From 68221fdd30fb9ba89219a4bd5a47870b2d1cf7e6 Mon Sep 17 00:00:00 2001 From: "Gabriel A. Devenyi" Date: Fri, 2 Jul 2021 16:13:18 -0400 Subject: [PATCH] ENH: Prepare for update to NIFTILIB3.0.1 --- .../ThirdParty/NIFTI/UpdateFromUpstream.sh | 5 +- Modules/ThirdParty/NIFTI/src/CMakeLists.txt | 1 + .../ThirdParty/NIFTI/src/nifti/CMakeLists.txt | 192 - .../NIFTI/src/nifti/CTestConfig.cmake | 15 - Modules/ThirdParty/NIFTI/src/nifti/LICENSE | 9 - Modules/ThirdParty/NIFTI/src/nifti/README | 77 - .../src/nifti/cmake/NIFTICPackConfig.cmake | 55 - .../NIFTI/src/nifti/cmake/NIFTIConfig.cmake | 1 - .../NIFTI/src/nifti/nifti2/CMakeLists.txt | 72 - .../NIFTI/src/nifti/nifti2/Makefile | 57 - .../NIFTI/src/nifti/nifti2/clib_02_nifti2.c | 168 - .../NIFTI/src/nifti/nifti2/nifti2.h | 117 - .../NIFTI/src/nifti/nifti2/nifti2_io.c | 9573 ----------------- .../NIFTI/src/nifti/nifti2/nifti2_io.h | 735 -- .../nifti2/nifti_regress_test/@show.diffs | 32 - .../src/nifti/nifti2/nifti_regress_test/@test | 80 - .../nifti2/nifti_regress_test/CMakeLists.txt | 0 .../nifti2/nifti_regress_test/README_regress | 50 - .../cmake_testscripts/bricks_test.sh | 35 - .../cmake_testscripts/comment_test.sh | 67 - .../cmake_testscripts/dci_test.sh | 48 - .../cmake_testscripts/dsets_test.sh | 63 - .../cmake_testscripts/dts_test.sh | 77 - .../cmake_testscripts/fetch_data_test.sh | 54 - .../cmake_testscripts/mod_header_test.sh | 62 - .../cmake_testscripts/newfiles_test.sh | 38 - .../nifti_regress_test/commands/c01.versions | 9 - .../nifti_regress_test/commands/c02.nt.help | 4 - .../nifti_regress_test/commands/c03.hist | 5 - .../commands/c04.disp.anat0.info | 7 - .../nifti_regress_test/commands/c05.mod.hdr | 9 - .../nifti_regress_test/commands/c06.add.ext | 22 - .../commands/c07.cbl.4bricks | 7 - .../commands/c08.dts.19.36.11 | 4 - .../commands/c09.dts4.compare | 9 - .../nifti_regress_test/commands/c10.dci.ts4 | 15 - .../commands/c10a.dci.run.210 | 15 - .../commands/c11.add.comment | 8 - .../commands/c12.check.comments | 7 - .../commands/c13.check.hdrs | 5 - .../commands/c14.make.dsets | 21 - .../nifti_regress_test/commands/c15.new.files | 21 - .../nifti_regress_test/commands/c16.rand.swap | 34 - .../nifti_regress_test/commands/c17.file.case | 33 - .../NIFTI/src/nifti/nifti2/nifti_tool.c | 5115 --------- .../NIFTI/src/nifti/nifti2/nifti_tool.h | 183 - .../NIFTI/src/nifti/niftilib/CMakeLists.txt | 110 - .../NIFTI/src/nifti/niftilib/Makefile | 56 - .../NIFTI/src/nifti/niftilib/nifti1.h | 1490 --- .../NIFTI/src/nifti/niftilib/nifti1_io.c | 7533 ------------- .../NIFTI/src/nifti/niftilib/nifti1_io.h | 555 - .../NIFTI/src/nifti/niftilib/nifti1_test.c | 107 - .../NIFTI/src/nifti/niftilib/nifti1_tool.c | 4199 -------- .../NIFTI/src/nifti/niftilib/nifti1_tool.h | 163 - .../src/nifti/niftilib/nifti_tester001.c | 695 -- .../src/nifti/niftilib/nifti_tester002.c | 38 - .../NIFTI/src/nifti/znzlib/CMakeLists.txt | 31 - .../NIFTI/src/nifti/znzlib/Makefile | 26 - .../NIFTI/src/nifti/znzlib/znzlib.c | 321 - .../NIFTI/src/nifti/znzlib/znzlib.h | 122 - 60 files changed, 3 insertions(+), 32659 deletions(-) delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/CMakeLists.txt delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/CTestConfig.cmake delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/LICENSE delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/README delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/cmake/NIFTICPackConfig.cmake delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/cmake/NIFTIConfig.cmake delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/CMakeLists.txt delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/Makefile delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/clib_02_nifti2.c delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti2.h delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti2_io.c delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti2_io.h delete mode 100755 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/@show.diffs delete mode 100755 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/@test delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/CMakeLists.txt delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/README_regress delete mode 100755 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/bricks_test.sh delete mode 100755 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/comment_test.sh delete mode 100755 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/dci_test.sh delete mode 100755 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/dsets_test.sh delete mode 100755 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/dts_test.sh delete mode 100755 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/fetch_data_test.sh delete mode 100755 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/mod_header_test.sh delete mode 100755 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/newfiles_test.sh delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c01.versions delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c02.nt.help delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c03.hist delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c04.disp.anat0.info delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c05.mod.hdr delete mode 100755 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c06.add.ext delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c07.cbl.4bricks delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c08.dts.19.36.11 delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c09.dts4.compare delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c10.dci.ts4 delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c10a.dci.run.210 delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c11.add.comment delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c12.check.comments delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c13.check.hdrs delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c14.make.dsets delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c15.new.files delete mode 100755 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c16.rand.swap delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c17.file.case delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_tool.c delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_tool.h delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/niftilib/CMakeLists.txt delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/niftilib/Makefile delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1.h delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_io.c delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_io.h delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_test.c delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_tool.c delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_tool.h delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti_tester001.c delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti_tester002.c delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/znzlib/CMakeLists.txt delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/znzlib/Makefile delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/znzlib/znzlib.c delete mode 100644 Modules/ThirdParty/NIFTI/src/nifti/znzlib/znzlib.h diff --git a/Modules/ThirdParty/NIFTI/UpdateFromUpstream.sh b/Modules/ThirdParty/NIFTI/UpdateFromUpstream.sh index da7deebd01c..55e96be4e8a 100755 --- a/Modules/ThirdParty/NIFTI/UpdateFromUpstream.sh +++ b/Modules/ThirdParty/NIFTI/UpdateFromUpstream.sh @@ -8,17 +8,16 @@ readonly name="nifti" readonly ownership="NIFTI Upstream " readonly subtree="Modules/ThirdParty/NIFTI/src/nifti" readonly repo="https://github.com/NIFTI-Imaging/nifti_clib.git" -readonly tag="master" +readonly tag="v3.0.1" readonly shortlog=false readonly paths=" CMakeLists.txt CTestConfig.cmake LICENSE -README +README.md cmake znzlib niftilib -nifti2 " extract_source () { diff --git a/Modules/ThirdParty/NIFTI/src/CMakeLists.txt b/Modules/ThirdParty/NIFTI/src/CMakeLists.txt index 2a09e220200..2e6863b98c9 100644 --- a/Modules/ThirdParty/NIFTI/src/CMakeLists.txt +++ b/Modules/ThirdParty/NIFTI/src/CMakeLists.txt @@ -13,6 +13,7 @@ set(NIFTI_USE_PACKAGING OFF CACHE BOOL "Do not use packaging from nifti when inc set(NIFTI_BUILD_APPLICATIONS OFF CACHE BOOL "Do not build applications provided by NIFTI" FORCE) # Testing is not compatible with ITK at the moment set(NIFTI_BUILD_TESTING OFF) # "Do not build nifit testing applications" +set(DOWNLOAD_TEST_DATA OFF) # Don't download testing data add_definitions(-DITKZLIB) set(NIFTI_INSTALL_EXPORT_NAME ${ITKNIFTI-targets}) # "Set the nifti package export target name" diff --git a/Modules/ThirdParty/NIFTI/src/nifti/CMakeLists.txt b/Modules/ThirdParty/NIFTI/src/nifti/CMakeLists.txt deleted file mode 100644 index 50118148667..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/CMakeLists.txt +++ /dev/null @@ -1,192 +0,0 @@ -cmake_minimum_required(VERSION 3.16.3 FATAL_ERROR) - -set(NIFTI_MAX_VALIDATED_CMAKE_VERSION "3.13.1") -if("${CMAKE_VERSION}" VERSION_LESS_EQUAL "${NIFTI_MAX_VALIDATED_CMAKE_VERSION}") - # As of 2018-12-04 NIFTI has been validated to build with cmake version 3.13.1 new policies. - # Set and use the newest cmake policies that are validated to work - set(NIFTI_CMAKE_POLICY_VERSION "${CMAKE_VERSION}") -else() - set(NIFTI_CMAKE_POLICY_VERSION "${NIFTI_MAX_VALIDATED_CMAKE_VERSION}") -endif() -cmake_policy(VERSION ${NIFTI_CMAKE_POLICY_VERSION}) - -set(NIFTI_HOMEPAGE_URL "https://nifti-imaging.github.io") -project(NIFTI - VERSION 2.1.0 - DESCRIPTION "Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format. nifti-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images." - LANGUAGES C) - -macro(set_if_not_defined var defaultvalue) -# Macro allowing to set a variable to its default value if not already defined. -# The default value is set with: -# (1) if set, the value environment variable . -# (2) if set, the value of local variable variable . -# (3) if none of the above, the value passed as a parameter. -# Setting the optional parameter 'OBFUSCATE' will display 'OBFUSCATED' instead of the real value. - set(_obfuscate FALSE) - foreach(arg ${ARGN}) - if(arg STREQUAL "OBFUSCATE") - set(_obfuscate TRUE) - endif() - endforeach() - if(DEFINED ENV{${var}} AND NOT DEFINED ${var}) - set(_value "$ENV{${var}}") - if(_obfuscate) - set(_value "OBFUSCATED") - endif() - message(STATUS "Setting '${var}' variable with environment variable value '${_value}'") - set(${var} $ENV{${var}}) - endif() - if(NOT DEFINED ${var}) - set(_value "${defaultvalue}") - if(_obfuscate) - set(_value "OBFUSCATED") - endif() - message(STATUS "Setting '${var}' variable with default value '${_value}'") - set(${var} "${defaultvalue}") - endif() -endmacro() - -set(CMAKE_INCLUDE_CURRENT_DIR ON) -set(CMAKE_INCLUDE_CURRENT_DIR_IN_INTERFACE ON) - - -# add option to build shared libraries. The default is OFF to maintain the -# current build behavior -option( BUILD_SHARED_LIBS "Toggle building shared libraries." OFF) - -#When including nifti as a subpackage, a prefix is often needed to avoid conflicts with sytem installed libraries. -set_if_not_defined(NIFTI_PACKAGE_PREFIX "") - -# Set default shared library version -# This library version will be applied to all libraries in the package -# unless it is not explicitely for a certain lib. -set(NIFTI_SHAREDLIB_VERSION ${NIFTI_VERSION_MAJOR}.${NIFTI_VERSION_MINOR}.${NIFTI_VERSION_PATCH} ) -string( REGEX MATCH "^[0-9]+" NIFTI_SHAREDLIB_SOVERSION ${NIFTI_SHAREDLIB_VERSION}) -if(BUILD_SHARED_LIBS AND NOT NIFTI_LIBRARY_PROPERTIES) - set(NIFTI_LIBRARY_PROPERTIES ${DEFAULT_SHARED_LIBS} - BUILD_SHARED_LIBS TRUE POSITION_INDEPENDENT_CODE TRUE VERSION ${NIFTI_SHAREDLIB_VERSION} SOVERSION ${NIFTI_SHAREDLIB_SOVERSION} - ) -endif() - -set_if_not_defined(NIFTI_INSTALL_RUNTIME_DIR "${CMAKE_INSTALL_PREFIX}/bin") -set_if_not_defined(NIFTI_INSTALL_LIBRARY_DIR "${CMAKE_INSTALL_PREFIX}/lib") -set_if_not_defined(NIFTI_INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_PREFIX}/include/nifti") -set_if_not_defined(NIFTI_ZLIB_LIBRARIES "") -if(NOT NIFTI_ZLIB_LIBRARIES) # If using a custom zlib library, skip the find package - ### USE AS STAND ALONE PACKAGE - find_package(ZLIB REQUIRED) - set(NIFTI_ZLIB_LIBRARIES ${ZLIB_LIBRARIES}) -endif() -#message(STATUS "---------------------ZLIB -${NIFTI_ZLIB_LIBRARIES}--") -add_definitions(-DHAVE_ZLIB) -# Modern CMake install COMPONENTS is being considered in upstream NIFTI -# Setting NIFTI_INSTALL_NO_DEVELOPMENT & NIFTI_INSTALL_NO_LIBRARIES to -# FALSE to make explicit that the development and libraries -# can not be skipped for installation. Use the install COMPONENTS -# features instead. -set(NIFTI_INSTALL_NO_DEVELOPMENT FALSE) -set(NIFTI_INSTALL_NO_LIBRARIES FALSE) - -####################################################################### -enable_testing() -include(CTest) -#Needs an if clause and more work before testing can take place. -set_if_not_defined(NIFTI_BUILD_TESTING ${BUILD_TESTING}) -if (NIFTI_BUILD_TESTING AND CMAKE_VERSION GREATER_EQUAL 3.11.0) # CMAKE VERSION 3.11.0 needed for fetching data with cmake - - include(FetchContent) # fetch data a configure time to simplify tests - # If new or changed data is needed, add that data to the https://github.com/NIFTI-Imaging/nifti-test-data repo - # make a new release, and then update the URL and hash (shasum -a 256 ). - FetchContent_Declare( fetch_testing_data - URL https://github.com/NIFTI-Imaging/nifti-test-data/archive/v3.0.0.tar.gz - URL_HASH SHA256=8a22554ca196f707f7c8cdc102e1a30117cd67da41d269390952683076ffcac8 - ) - FetchContent_GetProperties(fetch_testing_data) - if(NOT fetch_testing_data) - set(FETCHCONTENT_QUIET OFF) - message(STATUS "Downloading testing data... please wait") - FetchContent_Populate( fetch_testing_data ) - message(STATUS "download complete.") - endif() -endif() - -####################################################################### -add_subdirectory(znzlib) -add_subdirectory(niftilib) - -option(USE_NIFTICDF_CODE "Build nifticdf library and tools" ON) -mark_as_advanced(USE_NIFTICDF_CODE) -if(USE_NIFTICDF_CODE) - add_subdirectory(nifticdf) -endif() - -option(NIFTI_BUILD_APPLICATIONS "Build various utility tools" ON) -mark_as_advanced(NIFTI_BUILD_APPLICATIONS) - -option(USE_NIFTI2_CODE "Build the nifti2 library and tools" ON) -mark_as_advanced(USE_NIFTI2_CODE) -include(CMakeDependentOption) -cmake_dependent_option(USE_CIFTI_CODE "Build the cifti library and tools" OFF "USE_NIFTI2_CODE" OFF) -mark_as_advanced(USE_CIFTI_CODE) - -if( USE_NIFTI2_CODE ) - add_subdirectory(nifti2) - if( USE_CIFTI_CODE ) - add_subdirectory(cifti) - endif() -endif() - -option(USE_FSL_CODE "If OFF, The copyright of this code is questionable for inclusion with nifti." OFF) -mark_as_advanced(USE_FSL_CODE) -# the order of add_subdirectory is important! fsliolob has to preceed examples -# as otherwise FSLIOLIB_SOURCE_DIR is undefined and hence the examples -# will fail to compile -if(USE_FSL_CODE) - add_subdirectory(fsliolib) -endif() - -set_if_not_defined(NIFTI_INSTALL_EXPORT_NAME "NIFTITargets") -if(NIFTI_INSTALL_EXPORT_NAME EQUAL "NIFTITargets") - ####################################################################### - # CMake itself and can use some CMake facilities for creating the package files. - # This allows for find_package(NIFTI 2.1.0 NO_MODULE) to work for pulling in - # NIFTI libraries into an external project - include(CMakePackageConfigHelpers) - - write_basic_package_version_file( - "${CMAKE_CURRENT_BINARY_DIR}/NIFTI/NIFTIConfigVersion.cmake" - VERSION ${NIFTI_VERSION} - COMPATIBILITY AnyNewerVersion - ) - - export(EXPORT NIFTITargets - FILE "${CMAKE_CURRENT_BINARY_DIR}/NIFTI/NIFTITargets.cmake" - NAMESPACE ${NIFTI_PACKAGE_PREFIX}NIFTI:: - ) - configure_file(cmake/NIFTIConfig.cmake - "${CMAKE_CURRENT_BINARY_DIR}/NIFTI/NIFTIConfig.cmake" - COPYONLY - ) - - set(ConfigPackageLocation lib/cmake/NIFTI) - install(EXPORT NIFTITargets - FILE NIFTITargets.cmake - NAMESPACE ${NIFTI_PACKAGE_PREFIX}NIFTI:: - DESTINATION ${ConfigPackageLocation} - ) - install(FILES - cmake/NIFTIConfig.cmake - "${CMAKE_CURRENT_BINARY_DIR}/NIFTI/NIFTIConfigVersion.cmake" - DESTINATION ${ConfigPackageLocation} - COMPONENT Development - ) -endif() - -####################################################################### -## Add the cpack configuration settings last -option(NIFTI_USE_PACKAGING "Configure the packaging options for NIFTI" OFF) -mark_as_advanced(NIFTI_USE_PACKAGING) -if(NIFTI_USE_PACKAGING) - include(cmake/NIFTICPackConfig.cmake) -endif() diff --git a/Modules/ThirdParty/NIFTI/src/nifti/CTestConfig.cmake b/Modules/ThirdParty/NIFTI/src/nifti/CTestConfig.cmake deleted file mode 100644 index ec8515b304a..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/CTestConfig.cmake +++ /dev/null @@ -1,15 +0,0 @@ -## This file should be placed in the root directory of your project. -## Then modify the CMakeLists.txt file in the root directory of your -## project to incorporate the testing dashboard. -## -## # The following are required to submit to the CDash dashboard: -## enable_testing() -## include(CTest) - -set(CTEST_PROJECT_NAME "NIFTI") -set(CTEST_NIGHTLY_START_TIME "00:00:00 EST") - -set(CTEST_DROP_METHOD "http") -set(CTEST_DROP_SITE "my.cdash.org") -set(CTEST_DROP_LOCATION "/submit.php?project=nifti_clib") -set(CTEST_DROP_SITE_CDASH TRUE) diff --git a/Modules/ThirdParty/NIFTI/src/nifti/LICENSE b/Modules/ThirdParty/NIFTI/src/nifti/LICENSE deleted file mode 100644 index cd7ce5662d5..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/LICENSE +++ /dev/null @@ -1,9 +0,0 @@ -Niftilib has been developed by members of the NIFTI DFWG and volunteers in the -neuroimaging community and serves as a reference implementation of the nifti-1 -file format. - -http://nifti.nimh.nih.gov/ - -Nifticlib code is released into the public domain, developers are encouraged to -incorporate niftilib code into their applications, and, to contribute changes -and enhancements to niftilib. diff --git a/Modules/ThirdParty/NIFTI/src/nifti/README b/Modules/ThirdParty/NIFTI/src/nifti/README deleted file mode 100644 index a77d61d5567..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/README +++ /dev/null @@ -1,77 +0,0 @@ -Nifti-1 C libraries -------------------- - -Version 2.0.0 beta release Jul 2010 -Version 1.1.0 beta release Aug 2008 -Version 1.0.0 beta release Dec 2007 -Version 0.6 beta release Aug 2007 -Version 0.5 beta release May 2007 -Version 0.4 beta release Sept. 2006 -Version 0.3 beta release April 2006 -Version 0.2 beta release August 12, 2005 -Version 0.1 beta release March 11, 2005 - -niftilib code is released into the public domain. - - -Library directories -------------------- -znzlib -- low level library for handling read/write of compressed files. - -niftilib -- core i/o routines for reading and writing nifti-1 format files. - Primarily routines to read/write and manipulate the header field - information, including orientation matrices. Volume-wise, - timecourse-wise, access to image data. - -nifticdf -- functions to compute cumulative distributions and their inverses - -fsliolib -- i/o routines for reading and writing nifti-1 format files, higher - level than niftilib, includes routines for reading the data blob by - volume, timecourse, etc., and, addresses image orientation issues. - *** work in progress, subject to significant revision..... - -utils -- directory containing library utility programs (nifti_tool) - - - - -Destination directories ------------------------ -bin -- destination directory for installed programs -include -- destination directory for library header files -lib -- destination directory for compiled libraries -docs -- destination directory Doxygen html (created via "make doc") - - - -Example directories -------------------- -examples -- directory containing sample code using nifti reference library -real_easy -- code snippets to read nifti-1 files, not using nifti ref. lib. - - -Other directories ------------------ -Testing -- directory containing code to test the libraries -packaging -- spec file for building RPMs, and template package - description for Dev-Cpp (http://www.bloodshed.net/devcpp.html) - - - -Instructions to build ---------------------- - -command -- "make all" - - results will be left in the directories: bin/ include/ lib/ - -command -- "make help" - - will show more build options - - -For more information --------------------- - -See the niftilib webpage at http://niftilib.sourceforge.net/ -See the NIFTI webpage at http://nifti.nimh.nih.gov/ diff --git a/Modules/ThirdParty/NIFTI/src/nifti/cmake/NIFTICPackConfig.cmake b/Modules/ThirdParty/NIFTI/src/nifti/cmake/NIFTICPackConfig.cmake deleted file mode 100644 index f6cbd2d69bb..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/cmake/NIFTICPackConfig.cmake +++ /dev/null @@ -1,55 +0,0 @@ -#################################### -### Define information necessary for packaging with CPACK (https://gitlab.kitware.com/cmake/community/wikis/home#cpack) -### The last section is concerned with installing the binaries and making distributions. - -set_if_not_defined(CPACK_SOURCE_GENERATOR "TGZ;TZ;STGZ;TBZ2;ZIP") - -include(InstallRequiredSystemLibraries) - -set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "${NIFTI_PROJECT_DESCRIPTION}") -set(CPACK_PACKAGE_VENDOR "NIFTI DFWG") -set(CPACK_PACKAGE_DESCRIPTION_FILE "${NIFTI_SOURCE_DIR}/README") - -set(CPACK_RESOURCE_FILE_LICENSE "${NIFTI_SOURCE_DIR}/README") - -set(CPACK_PACKAGE_NAME "${PROJECT_NAME}") -set(CPACK_PACKAGE_VERSION_MAJOR "${NIFTI_VERSION_MAJOR}") -set(CPACK_PACKAGE_VERSION_MINOR "${NIFTI_VERSION_MINOR}") -set(CPACK_PACKAGE_VERSION_PATCH "${NIFTI_VERSION_PATCH}") - -set(CPACK_PACKAGE_INSTALL_DIRECTORY "NIFTI_${NIFTI_VERSION_MAJOR}.${NIFTI_VERSION_MINOR}.${NIFTI_VERSION_PATCH}") - -if(WIN32 AND NOT UNIX) - set(CPACK_PACKAGE_INSTALL_REGISTRY_KEY - "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}") - # There is a bug in NSI that does not handle full unix paths properly. Make - # sure there is at least one set of four (4) backlasshes. - set(CPACK_PACKAGE_ICON - "${CMake_SOURCE_DIR}/Utilities/Release\\\\InstallIcon.bmp") - set(CPACK_NSIS_INSTALLED_ICON_NAME "bin\\\\MyExecutable.exe") - set(CPACK_NSIS_DISPLAY_NAME "${CPACK_PACKAGE_INSTALL_DIRECTORY} NIFTI Project") - set(CPACK_NSIS_HELP_LINK "https:\\\\\\\\www.nitrc.org") - set(CPACK_NSIS_URL_INFO_ABOUT "https:\\\\\\\\www.nitrc.org") - set(CPACK_NSIS_CONTACT "xyz@domain.edu") - set(CPACK_NSIS_MODIFY_PATH ON) -else() - set(CPACK_STRIP_FILES OFF) - set(CPACK_SOURCE_STRIP_FILES OFF) -endif() -set(CPACK_PACKAGE_EXECUTABLES "nifti_tool;NIFTI") - -set(CPACK_PACKAGING_INSTALL_PREFIX ".") - -set(CPACK_SOURCE_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-dev") -set(CPACK_PACKAGE_DEFAULT_LOCATION "/opt/${CPACK_PACKAGE_NAME}") -set(CPACK_SET_DESTDIR ON) - -set(CPACK_SOURCE_IGNORE_FILES - "/.git/" - ".gitignore$" - ".*.swp$" - ".*~" - "Makefile\\\\.in$" -) - -include(CPack) diff --git a/Modules/ThirdParty/NIFTI/src/nifti/cmake/NIFTIConfig.cmake b/Modules/ThirdParty/NIFTI/src/nifti/cmake/NIFTIConfig.cmake deleted file mode 100644 index 4195e038a6e..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/cmake/NIFTIConfig.cmake +++ /dev/null @@ -1 +0,0 @@ -include("${CMAKE_CURRENT_LIST_DIR}/NIFTITargets.cmake") diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/CMakeLists.txt b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/CMakeLists.txt deleted file mode 100644 index e9f8330eec7..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/CMakeLists.txt +++ /dev/null @@ -1,72 +0,0 @@ -set(NIFTI_NIFTILIB2_NAME ${NIFTI_PACKAGE_PREFIX}nifti2) - -add_library(${NIFTI_NIFTILIB2_NAME} nifti2_io.c ) -target_link_libraries( ${NIFTI_NIFTILIB2_NAME} PUBLIC ${NIFTI_PACKAGE_PREFIX}niftiio) -target_include_directories(${NIFTI_NIFTILIB2_NAME} PUBLIC - $ - $ - ) - -if(NIFTI_BUILD_APPLICATIONS) - add_executable(${NIFTI_PACKAGE_PREFIX}nifti_tool nifti_tool.c) - target_link_libraries(${NIFTI_PACKAGE_PREFIX}nifti_tool PUBLIC ${NIFTI_NIFTILIB2_NAME}) - set(NIFTI2_APPS ${NIFTI_PACKAGE_PREFIX}nifti_tool) -endif() - -# Set lib version when buildung shared libs. -if(BUILD_SHARED_LIBS) - set_target_properties(${NIFTI_NIFTILIB2_NAME} PROPERTIES ${NIFTI_LIBRARY_PROPERTIES}) -endif() - -if(NOT NIFTI_INSTALL_NO_LIBRARIES) - install(TARGETS ${NIFTI_NIFTILIB2_NAME} ${NIFTI2_APPS} - EXPORT ${NIFTI_INSTALL_EXPORT_NAME} - RUNTIME DESTINATION ${NIFTI_INSTALL_RUNTIME_DIR} COMPONENT RuntimeLibraries - LIBRARY DESTINATION ${NIFTI_INSTALL_LIBRARY_DIR} COMPONENT RuntimeLibraries - ARCHIVE DESTINATION ${NIFTI_INSTALL_LIBRARY_DIR} COMPONENT Development - INCLUDES DESTINATION ${NIFTI_INSTALL_INCLUDE_DIR} - ) -endif() - -if(NOT NIFTI_INSTALL_NO_DEVELOPMENT) - file(GLOB __files "${CMAKE_CURRENT_SOURCE_DIR}/*.h") - install(FILES ${__files} - DESTINATION ${NIFTI_INSTALL_INCLUDE_DIR} - COMPONENT Development) -endif() - - -if(NIFTI_BUILD_TESTING AND NIFTI_BUILD_APPLICATIONS) - add_executable(${NIFTI_PACKAGE_PREFIX}clib_02_nifti2 clib_02_nifti2.c) - target_link_libraries(${NIFTI_PACKAGE_PREFIX}clib_02_nifti2 PUBLIC ${NIFTI_NIFTILIB2_NAME}) - - # Do all regression tests - add_test( NAME nifti_ver COMMAND $ -nifti_ver) - add_test( NAME nifti_tool_ver COMMAND $ -ver) - add_test( NAME nifti_help COMMAND $ -help) - add_test( NAME nifti_nifti_hist COMMAND $ -nifti_hist) - add_test( NAME nifti_hist COMMAND $ -hist) - - if (CMAKE_VERSION GREATER_EQUAL 3.11.0) # CMAKE VERSION 3.11.0 needed for fetching data with cmake - add_test( NAME nifti_disp_hdr COMMAND $ -disp_hdr -infiles ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data/anat0.nii ) - add_test( NAME nifti_disp_nim COMMAND $ -disp_nim -infiles ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data/anat0.nii ) - add_test( NAME nifti_disp_ext COMMAND $ -disp_ext -infiles ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data/anat0.nii ) - add_test( NAME nifti_header_check COMMAND $ -check_hdr -infiles ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data/anat0.nii ) - add_test( NAME nifti_nim_check COMMAND $ -check_nim -infiles ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data/anat0.nii ) - if(UNIX) # unix needed to run shell scripts - set(NIFTI_TEST_SCRIPT_DIR ${CMAKE_CURRENT_LIST_DIR}/nifti_regress_test/cmake_testscripts) - add_test( NAME nifti_modhdr_exts COMMAND sh ${NIFTI_TEST_SCRIPT_DIR}/mod_header_test.sh $ ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data ) - add_test( NAME nifti_bricks_test COMMAND sh ${NIFTI_TEST_SCRIPT_DIR}/bricks_test.sh $ ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data ) - - add_test( NAME nifti_dci_test COMMAND sh ${NIFTI_TEST_SCRIPT_DIR}/dci_test.sh $ ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data ) - add_test( NAME nifti_comment_test COMMAND sh ${NIFTI_TEST_SCRIPT_DIR}/comment_test.sh $ ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data ) - add_test( NAME nifti_dsets_test COMMAND sh ${NIFTI_TEST_SCRIPT_DIR}/dsets_test.sh $ ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data ) - add_test( NAME nifti_newfiles_test COMMAND sh ${NIFTI_TEST_SCRIPT_DIR}/newfiles_test.sh $ ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data ) - - add_test( NAME nifti_dts_test COMMAND sh ${NIFTI_TEST_SCRIPT_DIR}/dts_test.sh $ ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data ) - set_tests_properties( nifti_dts_test PROPERTIES DEPENDS nifti_bricks_test) - - - endif() - endif() -endif() diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/Makefile b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/Makefile deleted file mode 100644 index 8098385377d..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/Makefile +++ /dev/null @@ -1,57 +0,0 @@ - -# note the TARFILE_NAME embeds the release version number -TARFILE_NAME = nifti2clib-0.0.1 - -USEZLIB = -DHAVE_ZLIB - -## Compiler defines -CC = gcc -IFLAGS = -I. -I../niftilib -I../znzlib -CFLAGS = -Wall -std=gnu99 -pedantic $(USEZLIB) $(IFLAGS) - -LLIBS = -lz -lm - -MISC_OBJS = nifticdf.o znzlib.o -OBJS = nifti2_io.o $(MISC_OBJS) - -TOOLS = nifti_tool nifti1_tool nifti2_tool -EXAMPLES = clib_02_nifti2 - - -# -------------------------------------------------- -# default compile for C files -%.o : %.c %.h - $(CC) -c $(CFLAGS) $< -o $@ - -# -------------------------------------------------- -# main targets (primary is nifti_tool, for now) - -nifti_tool: nifti_tool.o nifti_tool.h nifti2objs - $(CC) -o $@ $(CFLAGS) $< $(OBJS) $(LLIBS) - -all: $(TOOLS) $(EXAMPLES) - -clean: - $(RM) *.o $(TOOLS) $(EXAMPLES) - -nifti2objs: $(OBJS) - -clib_02_nifti2: clib_02_nifti2.o nifti2objs - $(CC) -o $@ $(CFLAGS) $< $(OBJS) $(LLIBS) - -# -------------------------------------------------- -# targets from source residing elsewhere -nifticdf.o: - $(CC) -c $(CFLAGS) ../nifticdf/nifticdf.c -o $@ - -znzlib.o: - $(CC) -c $(CFLAGS) ../znzlib/znzlib.c -o $@ - -# maybe we want to build NIFTI-1 nifti_tool -nifti1_tool: $(MISC_OBJS) - $(CC) -o $@ -I../utils $(CFLAGS) \ - ../niftilib/nifti_tool.c ../niftilib/nifti1_io.c $(MISC_OBJS) $(LLIBS) - -# make non-clashing version -nifti2_tool: nifti_tool - cp -p nifti_tool nifti2_tool diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/clib_02_nifti2.c b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/clib_02_nifti2.c deleted file mode 100644 index fd4d0deb5b4..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/clib_02_nifti2.c +++ /dev/null @@ -1,168 +0,0 @@ -/* ---------------------------------------------------------------------- - * A basic example to read/write a nifti dataset (e.g. cp command). - * - * compile example (consider -pedantic or -Wall): - * - * gcc -o clib_02_nifti2 clib_02.nifti2.c \ - * -I../include -L../lib -lniftiio -lznz -lz -lm - * - * OR - * - * gcc -o clib_02_nifti2 clib_02.nifti2.c -I ../niftilib \ - * -I ../znzlib ../niftilib/nifti2_io.o ../znzlib/znzlib.o -lz -lm - * - * R Reynolds 3 Apr 2014 - *---------------------------------------------------------------------- - */ -#include - -#include -int disp_float(nifti_image * nim, int vol, int slice, int line, int offset); - -int show_help( void ) -{ - printf( - "clib_02_nifti2: short exmample of reading/writing NIfTI2\n" - "\n" - " This program is to demonstrate how to read a NIfTI-2 dataset,\n" - " set output filenames and write a NIfTI-2 dataset, all via the\n" - " standard NIfTI C library.\n" - "\n" - " basic usage: clib_02_nifti2 -input FILE_IN -output FILE_OUT\n" - " clib_02_nifti2 -input FILE_IN -disp_float_example\n" - "\n" - " options:\n" - "\n" - " -help : show this help\n" - " -disp_float_example : show some voxel's data\n" - " -input INFILE : specify input dataset\n" - " -output OUTFILE : specify output dataset\n" - " -verb LEVEL : set the verbose level to LEVEL\n" - "\n"); - return 0; -} - -int main(int argc, char * argv[]) -{ - nifti_image * nim=NULL; - char * fin=NULL, * fout=NULL; - int ac, disp_float_eg=0; - - if( argc < 2 ) return show_help(); /* typing '-help' is sooo much work */ - - /* process user options: 4 are valid presently */ - for( ac = 1; ac < argc; ac++ ) { - if( ! strncmp(argv[ac], "-h", 2) ) { - return show_help(); - } - else if( ! strcmp(argv[ac], "-disp_float_example") ) { - disp_float_eg = 1; - } - else if( ! strcmp(argv[ac], "-input") ) { - if( ++ac >= argc ) { - fprintf(stderr, "** missing argument for -input\n"); - return 1; - } - fin = argv[ac]; /* no string copy, just pointer assignment */ - } - else if( ! strcmp(argv[ac], "-output") ) { - if( ++ac >= argc ) { - fprintf(stderr, "** missing argument for -output\n"); - return 2; - } - fout = argv[ac]; - } - else if( ! strcmp(argv[ac], "-verb") ) { - if( ++ac >= argc ) { - fprintf(stderr, "** missing argument for -verb\n"); - return 2; - } - nifti_set_debug_level(atoi(argv[ac])); - } - else { - fprintf(stderr,"** invalid option, '%s'\n", argv[ac]); - return 1; - } - } - - if( !fin ) { fprintf(stderr, "** missing option '-input'\n"); return 1; } - /* read input dataset, including data */ - nim = nifti_image_read(fin, 1); - if( !nim ) { - fprintf(stderr,"** failed to read NIfTI image from '%s'\n", fin); - return 2; - } - - if( disp_float_eg ) disp_float(nim, 0, 1, 2, 3); - - if( !fout ) { fprintf(stderr, "-- no output requested \n"); return 0; } - - /* assign nifti_image fname/iname pair, based on output filename - (request to 'check' image and 'set_byte_order' here) */ - if( nifti_set_filenames(nim, fout, 1, 1) ) return 1; - - /* if we get here, write the output dataset */ - nifti_image_write( nim ); - - /* and clean up memory */ - nifti_image_free( nim ); - - return 0; -} - -int disp_float(nifti_image * nim, int vol, int slice, int line, int offset) -{ - float * dp, * d2; - long long lloff; - int nx, nxy, nxyz; - - if( ! nim ) return 1; - - if( nim->datatype != NIFTI_TYPE_FLOAT32 ) { - fprintf(stderr,"** datatype not float, have %s\n", - nifti_datatype_to_string(nim->datatype)); - return 1; - } - - nx = nim->nx; - nxy = nim->nx * nim->ny; - nxyz = nim->nx * nim->ny * nim->nz; - - /* set a float pointer to the beginning of the data, - so no more casting is needed */ - dp = (float *)nim->data; - - /* check limits */ - if( vol >= nim->nt || vol < 0 ) { - fprintf(stderr,"** vol index %d is out of range [0, %lld]\n", - vol, (long long)nim->nt-1); - return 1; - } - if( slice >= nim->nz || slice < 0 ) { - fprintf(stderr,"** slice index %d is out of range [0, %lld]\n", - slice, (long long)nim->nz-1); - return 1; - } - if( line >= nim->ny || line < 0 ) { - fprintf(stderr,"** line index %d is out of range [0, %lld]\n", - line, (long long)nim->ny-1); - return 1; - } - if( offset >= nim->nx || offset < 0 ) { - fprintf(stderr,"** offset %d is out of range [0, %lld]\n", - offset, (long long)nim->nx-1); - return 1; - } - - - d2 = dp + vol*nxyz + slice*nxy + line*nx + offset; - /* or */ - lloff = vol*nxyz + slice*nxy + line*nx + offset; - d2 = dp + lloff; - - printf("data[%d,%d,%d,%d] = %f\n", vol, slice, line, offset, *d2); - /* or */ - printf("data[%lld] = %f\n", lloff, dp[lloff]); - - return 0; /* success */ -} diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti2.h b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti2.h deleted file mode 100644 index ab47f3cdd4f..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti2.h +++ /dev/null @@ -1,117 +0,0 @@ -/** \file nifti2.h - \brief Header structure for NIFTI-2 format. - */ - -#ifndef __NIFTI2_HEADER -#define __NIFTI2_HEADER - -/*---------------------------------------------------------------------------*/ -/* Changes to the header from NIFTI-1 to NIFTI-2 are intended to allow for - larger and more accurate fields. The changes are as follows: - - - short dim[8] -> int64_t dim[8] - - float intent_p1,2,3 -> double intent_p1,2,3 (3 fields) - - float pixdim[8] -> double pixdim[8] - - float vox_offset -> int64_t vox_offset - - float scl_slope -> double scl_slope - - float scl_inter -> double scl_inter - - float cal_max -> double cal_max - - float cal_min -> double cal_min - - float slice_duration -> double slice_duration - - float toffset -> double toffset - - short slice_start -> int64_t slice_start - - short slice_end -> int64_t slice_end - - char slice_code -> int32_t slice_code - - char xyzt_units -> int32_t xyzt_units - - short intent_code -> int32_t intent_code - - short qform_code -> int32_t qform_code - - short sform_code -> int32_t sform_code - - float quatern_b,c,d -> double quatern_b,c,d (3 fields) - - float srow_x,y,z[4] -> double srow_x,y,z[4] (3 fields) - - char magic[4] -> char magic[8] - - char unused_str[15] -> padding added at the end of the header - - - previously unused fields have been removed: - data_type, db_name, extents, session_error, regular, glmax, glmin - - - the field order has been changed, notably with magic after sizeof_hdr - - 2 Jan, 2014 [rickr] ------------------------------------------------------------------------------*/ - -#include - -/*=================*/ -#ifdef __cplusplus -extern "C" { -#endif -/*=================*/ - -/*! \struct nifti_2_header - \brief Data structure defining the fields in the nifti2 header. - This binary header should be found at the beginning of a valid - NIFTI-2 header file. - */ - -/* hopefully cross-platform solution to byte padding added by some compilers */ -#pragma pack(push) -#pragma pack(1) - - /*****************************/ /***********************/ /************/ -struct nifti_2_header { /* NIFTI-2 usage */ /* NIFTI-1 usage */ /* offset */ - /*****************************/ /***********************/ /************/ - int32_t sizeof_hdr; /*!< MUST be 540 */ /* MUST be 348 */ /* 0 */ - char magic[8]; /*!< MUST be valid signature */ /* char magic[4] */ /* 4 */ - int16_t datatype; /*!< Defines data type! */ /* short datatype */ /* 12 */ - int16_t bitpix; /*!< Number bits/voxel */ /* short bitpix */ /* 14 */ - int64_t dim[8]; /*!< Data array dimensions */ /* short dim[8] */ /* 16 */ - double intent_p1; /*!< 1st intent parameter */ /* float intent_p1 */ /* 80 */ - double intent_p2; /*!< 2nd intent parameter */ /* float intent_p2 */ /* 88 */ - double intent_p3; /*!< 3rd intent parameter */ /* float intent_p3 */ /* 96 */ - double pixdim[8]; /*!< Grid spacings */ /* float pixdim[8] */ /* 104 */ - int64_t vox_offset; /*!< Offset into .nii file */ /* float vox_offset */ /* 168 */ - double scl_slope; /*!< Data scaling: slope */ /* float scl_slope */ /* 176 */ - double scl_inter; /*!< Data scaling: offset */ /* float scl_inter */ /* 184 */ - double cal_max; /*!< Max display intensity */ /* float cal_max */ /* 192 */ - double cal_min; /*!< Min display intensity */ /* float cal_min */ /* 200 */ - double slice_duration; /*!< Time for 1 slice */ /* float slice_duration*/ /* 208 */ - double toffset; /*!< Time axis shift */ /* float toffset */ /* 216 */ - int64_t slice_start; /*!< First slice index */ /* short slice_start */ /* 224 */ - int64_t slice_end; /*!< Last slice index */ /* short slice_end */ /* 232 */ - char descrip[80]; /*!< any text you like */ /* char descrip[80] */ /* 240 */ - char aux_file[24]; /*!< auxiliary filename */ /* char aux_file[24] */ /* 320 */ - int32_t qform_code; /*!< NIFTI_XFORM_* code */ /* short qform_code */ /* 344 */ - int32_t sform_code; /*!< NIFTI_XFORM_* code */ /* short sform_code */ /* 348 */ - double quatern_b; /*!< Quaternion b param */ /* float quatern_b */ /* 352 */ - double quatern_c; /*!< Quaternion c param */ /* float quatern_c */ /* 360 */ - double quatern_d; /*!< Quaternion d param */ /* float quatern_d */ /* 368 */ - double qoffset_x; /*!< Quaternion x shift */ /* float qoffset_x */ /* 376 */ - double qoffset_y; /*!< Quaternion y shift */ /* float qoffset_y */ /* 384 */ - double qoffset_z; /*!< Quaternion z shift */ /* float qoffset_z */ /* 392 */ - double srow_x[4]; /*!< 1st row affine transform*/ /* float srow_x[4] */ /* 400 */ - double srow_y[4]; /*!< 2nd row affine transform*/ /* float srow_y[4] */ /* 432 */ - double srow_z[4]; /*!< 3rd row affine transform*/ /* float srow_z[4] */ /* 464 */ - int32_t slice_code; /*!< Slice timing order */ /* char slice_code */ /* 496 */ - int32_t xyzt_units; /*!< Units of pixdim[1..4] */ /* char xyzt_units */ /* 500 */ - int32_t intent_code; /*!< NIFTI_INTENT_* code */ /* short intent_code */ /* 504 */ - char intent_name[16];/*!< name or meaning of data */ /* char intent_name[16]*/ /* 508 */ - char dim_info; /*!< MRI slice ordering */ /* char dim_info */ /* 524 */ - char unused_str[15]; /*!< unused, filled with \0 */ /* 525 */ -}; /****** total bytes: 540 */ -typedef struct nifti_2_header nifti_2_header; - -/* restore packing behavior */ -#pragma pack(pop) - -/* base swap test on the suggested version check, rather than dim[0] - swap4(348)==1543569408, swap4(540)==469893120 */ -#define NIFTI2_NEEDS_SWAP(h) \ - ((h).sizeof_hdr == 1543569408 || (h).sizeof_hdr == 469893120) - -/*=================*/ -#ifdef __cplusplus -} -#endif -/*=================*/ - -#endif /* __NIFTI2_HEADER */ diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti2_io.c b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti2_io.c deleted file mode 100644 index fdd3afebd42..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti2_io.c +++ /dev/null @@ -1,9573 +0,0 @@ -#define _NIFTI2_IO_C_ - -#include "nifti2_io.h" /* typedefs, prototypes, macros, etc. */ - -/*****===================================================================*****/ -/***** Sample functions to deal with NIFTI-1,2 and ANALYZE files *****/ -/*****...................................................................*****/ -/***** This code is released to the public domain. *****/ -/*****...................................................................*****/ -/***** Author: Robert W Cox, SSCC/DIRP/NIMH/NIH/DHHS/USA/EARTH *****/ -/***** Date: August 2003 *****/ -/*****...................................................................*****/ -/***** Neither the National Institutes of Health (NIH), nor any of its *****/ -/***** employees imply any warranty of usefulness of this software for *****/ -/***** any purpose, and do not assume any liability for damages, *****/ -/***** incidental or otherwise, caused by any use of this document. *****/ -/*****===================================================================*****/ - -/** \file nifti1_io.c - \brief main collection of nifti1 i/o routines - - written by Bob Cox, SSCC NIMH - - revised by Mark Jenkinson, FMRIB - - revised by Rick Reynolds, SSCC, NIMH - - revised by Kate Fissell, University of Pittsburgh - - The library history can be viewed via "nifti_tool -nifti_hist". -
The library version can be viewed via "nifti_tool -nifti_ver". - */ - -/*! global history and version strings, for printing */ -static char const * const gni1_history[] = -{ - "----------------------------------------------------------------------\n" - "history (of nifti-1 library changes):\n" - "\n", - "0.0 August, 2003 [rwcox]\n" - " (Robert W Cox of the National Institutes of Health, SSCC/DIRP/NIMH)\n" - " - initial version\n" - "\n", - "0.1 July/August, 2004 [Mark Jenkinson]\n" - " (FMRIB Centre, University of Oxford, UK)\n" - " - Mainly adding low-level IO and changing things to allow gzipped\n" - " files to be read and written\n" - " - Full backwards compatability should have been maintained\n" - "\n", - "0.2 16 Nov 2004 [rickr]\n" - " (Rick Reynolds of the National Institutes of Health, SSCC/DIRP/NIMH)\n" - " - included Mark's changes in the AFNI distribution (including znzlib/)\n" - " (HAVE_ZLIB is commented out for the standard distribution)\n" - " - modified nifti_validfilename() and nifti_makebasename()\n" - " - added nifti_find_file_extension()\n" - "\n", - "0.3 3 Dec 2004 [rickr]\n" - " - note: header extensions are not yet checked for\n" - " - added formatted history as global string, for printing\n" - " - added nifti_disp_lib_hist(), to display the nifti library history\n" - " - added nifti_disp_lib_version(), to display the nifti library history\n", - " - re-wrote nifti_findhdrname()\n" - " o used nifti_find_file_extension()\n" - " o changed order of file tests (default is .nii, depends on input)\n" - " o free hdrname on failure\n" - " - made similar changes to nifti_findimgname()\n" - " - check for NULL return from nifti_findhdrname() calls\n", - " - removed most of ERREX() macros\n" - " - modified nifti_image_read()\n" - " o added debug info and error checking (on gni_debug > 0, only)\n" - " o fail if workingname is NULL\n" - " o check for failure to open header file\n" - " o free workingname on failure\n" - " o check for failure of nifti_image_load()\n" - " o check for failure of nifti_convert_nhdr2nim()\n", - " - changed nifti_image_load() to int, and check nifti_read_buffer return\n" - " - changed nifti_read_buffer() to fail on short read, and to count float\n" - " fixes (to print on debug)\n" - " - changed nifti_image_infodump to print to stderr\n" - " - updated function header comments, or moved comments above header\n" - " - removed const keyword\n" - " - added LNI_FERR() macro for error reporting on input files\n" - "\n", - "0.4 10 Dec 2004 [rickr] - added header extensions\n" - " - in nifti1_io.h:\n" - " o added num_ext and ext_list to the definition of nifti_image\n" - " o made many functions static (more to follow)\n" - " o added LNI_MAX_NIA_EXT_LEN, for max nifti_type 3 extension length\n", - " - added __DATE__ to version output in nifti_disp_lib_version()\n" - " - added nifti_disp_matrix_orient() to print orientation information\n" - " - added '.nia' as a valid file extension in nifti_find_file_extension()\n" - " - added much more debug output\n" - " - in nifti_image_read(), in the case of an ASCII header, check for\n" - " extensions after the end of the header\n", - " - added nifti_read_extensions() function\n" - " - added nifti_read_next_extension() function\n" - " - added nifti_add_exten_to_list() function\n" - " - added nifti_check_extension() function\n" - " - added nifti_write_extensions() function\n" - " - added nifti_extension_size() function\n" - " - in nifti_set_iname_offest():\n" - " o adjust offset by the extension size and the extender size\n", - " o fixed the 'ceiling modulo 16' computation\n" - " - in nifti_image_write_hdr_img2(): \n" - " o added extension writing\n" - " o check for NULL return from nifti_findimgname()\n" - " - include number of extensions in nifti_image_to_ascii() output\n" - " - in nifti_image_from_ascii():\n" - " o return bytes_read as a parameter, computed from the final spos\n" - " o extract num_ext from ASCII header\n" - "\n", - "0.5 14 Dec 2004 [rickr] - added sub-brick reading functions\n" - " - added nifti_brick_list type to nifti1_io.h, along with new prototypes\n" - " - added main nifti_image_read_bricks() function, with description\n" - " - added nifti_image_load_bricks() - library function (requires nim)\n" - " - added valid_nifti_brick_list() - library function\n" - " - added free_NBL() - library function\n", - " - added update_nifti_image_for_brick_list() for dimension update\n" - " - added nifti_load_NBL_bricks(), nifti_alloc_NBL_mem(),\n" - " nifti_copynsort() and force_positive() (static functions)\n" - " - in nifti_image_read(), check for failed load only if read_data is set\n" - " - broke most of nifti_image_load() into nifti_image_load_prep()\n" - "\n", - "0.6 15 Dec 2004 [rickr] - added sub-brick writing functionality\n" - " - in nifti1_io.h, removed znzlib directory from include - all nifti\n" - " library files are now under the nifti directory\n" - " - nifti_read_extensions(): print no offset warning for nifti_type 3\n" - " - nifti_write_all_data():\n" - " o pass nifti_brick_list * NBL, for optional writing\n" - " o if NBL, write each sub-brick, sequentially\n", - " - nifti_set_iname_offset(): case 1 must have sizeof() cast to int\n" - " - pass NBL to nifti_image_write_hdr_img2(), and allow NBL or data\n" - " - added nifti_image_write_bricks() wrapper for ...write_hdr_img2()\n" - " - included compression abilities\n" - "\n", - "0.7 16 Dec 2004 [rickr] - minor changes to extension reading\n" - "\n", - "0.8 21 Dec 2004 [rickr] - restrict extension reading, and minor changes\n" - " - in nifti_image_read(), compute bytes for extensions (see remaining)\n" - " - in nifti_read_extensions(), pass 'remain' as space for extensions,\n" - " pass it to nifti_read_next_ext(), and update for each one read \n" - " - in nifti_check_extension(), require (size <= remain)\n", - " - in update_nifti_image_brick_list(), update nvox\n" - " - in nifti_image_load_bricks(), make explicit check for nbricks <= 0\n" - " - in int_force_positive(), check for (!list)\n" - " - in swap_nifti_header(), swap sizeof_hdr, and reorder to struct order\n" - " - change get_filesize functions to signed ( < 0 is no file or error )\n", - " - in nifti_validfilename(), lose redundant (len < 0) check\n" - " - make print_hex_vals() static\n" - " - in disp_nifti_1_header, restrict string field widths\n" - "\n", - "0.9 23 Dec 2004 [rickr] - minor changes\n" - " - broke ASCII header reading out of nifti_image_read(), into new\n" - " functions has_ascii_header() and read_ascii_image()\n", - " - check image_read failure and znzseek failure\n" - " - altered some debug output\n" - " - nifti_write_all_data() now returns an int\n" - "\n", - "0.10 29 Dec 2004 [rickr]\n" - " - renamed nifti_valid_extension() to nifti_check_extension()\n" - " - added functions nifti_makehdrname() and nifti_makeimgname()\n" - " - added function valid_nifti_extensions()\n" - " - in nifti_write_extensions(), check for validity before writing\n", - " - rewrote nifti_image_write_hdr_img2():\n" - " o set write_data and leave_open flags from write_opts\n" - " o add debug print statements\n" - " o use nifti_write_ascii_image() for the ascii case\n" - " o rewrote the logic of all cases to be easier to follow\n", - " - broke out code as nifti_write_ascii_image() function\n" - " - added debug to top-level write functions, and free the znzFile\n" - " - removed unused internal function nifti_image_open()\n" - "\n", - "0.11 30 Dec 2004 [rickr] - small mods\n" - " - moved static function prototypes from header to C file\n" - " - free extensions in nifti_image_free()\n" - "\n", - "1.0 07 Jan 2005 [rickr] - INITIAL RELEASE VERSION\n" - " - added function nifti_set_filenames()\n" - " - added function nifti_read_header()\n" - " - added static function nhdr_looks_good()\n" - " - added static function need_nhdr_swap()\n" - " - exported nifti_add_exten_to_list symbol\n", - " - fixed #bytes written in nifti_write_extensions()\n" - " - only modify offset if it is too small (nifti_set_iname_offset)\n" - " - added nifti_type 3 to nifti_makehdrname and nifti_makeimgname\n" - " - added function nifti_set_filenames()\n" - "\n", - "1.1 07 Jan 2005 [rickr]\n" - " - in nifti_read_header(), swap if needed\n" - "\n", - "1.2 07 Feb 2005 [kate fissell c/o rickr] \n" - " - nifti1.h: added doxygen comments for main struct and #define groups\n" - " - nifti1_io.h: added doxygen comments for file and nifti_image struct\n" - " - nifti1_io.h: added doxygen comments for file and some functions\n" - " - nifti1_io.c: changed nifti_copy_nim_info to use memcpy\n" - "\n", - "1.3 09 Feb 2005 [rickr]\n" - " - nifti1.h: added doxygen comments for extension structs\n" - " - nifti1_io.h: put most #defines in #ifdef _NIFTI1_IO_C_ block\n" - " - added a doxygen-style description to every exported function\n" - " - added doxygen-style comments within some functions\n" - " - re-exported many znzFile functions that I had made static\n" - " - re-added nifti_image_open (sorry, Mark)\n" - " - every exported function now has 'nifti' in the name (19 functions)\n", - " - made sure every alloc() has a failure test\n" - " - added nifti_copy_extensions function, for use in nifti_copy_nim_info\n" - " - nifti_is_gzfile: added initial strlen test\n" - " - nifti_set_filenames: added set_byte_order parameter option\n" - " (it seems appropriate to set the BO when new files are associated)\n" - " - disp_nifti_1_header: prints to stdout (a.o.t. stderr), with fflush\n" - "\n", - "1.4 23 Feb 2005 [rickr] - sourceforge merge\n" - " - merged into the nifti_io CVS directory structure at sourceforge.net\n" - " - merged in 4 changes by Mark, and re-added his const keywords\n" - " - cast some pointers to (void *) for -pedantic compile option\n" - " - added nifti_free_extensions()\n" - "\n", - "1.5 02 Mar 2005 [rickr] - started nifti global options\n" - " - gni_debug is now g_opts.debug\n" - " - added validity check parameter to nifti_read_header\n" - " - need_nhdr_swap no longer does test swaps on the stack\n" - "\n", - "1.6 05 April 2005 [rickr] - validation and collapsed_image_read\n" - " - added nifti_read_collapsed_image(), an interface for reading partial\n" - " datasets, specifying a subset of array indices\n" - " - for read_collapsed_image, added static functions: rci_read_data(),\n" - " rci_alloc_mem(), and make_pivot_list()\n", - " - added nifti_nim_is_valid() to check for consistency (more to do)\n" - " - added nifti_nim_has_valid_dims() to do many dimensions tests\n" - "\n", - "1.7 08 April 2005 [rickr]\n" - " - added nifti_update_dims_from_array() - to update dimensions\n" - " - modified nifti_makehdrname() and nifti_makeimgname():\n" - " if prefix has a valid extension, use it (else make one up)\n" - " - added nifti_get_intlist - for making an array of ints\n" - " - fixed init of NBL->bsize in nifti_alloc_NBL_mem() {thanks, Bob}\n" - "\n", - "1.8 14 April 2005 [rickr]\n" - " - added nifti_set_type_from_names(), for nifti_set_filenames()\n" - " (only updates type if number of files does not match it)\n" - " - added is_valid_nifti_type(), just to be sure\n" - " - updated description of nifti_read_collapsed_image() for *data change\n" - " (if *data is already set, assume memory exists for results)\n" - " - modified rci_alloc_mem() to allocate only if *data is NULL\n" - "\n", - "1.9 19 April 2005 [rickr]\n" - " - added extension codes NIFTI_ECODE_COMMENT and NIFTI_ECODE_XCEDE\n" - " - added nifti_type codes NIFTI_MAX_ECODE and NIFTI_MAX_FTYPE\n" - " - added nifti_add_extension() {exported}\n" - " - added nifti_fill_extension() as a static function\n" - " - added nifti_is_valid_ecode() {exported}\n", - " - nifti_type values are now NIFTI_FTYPE_* file codes\n" - " - in nifti_read_extensions(), decrement 'remain' by extender size, 4\n" - " - in nifti_set_iname_offset(), case 1, update if offset differs\n" - " - only output '-d writing nifti file' if debug > 1\n" - "\n", - "1.10 10 May 2005 [rickr]\n" - " - files are read using ZLIB only if they end in '.gz'\n" - "\n", - "1.11 12 August 2005 [kate fissell]\n" - " - Kate's 0.2 release packaging, for sourceforge\n" - "\n", - "1.12 17 August 2005 [rickr] - comment (doxygen) updates\n" - " - updated comments for most functions (2 updates from Cinly Ooi)\n" - " - added nifti_type_and_names_match()\n" - "\n", - "1.12a 24 August 2005 [rickr] - remove all tabs from Clibs/*/*.[ch]\n", - "1.12b 25 August 2005 [rickr] - changes by Hans Johnson\n", - "1.13 25 August 2005 [rickr]\n", - " - finished changes by Hans for Insight\n" - " - added const in all appropraite parameter locations (30-40)\n" - " (any pointer referencing data that will not change)\n" - " - shortened all string constants below 509 character limit\n" - "1.14 28 October 2005 [HJohnson]\n", - " - use nifti_set_filenames() in nifti_convert_nhdr2nim()\n" - "1.15 02 November 2005 [rickr]\n", - " - added skip_blank_ext to nifti_global_options\n" - " - added nifti_set_skip_blank_ext(), to set option\n" - " - if skip_blank_ext and no extensions, do not read/write extender\n" - "1.16 18 November 2005 [rickr]\n", - " - removed any test or access of dim[i], i>dim[0]\n" - " - do not set pixdim for collapsed dims to 1.0, leave them as they are\n" - " - added magic and dim[i] tests in nifti_hdr_looks_good()\n" - " - added 2 size_t casts\n" - "1.17 22 November 2005 [rickr]\n", - " - in hdr->nim, for i > dim[0], pass 0 or 1, else set to 1\n" - "1.18 02 March 2006 [rickr]\n", - " - in nifti_alloc_NBL_mem(), fixed nt=0 case from 1.17 change\n" - "1.19 23 May 2006 [HJohnson,rickr]\n", - " - nifti_write_ascii_image(): free(hstr)\n" - " - nifti_copy_extensions(): clear num_ext and ext_list\n" - "1.20 27 Jun 2006 [rickr]\n", - " - nifti_findhdrname(): fixed assign of efirst to match stated logic\n" - " (problem found by Atle Bjørnerud)\n" - "1.21 05 Sep 2006 [rickr] update for nifticlib-0.4 release\n", - " - was reminded to actually add nifti_set_skip_blank_ext()\n" - " - init g_opts.skip_blank_ext to 0\n" - "1.22 01 Jun 2007 nifticlib-0.5 release\n", - "1.23 05 Jun 2007 nifti_add_exten_to_list: revert on failure, free old list\n" - "1.24 07 Jun 2007 nifti_copy_extensions: use esize-8 for data size\n" - "1.25 12 Jun 2007 [rickr] EMPTY_IMAGE creation\n", - " - added nifti_make_new_header() - to create from dims/dtype\n" - " - added nifti_make_new_nim() - to create from dims/dtype/fill\n" - " - added nifti_is_valid_datatype(), and more debug info\n", - "1.26 27 Jul 2007 [rickr] handle single volumes > 2^31 bytes (but < 2^32)\n", - "1.27 28 Jul 2007 [rickr] nim->nvox, NBL-bsize are now type size_t\n" - "1.28 30 Jul 2007 [rickr] size_t updates\n", - "1.29 08 Aug 2007 [rickr] for list, valid_nifti_brick_list requires 3 dims\n" - "1.30 08 Nov 2007 [Yaroslav/rickr]\n" - " - fix ARM struct alignment problem in byte-swapping routines\n", - "1.31 29 Nov 2007 [rickr] for nifticlib-1.0.0\n" - " - added nifti_datatype_to/from_string routines\n" - " - added DT_RGBA32/NIFTI_TYPE_RGBA32 datatype macros (2304)\n" - " - added NIFTI_ECODE_FREESURFER (14)\n", - "1.32 08 Dec 2007 [rickr]\n" - " - nifti_hdr_looks_good() allows ANALYZE headers (req. by V. Luccio)\n" - " - added nifti_datatype_is_valid()\n", - "1.33 05 Feb 2008 [hansj,rickr] - block nia.gz use\n" - "1.34 13 Jun 2008 [rickr] - added nifti_compiled_with_zlib()\n" - "1.35 03 Aug 2008 [rickr]\n", - " - deal with swapping, so that CPU type does not affect output\n" - " (motivated by C Burns)\n" - " - added nifti_analyze75 structure and nifti_swap_as_analyze()\n" - " - previous swap_nifti_header is saved as old_swap_nifti_header\n" - " - also swap UNUSED fields in nifti_1_header struct\n", - "1.36 07 Oct 2008 [rickr]\n", - " - added nifti_NBL_matches_nim() check for write_bricks()\n" - "1.37 10 Mar 2009 [rickr]\n", - " - H Johnson cast updates (06 Feb)\n" - " - added NIFTI_ECODE_PYPICKLE for PyNIfTI (06 Feb)\n" - " - added NIFTI_ECODEs 18-28 for the LONI MiND group\n" - "1.38 28 Apr 2009 [rickr]\n", - " - uppercase extensions are now valid (requested by M. Coursolle)\n" - " - nifti_set_allow_upper_fext controls this option (req by C. Ooi)\n" - "1.39 23 Jun 2009 [rickr]: added 4 checks of alloc() returns\n", - "1.40 16 Mar 2010 [rickr]: added NIFTI_ECODE_VOXBO for D. Kimberg\n", - "1.41 28 Apr 2010 [rickr]: added NIFTI_ECODE_CARET for J. Harwell\n", - "1.42 06 Jul 2010 [rickr]: trouble with large (gz) files\n", - " - noted/investigated by M Hanke and Y Halchenko\n" - " - fixed znzread/write, noting example by M Adler\n" - " - changed nifti_swap_* routines/calls to take size_t (6)\n" - "1.43 07 Jul 2010 [rickr]: fixed znzR/W to again return nmembers\n", - "1.44 19 Jul 2013 [rickr]: ITK compatibility updates from H Johnson\n", - "----------------------------------------------------------------------\n" -}; - -/* rcr - todo - - - nifti_tool -copy_sform SFORM_DSET.nii -infile ORIG.nii -prefix PP - -copy_orient SFORM_DSET.nii -infile ORIG.nii -prefix PP - - - check converting nim 2 n2hdr - - update for n2 (and/or split from n1) - - is_nifti_file (maybe use nifti_header_version), nifti_hdr_looks_good - - extensions - - nifti_make_new_n1_header: check that dims are small enough (<2^15) - - nifti_convert_nim2nhdr: rename to nim2n1hdr and write nim2n2hdr - (maybe have nifti_convert_nim2nhdr wrap current version) - - nifti_set_iname_offset: n2 update via nifti_type - - track use of nifti_type - - nifti_image_write_hdr_img2: write nifti_2_header - */ - -static char const * const gni2_history[] = -{ - "----------------------------------------------------------------------\n" - "history (of nifti-2 library changes):\n" - "\n", - "2.00 02 Jan, 2014 [rickr]\n" - " Richard Reynolds of the National Institutes of Health, SSCC/DIRP/NIMH\n" - " - initial version - change types to 64-bit based on new nifti_image\n", - "2.01 04 Apr, 2014 [rickr]\n" - " - added functionality for both nifti-1 and -2 headers\n" - " (read/display/swap/convert2nim/make_new_n?_hdr)\n" - " - still needs much nifti-2 functionality\n", - "2.02 11 May, 2015 [rickr]\n" - " - added to repository 28 Apr, 2015\n" - " - nifti_read_header() now returns found header struct\n" - "2.03 23 Jul, 2015 [rickr]\n" - " - possibly alter dimensions on CIFTI read\n" - " - return N-1 headers in unknown version cases\n", - "2.04 05 Aug, 2015 [rickr]\n" - " - have writing try NIFTI-2 if NIFTI-1 seems insufficient\n" - "2.05 15 Apr, 2016 [rickr]\n" - " - print int64_t using PRId64 macro, (ugly, but no warnings)\n" - "2.06 01 Oct, 2018 [rickr]\n" - " - errors should all mention NIFTI, slight additional clarity\n" -}; - -static const char gni_version[] - = "nifti-2 library version 2.06 (1 October, 2018)"; - -/*! global nifti options structure - init with defaults */ -/* see 'option accessor functions' */ -static nifti_global_options g_opts = { - 1, /* debug level */ - 0, /* skip_blank_ext - skip extender if no extensions */ - 1, /* allow_upper_fext - allow uppercase file extensions */ - 0, /* alter_cifti - alter CIFTI dims to use nx,t,u,v*/ -}; - -char nifti1_magic[4] = { 'n', '+', '1', '\0' }; -char nifti2_magic[8] = { 'n', '+', '2', '\0', '\r', '\n', '\032', '\n' }; - -/*! global nifti types structure list (per type, ordered oldest to newest) */ -static const nifti_type_ele nifti_type_list[] = { - /* type nbyper swapsize name */ - { 0, 0, 0, "DT_UNKNOWN" }, - { 0, 0, 0, "DT_NONE" }, - { 1, 0, 0, "DT_BINARY" }, /* not usable */ - { 2, 1, 0, "DT_UNSIGNED_CHAR" }, - { 2, 1, 0, "DT_UINT8" }, - { 2, 1, 0, "NIFTI_TYPE_UINT8" }, - { 4, 2, 2, "DT_SIGNED_SHORT" }, - { 4, 2, 2, "DT_INT16" }, - { 4, 2, 2, "NIFTI_TYPE_INT16" }, - { 8, 4, 4, "DT_SIGNED_INT" }, - { 8, 4, 4, "DT_INT32" }, - { 8, 4, 4, "NIFTI_TYPE_INT32" }, - { 16, 4, 4, "DT_FLOAT" }, - { 16, 4, 4, "DT_FLOAT32" }, - { 16, 4, 4, "NIFTI_TYPE_FLOAT32" }, - { 32, 8, 4, "DT_COMPLEX" }, - { 32, 8, 4, "DT_COMPLEX64" }, - { 32, 8, 4, "NIFTI_TYPE_COMPLEX64" }, - { 64, 8, 8, "DT_DOUBLE" }, - { 64, 8, 8, "DT_FLOAT64" }, - { 64, 8, 8, "NIFTI_TYPE_FLOAT64" }, - { 128, 3, 0, "DT_RGB" }, - { 128, 3, 0, "DT_RGB24" }, - { 128, 3, 0, "NIFTI_TYPE_RGB24" }, - { 255, 0, 0, "DT_ALL" }, - { 256, 1, 0, "DT_INT8" }, - { 256, 1, 0, "NIFTI_TYPE_INT8" }, - { 512, 2, 2, "DT_UINT16" }, - { 512, 2, 2, "NIFTI_TYPE_UINT16" }, - { 768, 4, 4, "DT_UINT32" }, - { 768, 4, 4, "NIFTI_TYPE_UINT32" }, - { 1024, 8, 8, "DT_INT64" }, - { 1024, 8, 8, "NIFTI_TYPE_INT64" }, - { 1280, 8, 8, "DT_UINT64" }, - { 1280, 8, 8, "NIFTI_TYPE_UINT64" }, - { 1536, 16, 16, "DT_FLOAT128" }, - { 1536, 16, 16, "NIFTI_TYPE_FLOAT128" }, - { 1792, 16, 8, "DT_COMPLEX128" }, - { 1792, 16, 8, "NIFTI_TYPE_COMPLEX128" }, - { 2048, 32, 16, "DT_COMPLEX256" }, - { 2048, 32, 16, "NIFTI_TYPE_COMPLEX256" }, - { 2304, 4, 0, "DT_RGBA32" }, - { 2304, 4, 0, "NIFTI_TYPE_RGBA32" }, -}; - -/*---------------------------------------------------------------------------*/ -/* prototypes for internal functions - not part of exported library */ - -/* extension routines */ -static int nifti_read_extensions(nifti_image *nim, znzFile fp, int64_t remain); -static int nifti_read_next_extension( nifti1_extension * nex, nifti_image *nim, int remain, znzFile fp ); -static int nifti_check_extension(nifti_image *nim, int size,int code, int rem); -static void update_nifti_image_for_brick_list(nifti_image * nim, - int64_t nbricks); -static int nifti_add_exten_to_list(nifti1_extension * new_ext, - nifti1_extension ** list, int new_length); -static int nifti_fill_extension(nifti1_extension * ext, const char * data, - int len, int ecode); -static void compute_strides(int64_t *strides,const int64_t *size,int nbyper); - -/* NBL routines */ -static int nifti_load_NBL_bricks(nifti_image * nim , int64_t * slist, - int64_t * sindex, nifti_brick_list * NBL, znzFile fp ); -static int nifti_alloc_NBL_mem( nifti_image * nim, int64_t nbricks, - nifti_brick_list * nbl); -static int nifti_copynsort(int64_t nbricks, const int64_t *blist, - int64_t **slist, int64_t **sindex); -static int nifti_NBL_matches_nim(const nifti_image *nim, - const nifti_brick_list *NBL); - -/* for nifti_read_collapsed_image: */ -static int rci_read_data(nifti_image *nim, int *pivots, int64_t *prods, - int nprods, const int64_t dims[], char *data, - znzFile fp, int64_t base_offset); -static int rci_alloc_mem(void **data, int64_t prods[8], int nprods, int nbyper); -static int make_pivot_list(nifti_image * nim, const int64_t dims[], - int pivots[], int64_t prods[], int * nprods ); - -/* misc */ -static int compare_strlist (const char * str, char ** strlist, int len); -static int fileext_compare (const char * test_ext, const char * known_ext); -static int fileext_n_compare (const char * test_ext, - const char * known_ext, size_t maxlen); -static int is_mixedcase (const char * str); -static int is_uppercase (const char * str); -static int make_lowercase (char * str); -static int make_uppercase (char * str); -static int need_nhdr_swap (short dim0, int hdrsize); -static int print_hex_vals (const char * data, size_t nbytes, FILE * fp); -static int unescape_string (char *str); /* string utility functions */ -static char *escapize_string (const char *str); - -/* consider for export */ -static int nifti_ext_type_index(nifti_image * nim, int ecode); - -/* internal I/O routines */ -static znzFile nifti_image_load_prep( nifti_image *nim ); -static int has_ascii_header(znzFile fp); -/*---------------------------------------------------------------------------*/ - - -/* for calling from some main program */ - -/*----------------------------------------------------------------------*/ -/*! display the nifti library module history (via stdout) -*//*--------------------------------------------------------------------*/ -void nifti_disp_lib_hist( int ver ) -{ - int c, len; - - switch ( ver ) { - default: { - fprintf(stderr,"** NIFTI disp_lib_list: bad ver %d\n", ver); - break; - } - - case 0: - case 2: { - len = sizeof(gni2_history)/sizeof(char *); - for( c = 0; c < len; c++ ) - fputs(gni2_history[c], stdout); - break; - } - case 1: { - len = sizeof(gni1_history)/sizeof(char *); - for( c = 0; c < len; c++ ) - fputs(gni1_history[c], stdout); - break; - } - } -} - -/*----------------------------------------------------------------------*/ -/*! display the nifti library version (via stdout) -*//*--------------------------------------------------------------------*/ -void nifti_disp_lib_version( void ) -{ - printf("%s, compiled %s\n", gni_version, __DATE__); -} - - -/*----------------------------------------------------------------------*/ -/*! nifti_image_read_bricks - read nifti data as array of bricks - * - * 13 Dec 2004 [rickr] - * - * \param hname - filename of dataset to read (must be valid) - * \param nbricks - number of sub-bricks to read - * (if blist is valid, nbricks must be > 0) - * \param blist - list of sub-bricks to read - * (can be NULL; if NULL, read complete dataset) - * \param NBL - pointer to empty nifti_brick_list struct - * (must be a valid pointer) - * - * \return - *
nim - same as nifti_image_read, but - * nim->nt = NBL->nbricks (or nt*nu*nv*nw) - * nim->nu,nv,nw = 1 - * nim->data = NULL - *
NBL - filled with data volumes - * - * By default, this function will read the nifti dataset and break the data - * into a list of nt*nu*nv*nw sub-bricks, each having size nx*ny*nz elements. - * That is to say, instead of reading the entire dataset as a single array, - * break it up into sub-bricks (volumes), each of size nx*ny*nz elements. - * - * Note: in the returned nifti_image, nu, nv and nw will always be 1. The - * intention of this function is to collapse the dataset into a single - * array of volumes (of length nbricks or nt*nu*nv*nw). - * - * If 'blist' is valid, it is taken to be a list of sub-bricks, of length - * 'nbricks'. The data will still be separated into sub-bricks of size - * nx*ny*nz elements, but now 'nbricks' sub-bricks will be returned, of the - * caller's choosing via 'blist'. - * - * E.g. consider a dataset with 12 sub-bricks (numbered 0..11), and the - * following code: - * - * 
- * { nifti_brick_list   NB_orig, NB_select;
- *   nifti_image      * nim_orig, * nim_select;
- *   int                blist[5] = { 7, 0, 5, 5, 9 };
- *
- *   nim_orig   = nifti_image_read_bricks("myfile.nii", 0, NULL,  &NB_orig);
- *   nim_select = nifti_image_read_bricks("myfile.nii", 5, blist, &NB_select);
- * }
- *
- * - * Here, nim_orig gets the entire dataset, where NB_orig.nbricks = 12. But - * nim_select has NB_select.nbricks = 5. - * - * Note that the first case is not quite the same as just calling the - * nifti_image_read function, as here the data is separated into sub-bricks. - * - * Note that valid blist elements are in [0..nt*nu*nv*nw-1], - * or written [ 0 .. (dim[4]*dim[5]*dim[6]*dim[7] - 1) ]. - * - * Note that, as is the case with all of the reading functions, the - * data will be allocated, read in, and properly byte-swapped, if - * necessary. - * - * \sa nifti_image_load_bricks, nifti_free_NBL, valid_nifti_brick_list, - nifti_image_read -*//*----------------------------------------------------------------------*/ -nifti_image *nifti_image_read_bricks(const char * hname, int64_t nbricks, - const int64_t * blist, nifti_brick_list * NBL) -{ - nifti_image * nim; - - if( !hname || !NBL ){ - fprintf(stderr,"** nifti_image_read_bricks: bad params (%p,%p)\n", - hname, (void *)NBL); - return NULL; - } - - if( blist && nbricks <= 0 ){ - /* use PRId64 for printing int64_t 14 Apr 2016 */ - fprintf(stderr,"** nifti_image_read_bricks: bad nbricks, %" PRId64 "\n", - nbricks); - return NULL; - } - - nim = nifti_image_read(hname, 0); /* read header, but not data */ - - if( !nim ) return NULL; /* errors were already printed */ - - /* if we fail, free image and return */ - if( nifti_image_load_bricks(nim, nbricks, blist, NBL) <= 0 ){ - nifti_image_free(nim); - return NULL; - } - - if( blist ) update_nifti_image_for_brick_list(nim, nbricks); - - return nim; -} - - -/*---------------------------------------------------------------------- - * update_nifti_image_for_brick_list - update nifti_image - * - * When loading a specific brick list, the distinction between - * nt, nu, nv and nw is lost. So put everything in t, and set - * dim[0] = 4. - *----------------------------------------------------------------------*/ -static void update_nifti_image_for_brick_list( nifti_image * nim , - int64_t nbricks ) -{ - int64_t ndim; - - if( g_opts.debug > 2 ){ - fprintf(stderr,"+d updating image dimensions for %" PRId64 - " bricks in list\n", nbricks); - fprintf(stderr," ndim = %" PRId64 "\n",nim->ndim); - fprintf(stderr," nx,ny,nz,nt,nu,nv,nw: (%" PRId64 ",%" PRId64 - ",%" PRId64 ",%" PRId64 ",%" PRId64 ",%" PRId64 ",%" PRId64 ")\n", - nim->nx, nim->ny, nim->nz, nim->nt, nim->nu, nim->nv, nim->nw); - } - - nim->nt = nbricks; - nim->nu = nim->nv = nim->nw = 1; - nim->dim[4] = nbricks; - nim->dim[5] = nim->dim[6] = nim->dim[7] = 1; - - /* compute nvox */ - /* do not rely on dimensions above dim[0] 16 Nov 2005 [rickr] */ - for( nim->nvox = 1, ndim = 1; ndim <= nim->dim[0]; ndim++ ) - nim->nvox *= nim->dim[ndim]; - - /* update the dimensions to 4 or lower */ - for( ndim = 4; (ndim > 1) && (nim->dim[ndim] <= 1); ndim-- ) - ; - - if( g_opts.debug > 2 ){ - fprintf(stderr,"+d ndim = %" PRId64 " -> %" PRId64 "\n",nim->ndim, ndim); - fprintf(stderr," --> (%" PRId64 ",%" PRId64 ",%" PRId64 ",%" PRId64 - ",%" PRId64 ",%" PRId64 ",%" PRId64 ")\n", - nim->nx, nim->ny, nim->nz, nim->nt, nim->nu, nim->nv, nim->nw); - } - - nim->dim[0] = nim->ndim = ndim; -} - - -/*----------------------------------------------------------------------*/ -/*! nifti_update_dims_from_array - update nx, ny, ... from nim->dim[] - - Fix all the dimension information, based on a new nim->dim[]. - - Note: we assume that dim[0] will not increase. - - Check for updates to pixdim[], dx,..., nx,..., nvox, ndim, dim[0]. -*//*--------------------------------------------------------------------*/ -int nifti_update_dims_from_array( nifti_image * nim ) -{ - int c; - int64_t ndim; - - if( !nim ){ - fprintf(stderr,"** NIFTI update_dims: missing nim\n"); - return 1; - } - - if( g_opts.debug > 2 ){ - fprintf(stderr,"+d updating image dimensions given nim->dim:"); - for( c = 0; c < 8; c++ ) fprintf(stderr," %" PRId64, nim->dim[c]); - fputc('\n',stderr); - } - - /* verify dim[0] first */ - if(nim->dim[0] < 1 || nim->dim[0] > 7){ - fprintf(stderr,"** NIFTI: invalid dim[0], dim[] = "); - for( c = 0; c < 8; c++ ) fprintf(stderr," %" PRId64, nim->dim[c]); - fputc('\n',stderr); - return 1; - } - - /* set nx, ny ..., dx, dy, ..., one by one */ - - /* less than 1, set to 1, else copy */ - if(nim->dim[1] < 1) nim->nx = nim->dim[1] = 1; - else nim->nx = nim->dim[1]; - nim->dx = nim->pixdim[1]; - - /* if undefined, or less than 1, set to 1 */ - if(nim->dim[0] < 2 || (nim->dim[0] >= 2 && nim->dim[2] < 1)) - nim->ny = nim->dim[2] = 1; - else - nim->ny = nim->dim[2]; - /* copy delta values, in any case */ - nim->dy = nim->pixdim[2]; - - if(nim->dim[0] < 3 || (nim->dim[0] >= 3 && nim->dim[3] < 1)) - nim->nz = nim->dim[3] = 1; - else /* just copy vals from arrays */ - nim->nz = nim->dim[3]; - nim->dz = nim->pixdim[3]; - - if(nim->dim[0] < 4 || (nim->dim[0] >= 4 && nim->dim[4] < 1)) - nim->nt = nim->dim[4] = 1; - else /* just copy vals from arrays */ - nim->nt = nim->dim[4]; - nim->dt = nim->pixdim[4]; - - if(nim->dim[0] < 5 || (nim->dim[0] >= 5 && nim->dim[5] < 1)) - nim->nu = nim->dim[5] = 1; - else /* just copy vals from arrays */ - nim->nu = nim->dim[5]; - nim->du = nim->pixdim[5]; - - if(nim->dim[0] < 6 || (nim->dim[0] >= 6 && nim->dim[6] < 1)) - nim->nv = nim->dim[6] = 1; - else /* just copy vals from arrays */ - nim->nv = nim->dim[6]; - nim->dv = nim->pixdim[6]; - - if(nim->dim[0] < 7 || (nim->dim[0] >= 7 && nim->dim[7] < 1)) - nim->nw = nim->dim[7] = 1; - else /* just copy vals from arrays */ - nim->nw = nim->dim[7]; - nim->dw = nim->pixdim[7]; - - for( c = 1, nim->nvox = 1; c <= nim->dim[0]; c++ ) - nim->nvox *= nim->dim[c]; - - /* compute ndim, assuming it can be no larger than the old one */ - for( ndim = nim->dim[0]; (ndim > 1) && (nim->dim[ndim] <= 1); ndim-- ) - ; - - if( g_opts.debug > 2 ){ - fprintf(stderr,"+d ndim = %" PRId64 " -> %" PRId64 "\n",nim->ndim, ndim); - fprintf(stderr," --> (%" PRId64 ",%" PRId64 ",%" PRId64 ",%" PRId64 - ",%" PRId64 ",%" PRId64 ",%" PRId64 ")\n", - nim->nx, nim->ny, nim->nz, nim->nt, nim->nu, nim->nv, nim->nw); - } - - nim->dim[0] = nim->ndim = ndim; - - return 0; -} - - -/*----------------------------------------------------------------------*/ -/*! Load the image data from disk into an already-prepared image struct. - * - * \param nim - initialized nifti_image, without data - * \param nbricks - the length of blist (must be 0 if blist is NULL) - * \param blist - an array of xyz volume indices to read (can be NULL) - * \param NBL - pointer to struct where resulting data will be stored - * - * If blist is NULL, read all sub-bricks. - * - * \return the number of loaded bricks (NBL->nbricks), - * 0 on failure, < 0 on error - * - * NOTE: it is likely that another function will copy the data pointers - * out of NBL, in which case the only pointer the calling function - * will want to free is NBL->bricks (not each NBL->bricks[i]). -*//*--------------------------------------------------------------------*/ -int nifti_image_load_bricks( nifti_image * nim , int64_t nbricks, - const int64_t * blist, nifti_brick_list * NBL ) -{ - int64_t * slist = NULL, * sindex = NULL; - int rv; - znzFile fp; - - /* we can have blist == NULL */ - if( !nim || !NBL ){ - fprintf(stderr,"** nifti_image_load_bricks, bad params (%p,%p)\n", - (void *)nim, (void *)NBL); - return -1; - } - - if( blist && nbricks <= 0 ){ - if( g_opts.debug > 1 ) - fprintf(stderr,"-d load_bricks: received blist with nbricks = " - "%" PRId64 "," "ignoring blist\n", nbricks); - blist = NULL; /* pretend nothing was passed */ - } - - if( blist && ! valid_nifti_brick_list(nim, nbricks, blist, g_opts.debug>0) ) - return -1; - - /* for efficiency, let's read the file in order */ - if( blist && nifti_copynsort( nbricks, blist, &slist, &sindex ) != 0 ) - return -1; - - /* open the file and position the FILE pointer */ - fp = nifti_image_load_prep( nim ); - if( !fp ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** nifti_image_load_bricks, failed load_prep\n"); - if( blist ){ free(slist); free(sindex); } - return -1; - } - - /* this will flag to allocate defaults */ - if( !blist ) nbricks = 0; - if( nifti_alloc_NBL_mem( nim, nbricks, NBL ) != 0 ){ - if( blist ){ free(slist); free(sindex); } - znzclose(fp); - return -1; - } - - rv = nifti_load_NBL_bricks(nim, slist, sindex, NBL, fp); - - if( rv != 0 ){ - nifti_free_NBL( NBL ); /* failure! */ - NBL->nbricks = 0; /* repetative, but clear */ - } - - if( slist ){ free(slist); free(sindex); } - - znzclose(fp); - - return NBL->nbricks; -} - - -/*----------------------------------------------------------------------*/ -/*! nifti_free_NBL - free all pointers and clear structure - * - * note: this does not presume to free the structure pointer -*//*--------------------------------------------------------------------*/ -void nifti_free_NBL( nifti_brick_list * NBL ) -{ - int c; - - if( NBL->bricks ){ - for( c = 0; c < NBL->nbricks; c++ ) - if( NBL->bricks[c] ) free(NBL->bricks[c]); - free(NBL->bricks); - NBL->bricks = NULL; - } - - NBL->bsize = NBL->nbricks = 0; -} - - -/*---------------------------------------------------------------------- - * nifti_load_NBL_bricks - read the file data into the NBL struct - * - * return 0 on success, -1 on failure - *----------------------------------------------------------------------*/ -static int nifti_load_NBL_bricks( nifti_image * nim , int64_t * slist, - int64_t * sindex, nifti_brick_list * NBL, znzFile fp ) -{ - int64_t oposn, fposn; /* orig and current file positions */ - int64_t rv, test; - int64_t c; - int64_t prev, isrc, idest; /* previous/current sub-brick, and new index */ - - test = znztell(fp); /* store current file position */ - if( test < 0 ){ - fprintf(stderr,"** NIFTI load bricks: ztell failed??\n"); - return -1; - } - fposn = oposn = test; - - /* first, handle the default case, no passed blist */ - if( !slist ){ - for( c = 0; c < NBL->nbricks; c++ ) { - rv = nifti_read_buffer(fp, NBL->bricks[c], NBL->bsize, nim); - if( rv != NBL->bsize ){ - fprintf(stderr,"** NIFTI load bricks: cannot read brick %" PRId64 - " from '%s'\n", - c, nim->iname ? nim->iname : nim->fname); - return -1; - } - } - if( g_opts.debug > 1 ) - fprintf(stderr,"+d read %" PRId64 " default %" PRId64 - "-byte bricks from file %s\n", - NBL->nbricks, NBL->bsize, - nim->iname ? nim->iname:nim->fname ); - return 0; - } - - if( !sindex ){ - fprintf(stderr,"** NIFTI load_NBL_bricks: missing index list\n"); - return -1; - } - - prev = -1; /* use prev for previous sub-brick */ - for( c = 0; c < NBL->nbricks; c++ ){ - isrc = slist[c]; /* this is original brick index (c is new one) */ - idest = sindex[c]; /* this is the destination index for this data */ - - /* if this sub-brick is not the previous, we must read from disk */ - if( isrc != prev ){ - - /* if we are not looking at the correct sub-brick, scan forward */ - if( fposn != (oposn + isrc*NBL->bsize) ){ - fposn = oposn + isrc*NBL->bsize; - /* rcr - znz functions need to handle 64-bit cases, */ - /* see setting _FILE_OFFSET_BITS */ - if( znzseek(fp, fposn, SEEK_SET) < 0 ){ - fprintf(stderr,"** NIFTI: failed to locate brick %" PRId64 - " in file '%s'\n", - isrc, nim->iname ? nim->iname : nim->fname); - return -1; - } - } - - /* only 10,000 lines later and we're actually reading something! */ - rv = nifti_read_buffer(fp, NBL->bricks[idest], NBL->bsize, nim); - if( rv != NBL->bsize ){ - fprintf(stderr,"** NIFTI: failed to read brick %" PRId64 - " from file '%s'\n", - isrc, nim->iname ? nim->iname : nim->fname); - if( g_opts.debug > 1 ) - fprintf(stderr," (read %" PRId64 " of %" PRId64 " bytes)\n", - rv, NBL->bsize); - return -1; - } - fposn += NBL->bsize; - } else { - /* we have already read this sub-brick, just copy the previous one */ - /* note that this works because they are sorted */ - memcpy(NBL->bricks[idest], NBL->bricks[sindex[c-1]], NBL->bsize); - } - - prev = isrc; /* in any case, note the now previous sub-brick */ - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * nifti_alloc_NBL_mem - allocate memory for bricks - * - * return 0 on success, -1 on failure - *----------------------------------------------------------------------*/ -static int nifti_alloc_NBL_mem(nifti_image * nim, int64_t nbricks, - nifti_brick_list * nbl) -{ - int64_t c; - - /* if nbricks is not specified, use the default */ - if( nbricks > 0 ) nbl->nbricks = nbricks; - else { /* I missed this one with the 1.17 change 02 Mar 2006 [rickr] */ - nbl->nbricks = 1; - for( c = 4; c <= nim->ndim; c++ ) - nbl->nbricks *= nim->dim[c]; - } - - nbl->bsize = nim->nx * nim->ny * nim->nz * nim->nbyper; /* bytes */ - nbl->bricks = (void **)malloc(nbl->nbricks * sizeof(void *)); - - if( ! nbl->bricks ){ - fprintf(stderr,"** NIFTI NANM: failed to alloc %" PRId64 - " void ptrs\n",nbricks); - return -1; - } - - for( c = 0; c < nbl->nbricks; c++ ){ - nbl->bricks[c] = (void *)malloc(nbl->bsize); - if( ! nbl->bricks[c] ){ - fprintf(stderr,"** NIFTI NANM: failed to alloc %" PRId64 - " bytes for brick %" PRId64 "\n", nbl->bsize, c); - /* so free and clear everything before returning */ - while( c > 0 ){ - c--; - free(nbl->bricks[c]); - } - free(nbl->bricks); - nbl->bricks = NULL; - nbl->bsize = nbl->nbricks = 0; - return -1; - } - } - - if( g_opts.debug > 2 ) - fprintf(stderr,"+d NANM: alloc'd %" PRId64 " bricks of %" PRId64 - " bytes for NBL\n", nbl->nbricks, nbl->bsize); - - return 0; -} - - -/*---------------------------------------------------------------------- - * nifti_copynsort - copy int list, and sort with indices - * - * 1. duplicate the incoming list - * 2. create an sindex list, and init with 0..nbricks-1 - * 3. do a slow insertion sort on the small slist, along with sindex list - * 4. check results, just to be positive - * - * So slist is sorted, and sindex hold original positions. - * - * return 0 on success, -1 on failure - *----------------------------------------------------------------------*/ -static int nifti_copynsort(int64_t nbricks, const int64_t *blist, - int64_t ** slist, int64_t ** sindex) -{ - int64_t * stmp, * itmp; /* for ease of typing/reading */ - int64_t c1, c2, spos, tmp; - - *slist = (int64_t *)malloc(nbricks * sizeof(int64_t)); - *sindex = (int64_t *)malloc(nbricks * sizeof(int64_t)); - - if( !*slist || !*sindex ){ - fprintf(stderr,"** NIFTI NCS: failed to alloc %" PRId64 - " ints for sorting\n", nbricks); - if(*slist) free(*slist); /* maybe one succeeded */ - if(*sindex) free(*sindex); - return -1; - } - - /* init the lists */ - for( c1 = 0; c1 < nbricks; c1++ ) { - (*slist)[c1] = blist[c1]; - (*sindex)[c1] = c1; - } - - /* now actually sort slist */ - stmp = *slist; - itmp = *sindex; - for( c1 = 0; c1 < nbricks-1; c1++ ) { - /* find smallest value, init to current */ - spos = c1; - for( c2 = c1+1; c2 < nbricks; c2++ ) - if( stmp[c2] < stmp[spos] ) spos = c2; - if( spos != c1 ) /* swap: fine, don't maintain sub-order, see if I care */ - { - tmp = stmp[c1]; /* first swap the sorting values */ - stmp[c1] = stmp[spos]; - stmp[spos] = tmp; - - tmp = itmp[c1]; /* then swap the index values */ - itmp[c1] = itmp[spos]; - itmp[spos] = tmp; - } - } - - if( g_opts.debug > 2 ){ - fprintf(stderr, "+d sorted indexing list:\n"); - fprintf(stderr, " orig : "); - for( c1 = 0; c1 < nbricks; c1++ ) fprintf(stderr," %" PRId64, blist[c1]); - fprintf(stderr,"\n new : "); - for( c1 = 0; c1 < nbricks; c1++ ) fprintf(stderr," %" PRId64, stmp[c1]); - fprintf(stderr,"\n indices: "); - for( c1 = 0; c1 < nbricks; c1++ ) fprintf(stderr," %" PRId64, itmp[c1]); - fputc('\n', stderr); - } - - /* check the sort (why not? I've got time...) */ - for( c1 = 0; c1 < nbricks-1; c1++ ){ - if( (stmp[c1] > stmp[c1+1]) || (blist[itmp[c1]] != stmp[c1]) ){ - fprintf(stderr,"** NIFTI sorting screw-up, way to go, rick!\n"); - free(stmp); free(itmp); *slist = NULL; *sindex = NULL; - return -1; - } - } - - if( g_opts.debug > 2 ) fprintf(stderr,"-d sorting is okay\n"); - - return 0; -} - - -/*----------------------------------------------------------------------*/ -/*! valid_nifti_brick_list - check sub-brick list for image - * - * This function verifies that nbricks and blist are appropriate - * for use with this nim, based on the dimensions. - * - * \param nim nifti_image to check against - * \param nbricks number of brick indices in blist - * \param blist list of brick indices to check in nim - * \param disp_error if this flag is set, report errors to user - * - * \return 1 if valid, 0 if not -*//*--------------------------------------------------------------------*/ -int valid_nifti_brick_list(nifti_image * nim , int64_t nbricks, - const int64_t * blist, int disp_error) -{ - int64_t c, nsubs; - - if( !nim ){ - if( disp_error || g_opts.debug > 0 ) - fprintf(stderr,"** valid_nifti_brick_list: missing nifti image\n"); - return 0; - } - - if( nbricks <= 0 || !blist ){ - if( disp_error || g_opts.debug > 1 ) - fprintf(stderr,"** valid_nifti_brick_list: no brick list to check\n"); - return 0; - } - - if( nim->dim[0] < 3 ){ - if( disp_error || g_opts.debug > 1 ) - fprintf(stderr,"** NIFTI: cannot read explict brick list from %" PRId64 - "-D dataset\n", nim->dim[0]); - return 0; - } - - /* nsubs sub-brick is nt*nu*nv*nw */ - for( c = 4, nsubs = 1; c <= nim->dim[0]; c++ ) - nsubs *= nim->dim[c]; - - if( nsubs <= 0 ){ - fprintf(stderr,"** NIFTI VNBL warning: bad dim list (%" PRId64 ",%" - PRId64 ",%" PRId64 ",%" PRId64 ")\n", - nim->dim[4], nim->dim[5], nim->dim[6], nim->dim[7]); - return 0; - } - - for( c = 0; c < nbricks; c++ ) - if( (blist[c] < 0) || (blist[c] >= nsubs) ){ - if( disp_error || g_opts.debug > 1 ) - fprintf(stderr, - "** NIFTI volume index %" PRId64 " (#%" PRId64 ")" - " is out of range [0,%" PRId64 "]\n", blist[c], c, nsubs-1); - return 0; - } - - return 1; /* all is well */ -} - -/*----------------------------------------------------------------------*/ -/* verify that NBL struct is a valid data source for the image - * - * return 1 if so, 0 otherwise -*//*--------------------------------------------------------------------*/ -static int nifti_NBL_matches_nim(const nifti_image *nim, - const nifti_brick_list *NBL) -{ - int64_t volbytes = 0; /* bytes per volume */ - int64_t nvols = 0; - int ind, errs = 0; - - - if( !nim || !NBL ) { - if( g_opts.debug > 0 ) - fprintf(stderr,"** nifti_NBL_matches_nim: NULL pointer(s)\n"); - return 0; - } - - /* for nim, compute volbytes and nvols */ - if( nim->ndim > 0 ) { - /* first 3 indices are over a single volume */ - volbytes = (int64_t)nim->nbyper; - for( ind = 1; ind <= nim->ndim && ind < 4; ind++ ) - volbytes *= nim->dim[ind]; - - for( ind = 4, nvols = 1; ind <= nim->ndim; ind++ ) - nvols *= nim->dim[ind]; - } - - if( volbytes != NBL->bsize ) { - if( g_opts.debug > 1 ) - fprintf(stderr,"** NIFTI NBL/nim mismatch, volbytes = %" PRId64 - ", %" PRId64 "\n", NBL->bsize, volbytes); - errs++; - } - - if( nvols != NBL->nbricks ) { - if( g_opts.debug > 1 ) - fprintf(stderr,"** NIFTI NBL/nim mismatch, nvols = %" PRId64 - ", %" PRId64 "\n", NBL->nbricks, nvols); - errs++; - } - - if( errs ) return 0; - else if ( g_opts.debug > 2 ) - fprintf(stderr,"-- nim/NBL agree: nvols = %" PRId64 - ", nbytes = %" PRId64 "\n", nvols, volbytes); - - return 1; -} - -/* end of new nifti_image_read_bricks() functionality */ - -/*----------------------------------------------------------------------*/ -/*! display the orientation from the quaternian fields - * - * \param mesg if non-NULL, display this message first - * \param mat the matrix to convert to "nearest" orientation - * - * \return -1 if results cannot be determined, 0 if okay -*//*--------------------------------------------------------------------*/ -int nifti_disp_matrix_orient( const char * mesg, nifti_dmat44 mat ) -{ - int i, j, k; - - if ( mesg ) fputs( mesg, stderr ); /* use stdout? */ - - nifti_dmat44_to_orientation( mat, &i,&j,&k ); - if ( i <= 0 || j <= 0 || k <= 0 ) return -1; - - /* so we have good codes */ - fprintf(stderr, " i orientation = '%s'\n" - " j orientation = '%s'\n" - " k orientation = '%s'\n", - nifti_orientation_string(i), - nifti_orientation_string(j), - nifti_orientation_string(k) ); - return 0; -} - - -/*----------------------------------------------------------------------*/ -/*! duplicate the given string (alloc length+1) - * - * \return allocated pointer (or NULL on failure) -*//*--------------------------------------------------------------------*/ -char *nifti_strdup(const char *str) -{ - char *dup; - - if( !str ) return NULL; /* allow calls passing NULL */ - - dup = (char *)malloc(strlen(str) + 1); - - /* check for failure */ - if( dup ) strcpy(dup, str); - else fprintf(stderr,"** nifti_strdup: failed to alloc %" PRId64 - " bytes\n", (int64_t)(strlen(str)+1)); - - return dup; -} - - -/*---------------------------------------------------------------------------*/ -/*! Return a pointer to a string holding the name of a NIFTI datatype. - - \param dt NIfTI-1 datatype - - \return pointer to static string holding the datatype name - - \warning Do not free() or modify this string! - It points to static storage. - - \sa NIFTI1_DATATYPES group in nifti1.h -*//*-------------------------------------------------------------------------*/ -char const * nifti_datatype_string( int dt ) -{ - switch( dt ){ - case DT_UNKNOWN: return "UNKNOWN" ; - case DT_BINARY: return "BINARY" ; - case DT_INT8: return "INT8" ; - case DT_UINT8: return "UINT8" ; - case DT_INT16: return "INT16" ; - case DT_UINT16: return "UINT16" ; - case DT_INT32: return "INT32" ; - case DT_UINT32: return "UINT32" ; - case DT_INT64: return "INT64" ; - case DT_UINT64: return "UINT64" ; - case DT_FLOAT32: return "FLOAT32" ; - case DT_FLOAT64: return "FLOAT64" ; - case DT_FLOAT128: return "FLOAT128" ; - case DT_COMPLEX64: return "COMPLEX64" ; - case DT_COMPLEX128: return "COMPLEX128" ; - case DT_COMPLEX256: return "COMPLEX256" ; - case DT_RGB24: return "RGB24" ; - case DT_RGBA32: return "RGBA32" ; - } - return "**ILLEGAL**" ; -} - -/*----------------------------------------------------------------------*/ -/*! Determine if the datatype code dt is an integer type (1=YES, 0=NO). - - \return whether the given NIfTI-1 datatype code is valid - - \sa NIFTI1_DATATYPES group in nifti1.h -*//*--------------------------------------------------------------------*/ -int nifti_is_inttype( int dt ) -{ - switch( dt ){ - case DT_UNKNOWN: return 0 ; - case DT_BINARY: return 0 ; - case DT_INT8: return 1 ; - case DT_UINT8: return 1 ; - case DT_INT16: return 1 ; - case DT_UINT16: return 1 ; - case DT_INT32: return 1 ; - case DT_UINT32: return 1 ; - case DT_INT64: return 1 ; - case DT_UINT64: return 1 ; - case DT_FLOAT32: return 0 ; - case DT_FLOAT64: return 0 ; - case DT_FLOAT128: return 0 ; - case DT_COMPLEX64: return 0 ; - case DT_COMPLEX128: return 0 ; - case DT_COMPLEX256: return 0 ; - case DT_RGB24: return 1 ; - case DT_RGBA32: return 1 ; - } - return 0 ; -} - -/*---------------------------------------------------------------------------*/ -/*! Return a pointer to a string holding the name of a NIFTI units type. - - \param uu NIfTI-1 unit code - - \return pointer to static string for the given unit type - - \warning Do not free() or modify this string! - It points to static storage. - - \sa NIFTI1_UNITS group in nifti1.h -*//*-------------------------------------------------------------------------*/ -char const *nifti_units_string( int uu ) -{ - switch( uu ){ - case NIFTI_UNITS_METER: return "m" ; - case NIFTI_UNITS_MM: return "mm" ; - case NIFTI_UNITS_MICRON: return "um" ; - case NIFTI_UNITS_SEC: return "s" ; - case NIFTI_UNITS_MSEC: return "ms" ; - case NIFTI_UNITS_USEC: return "us" ; - case NIFTI_UNITS_HZ: return "Hz" ; - case NIFTI_UNITS_PPM: return "ppm" ; - case NIFTI_UNITS_RADS: return "rad/s" ; - } - return "Unknown" ; -} - -/*---------------------------------------------------------------------------*/ -/*! Return a pointer to a string holding the name of a NIFTI transform type. - - \param xx NIfTI-1 xform code - - \return pointer to static string describing xform code - - \warning Do not free() or modify this string! - It points to static storage. - - \sa NIFTI1_XFORM_CODES group in nifti1.h -*//*-------------------------------------------------------------------------*/ -char const *nifti_xform_string( int xx ) -{ - switch( xx ){ - case NIFTI_XFORM_SCANNER_ANAT: return "Scanner Anat" ; - case NIFTI_XFORM_ALIGNED_ANAT: return "Aligned Anat" ; - case NIFTI_XFORM_TALAIRACH: return "Talairach" ; - case NIFTI_XFORM_MNI_152: return "MNI_152" ; - } - return "Unknown" ; -} - -/*---------------------------------------------------------------------------*/ -/*! Return a pointer to a string holding the name of a NIFTI intent type. - - \param ii NIfTI-1 intent code - - \return pointer to static string describing code - - \warning Do not free() or modify this string! - It points to static storage. - - \sa NIFTI1_INTENT_CODES group in nifti1.h -*//*-------------------------------------------------------------------------*/ -char const *nifti_intent_string( int ii ) -{ - switch( ii ){ - case NIFTI_INTENT_CORREL: return "Correlation statistic" ; - case NIFTI_INTENT_TTEST: return "T-statistic" ; - case NIFTI_INTENT_FTEST: return "F-statistic" ; - case NIFTI_INTENT_ZSCORE: return "Z-score" ; - case NIFTI_INTENT_CHISQ: return "Chi-squared distribution" ; - case NIFTI_INTENT_BETA: return "Beta distribution" ; - case NIFTI_INTENT_BINOM: return "Binomial distribution" ; - case NIFTI_INTENT_GAMMA: return "Gamma distribution" ; - case NIFTI_INTENT_POISSON: return "Poisson distribution" ; - case NIFTI_INTENT_NORMAL: return "Normal distribution" ; - case NIFTI_INTENT_FTEST_NONC: return "F-statistic noncentral" ; - case NIFTI_INTENT_CHISQ_NONC: return "Chi-squared noncentral" ; - case NIFTI_INTENT_LOGISTIC: return "Logistic distribution" ; - case NIFTI_INTENT_LAPLACE: return "Laplace distribution" ; - case NIFTI_INTENT_UNIFORM: return "Uniform distribition" ; - case NIFTI_INTENT_TTEST_NONC: return "T-statistic noncentral" ; - case NIFTI_INTENT_WEIBULL: return "Weibull distribution" ; - case NIFTI_INTENT_CHI: return "Chi distribution" ; - case NIFTI_INTENT_INVGAUSS: return "Inverse Gaussian distribution" ; - case NIFTI_INTENT_EXTVAL: return "Extreme Value distribution" ; - case NIFTI_INTENT_PVAL: return "P-value" ; - - case NIFTI_INTENT_LOGPVAL: return "Log P-value" ; - case NIFTI_INTENT_LOG10PVAL: return "Log10 P-value" ; - - case NIFTI_INTENT_ESTIMATE: return "Estimate" ; - case NIFTI_INTENT_LABEL: return "Label index" ; - case NIFTI_INTENT_NEURONAME: return "NeuroNames index" ; - case NIFTI_INTENT_GENMATRIX: return "General matrix" ; - case NIFTI_INTENT_SYMMATRIX: return "Symmetric matrix" ; - case NIFTI_INTENT_DISPVECT: return "Displacement vector" ; - case NIFTI_INTENT_VECTOR: return "Vector" ; - case NIFTI_INTENT_POINTSET: return "Pointset" ; - case NIFTI_INTENT_TRIANGLE: return "Triangle" ; - case NIFTI_INTENT_QUATERNION: return "Quaternion" ; - - case NIFTI_INTENT_DIMLESS: return "Dimensionless number" ; - } - return "Unknown" ; -} - -/*---------------------------------------------------------------------------*/ -/*! Return a pointer to a string holding the name of a NIFTI slice_code. - - \param ss NIfTI-1 slice order code - - \return pointer to static string describing code - - \warning Do not free() or modify this string! - It points to static storage. - - \sa NIFTI1_SLICE_ORDER group in nifti1.h -*//*-------------------------------------------------------------------------*/ -char const *nifti_slice_string( int ss ) -{ - switch( ss ){ - case NIFTI_SLICE_SEQ_INC: return "sequential_increasing" ; - case NIFTI_SLICE_SEQ_DEC: return "sequential_decreasing" ; - case NIFTI_SLICE_ALT_INC: return "alternating_increasing" ; - case NIFTI_SLICE_ALT_DEC: return "alternating_decreasing" ; - case NIFTI_SLICE_ALT_INC2: return "alternating_increasing_2" ; - case NIFTI_SLICE_ALT_DEC2: return "alternating_decreasing_2" ; - } - return "Unknown" ; -} - -/*---------------------------------------------------------------------------*/ -/*! Return a pointer to a string holding the name of a NIFTI orientation. - - \param ii orientation code - - \return pointer to static string holding the orientation information - - \warning Do not free() or modify the return string! - It points to static storage. - - \sa NIFTI_L2R in nifti1_io.h -*//*-------------------------------------------------------------------------*/ -char const *nifti_orientation_string( int ii ) -{ - switch( ii ){ - case NIFTI_L2R: return "Left-to-Right" ; - case NIFTI_R2L: return "Right-to-Left" ; - case NIFTI_P2A: return "Posterior-to-Anterior" ; - case NIFTI_A2P: return "Anterior-to-Posterior" ; - case NIFTI_I2S: return "Inferior-to-Superior" ; - case NIFTI_S2I: return "Superior-to-Inferior" ; - } - return "Unknown" ; -} - -/*--------------------------------------------------------------------------*/ -/*! Given a datatype code, set number of bytes per voxel and the swapsize. - - \param datatype nifti1 datatype code - \param nbyper pointer to return value: number of bytes per voxel - \param swapsize pointer to return value: size of swap blocks - - \return appropriate values at nbyper and swapsize - - The swapsize is set to 0 if this datatype doesn't ever need swapping. - - \sa NIFTI1_DATATYPES in nifti1.h -*//*------------------------------------------------------------------------*/ -void nifti_datatype_sizes( int datatype , int *nbyper, int *swapsize ) -{ - int nb=0, ss=0 ; - switch( datatype ){ - case DT_INT8: - case DT_UINT8: nb = 1 ; ss = 0 ; break ; - - case DT_INT16: - case DT_UINT16: nb = 2 ; ss = 2 ; break ; - - case DT_RGB24: nb = 3 ; ss = 0 ; break ; - case DT_RGBA32: nb = 4 ; ss = 0 ; break ; - - case DT_INT32: - case DT_UINT32: - case DT_FLOAT32: nb = 4 ; ss = 4 ; break ; - - case DT_COMPLEX64: nb = 8 ; ss = 4 ; break ; - - case DT_FLOAT64: - case DT_INT64: - case DT_UINT64: nb = 8 ; ss = 8 ; break ; - - case DT_FLOAT128: nb = 16 ; ss = 16 ; break ; - - case DT_COMPLEX128: nb = 16 ; ss = 8 ; break ; - - case DT_COMPLEX256: nb = 32 ; ss = 16 ; break ; - } - - ASSIF(nbyper,nb) ; ASSIF(swapsize,ss) ; return ; -} - - -/*-----------------------------------------------------------------*/ -/*! copy between float and double mat44 types 10 Jul, 2015 [rickr] */ - -int nifti_mat44_to_dmat44(mat44 * fm, nifti_dmat44 * dm) -{ - int i, j; - if( !dm || !fm ) return 1; - for( i=0; i<4; i++ ) - for( j=0; j<4; j++ ) - dm->m[i][j] = (double)fm->m[i][j]; - return 0; -} - -int nifti_dmat44_to_mat44(nifti_dmat44 * dm, mat44 * fm) -{ - int i, j; - if( !dm || !fm ) return 1; - for( i=0; i<4; i++ ) - for( j=0; j<4; j++ ) - fm->m[i][j] = (float)dm->m[i][j]; - return 0; -} - - -/*---------------------------------------------------------------------------*/ -/*! Given the quaternion parameters (etc.), compute a transformation matrix - of doubles. - - See comments in nifti1.h for details. - - qb,qc,qd = quaternion parameters - - qx,qy,qz = offset parameters - - dx,dy,dz = grid stepsizes (non-negative inputs are set to 1.0) - - qfac = sign of dz step (< 0 is negative; >= 0 is positive) - - 
-   If qx=qy=qz=0, dx=dy=dz=1, then the output is a rotation matrix.
-   For qfac >= 0, the rotation is proper.
-   For qfac <  0, the rotation is improper.
-
- - \see "QUATERNION REPRESENTATION OF ROTATION MATRIX" in nifti1.h - \see nifti_mat44_to_quatern, nifti_make_orthog_mat44, - nifti_mat44_to_orientation - -*//*-------------------------------------------------------------------------*/ -nifti_dmat44 nifti_quatern_to_dmat44( double qb, double qc, double qd, - double qx, double qy, double qz, - double dx, double dy, double dz, double qfac ) -{ - nifti_dmat44 R ; - double a,b=qb,c=qc,d=qd , xd,yd,zd ; - - /* last row is always [ 0 0 0 1 ] */ - - R.m[3][0]=R.m[3][1]=R.m[3][2] = 0.0 ; R.m[3][3]= 1.0 ; - - /* compute a parameter from b,c,d */ - - a = 1.0l - (b*b + c*c + d*d) ; - if( a < 1.e-7l ){ /* special case */ - a = 1.0l / sqrt(b*b+c*c+d*d) ; - b *= a ; c *= a ; d *= a ; /* normalize (b,c,d) vector */ - a = 0.0l ; /* a = 0 ==> 180 degree rotation */ - } else{ - a = sqrt(a) ; /* angle = 2*arccos(a) */ - } - - /* load rotation matrix, including scaling factors for voxel sizes */ - - xd = (dx > 0.0) ? dx : 1.0l ; /* make sure are positive */ - yd = (dy > 0.0) ? dy : 1.0l ; - zd = (dz > 0.0) ? dz : 1.0l ; - - if( qfac < 0.0 ) zd = -zd ; /* left handedness? */ - - R.m[0][0] = (a*a+b*b-c*c-d*d) * xd; - R.m[0][1] = 2.0l * (b*c-a*d ) * yd ; - R.m[0][2] = 2.0l * (b*d+a*c ) * zd ; - R.m[1][0] = 2.0l * (b*c+a*d ) * xd ; - R.m[1][1] = (a*a+c*c-b*b-d*d) * yd; - R.m[1][2] = 2.0l * (c*d-a*b ) * zd ; - R.m[2][0] = 2.0l * (b*d-a*c ) * xd ; - R.m[2][1] = 2.0l * (c*d+a*b ) * yd ; - R.m[2][2] = (a*a+d*d-c*c-b*b) * zd; - - /* load offsets */ - - R.m[0][3] = qx ; R.m[1][3] = qy ; R.m[2][3] = qz ; - - return R ; -} - -/*---------------------------------------------------------------------------*/ -/*! Given the quaternion parameters (etc.), compute a transformation matrix. - - See comments in nifti1.h for details. - - qb,qc,qd = quaternion parameters - - qx,qy,qz = offset parameters - - dx,dy,dz = grid stepsizes (non-negative inputs are set to 1.0) - - qfac = sign of dz step (< 0 is negative; >= 0 is positive) - - 
-   If qx=qy=qz=0, dx=dy=dz=1, then the output is a rotation matrix.
-   For qfac >= 0, the rotation is proper.
-   For qfac <  0, the rotation is improper.
-
- - \see "QUATERNION REPRESENTATION OF ROTATION MATRIX" in nifti1.h - \see nifti_mat44_to_quatern, nifti_make_orthog_mat44, - nifti_mat44_to_orientation - -*//*-------------------------------------------------------------------------*/ -mat44 nifti_quatern_to_mat44( float qb, float qc, float qd, - float qx, float qy, float qz, - float dx, float dy, float dz, float qfac ) -{ - mat44 R ; - double a,b=qb,c=qc,d=qd , xd,yd,zd ; - - /* last row is always [ 0 0 0 1 ] */ - - R.m[3][0]=R.m[3][1]=R.m[3][2] = 0.0f ; R.m[3][3]= 1.0f ; - - /* compute a parameter from b,c,d */ - - a = 1.0l - (b*b + c*c + d*d) ; - if( a < 1.e-7l ){ /* special case */ - a = 1.0l / sqrt(b*b+c*c+d*d) ; - b *= a ; c *= a ; d *= a ; /* normalize (b,c,d) vector */ - a = 0.0l ; /* a = 0 ==> 180 degree rotation */ - } else{ - a = sqrt(a) ; /* angle = 2*arccos(a) */ - } - - /* load rotation matrix, including scaling factors for voxel sizes */ - - xd = (dx > 0.0) ? dx : 1.0l ; /* make sure are positive */ - yd = (dy > 0.0) ? dy : 1.0l ; - zd = (dz > 0.0) ? dz : 1.0l ; - - if( qfac < 0.0 ) zd = -zd ; /* left handedness? */ - - R.m[0][0] = (float)( (a*a+b*b-c*c-d*d) * xd) ; - R.m[0][1] = 2.0l * (b*c-a*d ) * yd ; - R.m[0][2] = 2.0l * (b*d+a*c ) * zd ; - R.m[1][0] = 2.0l * (b*c+a*d ) * xd ; - R.m[1][1] = (float)( (a*a+c*c-b*b-d*d) * yd) ; - R.m[1][2] = 2.0l * (c*d-a*b ) * zd ; - R.m[2][0] = 2.0l * (b*d-a*c ) * xd ; - R.m[2][1] = 2.0l * (c*d+a*b ) * yd ; - R.m[2][2] = (float)( (a*a+d*d-c*c-b*b) * zd) ; - - /* load offsets */ - - R.m[0][3] = qx ; R.m[1][3] = qy ; R.m[2][3] = qz ; - - return R ; -} - -/*---------------------------------------------------------------------------*/ -/*! Given the 3x4 upper corner of the matrix R, compute the quaternion - parameters that fit it. - - - Any NULL pointer on input won't get assigned (e.g., if you don't want - dx,dy,dz, just pass NULL in for those pointers). - - If the 3 input matrix columns are NOT orthogonal, they will be - orthogonalized prior to calculating the parameters, using - the polar decomposition to find the orthogonal matrix closest - to the column-normalized input matrix. - - However, if the 3 input matrix columns are NOT orthogonal, then - the matrix produced by nifti_quatern_to_dmat44 WILL have orthogonal - columns, so it won't be the same as the matrix input here. - This "feature" is because the NIFTI 'qform' transform is - deliberately not fully general -- it is intended to model a volume - with perpendicular axes. - - If the 3 input matrix columns are not even linearly independent, - you'll just have to take your luck, won't you? - - \see "QUATERNION REPRESENTATION OF ROTATION MATRIX" in nifti1.h - - \see nifti_quatern_to_dmat44, nifti_make_orthog_dmat44, - nifti_dmat44_to_orientation -*//*-------------------------------------------------------------------------*/ -void nifti_dmat44_to_quatern(nifti_dmat44 R , - double *qb, double *qc, double *qd, - double *qx, double *qy, double *qz, - double *dx, double *dy, double *dz, double *qfac ) -{ - double r11,r12,r13 , r21,r22,r23 , r31,r32,r33 ; - double xd,yd,zd , a,b,c,d ; - nifti_dmat33 P,Q ; - - /* offset outputs are read write out of input matrix */ - - ASSIF(qx,R.m[0][3]) ; ASSIF(qy,R.m[1][3]) ; ASSIF(qz,R.m[2][3]) ; - - /* load 3x3 matrix into local variables */ - - r11 = R.m[0][0] ; r12 = R.m[0][1] ; r13 = R.m[0][2] ; - r21 = R.m[1][0] ; r22 = R.m[1][1] ; r23 = R.m[1][2] ; - r31 = R.m[2][0] ; r32 = R.m[2][1] ; r33 = R.m[2][2] ; - - /* compute lengths of each column; these determine grid spacings */ - - xd = sqrt( r11*r11 + r21*r21 + r31*r31 ) ; - yd = sqrt( r12*r12 + r22*r22 + r32*r32 ) ; - zd = sqrt( r13*r13 + r23*r23 + r33*r33 ) ; - - /* if a column length is zero, patch the trouble */ - - if( xd == 0.0l ){ r11 = 1.0l ; r21 = r31 = 0.0l ; xd = 1.0l ; } - if( yd == 0.0l ){ r22 = 1.0l ; r12 = r32 = 0.0l ; yd = 1.0l ; } - if( zd == 0.0l ){ r33 = 1.0l ; r13 = r23 = 0.0l ; zd = 1.0l ; } - - /* assign the output lengths */ - - ASSIF(dx,xd) ; ASSIF(dy,yd) ; ASSIF(dz,zd) ; - - /* normalize the columns */ - - r11 /= xd ; r21 /= xd ; r31 /= xd ; - r12 /= yd ; r22 /= yd ; r32 /= yd ; - r13 /= zd ; r23 /= zd ; r33 /= zd ; - - /* At this point, the matrix has normal columns, but we have to allow - for the fact that the hideous user may not have given us a matrix - with orthogonal columns. - - So, now find the orthogonal matrix closest to the current matrix. - - One reason for using the polar decomposition to get this - orthogonal matrix, rather than just directly orthogonalizing - the columns, is so that inputting the inverse matrix to R - will result in the inverse orthogonal matrix at this point. - If we just orthogonalized the columns, this wouldn't necessarily hold. */ - - Q.m[0][0] = r11 ; Q.m[0][1] = r12 ; Q.m[0][2] = r13 ; /* load Q */ - Q.m[1][0] = r21 ; Q.m[1][1] = r22 ; Q.m[1][2] = r23 ; - Q.m[2][0] = r31 ; Q.m[2][1] = r32 ; Q.m[2][2] = r33 ; - - P = nifti_dmat33_polar(Q) ; /* P is orthog matrix closest to Q */ - - r11 = P.m[0][0] ; r12 = P.m[0][1] ; r13 = P.m[0][2] ; /* unload */ - r21 = P.m[1][0] ; r22 = P.m[1][1] ; r23 = P.m[1][2] ; - r31 = P.m[2][0] ; r32 = P.m[2][1] ; r33 = P.m[2][2] ; - - /* [ r11 r12 r13 ] */ - /* at this point, the matrix [ r21 r22 r23 ] is orthogonal */ - /* [ r31 r32 r33 ] */ - - /* compute the determinant to determine if it is proper */ - - zd = r11*r22*r33-r11*r32*r23-r21*r12*r33 - +r21*r32*r13+r31*r12*r23-r31*r22*r13 ; /* should be -1 or 1 */ - - if( zd > 0 ){ /* proper */ - ASSIF(qfac,1.0) ; - } else { /* improper ==> flip 3rd column */ - ASSIF(qfac,-1.0) ; - r13 = -r13 ; r23 = -r23 ; r33 = -r33 ; - } - - /* now, compute quaternion parameters */ - - a = r11 + r22 + r33 + 1.0l ; - - if( a > 0.5l ){ /* simplest case */ - a = 0.5l * sqrt(a) ; - b = 0.25l * (r32-r23) / a ; - c = 0.25l * (r13-r31) / a ; - d = 0.25l * (r21-r12) / a ; - } else { /* trickier case */ - xd = 1.0 + r11 - (r22+r33) ; /* 4*b*b */ - yd = 1.0 + r22 - (r11+r33) ; /* 4*c*c */ - zd = 1.0 + r33 - (r11+r22) ; /* 4*d*d */ - if( xd > 1.0 ){ - b = 0.5l * sqrt(xd) ; - c = 0.25l* (r12+r21) / b ; - d = 0.25l* (r13+r31) / b ; - a = 0.25l* (r32-r23) / b ; - } else if( yd > 1.0 ){ - c = 0.5l * sqrt(yd) ; - b = 0.25l* (r12+r21) / c ; - d = 0.25l* (r23+r32) / c ; - a = 0.25l* (r13-r31) / c ; - } else { - d = 0.5l * sqrt(zd) ; - b = 0.25l* (r13+r31) / d ; - c = 0.25l* (r23+r32) / d ; - a = 0.25l* (r21-r12) / d ; - } - if( a < 0.0l ){ b=-b ; c=-c ; d=-d; a=-a; } - } - - ASSIF(qb,b) ; ASSIF(qc,c) ; ASSIF(qd,d) ; - return ; -} - -/*---------------------------------------------------------------------------*/ -/*! Given the 3x4 upper corner of the matrix R, compute the quaternion - parameters that fit it. - - - Any NULL pointer on input won't get assigned (e.g., if you don't want - dx,dy,dz, just pass NULL in for those pointers). - - If the 3 input matrix columns are NOT orthogonal, they will be - orthogonalized prior to calculating the parameters, using - the polar decomposition to find the orthogonal matrix closest - to the column-normalized input matrix. - - However, if the 3 input matrix columns are NOT orthogonal, then - the matrix produced by nifti_quatern_to_mat44 WILL have orthogonal - columns, so it won't be the same as the matrix input here. - This "feature" is because the NIFTI 'qform' transform is - deliberately not fully general -- it is intended to model a volume - with perpendicular axes. - - If the 3 input matrix columns are not even linearly independent, - you'll just have to take your luck, won't you? - - \see "QUATERNION REPRESENTATION OF ROTATION MATRIX" in nifti1.h - - \see nifti_quatern_to_mat44, nifti_make_orthog_mat44, - nifti_mat44_to_orientation -*//*-------------------------------------------------------------------------*/ -void nifti_mat44_to_quatern( mat44 R , - float *qb, float *qc, float *qd, - float *qx, float *qy, float *qz, - float *dx, float *dy, float *dz, float *qfac ) -{ - double r11,r12,r13 , r21,r22,r23 , r31,r32,r33 ; - double xd,yd,zd , a,b,c,d ; - mat33 P,Q ; - - /* offset outputs are read write out of input matrix */ - - ASSIF(qx,R.m[0][3]) ; ASSIF(qy,R.m[1][3]) ; ASSIF(qz,R.m[2][3]) ; - - /* load 3x3 matrix into local variables */ - - r11 = R.m[0][0] ; r12 = R.m[0][1] ; r13 = R.m[0][2] ; - r21 = R.m[1][0] ; r22 = R.m[1][1] ; r23 = R.m[1][2] ; - r31 = R.m[2][0] ; r32 = R.m[2][1] ; r33 = R.m[2][2] ; - - /* compute lengths of each column; these determine grid spacings */ - - xd = sqrt( r11*r11 + r21*r21 + r31*r31 ) ; - yd = sqrt( r12*r12 + r22*r22 + r32*r32 ) ; - zd = sqrt( r13*r13 + r23*r23 + r33*r33 ) ; - - /* if a column length is zero, patch the trouble */ - - if( xd == 0.0l ){ r11 = 1.0l ; r21 = r31 = 0.0l ; xd = 1.0l ; } - if( yd == 0.0l ){ r22 = 1.0l ; r12 = r32 = 0.0l ; yd = 1.0l ; } - if( zd == 0.0l ){ r33 = 1.0l ; r13 = r23 = 0.0l ; zd = 1.0l ; } - - /* assign the output lengths */ - - ASSIF(dx,(float)xd) ; ASSIF(dy,(float)yd) ; ASSIF(dz,(float)zd) ; - - /* normalize the columns */ - - r11 /= xd ; r21 /= xd ; r31 /= xd ; - r12 /= yd ; r22 /= yd ; r32 /= yd ; - r13 /= zd ; r23 /= zd ; r33 /= zd ; - - /* At this point, the matrix has normal columns, but we have to allow - for the fact that the hideous user may not have given us a matrix - with orthogonal columns. - - So, now find the orthogonal matrix closest to the current matrix. - - One reason for using the polar decomposition to get this - orthogonal matrix, rather than just directly orthogonalizing - the columns, is so that inputting the inverse matrix to R - will result in the inverse orthogonal matrix at this point. - If we just orthogonalized the columns, this wouldn't necessarily hold. */ - - Q.m[0][0] = (float)r11 ; Q.m[0][1] = (float)r12 ; Q.m[0][2] = (float)r13 ; /* load Q */ - Q.m[1][0] = (float)r21 ; Q.m[1][1] = (float)r22 ; Q.m[1][2] = (float)r23 ; - Q.m[2][0] = (float)r31 ; Q.m[2][1] = (float)r32 ; Q.m[2][2] = (float)r33 ; - - P = nifti_mat33_polar(Q) ; /* P is orthog matrix closest to Q */ - - r11 = P.m[0][0] ; r12 = P.m[0][1] ; r13 = P.m[0][2] ; /* unload */ - r21 = P.m[1][0] ; r22 = P.m[1][1] ; r23 = P.m[1][2] ; - r31 = P.m[2][0] ; r32 = P.m[2][1] ; r33 = P.m[2][2] ; - - /* [ r11 r12 r13 ] */ - /* at this point, the matrix [ r21 r22 r23 ] is orthogonal */ - /* [ r31 r32 r33 ] */ - - /* compute the determinant to determine if it is proper */ - - zd = r11*r22*r33-r11*r32*r23-r21*r12*r33 - +r21*r32*r13+r31*r12*r23-r31*r22*r13 ; /* should be -1 or 1 */ - - if( zd > 0 ){ /* proper */ - ASSIF(qfac,1.0f) ; - } else { /* improper ==> flip 3rd column */ - ASSIF(qfac,-1.0f) ; - r13 = -r13 ; r23 = -r23 ; r33 = -r33 ; - } - - /* now, compute quaternion parameters */ - - a = r11 + r22 + r33 + 1.0l ; - - if( a > 0.5l ){ /* simplest case */ - a = 0.5l * sqrt(a) ; - b = 0.25l * (r32-r23) / a ; - c = 0.25l * (r13-r31) / a ; - d = 0.25l * (r21-r12) / a ; - } else { /* trickier case */ - xd = 1.0 + r11 - (r22+r33) ; /* 4*b*b */ - yd = 1.0 + r22 - (r11+r33) ; /* 4*c*c */ - zd = 1.0 + r33 - (r11+r22) ; /* 4*d*d */ - if( xd > 1.0 ){ - b = 0.5l * sqrt(xd) ; - c = 0.25l* (r12+r21) / b ; - d = 0.25l* (r13+r31) / b ; - a = 0.25l* (r32-r23) / b ; - } else if( yd > 1.0 ){ - c = 0.5l * sqrt(yd) ; - b = 0.25l* (r12+r21) / c ; - d = 0.25l* (r23+r32) / c ; - a = 0.25l* (r13-r31) / c ; - } else { - d = 0.5l * sqrt(zd) ; - b = 0.25l* (r13+r31) / d ; - c = 0.25l* (r23+r32) / d ; - a = 0.25l* (r21-r12) / d ; - } - if( a < 0.0l ){ b=-b ; c=-c ; d=-d; a=-a; } - } - - ASSIF(qb,(float)b) ; ASSIF(qc,(float)c) ; ASSIF(qd,(float)d) ; - return ; -} - -/*---------------------------------------------------------------------------*/ -/*! Compute the inverse of a bordered 4x4 matrix. - - 
-   - Some numerical code fragments were generated by Maple 8.
-   - If a singular matrix is input, the output matrix will be all zero.
-   - You can check for this by examining the [3][3] element, which will
-     be 1.0 for the normal case and 0.0 for the bad case.
-
-     The input matrix should have the form:
-        [ r11 r12 r13 v1 ]
-        [ r21 r22 r23 v2 ]
-        [ r31 r32 r33 v3 ]
-        [  0   0   0   1 ]
-
-*//*-------------------------------------------------------------------------*/ -nifti_dmat44 nifti_dmat44_inverse( nifti_dmat44 R ) -{ - double r11,r12,r13,r21,r22,r23,r31,r32,r33,v1,v2,v3 , deti ; - nifti_dmat44 Q ; - /* INPUT MATRIX IS: */ - r11 = R.m[0][0]; r12 = R.m[0][1]; r13 = R.m[0][2]; /* [ r11 r12 r13 v1 ] */ - r21 = R.m[1][0]; r22 = R.m[1][1]; r23 = R.m[1][2]; /* [ r21 r22 r23 v2 ] */ - r31 = R.m[2][0]; r32 = R.m[2][1]; r33 = R.m[2][2]; /* [ r31 r32 r33 v3 ] */ - v1 = R.m[0][3]; v2 = R.m[1][3]; v3 = R.m[2][3]; /* [ 0 0 0 1 ] */ - - deti = r11*r22*r33-r11*r32*r23-r21*r12*r33 - +r21*r32*r13+r31*r12*r23-r31*r22*r13 ; - - if( deti != 0.0l ) deti = 1.0l / deti ; - - Q.m[0][0] = deti*( r22*r33-r32*r23); - Q.m[0][1] = deti*(-r12*r33+r32*r13); - Q.m[0][2] = deti*( r12*r23-r22*r13); - Q.m[0][3] = deti*(-r12*r23*v3+r12*v2*r33+r22*r13*v3 - -r22*v1*r33-r32*r13*v2+r32*v1*r23); - - Q.m[1][0] = deti*(-r21*r33+r31*r23); - Q.m[1][1] = deti*( r11*r33-r31*r13); - Q.m[1][2] = deti*(-r11*r23+r21*r13); - Q.m[1][3] = deti*( r11*r23*v3-r11*v2*r33-r21*r13*v3 - +r21*v1*r33+r31*r13*v2-r31*v1*r23); - - Q.m[2][0] = deti*( r21*r32-r31*r22); - Q.m[2][1] = deti*(-r11*r32+r31*r12); - Q.m[2][2] = deti*( r11*r22-r21*r12); - Q.m[2][3] = deti*(-r11*r22*v3+r11*r32*v2+r21*r12*v3 - -r21*r32*v1-r31*r12*v2+r31*r22*v1); - - Q.m[3][0] = Q.m[3][1] = Q.m[3][2] = 0.0l ; - Q.m[3][3] = (deti == 0.0l) ? 0.0l : 1.0l ; /* failure flag if deti == 0 */ - - return Q ; -} - -/*---------------------------------------------------------------------------*/ -/*! Compute the inverse of a bordered 4x4 matrix. - - 
-   - Some numerical code fragments were generated by Maple 8.
-   - If a singular matrix is input, the output matrix will be all zero.
-   - You can check for this by examining the [3][3] element, which will
-     be 1.0 for the normal case and 0.0 for the bad case.
-
-     The input matrix should have the form:
-        [ r11 r12 r13 v1 ]
-        [ r21 r22 r23 v2 ]
-        [ r31 r32 r33 v3 ]
-        [  0   0   0   1 ]
-
-*//*-------------------------------------------------------------------------*/ -mat44 nifti_mat44_inverse( mat44 R ) -{ - double r11,r12,r13,r21,r22,r23,r31,r32,r33,v1,v2,v3 , deti ; - mat44 Q ; - /* INPUT MATRIX IS: */ - r11 = R.m[0][0]; r12 = R.m[0][1]; r13 = R.m[0][2]; /* [ r11 r12 r13 v1 ] */ - r21 = R.m[1][0]; r22 = R.m[1][1]; r23 = R.m[1][2]; /* [ r21 r22 r23 v2 ] */ - r31 = R.m[2][0]; r32 = R.m[2][1]; r33 = R.m[2][2]; /* [ r31 r32 r33 v3 ] */ - v1 = R.m[0][3]; v2 = R.m[1][3]; v3 = R.m[2][3]; /* [ 0 0 0 1 ] */ - - deti = r11*r22*r33-r11*r32*r23-r21*r12*r33 - +r21*r32*r13+r31*r12*r23-r31*r22*r13 ; - - if( deti != 0.0l ) deti = 1.0l / deti ; - - Q.m[0][0] = (float)( deti*( r22*r33-r32*r23) ) ; - Q.m[0][1] = (float)( deti*(-r12*r33+r32*r13) ) ; - Q.m[0][2] = (float)( deti*( r12*r23-r22*r13) ) ; - Q.m[0][3] = (float)( deti*(-r12*r23*v3+r12*v2*r33+r22*r13*v3 - -r22*v1*r33-r32*r13*v2+r32*v1*r23) ) ; - - Q.m[1][0] = (float)( deti*(-r21*r33+r31*r23) ) ; - Q.m[1][1] = (float)( deti*( r11*r33-r31*r13) ) ; - Q.m[1][2] = (float)( deti*(-r11*r23+r21*r13) ) ; - Q.m[1][3] = (float)( deti*( r11*r23*v3-r11*v2*r33-r21*r13*v3 - +r21*v1*r33+r31*r13*v2-r31*v1*r23) ) ; - - Q.m[2][0] = (float)( deti*( r21*r32-r31*r22) ) ; - Q.m[2][1] = (float)( deti*(-r11*r32+r31*r12) ) ; - Q.m[2][2] = (float)( deti*( r11*r22-r21*r12) ) ; - Q.m[2][3] = (float)( deti*(-r11*r22*v3+r11*r32*v2+r21*r12*v3 - -r21*r32*v1-r31*r12*v2+r31*r22*v1) ) ; - - Q.m[3][0] = Q.m[3][1] = Q.m[3][2] = 0.0l ; - Q.m[3][3] = (deti == 0.0l) ? 0.0l : 1.0l ; /* failure flag if deti == 0 */ - - return Q ; -} - -/*---------------------------------------------------------------------------*/ -/*! Input 9 floats and make an orthgonal nifti_dmat44 out of them. - - Each row is normalized, then nifti_mat33_polar() is used to orthogonalize - them. If row #3 (r31,r32,r33) is input as zero, then it will be taken to - be the cross product of rows #1 and #2. - - This function can be used to create a rotation matrix for transforming - an oblique volume to anatomical coordinates. For this application: - - row #1 (r11,r12,r13) is the direction vector along the image i-axis - - row #2 (r21,r22,r23) is the direction vector along the image j-axis - - row #3 (r31,r32,r33) is the direction vector along the slice direction - (if available; otherwise enter it as 0's) - - The first 2 rows can be taken from the DICOM attribute (0020,0037) - "Image Orientation (Patient)". - - After forming the rotation matrix, the complete affine transformation from - (i,j,k) grid indexes to (x,y,z) spatial coordinates can be computed by - multiplying each column by the appropriate grid spacing: - - column #1 (R.m[0][0],R.m[1][0],R.m[2][0]) by delta-x - - column #2 (R.m[0][1],R.m[1][1],R.m[2][1]) by delta-y - - column #3 (R.m[0][2],R.m[1][2],R.m[2][2]) by delta-z - - and by then placing the center (x,y,z) coordinates of voxel (0,0,0) into - the column #4 (R.m[0][3],R.m[1][3],R.m[2][3]). - - \sa nifti_quatern_to_dmat44, nifti_dmat44_to_quatern, - nifti_dmat44_to_orientation -*//*-------------------------------------------------------------------------*/ -nifti_dmat44 nifti_make_orthog_dmat44( double r11, double r12, double r13 , - double r21, double r22, double r23 , - double r31, double r32, double r33 ) -{ - nifti_dmat44 R ; - nifti_dmat33 Q , P ; - double val ; - - R.m[3][0] = R.m[3][1] = R.m[3][2] = 0.0l ; R.m[3][3] = 1.0l ; - - Q.m[0][0] = r11 ; Q.m[0][1] = r12 ; Q.m[0][2] = r13 ; /* load Q */ - Q.m[1][0] = r21 ; Q.m[1][1] = r22 ; Q.m[1][2] = r23 ; - Q.m[2][0] = r31 ; Q.m[2][1] = r32 ; Q.m[2][2] = r33 ; - - /* normalize row 1 */ - - val = Q.m[0][0]*Q.m[0][0] + Q.m[0][1]*Q.m[0][1] + Q.m[0][2]*Q.m[0][2] ; - if( val > 0.0l ){ - val = 1.0l / sqrt(val) ; - Q.m[0][0] *= val ; Q.m[0][1] *= val ; Q.m[0][2] *= val ; - } else { - Q.m[0][0] = 1.0l ; Q.m[0][1] = 0.0l ; Q.m[0][2] = 0.0l ; - } - - /* normalize row 2 */ - - val = Q.m[1][0]*Q.m[1][0] + Q.m[1][1]*Q.m[1][1] + Q.m[1][2]*Q.m[1][2] ; - if( val > 0.0l ){ - val = 1.0l / sqrt(val) ; - Q.m[1][0] *= val ; Q.m[1][1] *= val ; Q.m[1][2] *= val ; - } else { - Q.m[1][0] = 0.0l ; Q.m[1][1] = 1.0l ; Q.m[1][2] = 0.0l ; - } - - /* normalize row 3 */ - - val = Q.m[2][0]*Q.m[2][0] + Q.m[2][1]*Q.m[2][1] + Q.m[2][2]*Q.m[2][2] ; - if( val > 0.0l ){ - val = 1.0l / sqrt(val) ; - Q.m[2][0] *= val ; Q.m[2][1] *= val ; Q.m[2][2] *= val ; - } else { - Q.m[2][0] = Q.m[0][1]*Q.m[1][2] - Q.m[0][2]*Q.m[1][1] ; /* cross */ - Q.m[2][1] = Q.m[0][2]*Q.m[1][0] - Q.m[0][0]*Q.m[1][2] ; /* product */ - Q.m[2][2] = Q.m[0][0]*Q.m[1][1] - Q.m[0][1]*Q.m[1][0] ; - } - - P = nifti_dmat33_polar(Q) ; /* P is orthog matrix closest to Q */ - - R.m[0][0] = P.m[0][0] ; R.m[0][1] = P.m[0][1] ; R.m[0][2] = P.m[0][2] ; - R.m[1][0] = P.m[1][0] ; R.m[1][1] = P.m[1][1] ; R.m[1][2] = P.m[1][2] ; - R.m[2][0] = P.m[2][0] ; R.m[2][1] = P.m[2][1] ; R.m[2][2] = P.m[2][2] ; - - R.m[0][3] = R.m[1][3] = R.m[2][3] = 0.0f ; return R ; -} - -/*---------------------------------------------------------------------------*/ -/*! Input 9 floats and make an orthgonal mat44 out of them. - - Each row is normalized, then nifti_mat33_polar() is used to orthogonalize - them. If row #3 (r31,r32,r33) is input as zero, then it will be taken to - be the cross product of rows #1 and #2. - - This function can be used to create a rotation matrix for transforming - an oblique volume to anatomical coordinates. For this application: - - row #1 (r11,r12,r13) is the direction vector along the image i-axis - - row #2 (r21,r22,r23) is the direction vector along the image j-axis - - row #3 (r31,r32,r33) is the direction vector along the slice direction - (if available; otherwise enter it as 0's) - - The first 2 rows can be taken from the DICOM attribute (0020,0037) - "Image Orientation (Patient)". - - After forming the rotation matrix, the complete affine transformation from - (i,j,k) grid indexes to (x,y,z) spatial coordinates can be computed by - multiplying each column by the appropriate grid spacing: - - column #1 (R.m[0][0],R.m[1][0],R.m[2][0]) by delta-x - - column #2 (R.m[0][1],R.m[1][1],R.m[2][1]) by delta-y - - column #3 (R.m[0][2],R.m[1][2],R.m[2][2]) by delta-z - - and by then placing the center (x,y,z) coordinates of voxel (0,0,0) into - the column #4 (R.m[0][3],R.m[1][3],R.m[2][3]). - - \sa nifti_quatern_to_mat44, nifti_mat44_to_quatern, - nifti_mat44_to_orientation -*//*-------------------------------------------------------------------------*/ -mat44 nifti_make_orthog_mat44( float r11, float r12, float r13 , - float r21, float r22, float r23 , - float r31, float r32, float r33 ) -{ - mat44 R ; - mat33 Q , P ; - double val ; - - R.m[3][0] = R.m[3][1] = R.m[3][2] = 0.0l ; R.m[3][3] = 1.0l ; - - Q.m[0][0] = r11 ; Q.m[0][1] = r12 ; Q.m[0][2] = r13 ; /* load Q */ - Q.m[1][0] = r21 ; Q.m[1][1] = r22 ; Q.m[1][2] = r23 ; - Q.m[2][0] = r31 ; Q.m[2][1] = r32 ; Q.m[2][2] = r33 ; - - /* normalize row 1 */ - - val = Q.m[0][0]*Q.m[0][0] + Q.m[0][1]*Q.m[0][1] + Q.m[0][2]*Q.m[0][2] ; - if( val > 0.0l ){ - val = 1.0l / sqrt(val) ; - Q.m[0][0] *= (float)val ; Q.m[0][1] *= (float)val ; Q.m[0][2] *= (float)val ; - } else { - Q.m[0][0] = 1.0l ; Q.m[0][1] = 0.0l ; Q.m[0][2] = 0.0l ; - } - - /* normalize row 2 */ - - val = Q.m[1][0]*Q.m[1][0] + Q.m[1][1]*Q.m[1][1] + Q.m[1][2]*Q.m[1][2] ; - if( val > 0.0l ){ - val = 1.0l / sqrt(val) ; - Q.m[1][0] *= (float)val ; Q.m[1][1] *= (float)val ; Q.m[1][2] *= (float)val ; - } else { - Q.m[1][0] = 0.0l ; Q.m[1][1] = 1.0l ; Q.m[1][2] = 0.0l ; - } - - /* normalize row 3 */ - - val = Q.m[2][0]*Q.m[2][0] + Q.m[2][1]*Q.m[2][1] + Q.m[2][2]*Q.m[2][2] ; - if( val > 0.0l ){ - val = 1.0l / sqrt(val) ; - Q.m[2][0] *= (float)val ; Q.m[2][1] *= (float)val ; Q.m[2][2] *= (float)val ; - } else { - Q.m[2][0] = Q.m[0][1]*Q.m[1][2] - Q.m[0][2]*Q.m[1][1] ; /* cross */ - Q.m[2][1] = Q.m[0][2]*Q.m[1][0] - Q.m[0][0]*Q.m[1][2] ; /* product */ - Q.m[2][2] = Q.m[0][0]*Q.m[1][1] - Q.m[0][1]*Q.m[1][0] ; - } - - P = nifti_mat33_polar(Q) ; /* P is orthog matrix closest to Q */ - - R.m[0][0] = P.m[0][0] ; R.m[0][1] = P.m[0][1] ; R.m[0][2] = P.m[0][2] ; - R.m[1][0] = P.m[1][0] ; R.m[1][1] = P.m[1][1] ; R.m[1][2] = P.m[1][2] ; - R.m[2][0] = P.m[2][0] ; R.m[2][1] = P.m[2][1] ; R.m[2][2] = P.m[2][2] ; - - R.m[0][3] = R.m[1][3] = R.m[2][3] = 0.0f ; return R ; -} - -/*----------------------------------------------------------------------*/ -/*! compute the inverse of a 3x3 matrix -*//*--------------------------------------------------------------------*/ -nifti_dmat33 nifti_dmat33_inverse( nifti_dmat33 R ) /* inverse of 3x3 matrix */ -{ - double r11,r12,r13,r21,r22,r23,r31,r32,r33 , deti ; - nifti_dmat33 Q ; - /* INPUT MATRIX: */ - r11 = R.m[0][0]; r12 = R.m[0][1]; r13 = R.m[0][2]; /* [ r11 r12 r13 ] */ - r21 = R.m[1][0]; r22 = R.m[1][1]; r23 = R.m[1][2]; /* [ r21 r22 r23 ] */ - r31 = R.m[2][0]; r32 = R.m[2][1]; r33 = R.m[2][2]; /* [ r31 r32 r33 ] */ - - deti = r11*r22*r33-r11*r32*r23-r21*r12*r33 - +r21*r32*r13+r31*r12*r23-r31*r22*r13 ; - - if( deti != 0.0l ) deti = 1.0l / deti ; - - Q.m[0][0] = deti*( r22*r33-r32*r23); - Q.m[0][1] = deti*(-r12*r33+r32*r13); - Q.m[0][2] = deti*( r12*r23-r22*r13); - - Q.m[1][0] = deti*(-r21*r33+r31*r23); - Q.m[1][1] = deti*( r11*r33-r31*r13); - Q.m[1][2] = deti*(-r11*r23+r21*r13); - - Q.m[2][0] = deti*( r21*r32-r31*r22); - Q.m[2][1] = deti*(-r11*r32+r31*r12); - Q.m[2][2] = deti*( r11*r22-r21*r12); - - return Q ; -} - -/*----------------------------------------------------------------------*/ -/*! compute the inverse of a 3x3 matrix -*//*--------------------------------------------------------------------*/ -mat33 nifti_mat33_inverse( mat33 R ) /* inverse of 3x3 matrix */ -{ - double r11,r12,r13,r21,r22,r23,r31,r32,r33 , deti ; - mat33 Q ; - /* INPUT MATRIX: */ - r11 = R.m[0][0]; r12 = R.m[0][1]; r13 = R.m[0][2]; /* [ r11 r12 r13 ] */ - r21 = R.m[1][0]; r22 = R.m[1][1]; r23 = R.m[1][2]; /* [ r21 r22 r23 ] */ - r31 = R.m[2][0]; r32 = R.m[2][1]; r33 = R.m[2][2]; /* [ r31 r32 r33 ] */ - - deti = r11*r22*r33-r11*r32*r23-r21*r12*r33 - +r21*r32*r13+r31*r12*r23-r31*r22*r13 ; - - if( deti != 0.0l ) deti = 1.0l / deti ; - - Q.m[0][0] = (float)( deti*( r22*r33-r32*r23) ) ; - Q.m[0][1] = (float)( deti*(-r12*r33+r32*r13) ) ; - Q.m[0][2] = (float)( deti*( r12*r23-r22*r13) ) ; - - Q.m[1][0] = (float)( deti*(-r21*r33+r31*r23) ) ; - Q.m[1][1] = (float)( deti*( r11*r33-r31*r13) ) ; - Q.m[1][2] = (float)( deti*(-r11*r23+r21*r13) ) ; - - Q.m[2][0] = (float)( deti*( r21*r32-r31*r22) ) ; - Q.m[2][1] = (float)( deti*(-r11*r32+r31*r12) ) ; - Q.m[2][2] = (float)( deti*( r11*r22-r21*r12) ) ; - - return Q ; -} - -/*----------------------------------------------------------------------*/ -/*! compute the determinant of a 3x3 matrix -*//*--------------------------------------------------------------------*/ -double nifti_dmat33_determ( nifti_dmat33 R ) /* determinant of 3x3 matrix */ -{ - double r11,r12,r13,r21,r22,r23,r31,r32,r33 ; - /* INPUT MATRIX: */ - r11 = R.m[0][0]; r12 = R.m[0][1]; r13 = R.m[0][2]; /* [ r11 r12 r13 ] */ - r21 = R.m[1][0]; r22 = R.m[1][1]; r23 = R.m[1][2]; /* [ r21 r22 r23 ] */ - r31 = R.m[2][0]; r32 = R.m[2][1]; r33 = R.m[2][2]; /* [ r31 r32 r33 ] */ - - return (r11*r22*r33-r11*r32*r23-r21*r12*r33 - +r21*r32*r13+r31*r12*r23-r31*r22*r13) ; -} - -/*----------------------------------------------------------------------*/ -/*! compute the determinant of a 3x3 matrix -*//*--------------------------------------------------------------------*/ -float nifti_mat33_determ( mat33 R ) /* determinant of 3x3 matrix */ -{ - double r11,r12,r13,r21,r22,r23,r31,r32,r33 ; - /* INPUT MATRIX: */ - r11 = R.m[0][0]; r12 = R.m[0][1]; r13 = R.m[0][2]; /* [ r11 r12 r13 ] */ - r21 = R.m[1][0]; r22 = R.m[1][1]; r23 = R.m[1][2]; /* [ r21 r22 r23 ] */ - r31 = R.m[2][0]; r32 = R.m[2][1]; r33 = R.m[2][2]; /* [ r31 r32 r33 ] */ - - return (float)(r11*r22*r33-r11*r32*r23-r21*r12*r33 - +r21*r32*r13+r31*r12*r23-r31*r22*r13) ; -} - -/*----------------------------------------------------------------------*/ -/*! compute the max row norm of a 3x3 matrix -*//*--------------------------------------------------------------------*/ -double nifti_dmat33_rownorm( nifti_dmat33 A ) /* max row norm of 3x3 matrix */ -{ - double r1,r2,r3 ; - - r1 = fabs(A.m[0][0])+fabs(A.m[0][1])+fabs(A.m[0][2]); - r2 = fabs(A.m[1][0])+fabs(A.m[1][1])+fabs(A.m[1][2]); - r3 = fabs(A.m[2][0])+fabs(A.m[2][1])+fabs(A.m[2][2]); - if( r1 < r2 ) r1 = r2 ; - if( r1 < r3 ) r1 = r3 ; - return r1 ; -} - -/*----------------------------------------------------------------------*/ -/*! compute the max row norm of a 3x3 matrix -*//*--------------------------------------------------------------------*/ -float nifti_mat33_rownorm( mat33 A ) /* max row norm of 3x3 matrix */ -{ - float r1,r2,r3 ; - - r1 = (float)( fabs(A.m[0][0])+fabs(A.m[0][1])+fabs(A.m[0][2]) ) ; - r2 = (float)( fabs(A.m[1][0])+fabs(A.m[1][1])+fabs(A.m[1][2]) ) ; - r3 = (float)( fabs(A.m[2][0])+fabs(A.m[2][1])+fabs(A.m[2][2]) ) ; - if( r1 < r2 ) r1 = r2 ; - if( r1 < r3 ) r1 = r3 ; - return r1 ; -} - -/*----------------------------------------------------------------------*/ -/*! compute the max column norm of a 3x3 matrix -*//*--------------------------------------------------------------------*/ -double nifti_dmat33_colnorm( nifti_dmat33 A )/* max column norm of 3x3 matrix */ -{ - double r1,r2,r3 ; - - r1 = fabs(A.m[0][0])+fabs(A.m[1][0])+fabs(A.m[2][0]); - r2 = fabs(A.m[0][1])+fabs(A.m[1][1])+fabs(A.m[2][1]); - r3 = fabs(A.m[0][2])+fabs(A.m[1][2])+fabs(A.m[2][2]); - if( r1 < r2 ) r1 = r2 ; - if( r1 < r3 ) r1 = r3 ; - return r1 ; -} - -/*----------------------------------------------------------------------*/ -/*! compute the max column norm of a 3x3 matrix -*//*--------------------------------------------------------------------*/ -float nifti_mat33_colnorm( mat33 A ) /* max column norm of 3x3 matrix */ -{ - float r1,r2,r3 ; - - r1 = (float)( fabs(A.m[0][0])+fabs(A.m[1][0])+fabs(A.m[2][0]) ) ; - r2 = (float)( fabs(A.m[0][1])+fabs(A.m[1][1])+fabs(A.m[2][1]) ) ; - r3 = (float)( fabs(A.m[0][2])+fabs(A.m[1][2])+fabs(A.m[2][2]) ) ; - if( r1 < r2 ) r1 = r2 ; - if( r1 < r3 ) r1 = r3 ; - return r1 ; -} - -/*----------------------------------------------------------------------*/ -/*! multiply 2 3x3 matrices -*//*--------------------------------------------------------------------*/ -nifti_dmat33 nifti_dmat33_mul( nifti_dmat33 A , nifti_dmat33 B ) -/* multiply 2 3x3 matrices */ -{ - nifti_dmat33 C ; int i,j ; - for( i=0 ; i < 3 ; i++ ) - for( j=0 ; j < 3 ; j++ ) - C.m[i][j] = A.m[i][0] * B.m[0][j] - + A.m[i][1] * B.m[1][j] - + A.m[i][2] * B.m[2][j] ; - return C ; -} - -/*----------------------------------------------------------------------*/ -/*! multiply 2 3x3 matrices -*//*--------------------------------------------------------------------*/ -mat33 nifti_mat33_mul( mat33 A , mat33 B ) /* multiply 2 3x3 matrices */ -{ - mat33 C ; int i,j ; - for( i=0 ; i < 3 ; i++ ) - for( j=0 ; j < 3 ; j++ ) - C.m[i][j] = A.m[i][0] * B.m[0][j] - + A.m[i][1] * B.m[1][j] - + A.m[i][2] * B.m[2][j] ; - return C ; -} - -/*---------------------------------------------------------------------------*/ -/*! polar decomposition of a 3x3 matrix - - This finds the closest orthogonal matrix to input A - (in both the Frobenius and L2 norms). - - Algorithm is that from NJ Higham, SIAM J Sci Stat Comput, 7:1160-1174. -*//*-------------------------------------------------------------------------*/ -nifti_dmat33 nifti_dmat33_polar( nifti_dmat33 A ) -{ - nifti_dmat33 X , Y , Z ; - double alp,bet,gam,gmi , dif=1.0 ; - int k=0 ; - - X = A ; - - /* force matrix to be nonsingular */ - - gam = nifti_dmat33_determ(X) ; - while( gam == 0.0 ){ /* perturb matrix */ - gam = 0.00001 * ( 0.001 + nifti_dmat33_rownorm(X) ); - X.m[0][0] += gam ; X.m[1][1] += gam ; X.m[2][2] += gam ; - gam = nifti_dmat33_determ(X) ; - } - - while(1){ - Y = nifti_dmat33_inverse(X) ; - if( dif > 0.3 ){ /* far from convergence */ - alp = sqrt( nifti_dmat33_rownorm(X) * nifti_dmat33_colnorm(X) ); - bet = sqrt( nifti_dmat33_rownorm(Y) * nifti_dmat33_colnorm(Y) ); - gam = sqrt( bet / alp ); - gmi = 1.0 / gam; - } else { - gam = gmi = 1.0f ; /* close to convergence */ - } - Z.m[0][0] = 0.5 * ( gam*X.m[0][0] + gmi*Y.m[0][0] ); - Z.m[0][1] = 0.5 * ( gam*X.m[0][1] + gmi*Y.m[1][0] ); - Z.m[0][2] = 0.5 * ( gam*X.m[0][2] + gmi*Y.m[2][0] ); - Z.m[1][0] = 0.5 * ( gam*X.m[1][0] + gmi*Y.m[0][1] ); - Z.m[1][1] = 0.5 * ( gam*X.m[1][1] + gmi*Y.m[1][1] ); - Z.m[1][2] = 0.5 * ( gam*X.m[1][2] + gmi*Y.m[2][1] ); - Z.m[2][0] = 0.5 * ( gam*X.m[2][0] + gmi*Y.m[0][2] ); - Z.m[2][1] = 0.5 * ( gam*X.m[2][1] + gmi*Y.m[1][2] ); - Z.m[2][2] = 0.5 * ( gam*X.m[2][2] + gmi*Y.m[2][2] ); - - dif = fabs(Z.m[0][0]-X.m[0][0])+fabs(Z.m[0][1]-X.m[0][1]) - +fabs(Z.m[0][2]-X.m[0][2])+fabs(Z.m[1][0]-X.m[1][0]) - +fabs(Z.m[1][1]-X.m[1][1])+fabs(Z.m[1][2]-X.m[1][2]) - +fabs(Z.m[2][0]-X.m[2][0])+fabs(Z.m[2][1]-X.m[2][1]) - +fabs(Z.m[2][2]-X.m[2][2]); - - k = k+1 ; - if( k > 100 || dif < 3.e-6 ) break ; /* convergence or exhaustion */ - X = Z ; - } - - return Z ; -} - -/*---------------------------------------------------------------------------*/ -/*! polar decomposition of a 3x3 matrix - - This finds the closest orthogonal matrix to input A - (in both the Frobenius and L2 norms). - - Algorithm is that from NJ Higham, SIAM J Sci Stat Comput, 7:1160-1174. -*//*-------------------------------------------------------------------------*/ -mat33 nifti_mat33_polar( mat33 A ) -{ - mat33 X , Y , Z ; - float alp,bet,gam,gmi , dif=1.0f ; - int k=0 ; - - X = A ; - - /* force matrix to be nonsingular */ - - gam = nifti_mat33_determ(X) ; - while( gam == 0.0 ){ /* perturb matrix */ - gam = (float)( 0.00001 * ( 0.001 + nifti_mat33_rownorm(X) ) ) ; - X.m[0][0] += gam ; X.m[1][1] += gam ; X.m[2][2] += gam ; - gam = nifti_mat33_determ(X) ; - } - - while(1){ - Y = nifti_mat33_inverse(X) ; - if( dif > 0.3 ){ /* far from convergence */ - alp = (float)( sqrt( nifti_mat33_rownorm(X) * nifti_mat33_colnorm(X) ) ) ; - bet = (float)( sqrt( nifti_mat33_rownorm(Y) * nifti_mat33_colnorm(Y) ) ) ; - gam = (float)( sqrt( bet / alp ) ) ; - gmi = (float)( 1.0 / gam ) ; - } else { - gam = gmi = 1.0f ; /* close to convergence */ - } - Z.m[0][0] = (float)( 0.5 * ( gam*X.m[0][0] + gmi*Y.m[0][0] ) ) ; - Z.m[0][1] = (float)( 0.5 * ( gam*X.m[0][1] + gmi*Y.m[1][0] ) ) ; - Z.m[0][2] = (float)( 0.5 * ( gam*X.m[0][2] + gmi*Y.m[2][0] ) ) ; - Z.m[1][0] = (float)( 0.5 * ( gam*X.m[1][0] + gmi*Y.m[0][1] ) ) ; - Z.m[1][1] = (float)( 0.5 * ( gam*X.m[1][1] + gmi*Y.m[1][1] ) ) ; - Z.m[1][2] = (float)( 0.5 * ( gam*X.m[1][2] + gmi*Y.m[2][1] ) ) ; - Z.m[2][0] = (float)( 0.5 * ( gam*X.m[2][0] + gmi*Y.m[0][2] ) ) ; - Z.m[2][1] = (float)( 0.5 * ( gam*X.m[2][1] + gmi*Y.m[1][2] ) ) ; - Z.m[2][2] = (float)( 0.5 * ( gam*X.m[2][2] + gmi*Y.m[2][2] ) ) ; - - dif = (float)( fabs(Z.m[0][0]-X.m[0][0])+fabs(Z.m[0][1]-X.m[0][1]) - +fabs(Z.m[0][2]-X.m[0][2])+fabs(Z.m[1][0]-X.m[1][0]) - +fabs(Z.m[1][1]-X.m[1][1])+fabs(Z.m[1][2]-X.m[1][2]) - +fabs(Z.m[2][0]-X.m[2][0])+fabs(Z.m[2][1]-X.m[2][1]) - +fabs(Z.m[2][2]-X.m[2][2]) ); - - k = k+1 ; - if( k > 100 || dif < 3.e-6 ) break ; /* convergence or exhaustion */ - X = Z ; - } - - return Z ; -} - -/*---------------------------------------------------------------------------*/ -/*! compute the (closest) orientation from a 4x4 ijk->xyz tranformation matrix - - 
-   Input:  4x4 matrix that transforms (i,j,k) indexes to (x,y,z) coordinates,
-           where +x=Right, +y=Anterior, +z=Superior.
-           (Only the upper-left 3x3 corner of R is used herein.)
-   Output: 3 orientation codes that correspond to the closest "standard"
-           anatomical orientation of the (i,j,k) axes.
-   Method: Find which permutation of (x,y,z) has the smallest angle to the
-           (i,j,k) axes directions, which are the columns of the R matrix.
-   Errors: The codes returned will be zero.
-
-   For example, an axial volume might get return values of
-     *icod = NIFTI_R2L   (i axis is mostly Right to Left)
-     *jcod = NIFTI_P2A   (j axis is mostly Posterior to Anterior)
-     *kcod = NIFTI_I2S   (k axis is mostly Inferior to Superior)
-
- - \see "QUATERNION REPRESENTATION OF ROTATION MATRIX" in nifti1.h - - \see nifti_quatern_to_mat44, nifti_mat44_to_quatern, - nifti_make_orthog_mat44 -*//*-------------------------------------------------------------------------*/ -void nifti_dmat44_to_orientation( nifti_dmat44 R , - int *icod, int *jcod, int *kcod ) -{ - double xi,xj,xk , yi,yj,yk , zi,zj,zk , val,detQ,detP ; - nifti_dmat33 P , Q , M ; - int i,j,k=0,p,q,r , ibest,jbest,kbest,pbest,qbest,rbest ; - double vbest ; - - if( icod == NULL || jcod == NULL || kcod == NULL ) return ; /* bad */ - - *icod = *jcod = *kcod = 0 ; /* error returns, if sh*t happens */ - - /* load column vectors for each (i,j,k) direction from matrix */ - - /*-- i axis --*/ /*-- j axis --*/ /*-- k axis --*/ - - xi = R.m[0][0] ; xj = R.m[0][1] ; xk = R.m[0][2] ; - yi = R.m[1][0] ; yj = R.m[1][1] ; yk = R.m[1][2] ; - zi = R.m[2][0] ; zj = R.m[2][1] ; zk = R.m[2][2] ; - - /* normalize column vectors to get unit vectors along each ijk-axis */ - - /* normalize i axis */ - - val = sqrt( xi*xi + yi*yi + zi*zi ) ; - if( val == 0.0 ) return ; /* stupid input */ - xi /= val ; yi /= val ; zi /= val ; - - /* normalize j axis */ - - val = sqrt( xj*xj + yj*yj + zj*zj ) ; - if( val == 0.0 ) return ; /* stupid input */ - xj /= val ; yj /= val ; zj /= val ; - - /* orthogonalize j axis to i axis, if needed */ - - val = xi*xj + yi*yj + zi*zj ; /* dot product between i and j */ - if( fabs(val) > 1.e-4 ){ - xj -= val*xi ; yj -= val*yi ; zj -= val*zi ; - val = sqrt( xj*xj + yj*yj + zj*zj ) ; /* must renormalize */ - if( val == 0.0 ) return ; /* j was parallel to i? */ - xj /= val ; yj /= val ; zj /= val ; - } - - /* normalize k axis; if it is zero, make it the cross product i x j */ - - val = sqrt( xk*xk + yk*yk + zk*zk ) ; - if( val == 0.0 ){ xk = yi*zj-zi*yj; yk = zi*xj-zj*xi ; zk=xi*yj-yi*xj ; } - else { xk /= val ; yk /= val ; zk /= val ; } - - /* orthogonalize k to i */ - - val = xi*xk + yi*yk + zi*zk ; /* dot product between i and k */ - if( fabs(val) > 1.e-4 ){ - xk -= val*xi ; yk -= val*yi ; zk -= val*zi ; - val = sqrt( xk*xk + yk*yk + zk*zk ) ; - if( val == 0.0 ) return ; /* bad */ - xk /= val ; yk /= val ; zk /= val ; - } - - /* orthogonalize k to j */ - - val = xj*xk + yj*yk + zj*zk ; /* dot product between j and k */ - if( fabs(val) > 1.e-4 ){ - xk -= val*xj ; yk -= val*yj ; zk -= val*zj ; - val = sqrt( xk*xk + yk*yk + zk*zk ) ; - if( val == 0.0 ) return ; /* bad */ - xk /= val ; yk /= val ; zk /= val ; - } - - Q.m[0][0] = xi ; Q.m[0][1] = xj ; Q.m[0][2] = xk ; - Q.m[1][0] = yi ; Q.m[1][1] = yj ; Q.m[1][2] = yk ; - Q.m[2][0] = zi ; Q.m[2][1] = zj ; Q.m[2][2] = zk ; - - /* at this point, Q is the rotation matrix from (i,j,k) to (x,y,z) axes */ - - detQ = nifti_dmat33_determ( Q ) ; - if( detQ == 0.0 ) return ; /* shouldn't happen unless user is a DUFIS */ - - /* Build and test all possible +1/-1 coordinate permutation matrices P; - then find the P such that the rotation matrix M=PQ is closest to the - identity, in the sense of M having the smallest total rotation angle. */ - - /* Despite the formidable looking 6 nested loops, there are - only 3*3*3*2*2*2 = 216 passes, which will run very quickly. */ - - vbest = -666.0 ; ibest=pbest=qbest=rbest=1 ; jbest=2 ; kbest=3 ; - for( i=1 ; i <= 3 ; i++ ){ /* i = column number to use for row #1 */ - for( j=1 ; j <= 3 ; j++ ){ /* j = column number to use for row #2 */ - if( i == j ) continue ; - for( k=1 ; k <= 3 ; k++ ){ /* k = column number to use for row #3 */ - if( i == k || j == k ) continue ; - P.m[0][0] = P.m[0][1] = P.m[0][2] = - P.m[1][0] = P.m[1][1] = P.m[1][2] = - P.m[2][0] = P.m[2][1] = P.m[2][2] = 0.0 ; - for( p=-1 ; p <= 1 ; p+=2 ){ /* p,q,r are -1 or +1 */ - for( q=-1 ; q <= 1 ; q+=2 ){ /* and go into rows #1,2,3 */ - for( r=-1 ; r <= 1 ; r+=2 ){ - P.m[0][i-1] = p ; P.m[1][j-1] = q ; P.m[2][k-1] = r ; - detP = nifti_dmat33_determ(P) ; /* sign of permutation */ - if( detP * detQ <= 0.0 ) continue ; /* doesn't match sign of Q */ - M = nifti_dmat33_mul(P,Q) ; - - /* angle of M rotation = 2.0*acos(0.5*sqrt(1.0+trace(M))) */ - /* we want largest trace(M) == smallest angle == M nearest to I */ - - val = M.m[0][0] + M.m[1][1] + M.m[2][2] ; /* trace */ - if( val > vbest ){ - vbest = val ; - ibest = i ; jbest = j ; kbest = k ; - pbest = p ; qbest = q ; rbest = r ; - } - }}}}}} - - /* At this point ibest is 1 or 2 or 3; pbest is -1 or +1; etc. - - The matrix P that corresponds is the best permutation approximation - to Q-inverse; that is, P (approximately) takes (x,y,z) coordinates - to the (i,j,k) axes. - - For example, the first row of P (which contains pbest in column ibest) - determines the way the i axis points relative to the anatomical - (x,y,z) axes. If ibest is 2, then the i axis is along the y axis, - which is direction P2A (if pbest > 0) or A2P (if pbest < 0). - - So, using ibest and pbest, we can assign the output code for - the i axis. Mutatis mutandis for the j and k axes, of course. */ - - switch( ibest*pbest ){ - case 1: i = NIFTI_L2R ; break ; - case -1: i = NIFTI_R2L ; break ; - case 2: i = NIFTI_P2A ; break ; - case -2: i = NIFTI_A2P ; break ; - case 3: i = NIFTI_I2S ; break ; - case -3: i = NIFTI_S2I ; break ; - } - - switch( jbest*qbest ){ - case 1: j = NIFTI_L2R ; break ; - case -1: j = NIFTI_R2L ; break ; - case 2: j = NIFTI_P2A ; break ; - case -2: j = NIFTI_A2P ; break ; - case 3: j = NIFTI_I2S ; break ; - case -3: j = NIFTI_S2I ; break ; - } - - switch( kbest*rbest ){ - case 1: k = NIFTI_L2R ; break ; - case -1: k = NIFTI_R2L ; break ; - case 2: k = NIFTI_P2A ; break ; - case -2: k = NIFTI_A2P ; break ; - case 3: k = NIFTI_I2S ; break ; - case -3: k = NIFTI_S2I ; break ; - } - - *icod = i ; *jcod = j ; *kcod = k ; return ; -} - -/*---------------------------------------------------------------------------*/ -/*! compute the (closest) orientation from a 4x4 ijk->xyz tranformation matrix - - 
-   Input:  4x4 matrix that transforms (i,j,k) indexes to (x,y,z) coordinates,
-           where +x=Right, +y=Anterior, +z=Superior.
-           (Only the upper-left 3x3 corner of R is used herein.)
-   Output: 3 orientation codes that correspond to the closest "standard"
-           anatomical orientation of the (i,j,k) axes.
-   Method: Find which permutation of (x,y,z) has the smallest angle to the
-           (i,j,k) axes directions, which are the columns of the R matrix.
-   Errors: The codes returned will be zero.
-
-   For example, an axial volume might get return values of
-     *icod = NIFTI_R2L   (i axis is mostly Right to Left)
-     *jcod = NIFTI_P2A   (j axis is mostly Posterior to Anterior)
-     *kcod = NIFTI_I2S   (k axis is mostly Inferior to Superior)
-
- - \see "QUATERNION REPRESENTATION OF ROTATION MATRIX" in nifti1.h - - \see nifti_quatern_to_mat44, nifti_mat44_to_quatern, - nifti_make_orthog_mat44 -*//*-------------------------------------------------------------------------*/ -void nifti_mat44_to_orientation( mat44 R , int *icod, int *jcod, int *kcod ) -{ - float xi,xj,xk , yi,yj,yk , zi,zj,zk , val,detQ,detP ; - mat33 P , Q , M ; - int i,j,k=0,p,q,r , ibest,jbest,kbest,pbest,qbest,rbest ; - float vbest ; - - if( icod == NULL || jcod == NULL || kcod == NULL ) return ; /* bad */ - - *icod = *jcod = *kcod = 0 ; /* error returns, if sh*t happens */ - - /* load column vectors for each (i,j,k) direction from matrix */ - - /*-- i axis --*/ /*-- j axis --*/ /*-- k axis --*/ - - xi = R.m[0][0] ; xj = R.m[0][1] ; xk = R.m[0][2] ; - yi = R.m[1][0] ; yj = R.m[1][1] ; yk = R.m[1][2] ; - zi = R.m[2][0] ; zj = R.m[2][1] ; zk = R.m[2][2] ; - - /* normalize column vectors to get unit vectors along each ijk-axis */ - - /* normalize i axis */ - - val = (float)sqrt( xi*xi + yi*yi + zi*zi ) ; - if( val == 0.0 ) return ; /* stupid input */ - xi /= val ; yi /= val ; zi /= val ; - - /* normalize j axis */ - - val = (float)sqrt( xj*xj + yj*yj + zj*zj ) ; - if( val == 0.0 ) return ; /* stupid input */ - xj /= val ; yj /= val ; zj /= val ; - - /* orthogonalize j axis to i axis, if needed */ - - val = xi*xj + yi*yj + zi*zj ; /* dot product between i and j */ - if( fabs(val) > 1.e-4 ){ - xj -= val*xi ; yj -= val*yi ; zj -= val*zi ; - val = (float)sqrt( xj*xj + yj*yj + zj*zj ) ; /* must renormalize */ - if( val == 0.0 ) return ; /* j was parallel to i? */ - xj /= val ; yj /= val ; zj /= val ; - } - - /* normalize k axis; if it is zero, make it the cross product i x j */ - - val = (float)sqrt( xk*xk + yk*yk + zk*zk ) ; - if( val == 0.0 ){ xk = yi*zj-zi*yj; yk = zi*xj-zj*xi ; zk=xi*yj-yi*xj ; } - else { xk /= val ; yk /= val ; zk /= val ; } - - /* orthogonalize k to i */ - - val = xi*xk + yi*yk + zi*zk ; /* dot product between i and k */ - if( fabs(val) > 1.e-4 ){ - xk -= val*xi ; yk -= val*yi ; zk -= val*zi ; - val = (float)sqrt( xk*xk + yk*yk + zk*zk ) ; - if( val == 0.0 ) return ; /* bad */ - xk /= val ; yk /= val ; zk /= val ; - } - - /* orthogonalize k to j */ - - val = xj*xk + yj*yk + zj*zk ; /* dot product between j and k */ - if( fabs(val) > 1.e-4 ){ - xk -= val*xj ; yk -= val*yj ; zk -= val*zj ; - val = (float)sqrt( xk*xk + yk*yk + zk*zk ) ; - if( val == 0.0 ) return ; /* bad */ - xk /= val ; yk /= val ; zk /= val ; - } - - Q.m[0][0] = xi ; Q.m[0][1] = xj ; Q.m[0][2] = xk ; - Q.m[1][0] = yi ; Q.m[1][1] = yj ; Q.m[1][2] = yk ; - Q.m[2][0] = zi ; Q.m[2][1] = zj ; Q.m[2][2] = zk ; - - /* at this point, Q is the rotation matrix from the (i,j,k) to (x,y,z) axes */ - - detQ = nifti_mat33_determ( Q ) ; - if( detQ == 0.0 ) return ; /* shouldn't happen unless user is a DUFIS */ - - /* Build and test all possible +1/-1 coordinate permutation matrices P; - then find the P such that the rotation matrix M=PQ is closest to the - identity, in the sense of M having the smallest total rotation angle. */ - - /* Despite the formidable looking 6 nested loops, there are - only 3*3*3*2*2*2 = 216 passes, which will run very quickly. */ - - vbest = -666.0f ; ibest=pbest=qbest=rbest=1 ; jbest=2 ; kbest=3 ; - for( i=1 ; i <= 3 ; i++ ){ /* i = column number to use for row #1 */ - for( j=1 ; j <= 3 ; j++ ){ /* j = column number to use for row #2 */ - if( i == j ) continue ; - for( k=1 ; k <= 3 ; k++ ){ /* k = column number to use for row #3 */ - if( i == k || j == k ) continue ; - P.m[0][0] = P.m[0][1] = P.m[0][2] = - P.m[1][0] = P.m[1][1] = P.m[1][2] = - P.m[2][0] = P.m[2][1] = P.m[2][2] = 0.0f ; - for( p=-1 ; p <= 1 ; p+=2 ){ /* p,q,r are -1 or +1 */ - for( q=-1 ; q <= 1 ; q+=2 ){ /* and go into rows #1,2,3 */ - for( r=-1 ; r <= 1 ; r+=2 ){ - P.m[0][i-1] = p ; P.m[1][j-1] = q ; P.m[2][k-1] = r ; - detP = nifti_mat33_determ(P) ; /* sign of permutation */ - if( detP * detQ <= 0.0 ) continue ; /* doesn't match sign of Q */ - M = nifti_mat33_mul(P,Q) ; - - /* angle of M rotation = 2.0*acos(0.5*sqrt(1.0+trace(M))) */ - /* we want largest trace(M) == smallest angle == M nearest to I */ - - val = M.m[0][0] + M.m[1][1] + M.m[2][2] ; /* trace */ - if( val > vbest ){ - vbest = val ; - ibest = i ; jbest = j ; kbest = k ; - pbest = p ; qbest = q ; rbest = r ; - } - }}}}}} - - /* At this point ibest is 1 or 2 or 3; pbest is -1 or +1; etc. - - The matrix P that corresponds is the best permutation approximation - to Q-inverse; that is, P (approximately) takes (x,y,z) coordinates - to the (i,j,k) axes. - - For example, the first row of P (which contains pbest in column ibest) - determines the way the i axis points relative to the anatomical - (x,y,z) axes. If ibest is 2, then the i axis is along the y axis, - which is direction P2A (if pbest > 0) or A2P (if pbest < 0). - - So, using ibest and pbest, we can assign the output code for - the i axis. Mutatis mutandis for the j and k axes, of course. */ - - switch( ibest*pbest ){ - case 1: i = NIFTI_L2R ; break ; - case -1: i = NIFTI_R2L ; break ; - case 2: i = NIFTI_P2A ; break ; - case -2: i = NIFTI_A2P ; break ; - case 3: i = NIFTI_I2S ; break ; - case -3: i = NIFTI_S2I ; break ; - } - - switch( jbest*qbest ){ - case 1: j = NIFTI_L2R ; break ; - case -1: j = NIFTI_R2L ; break ; - case 2: j = NIFTI_P2A ; break ; - case -2: j = NIFTI_A2P ; break ; - case 3: j = NIFTI_I2S ; break ; - case -3: j = NIFTI_S2I ; break ; - } - - switch( kbest*rbest ){ - case 1: k = NIFTI_L2R ; break ; - case -1: k = NIFTI_R2L ; break ; - case 2: k = NIFTI_P2A ; break ; - case -2: k = NIFTI_A2P ; break ; - case 3: k = NIFTI_I2S ; break ; - case -3: k = NIFTI_S2I ; break ; - } - - *icod = i ; *jcod = j ; *kcod = k ; return ; -} - -/*---------------------------------------------------------------------------*/ -/* Routines to swap byte arrays in various ways: - - 2 at a time: ab -> ba [short] - - 4 at a time: abcd -> dcba [int, float] - - 8 at a time: abcdDCBA -> ABCDdcba [long long, double] - - 16 at a time: abcdefghHGFEDCBA -> ABCDEFGHhgfedcba [long double] ------------------------------------------------------------------------------*/ - -/*----------------------------------------------------------------------*/ -/*! swap each byte pair from the given list of n pairs - * - * Due to alignment of structures at some architectures (e.g. on ARM), - * stick to char varaibles. - * Fixes http://bugs.debian.org/446893 Yaroslav - * -*//*--------------------------------------------------------------------*/ -void nifti_swap_2bytes( int64_t n , void *ar ) /* 2 bytes at a time */ -{ - int64_t ii ; - unsigned char * cp1 = (unsigned char *)ar, * cp2 ; - unsigned char tval; - - for( ii=0 ; ii < n ; ii++ ){ - cp2 = cp1 + 1; - tval = *cp1; *cp1 = *cp2; *cp2 = tval; - cp1 += 2; - } - return ; -} - -/*----------------------------------------------------------------------*/ -/*! swap 4 bytes at a time from the given list of n sets of 4 bytes -*//*--------------------------------------------------------------------*/ -void nifti_swap_4bytes( int64_t n , void *ar ) /* 4 bytes at a time */ -{ - int64_t ii ; - unsigned char * cp0 = (unsigned char *)ar, * cp1, * cp2 ; - unsigned char tval ; - - for( ii=0 ; ii < n ; ii++ ){ - cp1 = cp0; cp2 = cp0+3; - tval = *cp1; *cp1 = *cp2; *cp2 = tval; - cp1++; cp2--; - tval = *cp1; *cp1 = *cp2; *cp2 = tval; - cp0 += 4; - } - return ; -} - -/*----------------------------------------------------------------------*/ -/*! swap 8 bytes at a time from the given list of n sets of 8 bytes - * - * perhaps use this style for the general Nbytes, as Yaroslav suggests -*//*--------------------------------------------------------------------*/ -void nifti_swap_8bytes( int64_t n , void *ar ) /* 8 bytes at a time */ -{ - int64_t ii ; - unsigned char * cp0 = (unsigned char *)ar, * cp1, * cp2 ; - unsigned char tval ; - - for( ii=0 ; ii < n ; ii++ ){ - cp1 = cp0; cp2 = cp0+7; - while ( cp2 > cp1 ) /* unroll? */ - { - tval = *cp1 ; *cp1 = *cp2 ; *cp2 = tval ; - cp1++; cp2--; - } - cp0 += 8; - } - return ; -} - -/*----------------------------------------------------------------------*/ -/*! swap 16 bytes at a time from the given list of n sets of 16 bytes -*//*--------------------------------------------------------------------*/ -void nifti_swap_16bytes( int64_t n , void *ar ) /* 16 bytes at a time */ -{ - int64_t ii ; - unsigned char * cp0 = (unsigned char *)ar, * cp1, * cp2 ; - unsigned char tval ; - - for( ii=0 ; ii < n ; ii++ ){ - cp1 = cp0; cp2 = cp0+15; - while ( cp2 > cp1 ) - { - tval = *cp1 ; *cp1 = *cp2 ; *cp2 = tval ; - cp1++; cp2--; - } - cp0 += 16; - } - return ; -} - -#if 0 /* not important: save for version update 6 Jul 2010 [rickr] */ - -/*----------------------------------------------------------------------*/ -/*! generic: swap siz bytes at a time from the given list of n sets -*//*--------------------------------------------------------------------*/ -void nifti_swap_bytes( int64_t n , int siz , void *ar ) -{ - int64_t ii ; - unsigned char * cp0 = (unsigned char *)ar, * cp1, * cp2 ; - unsigned char tval ; - - for( ii=0 ; ii < n ; ii++ ){ - cp1 = cp0; cp2 = cp0+(siz-1); - while ( cp2 > cp1 ) - { - tval = *cp1 ; *cp1 = *cp2 ; *cp2 = tval ; - cp1++; cp2--; - } - cp0 += siz; - } - return ; -} -#endif - -/*---------------------------------------------------------------------------*/ - -/*----------------------------------------------------------------------*/ -/*! based on siz, call the appropriate nifti_swap_Nbytes() function -*//*--------------------------------------------------------------------*/ -void nifti_swap_Nbytes( int64_t n , int siz , void *ar ) /* subsuming case */ -{ - switch( siz ){ - case 2: nifti_swap_2bytes ( n , ar ) ; break ; - case 4: nifti_swap_4bytes ( n , ar ) ; break ; - case 8: nifti_swap_8bytes ( n , ar ) ; break ; - case 16: nifti_swap_16bytes( n , ar ) ; break ; - default: /* nifti_swap_bytes ( n , siz, ar ) ; */ - fprintf(stderr,"** NIfTI: cannot swap in %d byte blocks\n", siz); - break ; - } - return ; -} - - -/*-------------------------------------------------------------------------*/ -/*! Byte swap NIFTI file header, depending on the version. -*//*---------------------------------------------------------------------- */ -void swap_nifti_header( void * hdr , int ni_ver ) -{ - if ( ni_ver == 0 ) nifti_swap_as_analyze((nifti_analyze75 *)hdr); - else if( ni_ver == 1 ) nifti_swap_as_nifti1((nifti_1_header *)hdr); - else if( ni_ver == 2 ) nifti_swap_as_nifti2((nifti_2_header *)hdr); - else if( ni_ver >= 0 && ni_ver <= 9 ) { - fprintf(stderr,"** swap_nifti_header: not ready for version %d\n",ni_ver); - } else { - fprintf(stderr,"** swap_nifti_header: illegal version %d\n", ni_ver); - } -} - - -/*-------------------------------------------------------------------------*/ -/*! Byte swap NIFTI-2 file header. -*//*---------------------------------------------------------------------- */ -void nifti_swap_as_nifti2( nifti_2_header * h ) -{ - if ( ! h ) { - fprintf(stderr,"** nifti_swap_as_nifti2: NULL pointer\n"); - return; - } - - nifti_swap_4bytes(1, &h->sizeof_hdr); - - nifti_swap_2bytes(1, &h->datatype); - nifti_swap_2bytes(1, &h->bitpix); - - nifti_swap_8bytes(8, h->dim); - nifti_swap_8bytes(1, &h->intent_p1); - nifti_swap_8bytes(1, &h->intent_p2); - nifti_swap_8bytes(1, &h->intent_p3); - nifti_swap_8bytes(8, h->pixdim); - - nifti_swap_8bytes(1, &h->vox_offset); - nifti_swap_8bytes(1, &h->scl_slope); - nifti_swap_8bytes(1, &h->scl_inter); - nifti_swap_8bytes(1, &h->cal_max); - nifti_swap_8bytes(1, &h->cal_min); - nifti_swap_8bytes(1, &h->slice_duration); - nifti_swap_8bytes(1, &h->toffset); - nifti_swap_8bytes(1, &h->slice_start); - nifti_swap_8bytes(1, &h->slice_end); - - nifti_swap_4bytes(1, &h->qform_code); - nifti_swap_4bytes(1, &h->sform_code); - - nifti_swap_8bytes(1, &h->quatern_b); - nifti_swap_8bytes(1, &h->quatern_c); - nifti_swap_8bytes(1, &h->quatern_d); - nifti_swap_8bytes(1, &h->qoffset_x); - nifti_swap_8bytes(1, &h->qoffset_y); - nifti_swap_8bytes(1, &h->qoffset_z); - - nifti_swap_8bytes(4, h->srow_x); - nifti_swap_8bytes(4, h->srow_y); - nifti_swap_8bytes(4, h->srow_z); - - nifti_swap_4bytes(1, &h->slice_code); - nifti_swap_4bytes(1, &h->xyzt_units); - nifti_swap_4bytes(1, &h->intent_code); -} - -/*-------------------------------------------------------------------------*/ -/*! Byte swap NIFTI-1 file header in various places and ways. - * return 0 on success -*//*---------------------------------------------------------------------- */ -void nifti_swap_as_nifti1( nifti_1_header * h ) -{ - if ( ! h ) { - fprintf(stderr,"** nifti_swap_as_nifti1: NULL pointer\n"); - return; - } - - nifti_swap_4bytes(1, &h->sizeof_hdr); - nifti_swap_4bytes(1, &h->extents); - nifti_swap_2bytes(1, &h->session_error); - - nifti_swap_2bytes(8, h->dim); - nifti_swap_4bytes(1, &h->intent_p1); - nifti_swap_4bytes(1, &h->intent_p2); - nifti_swap_4bytes(1, &h->intent_p3); - - nifti_swap_2bytes(1, &h->intent_code); - nifti_swap_2bytes(1, &h->datatype); - nifti_swap_2bytes(1, &h->bitpix); - nifti_swap_2bytes(1, &h->slice_start); - - nifti_swap_4bytes(8, h->pixdim); - - nifti_swap_4bytes(1, &h->vox_offset); - nifti_swap_4bytes(1, &h->scl_slope); - nifti_swap_4bytes(1, &h->scl_inter); - nifti_swap_2bytes(1, &h->slice_end); - - nifti_swap_4bytes(1, &h->cal_max); - nifti_swap_4bytes(1, &h->cal_min); - nifti_swap_4bytes(1, &h->slice_duration); - nifti_swap_4bytes(1, &h->toffset); - nifti_swap_4bytes(1, &h->glmax); - nifti_swap_4bytes(1, &h->glmin); - - nifti_swap_2bytes(1, &h->qform_code); - nifti_swap_2bytes(1, &h->sform_code); - - nifti_swap_4bytes(1, &h->quatern_b); - nifti_swap_4bytes(1, &h->quatern_c); - nifti_swap_4bytes(1, &h->quatern_d); - nifti_swap_4bytes(1, &h->qoffset_x); - nifti_swap_4bytes(1, &h->qoffset_y); - nifti_swap_4bytes(1, &h->qoffset_z); - - nifti_swap_4bytes(4, h->srow_x); - nifti_swap_4bytes(4, h->srow_y); - nifti_swap_4bytes(4, h->srow_z); -} - -/*-------------------------------------------------------------------------*/ -/*! Byte swap as an ANALYZE 7.5 header - * - * return non-zero on failure -*//*---------------------------------------------------------------------- */ -void nifti_swap_as_analyze( nifti_analyze75 * h ) -{ - if ( ! h ) { - fprintf(stderr,"** nifti_swap_as_analyze: NULL pointer\n"); - return; - } - - nifti_swap_4bytes(1, &h->sizeof_hdr); - nifti_swap_4bytes(1, &h->extents); - nifti_swap_2bytes(1, &h->session_error); - - nifti_swap_2bytes(8, h->dim); - nifti_swap_2bytes(1, &h->unused8); - nifti_swap_2bytes(1, &h->unused9); - nifti_swap_2bytes(1, &h->unused10); - nifti_swap_2bytes(1, &h->unused11); - nifti_swap_2bytes(1, &h->unused12); - nifti_swap_2bytes(1, &h->unused13); - nifti_swap_2bytes(1, &h->unused14); - - nifti_swap_2bytes(1, &h->datatype); - nifti_swap_2bytes(1, &h->bitpix); - nifti_swap_2bytes(1, &h->dim_un0); - - nifti_swap_4bytes(8, h->pixdim); - - nifti_swap_4bytes(1, &h->vox_offset); - nifti_swap_4bytes(1, &h->funused1); - nifti_swap_4bytes(1, &h->funused2); - nifti_swap_4bytes(1, &h->funused3); - - nifti_swap_4bytes(1, &h->cal_max); - nifti_swap_4bytes(1, &h->cal_min); - nifti_swap_4bytes(1, &h->compressed); - nifti_swap_4bytes(1, &h->verified); - nifti_swap_4bytes(1, &h->glmax); - nifti_swap_4bytes(1, &h->glmin); - - nifti_swap_4bytes(1, &h->views); - nifti_swap_4bytes(1, &h->vols_added); - nifti_swap_4bytes(1, &h->start_field); - nifti_swap_4bytes(1, &h->field_skip); - - nifti_swap_4bytes(1, &h->omax); - nifti_swap_4bytes(1, &h->omin); - nifti_swap_4bytes(1, &h->smax); - nifti_swap_4bytes(1, &h->smin); -} - -/*-------------------------------------------------------------------------*/ -/*! OLD VERSION of swap_nifti_header (left for undo/compare operations) - - Byte swap NIFTI-1 file header in various places and ways. - - If is_nifti is nonzero, will also swap the NIFTI-specific - components of the header; otherwise, only the components - common to NIFTI and ANALYZE will be swapped. -*//*---------------------------------------------------------------------- */ -void old_swap_nifti_header( nifti_1_header *h , int is_nifti ) -{ - /* this stuff is always present, for ANALYZE and NIFTI */ - - swap_4(h->sizeof_hdr) ; - nifti_swap_2bytes( 8 , h->dim ) ; - nifti_swap_4bytes( 8 , h->pixdim ) ; - - swap_2(h->datatype) ; - swap_2(h->bitpix) ; - - swap_4(h->vox_offset); swap_4(h->cal_max); swap_4(h->cal_min); - - /* this stuff is NIFTI specific */ - - if( is_nifti ){ - swap_4(h->intent_p1); swap_4(h->intent_p2); swap_4(h->intent_p3); - swap_2(h->intent_code); - - swap_2(h->slice_start); swap_2(h->slice_end); - swap_4(h->scl_slope); swap_4(h->scl_inter); - swap_4(h->slice_duration); swap_4(h->toffset); - - swap_2(h->qform_code); swap_2(h->sform_code); - swap_4(h->quatern_b); swap_4(h->quatern_c); swap_4(h->quatern_d); - swap_4(h->qoffset_x); swap_4(h->qoffset_y); swap_4(h->qoffset_z); - nifti_swap_4bytes(4,h->srow_x); - nifti_swap_4bytes(4,h->srow_y); - nifti_swap_4bytes(4,h->srow_z); - } - return ; -} - - -#define USE_STAT -#ifdef USE_STAT -/*---------------------------------------------------------------------------*/ -/* Return the file length (0 if file not found or has no contents). - This is a Unix-specific function, since it uses stat(). ------------------------------------------------------------------------------*/ -#include -#include - -/*---------------------------------------------------------------------------*/ -/*! return the size of a file, in bytes - - \return size of file on success, -1 on error or no file - - changed to return int, -1 means no file or error 20 Dec 2004 [rickr] -*//*-------------------------------------------------------------------------*/ -int64_t nifti_get_filesize( const char *pathname ) -{ - struct stat buf ; int ii ; - - if( pathname == NULL || *pathname == '\0' ) return -1 ; - ii = stat( pathname , &buf ); if( ii != 0 ) return -1 ; - return buf.st_size ; -} - -#else /*---------- non-Unix version of the above, less efficient -----------*/ - -int64_t nifti_get_filesize( const char *pathname ) -{ - znzFile fp ; int64_t len ; - - if( pathname == NULL || *pathname == '\0' ) return -1 ; - fp = znzopen(pathname,"rb",0); if( znz_isnull(fp) ) return -1 ; - znzseek(fp,0L,SEEK_END) ; len = znztell(fp) ; - znzclose(fp) ; return len ; -} - -#endif /* USE_STAT */ - - -/*----------------------------------------------------------------------*/ -/*! return the total volume size, in bytes - - This is computed as nvox * nbyper. -*//*--------------------------------------------------------------------*/ -int64_t nifti_get_volsize(const nifti_image *nim) -{ - return (int64_t)nim->nbyper * nim->nvox ; /* total bytes */ -} - - -/*--------------------------------------------------------------------------*/ -/* Support functions for filenames in read and write - - allows for gzipped files -*/ - - -/*----------------------------------------------------------------------*/ -/*! simple check for file existence - - \return 1 on existence, 0 otherwise -*//*--------------------------------------------------------------------*/ -int nifti_fileexists(const char* fname) -{ - znzFile fp; - fp = znzopen( fname , "rb" , 1 ) ; - if( !znz_isnull(fp) ) { znzclose(fp); return 1; } - return 0; /* fp is NULL */ -} - -/*----------------------------------------------------------------------*/ -/*! return whether the filename is valid - - Note: uppercase extensions are now valid. 27 Apr 2009 [rickr] - - The name is considered valid if the file basename has length greater than - zero, AND one of the valid nifti extensions is provided. - fname input | return | - =============================== - "myimage" | 0 | - "myimage.tif" | 0 | - "myimage.tif.gz" | 0 | - "myimage.nii" | 1 | - ".nii" | 0 | - ".myhiddenimage" | 0 | - ".myhiddenimage.nii" | 1 | -*//*--------------------------------------------------------------------*/ -int nifti_is_complete_filename(const char* fname) -{ - const char * ext; - - /* check input file(s) for sanity */ - if( fname == NULL || *fname == '\0' ){ - if ( g_opts.debug > 1 ) - fprintf(stderr,"-- empty filename in nifti_validfilename()\n"); - return 0; - } - - ext = nifti_find_file_extension(fname); - if ( ext == NULL ) { /*Invalid extension given */ - if ( g_opts.debug > 0 ) - fprintf(stderr,"-- no nifti valid extension for filename '%s'\n", fname); - return 0; - } - - if ( ext && ext == fname ) { /* then no filename prefix */ - if ( g_opts.debug > 0 ) - fprintf(stderr,"-- no prefix for filename '%s'\n", fname); - return 0; - } - return 1; -} - -/*----------------------------------------------------------------------*/ -/*! return whether the filename is valid - - Allow uppercase extensions as valid. 27 Apr 2009 [rickr] - Any .gz extension case must match the base extension case. - - The name is considered valid if its length is positive, excluding - any nifti filename extension. - fname input | return | result of nifti_makebasename - ==================================================================== - "myimage" | 1 | "myimage" - "myimage.tif" | 1 | "myimage.tif" - "myimage.tif.gz" | 1 | "myimage.tif" - "myimage.nii" | 1 | "myimage" - ".nii" | 0 | - ".myhiddenimage" | 1 | ".myhiddenimage" - ".myhiddenimage.nii | 1 | ".myhiddenimage" -*//*--------------------------------------------------------------------*/ -int nifti_validfilename(const char* fname) -{ - const char * ext; - - /* check input file(s) for sanity */ - if( fname == NULL || *fname == '\0' ){ - if ( g_opts.debug > 1 ) - fprintf(stderr,"-- empty filename in nifti_validfilename()\n"); - return 0; - } - - ext = nifti_find_file_extension(fname); - - if ( ext && ext == fname ) { /* then no filename prefix */ - if ( g_opts.debug > 0 ) - fprintf(stderr,"-- no prefix for filename '%s'\n", fname); - return 0; - } - - return 1; -} - -/*----------------------------------------------------------------------*/ -/*! check the end of the filename for a valid nifti extension - - Valid extensions are currently .nii, .hdr, .img, .nia, - or any of them followed by .gz. Note that '.' is part of - the extension. - - Uppercase extensions are also valid, but not mixed case. - - \return a pointer to the extension substring within the original - function input parameter name, or NULL if not found. - \caution Note that if the input parameter is is immutabale - (i.e. a const char *) then this function performs an - implicit casting away of the mutability constraint and - the return parameter will appear as a mutable - even though it is part of the immuttable string. -*//*--------------------------------------------------------------------*/ -char * nifti_find_file_extension( const char * name ) -{ - const char * ext; - char extcopy[8]; - int len; - char extnii[8] = ".nii"; /* modifiable, for possible uppercase */ - char exthdr[8] = ".hdr"; /* (leave space for .gz) */ - char extimg[8] = ".img"; - char extnia[8] = ".nia"; - char extgz[4] = ".gz"; - char * elist[4] = { NULL, NULL, NULL, NULL}; - - /* stupid compiler... */ - elist[0] = extnii; elist[1] = exthdr; elist[2] = extimg; elist[3] = extnia; - - if ( ! name ) return NULL; - - len = (int)strlen(name); - if ( len < 4 ) return NULL; - - ext = name + len - 4; - - /* make manipulation copy, and possibly convert to lowercase */ - strcpy(extcopy, ext); - if( g_opts.allow_upper_fext ) make_lowercase(extcopy); - - /* if it look like a basic extension, fail or return it */ - if( compare_strlist(extcopy, elist, 4) >= 0 ) { - if( is_mixedcase(ext) ) { - fprintf(stderr,"** NIFTI: mixed case extension '%s' is not valid\n", - ext); - return NULL; - } - else return (char *)ext; /* Cast away the constness of the input parameter */ - } - -#ifdef HAVE_ZLIB - if ( len < 7 ) return NULL; - - ext = name + len - 7; - - /* make manipulation copy, and possibly convert to lowercase */ - strcpy(extcopy, ext); - if( g_opts.allow_upper_fext ) make_lowercase(extcopy); - - /* go after .gz extensions using the modifiable strings */ - strcat(elist[0], extgz); strcat(elist[1], extgz); strcat(elist[2], extgz); - - if( compare_strlist(extcopy, elist, 3) >= 0 ) { - if( is_mixedcase(ext) ) { - fprintf(stderr,"** NIFTI: mixed case extension '%s' is not valid\n", - ext); - return NULL; - } - else return (char *)ext; /* Cast away the constness of the input parameter */ - } - -#endif - - if( g_opts.debug > 1 ) - fprintf(stderr,"** find_file_ext: failed for name '%s'\n", name); - - return NULL; -} - -/*----------------------------------------------------------------------*/ -/*! return whether the filename ends in ".gz" -*//*--------------------------------------------------------------------*/ -int nifti_is_gzfile(const char* fname) -{ - /* return true if the filename ends with .gz */ - if (fname == NULL) { return 0; } -#ifdef HAVE_ZLIB - { /* just so len doesn't generate compile warning */ - int len; - len = (int)strlen(fname); - if (len < 3) return 0; /* so we don't search before the name */ - if (fileext_compare(fname + strlen(fname) - 3,".gz")==0) { return 1; } - } -#endif - return 0; -} - -/*----------------------------------------------------------------------*/ -/*! return whether the given library was compiled with HAVE_ZLIB set -*//*--------------------------------------------------------------------*/ -int nifti_compiled_with_zlib(void) -{ -#ifdef HAVE_ZLIB - return 1; -#else - return 0; -#endif -} - -/*----------------------------------------------------------------------*/ -/*! duplicate the filename, while clearing any extension - - This allocates memory for basename which should eventually be freed. -*//*--------------------------------------------------------------------*/ -char * nifti_makebasename(const char* fname) -{ - char *basename; - const char *ext; - - basename=nifti_strdup(fname); - - ext = nifti_find_file_extension(basename); - if ( ext ) - { - basename[strlen(basename)-strlen(ext)] = '\0'; /* clear out extension */ - } - - return basename; /* in either case */ -} - -/*----------------------------------------------------------------------*/ -/* option accessor functions */ -/*----------------------------------------------------------------------*/ - -/*----------------------------------------------------------------------*/ -/*! set nifti's global debug level, for status reporting - - - 0 : quiet, nothing is printed to the terminal, but errors - - 1 : normal execution (the default) - - 2, 3 : more details -*//*--------------------------------------------------------------------*/ -void nifti_set_debug_level( int level ) -{ - g_opts.debug = level; -} - -/*----------------------------------------------------------------------*/ -/*! set nifti's global skip_blank_ext flag 5 Sep 2006 [rickr] - - explicitly set to 0 or 1 -*//*--------------------------------------------------------------------*/ -void nifti_set_skip_blank_ext( int skip ) -{ - g_opts.skip_blank_ext = skip ? 1 : 0; -} - -/*----------------------------------------------------------------------*/ -/*! set nifti's global allow_upper_fext flag 28 Apr 2009 [rickr] - - explicitly set to 0 or 1 -*//*--------------------------------------------------------------------*/ -void nifti_set_allow_upper_fext( int allow ) -{ - g_opts.allow_upper_fext = allow ? 1 : 0; -} - -/*----------------------------------------------------------------------*/ -/*! get nifti's global alter_cifti flag 22 Jul 2015 [rickr] -*//*--------------------------------------------------------------------*/ -int nifti_get_alter_cifti( void ) -{ - return g_opts.alter_cifti; -} - -/*----------------------------------------------------------------------*/ -/*! set nifti's global alter_cifti flag 22 Jul 2015 [rickr] - - explicitly set to 0 or 1 -*//*--------------------------------------------------------------------*/ -void nifti_set_alter_cifti( int alter_cifti ) -{ - g_opts.alter_cifti = alter_cifti ? 1 : 0; -} - -/*----------------------------------------------------------------------*/ -/*! check current directory for existing header file - - \return filename of header on success and NULL if no appropriate file - could be found - - If fname has an uppercase extension, check for uppercase files. - - NB: it allocates memory for hdrname which should be freed - when no longer required -*//*-------------------------------------------------------------------*/ -char * nifti_findhdrname(const char* fname) -{ - char *basename, *hdrname; - const char *ext; - char elist[2][5] = { ".hdr", ".nii" }; - char extzip[4] = ".gz"; - int efirst = 1; /* init to .nii extension */ - int eisupper = 0; /* init to lowercase extensions */ - - /**- check input file(s) for sanity */ - if( !nifti_validfilename(fname) ) return NULL; - - basename = nifti_makebasename(fname); - if( !basename ) return NULL; /* only on string alloc failure */ - - /**- return filename if it has a valid extension and exists - (except if it is an .img file (and maybe .gz)) */ - ext = nifti_find_file_extension(fname); - - if( ext ) eisupper = is_uppercase(ext); /* do we look for uppercase? */ - - /* if the file exists and is a valid header name (not .img), return it */ - if ( ext && nifti_fileexists(fname) ) { - /* allow for uppercase extension */ - if ( fileext_n_compare(ext,".img",4) != 0 ){ - hdrname = nifti_strdup(fname); - free(basename); - return hdrname; - } else - efirst = 0; /* note for below */ - } - - /* So the requested name is a basename, contains .img, or does not exist. */ - /* In any case, use basename. */ - - /**- if .img, look for .hdr, .hdr.gz, .nii, .nii.gz, in that order */ - /**- else, look for .nii, .nii.gz, .hdr, .hdr.gz, in that order */ - - /* if we get more extension choices, this could be a loop */ - - /* note: efirst is 0 in the case of ".img" */ - - /* if the user passed an uppercase entension (.IMG), search for uppercase */ - if( eisupper ) { - make_uppercase(elist[0]); - make_uppercase(elist[1]); - make_uppercase(extzip); - } - - hdrname = (char *)calloc(sizeof(char),strlen(basename)+8); - if( !hdrname ){ - fprintf(stderr,"** nifti_findhdrname: failed to alloc hdrname\n"); - free(basename); - return NULL; - } - - strcpy(hdrname,basename); - strcat(hdrname,elist[efirst]); - if (nifti_fileexists(hdrname)) { free(basename); return hdrname; } -#ifdef HAVE_ZLIB - strcat(hdrname,extzip); - if (nifti_fileexists(hdrname)) { free(basename); return hdrname; } -#endif - - /* okay, try the other possibility */ - - efirst = 1 - efirst; - - strcpy(hdrname,basename); - strcat(hdrname,elist[efirst]); - if (nifti_fileexists(hdrname)) { free(basename); return hdrname; } -#ifdef HAVE_ZLIB - strcat(hdrname,extzip); - if (nifti_fileexists(hdrname)) { free(basename); return hdrname; } -#endif - - /**- if nothing has been found, return NULL */ - free(basename); - free(hdrname); - return NULL; -} - - -/*------------------------------------------------------------------------*/ -/*! check current directory for existing image file - - \param fname filename to check for - \nifti_type nifti_type for dataset - this determines whether to - first check for ".nii" or ".img" (since both may exist) - - \return filename of data/img file on success and NULL if no appropriate - file could be found - - If fname has a valid, uppercase extension, apply all extensions as - uppercase. - - NB: it allocates memory for the image filename, which should be freed - when no longer required -*//*---------------------------------------------------------------------*/ -char * nifti_findimgname(const char* fname , int nifti_type) -{ - /* store all extensions as strings, in case we need to go uppercase */ - char *basename, *imgname, elist[2][5] = { ".nii", ".img" }; - char extzip[4] = ".gz"; - char extnia[5] = ".nia"; - const char *ext; - int first; /* first extension to use */ - - /* check input file(s) for sanity */ - if( !nifti_validfilename(fname) ) return NULL; - - basename = nifti_makebasename(fname); - imgname = (char *)calloc(sizeof(char),strlen(basename)+8); - if( !imgname ){ - fprintf(stderr,"** nifti_findimgname: failed to alloc imgname\n"); - free(basename); - return NULL; - } - - /* if we are looking for uppercase, apply the fact now */ - ext = nifti_find_file_extension(fname); - if( ext && is_uppercase(ext) ) { - make_uppercase(elist[0]); - make_uppercase(elist[1]); - make_uppercase(extzip); - make_uppercase(extnia); - } - - /* only valid extension for ASCII type is .nia, handle first */ - if( nifti_type == NIFTI_FTYPE_ASCII ){ - strcpy(imgname,basename); - strcat(imgname,extnia); - if (nifti_fileexists(imgname)) { free(basename); return imgname; } - - } else { - - /**- test for .nii and .img (don't assume input type from image type) */ - /**- if nifti_type = 1, check for .nii first, else .img first */ - - /* if we get 3 or more extensions, can make a loop here... */ - - if (nifti_type == NIFTI_FTYPE_NIFTI1_1) first = 0; /* should match .nii */ - else first = 1; /* should match .img */ - - strcpy(imgname,basename); - strcat(imgname,elist[first]); - if (nifti_fileexists(imgname)) { free(basename); return imgname; } -#ifdef HAVE_ZLIB /* then also check for .gz */ - strcat(imgname,extzip); - if (nifti_fileexists(imgname)) { free(basename); return imgname; } -#endif - - /* failed to find image file with expected extension, try the other */ - - strcpy(imgname,basename); - strcat(imgname,elist[1-first]); /* can do this with only 2 choices */ - if (nifti_fileexists(imgname)) { free(basename); return imgname; } -#ifdef HAVE_ZLIB /* then also check for .gz */ - strcat(imgname,extzip); - if (nifti_fileexists(imgname)) { free(basename); return imgname; } -#endif - } - - /**- if nothing has been found, return NULL */ - free(basename); - free(imgname); - return NULL; -} - - -/*----------------------------------------------------------------------*/ -/*! creates a filename for storing the header, based on nifti_type - - \param prefix - this will be copied before the suffix is added - \param nifti_type - determines the extension, unless one is in prefix - \param check - check for existence (fail condition) - \param comp - add .gz for compressed name - - Note that if prefix provides a file suffix, nifti_type is not used. - - NB: this allocates memory which should be freed - - \sa nifti_set_filenames -*//*-------------------------------------------------------------------*/ -char * nifti_makehdrname(const char * prefix, int nifti_type, int check, - int comp) -{ - char * iname; - const char * ext; - char extnii[5] = ".nii"; /* modifiable, for possible uppercase */ - char exthdr[5] = ".hdr"; - char extimg[5] = ".img"; - char extnia[5] = ".nia"; - char extgz[5] = ".gz"; - - if( !nifti_validfilename(prefix) ) return NULL; - - /* add space for extension, optional ".gz", and null char */ - iname = (char *)calloc(sizeof(char),strlen(prefix)+8); - if( !iname ){ - fprintf(stderr,"** NIFTI small malloc failure!\n"); - return NULL; - } - strcpy(iname, prefix); - - /* use any valid extension */ - if( (ext = nifti_find_file_extension(iname)) != NULL ){ - /* if uppercase, convert all extensions */ - if( is_uppercase(ext) ) { - make_uppercase(extnii); - make_uppercase(exthdr); - make_uppercase(extimg); - make_uppercase(extnia); - make_uppercase(extgz); - } - - if( strncmp(ext,extimg,4) == 0 ) - { - memcpy(&(iname[strlen(iname)-strlen(ext)]),exthdr,4); /* then convert img name to hdr */ - } - } - /* otherwise, make one up */ - else if( nifti_type == NIFTI_FTYPE_NIFTI1_1 ) strcat(iname, extnii); - else if( nifti_type == NIFTI_FTYPE_ASCII ) strcat(iname, extnia); - else strcat(iname, exthdr); - -#ifdef HAVE_ZLIB /* if compression is requested, make sure of suffix */ - if( comp && (!ext || !strstr(iname,extgz)) ) strcat(iname,extgz); -#endif - - /* check for existence failure */ - if( check && nifti_fileexists(iname) ){ - fprintf(stderr,"** failure: NIFTI header file '%s' already exists\n", - iname); - free(iname); - return NULL; - } - - if(g_opts.debug > 2) fprintf(stderr,"+d made header filename '%s'\n", iname); - - return iname; -} - - -/*----------------------------------------------------------------------*/ -/*! creates a filename for storing the image, based on nifti_type - - \param prefix - this will be copied before the suffix is added - \param nifti_type - determines the extension, unless provided by prefix - \param check - check for existence (fail condition) - \param comp - add .gz for compressed name - - Note that if prefix provides a file suffix, nifti_type is not used. - - NB: it allocates memory which should be freed - - \sa nifti_set_filenames -*//*-------------------------------------------------------------------*/ -char * nifti_makeimgname(const char * prefix, int nifti_type, int check, - int comp) -{ - char * iname; - const char * ext; - char extnii[5] = ".nii"; /* modifiable, for possible uppercase */ - char exthdr[5] = ".hdr"; - char extimg[5] = ".img"; - char extnia[5] = ".nia"; - char extgz[5] = ".gz"; - - if( !nifti_validfilename(prefix) ) return NULL; - - /* add space for extension, optional ".gz", and null char */ - iname = (char *)calloc(sizeof(char),strlen(prefix)+8); - if( !iname ){ - fprintf(stderr,"** NIFTI: small malloc failure!\n"); - return NULL; - } - strcpy(iname, prefix); - - /* use any valid extension */ - if( (ext = nifti_find_file_extension(iname)) != NULL ){ - /* if uppercase, convert all extensions */ - if( is_uppercase(ext) ) { - make_uppercase(extnii); - make_uppercase(exthdr); - make_uppercase(extimg); - make_uppercase(extnia); - make_uppercase(extgz); - } - - if( strncmp(ext,exthdr,4) == 0 ) - { - memcpy(&(iname[strlen(iname)-strlen(ext)]),extimg,4); /* then convert hdr name to img */ - } - } - /* otherwise, make one up */ - else if( nifti_type == NIFTI_FTYPE_NIFTI1_1 ) strcat(iname, extnii); - else if( nifti_type == NIFTI_FTYPE_ASCII ) strcat(iname, extnia); - else strcat(iname, extimg); - -#ifdef HAVE_ZLIB /* if compression is requested, make sure of suffix */ - if( comp && (!ext || !strstr(iname,extgz)) ) strcat(iname,extgz); -#endif - - /* check for existence failure */ - if( check && nifti_fileexists(iname) ){ - fprintf(stderr,"** NIFTI failure: image file '%s' already exists\n", - iname); - free(iname); - return NULL; - } - - if( g_opts.debug > 2 ) fprintf(stderr,"+d made image filename '%s'\n",iname); - - return iname; -} - - -/*----------------------------------------------------------------------*/ -/*! create and set new filenames, based on prefix and image type - - \param nim pointer to nifti_image in which to set filenames - \param prefix (required) prefix for output filenames - \param check check for previous existence of filename - (existence is an error condition) - \param set_byte_order flag to set nim->byteorder here - (this is probably a logical place to do so) - - \return 0 on successful update - - \warning this will free() any existing names and create new ones - - \sa nifti_makeimgname, nifti_makehdrname, nifti_type_and_names_match -*//*--------------------------------------------------------------------*/ -int nifti_set_filenames( nifti_image * nim, const char * prefix, int check, - int set_byte_order ) -{ - int comp = nifti_is_gzfile(prefix); - - if( !nim || !prefix ){ - fprintf(stderr,"** nifti_set_filenames, bad params %p, %p\n", - (void *)nim,prefix); - return -1; - } - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d modifying output filenames using prefix %s\n", prefix); - - /* set and test output filenames */ - if( nim->fname ) free(nim->fname); - if( nim->iname ) free(nim->iname); - nim->iname = NULL; - nim->fname = nifti_makehdrname(prefix, nim->nifti_type, check, comp); - if( nim->fname ) - nim->iname = nifti_makeimgname(prefix, nim->nifti_type, check, comp); - if( !nim->fname || !nim->iname ) return -1; /* failure */ - - if( set_byte_order ) nim->byteorder = nifti_short_order() ; - - if( nifti_set_type_from_names(nim) < 0 ) - return -1; - - if( g_opts.debug > 2 ) - fprintf(stderr,"+d have new filenames %s and %s\n",nim->fname,nim->iname); - - return 0; -} - - -/*--------------------------------------------------------------------------*/ -/*! check whether nifti_type matches fname and iname for the nifti_image - - - if type 0 or 2, expect .hdr/.img pair - - if type 1, expect .nii (and names must match) - - \param nim given nifti_image - \param show_warn if set, print a warning message for any mis-match - - \return - - 1 if the values seem to match - - 0 if there is a mis-match - - -1 if there is not sufficient information to create file(s) - - \sa NIFTI_FTYPE_* codes in nifti1_io.h - \sa nifti_set_type_from_names, is_valid_nifti_type -*//*------------------------------------------------------------------------*/ -int nifti_type_and_names_match( nifti_image * nim, int show_warn ) -{ - char func[] = "nifti_type_and_names_match"; - const char * ext_h; /* header filename extension */ - const char * ext_i; /* image filename extension */ - int errs = 0; /* error counter */ - - /* sanity checks */ - if( !nim ){ - if( show_warn ) fprintf(stderr,"** %s: missing nifti_image\n", func); - return -1; - } - if( !nim->fname ){ - if( show_warn ) fprintf(stderr,"** %s: missing header filename\n", func); - errs++; - } - if( !nim->iname ){ - if( show_warn ) fprintf(stderr,"** %s: missing image filename\n", func); - errs++; - } - if( !is_valid_nifti_type(nim->nifti_type) ){ - if( show_warn ) - fprintf(stderr,"** %s: bad nifti_type %d\n", func, nim->nifti_type); - errs++; - } - - if( errs ) return -1; /* then do not proceed */ - - /* get pointers to extensions */ - ext_h = nifti_find_file_extension( nim->fname ); - ext_i = nifti_find_file_extension( nim->iname ); - - /* check for filename extensions */ - if( !ext_h ){ - if( show_warn ) - fprintf(stderr,"-d missing NIFTI extension in header filename, %s\n", - nim->fname); - errs++; - } - if( !ext_i ){ - if( show_warn ) - fprintf(stderr,"-d missing NIFTI extension in image filename, %s\n", - nim->iname); - errs++; - } - - if( errs ) return 0; /* do not proceed, but this is just a mis-match */ - - /* general tests */ - if( nim->nifti_type == NIFTI_FTYPE_NIFTI1_1 ){ /* .nii */ - if( fileext_n_compare(ext_h,".nii",4) ) { - if( show_warn ) - fprintf(stderr, - "-d NIFTI_FTYPE 1, but no .nii extension in header filename, %s\n", - nim->fname); - errs++; - } - if( fileext_n_compare(ext_i,".nii",4) ) { - if( show_warn ) - fprintf(stderr, - "-d NIFTI_FTYPE 1, but no .nii extension in image filename, %s\n", - nim->iname); - errs++; - } - if( strcmp(nim->fname, nim->iname) != 0 ){ - if( show_warn ) - fprintf(stderr, - "-d NIFTI_FTYPE 1, but header and image filenames differ: %s, %s\n", - nim->fname, nim->iname); - errs++; - } - } - else if( (nim->nifti_type == NIFTI_FTYPE_NIFTI1_2) || /* .hdr/.img */ - (nim->nifti_type == NIFTI_FTYPE_ANALYZE) ) - { - if( fileext_n_compare(ext_h,".hdr",4) != 0 ){ - if( show_warn ) - fprintf(stderr,"-d no '.hdr' extension, but NIFTI type is %d, %s\n", - nim->nifti_type, nim->fname); - errs++; - } - if( fileext_n_compare(ext_i,".img",4) != 0 ){ - if( show_warn ) - fprintf(stderr,"-d no '.img' extension, but NIFTI type is %d, %s\n", - nim->nifti_type, nim->iname); - errs++; - } - } - /* ignore any other nifti_type */ - - return 1; -} - -/* like strcmp, but also check against capitalization of known_ext - * (test as local string, with max length 7) */ -static int fileext_compare(const char * test_ext, const char * known_ext) -{ - char caps[8] = ""; - size_t c,len; - /* if equal, don't need to check case (store to avoid multiple calls) */ - const int cmp = strcmp(test_ext, known_ext); - if( cmp == 0 ) return cmp; - - /* if anything odd, use default */ - if( !test_ext || !known_ext ) return cmp; - - len = strlen(known_ext); - if( len > 7 ) return cmp; - - /* if here, strings are different but need to check upper-case */ - - for(c = 0; c < len; c++ ) caps[c] = toupper((int) known_ext[c]); - caps[c] = '\0'; - - return strcmp(test_ext, caps); -} - -/* like strncmp, but also check against capitalization of known_ext - * (test as local string, with max length 7) */ -static int fileext_n_compare(const char * test_ext, - const char * known_ext, size_t maxlen) -{ - char caps[8] = ""; - size_t c,len; - /* if equal, don't need to check case (store to avoid multiple calls) */ - const int cmp = strncmp(test_ext, known_ext, maxlen); - if( cmp == 0 ) return cmp; - - /* if anything odd, use default */ - if( !test_ext || !known_ext ) return cmp; - - len = strlen(known_ext); - if( len > maxlen ) len = maxlen; /* ignore anything past maxlen */ - if( len > 7 ) return cmp; - - /* if here, strings are different but need to check upper-case */ - for(c = 0; c < len; c++ ) caps[c] = toupper((int) known_ext[c]); - caps[c] = '\0'; - - return strncmp(test_ext, caps, maxlen); -} - -/* return 1 if there are uppercase but no lowercase */ -static int is_uppercase(const char * str) -{ - size_t c; - int hasupper = 0; - - if( !str || !*str ) return 0; - - for(c = 0; c < strlen(str); c++ ) { - if( islower((int) str[c]) ) return 0; - if( !hasupper && isupper((int) str[c]) ) hasupper = 1; - } - - return hasupper; -} - -/* return 1 if there are both uppercase and lowercase characters */ -static int is_mixedcase(const char * str) -{ - size_t c; - int hasupper = 0, haslower = 0; - - if( !str || !*str ) return 0; - - for(c = 0; c < strlen(str); c++ ) { - if( !haslower && islower((int) str[c]) ) haslower = 1; - if( !hasupper && isupper((int) str[c]) ) hasupper = 1; - - if( haslower && hasupper ) return 1; - } - - return 0; -} - -/* convert any lowercase chars to uppercase */ -static int make_uppercase(char * str) -{ - size_t c; - - if( !str || !*str ) return 0; - - for(c = 0; c < strlen(str); c++ ) - if( islower((int) str[c]) ) str[c] = toupper((int) str[c]); - - return 0; -} - -/* convert any uppercase chars to lowercase */ -static int make_lowercase(char * str) -{ - size_t c; - if( !str || !*str ) return 0; - - for(c = 0; c < strlen(str); c++ ) - if( isupper((int) str[c]) ) str[c] = tolower((int) str[c]); - - return 0; -} - -/* run strcmp against of list of strings - * return index of equality, if found - * else return -1 */ -static int compare_strlist(const char * str, char ** strlist, int len) -{ - int c; - if( len <= 0 || !str || !strlist ) return -1; - for( c = 0; c < len; c++ ) - if( strlist[c] && !strcmp(str, strlist[c]) ) return c; - return -1; -} - -/*--------------------------------------------------------------------------*/ -/*! check whether the given type is on the "approved" list - - The code is valid if it is non-negative, and does not exceed - NIFTI_MAX_FTYPE. - - \return 1 if nifti_type is valid, 0 otherwise - \sa NIFTI_FTYPE_* codes in nifti1_io.h -*//*------------------------------------------------------------------------*/ -int is_valid_nifti_type( int nifti_type ) -{ - if( nifti_type >= NIFTI_FTYPE_ANALYZE && /* smallest type, 0 */ - nifti_type <= NIFTI_MAX_FTYPE ) - return 1; - return 0; -} - - -/*--------------------------------------------------------------------------*/ -/*! check whether the given type is on the "approved" list - - The type is explicitly checked against the NIFTI_TYPE_* list - in nifti1.h. - - \return 1 if dtype is valid, 0 otherwise - \sa NIFTI_TYPE_* codes in nifti1.h -*//*------------------------------------------------------------------------*/ -int nifti_is_valid_datatype( int dtype ) -{ - if( dtype == NIFTI_TYPE_UINT8 || - dtype == NIFTI_TYPE_INT16 || - dtype == NIFTI_TYPE_INT32 || - dtype == NIFTI_TYPE_FLOAT32 || - dtype == NIFTI_TYPE_COMPLEX64 || - dtype == NIFTI_TYPE_FLOAT64 || - dtype == NIFTI_TYPE_RGB24 || - dtype == NIFTI_TYPE_RGBA32 || - dtype == NIFTI_TYPE_INT8 || - dtype == NIFTI_TYPE_UINT16 || - dtype == NIFTI_TYPE_UINT32 || - dtype == NIFTI_TYPE_INT64 || - dtype == NIFTI_TYPE_UINT64 || - dtype == NIFTI_TYPE_FLOAT128 || - dtype == NIFTI_TYPE_COMPLEX128 || - dtype == NIFTI_TYPE_COMPLEX256 ) return 1; - return 0; -} - - -/*--------------------------------------------------------------------------*/ -/*! set the nifti_type field based on fname and iname - - Note that nifti_type is changed only when it does not match - the filenames. - - \return 0 on success, -1 on error - - \sa is_valid_nifti_type, nifti_type_and_names_match -*//*------------------------------------------------------------------------*/ -int nifti_set_type_from_names( nifti_image * nim ) -{ - /* error checking first */ - if( !nim ){ fprintf(stderr,"** NSTFN: no nifti_image\n"); return -1; } - - if( !nim->fname || !nim->iname ){ - fprintf(stderr,"** NIFTI_STFN: NULL filename(s) fname @ %p, iname @ %p\n", - nim->fname, nim->iname); - return -1; - } - - if( ! nifti_validfilename ( nim->fname ) || - ! nifti_validfilename ( nim->iname ) || - ! nifti_find_file_extension( nim->fname ) || - ! nifti_find_file_extension( nim->iname ) - ) { - fprintf(stderr,"** NIFTI_STFN: invalid filename(s) " - "fname='%s', iname='%s'\n", - nim->fname, nim->iname); - return -1; - } - - if( g_opts.debug > 2 ) - fprintf(stderr,"-d verify nifti_type from filenames: %d",nim->nifti_type); - - /* type should be NIFTI_FTYPE_ASCII if extension is .nia */ - if( (fileext_compare(nifti_find_file_extension(nim->fname),".nia")==0)){ - nim->nifti_type = NIFTI_FTYPE_ASCII; - } else { - /* not too picky here, do what must be done, and then verify */ - if( strcmp(nim->fname, nim->iname) == 0 ) /* one file, type 1 */ - nim->nifti_type = NIFTI_FTYPE_NIFTI1_1; - else if( nim->nifti_type == NIFTI_FTYPE_NIFTI1_1 ) /* cannot be type 1 */ - nim->nifti_type = NIFTI_FTYPE_NIFTI1_2; - } - - if( g_opts.debug > 2 ) fprintf(stderr," -> %d\n",nim->nifti_type); - - if( g_opts.debug > 1 ) /* warn user about anything strange */ - nifti_type_and_names_match(nim, 1); - - if( is_valid_nifti_type(nim->nifti_type) ) return 0; /* success! */ - - fprintf(stderr,"** NSTFN: bad nifti_type %d, for '%s' and '%s'\n", - nim->nifti_type, nim->fname, nim->iname); - - return -1; -} - - -/*--------------------------------------------------------------------------*/ -/*! Determine if this is a NIFTI-formatted file. - - 
-   \return  0 if file looks like ANALYZE 7.5 [checks sizeof_hdr field == 348]
-            1 if file marked as NIFTI (header+data in 1 file)
-            2 if file marked as NIFTI (header+data in 2 files)
-           -1 if it can't tell, file doesn't exist, etc.
-
-*//*------------------------------------------------------------------------*/ -int is_nifti_file( const char *hname ) -{ - nifti_1_header nhdr ; - znzFile fp ; - int ii ; - char *tmpname; - -/* rcr - update to check for nifti-1 or -2 */ - - /* bad input name? */ - - if( !nifti_validfilename(hname) ) return -1 ; - - /* open file */ - - tmpname = nifti_findhdrname(hname); - if( tmpname == NULL ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** NIFTI: no header file found for '%s'\n",hname); - return -1; - } - fp = znzopen( tmpname , "rb" , nifti_is_gzfile(tmpname) ) ; - free(tmpname); - if (znz_isnull(fp)) return -1 ; /* bad open? */ - - /* read header, close file */ - - ii = (int)znzread( &nhdr , 1 , sizeof(nhdr) , fp ) ; - znzclose( fp ) ; - if( ii < (int) sizeof(nhdr) ) return -1 ; /* bad read? */ - - /* check for NIFTI-ness */ - - if( NIFTI_VERSION(nhdr) != 0 ){ - return ( NIFTI_ONEFILE(nhdr) ) ? 1 : 2 ; - } - - /* check for ANALYZE-ness (sizeof_hdr field == 348) */ - - ii = nhdr.sizeof_hdr ; - if( ii == (int)sizeof(nhdr) ) return 0 ; /* matches */ - - /* try byte-swapping header */ - - swap_4(ii) ; - if( ii == (int)sizeof(nhdr) ) return 0 ; /* matches */ - - return -1 ; /* not good */ -} - -static int print_hex_vals( const char * data, size_t nbytes, FILE * fp ) -{ - size_t c; - - if ( !data || nbytes < 1 || !fp ) return -1; - - fputs("0x", fp); - for ( c = 0; c < nbytes; c++ ) - fprintf(fp, " %02x", data[c]); - - return 0; -} - -/*----------------------------------------------------------------------*/ -/*! display the contents of the nifti_1_header (send to stdout) - - \param info if non-NULL, print this character string - \param hp pointer to nifti_1_header -*//*--------------------------------------------------------------------*/ -int disp_nifti_1_header( const char * info, const nifti_1_header * hp ) -{ - int c; - - fputs( "-------------------------------------------------------\n", stdout ); - if ( info ) fputs( info, stdout ); - if ( !hp ){ fputs(" ** no nifti_1_header to display!\n",stdout); return 1; } - - fprintf(stdout," nifti_1_header :\n" - " sizeof_hdr = %d\n" - " data_type[10] = ", hp->sizeof_hdr); - print_hex_vals(hp->data_type, 10, stdout); - fprintf(stdout, "\n" - " db_name[18] = "); - print_hex_vals(hp->db_name, 18, stdout); - fprintf(stdout, "\n" - " extents = %d\n" - " session_error = %d\n" - " regular = 0x%x\n" - " dim_info = 0x%x\n", - hp->extents, hp->session_error, hp->regular, hp->dim_info ); - fprintf(stdout, " dim[8] ="); - for ( c = 0; c < 8; c++ ) fprintf(stdout," %d", hp->dim[c]); - fprintf(stdout, "\n" - " intent_p1 = %f\n" - " intent_p2 = %f\n" - " intent_p3 = %f\n" - " intent_code = %d\n" - " datatype = %d\n" - " bitpix = %d\n" - " slice_start = %d\n" - " pixdim[8] =", - hp->intent_p1, hp->intent_p2, hp->intent_p3, hp->intent_code, - hp->datatype, hp->bitpix, hp->slice_start); - /* break pixdim over 2 lines */ - for ( c = 0; c < 4; c++ ) fprintf(stdout," %f", hp->pixdim[c]); - fprintf(stdout, "\n "); - for ( c = 4; c < 8; c++ ) fprintf(stdout," %f", hp->pixdim[c]); - fprintf(stdout, "\n" - " vox_offset = %f\n" - " scl_slope = %f\n" - " scl_inter = %f\n" - " slice_end = %d\n" - " slice_code = %d\n" - " xyzt_units = 0x%x\n" - " cal_max = %f\n" - " cal_min = %f\n" - " slice_duration = %f\n" - " toffset = %f\n" - " glmax = %d\n" - " glmin = %d\n", - hp->vox_offset, hp->scl_slope, hp->scl_inter, hp->slice_end, - hp->slice_code, hp->xyzt_units, hp->cal_max, hp->cal_min, - hp->slice_duration, hp->toffset, hp->glmax, hp->glmin); - fprintf(stdout, - " descrip = '%.80s'\n" - " aux_file = '%.24s'\n" - " qform_code = %d\n" - " sform_code = %d\n" - " quatern_b = %f\n" - " quatern_c = %f\n" - " quatern_d = %f\n" - " qoffset_x = %f\n" - " qoffset_y = %f\n" - " qoffset_z = %f\n" - " srow_x[4] = %f, %f, %f, %f\n" - " srow_y[4] = %f, %f, %f, %f\n" - " srow_z[4] = %f, %f, %f, %f\n" - " intent_name = '%-.16s'\n" - " magic = '%-.4s'\n", - hp->descrip, hp->aux_file, hp->qform_code, hp->sform_code, - hp->quatern_b, hp->quatern_c, hp->quatern_d, - hp->qoffset_x, hp->qoffset_y, hp->qoffset_z, - hp->srow_x[0], hp->srow_x[1], hp->srow_x[2], hp->srow_x[3], - hp->srow_y[0], hp->srow_y[1], hp->srow_y[2], hp->srow_y[3], - hp->srow_z[0], hp->srow_z[1], hp->srow_z[2], hp->srow_z[3], - hp->intent_name, hp->magic); - fputs( "-------------------------------------------------------\n", stdout ); - fflush(stdout); - - return 0; -} - - -/*----------------------------------------------------------------------*/ -/*! display the contents of the nifti_2_header (send to stdout) - - \param info if non-NULL, print this character string - \param hp pointer to nifti_2_header -*//*--------------------------------------------------------------------*/ -int disp_nifti_2_header( const char * info, const nifti_2_header * hp ) -{ - FILE * fp = stdout; - int c; - - fputs( "-------------------------------------------------------\n", fp ); - if ( info ) fputs( info, fp ); - if ( !hp ){ fputs(" ** no nifti_2_header to display!\n",fp); return 1; } - - /* print fields one by one, makes changing order and copying easier */ - - fprintf(fp," nifti_2_header :\n"); - fprintf(fp," sizeof_hdr = %d\n", hp->sizeof_hdr); - fprintf(fp," magic[8] = '%-.4s' + ", hp->magic); - print_hex_vals(hp->magic+4, 4, fp); fputc('\n', fp); - - fprintf(fp," datatype = %d (%s)\n", - hp->datatype, nifti_datatype_to_string(hp->datatype)); - fprintf(fp," bitpix = %d\n", hp->bitpix); - fprintf(fp, " dim[8] ="); - for ( c = 0; c < 8; c++ ) fprintf(fp," %" PRId64, hp->dim[c]); - fputc('\n', fp); - - fprintf(fp, " intent_p1 = %lf\n", hp->intent_p1); - fprintf(fp, " intent_p2 = %lf\n", hp->intent_p2); - fprintf(fp, " intent_p3 = %lf\n", hp->intent_p3); - fprintf(fp, " pixdim[8] ="); - for ( c = 0; c < 8; c++ ) fprintf(fp," %lf", hp->pixdim[c]); - fputc('\n', fp); - - fprintf(fp, " vox_offset = %" PRId64 "\n", hp->vox_offset); - - fprintf(fp, " scl_slope = %lf\n", hp->scl_slope); - fprintf(fp, " scl_inter = %lf\n", hp->scl_inter); - fprintf(fp, " cal_max = %lf\n", hp->cal_max); - fprintf(fp, " cal_min = %lf\n", hp->cal_min); - fprintf(fp, " slice_duration = %lf\n", hp->slice_duration); - fprintf(fp, " toffset = %lf\n", hp->toffset); - - fprintf(fp, " slice_start = %" PRId64 "\n", hp->slice_start); - fprintf(fp, " slice_end = %" PRId64 "\n", hp->slice_end); - - fprintf(fp, " descrip = '%.80s'\n", hp->descrip); - fprintf(fp, " aux_file = '%.24s'\n", hp->aux_file); - - fprintf(fp, " qform_code = %d\n", hp->qform_code); - fprintf(fp, " sform_code = %d\n", hp->sform_code); - - fprintf(fp, " quatern_b = %lf\n", hp->quatern_b); - fprintf(fp, " quatern_c = %lf\n", hp->quatern_c); - fprintf(fp, " quatern_d = %lf\n", hp->quatern_d); - fprintf(fp, " qoffset_x = %lf\n", hp->qoffset_x); - fprintf(fp, " qoffset_y = %lf\n", hp->qoffset_y); - fprintf(fp, " qoffset_z = %lf\n", hp->qoffset_z); - fprintf(fp, " srow_x[4] = %lf, %lf, %lf, %lf\n", - hp->srow_x[0], hp->srow_x[1], hp->srow_x[2], hp->srow_x[3]); - fprintf(fp, " srow_y[4] = %lf, %lf, %lf, %lf\n", - hp->srow_y[0], hp->srow_y[1], hp->srow_y[2], hp->srow_y[3]); - fprintf(fp, " srow_z[4] = %lf, %lf, %lf, %lf\n", - hp->srow_z[0], hp->srow_z[1], hp->srow_z[2], hp->srow_z[3]); - - fprintf(fp, " slice_code = %d\n", hp->slice_code); - fprintf(fp, " xyzt_units = %d\n", hp->xyzt_units); - fprintf(fp, " intent_code = %d\n", hp->intent_code); - - fprintf(fp, " intent_name = '%-.16s'\n", hp->intent_name); - fprintf(fp, " dim_info = 0x%02x\n",(unsigned char)hp->dim_info); - fprintf(fp, " unused_str = 0x "); - for ( c = 0; c < 15; c++ ) fprintf(fp," %02x", hp->unused_str[c]); - fputc('\n', fp); - - fputs( "-------------------------------------------------------\n", fp ); - fflush(fp); - - return 0; -} - - -#undef ERREX -#define ERREX(msg) \ - do{ fprintf(stderr,"** ERROR: nifti_convert_n1hdr2nim: %s\n", (msg) ) ; \ - return NULL ; } while(0) - -/*----------------------------------------------------------------------*/ -/*! convert a nifti_1_header into a nift1_image - - \return an allocated nifti_image, or NULL on failure -*//*--------------------------------------------------------------------*/ -nifti_image* nifti_convert_n1hdr2nim(nifti_1_header nhdr, const char * fname) -{ - int ii , doswap , ioff ; - int ni_ver , is_onefile ; - nifti_image *nim; - - nim = (nifti_image *)calloc( 1 , sizeof(nifti_image) ) ; - if( !nim ) ERREX("failed to allocate nifti image"); - - /* be explicit with pointers */ - nim->fname = NULL; - nim->iname = NULL; - nim->data = NULL; - - /**- check if we must swap bytes */ - - doswap = need_nhdr_swap(nhdr.dim[0], nhdr.sizeof_hdr); /* swap data flag */ - - if( doswap < 0 ){ - free(nim); - if( doswap == -1 ) ERREX("bad dim[0]") ; - ERREX("bad sizeof_hdr") ; /* else */ - } - - /**- determine if this is a NIFTI-1 compliant header */ - - ni_ver = NIFTI_VERSION(nhdr) ; - /* - * before swapping header, record the Analyze75 orient code - */ - if(ni_ver == 0) - { - /**- in analyze75, the orient code is at the same address as - * qform_code, but it's just one byte - * the qform_code will be zero, at which point you can check - * analyze75_orient if you care to. - */ - unsigned char c = *((char *)(&nhdr.qform_code)); - nim->analyze75_orient = (analyze_75_orient_code)c; - } - if( doswap ) { - if ( g_opts.debug > 3 ) disp_nifti_1_header("-d ni1 pre-swap: ", &nhdr); - swap_nifti_header( &nhdr , ni_ver ) ; - } - - if ( g_opts.debug > 2 ) disp_nifti_1_header("-d nhdr2nim : ", &nhdr); - - if( nhdr.datatype == DT_BINARY || nhdr.datatype == DT_UNKNOWN ) - { - free(nim); - ERREX("bad datatype") ; - } - - if( nhdr.dim[1] <= 0 ) - { - free(nim); - ERREX("bad dim[1]") ; - } - - /* fix bad dim[] values in the defined dimension range */ - for( ii=2 ; ii <= nhdr.dim[0] ; ii++ ) - if( nhdr.dim[ii] <= 0 ) nhdr.dim[ii] = 1 ; - - /* fix any remaining bad dim[] values, so garbage does not propagate */ - /* (only values 0 or 1 seem rational, otherwise set to arbirary 1) */ - for( ii=nhdr.dim[0]+1 ; ii <= 7 ; ii++ ) - if( nhdr.dim[ii] != 1 && nhdr.dim[ii] != 0) nhdr.dim[ii] = 1 ; - -#if 0 /* rely on dim[0], do not attempt to modify it 16 Nov 2005 [rickr] */ - - /**- get number of dimensions (ignoring dim[0] now) */ - for( ii=7 ; ii >= 2 ; ii-- ) /* loop backwards until we */ - if( nhdr.dim[ii] > 1 ) break ; /* find a dim bigger than 1 */ - ndim = ii ; -#endif - - /**- set bad grid spacings to 1.0 */ - - for( ii=1 ; ii <= nhdr.dim[0] ; ii++ ){ - if( nhdr.pixdim[ii] == 0.0 || - !IS_GOOD_FLOAT(nhdr.pixdim[ii]) ) nhdr.pixdim[ii] = 1.0f ; - } - - is_onefile = (ni_ver > 0) && NIFTI_ONEFILE(nhdr) ; - - if( ni_ver ) nim->nifti_type = (is_onefile) ? NIFTI_FTYPE_NIFTI1_1 - : NIFTI_FTYPE_NIFTI1_2 ; - else nim->nifti_type = NIFTI_FTYPE_ANALYZE ; - - ii = nifti_short_order() ; - if( doswap ) nim->byteorder = REVERSE_ORDER(ii) ; - else nim->byteorder = ii ; - - - /**- set dimensions of data array */ - - nim->ndim = nim->dim[0] = nhdr.dim[0]; - nim->nx = nim->dim[1] = nhdr.dim[1]; - nim->ny = nim->dim[2] = nhdr.dim[2]; - nim->nz = nim->dim[3] = nhdr.dim[3]; - nim->nt = nim->dim[4] = nhdr.dim[4]; - nim->nu = nim->dim[5] = nhdr.dim[5]; - nim->nv = nim->dim[6] = nhdr.dim[6]; - nim->nw = nim->dim[7] = nhdr.dim[7]; - - for( ii=1, nim->nvox=1; ii <= nhdr.dim[0]; ii++ ) - nim->nvox *= nhdr.dim[ii]; - - /**- set the type of data in voxels and how many bytes per voxel */ - - nim->datatype = nhdr.datatype ; - - nifti_datatype_sizes( nim->datatype , &(nim->nbyper) , &(nim->swapsize) ) ; - if( nim->nbyper == 0 ){ free(nim); ERREX("bad datatype"); } - - /**- set the grid spacings */ - - nim->dx = nim->pixdim[1] = nhdr.pixdim[1] ; - nim->dy = nim->pixdim[2] = nhdr.pixdim[2] ; - nim->dz = nim->pixdim[3] = nhdr.pixdim[3] ; - nim->dt = nim->pixdim[4] = nhdr.pixdim[4] ; - nim->du = nim->pixdim[5] = nhdr.pixdim[5] ; - nim->dv = nim->pixdim[6] = nhdr.pixdim[6] ; - nim->dw = nim->pixdim[7] = nhdr.pixdim[7] ; - - /**- compute qto_xyz transformation from pixel indexes (i,j,k) to (x,y,z) */ - - if( !ni_ver || nhdr.qform_code <= 0 ){ - /**- if not nifti or qform_code <= 0, use grid spacing for qto_xyz */ - - nim->qto_xyz.m[0][0] = nim->dx ; /* grid spacings */ - nim->qto_xyz.m[1][1] = nim->dy ; /* along diagonal */ - nim->qto_xyz.m[2][2] = nim->dz ; - - /* off diagonal is zero */ - - nim->qto_xyz.m[0][1]=nim->qto_xyz.m[0][2]=nim->qto_xyz.m[0][3] = 0.0f; - nim->qto_xyz.m[1][0]=nim->qto_xyz.m[1][2]=nim->qto_xyz.m[1][3] = 0.0f; - nim->qto_xyz.m[2][0]=nim->qto_xyz.m[2][1]=nim->qto_xyz.m[2][3] = 0.0f; - - /* last row is always [ 0 0 0 1 ] */ - - nim->qto_xyz.m[3][0]=nim->qto_xyz.m[3][1]=nim->qto_xyz.m[3][2] = 0.0f; - nim->qto_xyz.m[3][3]= 1.0f ; - - nim->qform_code = NIFTI_XFORM_UNKNOWN ; - - if( g_opts.debug > 1 ) fprintf(stderr,"-d no qform provided\n"); - } else { - /**- else NIFTI: use the quaternion-specified transformation */ - - nim->quatern_b = FIXED_FLOAT( nhdr.quatern_b ) ; - nim->quatern_c = FIXED_FLOAT( nhdr.quatern_c ) ; - nim->quatern_d = FIXED_FLOAT( nhdr.quatern_d ) ; - - nim->qoffset_x = FIXED_FLOAT(nhdr.qoffset_x) ; - nim->qoffset_y = FIXED_FLOAT(nhdr.qoffset_y) ; - nim->qoffset_z = FIXED_FLOAT(nhdr.qoffset_z) ; - - nim->qfac = (nhdr.pixdim[0] < 0.0) ? -1.0f : 1.0f ; /* left-handedness? */ - - nim->qto_xyz = nifti_quatern_to_dmat44( - nim->quatern_b, nim->quatern_c, nim->quatern_d, - nim->qoffset_x, nim->qoffset_y, nim->qoffset_z, - nim->dx , nim->dy , nim->dz , - nim->qfac ) ; - - nim->qform_code = nhdr.qform_code ; - - if( g_opts.debug > 1 ) - nifti_disp_matrix_orient("-d qform orientations:\n", nim->qto_xyz); - } - - /**- load inverse transformation (x,y,z) -> (i,j,k) */ - - nim->qto_ijk = nifti_dmat44_inverse( nim->qto_xyz ) ; - - /**- load sto_xyz affine transformation, if present */ - - if( !ni_ver || nhdr.sform_code <= 0 ){ - /**- if not nifti or sform_code <= 0, then no sto transformation */ - - nim->sform_code = NIFTI_XFORM_UNKNOWN ; - - if( g_opts.debug > 1 ) fprintf(stderr,"-d no sform provided\n"); - - } else { - /**- else set the sto transformation from srow_*[] */ - - nim->sto_xyz.m[0][0] = nhdr.srow_x[0] ; - nim->sto_xyz.m[0][1] = nhdr.srow_x[1] ; - nim->sto_xyz.m[0][2] = nhdr.srow_x[2] ; - nim->sto_xyz.m[0][3] = nhdr.srow_x[3] ; - - nim->sto_xyz.m[1][0] = nhdr.srow_y[0] ; - nim->sto_xyz.m[1][1] = nhdr.srow_y[1] ; - nim->sto_xyz.m[1][2] = nhdr.srow_y[2] ; - nim->sto_xyz.m[1][3] = nhdr.srow_y[3] ; - - nim->sto_xyz.m[2][0] = nhdr.srow_z[0] ; - nim->sto_xyz.m[2][1] = nhdr.srow_z[1] ; - nim->sto_xyz.m[2][2] = nhdr.srow_z[2] ; - nim->sto_xyz.m[2][3] = nhdr.srow_z[3] ; - - /* last row is always [ 0 0 0 1 ] */ - - nim->sto_xyz.m[3][0]=nim->sto_xyz.m[3][1]=nim->sto_xyz.m[3][2] = 0.0f; - nim->sto_xyz.m[3][3]= 1.0f ; - - nim->sto_ijk = nifti_dmat44_inverse( nim->sto_xyz ) ; - - nim->sform_code = nhdr.sform_code ; - - if( g_opts.debug > 1 ) - nifti_disp_matrix_orient("-d sform orientations:\n", nim->sto_xyz); - } - - /**- set miscellaneous NIFTI stuff */ - - if( ni_ver ){ - nim->scl_slope = FIXED_FLOAT( nhdr.scl_slope ) ; - nim->scl_inter = FIXED_FLOAT( nhdr.scl_inter ) ; - - nim->intent_code = nhdr.intent_code ; - - nim->intent_p1 = FIXED_FLOAT( nhdr.intent_p1 ) ; - nim->intent_p2 = FIXED_FLOAT( nhdr.intent_p2 ) ; - nim->intent_p3 = FIXED_FLOAT( nhdr.intent_p3 ) ; - - nim->toffset = FIXED_FLOAT( nhdr.toffset ) ; - - memcpy(nim->intent_name,nhdr.intent_name,15); nim->intent_name[15] = '\0'; - - nim->xyz_units = XYZT_TO_SPACE(nhdr.xyzt_units) ; - nim->time_units = XYZT_TO_TIME (nhdr.xyzt_units) ; - - nim->freq_dim = DIM_INFO_TO_FREQ_DIM ( nhdr.dim_info ) ; - nim->phase_dim = DIM_INFO_TO_PHASE_DIM( nhdr.dim_info ) ; - nim->slice_dim = DIM_INFO_TO_SLICE_DIM( nhdr.dim_info ) ; - - nim->slice_code = nhdr.slice_code ; - nim->slice_start = nhdr.slice_start ; - nim->slice_end = nhdr.slice_end ; - nim->slice_duration = FIXED_FLOAT(nhdr.slice_duration) ; - } - - /**- set Miscellaneous ANALYZE stuff */ - - nim->cal_min = FIXED_FLOAT(nhdr.cal_min) ; - nim->cal_max = FIXED_FLOAT(nhdr.cal_max) ; - - memcpy(nim->descrip ,nhdr.descrip ,79) ; nim->descrip [79] = '\0' ; - memcpy(nim->aux_file,nhdr.aux_file,23) ; nim->aux_file[23] = '\0' ; - - /**- set ioff from vox_offset (but at least sizeof(header)) */ - - is_onefile = ni_ver && NIFTI_ONEFILE(nhdr) ; - - if( is_onefile ){ - ioff = (int)nhdr.vox_offset ; - if( ioff < (int) sizeof(nhdr) ) ioff = (int) sizeof(nhdr) ; - } else { - ioff = (int)nhdr.vox_offset ; - } - nim->iname_offset = ioff ; - - - /**- deal with file names if set */ - if (fname!=NULL) { - nifti_set_filenames(nim,fname,0,0); - if (nim->iname==NULL) { ERREX("bad filename"); } - } else { - nim->fname = NULL; - nim->iname = NULL; - } - - /* clear extension fields */ - nim->num_ext = 0; - nim->ext_list = NULL; - - return nim; -} - -#undef ERREX -#define ERREX(msg) \ - do{ fprintf(stderr,"** ERROR: nifti_convert_n2hdr2nim: %s\n", (msg) ) ; \ - return NULL ; } while(0) - -/*----------------------------------------------------------------------*/ -/*! convert a nifti_1_header into a nift1_image - - \return an allocated nifti_image, or NULL on failure -*//*--------------------------------------------------------------------*/ -nifti_image* nifti_convert_n2hdr2nim(nifti_2_header nhdr, const char * fname) -{ - int ii, doswap, ni_ver, is_onefile; - nifti_image *nim; - - nim = (nifti_image *)calloc( 1 , sizeof(nifti_image) ) ; - if( !nim ) ERREX("failed to allocate nifti image"); - - /* be explicit with pointers */ - nim->fname = NULL; - nim->iname = NULL; - nim->data = NULL; - - /**- check if we must swap bytes */ - - doswap = NIFTI2_NEEDS_SWAP(nhdr); /* swap data flag */ - - /**- determine if this is a NIFTI-2 compliant header */ - - ni_ver = NIFTI_VERSION(nhdr) ; - if(ni_ver != 2) { - free(nim); - fprintf(stderr,"** convert NIFTI-2 hdr2nim: bad version %d\n", ni_ver); - return NULL; - } - - if( doswap ) { - if ( g_opts.debug > 3 ) disp_nifti_2_header("-d n2 pre-swap: ", &nhdr); - swap_nifti_header( &nhdr , ni_ver ) ; - } else if ( g_opts.debug > 3 ) fprintf(stderr,"-- n2hdr2nim: no swap\n"); - - if ( g_opts.debug > 2 ) disp_nifti_2_header("-d n2hdr2nim : ", &nhdr); - - if( nhdr.datatype == DT_BINARY || nhdr.datatype == DT_UNKNOWN ) - { - free(nim); - ERREX("bad datatype") ; - } - - if( nhdr.dim[1] <= 0 ) - { - free(nim); - ERREX("bad dim[1]") ; - } - - /* fix bad dim[] values in the defined dimension range */ - for( ii=2 ; ii <= nhdr.dim[0] ; ii++ ) - if( nhdr.dim[ii] <= 0 ) nhdr.dim[ii] = 1 ; - - /* fix any remaining bad dim[] values, so garbage does not propagate */ - /* (only values 0 or 1 seem rational, otherwise set to arbirary 1) */ - for( ii=nhdr.dim[0]+1 ; ii <= 7 ; ii++ ) - if( nhdr.dim[ii] != 1 && nhdr.dim[ii] != 0) nhdr.dim[ii] = 1 ; - - /**- set bad grid spacings to 1.0 */ - for( ii=1 ; ii <= nhdr.dim[0] ; ii++ ){ - if( nhdr.pixdim[ii] == 0.0 || - !IS_GOOD_FLOAT(nhdr.pixdim[ii]) ) nhdr.pixdim[ii] = 1.0 ; - } - - is_onefile = (ni_ver > 0) && NIFTI_ONEFILE(nhdr) ; - - nim->nifti_type = (is_onefile) ? NIFTI_FTYPE_NIFTI1_1 : NIFTI_FTYPE_NIFTI1_2; - - ii = nifti_short_order() ; - if( doswap ) nim->byteorder = REVERSE_ORDER(ii) ; - else nim->byteorder = ii ; - - - /**- set dimensions of data array */ - - nim->ndim = nim->dim[0] = nhdr.dim[0]; - nim->nx = nim->dim[1] = nhdr.dim[1]; - nim->ny = nim->dim[2] = nhdr.dim[2]; - nim->nz = nim->dim[3] = nhdr.dim[3]; - nim->nt = nim->dim[4] = nhdr.dim[4]; - nim->nu = nim->dim[5] = nhdr.dim[5]; - nim->nv = nim->dim[6] = nhdr.dim[6]; - nim->nw = nim->dim[7] = nhdr.dim[7]; - - for( ii=1, nim->nvox=1; ii <= nhdr.dim[0]; ii++ ) - nim->nvox *= nhdr.dim[ii]; - - /**- set the type of data in voxels and how many bytes per voxel */ - - nim->datatype = nhdr.datatype ; - - nifti_datatype_sizes( nim->datatype , &(nim->nbyper) , &(nim->swapsize) ) ; - if( nim->nbyper == 0 ){ free(nim); ERREX("bad datatype"); } - - /**- set the grid spacings */ - - nim->dx = nim->pixdim[1] = nhdr.pixdim[1] ; - nim->dy = nim->pixdim[2] = nhdr.pixdim[2] ; - nim->dz = nim->pixdim[3] = nhdr.pixdim[3] ; - nim->dt = nim->pixdim[4] = nhdr.pixdim[4] ; - nim->du = nim->pixdim[5] = nhdr.pixdim[5] ; - nim->dv = nim->pixdim[6] = nhdr.pixdim[6] ; - nim->dw = nim->pixdim[7] = nhdr.pixdim[7] ; - - /**- compute qto_xyz transformation from pixel indexes (i,j,k) to (x,y,z) */ - - if( !ni_ver || nhdr.qform_code <= 0 ){ - /**- if not nifti or qform_code <= 0, use grid spacing for qto_xyz */ - - nim->qto_xyz.m[0][0] = nim->dx ; /* grid spacings */ - nim->qto_xyz.m[1][1] = nim->dy ; /* along diagonal */ - nim->qto_xyz.m[2][2] = nim->dz ; - - /* off diagonal is zero */ - - nim->qto_xyz.m[0][1]=nim->qto_xyz.m[0][2]=nim->qto_xyz.m[0][3] = 0.0f; - nim->qto_xyz.m[1][0]=nim->qto_xyz.m[1][2]=nim->qto_xyz.m[1][3] = 0.0f; - nim->qto_xyz.m[2][0]=nim->qto_xyz.m[2][1]=nim->qto_xyz.m[2][3] = 0.0f; - - /* last row is always [ 0 0 0 1 ] */ - - nim->qto_xyz.m[3][0]=nim->qto_xyz.m[3][1]=nim->qto_xyz.m[3][2] = 0.0f; - nim->qto_xyz.m[3][3]= 1.0f ; - - nim->qform_code = NIFTI_XFORM_UNKNOWN ; - - if( g_opts.debug > 1 ) fprintf(stderr,"-d no qform provided\n"); - } else { - /**- else NIFTI: use the quaternion-specified transformation */ - - nim->quatern_b = FIXED_FLOAT( nhdr.quatern_b ) ; - nim->quatern_c = FIXED_FLOAT( nhdr.quatern_c ) ; - nim->quatern_d = FIXED_FLOAT( nhdr.quatern_d ) ; - - nim->qoffset_x = FIXED_FLOAT(nhdr.qoffset_x) ; - nim->qoffset_y = FIXED_FLOAT(nhdr.qoffset_y) ; - nim->qoffset_z = FIXED_FLOAT(nhdr.qoffset_z) ; - - nim->qfac = (nhdr.pixdim[0] < 0.0) ? -1.0 : 1.0 ; /* left-handedness? */ - - nim->qto_xyz = nifti_quatern_to_dmat44( - nim->quatern_b, nim->quatern_c, nim->quatern_d, - nim->qoffset_x, nim->qoffset_y, nim->qoffset_z, - nim->dx , nim->dy , nim->dz , - nim->qfac ) ; - - nim->qform_code = nhdr.qform_code ; - - if( g_opts.debug > 1 ) - nifti_disp_matrix_orient("-d qform orientations:\n", nim->qto_xyz); - } - - /**- load inverse transformation (x,y,z) -> (i,j,k) */ - - nim->qto_ijk = nifti_dmat44_inverse( nim->qto_xyz ) ; - - /**- load sto_xyz affine transformation, if present */ - - if( !ni_ver || nhdr.sform_code <= 0 ){ - /**- if not nifti or sform_code <= 0, then no sto transformation */ - - nim->sform_code = NIFTI_XFORM_UNKNOWN ; - - if( g_opts.debug > 1 ) fprintf(stderr,"-d no sform provided\n"); - - } else { - /**- else set the sto transformation from srow_*[] */ - - nim->sto_xyz.m[0][0] = nhdr.srow_x[0] ; - nim->sto_xyz.m[0][1] = nhdr.srow_x[1] ; - nim->sto_xyz.m[0][2] = nhdr.srow_x[2] ; - nim->sto_xyz.m[0][3] = nhdr.srow_x[3] ; - - nim->sto_xyz.m[1][0] = nhdr.srow_y[0] ; - nim->sto_xyz.m[1][1] = nhdr.srow_y[1] ; - nim->sto_xyz.m[1][2] = nhdr.srow_y[2] ; - nim->sto_xyz.m[1][3] = nhdr.srow_y[3] ; - - nim->sto_xyz.m[2][0] = nhdr.srow_z[0] ; - nim->sto_xyz.m[2][1] = nhdr.srow_z[1] ; - nim->sto_xyz.m[2][2] = nhdr.srow_z[2] ; - nim->sto_xyz.m[2][3] = nhdr.srow_z[3] ; - - /* last row is always [ 0 0 0 1 ] */ - - nim->sto_xyz.m[3][0]=nim->sto_xyz.m[3][1]=nim->sto_xyz.m[3][2] = 0.0f; - nim->sto_xyz.m[3][3]= 1.0f ; - - nim->sto_ijk = nifti_dmat44_inverse( nim->sto_xyz ) ; - - nim->sform_code = nhdr.sform_code ; - - if( g_opts.debug > 1 ) - nifti_disp_matrix_orient("-d sform orientations:\n", nim->sto_xyz); - } - - /**- set miscellaneous NIFTI stuff */ - - if( ni_ver ){ - nim->scl_slope = FIXED_FLOAT( nhdr.scl_slope ) ; - nim->scl_inter = FIXED_FLOAT( nhdr.scl_inter ) ; - - nim->intent_code = nhdr.intent_code ; - - nim->intent_p1 = FIXED_FLOAT( nhdr.intent_p1 ) ; - nim->intent_p2 = FIXED_FLOAT( nhdr.intent_p2 ) ; - nim->intent_p3 = FIXED_FLOAT( nhdr.intent_p3 ) ; - - nim->toffset = FIXED_FLOAT( nhdr.toffset ) ; - - memcpy(nim->intent_name,nhdr.intent_name,15); nim->intent_name[15] = '\0'; - - nim->xyz_units = XYZT_TO_SPACE(nhdr.xyzt_units) ; - nim->time_units = XYZT_TO_TIME (nhdr.xyzt_units) ; - - nim->freq_dim = DIM_INFO_TO_FREQ_DIM ( nhdr.dim_info ) ; - nim->phase_dim = DIM_INFO_TO_PHASE_DIM( nhdr.dim_info ) ; - nim->slice_dim = DIM_INFO_TO_SLICE_DIM( nhdr.dim_info ) ; - - nim->slice_code = nhdr.slice_code ; - nim->slice_start = nhdr.slice_start ; - nim->slice_end = nhdr.slice_end ; - nim->slice_duration = FIXED_FLOAT(nhdr.slice_duration) ; - } - - /**- set Miscellaneous ANALYZE stuff */ - - nim->cal_min = FIXED_FLOAT(nhdr.cal_min) ; - nim->cal_max = FIXED_FLOAT(nhdr.cal_max) ; - - memcpy(nim->descrip ,nhdr.descrip ,79) ; nim->descrip [79] = '\0' ; - memcpy(nim->aux_file,nhdr.aux_file,23) ; nim->aux_file[23] = '\0' ; - - /**- set ioff from vox_offset (but at least sizeof(header)) */ - - nim->iname_offset = nhdr.vox_offset; - if( is_onefile && nhdr.vox_offset < (int64_t)sizeof(nhdr) ) - nim->iname_offset = (int64_t)sizeof(nhdr); - - /**- deal with file names if set */ - if (fname!=NULL) { - nifti_set_filenames(nim,fname,0,0); - if (nim->iname==NULL) { ERREX("bad filename"); } - } else { - nim->fname = NULL; - nim->iname = NULL; - } - - /* clear extension fields */ - nim->num_ext = 0; - nim->ext_list = NULL; - - return nim; -} - -#undef ERREX -#define ERREX(msg) \ - do{ fprintf(stderr,"** ERROR: nifti_image_open(%s): %s\n", \ - (hname != NULL) ? hname : "(null)" , (msg) ) ; \ - return fptr ; } while(0) - -/*************************************************************** - * nifti_image_open - ***************************************************************/ -/*! znzFile nifti_image_open( char *hname, char *opts , nifti_image **nim) - \brief Read in NIFTI-1 or ANALYZE-7.5 file (pair) header information into a nifti_image struct. - - - The image data is not read from disk (it may be read later using - nifti_image_load(), for example). - - The image data will be stored in whatever data format the - input data is; no scaling will be applied. - - DT_BINARY data is not supported. - - nifti_image_free() can be used to delete the returned struct, - when you are done with it. - - \param hname filename of dataset .hdr or .nii file - \param opts options string for opening the header file - \param nim pointer to pointer to nifti_image struct - (this routine allocates the nifti_image struct) - \return file pointer (gzippable) to the file with the image data, - ready for reading. -
NULL if something fails badly. - \sa nifti_image_load, nifti_image_free - */ -znzFile nifti_image_open(const char * hname, char * opts, nifti_image ** nim) -{ - znzFile fptr=NULL; - /* open the hdr and reading it in, but do not load the data */ - *nim = nifti_image_read(hname,0); - /* open the image file, ready for reading (compressed works for all reads) */ - if( ((*nim) == NULL) || ((*nim)->iname == NULL) || - ((*nim)->nbyper <= 0) || ((*nim)->nvox <= 0) ) - ERREX("bad header info") ; - - /* open image data file */ - fptr = znzopen( (*nim)->iname, opts, nifti_is_gzfile((*nim)->iname) ); - if( znz_isnull(fptr) ) ERREX("Can't open data file") ; - - return fptr; -} - - -/*----------------------------------------------------------------------*/ -/*! return an allocated and filled nifti_1_header struct - - Read the binary header from disk, and swap bytes if necessary. - - \return an allocated nifti_1_header struct, or NULL on failure - - \param hname name of file containing header - \param swapped if not NULL, return whether header bytes were swapped - \param check flag to check for invalid nifti_1_header - - \warning ASCII header type is not supported - - \sa nifti_image_read, nifti_image_free, nifti_image_read_bricks -*//*--------------------------------------------------------------------*/ -nifti_1_header * nifti_read_n1_hdr(const char * hname, int *swapped, int check) -{ - nifti_1_header nhdr, * hptr; - znzFile fp; - int bytes, lswap; - char * hfile; - char fname[] = { "nifti_read_n1_hdr" }; - - /* determine file name to use for header */ - hfile = nifti_findhdrname(hname); - if( hfile == NULL ){ - if( g_opts.debug > 0 ) - LNI_FERR(fname,"failed to find header file for", hname); - return NULL; - } else if( g_opts.debug > 1 ) - fprintf(stderr,"-d %s: found header filename '%s'\n",fname,hfile); - - fp = znzopen( hfile, "rb", nifti_is_gzfile(hfile) ); - if( znz_isnull(fp) ){ - if( g_opts.debug > 0 ) LNI_FERR(fname,"failed to open header file",hfile); - free(hfile); - return NULL; - } - - free(hfile); /* done with filename */ - - if( has_ascii_header(fp) == 1 ){ - znzclose( fp ); - if( g_opts.debug > 0 ) - LNI_FERR(fname,"ASCII header type not supported",hname); - return NULL; - } - - /* read the binary header */ - bytes = (int)znzread( &nhdr, 1, sizeof(nhdr), fp ); - znzclose( fp ); /* we are done with the file now */ - - if( bytes < (int)sizeof(nhdr) ){ - if( g_opts.debug > 0 ){ - LNI_FERR(fname,"bad binary header read for file", hname); - fprintf(stderr," - read %d of %d bytes\n",bytes, (int)sizeof(nhdr)); - } - return NULL; - } - - /* now just decide on byte swapping */ - lswap = need_nhdr_swap(nhdr.dim[0], nhdr.sizeof_hdr); /* swap data flag */ - if( check && lswap < 0 ){ - LNI_FERR(fname,"bad nifti_1_header for file", hname); - return NULL; - } else if ( lswap < 0 ) { - lswap = 0; /* if swapping does not help, don't do it */ - if(g_opts.debug > 1) fprintf(stderr,"-- swap failure, none applied\n"); - } - - if( lswap ) { - if ( g_opts.debug > 3 ) disp_nifti_1_header("-d nhdr pre-swap: ", &nhdr); - swap_nifti_header( &nhdr , NIFTI_VERSION(nhdr) ) ; - } - - if ( g_opts.debug > 2 ) disp_nifti_1_header("-d nhdr post-swap: ", &nhdr); - - if ( check && ! nifti_hdr1_looks_good(&nhdr) ){ - LNI_FERR(fname,"nifti_1_header looks bad for file", hname); - return NULL; - } - - /* all looks good, so allocate memory for and return the header */ - hptr = (nifti_1_header *)malloc(sizeof(nifti_1_header)); - if( ! hptr ){ - fprintf(stderr,"** nifti_read_hdr: failed to alloc nifti_1_header\n"); - return NULL; - } - - if( swapped ) *swapped = lswap; /* only if they care */ - - memcpy(hptr, &nhdr, sizeof(nifti_1_header)); - - return hptr; -} - - -/*----------------------------------------------------------------------*/ -/*! return an allocated and filled nifti_2_header struct - - Read the binary header from disk, and swap bytes if necessary. - - \return an allocated nifti_2_header struct, or NULL on failure - - \param hname name of file containing header - \param swapped if not NULL, return whether header bytes were swapped - \param check flag to check for invalid nifti_2_header - - \warning ASCII header type is not supported - - \sa nifti_read_header, nifti_read_n1_hdr, - nifti_image_read, nifti_image_read_bricks -*//*--------------------------------------------------------------------*/ -nifti_2_header * nifti_read_n2_hdr(const char * hname, int * swapped, - int check) -{ - nifti_2_header nhdr, * hptr; - znzFile fp; - int bytes, lswap; - char * hfile; - char fname[] = { "nifti_read_n2_hdr" }; - - /* determine file name to use for header */ - hfile = nifti_findhdrname(hname); - if( hfile == NULL ){ - if( g_opts.debug > 0 ) - LNI_FERR(fname,"failed to find header file for", hname); - return NULL; - } else if( g_opts.debug > 1 ) - fprintf(stderr,"-d %s: found N2 header filename '%s'\n",fname,hfile); - - fp = znzopen( hfile, "rb", nifti_is_gzfile(hfile) ); - if( znz_isnull(fp) ){ - if( g_opts.debug > 0 ) - LNI_FERR(fname,"failed to open N2 header file",hfile); - free(hfile); - return NULL; - } - - free(hfile); /* done with filename */ - - if( has_ascii_header(fp) == 1 ){ - znzclose( fp ); - if( g_opts.debug > 0 ) - LNI_FERR(fname,"ASCII header type not supported for NIFTI-2",hname); - return NULL; - } - - /* read the binary header */ - bytes = (int)znzread( &nhdr, 1, sizeof(nhdr), fp ); - znzclose( fp ); /* we are done with the file now */ - - if( bytes < (int)sizeof(nhdr) ){ - if( g_opts.debug > 0 ){ - LNI_FERR(fname,"bad binary header read for N2 file", hname); - fprintf(stderr," - read %d of %d bytes\n",bytes, (int)sizeof(nhdr)); - } - return NULL; - } - - /* now just decide on byte swapping */ - lswap = NIFTI2_NEEDS_SWAP(nhdr); - if( lswap ) { - if ( g_opts.debug > 3 ) disp_nifti_2_header("-d n2hdr pre-swap: ", &nhdr); - swap_nifti_header( &nhdr , 2 ); /* use explicit version */ - } - - if ( g_opts.debug > 2 ) disp_nifti_2_header("-d nhdr post-swap: ", &nhdr); - - if ( check && ! nifti_hdr2_looks_good(&nhdr) ){ - LNI_FERR(fname,"nifti_2_header looks bad for file", hname); - return NULL; - } - - /* all looks good, so allocate memory for and return the header */ - hptr = (nifti_2_header *)malloc(sizeof(nifti_2_header)); - if( ! hptr ){ - fprintf(stderr,"** nifti2_read_hdr: failed to alloc nifti_2_header\n"); - return NULL; - } - - if( swapped ) *swapped = lswap; /* only if they care */ - - memcpy(hptr, &nhdr, sizeof(nifti_2_header)); - - return hptr; -} - - -/*----------------------------------------------------------------------*/ -/*! decide if this nifti_1_header structure looks reasonable - - Check dim[0], dim[1], sizeof_hdr, and datatype. - Check magic string for "n+1". - Maybe more tests will follow. - - \return 1 if the header seems valid, 0 otherwise - - \sa nifti_nim_is_valid, valid_nifti_extensions -*//*--------------------------------------------------------------------*/ -int nifti_hdr1_looks_good(const nifti_1_header * hdr) -{ - int ni_ver, c, errs = 0; - - /* check dim[0] and sizeof_hdr */ - if( need_nhdr_swap(hdr->dim[0], hdr->sizeof_hdr) < 0 ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** NIFTI: bad hdr1 fields: dim0, sizeof_hdr = %d, %d\n", - hdr->dim[0], hdr->sizeof_hdr); - errs++; - } - - /* check the valid dimension sizes (maybe dim[0] is bad) */ - for( c = 1; c <= hdr->dim[0] && c <= 7; c++ ) - if( hdr->dim[c] <= 0 ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** NIFTI: bad nhdr field: dim[%d] = %d\n", - c,hdr->dim[c]); - errs++; - } - - ni_ver = NIFTI_VERSION(*hdr); /* determine header type */ - - if( ni_ver > 0 ){ /* NIFTI */ - - if( ! nifti_datatype_is_valid(hdr->datatype, 1) ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** bad NIFTI datatype in hdr, %d\n",hdr->datatype); - errs++; - } - - } else { /* ANALYZE 7.5 */ - - if( g_opts.debug > 1 ) { /* maybe tell user it's an ANALYZE hdr */ - fprintf(stderr, - "-- nhdr magic field implies ANALYZE: magic = '%.4s' : ",hdr->magic); - print_hex_vals(hdr->magic, 4, stderr); fputc('\n', stderr); - } - - if( ! nifti_datatype_is_valid(hdr->datatype, 0) ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** NIFTI: bad ANALYZE datatype in hdr, %d\n", - hdr->datatype); - errs++; - } - } - - if( errs ) return 0; /* problems */ - - if( g_opts.debug > 2 ) fprintf(stderr,"-d nifti header looks good\n"); - - return 1; /* looks good */ -} - - -/*----------------------------------------------------------------------*/ -/*! check that sizeof() returns the proper size - * - * if ni_ver is valid (1 or 2 right now), check those sizes - * if ni_ver == 0, check all known sizes - * else whine and fail -*//*--------------------------------------------------------------------*/ -int nifti_valid_header_size(int ni_ver, int whine) -{ - int size, errs=0, checks=0; - - if ( !ni_ver || (ni_ver == 1) ) { - size = 348; - checks++; - if( sizeof(nifti_1_header) != size ) { - if( whine ) - fprintf(stderr, - "** warning: sizeof(nifti_1_header) = %d, expected %d\n", - (int)sizeof(nifti_1_header), size); - errs++; - } - } - - if ( !ni_ver || (ni_ver == 2) ) { - size = 540; - checks++; - if( sizeof(nifti_2_header) != size ) { - if( whine ) - fprintf(stderr, - "** warning: sizeof(nifti_2_header) = %d, expected %d\n", - (int)sizeof(nifti_2_header), size); - errs++; - } - } - - if ( ! checks ) { - fprintf(stderr,"** nifti_valid_header_size: bad ni_ver = %d\n",ni_ver); - return 0; - } - - return errs ? 0 : 1; /* though !errs seems more fun */ -} - - -/*----------------------------------------------------------------------*/ -/*! decide if this nifti_2_header structure looks reasonable - * swapping should have already happened - - Check sizeof() and sizeof_hdr. - Check dim[0], dim[i], and datatype. - Check magic string for "n+2". - - \return 1 if the header seems valid, 0 otherwise - - \sa nifti_nim_is_valid, valid_nifti_extensions -*//*--------------------------------------------------------------------*/ -int nifti_hdr2_looks_good(const nifti_2_header * hdr) -{ - int ni_ver, c, errs = 0; - int64_t d0; - - if( !hdr ) { fprintf(stderr,"** NIFTI n2hdr: hdr is NULL\n"); return 0; } - - /* for now, just warn if the header sizes are not right */ - if( g_opts.debug > 0 ) (void)nifti_valid_header_size(0, 1); - - if( hdr->sizeof_hdr != sizeof(nifti_2_header) ) { - if( g_opts.debug > 0 ) - fprintf(stderr,"** NIFTI bad n2hdr: sizeof_hdr = %d\n", - hdr->sizeof_hdr); - errs++; - } - - /* check the valid dimension sizes (maybe dim[0] is bad) */ - d0 = hdr->dim[0]; - if( d0 < 0 || d0 > 7 ) { - if( g_opts.debug > 0 ) - fprintf(stderr,"** NIFTI: bad n2hdr: dim0 = %" PRId64 "\n", d0); - errs++; - } else { /* only check dims if d0 is okay */ - for( c = 1; c <= d0; c++ ) - if( hdr->dim[c] <= 0 ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** NIFTI: bad nhdr field: dim[%d] = %" PRId64 "\n", - c, hdr->dim[c]); - errs++; - } - } - - ni_ver = NIFTI_VERSION(*hdr); /* note version */ - - if( ! nifti_datatype_is_valid(hdr->datatype, ni_ver) ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** bad %s NIFTI datatype in hdr, %d\n", - ni_ver ? "NIFTI" : "ANALYZE", hdr->datatype); - errs++; - } - - /* NIFTI_VERSION must return 2, or else sizes will not match */ - if( ni_ver != 2 || memcmp((hdr->magic+4), nifti2_magic+4, 4) ) { - if( g_opts.debug > 0 ) { - fprintf(stderr, "-- header magic not NIFTI-2, magic = '%.4s' + ", - hdr->magic); - print_hex_vals(hdr->magic+4, 4, stderr); fputc('\n', stderr); - } - errs++; - } - - if( errs ) return 0; /* problems */ - - if( g_opts.debug > 2 ) fprintf(stderr,"-d nifti header looks good\n"); - - return 1; /* looks good */ -} - - -/*---------------------------------------------------------------------- - * check whether byte swapping is needed - * - * dim[0] should be in [0,7], and sizeof_hdr should be accurate - * - * \returns > 0 : needs swap - * 0 : does not need swap - * < 0 : error condition - *----------------------------------------------------------------------*/ -static int need_nhdr_swap( short dim0, int hdrsize ) -{ - short d0 = dim0; /* so we won't have to swap them on the stack */ - int hsize = hdrsize; - - if( d0 != 0 ){ /* then use it for the check */ - if( d0 > 0 && d0 <= 7 ) return 0; - - nifti_swap_2bytes(1, &d0); /* swap? */ - if( d0 > 0 && d0 <= 7 ) return 1; - - if( g_opts.debug > 1 ){ - fprintf(stderr,"** NIFTI: bad swapped d0 = %d, unswapped = ", d0); - nifti_swap_2bytes(1, &d0); /* swap? */ - fprintf(stderr,"%d\n", d0); - } - - return -1; /* bad, naughty d0 */ - } - - /* dim[0] == 0 should not happen, but could, so try hdrsize */ - if( hsize == sizeof(nifti_1_header) ) return 0; - - nifti_swap_4bytes(1, &hsize); /* swap? */ - if( hsize == sizeof(nifti_1_header) ) return 1; - - if( g_opts.debug > 1 ){ - fprintf(stderr,"** NIFTI: bad swapped hsize = %d, unswapped = ", hsize); - nifti_swap_4bytes(1, &hsize); /* swap? */ - fprintf(stderr,"%d\n", hsize); - } - - return -2; /* bad, naughty hsize */ -} - - -/* use macro LNI_FILE_ERROR instead of ERREX() -#undef ERREX -#define ERREX(msg) \ - do{ fprintf(stderr,"** ERROR: nifti_image_read(%s): %s\n", \ - (hname != NULL) ? hname : "(null)" , (msg) ) ; \ - return NULL ; } while(0) -*/ - - -/*************************************************************** - * nifti_read_header - ***************************************************************/ -/*! \brief Read and return a nifti header, along with the found type - - - The data buffer will be byteswapped if necessary. - - The data buffer will not be scaled. - - The data buffer is allocated with calloc(). - - \param hname filename of the nifti dataset - \param nver : - \return A void pointer, which should be cast based on the returned nver. - It points to an allocated header struct. -*/ -void * nifti_read_header( const char *hname, int *nver, int check ) -{ - nifti_1_header n1hdr; - nifti_2_header n2hdr; - znzFile fp; - void * hresult = NULL; - int64_t remain, h1size=0, h2size=0; - char fname[] = { "nifti_read_header" }; - char *hfile=NULL, *posn; - int ii, ni_ver; - - if( g_opts.debug > 2 ){ - fprintf(stderr,"-d reading header from '%s'",hname); - fprintf(stderr,", HAVE_ZLIB = %d\n", nifti_compiled_with_zlib()); - } - - /**- determine filename to use for header */ - hfile = nifti_findhdrname(hname); - if( hfile == NULL ){ - if(g_opts.debug > 0) - LNI_FERR(fname,"failed to find header file for", hname); - return NULL; /* check return */ - } else if( g_opts.debug > 2 ) - fprintf(stderr,"-d %s: found header filename '%s'\n",fname,hfile); - - h1size = sizeof(nifti_1_header); - h2size = sizeof(nifti_2_header); - - /**- open file, separate reading of header, extensions and data */ - fp = znzopen(hfile, "rb", nifti_is_gzfile(hfile)); - if( znz_isnull(fp) ){ - if( g_opts.debug > 0 ) LNI_FERR(fname,"failed to open header file",hfile); - free(hfile); - return NULL; - } - - /**- next read into nifti_1_header and determine nifti type */ - ii = (int)znzread(&n1hdr, 1, h1size, fp); - - if( ii < (int)h1size ){ /* failure? */ - if( g_opts.debug > 0 ){ - LNI_FERR(fname,"bad binary header read for file", hfile); - fprintf(stderr," - read %d of %d bytes\n",ii, (int)h1size); - } - znzclose(fp) ; - free(hfile); - return NULL; - } - - /* find out what type of header we have */ - ni_ver = nifti_header_version((char *)&n1hdr, h1size); - if( g_opts.debug > 2 ) - fprintf(stderr,"-- %s: NIFTI version = %d\n", fname, ni_ver); - - /* maybe set return NIFTI version */ - if( nver ) *nver = ni_ver; - - /* if NIFTI-2, copy and finish reading header */ - if ( ni_ver == 2 ) { - if( g_opts.debug > 2 ) - fprintf(stderr,"-- %s: copying and filling NIFTI-2 header...\n",fname); - memcpy(&n2hdr, &n1hdr, h1size); /* copy first part */ - remain = h2size - h1size; - posn = (char *)&n2hdr + h1size; - ii = (int)znzread(posn, 1, remain, fp); /* read remaining part */ - if( ii < (int)remain) { - LNI_FERR(fname,"short NIFTI-2 header read for file", hfile); - znzclose(fp); free(hfile); return NULL; - } - } - - /* clean up */ - znzclose(fp); - free(hfile); - - /* allocate header space and return */ - if( ni_ver == 0 || ni_ver == 1 ) { - hresult = malloc(h1size); - if( ! hresult ) { - LNI_FERR(fname,"failed to alloc NIFTI-1 header for file", hname); - return NULL; - } - memcpy(hresult, (void *)&n1hdr, h1size); - - if ( check && ! nifti_hdr1_looks_good(hresult) ){ - LNI_FERR(fname,"nifti_1_header looks bad for file", hname); - return hresult; - } - } else if ( ni_ver == 2 ) { - hresult = malloc(h2size); - if( ! hresult ) { - LNI_FERR(fname,"failed to alloc NIFTI-2 header for file", hname); - return NULL; - } - memcpy(hresult, &n2hdr, h2size); - - if ( check && ! nifti_hdr2_looks_good(hresult) ){ - LNI_FERR(fname,"nifti_2_header looks bad for file", hname); - return hresult; - } - } else { - if( g_opts.debug > 0 ) - fprintf(stderr, "** %s: bad nifti header version %d\n", hname, ni_ver); - - /* return a nifti-1 header anyway */ - hresult = malloc(h1size); - if( ! hresult ) { - LNI_FERR(fname,"failed to alloc NIFTI-?? header for file", hname); - return NULL; - } - memcpy(hresult, (void *)&n1hdr, h1size); - } - - if( g_opts.debug > 1 ) - fprintf(stderr,"-- returning NIFTI-%d header in %s\n", ni_ver, hname); - - return hresult; -} - - -/*************************************************************** - * nifti_image_read - ***************************************************************/ -/*! \brief Read a nifti header and optionally the data, creating a nifti_image. - - - The data buffer will be byteswapped if necessary. - - The data buffer will not be scaled. - - The data buffer is allocated with calloc(). - - \param hname filename of the nifti dataset - \param read_data Flag, true=read data blob, false=don't read blob. - \return A pointer to the nifti_image data structure. - - \sa nifti_image_free, nifti_free_extensions, nifti_image_read_bricks -*/ -nifti_image *nifti_image_read( const char *hname , int read_data ) -{ - nifti_1_header n1hdr; - nifti_2_header n2hdr; - nifti_image *nim; - znzFile fp; - int rv, ii, ni_ver, onefile=0; - int64_t filesize, remain, h1size=0, h2size=0; - char fname[] = { "nifti_image_read" }; - char *hfile=NULL, *posn; - - if( g_opts.debug > 1 ){ - fprintf(stderr,"-d image_read from '%s', read_data = %d",hname,read_data); - fprintf(stderr,", HAVE_ZLIB = %d\n", nifti_compiled_with_zlib()); - } - - /**- determine filename to use for header */ - hfile = nifti_findhdrname(hname); - if( hfile == NULL ){ - if(g_opts.debug > 0) - LNI_FERR(fname,"failed to find header file for", hname); - return NULL; /* check return */ - } else if( g_opts.debug > 1 ) - fprintf(stderr,"-d %s: found header filename '%s'\n",fname,hfile); - - if( nifti_is_gzfile(hfile) ) filesize = -1; /* unknown */ - else filesize = nifti_get_filesize(hfile); - - /**- open file, separate reading of header, extensions and data */ - fp = znzopen(hfile, "rb", nifti_is_gzfile(hfile)); - if( znz_isnull(fp) ){ - if( g_opts.debug > 0 ) LNI_FERR(fname,"failed to open header file",hfile); - free(hfile); - return NULL; - } - - /**- first try to read dataset as ASCII (and return if so) */ - rv = has_ascii_header( fp ); - if( rv < 0 ){ - if( g_opts.debug > 0 ) LNI_FERR(fname,"short header read",hfile); - znzclose( fp ); - free(hfile); - return NULL; - } - else if ( rv == 1 ) /* process special file type */ - return nifti_read_ascii_image( fp, hfile, filesize, read_data ); - - h1size = sizeof(nifti_1_header); - h2size = sizeof(nifti_2_header); - - /**- next read into nifti_1_header and determine nifti type */ - ii = (int)znzread(&n1hdr, 1, h1size, fp); - - if( ii < (int)h1size ){ /* failure? */ - if( g_opts.debug > 0 ){ - LNI_FERR(fname,"bad binary header read for file", hfile); - fprintf(stderr," - read %d of %d bytes\n",ii, (int)h1size); - } - znzclose(fp) ; - free(hfile); - return NULL; - } - - /* find out what type of header we have */ - ni_ver = nifti_header_version((char *)&n1hdr, h1size); - if( g_opts.debug > 2 ) - fprintf(stderr,"-- %s: NIFTI version = %d\n", fname, ni_ver); - - if( ni_ver == 0 || ni_ver == 1 ) { - nim = nifti_convert_n1hdr2nim(n1hdr,hfile); - onefile = NIFTI_ONEFILE(n1hdr); - } else if ( ni_ver == 2 ) { - /* fill nifti-2 header and convert */ - if( g_opts.debug > 2 ) - fprintf(stderr,"-- %s: copying and filling NIFTI-2 header...\n",fname); - memcpy(&n2hdr, &n1hdr, h1size); /* copy first part */ - remain = h2size - h1size; - posn = (char *)&n2hdr + h1size; - ii = (int)znzread(posn, 1, remain, fp); /* read remaining part */ - if( ii < (int)remain) { - LNI_FERR(fname,"short NIFTI-2 header read for file", hfile); - znzclose(fp); free(hfile); return NULL; - } - nim = nifti_convert_n2hdr2nim(n2hdr,hfile); - onefile = NIFTI_ONEFILE(n2hdr); - } else { - if( g_opts.debug > 0 ) - fprintf(stderr,"** %s: bad nifti im header version %d\n",fname,ni_ver); - znzclose(fp); free(hfile); return NULL; - } - - if( nim == NULL ){ - znzclose( fp ) ; /* close the file */ - if( g_opts.debug > 0 ) - LNI_FERR(fname,"cannot create nifti image from header",hfile); - free(hfile); /* had to save this for debug message */ - return NULL; - } - - if( g_opts.debug > 3 ){ - fprintf(stderr,"+d nifti_image_read(), have nifti image:\n"); - if( g_opts.debug > 2 ) nifti_image_infodump(nim); - } - - /**- check for extensions (any errors here means no extensions) */ - if ( onefile ) remain = nim->iname_offset; - else remain = filesize; - - if ( ni_ver <= 1 ) remain -= h1size; - else remain -= h2size; - - (void)nifti_read_extensions(nim, fp, remain); - - znzclose( fp ) ; /* close the file */ - free(hfile); - - if ( g_opts.alter_cifti && nifti_looks_like_cifti(nim) ) - nifti_alter_cifti_dims(nim); - - /**- read the data if desired, then bug out */ - if( read_data ){ - if( nifti_image_load( nim ) < 0 ){ - nifti_image_free(nim); /* take ball, go home. */ - return NULL; - } - } - else nim->data = NULL ; - - return nim ; -} - - -/*---------------------------------------------------------------------- - # return the index of the first occurrence of the given ecode, else -1 - *----------------------------------------------------------------------*/ -static int nifti_ext_type_index(nifti_image * nim, int ecode) -{ - int ind; - - if ( !nim || ecode < 0 ) return -1; - - for( ind = 0; ind < nim->num_ext; ind++ ) - if( nim->ext_list[ind].ecode == ecode ) - return ind; - - return -1; -} - -/*---------------------------------------------------------------------- - *! does this dataset look like CIFTI? - * - * check dimensions and extension ecodes for CIFTI - * - * should have - nx=ny=nz=nt=1, nu,nv>1, nw optional - * - CIFTI extension - *----------------------------------------------------------------------*/ -int nifti_looks_like_cifti(nifti_image * nim) -{ - if( ! nim ) return 0; - - if( nifti_ext_type_index(nim, NIFTI_ECODE_CIFTI) < 0 ) return 0; - - if( nim->nx > 1 || nim->ny > 1 || nim->nz > 1 || nim->nt > 1 ) return 0; - - if( nim->nu > 1 || nim->nv > 1 ) return 1; /* looks like it */ - - return 0; -} - -/*---------------------------------------------------------------------- - *! alter the dims[] from CIFTI style - * - * convert nu -> nx, nv -> nt/nu, nw -> nv - *----------------------------------------------------------------------*/ -int nifti_alter_cifti_dims(nifti_image * nim) -{ - if( ! nifti_looks_like_cifti(nim) ) return 0; - - /* the main effect, move position axis to x ... */ - if( nim->nu > 1 || nim->dim[5] ) { - nim->nx = nim->nu; - nim->nu = 1; - - nim->dim[1] = nim->dim[5]; - nim->dim[5] = 1; - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * has_ascii_header - see if the NIFTI header is an ASCII format - * - * If the file starts with the ASCII string " 1 ) - fprintf(stderr,"-d %s: have ASCII NIFTI file of size %d\n",fname,slen); - - if( slen > 65530 ) slen = 65530 ; - sbuf = (char *)calloc(sizeof(char),slen+1) ; - if( !sbuf ){ - fprintf(stderr,"** %s: failed to alloc %d bytes for sbuf",lfunc,65530); - free(fname); znzclose(fp); return NULL; - } - znzread( sbuf , 1 , slen , fp ) ; - nim = nifti_image_from_ascii( sbuf, &txt_size ) ; free( sbuf ) ; - if( nim == NULL ){ - LNI_FERR(lfunc,"failed nifti_image_from_ascii()",fname); - free(fname); znzclose(fp); return NULL; - } - nim->nifti_type = NIFTI_FTYPE_ASCII ; - - /* compute remaining space for extensions */ - remain = flen - txt_size - (int)nifti_get_volsize(nim); - if( remain > 4 ){ - /* read extensions (reposition file pointer, first) */ - znzseek(fp, txt_size, SEEK_SET); - (void) nifti_read_extensions(nim, fp, (int64_t)remain); - } - - free(fname); - znzclose( fp ) ; - - nim->iname_offset = -1 ; /* check from the end of the file */ - - if( read_data ) rv = nifti_image_load( nim ) ; - else nim->data = NULL ; - - /* check for nifti_image_load() failure, maybe bail out */ - if( read_data && rv != 0 ){ - if( g_opts.debug > 1 ) - fprintf(stderr,"-d failed image_load, free nifti image struct\n"); - free(nim); - return NULL; - } - - return nim ; -} - - -/*---------------------------------------------------------------------- - * Read the extensions into the nifti_image struct 08 Dec 2004 [rickr] - * - * This function is called just after the header struct is read in, and - * it is assumed the file pointer has not moved. The value in remain - * is assumed to be accurate, reflecting the bytes of space for potential - * extensions. - * - * return the number of extensions read in, or < 0 on error - *----------------------------------------------------------------------*/ -static int nifti_read_extensions( nifti_image *nim, znzFile fp, int64_t remain ) -{ - nifti1_extender extdr; /* defines extension existence */ - nifti1_extension extn; /* single extension to process */ - nifti1_extension * Elist; /* list of processed extensions */ - int64_t posn, count; - - /* rcr n2 - add and use nifti2_extension type? */ - - if( !nim || znz_isnull(fp) ) { - if( g_opts.debug > 0 ) - fprintf(stderr,"** nifti_read_extensions: bad inputs (%p,%p)\n", - (void *)nim, (void *)fp); - return -1; - } - - posn = znztell(fp); - - if( g_opts.debug > 2 ) - fprintf(stderr,"-d nre: posn=%" PRId64 ", offset=%" PRId64 - ", type=%d, remain=%" PRId64 "\n", - posn, nim->iname_offset, nim->nifti_type, remain); - - if( remain < 16 ){ - if( g_opts.debug > 2 ){ - if( g_opts.skip_blank_ext ) - fprintf(stderr,"-d no extender in '%s' is okay, as " - "skip_blank_ext is set\n",nim->fname); - else - fprintf(stderr,"-d remain=%" PRId64 ", no space for extensions\n", - remain); - } - return 0; - } - - count = znzread( extdr.extension, 1, 4, fp ); /* get extender */ - - if( count < 4 ){ - if( g_opts.debug > 1 ) - fprintf(stderr,"-d file '%s' is too short for an extender\n", - nim->fname); - return 0; - } - - if( extdr.extension[0] != 1 ){ - if( g_opts.debug > 2 ) - fprintf(stderr,"-d extender[0] (%d) shows no extensions for '%s'\n", - extdr.extension[0], nim->fname); - return 0; - } - - remain -= 4; - if( g_opts.debug > 2 ) - fprintf(stderr,"-d found valid 4-byte extender, remain = %" PRId64 "\n", - remain); - - /* so we expect extensions, but have no idea of how many there may be */ - - count = 0; - Elist = NULL; - while (nifti_read_next_extension(&extn, nim, remain, fp) > 0) - { - if( nifti_add_exten_to_list(&extn, &Elist, (int)count+1) < 0 ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** NIFTI: failed adding ext %" PRId64 " to list\n", - count); - return -1; - } - - /* we have a new extension */ - if( g_opts.debug > 1 ){ - fprintf(stderr,"+d found extension #%" PRId64 - ", code = 0x%x, size = %d\n", - count, extn.ecode, extn.esize); - if( extn.ecode == NIFTI_ECODE_AFNI && g_opts.debug > 2 ) /* ~XML */ - fprintf(stderr," AFNI extension: %.*s\n", - extn.esize-8,extn.edata); - else if( extn.ecode == NIFTI_ECODE_COMMENT && g_opts.debug > 2 ) - fprintf(stderr," COMMENT extension: %.*s\n", /* TEXT */ - extn.esize-8,extn.edata); - } - remain -= extn.esize; - count++; - } - - if( g_opts.debug > 2 ) - fprintf(stderr,"+d found %" PRId64 " extension(s)\n", count); - /* rcr n2 - allow int64_t num ext? */ - nim->num_ext = (int)count; - nim->ext_list = Elist; - - return count; -} - - -/*----------------------------------------------------------------------*/ -/*! nifti_add_extension - add an extension, with a copy of the data - - Add an extension to the nim->ext_list array. - Fill this extension with a copy of the data, noting the - length and extension code. - - \param nim - nifti_image to add extension to - \param data - raw extension data - \param length - length of raw extension data - \param ecode - extension code - - \sa extension codes NIFTI_ECODE_* in nifti1_io.h - \sa nifti_free_extensions, valid_nifti_extensions, nifti_copy_extensions - - \return 0 on success, -1 on error (and free the entire list) -*//*--------------------------------------------------------------------*/ -int nifti_add_extension(nifti_image *nim, const char * data, int len, int ecode) -{ - nifti1_extension ext; - - /* error are printed in functions */ - if( nifti_fill_extension(&ext, data, len, ecode) ) return -1; - if( nifti_add_exten_to_list(&ext, &nim->ext_list, nim->num_ext+1)) return -1; - - nim->num_ext++; /* success, so increment */ - - return 0; -} - - -/*----------------------------------------------------------------------*/ -/* nifti_add_exten_to_list - add a new nifti1_extension to the list - - We will append via "malloc, copy and free", because on an error, - the list will revert to the previous one (sorry realloc(), only - quality dolphins get to become part of St@rk!st brand tunafish). - - return 0 on success, -1 on error (and free the entire list) -*//*--------------------------------------------------------------------*/ -static int nifti_add_exten_to_list( nifti1_extension * new_ext, - nifti1_extension ** list, int new_length ) -{ - nifti1_extension * tmplist; - - tmplist = *list; - *list = (nifti1_extension *)malloc(new_length * sizeof(nifti1_extension)); - - /* check for failure first */ - if( ! *list ){ - fprintf(stderr,"** NIFTI: failed to alloc %d ext structs (%d bytes)\n", - new_length, new_length*(int)sizeof(nifti1_extension)); - if( !tmplist ) return -1; /* no old list to lose */ - - *list = tmplist; /* reset list to old one */ - return -1; - } - - /* if an old list exists, copy the pointers and free the list */ - if( tmplist ){ - memcpy(*list, tmplist, (new_length-1)*sizeof(nifti1_extension)); - free(tmplist); - } - - /* for some reason, I just don't like struct copy... */ - (*list)[new_length-1].esize = new_ext->esize; - (*list)[new_length-1].ecode = new_ext->ecode; - (*list)[new_length-1].edata = new_ext->edata; - - if( g_opts.debug > 2 ) - fprintf(stderr,"+d allocated and appended extension #%d to list\n", - new_length); - - return 0; -} - - -/*----------------------------------------------------------------------*/ -/* nifti_fill_extension - given data and length, fill an extension struct - - Allocate memory for data, copy data, set the size and code. - - return 0 on success, -1 on error (and free the entire list) -*//*--------------------------------------------------------------------*/ -static int nifti_fill_extension( nifti1_extension *ext, const char * data, - int len, int ecode) -{ - int esize; - - if( !ext || !data || len < 0 ){ - fprintf(stderr,"** NIFTI fill_ext: bad params (%p,%p,%d)\n", - (void *)ext, data, len); - return -1; - } else if( ! nifti_is_valid_ecode(ecode) ){ - fprintf(stderr,"** NIFTI fill_ext: invalid ecode %d\n", ecode); - /* should not be fatal 29 Apr 2015 [rickr] */ - } - - /* compute esize, first : len+8, and take ceiling up to a mult of 16 */ - esize = len+8; - if( esize & 0xf ) esize = (esize + 0xf) & ~0xf; - ext->esize = esize; - - /* allocate esize-8 (maybe more than len), using calloc for fill */ - ext->edata = (char *)calloc(esize-8, sizeof(char)); - if( !ext->edata ){ - fprintf(stderr,"** NIFTI NFE: failed to alloc %d bytes for extension\n", - len); - return -1; - } - - memcpy(ext->edata, data, len); /* copy the data, using len */ - ext->ecode = ecode; /* set the ecode */ - - if( g_opts.debug > 2 ) - fprintf(stderr,"+d alloc %d bytes for ext len %d, ecode %d, esize %d\n", - esize-8, len, ecode, esize); - - return 0; -} - - -/*---------------------------------------------------------------------- - * nifti_read_next_extension - read a single extension from the file - * - * return (>= 0 is okay): - * - * success : esize - * no extension : 0 - * error : -1 - *----------------------------------------------------------------------*/ -static int nifti_read_next_extension( nifti1_extension * nex, nifti_image *nim, - int remain, znzFile fp ) -{ - int swap = nim->byteorder != nifti_short_order(); - int count, size, code; - - /* first clear nex */ - nex->esize = nex->ecode = 0; - nex->edata = NULL; - - if( remain < 16 ){ - if( g_opts.debug > 2 ) - fprintf(stderr,"-d only %d bytes remain, so no extension\n", remain); - return 0; - } - - /* must start with 4-byte size and code */ - count = (int)znzread( &size, 4, 1, fp ); - if( count == 1 ) count += (int)znzread( &code, 4, 1, fp ); - - if( count != 2 ){ - if( g_opts.debug > 2 ) - fprintf(stderr,"-d current extension read failed\n"); - znzseek(fp, -4*count, SEEK_CUR); /* back up past any read */ - return 0; /* no extension, no error condition */ - } - - if( swap ){ - if( g_opts.debug > 2 ) - fprintf(stderr,"-d pre-swap exts: code %d, size %d\n", code, size); - - nifti_swap_4bytes(1, &size); - nifti_swap_4bytes(1, &code); - } - - if( g_opts.debug > 2 ) - fprintf(stderr,"-d potential extension: code %d, size %d\n", code, size); - - if( !nifti_check_extension(nim, size, code, remain) ){ - if( znzseek(fp, -8, SEEK_CUR) < 0 ){ /* back up past any read */ - fprintf(stderr,"** NIFTI: failure to back out of extension read!\n"); - return -1; - } - return 0; - } - - /* now get the actual data */ - nex->esize = size; - nex->ecode = code; - - size -= 8; /* subtract space for size and code in extension */ - nex->edata = (char *)malloc(size * sizeof(char)); - if( !nex->edata ){ - fprintf(stderr,"** NIFTI: failed to allocate %d bytes for extension\n", - size); - return -1; - } - - count = (int)znzread(nex->edata, 1, size, fp); - if( count < size ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"-d read only %d (of %d) bytes for extension\n", - count, size); - free(nex->edata); - nex->edata = NULL; - return -1; - } - - /* success! */ - if( g_opts.debug > 2 ) - fprintf(stderr,"+d successfully read extension, code %d, size %d\n", - nex->ecode, nex->esize); - - return nex->esize; -} - - -/*----------------------------------------------------------------------*/ -/*! for each extension, check code, size and data pointer -*//*--------------------------------------------------------------------*/ -int valid_nifti_extensions(const nifti_image * nim) -{ - nifti1_extension * ext; - int c, errs; - - if( nim->num_ext <= 0 || nim->ext_list == NULL ){ - if( g_opts.debug > 2 ) fprintf(stderr,"-d empty extension list\n"); - return 0; - } - - /* for each extension, check code, size and data pointer */ - ext = nim->ext_list; - errs = 0; - for ( c = 0; c < nim->num_ext; c++ ){ - if( ! nifti_is_valid_ecode(ext->ecode) ) { - if( g_opts.debug > 1 ) - fprintf(stderr,"-d ext %d, invalid code %d\n", c, ext->ecode); - /* should not be fatal 29 Apr 2015 [rickr] */ - } - - if( ext->esize <= 0 ){ - if( g_opts.debug > 1 ) - fprintf(stderr,"-d ext %d, bad size = %d\n", c, ext->esize); - errs++; - } else if( ext->esize & 0xf ){ - if( g_opts.debug > 1 ) - fprintf(stderr,"-d ext %d, size %d not multiple of 16\n", - c, ext->esize); - errs++; - } - - if( ext->edata == NULL ){ - if( g_opts.debug > 1 ) fprintf(stderr,"-d ext %d, missing data\n", c); - errs++; - } - - ext++; - } - - if( errs > 0 ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"-d had %d extension errors, none will be written\n", - errs); - return 0; - } - - /* if we're here, we're good */ - return 1; -} - -/*----------------------------------------------------------------------*/ -/*! determine NIFTI version from buffer (check sizeof_hdr and magic) - - \return -1 on error, else NIFTI version - *//*--------------------------------------------------------------------*/ -int nifti_header_version(const char * buf, size_t nbytes){ - nifti_1_header *n1p = (nifti_1_header *)buf; - nifti_2_header *n2p = (nifti_2_header *)buf; - char fname[] = { "nifti_header_version" }; - int sizeof_hdr, sver, nver; - - if( !buf ) { - if(g_opts.debug > 0) - fprintf(stderr,"** %s: have NULL buffer pointer", fname); - return -1; - } - - if( nbytes < sizeof(nifti_1_header) ) { - if(g_opts.debug > 0) - fprintf(stderr,"** %s: nbytes=%zu, too small for test", fname, nbytes); - return -1; - } - - /* try to determine the version based on sizeof_hdr */ - sver = -1; - sizeof_hdr = n1p->sizeof_hdr; - if ( sizeof_hdr == (int)sizeof(nifti_1_header) ) sver = 1; - else if( sizeof_hdr == (int)sizeof(nifti_2_header) ) sver = 2; - else { /* try swapping */ - nifti_swap_4bytes(1, &sizeof_hdr); - if ( sizeof_hdr == (int)sizeof(nifti_1_header) ) sver = 1; - else if( sizeof_hdr == (int)sizeof(nifti_2_header) ) sver = 2; - } - - /* and check magic field */ - if ( sver == 1 ) nver = NIFTI_VERSION(*n1p); - else if ( sver == 2 ) nver = NIFTI_VERSION(*n2p); - else nver = -1; - - /* now compare and return */ - - if( g_opts.debug > 2 ) - fprintf(stderr,"-- %s: size ver = %d, ni ver = %d\n", fname, sver, nver); - - if( sver == 1 ) { - nver = NIFTI_VERSION(*n1p); - if( nver == 0 ) return 0; /* ANALYZE */ - if( nver == 1 ) return 1; /* NIFTI-1 */ - if( g_opts.debug > 1 ) - fprintf(stderr,"** %s: bad NIFTI-1 magic= %.4s", fname, n1p->magic); - return -1; - } else if ( sver == 2 ) { - nver = NIFTI_VERSION(*n2p); - if( nver == 2 ) return 2; /* NIFTI-2 */ - if( g_opts.debug > 1 ) - fprintf(stderr,"** %s: bad NIFTI-2 magic4= %.4s", fname, n2p->magic); - return -1; - } - - /* failure */ - - if( g_opts.debug > 0 ) - fprintf(stderr,"** %s: bad sizeof_hdr = %d\n", fname, n1p->sizeof_hdr); - - return -1; -} - - - -/*----------------------------------------------------------------------*/ -/*! check whether the extension code is valid - - \return 1 if valid, 0 otherwise -*//*--------------------------------------------------------------------*/ -int nifti_is_valid_ecode( int ecode ) -{ - if( ecode < NIFTI_ECODE_IGNORE || /* minimum code number (0) */ - ecode > NIFTI_MAX_ECODE || /* maximum code number */ - ecode & 1 ) /* cannot be odd */ - return 0; - - return 1; -} - - -/*---------------------------------------------------------------------- - * check for valid size and code, as well as can be done - *----------------------------------------------------------------------*/ -static int nifti_check_extension(nifti_image *nim, int size, int code, int rem) -{ - /* check for bad code before bad size */ - if( ! nifti_is_valid_ecode(code) ) { - if( g_opts.debug > 2 ) - fprintf(stderr,"-d invalid extension code %d\n",code); - /* should not be fatal 29 Apr 2015 [rickr] */ - } - - if( size < 16 ){ - if( g_opts.debug > 2 ) - fprintf(stderr,"-d ext size %d, no extension\n",size); - return 0; - } - - if( size > rem ){ - if( g_opts.debug > 2 ) - fprintf(stderr,"-d ext size %d, space %d, no extension\n", size, rem); - return 0; - } - - if( size & 0xf ){ - if( g_opts.debug > 2 ) - fprintf(stderr,"-d nifti extension size %d not multiple of 16\n",size); - return 0; - } - - if( nim->nifti_type == NIFTI_FTYPE_ASCII && size > LNI_MAX_NIA_EXT_LEN ){ - if( g_opts.debug > 2 ) - fprintf(stderr,"-d NVE, bad nifti_type 3 size %d\n", size); - return 0; - } - - return 1; -} - - -/*---------------------------------------------------------------------- - * nifti_image_load_prep - prepare to read data - * - * Check nifti_image fields, open the file and seek to the appropriate - * offset for reading. - * - * return NULL on failure - *----------------------------------------------------------------------*/ -static znzFile nifti_image_load_prep( nifti_image *nim ) -{ - /* set up data space, open data file and seek, then call nifti_read_buffer */ - int64_t ntot , ii , ioff; - znzFile fp; - char *tmpimgname; - char fname[] = { "nifti_image_load_prep" }; - - /**- perform sanity checks */ - if( nim == NULL || nim->iname == NULL || - nim->nbyper <= 0 || nim->nvox <= 0 ) - { - if ( g_opts.debug > 0 ){ - if( !nim ) fprintf(stderr,"** ERROR: N_image_load: no nifti image\n"); - else fprintf(stderr,"** ERROR: nifti_image_load: bad params (%p,%d," - "%" PRId64 ")\n", nim->iname, nim->nbyper, nim->nvox); - } - return NULL; - } - - ntot = nifti_get_volsize(nim) ; /* total bytes to read */ - - /**- open image data file */ - - tmpimgname = nifti_findimgname(nim->iname , nim->nifti_type); - if( tmpimgname == NULL ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** NIFTI: no image file found for '%s'\n",nim->iname); - return NULL; - } - - fp = znzopen(tmpimgname, "rb", nifti_is_gzfile(tmpimgname)); - if (znz_isnull(fp)){ - if(g_opts.debug > 0) LNI_FERR(fname,"cannot open data file",tmpimgname); - free(tmpimgname); - return NULL; /* bad open? */ - } - free(tmpimgname); - - /**- get image offset: a negative offset means to figure from end of file */ - if( nim->iname_offset < 0 ){ - if( nifti_is_gzfile(nim->iname) ){ - if( g_opts.debug > 0 ) - LNI_FERR(fname,"negative offset for compressed file",nim->iname); - znzclose(fp); - return NULL; - } - ii = nifti_get_filesize( nim->iname ) ; - if( ii <= 0 ){ - if( g_opts.debug > 0 ) LNI_FERR(fname,"empty data file",nim->iname); - znzclose(fp); - return NULL; - } - ioff = (ii > ntot) ? ii-ntot : 0 ; - } else { /* non-negative offset */ - ioff = nim->iname_offset ; /* means use it directly */ - } - - /**- seek to the appropriate read position */ - if( znzseek(fp , (long)ioff , SEEK_SET) < 0 ){ - fprintf(stderr,"** NIFTI: could not seek to offset %" PRId64 - " in file '%s'\n", - ioff, nim->iname); - znzclose(fp); - return NULL; - } - - /**- and return the File pointer */ - return fp; -} - - -/*---------------------------------------------------------------------- - * nifti_image_load - *----------------------------------------------------------------------*/ -/*! \fn int nifti_image_load( nifti_image *nim ) - \brief Load the image blob into a previously initialized nifti_image. - - - If not yet set, the data buffer is allocated with calloc(). - - The data buffer will be byteswapped if necessary. - - The data buffer will not be scaled. - - This function is used to read the image from disk. It should be used - after a function such as nifti_image_read(), so that the nifti_image - structure is already initialized. - - \param nim pointer to a nifti_image (previously initialized) - \return 0 on success, -1 on failure - \sa nifti_image_read, nifti_image_free, nifti_image_unload -*/ -int nifti_image_load( nifti_image *nim ) -{ - /* set up data space, open data file and seek, then call nifti_read_buffer */ - int64_t ntot , ii ; - znzFile fp ; - - /**- open the file and position the FILE pointer */ - fp = nifti_image_load_prep( nim ); - - if( fp == NULL ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** nifti_image_load, failed load_prep\n"); - return -1; - } - - ntot = nifti_get_volsize(nim); - - /**- if the data pointer is not yet set, get memory space for the image */ - - if( nim->data == NULL ) - { - nim->data = (void *)calloc(1,ntot) ; /* create image memory */ - if( nim->data == NULL ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** NIFTI: failed to alloc %d bytes for image data\n", - (int)ntot); - znzclose(fp); - return -1; - } - } - - /**- now that everything is set up, do the reading */ - ii = nifti_read_buffer(fp,nim->data,ntot,nim); - if( ii < ntot ){ - znzclose(fp) ; - free(nim->data) ; - nim->data = NULL ; - return -1 ; /* errors were printed in nifti_read_buffer() */ - } - - /**- close the file */ - znzclose( fp ) ; - - return 0 ; -} - - -/* 30 Nov 2004 [rickr] -#undef ERREX -#define ERREX(msg) \ - do{ fprintf(stderr,"** ERROR: nifti_read_buffer: %s\n",(msg)) ; \ - return 0; } while(0) -*/ - -/*----------------------------------------------------------------------*/ -/*! read ntot bytes of data from an open file and byte swaps if necessary - - note that nifti_image is required for information on datatype, bsize - (for any needed byte swapping), etc. - - This function does not allocate memory, so dataptr must be valid. -*//*--------------------------------------------------------------------*/ -int64_t nifti_read_buffer(znzFile fp, void* dataptr, int64_t ntot, - nifti_image *nim) -{ - int64_t ii; - - if( dataptr == NULL ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** ERROR: nifti_read_buffer: NULL dataptr\n"); - return -1; - } - - ii = znzread( dataptr , 1 , ntot , fp ) ; /* data input */ - - /* if read was short, fail */ - if( ii < ntot ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"++ WARNING: nifti_read_buffer(%s):\n" - " data bytes needed = %" PRId64 "\n" - " data bytes input = %" PRId64 "\n" - " number missing = %" PRId64 " (set to 0)\n", - nim->iname , ntot , ii , (ntot-ii) ) ; - /* memset( (char *)(dataptr)+ii , 0 , ntot-ii ) ; now failure [rickr] */ - return -1 ; - } - - if( g_opts.debug > 2 ) - fprintf(stderr,"+d nifti_read_buffer: read %" PRId64 " bytes\n", ii); - - /* byte swap array if needed */ - - /* ntot/swapsize might not fit as int, use int64_t 6 Jul 2010 [rickr] */ - if( nim->swapsize > 1 && nim->byteorder != nifti_short_order() ) { - if( g_opts.debug > 1 ) - fprintf(stderr,"+d nifti_read_buffer: swapping data bytes...\n"); - nifti_swap_Nbytes( (int)(ntot / nim->swapsize), nim->swapsize , dataptr ) ; - } - -#ifdef isfinite -{ - /* check input float arrays for goodness, and fix bad floats */ - int fix_count = 0 ; - - switch( nim->datatype ){ - - case NIFTI_TYPE_FLOAT32: - case NIFTI_TYPE_COMPLEX64:{ - float *far = (float *)dataptr ; int64_t jj,nj ; - nj = ntot / sizeof(float) ; - for( jj=0 ; jj < nj ; jj++ ) /* count fixes 30 Nov 2004 [rickr] */ - if( !IS_GOOD_FLOAT(far[jj]) ){ - far[jj] = 0 ; - fix_count++ ; - } - } - break ; - - case NIFTI_TYPE_FLOAT64: - case NIFTI_TYPE_COMPLEX128:{ - double *far = (double *)dataptr ; int64_t jj,nj ; - nj = ntot / sizeof(double) ; - for( jj=0 ; jj < nj ; jj++ ) /* count fixes 30 Nov 2004 [rickr] */ - if( !IS_GOOD_FLOAT(far[jj]) ){ - far[jj] = 0 ; - fix_count++ ; - } - } - break ; - - } - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d in image, %d bad floats were set to 0\n", fix_count); -} -#endif - - return ii; -} - -/*--------------------------------------------------------------------------*/ -/*! Unload the data in a nifti_image struct, but keep the metadata. -*//*------------------------------------------------------------------------*/ -void nifti_image_unload( nifti_image *nim ) -{ - if( nim != NULL && nim->data != NULL ){ - free(nim->data) ; nim->data = NULL ; - } - return ; -} - -/*--------------------------------------------------------------------------*/ -/*! free 'everything' about a nifti_image struct (including the passed struct) - - free (only fields which are not NULL): - - fname and iname - - data - - any ext_list[i].edata - - ext_list - - nim -*//*------------------------------------------------------------------------*/ -void nifti_image_free( nifti_image *nim ) -{ - if( nim == NULL ) return ; - if( nim->fname != NULL ) free(nim->fname) ; - if( nim->iname != NULL ) free(nim->iname) ; - if( nim->data != NULL ) free(nim->data ) ; - (void)nifti_free_extensions( nim ) ; - free(nim) ; return ; -} - - -/*--------------------------------------------------------------------------*/ -/*! free the nifti extensions - - - If any edata pointer is set in the extension list, free() it. - - Free ext_list, if it is set. - - Clear num_ext and ext_list from nim. - - \return 0 on success, -1 on error - - \sa nifti_add_extension, nifti_copy_extensions -*//*------------------------------------------------------------------------*/ -int nifti_free_extensions( nifti_image *nim ) -{ - int c ; - if( nim == NULL ) return -1; - if( nim->num_ext > 0 && nim->ext_list ){ - for( c = 0; c < nim->num_ext; c++ ) - if ( nim->ext_list[c].edata ) free(nim->ext_list[c].edata); - free(nim->ext_list); - } - /* or if it is inconsistent, warn the user (if we are not in quiet mode) */ - else if ( (nim->num_ext > 0 || nim->ext_list != NULL) && (g_opts.debug > 0) ) - fprintf(stderr,"** warning: nifti extension num/ptr mismatch (%d,%p)\n", - nim->num_ext, (void *)nim->ext_list); - - if( g_opts.debug > 2 ) - fprintf(stderr,"+d free'd %d extension(s)\n", nim->num_ext); - - nim->num_ext = 0; - nim->ext_list = NULL; - - return 0; -} - - -/*--------------------------------------------------------------------------*/ -/*! Print to stdout some info about a nifti_image struct. -*//*------------------------------------------------------------------------*/ -void nifti_image_infodump( const nifti_image *nim ) -{ - char *str = nifti_image_to_ascii( nim ) ; - /* stdout -> stderr 2 Dec 2004 [rickr] */ - if( str != NULL ){ fputs(str,stderr) ; free(str) ; } - return ; -} - - -/*-------------------------------------------------------------------------- - * nifti_write_buffer just check for a null znzFile and call znzwrite - *--------------------------------------------------------------------------*/ -/*! \fn int64_t nifti_write_buffer(znzFile fp, void *buffer, int64_t numbytes) - \brief write numbytes of buffer to file, fp - - \param fp File pointer (from znzopen) to gzippable nifti datafile - \param buffer data buffer to be written - \param numbytes number of bytes in buffer to write - \return number of bytes successfully written -*/ -int64_t nifti_write_buffer(znzFile fp, const void *buffer, int64_t numbytes) -{ - /* Write all the image data at once (no swapping here) */ - int64_t ss; - if (znz_isnull(fp)){ - fprintf(stderr,"** ERROR: nifti_write_buffer: null file pointer\n"); - return 0; - } - ss = znzwrite( (const void*)buffer , 1 , numbytes , fp ) ; - return ss; -} - - -/*----------------------------------------------------------------------*/ -/*! write the nifti_image data to file (from nim->data or from NBL) - - If NBL is not NULL, write the data from that structure. Otherwise, - write it out from nim->data. No swapping is done here. - - \param fp : File pointer - \param nim : nifti_image corresponding to the data - \param NBL : optional source of write data (if NULL use nim->data) - - \return 0 on success, -1 on failure - - Note: the nifti_image byte_order is set as that of the current CPU. - This is because such a conversion was made to the data upon - reading, while byte_order was not set (so the programs would - know what format the data was on disk). Effectively, since - byte_order should match what is on disk, it should bet set to - that of the current CPU whenever new filenames are assigned. -*//*--------------------------------------------------------------------*/ -int nifti_write_all_data(znzFile fp, nifti_image * nim, - const nifti_brick_list * NBL) -{ - int64_t ss, bnum; - - if( !NBL ){ /* just write one buffer and get out of here */ - if( nim->data == NULL ){ - fprintf(stderr,"** NIFTI ERROR (NWAD): no image data to write\n"); - return -1; - } - - ss = nifti_write_buffer(fp,nim->data,nim->nbyper * nim->nvox); - if (ss < nim->nbyper * nim->nvox){ - fprintf(stderr, - "** NIFTI ERROR (NWAD): wrote only %" PRId64 " of %" PRId64 - " bytes to file\n", - ss, nim->nbyper * nim->nvox); - return -1; - } - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d wrote single image of %" PRId64 " bytes\n", ss); - } else { - if( ! NBL->bricks || NBL->nbricks <= 0 || NBL->bsize <= 0 ){ - fprintf(stderr,"** NIFTI error (NWAD): no brick data to write (%p,%" - PRId64 ",%" PRId64 ")\n", - (void *)NBL->bricks, NBL->nbricks, NBL->bsize); - return -1; - } - - for( bnum = 0; bnum < NBL->nbricks; bnum++ ){ - ss = nifti_write_buffer(fp, NBL->bricks[bnum], NBL->bsize); - if( ss < NBL->bsize ){ - fprintf(stderr, - "** NIFTI ERROR (NWAD): wrote only %" PRId64 " of %" PRId64 - " bytes of brick %" PRId64 " of %" PRId64 " to file\n", - ss, NBL->bsize, bnum+1, NBL->nbricks); - return -1; - } - } - if( g_opts.debug > 1 ) - fprintf(stderr,"+d wrote image of %" PRId64 - " brick(s), each of %" PRId64 " bytes\n", - NBL->nbricks, NBL->bsize); - } - - /* mark as being in this CPU byte order */ - nim->byteorder = nifti_short_order() ; - - return 0; -} - -/* return number of extensions written, or -1 on error */ -static int nifti_write_extensions(znzFile fp, nifti_image *nim) -{ - nifti1_extension * list; - char extdr[4] = { 0, 0, 0, 0 }; - int c, size, ok = 1; - - if( znz_isnull(fp) || !nim || nim->num_ext < 0 ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** nifti_write_extensions, bad params\n"); - return -1; - } - - /* if no extensions and user requests it, skip extender */ - if( g_opts.skip_blank_ext && (nim->num_ext == 0 || ! nim->ext_list ) ){ - if( g_opts.debug > 1 ) - fprintf(stderr,"-d no exts and skip_blank_ext set, " - "so skipping 4-byte extender\n"); - return 0; - } - - /* if invalid extension list, clear num_ext */ - if( ! valid_nifti_extensions(nim) ) nim->num_ext = 0; - - /* write out extender block */ - if( nim->num_ext > 0 ) extdr[0] = 1; - if( nifti_write_buffer(fp, extdr, 4) != 4 ){ - fprintf(stderr,"** NIFTI ERROR: failed to write extender\n"); - return -1; - } - - list = nim->ext_list; - for ( c = 0; c < nim->num_ext; c++ ){ - size = (int)nifti_write_buffer(fp, &list->esize, sizeof(int)); - ok = (size == (int)sizeof(int)); - if( ok ){ - size = (int)nifti_write_buffer(fp, &list->ecode, sizeof(int)); - ok = (size == (int)sizeof(int)); - } - if( ok ){ - size = (int)nifti_write_buffer(fp, list->edata, list->esize - 8); - ok = (size == list->esize - 8); - } - - if( !ok ){ - fprintf(stderr,"** NIFTI: failed while writing extension #%d\n",c); - return -1; - } else if ( g_opts.debug > 2 ) - fprintf(stderr,"+d wrote extension %d of %d bytes\n", c, size); - - list++; - } - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d wrote out %d extension(s)\n", nim->num_ext); - - return nim->num_ext; -} - - -/*----------------------------------------------------------------------*/ -/*! basic initialization of a nifti_image struct (to a 1x1x1 image) -*//*--------------------------------------------------------------------*/ -nifti_image* nifti_simple_init_nim(void) -{ - nifti_image *nim; - nifti_2_header nhdr; - int nbyper, swapsize; - - memset(&nhdr,0,sizeof(nhdr)) ; /* zero out header, to be safe */ - - nhdr.sizeof_hdr = sizeof(nhdr) ; - - nhdr.dim[0] = 3 ; - nhdr.dim[1] = 1 ; nhdr.dim[2] = 1 ; nhdr.dim[3] = 1 ; - nhdr.dim[4] = 0 ; - - nhdr.pixdim[0] = 0.0 ; - nhdr.pixdim[1] = 1.0 ; nhdr.pixdim[2] = 1.0 ; nhdr.pixdim[3] = 1.0 ; - - nhdr.datatype = DT_FLOAT32 ; - nifti_datatype_sizes( nhdr.datatype , &nbyper, &swapsize ); - nhdr.bitpix = 8 * nbyper ; - - memcpy(nhdr.magic, nifti2_magic, 8); /* init to single file */ - - nim = nifti_convert_n2hdr2nim(nhdr,NULL); - nim->fname = NULL; - nim->iname = NULL; - return nim; -} - - -/*----------------------------------------------------------------------*/ -/*! basic initialization of a nifti_2_header struct (with given dimensions) - - Return an allocated nifti_2_header struct, based on the given - dimensions and datatype. - - \param arg_dims : optional dim[8] array (default {3,1,1,1,0,0,0,0}) - \param arg_dtype : optional datatype (default DT_FLOAT32) - - \return pointer to allocated nifti_2_header struct -*//*--------------------------------------------------------------------*/ -nifti_2_header * nifti_make_new_n2_header(const int64_t arg_dims[], - int arg_dtype) -{ - nifti_2_header * nhdr; - const int64_t default_dims[8] = { 3, 1, 1, 1, 0, 0, 0, 0 }; - const int64_t * dim; /* either passed or default dims */ - int dtype; /* either passed or default dtype */ - int c, nbyper, swapsize; - - /* if arg_dims is passed, apply it */ - if( arg_dims ) dim = arg_dims; - else dim = default_dims; - - /* validate dim: if there is any problem, apply default_dims */ - if( dim[0] < 1 || dim[0] > 7 ) { - fprintf(stderr,"** nifti_simple_hdr_with_dims: bad dim[0]=%" PRId64 "\n", - dim[0]); - dim = default_dims; - } else { - for( c = 1; c <= dim[0]; c++ ) - if( dim[c] < 1 ) - { - fprintf(stderr, - "** nifti_simple_hdr_with_dims: bad dim[%d]=%" PRId64 "\n", - c, dim[c]); - dim = default_dims; - break; - } - } - - /* validate dtype, too */ - dtype = arg_dtype; - if( ! nifti_is_valid_datatype(dtype) ) { - fprintf(stderr,"** nifti_simple_hdr_with_dims: bad dtype %d\n",dtype); - dtype = DT_FLOAT32; - } - - /* now populate the header struct */ - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d make_new_n2_header, dim[0] = %" PRId64 - ", datatype = %d\n", - dim[0], dtype); - - nhdr = (nifti_2_header *)calloc(1,sizeof(nifti_2_header)); - if( !nhdr ){ - fprintf(stderr,"** NIFTI make_new_n2_header: failed to alloc hdr\n"); - return NULL; - } - - nhdr->sizeof_hdr = sizeof(nifti_2_header) ; - - /* init dim and pixdim */ - nhdr->dim[0] = dim[0]; - nhdr->pixdim[0] = 0.0; - for( c = 1; c <= dim[0]; c++ ) { - nhdr->dim[c] = dim[c]; - nhdr->pixdim[c] = 1.0; - } - - nhdr->datatype = dtype ; - nifti_datatype_sizes( nhdr->datatype , &nbyper, &swapsize ); - nhdr->bitpix = 8 * nbyper ; - - memcpy(nhdr->magic, nifti2_magic, 8); /* init to single file */ - - return nhdr; -} - - -/*----------------------------------------------------------------------*/ -/*! basic initialization of a nifti_1_header struct (with given dimensions) - - Return an allocated nifti_1_header struct, based on the given - dimensions and datatype. - - \param arg_dims : optional dim[8] array (default {3,1,1,1,0,0,0,0}) - \param arg_dtype : optional datatype (default DT_FLOAT32) - - \return pointer to allocated nifti_1_header struct -*//*--------------------------------------------------------------------*/ -nifti_1_header * nifti_make_new_n1_header(const int64_t arg_dims[], - int arg_dtype) -{ - nifti_1_header * nhdr; - const int64_t default_dims[8] = { 3, 1, 1, 1, 0, 0, 0, 0 }; - const int64_t * dim; /* either passed or default dims */ - int dtype; /* either passed or default dtype */ - int c, nbyper, swapsize; - - /* if arg_dims is passed, apply it */ - if( arg_dims ) dim = arg_dims; - else dim = default_dims; - - /* validate dim: if there is any problem, apply default_dims */ - if( dim[0] < 1 || dim[0] > 7 ) { - fprintf(stderr,"** nifti_simple_hdr_with_dims: bad dim[0]=%" PRId64 "\n", - dim[0]); - dim = default_dims; - } else { - for( c = 1; c <= dim[0]; c++ ) - if( dim[c] < 1 ) - { - fprintf(stderr, - "** nifti_simple_hdr_with_dims: bad dim[%d]=%" PRId64 "\n", c, dim[c]); - dim = default_dims; - break; - } - } - - /* validate dtype, too */ - dtype = arg_dtype; - if( ! nifti_is_valid_datatype(dtype) ) { - fprintf(stderr,"** nifti_simple_hdr_with_dims: bad dtype %d\n",dtype); - dtype = DT_FLOAT32; - } - - /* now populate the header struct */ - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d make_new_n1_header, dim[0] = %" PRId64 - ", datatype = %d\n", - dim[0], dtype); - - nhdr = (nifti_1_header *)calloc(1,sizeof(nifti_1_header)); - if( !nhdr ){ - fprintf(stderr,"** NIFTI make_new_n1_header: failed to alloc hdr\n"); - return NULL; - } - - nhdr->sizeof_hdr = sizeof(nifti_1_header) ; - nhdr->regular = 'r' ; /* for some stupid reason */ - - /* init dim and pixdim */ - nhdr->dim[0] = (int)dim[0]; /* rcr n2 - check dim sizes for nifti-1 */ - /* (verify vals are < 2^15) */ - nhdr->pixdim[0] = 0.0f; - for( c = 1; c <= dim[0]; c++ ) { - nhdr->dim[c] = (int)dim[c]; - nhdr->pixdim[c] = 1.0f; - } - - nhdr->datatype = dtype ; - nifti_datatype_sizes( nhdr->datatype , &nbyper, &swapsize ); - nhdr->bitpix = 8 * nbyper ; - - strcpy(nhdr->magic, "n+1"); /* init to single file */ - - return nhdr; -} - - -/*----------------------------------------------------------------------*/ -/*! basic creation of a nifti_image struct - - Create a nifti_image from the given dimensions and data type. - Optinally, allocate zero-filled data. - - \param dims : optional dim[8] (default {3,1,1,1,0,0,0,0}) - \param datatype : optional datatype (default DT_FLOAT32) - \param data_fill : if flag is set, allocate zero-filled data for image - - \return pointer to allocated nifti_image struct -*//*--------------------------------------------------------------------*/ -nifti_image * nifti_make_new_nim(const int64_t dims[], int datatype, - int data_fill) -{ - nifti_image * nim; - nifti_2_header * nhdr; - - nhdr = nifti_make_new_n2_header(dims, datatype); - if( !nhdr ) return NULL; /* error already printed */ - - nim = nifti_convert_n2hdr2nim(*nhdr,NULL); - free(nhdr); /* in any case, we are done with this */ - if( !nim ){ - fprintf(stderr,"** NMNN: nifti_convert_n2hdr2nim failure\n"); - return NULL; - } - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d nifti_make_new_nim, data_fill = %d\n",data_fill); - - if( data_fill ) { - nim->data = calloc(nim->nvox, nim->nbyper); - - /* if we cannot allocate data, take ball and go home */ - if( !nim->data ) { - fprintf(stderr,"** NIFTI NMNN: failed to alloc %" PRId64 - " bytes for data\n", nim->nvox*nim->nbyper); - nifti_image_free(nim); - nim = NULL; - } - } - - return nim; -} - -#undef N_CHECK_2BYTE_VAL -#define N_CHECK_2BYTE_VAL(fn) do { if( ! NIFTI_IS_16_BIT_INT(nim->fn) ) { \ - fprintf(stderr,"** nim->%s = %" PRId64 \ - " does not fit into NIFTI-1 header\n", \ - #fn, (int64_t)nim->fn); return 1; } } while(0) - - -/*----------------------------------------------------------------------*/ -/*! convert a nifti_image structure to a nifti_1_header struct - - No allocation is done, this should be used via structure copy. - As in: - 
-    nifti_1_header my_header;
-    my_header = nifti_convert_nim2n1hdr(my_nim_pointer);
-
-*//*--------------------------------------------------------------------*/ -int nifti_convert_nim2n1hdr(const nifti_image * nim, nifti_1_header * hdr) -{ - nifti_1_header nhdr; - - if( !hdr ) { - fprintf(stderr,"** nifti_CN2N1hdr: no hdr to fill\n"); - return 1; - } - - memset(&nhdr,0,sizeof(nhdr)) ; /* zero out header, to be safe */ - - - /**- load the ANALYZE-7.5 generic parts of the header struct */ - - nhdr.sizeof_hdr = sizeof(nhdr) ; - nhdr.regular = 'r' ; /* for some stupid reason */ - - N_CHECK_2BYTE_VAL(ndim); - N_CHECK_2BYTE_VAL(nx); - N_CHECK_2BYTE_VAL(ny); - N_CHECK_2BYTE_VAL(nz); - N_CHECK_2BYTE_VAL(nt); - N_CHECK_2BYTE_VAL(nu); - N_CHECK_2BYTE_VAL(nv); - N_CHECK_2BYTE_VAL(nw); - N_CHECK_2BYTE_VAL(datatype); - N_CHECK_2BYTE_VAL(nbyper); - - nhdr.dim[0] = nim->ndim ; - nhdr.dim[1] = nim->nx ; nhdr.dim[2] = nim->ny ; nhdr.dim[3] = nim->nz ; - nhdr.dim[4] = nim->nt ; nhdr.dim[5] = nim->nu ; nhdr.dim[6] = nim->nv ; - nhdr.dim[7] = nim->nw ; - - nhdr.pixdim[0] = 0.0f ; - nhdr.pixdim[1] = nim->dx ; nhdr.pixdim[2] = nim->dy ; - nhdr.pixdim[3] = nim->dz ; nhdr.pixdim[4] = nim->dt ; - nhdr.pixdim[5] = nim->du ; nhdr.pixdim[6] = nim->dv ; - nhdr.pixdim[7] = nim->dw ; - - nhdr.datatype = nim->datatype ; - nhdr.bitpix = 8 * nim->nbyper ; - - if( nim->cal_max > nim->cal_min ){ - nhdr.cal_max = nim->cal_max ; - nhdr.cal_min = nim->cal_min ; - } - - if( nim->scl_slope != 0.0 ){ - nhdr.scl_slope = nim->scl_slope ; - nhdr.scl_inter = nim->scl_inter ; - } - - if( nim->descrip[0] != '\0' ){ - memcpy(nhdr.descrip ,nim->descrip ,79) ; nhdr.descrip[79] = '\0' ; - } - if( nim->aux_file[0] != '\0' ){ - memcpy(nhdr.aux_file ,nim->aux_file ,23) ; nhdr.aux_file[23] = '\0' ; - } - - /**- Load NIFTI specific stuff into the header */ - - if( nim->nifti_type > NIFTI_FTYPE_ANALYZE ){ /* then not ANALYZE */ - - if( nim->nifti_type == NIFTI_FTYPE_NIFTI1_1 ) strcpy(nhdr.magic,"n+1") ; - else strcpy(nhdr.magic,"ni1") ; - - nhdr.pixdim[1] = (float)fabs(nhdr.pixdim[1]) ; - nhdr.pixdim[2] = (float)fabs(nhdr.pixdim[2]) ; - nhdr.pixdim[3] = (float)fabs(nhdr.pixdim[3]) ; - nhdr.pixdim[4] = (float)fabs(nhdr.pixdim[4]) ; - nhdr.pixdim[5] = (float)fabs(nhdr.pixdim[5]) ; - nhdr.pixdim[6] = (float)fabs(nhdr.pixdim[6]) ; - nhdr.pixdim[7] = (float)fabs(nhdr.pixdim[7]) ; - - N_CHECK_2BYTE_VAL(intent_code); - N_CHECK_2BYTE_VAL(qform_code); - N_CHECK_2BYTE_VAL(sform_code); - - nhdr.intent_code = nim->intent_code ; - nhdr.intent_p1 = nim->intent_p1 ; - nhdr.intent_p2 = nim->intent_p2 ; - nhdr.intent_p3 = nim->intent_p3 ; - if( nim->intent_name[0] != '\0' ){ - memcpy(nhdr.intent_name,nim->intent_name,15) ; - nhdr.intent_name[15] = '\0' ; - } - - nhdr.vox_offset = (float) nim->iname_offset ; - nhdr.xyzt_units = SPACE_TIME_TO_XYZT( nim->xyz_units, nim->time_units ) ; - nhdr.toffset = nim->toffset ; - - if( nim->qform_code > 0 ){ - nhdr.qform_code = nim->qform_code ; - nhdr.quatern_b = nim->quatern_b ; - nhdr.quatern_c = nim->quatern_c ; - nhdr.quatern_d = nim->quatern_d ; - nhdr.qoffset_x = nim->qoffset_x ; - nhdr.qoffset_y = nim->qoffset_y ; - nhdr.qoffset_z = nim->qoffset_z ; - nhdr.pixdim[0] = (nim->qfac >= 0.0) ? 1.0f : -1.0f ; - } - - if( nim->sform_code > 0 ){ - nhdr.sform_code = nim->sform_code ; - nhdr.srow_x[0] = nim->sto_xyz.m[0][0] ; - nhdr.srow_x[1] = nim->sto_xyz.m[0][1] ; - nhdr.srow_x[2] = nim->sto_xyz.m[0][2] ; - nhdr.srow_x[3] = nim->sto_xyz.m[0][3] ; - nhdr.srow_y[0] = nim->sto_xyz.m[1][0] ; - nhdr.srow_y[1] = nim->sto_xyz.m[1][1] ; - nhdr.srow_y[2] = nim->sto_xyz.m[1][2] ; - nhdr.srow_y[3] = nim->sto_xyz.m[1][3] ; - nhdr.srow_z[0] = nim->sto_xyz.m[2][0] ; - nhdr.srow_z[1] = nim->sto_xyz.m[2][1] ; - nhdr.srow_z[2] = nim->sto_xyz.m[2][2] ; - nhdr.srow_z[3] = nim->sto_xyz.m[2][3] ; - } - - N_CHECK_2BYTE_VAL(sform_code); - N_CHECK_2BYTE_VAL(slice_start); - N_CHECK_2BYTE_VAL(slice_end); - - nhdr.dim_info = FPS_INTO_DIM_INFO( nim->freq_dim , - nim->phase_dim , nim->slice_dim ) ; - nhdr.slice_code = nim->slice_code ; - nhdr.slice_start = nim->slice_start ; - nhdr.slice_end = nim->slice_end ; - nhdr.slice_duration = nim->slice_duration ; - } - - memcpy(hdr, &nhdr, sizeof(nhdr)); - - return 0; -} - - -/*----------------------------------------------------------------------*/ -/*! convert a nifti_image structure to a nifti_2_header struct - - No allocation is done, this should be used via structure copy. - As in: - 
-    nifti_2_header my_header;
-    my_header = nifti_convert_nim2n2hdr(my_nim_pointer);
-
-*//*--------------------------------------------------------------------*/ -int nifti_convert_nim2n2hdr(const nifti_image * nim, nifti_2_header * hdr) -{ - nifti_2_header nhdr; - - if( !hdr ) { - fprintf(stderr,"** nifti_CN2N2hdr: no hdr to fill\n"); - return 1; - } - - memset(&nhdr,0,sizeof(nhdr)) ; /* zero out header, to be safe */ - - - /**- load the ANALYZE-7.5 generic parts of the header struct */ - - nhdr.sizeof_hdr = sizeof(nhdr) ; - if( nim->nifti_type == NIFTI_FTYPE_NIFTI2_1 ) strcpy(nhdr.magic,"n+2") ; - else strcpy(nhdr.magic,"ni2") ; - - nhdr.datatype = nim->datatype ; - nhdr.bitpix = 8 * nim->nbyper ; - - nhdr.dim[0] = nim->ndim ; - nhdr.dim[1] = nim->nx ; nhdr.dim[2] = nim->ny ; nhdr.dim[3] = nim->nz ; - nhdr.dim[4] = nim->nt ; nhdr.dim[5] = nim->nu ; nhdr.dim[6] = nim->nv ; - nhdr.dim[7] = nim->nw ; - - nhdr.intent_p1 = nim->intent_p1 ; - nhdr.intent_p2 = nim->intent_p2 ; - nhdr.intent_p3 = nim->intent_p3 ; - - nhdr.pixdim[0] = 0.0 ; - nhdr.pixdim[1] = fabs(nim->dx) ; nhdr.pixdim[2] = fabs(nim->dy) ; - nhdr.pixdim[3] = fabs(nim->dz) ; nhdr.pixdim[4] = fabs(nim->dt) ; - nhdr.pixdim[5] = fabs(nim->du) ; nhdr.pixdim[6] = fabs(nim->dv) ; - nhdr.pixdim[7] = fabs(nim->dw) ; - - nhdr.vox_offset = nim->iname_offset ; - - nhdr.scl_slope = nim->scl_slope ; - nhdr.scl_inter = nim->scl_inter ; - - nhdr.cal_max = nim->cal_max ; - nhdr.cal_min = nim->cal_min ; - - nhdr.slice_duration = nim->slice_duration ; - nhdr.toffset = nim->toffset ; - nhdr.slice_start = nim->slice_start ; - nhdr.slice_end = nim->slice_end ; - - if( nim->descrip[0] != '\0' ){ - memcpy(nhdr.descrip ,nim->descrip ,79) ; nhdr.descrip[79] = '\0' ; - } - if( nim->aux_file[0] != '\0' ){ - memcpy(nhdr.aux_file ,nim->aux_file ,23) ; nhdr.aux_file[23] = '\0' ; - } - - if( nim->qform_code > 0 ){ - nhdr.qform_code = nim->qform_code ; - nhdr.quatern_b = nim->quatern_b ; - nhdr.quatern_c = nim->quatern_c ; - nhdr.quatern_d = nim->quatern_d ; - nhdr.qoffset_x = nim->qoffset_x ; - nhdr.qoffset_y = nim->qoffset_y ; - nhdr.qoffset_z = nim->qoffset_z ; - nhdr.pixdim[0] = (nim->qfac >= 0.0) ? 1.0f : -1.0f ; - } - - if( nim->sform_code > 0 ){ - nhdr.sform_code = nim->sform_code ; - nhdr.srow_x[0] = nim->sto_xyz.m[0][0] ; - nhdr.srow_x[1] = nim->sto_xyz.m[0][1] ; - nhdr.srow_x[2] = nim->sto_xyz.m[0][2] ; - nhdr.srow_x[3] = nim->sto_xyz.m[0][3] ; - nhdr.srow_y[0] = nim->sto_xyz.m[1][0] ; - nhdr.srow_y[1] = nim->sto_xyz.m[1][1] ; - nhdr.srow_y[2] = nim->sto_xyz.m[1][2] ; - nhdr.srow_y[3] = nim->sto_xyz.m[1][3] ; - nhdr.srow_z[0] = nim->sto_xyz.m[2][0] ; - nhdr.srow_z[1] = nim->sto_xyz.m[2][1] ; - nhdr.srow_z[2] = nim->sto_xyz.m[2][2] ; - nhdr.srow_z[3] = nim->sto_xyz.m[2][3] ; - } - - nhdr.slice_code = nim->slice_code ; - nhdr.xyzt_units = SPACE_TIME_TO_XYZT( nim->xyz_units, nim->time_units ) ; - nhdr.intent_code = nim->intent_code ; - if( nim->intent_name[0] != '\0' ){ - memcpy(nhdr.intent_name,nim->intent_name,15) ; - nhdr.intent_name[15] = '\0' ; - } - - nhdr.dim_info = FPS_INTO_DIM_INFO( nim->freq_dim , - nim->phase_dim , nim->slice_dim ) ; - - nhdr.unused_str[0] = '\0' ; /* not needed, but complete */ - - memcpy(hdr, &nhdr, sizeof(nhdr)); - - return 0; -} - - -/*----------------------------------------------------------------------*/ -/*! \fn int nifti_copy_extensions(nifti_image * nim_dest, nifti_image * nim_src) - \brief copy the nifti1_extension list from src to dest - - Duplicate the list of nifti1_extensions. The dest structure must - be clear of extensions. - \return 0 on success, -1 on failure - - \sa nifti_add_extension, nifti_free_extensions -*/ -int nifti_copy_extensions(nifti_image * nim_dest, const nifti_image * nim_src) -{ - char * data; - int64_t bytes; - int c, size, old_size; - - if( nim_dest->num_ext > 0 || nim_dest->ext_list != NULL ){ - fprintf(stderr,"** NIFTI: will not copy over existing extensions\n"); - return -1; - } - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d duplicating %d extension(s)\n", nim_src->num_ext); - - if( nim_src->num_ext <= 0 ) return 0; - - bytes = nim_src->num_ext * sizeof(nifti1_extension); /* I'm lazy */ - nim_dest->ext_list = (nifti1_extension *)malloc(bytes); - if( !nim_dest->ext_list ){ - fprintf(stderr,"** failed to allocate %d nifti1_extension structs\n", - nim_src->num_ext); - return -1; - } - - /* copy the extension data */ - nim_dest->num_ext = 0; - for( c = 0; c < nim_src->num_ext; c++ ){ - size = old_size = nim_src->ext_list[c].esize; - if( size & 0xf ) size = (size + 0xf) & ~0xf; /* make multiple of 16 */ - if( g_opts.debug > 2 ) - fprintf(stderr,"+d dup'ing ext #%d of size %d (from size %d)\n", - c, size, old_size); - /* data length is size-8, as esize includes space for esize and ecode */ - data = (char *)calloc(size-8,sizeof(char)); /* maybe size > old */ - if( !data ){ - fprintf(stderr,"** NIFTI: failed to alloc %d bytes for extention\n", - size); - if( c == 0 ) { free(nim_dest->ext_list); nim_dest->ext_list = NULL; } - /* otherwise, keep what we have (a.o.t. deleting them all) */ - return -1; - } - /* finally, fill the new structure */ - nim_dest->ext_list[c].esize = size; - nim_dest->ext_list[c].ecode = nim_src->ext_list[c].ecode; - nim_dest->ext_list[c].edata = data; - memcpy(data, nim_src->ext_list[c].edata, old_size-8); - - nim_dest->num_ext++; - } - - return 0; -} - - -/*----------------------------------------------------------------------*/ -/*! compute the total size of all extensions - - \return the total of all esize fields - - Note that each esize includes 4 bytes for ecode, 4 bytes for esize, - and the bytes used for the data. Each esize also needs to be a - multiple of 16, so it may be greater than the sum of its 3 parts. -*//*--------------------------------------------------------------------*/ -int nifti_extension_size(nifti_image *nim) -{ - int c, size = 0; - - if( !nim || nim->num_ext <= 0 ) return 0; - - if( g_opts.debug > 2 ) fprintf(stderr,"-d ext sizes:"); - - for ( c = 0; c < nim->num_ext; c++ ){ - size += nim->ext_list[c].esize; - if( g_opts.debug > 2 ) fprintf(stderr," %d",nim->ext_list[c].esize); - } - - if( g_opts.debug > 2 ) fprintf(stderr," (total = %d)\n",size); - - return size; -} - - -/*----------------------------------------------------------------------*/ -/*! set the nifti_image iname_offset field, based on nifti_type - - - if writing to 2 files, set offset to 0 - - if writing to a single NIFTI-1 file, set the offset to - 352 + total extension size, then align to 16-byte boundary - - if writing an ASCII header, set offset to -1 -*//*--------------------------------------------------------------------*/ -void nifti_set_iname_offset(nifti_image *nim) -{ - int64_t offset; - - switch( nim->nifti_type ){ - - default: /* writing into 2 files */ - /* we only write files with 0 offset in the 2 file format */ - nim->iname_offset = 0 ; - break ; - - /* NIFTI-1 single binary file - always update */ - case NIFTI_FTYPE_NIFTI1_1: - offset = nifti_extension_size(nim)+sizeof(nifti_1_header)+4; - /* be sure offset is aligned to a 16 byte boundary */ - if ( ( offset % 16 ) != 0 ) offset = ((offset + 0xf) & ~0xf); - if( nim->iname_offset != offset ){ - if( g_opts.debug > 1 ) - fprintf(stderr,"+d changing offset from %" PRId64 " to %" PRId64 - "\n", nim->iname_offset, offset); - nim->iname_offset = offset; - } - break ; - - /* non-standard case: NIFTI-1 ASCII header + binary data (single file) */ - case NIFTI_FTYPE_ASCII: - nim->iname_offset = -1 ; /* compute offset from filesize */ - break ; - } -} - - -/*----------------------------------------------------------------------*/ -/*! write the nifti_image dataset to disk, optionally including data - - This is just a front-end for nifti_image_write_hdr_img2. - - \param nim nifti_image to write to disk - \param write_data write options (see nifti_image_write_hdr_img2) - \param opts file open options ("wb" from nifti_image_write) - - \sa nifti_image_write, nifti_image_write_hdr_img2, nifti_image_free, - nifti_set_filenames -*//*--------------------------------------------------------------------*/ -znzFile nifti_image_write_hdr_img( nifti_image *nim , int write_data , - const char* opts ) -{ - return nifti_image_write_hdr_img2(nim,write_data,opts,NULL,NULL); -} - - -#undef ERREX -#define ERREX(msg) \ - do{ fprintf(stderr,"** ERROR: nifti_image_write_hdr_img: %s\n",(msg)) ; \ - return fp ; } while(0) - - -/* ----------------------------------------------------------------------*/ -/*! This writes the header (and optionally the image data) to file - * - * If the image data file is left open it returns a valid znzFile handle. - * It also uses imgfile as the open image file is not null, and modifies - * it inside. - * - * \param nim nifti_image to write to disk - * \param write_opts flags whether to write data and/or close file (see below) - * \param opts file-open options, probably "wb" from nifti_image_write() - * \param imgfile optional open znzFile struct, for writing image data - (may be NULL) - * \param NBL optional nifti_brick_list, containing the image data - (may be NULL) - * - * Values for write_opts mode are based on two binary flags - * ( 0/1 for no-write/write data, and 0/2 for close/leave-open files ) : - * - 0 = do not write data and close (do not open data file) - * - 1 = write data and close - * - 2 = do not write data and leave data file open - * - 3 = write data and leave data file open - * - * \sa nifti_image_write, nifti_image_write_hdr_img, nifti_image_free, - * nifti_set_filenames -*//*---------------------------------------------------------------------*/ -znzFile nifti_image_write_hdr_img2(nifti_image *nim, int write_opts, - const char * opts, znzFile imgfile, const nifti_brick_list * NBL) -{ - nifti_1_header n1hdr ; - nifti_2_header n2hdr ; - znzFile fp=NULL; - int64_t ss ; - int write_data, leave_open; - int nver=1, hsize=(int)sizeof(nifti_1_header); /* 5 Aug 2015 */ - char func[] = { "nifti_image_write_hdr_img2" }; - - write_data = write_opts & 1; /* just separate the bits now */ - leave_open = write_opts & 2; - - if( ! nim ) ERREX("NULL input") ; - if( ! nifti_validfilename(nim->fname) ) ERREX("bad fname input") ; - if( write_data && ! nim->data && ! NBL ) ERREX("no image data") ; - - if( write_data && NBL && ! nifti_NBL_matches_nim(nim, NBL) ) - ERREX("NBL does not match nim"); - - nifti_set_iname_offset(nim); - - if( g_opts.debug > 1 ){ - fprintf(stderr,"-d writing nifti file '%s'...\n", nim->fname); - if( g_opts.debug > 2 ) - fprintf(stderr,"-d nifti type %d, offset %" PRId64 "\n", - nim->nifti_type, nim->iname_offset); - } - - if( nim->nifti_type == NIFTI_FTYPE_ASCII ) /* non-standard case */ - return nifti_write_ascii_image(nim,NBL,opts,write_data,leave_open); - - /* create the nifti header struct 5 Aug, 2015 [rickr] - - default is NIFTI-1 (option?) - - if that fails try NIFTI-2 - */ - if( nifti_convert_nim2n1hdr(nim, &n1hdr) ) { - if( nifti_convert_nim2n2hdr(nim, &n2hdr) ) return NULL; - fprintf(stderr,"+d writing %s as NIFTI-2, instead...\n", nim->fname); - nver = 2; /* we will write NIFTI-2 */ - hsize = (int)sizeof(nifti_2_header); - } - - /* if writing to 2 files, make sure iname is set and different from fname */ - if( nim->nifti_type != NIFTI_FTYPE_NIFTI1_1 ){ - if( nim->iname && strcmp(nim->iname,nim->fname) == 0 ){ - free(nim->iname) ; nim->iname = NULL ; - } - if( nim->iname == NULL ){ /* then make a new one */ - nim->iname = nifti_makeimgname(nim->fname,nim->nifti_type,0,0); - if( nim->iname == NULL ) return NULL; - } - } - - /* if we have an imgfile and will write the header there, use it */ - if( ! znz_isnull(imgfile) && nim->nifti_type == NIFTI_FTYPE_NIFTI1_1 ){ - if( g_opts.debug > 2 ) fprintf(stderr,"+d using passed file for hdr\n"); - fp = imgfile; - } - else { - if( g_opts.debug > 2 ) - fprintf(stderr,"+d opening output file %s [%s]\n",nim->fname,opts); - fp = znzopen( nim->fname , opts , nifti_is_gzfile(nim->fname) ) ; - if( znz_isnull(fp) ){ - LNI_FERR(func,"cannot open output file",nim->fname); - return fp; - } - } - - /* write the header and extensions */ - - if( nver == 2 ) ss = znzwrite(&n2hdr , 1 , hsize , fp); /* write header */ - else ss = znzwrite(&n1hdr , 1 , hsize , fp); /* write header */ - - if( ss < hsize ){ - LNI_FERR(func,"bad header write to output file",nim->fname); - znzclose(fp); return fp; - } - - /* partial file exists, and errors have been printed, so ignore return */ - if( nim->nifti_type != NIFTI_FTYPE_ANALYZE ) - (void)nifti_write_extensions(fp,nim); - - /* if the header is all we want, we are done */ - if( ! write_data && ! leave_open ){ - if( g_opts.debug > 2 ) fprintf(stderr,"-d header is all we want: done\n"); - znzclose(fp); return(fp); - } - - if( nim->nifti_type != NIFTI_FTYPE_NIFTI1_1 ){ /* get a new file pointer */ - znzclose(fp); /* first, close header file */ - if( ! znz_isnull(imgfile) ){ - if(g_opts.debug > 2) fprintf(stderr,"+d using passed file for img\n"); - fp = imgfile; - } - else { - if( g_opts.debug > 2 ) - fprintf(stderr,"+d opening img file '%s'\n", nim->iname); - fp = znzopen( nim->iname , opts , nifti_is_gzfile(nim->iname) ) ; - if( znz_isnull(fp) ) ERREX("cannot open image file") ; - } - } - - znzseek(fp, nim->iname_offset, SEEK_SET); /* in any case, seek to offset */ - - if( write_data ) nifti_write_all_data(fp,nim,NBL); - if( ! leave_open ) znzclose(fp); - - return fp; -} - - -/*----------------------------------------------------------------------*/ -/*! write a nifti_image to disk in ASCII format -*//*--------------------------------------------------------------------*/ -znzFile nifti_write_ascii_image(nifti_image *nim, const nifti_brick_list * NBL, - const char *opts, int write_data, int leave_open) -{ - znzFile fp; - char * hstr; - - hstr = nifti_image_to_ascii( nim ) ; /* get header in ASCII form */ - if( ! hstr ){ fprintf(stderr,"** failed image_to_ascii()\n"); return NULL; } - - fp = znzopen( nim->fname , opts , nifti_is_gzfile(nim->fname) ) ; - if( znz_isnull(fp) ){ - free(hstr); - fprintf(stderr,"** NIFTI: failed to open '%s' for ascii write\n", - nim->fname); - return fp; - } - - znzputs(hstr,fp); /* header */ - nifti_write_extensions(fp,nim); /* extensions */ - - if ( write_data ) { nifti_write_all_data(fp,nim,NBL); } /* data */ - if ( ! leave_open ) { znzclose(fp); } - free(hstr); - return fp; /* returned but may be closed */ -} - - -/*--------------------------------------------------------------------------*/ -/*! Write a nifti_image to disk. - - Since data is properly byte-swapped upon reading, it is assumed - to be in the byte-order of the current CPU at write time. Thus, - nim->byte_order should match that of the current CPU. Note that - the nifti_set_filenames() function takes the flag, set_byte_order. - - The following fields of nim affect how the output appears: - - nifti_type = 0 ==> ANALYZE-7.5 format file pair will be written - - nifti_type = 1 ==> NIFTI-1 format single file will be written - (data offset will be 352+extensions) - - nifti_type = 2 ==> NIFTI_1 format file pair will be written - - nifti_type = 3 ==> NIFTI_1 ASCII single file will be written - - fname is the name of the output file (header or header+data) - - if a file pair is being written, iname is the name of the data file - - existing files WILL be overwritten with extreme prejudice - - if qform_code > 0, the quatern_*, qoffset_*, and qfac fields determine - the qform output, NOT the qto_xyz matrix; if you want to compute these - fields from the qto_xyz matrix, you can use the utility function - nifti_mat44_to_quatern() - - \sa nifti_image_write_bricks, nifti_image_free, nifti_set_filenames, - nifti_image_write_hdr_img -*//*------------------------------------------------------------------------*/ -void nifti_image_write( nifti_image *nim ) -{ - znzFile fp = nifti_image_write_hdr_img(nim,1,"wb"); - if( fp ){ - if( g_opts.debug > 2 ) fprintf(stderr,"-d niw: done with znzFile\n"); - free(fp); - } - if( g_opts.debug > 1 ) fprintf(stderr,"-d nifti_image_write: done\n"); -} - - -/*----------------------------------------------------------------------*/ -/*! similar to nifti_image_write, but data is in NBL struct, not nim->data - - \sa nifti_image_write, nifti_image_free, nifti_set_filenames, nifti_free_NBL -*//*--------------------------------------------------------------------*/ -void nifti_image_write_bricks( nifti_image *nim, const nifti_brick_list * NBL ) -{ - znzFile fp = nifti_image_write_hdr_img2(nim,1,"wb",NULL,NBL); - if( fp ){ - if( g_opts.debug > 2 ) fprintf(stderr,"-d niwb: done with znzFile\n"); - free(fp); - } - if( g_opts.debug > 1 ) fprintf(stderr,"-d niwb: done writing bricks\n"); -} - - -/*----------------------------------------------------------------------*/ -/*! copy the nifti_image structure, without data - - Duplicate the structure, including fname, iname and extensions. - Leave the data pointer as NULL. -*//*--------------------------------------------------------------------*/ -nifti_image * nifti_copy_nim_info(const nifti_image * src) -{ - nifti_image *dest; - dest = (nifti_image *)calloc(1,sizeof(nifti_image)); - if( !dest ){ - fprintf(stderr,"** NCNI: failed to alloc nifti_image\n"); - return NULL; - } - memcpy(dest, src, sizeof(nifti_image)); - if( src->fname ) dest->fname = nifti_strdup(src->fname); - if( src->iname ) dest->iname = nifti_strdup(src->iname); - dest->num_ext = 0; - dest->ext_list = NULL; - /* errors will be printed in NCE(), continue in either case */ - (void)nifti_copy_extensions(dest, src); - - dest->data = NULL; - - return dest; -} - - -/*------------------------------------------------------------------------*/ -/* Un-escape a C string in place -- that is, convert XML escape sequences - back into their characters. (This can be done in place since the - replacement is always smaller than the input.) Escapes recognized are: - - < -> < - - > -> > - - " -> " - - ' -> ' - - & -> & - Also replace CR LF pair (Microsoft), or CR alone (Macintosh) with - LF (Unix), per the XML standard. - Return value is number of replacements made (if you care). ---------------------------------------------------------------------------*/ - -#undef CR -#undef LF -#define CR 0x0D -#define LF 0x0A - -static int unescape_string( char *str ) -{ - int ii,jj , nn,ll ; - - if( str == NULL ) return 0 ; /* no string? */ - ll = (int)strlen(str) ; if( ll == 0 ) return 0 ; - - /* scan for escapes: &something; */ - - for( ii=jj=nn=0 ; ii': lout += 4 ; break ; /* replace '<' with "<" */ - - case '"' : - case '\'': lout += 6 ; break ; /* replace '"' with """ */ - - case CR: - case LF: lout += 6 ; break ; /* replace CR with " " - LF with " " */ - - default: lout++ ; break ; /* copy all other chars */ - } - } - out = (char *)calloc(1,lout) ; /* allocate output string */ - if( !out ){ - fprintf(stderr,"** NIFTI escapize_string: failed to alloc %d bytes\n", - lout); - return NULL; - } - out[0] = '\'' ; /* opening quote mark */ - for( ii=0,jj=1 ; ii < lstr ; ii++ ){ - switch( str[ii] ){ - default: out[jj++] = str[ii] ; break ; /* normal characters */ - - case '&': memcpy(out+jj,"&",5) ; jj+=5 ; break ; - - case '<': memcpy(out+jj,"<",4) ; jj+=4 ; break ; - case '>': memcpy(out+jj,">",4) ; jj+=4 ; break ; - - case '"' : memcpy(out+jj,""",6) ; jj+=6 ; break ; - - case '\'': memcpy(out+jj,"'",6) ; jj+=6 ; break ; - - case CR: memcpy(out+jj," ",6) ; jj+=6 ; break ; - case LF: memcpy(out+jj," ",6) ; jj+=6 ; break ; - } - } - out[jj++] = '\'' ; /* closing quote mark */ - out[jj] = '\0' ; /* terminate the string */ - return out ; -} - -/*---------------------------------------------------------------------------*/ -/*! Dump the information in a NIFTI image header to an XML-ish ASCII string - that can later be converted back into a NIFTI header in - nifti_image_from_ascii(). - - The resulting string can be free()-ed when you are done with it. -*//*-------------------------------------------------------------------------*/ -char *nifti_image_to_ascii( const nifti_image *nim ) -{ - char *buf , *ebuf ; int nbuf ; - - if( nim == NULL ) return NULL ; /* stupid caller */ - - buf = (char *)calloc(1,65534); nbuf = 0; /* longer than needed, to be safe */ - if( !buf ){ - fprintf(stderr,"** NIFTI NITA: failed to alloc %d bytes\n",65534); - return NULL; - } - - sprintf( buf , "nifti_type == NIFTI_FTYPE_NIFTI1_1) ? "NIFTI-1+" - :(nim->nifti_type == NIFTI_FTYPE_NIFTI1_2) ? "NIFTI-1" - :(nim->nifti_type == NIFTI_FTYPE_ASCII ) ? "NIFTI-1A" - : "ANALYZE-7.5" ) ; - - /** Strings that we don't control (filenames, etc.) that might - contain "weird" characters (like quotes) are "escaped": - - A few special characters are replaced by XML-style escapes, using - the function escapize_string(). - - On input, function unescape_string() reverses this process. - - The result is that the NIFTI ASCII-format header is XML-compliant. */ - - ebuf = escapize_string(nim->fname) ; - sprintf( buf+strlen(buf) , " header_filename = %s\n",ebuf); free(ebuf); - - ebuf = escapize_string(nim->iname) ; - sprintf( buf+strlen(buf) , " image_filename = %s\n", ebuf); free(ebuf); - - sprintf( buf+strlen(buf) , " image_offset = '%" PRId64 "'\n" , - nim->iname_offset ); - - sprintf( buf+strlen(buf), " ndim = '%" PRId64 "'\n",nim->ndim); - sprintf( buf+strlen(buf), " nx = '%" PRId64 "'\n", nim->nx ); - if( nim->ndim > 1 ) - sprintf( buf+strlen(buf), " ny = '%" PRId64 "'\n", nim->ny ); - if( nim->ndim > 2 ) - sprintf( buf+strlen(buf), " nz = '%" PRId64 "'\n", nim->nz ); - if( nim->ndim > 3 ) - sprintf( buf+strlen(buf), " nt = '%" PRId64 "'\n", nim->nt ); - if( nim->ndim > 4 ) - sprintf( buf+strlen(buf), " nu = '%" PRId64 "'\n", nim->nu ); - if( nim->ndim > 5 ) - sprintf( buf+strlen(buf), " nv = '%" PRId64 "'\n", nim->nv ); - if( nim->ndim > 6 ) - sprintf( buf+strlen(buf), " nw = '%" PRId64 "'\n", nim->nw ); - - sprintf( buf+strlen(buf), " dx = '%g'\n", nim->dx ); - if( nim->ndim > 1 ) sprintf( buf+strlen(buf), " dy = '%g'\n", nim->dy ); - if( nim->ndim > 2 ) sprintf( buf+strlen(buf), " dz = '%g'\n", nim->dz ); - if( nim->ndim > 3 ) sprintf( buf+strlen(buf), " dt = '%g'\n", nim->dt ); - if( nim->ndim > 4 ) sprintf( buf+strlen(buf), " du = '%g'\n", nim->du ); - if( nim->ndim > 5 ) sprintf( buf+strlen(buf), " dv = '%g'\n", nim->dv ); - if( nim->ndim > 6 ) sprintf( buf+strlen(buf), " dw = '%g'\n", nim->dw ); - - sprintf( buf+strlen(buf) , " datatype = '%d'\n" , nim->datatype ) ; - sprintf( buf+strlen(buf) , " datatype_name = '%s'\n" , - nifti_datatype_string(nim->datatype) ) ; - - sprintf( buf+strlen(buf) , " nvox = '%" PRId64 "'\n" , nim->nvox ) ; - sprintf( buf+strlen(buf) , " nbyper = '%d'\n" , nim->nbyper ) ; - - sprintf( buf+strlen(buf) , " byteorder = '%s'\n" , - (nim->byteorder==MSB_FIRST) ? "MSB_FIRST" : "LSB_FIRST" ) ; - - if( nim->cal_min < nim->cal_max ){ - sprintf( buf+strlen(buf) , " cal_min = '%g'\n", nim->cal_min ) ; - sprintf( buf+strlen(buf) , " cal_max = '%g'\n", nim->cal_max ) ; - } - - if( nim->scl_slope != 0.0 ){ - sprintf( buf+strlen(buf) , " scl_slope = '%g'\n" , nim->scl_slope ) ; - sprintf( buf+strlen(buf) , " scl_inter = '%g'\n" , nim->scl_inter ) ; - } - - if( nim->intent_code > 0 ){ - sprintf( buf+strlen(buf) , " intent_code = '%d'\n", nim->intent_code ) ; - sprintf( buf+strlen(buf) , " intent_code_name = '%s'\n" , - nifti_intent_string(nim->intent_code) ) ; - sprintf( buf+strlen(buf) , " intent_p1 = '%g'\n" , nim->intent_p1 ) ; - sprintf( buf+strlen(buf) , " intent_p2 = '%g'\n" , nim->intent_p2 ) ; - sprintf( buf+strlen(buf) , " intent_p3 = '%g'\n" , nim->intent_p3 ) ; - - if( nim->intent_name[0] != '\0' ){ - ebuf = escapize_string(nim->intent_name) ; - sprintf( buf+strlen(buf) , " intent_name = %s\n",ebuf) ; - free(ebuf) ; - } - } - - if( nim->toffset != 0.0 ) - sprintf( buf+strlen(buf) , " toffset = '%g'\n",nim->toffset ) ; - - if( nim->xyz_units > 0 ) - sprintf( buf+strlen(buf) , - " xyz_units = '%d'\n" - " xyz_units_name = '%s'\n" , - nim->xyz_units , nifti_units_string(nim->xyz_units) ) ; - - if( nim->time_units > 0 ) - sprintf( buf+strlen(buf) , - " time_units = '%d'\n" - " time_units_name = '%s'\n" , - nim->time_units , nifti_units_string(nim->time_units) ) ; - - if( nim->freq_dim > 0 ) - sprintf( buf+strlen(buf) , " freq_dim = '%d'\n",nim->freq_dim ) ; - if( nim->phase_dim > 0 ) - sprintf( buf+strlen(buf) , " phase_dim = '%d'\n",nim->phase_dim ) ; - if( nim->slice_dim > 0 ) - sprintf( buf+strlen(buf) , " slice_dim = '%d'\n",nim->slice_dim ) ; - if( nim->slice_code > 0 ) - sprintf( buf+strlen(buf) , - " slice_code = '%d'\n" - " slice_code_name = '%s'\n" , - nim->slice_code , nifti_slice_string(nim->slice_code) ) ; - if( nim->slice_start >= 0 && nim->slice_end > nim->slice_start ) - sprintf( buf+strlen(buf) , - " slice_start = '%" PRId64 "'\n" - " slice_end = '%" PRId64 "'\n", - nim->slice_start , nim->slice_end ) ; - if( nim->slice_duration != 0.0 ) - sprintf( buf+strlen(buf) , " slice_duration = '%g'\n", - nim->slice_duration ) ; - - if( nim->descrip[0] != '\0' ){ - ebuf = escapize_string(nim->descrip) ; - sprintf( buf+strlen(buf) , " descrip = %s\n",ebuf) ; - free(ebuf) ; - } - - if( nim->aux_file[0] != '\0' ){ - ebuf = escapize_string(nim->aux_file) ; - sprintf( buf+strlen(buf) , " aux_file = %s\n",ebuf) ; - free(ebuf) ; - } - - if( nim->qform_code > 0 ){ - int i,j,k ; - - sprintf( buf+strlen(buf) , - " qform_code = '%d'\n" - " qform_code_name = '%s'\n" - " qto_xyz_matrix = '%g %g %g %g %g %g %g %g %g %g %g %g %g %g %g %g'\n" , - nim->qform_code , nifti_xform_string(nim->qform_code) , - nim->qto_xyz.m[0][0] , nim->qto_xyz.m[0][1] , - nim->qto_xyz.m[0][2] , nim->qto_xyz.m[0][3] , - nim->qto_xyz.m[1][0] , nim->qto_xyz.m[1][1] , - nim->qto_xyz.m[1][2] , nim->qto_xyz.m[1][3] , - nim->qto_xyz.m[2][0] , nim->qto_xyz.m[2][1] , - nim->qto_xyz.m[2][2] , nim->qto_xyz.m[2][3] , - nim->qto_xyz.m[3][0] , nim->qto_xyz.m[3][1] , - nim->qto_xyz.m[3][2] , nim->qto_xyz.m[3][3] ) ; - - sprintf( buf+strlen(buf) , - " qto_ijk_matrix = '%g %g %g %g %g %g %g %g %g %g %g %g %g %g %g %g'\n" , - nim->qto_ijk.m[0][0] , nim->qto_ijk.m[0][1] , - nim->qto_ijk.m[0][2] , nim->qto_ijk.m[0][3] , - nim->qto_ijk.m[1][0] , nim->qto_ijk.m[1][1] , - nim->qto_ijk.m[1][2] , nim->qto_ijk.m[1][3] , - nim->qto_ijk.m[2][0] , nim->qto_ijk.m[2][1] , - nim->qto_ijk.m[2][2] , nim->qto_ijk.m[2][3] , - nim->qto_ijk.m[3][0] , nim->qto_ijk.m[3][1] , - nim->qto_ijk.m[3][2] , nim->qto_ijk.m[3][3] ) ; - - sprintf( buf+strlen(buf) , - " quatern_b = '%g'\n" - " quatern_c = '%g'\n" - " quatern_d = '%g'\n" - " qoffset_x = '%g'\n" - " qoffset_y = '%g'\n" - " qoffset_z = '%g'\n" - " qfac = '%g'\n" , - nim->quatern_b , nim->quatern_c , nim->quatern_d , - nim->qoffset_x , nim->qoffset_y , nim->qoffset_z , nim->qfac ) ; - - nifti_dmat44_to_orientation( nim->qto_xyz , &i,&j,&k ) ; - if( i > 0 && j > 0 && k > 0 ) - sprintf( buf+strlen(buf) , - " qform_i_orientation = '%s'\n" - " qform_j_orientation = '%s'\n" - " qform_k_orientation = '%s'\n" , - nifti_orientation_string(i) , - nifti_orientation_string(j) , - nifti_orientation_string(k) ) ; - } - - if( nim->sform_code > 0 ){ - int i,j,k ; - - sprintf( buf+strlen(buf) , - " sform_code = '%d'\n" - " sform_code_name = '%s'\n" - " sto_xyz_matrix = '%g %g %g %g %g %g %g %g %g %g %g %g %g %g %g %g'\n" , - nim->sform_code , nifti_xform_string(nim->sform_code) , - nim->sto_xyz.m[0][0] , nim->sto_xyz.m[0][1] , - nim->sto_xyz.m[0][2] , nim->sto_xyz.m[0][3] , - nim->sto_xyz.m[1][0] , nim->sto_xyz.m[1][1] , - nim->sto_xyz.m[1][2] , nim->sto_xyz.m[1][3] , - nim->sto_xyz.m[2][0] , nim->sto_xyz.m[2][1] , - nim->sto_xyz.m[2][2] , nim->sto_xyz.m[2][3] , - nim->sto_xyz.m[3][0] , nim->sto_xyz.m[3][1] , - nim->sto_xyz.m[3][2] , nim->sto_xyz.m[3][3] ) ; - - sprintf( buf+strlen(buf) , - " sto_ijk matrix = '%g %g %g %g %g %g %g %g %g %g %g %g %g %g %g %g'\n" , - nim->sto_ijk.m[0][0] , nim->sto_ijk.m[0][1] , - nim->sto_ijk.m[0][2] , nim->sto_ijk.m[0][3] , - nim->sto_ijk.m[1][0] , nim->sto_ijk.m[1][1] , - nim->sto_ijk.m[1][2] , nim->sto_ijk.m[1][3] , - nim->sto_ijk.m[2][0] , nim->sto_ijk.m[2][1] , - nim->sto_ijk.m[2][2] , nim->sto_ijk.m[2][3] , - nim->sto_ijk.m[3][0] , nim->sto_ijk.m[3][1] , - nim->sto_ijk.m[3][2] , nim->sto_ijk.m[3][3] ) ; - - nifti_dmat44_to_orientation( nim->sto_xyz , &i,&j,&k ) ; - if( i > 0 && j > 0 && k > 0 ) - sprintf( buf+strlen(buf) , - " sform_i_orientation = '%s'\n" - " sform_j_orientation = '%s'\n" - " sform_k_orientation = '%s'\n" , - nifti_orientation_string(i) , - nifti_orientation_string(j) , - nifti_orientation_string(k) ) ; - } - - sprintf( buf+strlen(buf) , " num_ext = '%d'\n", nim->num_ext ) ; - - sprintf( buf+strlen(buf) , "/>\n" ) ; /* XML-ish closer */ - - nbuf = (int)strlen(buf) ; - buf = (char *)realloc((void *)buf, nbuf+1); /* cut back to proper length */ - if( !buf ) fprintf(stderr,"** NIFTI NITA: failed to realloc %d bytes\n", - nbuf+1); - return buf ; -} - -/*---------------------------------------------------------------------------*/ - -/*----------------------------------------------------------------------*/ -/*! get the byte order for this CPU - - - LSB_FIRST means least significant byte, first (little endian) - - MSB_FIRST means most significant byte, first (big endian) -*//*--------------------------------------------------------------------*/ -int nifti_short_order(void) /* determine this CPU's byte order */ -{ - union { unsigned char bb[2] ; - short ss ; } fred ; - - fred.bb[0] = 1 ; fred.bb[1] = 0 ; - - return (fred.ss == 1) ? LSB_FIRST : MSB_FIRST ; -} - -/*---------------------------------------------------------------------------*/ - -#undef QQNUM -#undef QNUM -#undef QSTR - -/* macro to check lhs string against "n1"; if it matches, - interpret rhs string as a number, and put it into nim->"n2" */ - -#define QQNUM(n1,n2,tt) if( strcmp(lhs,#n1)==0 ) nim->n2=(tt)strtod(rhs,NULL) - -/* same, but where "n1" == "n2" */ - -#define QNUM(nam,tt) QQNUM(nam,nam,tt) - -/* macro to check lhs string against "nam"; if it matches, - put rhs string into nim->"nam" string, with max length = "ml" */ - -#define QSTR(nam,ml) if( strcmp(lhs,#nam) == 0 ) \ - strncpy(nim->nam,rhs,ml), nim->nam[ml]='\0' - -/*---------------------------------------------------------------------------*/ -/*! Take an XML-ish ASCII string and create a NIFTI image header to match. - - NULL is returned if enough information isn't present in the input string. - - The image data can later be loaded with nifti_image_load(). - - The struct returned here can be liberated with nifti_image_free(). - - Not a lot of error checking is done here to make sure that the - input values are reasonable! -*//*-------------------------------------------------------------------------*/ -nifti_image *nifti_image_from_ascii( const char *str, int * bytes_read ) -{ - char lhs[1024] , rhs[1024] ; - int ii , spos, nn ; - nifti_image *nim ; /* will be output */ - - if( str == NULL || *str == '\0' ) return NULL ; /* bad input!? */ - - /* scan for opening string */ - - spos = 0 ; - ii = sscanf( str+spos , "%1023s%n" , lhs , &nn ) ; spos += nn ; - if( ii == 0 || strcmp(lhs,"nx = nim->ny = nim->nz = nim->nt - = nim->nu = nim->nv = nim->nw = 1 ; - nim->dx = nim->dy = nim->dz = nim->dt - = nim->du = nim->dv = nim->dw = 0 ; - nim->qfac = 1.0f ; - - nim->byteorder = nifti_short_order() ; - - /* starting at str[spos], scan for "equations" of the form - lhs = 'rhs' - and assign rhs values into the struct component named by lhs */ - - while(1){ - - while( isspace((int) str[spos]) ) spos++ ; /* skip whitespace */ - if( str[spos] == '\0' ) break ; /* end of string? */ - - /* get lhs string */ - - ii = sscanf( str+spos , "%1023s%n" , lhs , &nn ) ; spos += nn ; - if( ii == 0 || strcmp(lhs,"/>") == 0 ) break ; /* end of input? */ - - /* skip whitespace and the '=' marker */ - - while( isspace((int) str[spos]) || str[spos] == '=' ) spos++ ; - if( str[spos] == '\0' ) break ; /* end of string? */ - - /* if next character is a quote ', copy everything up to next ' - otherwise, copy everything up to next nonblank */ - - if( str[spos] == '\'' ){ - ii = spos+1 ; - while( str[ii] != '\0' && str[ii] != '\'' ) ii++ ; - nn = ii-spos-1 ; if( nn > 1023 ) nn = 1023 ; - memcpy(rhs,str+spos+1,nn) ; rhs[nn] = '\0' ; - spos = (str[ii] == '\'') ? ii+1 : ii ; - } else { - ii = sscanf( str+spos , "%1023s%n" , rhs , &nn ) ; spos += nn ; - if( ii == 0 ) break ; /* nothing found? */ - } - unescape_string(rhs) ; /* remove any XML escape sequences */ - - /* Now can do the assignment, based on lhs string. - Start with special cases that don't fit the QNUM/QSTR macros. */ - - if( strcmp(lhs,"nifti_type") == 0 ){ - if( strcmp(rhs,"ANALYZE-7.5") == 0 ) - nim->nifti_type = NIFTI_FTYPE_ANALYZE ; - else if( strcmp(rhs,"NIFTI-1+") == 0 ) - nim->nifti_type = NIFTI_FTYPE_NIFTI1_1 ; - else if( strcmp(rhs,"NIFTI-1") == 0 ) - nim->nifti_type = NIFTI_FTYPE_NIFTI1_2 ; - else if( strcmp(rhs,"NIFTI-1A") == 0 ) - nim->nifti_type = NIFTI_FTYPE_ASCII ; - } - else if( strcmp(lhs,"header_filename") == 0 ){ - nim->fname = nifti_strdup(rhs) ; - } - else if( strcmp(lhs,"image_filename") == 0 ){ - nim->iname = nifti_strdup(rhs) ; - } - else if( strcmp(lhs,"sto_xyz_matrix") == 0 ){ - sscanf( rhs , "%lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf" , - &(nim->sto_xyz.m[0][0]) , &(nim->sto_xyz.m[0][1]) , - &(nim->sto_xyz.m[0][2]) , &(nim->sto_xyz.m[0][3]) , - &(nim->sto_xyz.m[1][0]) , &(nim->sto_xyz.m[1][1]) , - &(nim->sto_xyz.m[1][2]) , &(nim->sto_xyz.m[1][3]) , - &(nim->sto_xyz.m[2][0]) , &(nim->sto_xyz.m[2][1]) , - &(nim->sto_xyz.m[2][2]) , &(nim->sto_xyz.m[2][3]) , - &(nim->sto_xyz.m[3][0]) , &(nim->sto_xyz.m[3][1]) , - &(nim->sto_xyz.m[3][2]) , &(nim->sto_xyz.m[3][3]) ) ; - } - else if( strcmp(lhs,"byteorder") == 0 ){ - if( strcmp(rhs,"MSB_FIRST") == 0 ) nim->byteorder = MSB_FIRST ; - if( strcmp(rhs,"LSB_FIRST") == 0 ) nim->byteorder = LSB_FIRST ; - } - else QQNUM(image_offset,iname_offset,int) ; - else QNUM(datatype,short int) ; - else QNUM(ndim,int) ; - else QNUM(nx,int) ; - else QNUM(ny,int) ; - else QNUM(nz,int) ; - else QNUM(nt,int) ; - else QNUM(nu,int) ; - else QNUM(nv,int) ; - else QNUM(nw,int) ; - else QNUM(dx,float) ; - else QNUM(dy,float) ; - else QNUM(dz,float) ; - else QNUM(dt,float) ; - else QNUM(du,float) ; - else QNUM(dv,float) ; - else QNUM(dw,float) ; - else QNUM(cal_min,float) ; - else QNUM(cal_max,float) ; - else QNUM(scl_slope,float) ; - else QNUM(scl_inter,float) ; - else QNUM(intent_code,short) ; - else QNUM(intent_p1,float) ; - else QNUM(intent_p2,float) ; - else QNUM(intent_p3,float) ; - else QSTR(intent_name,15) ; - else QNUM(toffset,float) ; - else QNUM(xyz_units,int) ; - else QNUM(time_units,int) ; - else QSTR(descrip,79) ; - else QSTR(aux_file,23) ; - else QNUM(qform_code,int) ; - else QNUM(quatern_b,float) ; - else QNUM(quatern_c,float) ; - else QNUM(quatern_d,float) ; - else QNUM(qoffset_x,float) ; - else QNUM(qoffset_y,float) ; - else QNUM(qoffset_z,float) ; - else QNUM(qfac,float) ; - else QNUM(sform_code,int) ; - else QNUM(freq_dim,int) ; - else QNUM(phase_dim,int) ; - else QNUM(slice_dim,int) ; - else QNUM(slice_code,int) ; - else QNUM(slice_start,int) ; - else QNUM(slice_end,int) ; - else QNUM(slice_duration,float) ; - else QNUM(num_ext,int) ; - - } /* end of while loop */ - - if( bytes_read ) *bytes_read = spos+1; /* "process" last '\n' */ - - /* do miscellaneous checking and cleanup */ - - if( nim->ndim <= 0 ){ nifti_image_free(nim); return NULL; } /* bad! */ - - nifti_datatype_sizes( nim->datatype, &(nim->nbyper), &(nim->swapsize) ); - if( nim->nbyper == 0 ){ nifti_image_free(nim); return NULL; } /* bad! */ - - nim->dim[0] = nim->ndim ; - nim->dim[1] = nim->nx ; nim->pixdim[1] = nim->dx ; - nim->dim[2] = nim->ny ; nim->pixdim[2] = nim->dy ; - nim->dim[3] = nim->nz ; nim->pixdim[3] = nim->dz ; - nim->dim[4] = nim->nt ; nim->pixdim[4] = nim->dt ; - nim->dim[5] = nim->nu ; nim->pixdim[5] = nim->du ; - nim->dim[6] = nim->nv ; nim->pixdim[6] = nim->dv ; - nim->dim[7] = nim->nw ; nim->pixdim[7] = nim->dw ; - - nim->nvox = (int64_t)nim->nx * nim->ny * nim->nz - * nim->nt * nim->nu * nim->nv * nim->nw ; - - if( nim->qform_code > 0 ) - nim->qto_xyz = nifti_quatern_to_dmat44( - nim->quatern_b, nim->quatern_c, nim->quatern_d, - nim->qoffset_x, nim->qoffset_y, nim->qoffset_z, - nim->dx , nim->dy , nim->dz , - nim->qfac ) ; - else - nim->qto_xyz = nifti_quatern_to_dmat44( - 0.0 , 0.0 , 0.0 , 0.0 , 0.0 , 0.0 , - nim->dx , nim->dy , nim->dz , 0.0 ) ; - - - nim->qto_ijk = nifti_dmat44_inverse( nim->qto_xyz ) ; - - if( nim->sform_code > 0 ) - nim->sto_ijk = nifti_dmat44_inverse( nim->sto_xyz ) ; - - return nim ; -} - - -/*---------------------------------------------------------------------------*/ -/*! validate the nifti_image - - \return 1 if the structure seems valid, otherwise 0 - - \sa nifti_nim_has_valid_dims, nifti_hdr1_looks_good -*//*-------------------------------------------------------------------------*/ -int nifti_nim_is_valid(nifti_image * nim, int complain) -{ - int errs = 0; - - if( !nim ){ - fprintf(stderr,"** NIFTI is_valid_nim: nim is NULL\n"); - return 0; - } - - if( g_opts.debug > 2 ) fprintf(stderr,"-d nim_is_valid check...\n"); - - /**- check that dim[] matches the individual values ndim, nx, ny, ... */ - if( ! nifti_nim_has_valid_dims(nim,complain) ){ - if( !complain ) return 0; - errs++; - } - - /* might check nbyper, pixdim, q/sforms, swapsize, nifti_type, ... */ - - /**- be explicit in return of 0 or 1 */ - if( errs > 0 ) return 0; - else return 1; -} - -/*---------------------------------------------------------------------------*/ -/*! validate nifti dimensions - - \return 1 if valid, 0 if not - - \sa nifti_nim_is_valid, nifti_hdr1_looks_good - - rely on dim[] as the master -*//*-------------------------------------------------------------------------*/ -int nifti_nim_has_valid_dims(nifti_image * nim, int complain) -{ - int64_t prod, c; - int errs = 0; - - /**- start with dim[0]: failure here is considered terminal */ - if( nim->dim[0] <= 0 || nim->dim[0] > 7 ){ - errs++; - if( complain ) - fprintf(stderr,"** NIFTI NVd: dim[0] (%" PRId64 - ") out of range [1,7]\n", nim->dim[0]); - return 0; - } - - /**- check whether ndim equals dim[0] */ - if( nim->ndim != nim->dim[0] ){ - errs++; - if( ! complain ) return 0; - fprintf(stderr,"** NIFTI NVd: ndim != dim[0] (%" PRId64 ",%" PRId64 ")\n", - nim->ndim,nim->dim[0]); - } - - /**- compare each dim[i] to the proper nx, ny, ... */ - if( ( (nim->dim[0] >= 1) && (nim->dim[1] != nim->nx) ) || - ( (nim->dim[0] >= 2) && (nim->dim[2] != nim->ny) ) || - ( (nim->dim[0] >= 3) && (nim->dim[3] != nim->nz) ) || - ( (nim->dim[0] >= 4) && (nim->dim[4] != nim->nt) ) || - ( (nim->dim[0] >= 5) && (nim->dim[5] != nim->nu) ) || - ( (nim->dim[0] >= 6) && (nim->dim[6] != nim->nv) ) || - ( (nim->dim[0] >= 7) && (nim->dim[7] != nim->nw) ) ){ - errs++; - if( !complain ) return 0; - fprintf(stderr,"** NIFTI NVd mismatch: dims = %" PRId64 ",%" PRId64 - ",%" PRId64 ",%" PRId64 ",%" PRId64 ",%" PRId64 ",%" PRId64 "\n" - " nxyz... = %" PRId64 ",%" PRId64 ",%" PRId64 - ",%" PRId64 ",%" PRId64 ",%" PRId64 ",%" PRId64 "\n", - nim->dim[1], nim->dim[2], nim->dim[3], - nim->dim[4], nim->dim[5], nim->dim[6], nim->dim[7], - nim->nx, nim->ny, nim->nz, - nim->nt, nim->nu, nim->nv, nim->nw ); - } - - if( g_opts.debug > 2 ){ - fprintf(stderr,"-d check dim[%" PRId64 "] =", nim->dim[0]); - for( c = 0; c < 7; c++ ) fprintf(stderr," %" PRId64 "", nim->dim[c]); - fputc('\n', stderr); - } - - /**- check the dimensions, and that their product matches nvox */ - prod = 1; - for( c = 1; c <= nim->dim[0]; c++ ){ - if( nim->dim[c] > 0) - prod *= nim->dim[c]; - else if( nim->dim[c] <= 0 ){ - if( !complain ) return 0; - fprintf(stderr,"** NIFTI NVd: dim[%" PRId64 "] (=%" PRId64 ") <= 0\n", - c, nim->dim[c]); - errs++; - } - } - if( prod != nim->nvox ){ - if( ! complain ) return 0; - fprintf(stderr,"** NIFTI NVd: nvox does not match %" PRId64 - "-dim product (%" PRId64 ", %" PRId64 ")\n", - nim->dim[0], nim->nvox, prod); - errs++; - } - - /**- if debug, warn about any remaining dim that is neither 0, nor 1 */ - /* (values in dims above dim[0] are undefined, as reminded by Cinly - Ooi and Alle Meije Wink) 16 Nov 2005 [rickr] */ - if( g_opts.debug > 1 ) - for( c = nim->dim[0]+1; c <= 7; c++ ) - if( nim->dim[c] != 0 && nim->dim[c] != 1 ) - fprintf(stderr,"** NIFTI NVd warning: dim[%" PRId64 "] = %" PRId64 - ", but ndim = %" PRId64 "\n", - c, nim->dim[c], nim->dim[0]); - - if( g_opts.debug > 2 ) - fprintf(stderr,"-d nim_has_valid_dims check, errs = %d\n", errs); - - /**- return invalid or valid */ - if( errs > 0 ) return 0; - else return 1; -} - - -/*---------------------------------------------------------------------------*/ -/*! read a nifti image, collapsed across dimensions according to dims[8] 
-
-    This function may be used to read parts of a nifti dataset, such as
-    the time series for a single voxel, or perhaps a slice.  It is similar
-    to nifti_image_load(), though the passed 'data' parameter is used for
-    returning the image, not nim->data.
-
-    \param nim  given nifti_image struct, corresponding to the data file
-    \param dims given list of dimensions (see below)
-    \param data pointer to data pointer (if *data is NULL, data will be
-                allocated, otherwise not)
-
-    Here, dims is an array of 8 ints, similar to nim->dim[8].  While dims[0]
-    is unused at this point, the other indices specify which dimensions to
-    collapse (and at which index), and which not to collapse.  If dims[i] is
-    set to -1, then that entire dimension will be read in, from index 0 to
-    index (nim->dim[i] - 1).  If dims[i] >= 0, then only that index will be
-    read in (so dims[i] must also be < nim->dim[i]).
-
-    Example: given  nim->dim[8] = { 4, 64, 64, 21, 80, 1, 1, 1 } (4-D dataset)
-
-      if dims[8] = { 0,  5,  4, 17, -1, -1, -1, -1 }
-         -> read time series for voxel i,j,k = 5,4,17
-
-      if dims[8] = { 0, -1, -1, -1, 17, -1, -1, -1 }
-         -> read single volume at time point 17
-
-    Example: given  nim->dim[8] = { 6, 64, 64, 21, 80, 4, 3, 1 } (6-D dataset)
-
-      if dims[8] = { 0, 5, 4, 17, -1, 2, 1, 0 }
-         -> read time series for the voxel i,j,k = 5,4,17, and dim 5,6 = 2,1
-
-      if dims[8] = { 0, 5, 4, -1, -1, 0, 0, 0 }
-         -> read time series for slice at i,j = 5,4, and dim 5,6,7 = 0,0,0
-            (note that dims[7] is not relevant, but must be 0 or -1)
-
-    If *data is NULL, then *data will be set as a pointer to new memory,
-    allocated here for the resulting collapsed image data.
-
-      e.g. { int    dims[8] = { 0,  5,  4, 17, -1, -1, -1, -1 };
-             void * data    = NULL;
-             ret_val = nifti_read_collapsed_image(nim, dims, &data);
-             if( ret_val > 0 ){
-                process_time_series(data);
-                if( data != NULL ) free(data);
-             }
-           }
-
-    NOTE: If *data is not NULL, then it will be assumed that it points to
-          valid memory, sufficient to hold the results.  This is done for
-          speed and possibly repeated calls to this function.
-
-      e.g. { int64_t dims[8] = { 0,  -1, -1, -1, -1, -1, -1, -1 };
-             void  * data    = NULL;
-             for( zslice = 0; zslice < nzslices; zslice++ ){
-                dims[3] = zslice;
-                ret_val = nifti_read_collapsed_image(nim, dims, &data);
-                if( ret_val > 0 ) process_slice(zslice, data);
-             }
-             if( data != NULL ) free(data);
-           }
-
-    \return
-        -  the total number of bytes read, or < 0 on failure
-        -  the read and byte-swapped data, in 'data'
- - \sa nifti_image_read, nifti_image_free, nifti_image_read_bricks - nifti_image_load -*//*-------------------------------------------------------------------------*/ -int64_t nifti_read_collapsed_image( nifti_image * nim, const int64_t dims [8], - void ** data ) -{ - znzFile fp; - int64_t prods[8]; /* sizes are bounded by dims[], so 8 */ - int pivots[8], nprods; /* sizes are bounded by dims[], so 8 */ - int64_t c, bytes; - - /** - check pointers for sanity */ - if( !nim || !dims || !data ){ - fprintf(stderr,"** nifti_RCI: bad params %p, %p, %p\n", - (void *)nim, (const void *)dims, (void *)data); - return -1; - } - - if( g_opts.debug > 2 ){ - fprintf(stderr,"-d read_collapsed_image:\n dims ="); - for(c = 0; c < 8; c++) fprintf(stderr," %3" PRId64 "", dims[c]); - fprintf(stderr,"\n nim->dims ="); - for(c = 0; c < 8; c++) fprintf(stderr," %3" PRId64 "", nim->dim[c]); - fputc('\n', stderr); - } - - /** - verify that dim[] makes sense */ - if( ! nifti_nim_is_valid(nim, g_opts.debug > 0) ){ - fprintf(stderr,"** NIFTI: invalid nim (file is '%s')\n", nim->fname ); - return -1; - } - - /** - verify that dims[] makes sense for this dataset */ - for( c = 1; c <= nim->dim[0]; c++ ){ - if( dims[c] >= nim->dim[c] ){ - fprintf(stderr,"** nifti_RCI: dims[%" PRId64 "] >= nim->dim[%" PRId64 - "] (%" PRId64 ",%" PRId64 ")\n", - c, c, dims[c], nim->dim[c]); - return -1; - } - } - - /** - prepare pivot list - pivots are fixed indices */ - if( make_pivot_list(nim, dims, pivots, prods, &nprods) < 0 ) return -1; - - bytes = rci_alloc_mem(data, prods, nprods, nim->nbyper); - if( bytes < 0 ) return -1; - - /** - open the image file for reading at the appropriate offset */ - fp = nifti_image_load_prep( nim ); - if( ! fp ){ free(*data); *data = NULL; return -1; } /* failure */ - - /** - call the recursive reading function, passing nim, the pivot info, - location to store memory, and file pointer and position */ - c = rci_read_data(nim, pivots, prods, nprods, dims, (char *)*data, fp, - znztell(fp)); - znzclose(fp); /* in any case, close the file */ - if( c < 0 ){ free(*data); *data = NULL; return -1; } /* failure */ - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d read %" PRId64 " bytes of collapsed image from %s\n", - bytes, nim->fname); - - return bytes; -} - - -/* local function to find strides per dimension. assumes 7D size and -** stride array. -*/ -static void -compute_strides(int64_t *strides,const int64_t *size,int nbyper) -{ - int i; - strides[0] = nbyper; - for(i = 1; i < 7; i++) - { - strides[i] = size[i-1] * strides[i-1]; - } -} - -/*---------------------------------------------------------------------------*/ -/*! read an arbitrary subregion from a nifti image - - This function may be used to read a single arbitary subregion of any - rectangular size from a nifti dataset, such as a small 5x5x5 subregion - around the center of a 3D image. - - \param nim given nifti_image struct, corresponding to the data file - \param start_index the index location of first voxel that will be returned - \param region_size the size of the subregion to be returned - \param data pointer to data pointer (if *data is NULL, data will be - allocated, otherwise not) - - Example: given nim->dim[8] = {3, 64, 64, 64, 1, 1, 1, 1 } (3-D dataset) - - if start_index[7] = { 29, 29, 29, 0, 0, 0, 0 } and - region_size[7] = { 5, 5, 5, 1, 1, 1, 1 } - -> read 5x5x5 region starting with the first voxel at (29,29,29) - - NOTE: If *data is not NULL, then it will be assumed that it points to - valid memory, sufficient to hold the results. This is done for - speed and possibly repeated calls to this function. - \return - - the total number of bytes read, or < 0 on failure - - the read and byte-swapped data, in 'data' - - \sa nifti_image_read, nifti_image_free, nifti_image_read_bricks - nifti_image_load, nifti_read_collapsed_image -*//*-------------------------------------------------------------------------*/ -int64_t nifti_read_subregion_image( nifti_image * nim, - int64_t *start_index, - int64_t *region_size, - void ** data ) -{ - znzFile fp; /* file to read */ - int64_t i,j,k,l,m,n; /* indices for dims */ - int64_t bytes = 0; /* total # bytes read */ - int64_t total_alloc_size; /* size of buffer allocation */ - char *readptr; /* where in *data to read next */ - int64_t strides[7]; /* strides between dimensions */ - int64_t collapsed_dims[8]; /* for read_collapsed_image */ - int64_t *image_size; /* pointer to dimensions in header */ - int64_t initial_offset; - int64_t offset; /* seek offset for reading current row */ - - /* probably ignored, but set to ndim for consistency*/ - collapsed_dims[0] = nim->ndim; - - /* build a dims array for collapsed image read */ - for(i = 0; i < nim->ndim; i++) { - /* if you take the whole extent in this dimension */ - if(start_index[i] == 0 && region_size[i] == nim->dim[i+1]) - collapsed_dims[i+1] = -1; - /* if you specify a single element in this dimension */ - else if(region_size[i] == 1) - collapsed_dims[i+1] = start_index[i]; - else - collapsed_dims[i+1] = -2; /* sentinel value */ - } - /* fill out end of collapsed_dims */ - for(i = nim->ndim ; i < 7; i++) - collapsed_dims[i+1] = -1; - - /* check to see whether collapsed read is possible */ - for(i = 1; i <= nim->ndim; i++) - if(collapsed_dims[i] == -2) break; - - /* if you get through all the dimensions without hitting - ** a subrange of size > 1, a collapsed read is possible - */ - if(i > nim->ndim) - return nifti_read_collapsed_image(nim, collapsed_dims, data); - - /* point past first element of dim, which holds nim->ndim */ - image_size = &(nim->dim[1]); - - /* check region sizes for sanity */ - for(i = 0; i < nim->ndim; i++) - if(start_index[i] + region_size[i] > image_size[i]) { - if(g_opts.debug > 1) - fprintf(stderr,"region doesn't fit within image size\n"); - return -1; - } - - /* get the file open */ - fp = nifti_image_load_prep( nim ); - /* the current offset is just past the nifti header, save - * location so that SEEK_SET can be used below - */ - initial_offset = znztell(fp); - /* get strides*/ - compute_strides(strides,image_size,nim->nbyper); - - total_alloc_size = nim->nbyper; /* size of pixel */ - - /* find alloc size */ - for(i = 0; i < nim->ndim; i++) total_alloc_size *= region_size[i]; - - /* allocate buffer, if necessary */ - if(! *data) *data = (void *)malloc(total_alloc_size); - - if(! *data) { - if(g_opts.debug > 1) - fprintf(stderr,"allocation of %" PRId64 " bytes failed\n", - total_alloc_size); - return -1; - } - - /* point to start of data buffer as char * */ - readptr = *((char **)data); - { - /* can't assume that start_index and region_size have any more than - ** nim->ndim elements so make local copies, filled out to seven elements - */ - int64_t si[7], rs[7]; - for(i = 0; i < nim->ndim; i++) { - si[i] = start_index[i]; - rs[i] = region_size[i]; - } - for(i = nim->ndim; i < 7; i++) { - si[i] = 0; - rs[i] = 1; - } - - /* loop through subregion and read a row at a time */ - for(i = si[6]; i < (si[6] + rs[6]); i++) { - for(j = si[5]; j < (si[5] + rs[5]); j++) { - for(k = si[4]; k < (si[4] + rs[4]); k++) { - for(l = si[3]; l < (si[3] + rs[3]); l++) { - for(m = si[2]; m < (si[2] + rs[2]); m++) { - for(n = si[1]; n < (si[1] + rs[1]); n++) { - int64_t nread,read_amount; - offset = initial_offset + - (i * strides[6]) + - (j * strides[5]) + - (k * strides[4]) + - (l * strides[3]) + - (m * strides[2]) + - (n * strides[1]) + - (si[0] * strides[0]); - znzseek(fp, offset, SEEK_SET); /* seek to current row */ - read_amount = rs[0] * nim->nbyper; /* read a row of subregion */ - nread = nifti_read_buffer(fp, readptr, read_amount, nim); - if(nread != read_amount) { - if(g_opts.debug > 1) { - fprintf(stderr,"read of %" PRId64 " bytes failed\n", - read_amount); - return -1; - } - } - bytes += nread; - readptr += read_amount; - } - } - } - } - } - } - } - return bytes; -} - - -/* read the data from the file pointed to by fp - - - this a recursive function, so start with the base case - - data is now (char *) for easy incrementing - - return 0 on success, < 0 on failure -*/ -static int rci_read_data(nifti_image * nim, int * pivots, int64_t * prods, - int nprods, const int64_t dims[], char * data, - znzFile fp, int64_t base_offset) -{ - int64_t sublen, offset, read_size; - int c; - - /* bad check first - base_offset may not have been checked */ - if( nprods <= 0 ){ - fprintf(stderr,"** NIFTI rci_read_data, bad prods, %d\n", nprods); - return -1; - } - - /* base case: actually read the data */ - if( nprods == 1 ){ - int64_t nread, bytes; - - /* make sure things look good here */ - if( *pivots != 0 ){ - fprintf(stderr,"** NIFTI rciRD: final pivot == %d!\n", *pivots); - return -1; - } - - /* so just seek and read (prods[0] * nbyper) bytes from the file */ - znzseek(fp, base_offset, SEEK_SET); - bytes = prods[0] * nim->nbyper; - nread = nifti_read_buffer(fp, data, bytes, nim); - if( nread != bytes ){ - fprintf(stderr,"** NIFTI rciRD: read only %" PRId64 " of %" PRId64 - " bytes from '%s'\n", - nread, bytes, nim->fname); - return -1; - } else if( g_opts.debug > 3 ) - fprintf(stderr,"+d successful read of %" PRId64 - " bytes at offset %" PRId64 "\n", - bytes, base_offset); - - return 0; /* done with base case - return success */ - } - - /* not the base case, so do a set of reduced reads */ - - /* compute size of sub-brick: all dimensions below pivot */ - for( c = 1, sublen = 1; c < *pivots; c++ ) sublen *= nim->dim[c]; - - /* compute number of values to read, i.e. remaining prods */ - for( c = 1, read_size = 1; c < nprods; c++ ) read_size *= prods[c]; - read_size *= nim->nbyper; /* and multiply by bytes per voxel */ - - /* now repeatedly compute offsets, and recursively read */ - for( c = 0; c < prods[0]; c++ ){ - /* offset is (c * sub-block size (including pivot dim)) */ - /* + (dims[] index into pivot sub-block) */ - /* the unneeded multiplication is to make this more clear */ - offset = (int64_t)c * sublen * nim->dim[*pivots] + - (int64_t)sublen * dims[*pivots]; - offset *= nim->nbyper; - - if( g_opts.debug > 3 ) - fprintf(stderr,"-d reading %" PRId64 " bytes, foff %" PRId64 - " + %" PRId64 ", doff %" PRId64 "\n", - read_size, base_offset, offset, c*read_size); - - /* now read the next level down, adding this offset */ - if( rci_read_data(nim, pivots+1, prods+1, nprods-1, dims, - data + c * read_size, fp, base_offset + offset) < 0 ) - return -1; - } - - return 0; -} - - -/* allocate memory for all collapsed image data - - If *data is already set, do not allocate, but still calculate - size for debug report. - - return total size on success, and < 0 on failure -*/ -static int rci_alloc_mem(void **data, int64_t prods[8], int nprods, int nbyper ) -{ - int64_t size; - int memindex; - - if( nbyper < 0 || nprods < 1 || nprods > 8 ){ - fprintf(stderr,"** NIFTI rci_am: bad params, %d, %d\n", nbyper, nprods); - return -1; - } - - for( memindex = 0, size = 1; memindex < nprods; memindex++ ) - size *= prods[memindex]; - - size *= nbyper; - - if( ! *data ){ /* then allocate what is needed */ - if( g_opts.debug > 1 ) - fprintf(stderr,"+d alloc %" PRId64 - " (%" PRId64 " x %d) bytes for collapsed image\n", - size, size/nbyper, nbyper); - - *data = malloc(size); /* actually allocate the memory */ - if( ! *data ){ - fprintf(stderr,"** NIFTI rci_am: failed to alloc %" PRId64 - " bytes for data\n", size); - return -1; - } - } else if( g_opts.debug > 1 ) - fprintf(stderr,"-d rci_am: *data already set, need %" PRId64 - " x %d bytes\n", - size/nbyper, nbyper); - - return size; -} - - -/* prepare a pivot list for reading - - The pivot points are the indices into dims where the calling function - wants to collapse a dimension. The last pivot should always be zero - (note that we have space for that in the lists). -*/ -static int make_pivot_list(nifti_image *nim, const int64_t dims[], int pivots[], - int64_t prods[], int * nprods ) -{ - int len, dind; - - len = 0; - dind = nim->dim[0]; - while( dind > 0 ){ - prods[len] = 1; - while( dind > 0 && (nim->dim[dind] == 1 || dims[dind] == -1) ){ - prods[len] *= nim->dim[dind]; - dind--; - } - pivots[len] = dind; - len++; - dind--; /* fine, let it drop out at -1 */ - } - - /* make sure to include 0 as a pivot (instead of just 1, if it is) */ - if( pivots[len-1] != 0 ){ - pivots[len] = 0; - prods[len] = 1; - len++; - } - - *nprods = len; - - if( g_opts.debug > 2 ){ - fprintf(stderr,"+d pivot list created, pivots :"); - for(dind = 0; dind < len; dind++) - fprintf(stderr," %d", pivots[dind]); - fprintf(stderr,", prods :"); - for(dind = 0; dind < len; dind++) - fprintf(stderr," %" PRId64 "", prods[dind]); - fputc('\n',stderr); - } - - return 0; -} - - -#undef ISEND -#define ISEND(c) ( (c)==']' || (c)=='}' || (c)=='\0' ) - -/*---------------------------------------------------------------------*/ -/*! Get an integer list in the range 0..(nvals-1), from the - character string str. If we call the output pointer fred, - then fred[0] = number of integers in the list (> 0), and - fred[i] = i-th integer in the list for i=1..fred[0]. - If on return, fred == NULL or fred[0] == 0, then something is - wrong, and the caller must deal with that. - - Syntax of input string: - - initial '{' or '[' is skipped, if present - - ends when '}' or ']' or end of string is found - - contains entries separated by commas - - entries have one of these forms: - - a single number - - a dollar sign '$', which means nvals-1 - - a sequence of consecutive numbers in the form "a..b" or - "a-b", where "a" and "b" are single numbers (or '$') - - a sequence of evenly spaced numbers in the form - "a..b(c)" or "a-b(c)", where "c" encodes the step - - Example: "[2,7..4,3..9(2)]" decodes to the list - 2 7 6 5 4 3 5 7 9 - - entries should be in the range 0..nvals-1 - - (borrowed, with permission, from thd_intlist.c) -*//*-------------------------------------------------------------------*/ -int64_t * nifti_get_int64list( int64_t nvals , const char * str ) -{ - int64_t *subv = NULL ; - int64_t ii , nout ; - int64_t ibot,itop,istep , nused ; - int ipos , slen ; - char *cpt ; - - /* Meaningless input? */ - if( nvals < 1 ) return NULL ; - - /* No selection list? */ - if( str == NULL || str[0] == '\0' ) return NULL ; - - /* skip initial '[' or '{' */ - subv = (int64_t *)malloc( sizeof(int64_t) * 2 ) ; - if( !subv ) { - fprintf(stderr,"** nifti_get_intlist: failed alloc of 2 ints\n"); - return NULL; - } - subv[0] = nout = 0 ; - - ipos = 0 ; - if( str[ipos] == '[' || str[ipos] == '{' ) ipos++ ; - - if( g_opts.debug > 1 ) - fprintf(stderr,"-d making int_list (vals = %" PRId64 ") from '%s'\n", - nvals, str); - - /**- for each sub-selector until end of input... */ - - slen = (int)strlen(str) ; - while( ipos < slen && !ISEND(str[ipos]) ){ - - while( isspace((int) str[ipos]) ) ipos++ ; /* skip blanks */ - if( ISEND(str[ipos]) ) break ; /* done */ - - /**- get starting value */ - - if( str[ipos] == '$' ){ /* special case */ - ibot = nvals-1 ; ipos++ ; - } else { /* decode an integer */ - ibot = strtoll( str+ipos , &cpt , 10 ) ; - if( ibot < 0 ){ - fprintf(stderr,"** NIFTI ERROR: list index %" PRId64 - " is out of range 0..%" PRId64 "\n", - ibot,nvals-1) ; - free(subv) ; return NULL ; - } - if( ibot >= nvals ){ - fprintf(stderr,"** NIFTI ERROR: list index %" PRId64 - " is out of range 0..%" PRId64 "\n", - ibot,nvals-1) ; - free(subv) ; return NULL ; - } - nused = (cpt-(str+ipos)) ; - if( ibot == 0 && nused == 0 ){ - fprintf(stderr,"** NIFTI : list syntax error '%s'\n",str+ipos) ; - free(subv) ; return NULL ; - } - ipos += nused ; - } - - while( isspace((int) str[ipos]) ) ipos++ ; /* skip blanks */ - - /**- if that's it for this sub-selector, add one value to list */ - - if( str[ipos] == ',' || ISEND(str[ipos]) ){ - nout++ ; - subv = (int64_t *)realloc( (char *)subv , sizeof(int64_t)*(nout+1) ) ; - if( !subv ) { - fprintf(stderr,"** nifti_get_intlist: failed realloc of %" PRId64 - " ints\n", nout+1); - return NULL; - } - subv[0] = nout ; - subv[nout] = ibot ; - if( ISEND(str[ipos]) ) break ; /* done */ - ipos++ ; continue ; /* re-start loop at next sub-selector */ - } - - /**- otherwise, must have '..' or '-' as next inputs */ - - if( str[ipos] == '-' ){ - ipos++ ; - } else if( str[ipos] == '.' && str[ipos+1] == '.' ){ - ipos++ ; ipos++ ; - } else { - fprintf(stderr,"** NIFTI ERROR: index list syntax is bad: '%s'\n", - str+ipos) ; - free(subv) ; return NULL ; - } - - /**- get ending value for loop now */ - - if( str[ipos] == '$' ){ /* special case */ - itop = nvals-1 ; ipos++ ; - } else { /* decode an integer */ - itop = strtoll( str+ipos , &cpt , 10 ) ; - if( itop < 0 ){ - fprintf(stderr,"** NIFTI ERROR: index %" PRId64 - " is out of range 0..%" PRId64 "\n", - itop,nvals-1) ; - free(subv) ; return NULL ; - } - if( itop >= nvals ){ - fprintf(stderr,"** NIFTI ERROR: index %" PRId64 - " is out of range 0..%" PRId64 "\n", - itop,nvals-1) ; - free(subv) ; return NULL ; - } - nused = (cpt-(str+ipos)) ; - if( itop == 0 && nused == 0 ){ - fprintf(stderr,"** NIFTI: index list syntax error '%s'\n", - str+ipos) ; - free(subv) ; return NULL ; - } - ipos += nused ; - } - - /**- set default loop step */ - - istep = (ibot <= itop) ? 1 : -1 ; - - while( isspace((int) str[ipos]) ) ipos++ ; /* skip blanks */ - - /**- check if we have a non-default loop step */ - - if( str[ipos] == '(' ){ /* decode an integer */ - ipos++ ; - istep = strtoll( str+ipos , &cpt , 10 ) ; - if( istep == 0 ){ - fprintf(stderr,"** NIFTI ERROR: index loop step is 0!\n") ; - free(subv) ; return NULL ; - } - nused = (cpt-(str+ipos)) ; - ipos += nused ; - if( str[ipos] == ')' ) ipos++ ; - if( (ibot-itop)*istep > 0 ){ - fprintf(stderr,"** NIFTI WARNING: index list '%" PRId64 "..%" PRId64 - "(%" PRId64 ")' means nothing\n", - ibot,itop,istep ) ; - } - } - - /**- add values to output */ - - for( ii=ibot ; (ii-itop)*istep <= 0 ; ii += istep ){ - nout++ ; - subv = (int64_t *)realloc( (char *)subv , sizeof(int64_t)*(nout+1) ) ; - if( !subv ) { - fprintf(stderr,"** nifti_get_intlist: failed realloc of %" PRId64 - " ints\n", nout+1); - return NULL; - } - subv[0] = nout ; - subv[nout] = ii ; - } - - /**- check if we have a comma to skip over */ - - while( isspace((int) str[ipos]) ) ipos++ ; /* skip blanks */ - if( str[ipos] == ',' ) ipos++ ; /* skip commas */ - - } /* end of loop through selector string */ - - if( g_opts.debug > 1 ) { - fprintf(stderr,"+d int_list (vals = %" PRId64 "): ", subv[0]); - for( ii = 1; ii <= subv[0]; ii++ ) - fprintf(stderr,"%" PRId64 " ", subv[ii]); - fputc('\n',stderr); - } - - if( subv[0] == 0 ){ free(subv); subv = NULL; } - return subv ; -} - -/*! a 32-bit version of nifti_get_int64list */ -int * nifti_get_intlist( int nvals , const char * str ) -{ - int *ilist=NULL; - int64_t *i64list=NULL, nints, index; - - i64list = nifti_get_int64list((int64_t)nvals, str); - if( !i64list ) return NULL; - - /* check that the length is between 1 and INT_MAX */ - nints = i64list[0]; - if( nints <= 0 ) { free(i64list); return NULL; } - - if( nints > INT_MAX ) { - fprintf(stderr,"** nifti_get_intlist: %" PRId64 - " ints is too long for 32-bits\n", nints); - free(i64list); - return NULL; - } - - /* have a valid result, copy as ints */ - ilist = (int *)malloc((nints+1) * sizeof(int)); - if( !ilist ) { - fprintf(stderr,"** nifti_get_intlist: failed to alloc %" PRId64 " ints\n", - nints); - free(i64list); - return NULL; - } - - /* copy list, including length at index 0 */ - for( index=0; index <= nints; index++ ) { - if( i64list[index] > INT_MAX ) { - fprintf(stderr,"** nifti_get_intlist: value %" PRId64 - " too big for 32-bits\n", - i64list[index]); - free(ilist); - free(i64list); - return NULL; - } - ilist[index] = (int)i64list[index]; - } - - free(i64list); - - return ilist; -} - -/*---------------------------------------------------------------------*/ -/*! Given a NIFTI_TYPE string, such as "NIFTI_TYPE_INT16", return the - * corresponding integral type code. The type code is the macro - * value defined in nifti1.h. -*//*-------------------------------------------------------------------*/ -int nifti_datatype_from_string( const char * name ) -{ - int tablen = sizeof(nifti_type_list)/sizeof(nifti_type_ele); - int c; - - if( !name ) return DT_UNKNOWN; - - for( c = tablen-1; c > 0; c-- ) - if( !strcmp(name, nifti_type_list[c].name) ) - break; - - return nifti_type_list[c].type; -} - - -/*---------------------------------------------------------------------*/ -/*! Given a NIFTI_TYPE value, such as NIFTI_TYPE_INT16, return the - * corresponding macro label as a string. The dtype code is the - * macro value defined in nifti1.h. -*//*-------------------------------------------------------------------*/ -const char * nifti_datatype_to_string( int dtype ) -{ - int tablen = sizeof(nifti_type_list)/sizeof(nifti_type_ele); - int c; - - for( c = tablen-1; c > 0; c-- ) - if( nifti_type_list[c].type == dtype ) - break; - - return nifti_type_list[c].name; -} - - -/*---------------------------------------------------------------------*/ -/*! Determine whether dtype is a valid NIFTI_TYPE. - * - * DT_UNKNOWN is considered invalid - * - * The only difference 'for_nifti' makes is that DT_BINARY - * should be invalid for a NIfTI dataset. -*//*-------------------------------------------------------------------*/ -int nifti_datatype_is_valid( int dtype, int for_nifti ) -{ - int tablen = sizeof(nifti_type_list)/sizeof(nifti_type_ele); - int c; - - /* special case */ - if( for_nifti && dtype == DT_BINARY ) return 0; - - for( c = tablen-1; c > 0; c-- ) - if( nifti_type_list[c].type == dtype ) - return 1; - - return 0; -} - - -/*---------------------------------------------------------------------*/ -/*! Only as a test, verify that the new nifti_type_list table matches - * the the usage of nifti_datatype_sizes (which could be changed to - * use the table, if there were interest). - * - * return the number of errors (so 0 is success, as usual) -*//*-------------------------------------------------------------------*/ -int nifti_test_datatype_sizes(int verb) -{ - int tablen = sizeof(nifti_type_list)/sizeof(nifti_type_ele); - int nbyper, ssize; - int c, errs = 0; - - for( c = 0; c < tablen; c++ ) - { - nbyper = ssize = -1; - nifti_datatype_sizes(nifti_type_list[c].type, &nbyper, &ssize); - if( nbyper < 0 || ssize < 0 || - nbyper != nifti_type_list[c].nbyper || - ssize != nifti_type_list[c].swapsize ) - { - if( verb || g_opts.debug > 2 ) - fprintf(stderr, "** NIFTI type mismatch: " - "%s, %d, %d, %d : %d, %d\n", - nifti_type_list[c].name, nifti_type_list[c].type, - nifti_type_list[c].nbyper, nifti_type_list[c].swapsize, - nbyper, ssize); - errs++; - } - } - - if( errs ) - fprintf(stderr,"** nifti_test_datatype_sizes: found %d errors\n",errs); - else if( verb || g_opts.debug > 1 ) - fprintf(stderr,"-- nifti_test_datatype_sizes: all OK\n"); - - return errs; -} - - -/*---------------------------------------------------------------------*/ -/*! Display the nifti_type_list table. - * - * if which == 1 : display DT_* - * if which == 2 : display NIFTI_TYPE* - * else : display all -*//*-------------------------------------------------------------------*/ -int nifti_disp_type_list( int which ) -{ - const char * style; - int tablen = sizeof(nifti_type_list)/sizeof(nifti_type_ele); - int lwhich, c; - - if ( which == 1 ){ lwhich = 1; style = "DT_"; } - else if( which == 2 ){ lwhich = 2; style = "NIFTI_TYPE_"; } - else { lwhich = 3; style = "ALL"; } - - printf("nifti_type_list entries (%s) :\n" - " name type nbyper swapsize\n" - " --------------------- ---- ------ --------\n", style); - - for( c = 0; c < tablen; c++ ) - if( (lwhich & 1 && nifti_type_list[c].name[0] == 'D') || - (lwhich & 2 && nifti_type_list[c].name[0] == 'N') ) - printf(" %-22s %5d %3d %5d\n", - nifti_type_list[c].name, - nifti_type_list[c].type, - nifti_type_list[c].nbyper, - nifti_type_list[c].swapsize); - - return 0; -} diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti2_io.h b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti2_io.h deleted file mode 100644 index 101350e5e63..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti2_io.h +++ /dev/null @@ -1,735 +0,0 @@ -/** \file nifti2_io.h - \brief Data structures for using nifti2_io API. - - Written by Bob Cox, SSCC NIMH - - Revisions by Rick Reynolds, SSCC NIMH - */ -#ifndef _NIFTI2_IO_HEADER_ -#define _NIFTI2_IO_HEADER_ - -#include -#include -#include -#include -#include -#include -#include - -#ifndef DONT_INCLUDE_ANALYZE_STRUCT -#define DONT_INCLUDE_ANALYZE_STRUCT /*** not needed herein ***/ -#endif -#include "nifti1.h" /*** NIFTI-1 header specification ***/ -#include "nifti2.h" /*** NIFTI-2 header specification ***/ - -#include - -/*=================*/ -#ifdef __cplusplus -extern "C" { -#endif -/*=================*/ - -/*****===================================================================*****/ -/***** File nifti2_io.h == Declarations for nifti2_io.c *****/ -/*****...................................................................*****/ -/***** This code is a modification of nifti1_io.h. *****/ -/*****...................................................................*****/ -/***** This code is released to the public domain. *****/ -/*****...................................................................*****/ -/***** Author: Robert W Cox, SSCC/DIRP/NIMH/NIH/DHHS/USA/EARTH *****/ -/***** Date: August 2003 *****/ -/*****...................................................................*****/ -/***** Neither the National Institutes of Health (NIH), nor any of its *****/ -/***** employees imply any warranty of usefulness of this software for *****/ -/***** any purpose, and do not assume any liability for damages, *****/ -/***** incidental or otherwise, caused by any use of this document. *****/ -/*****===================================================================*****/ - -/* ...................................................................... - Modified by: Mark Jenkinson (FMRIB Centre, University of Oxford, UK) - Date: July/August 2004 - - Mainly adding low-level IO and changing things to allow gzipped files - to be read and written - Full backwards compatability should have been maintained - - ...................................................................... - Modified by: Rick Reynolds (SSCC/DIRP/NIMH, National Institutes of Health) - Date: December 2004 - - Modified and added many routines for I/O, particularly involving - extensions and nifti_brick_list. - - ...................................................................... - Modified by: Rick Reynolds (SSCC/DIRP/NIMH, National Institutes of Health) - Date: August 2013 - - Converted to be based on nifti_2_header. - - ** NOT BACKWARD COMPATABLE ** - - These routines will read/write both NIFTI-1 and NIFTI-2 image files, - but modification to the _calling_ routies is necessary, since: - - a. the main nifti_image type has changed (to nifti2_image) - b. some image field types have been altered (to have larger size) - c. some routines have been changed to apply to multiple NIFTI types -*/ - -/********************** Some sample data structures **************************/ - -typedef struct { /** 4x4 matrix struct **/ - float m[4][4] ; -} mat44 ; - -typedef struct { /** 3x3 matrix struct **/ - float m[3][3] ; -} mat33 ; - -typedef struct { /** 4x4 matrix struct (double) **/ - double m[4][4] ; -} nifti_dmat44 ; - -typedef struct { /** 3x3 matrix struct (double) **/ - double m[3][3] ; -} nifti_dmat33 ; - -/*...........................................................................*/ - -/*! \enum analyze_75_orient_code - * \brief Old-style analyze75 orientation - * codes. - */ -typedef enum _analyze75_orient_code { - a75_transverse_unflipped = 0, - a75_coronal_unflipped = 1, - a75_sagittal_unflipped = 2, - a75_transverse_flipped = 3, - a75_coronal_flipped = 4, - a75_sagittal_flipped = 5, - a75_orient_unknown = 6 -} analyze_75_orient_code; - -/*! \struct nifti_image - \brief High level data structure for open nifti datasets in the - nifti2_io API. Note that this structure is not part of the - nifti2 format definition; it is used to implement one API - for reading/writing datasets in the nifti1 or nifti2 formats. - - Field types changed for NIFTI-2 (note: ALL floats to doubles): - nx, ny, ..., nw, dim, nvox, - dx, dy, ..., dw, pixdim, - scl_slope, scl_inter, cal_min, cal_max, - slice_start, slice_end, slice_duration, - quatern_b,c,d, qoffset_x,y,z, qfac, - qto_xyz,ijk, sto_xyz,ijk, - toffset, intent_p1,2,3, iname_offset - */ -typedef struct { /*!< Image storage struct **/ - - int64_t ndim ; /*!< last dimension greater than 1 (1..7) */ - int64_t nx ; /*!< dimensions of grid array */ - int64_t ny ; /*!< dimensions of grid array */ - int64_t nz ; /*!< dimensions of grid array */ - int64_t nt ; /*!< dimensions of grid array */ - int64_t nu ; /*!< dimensions of grid array */ - int64_t nv ; /*!< dimensions of grid array */ - int64_t nw ; /*!< dimensions of grid array */ - int64_t dim[8] ; /*!< dim[0]=ndim, dim[1]=nx, etc. */ - int64_t nvox ; /*!< number of voxels = nx*ny*nz*...*nw */ - int nbyper ; /*!< bytes per voxel, matches datatype */ - int datatype ; /*!< type of data in voxels: DT_* code */ - - double dx ; /*!< grid spacings */ - double dy ; /*!< grid spacings */ - double dz ; /*!< grid spacings */ - double dt ; /*!< grid spacings */ - double du ; /*!< grid spacings */ - double dv ; /*!< grid spacings */ - double dw ; /*!< grid spacings */ - double pixdim[8] ; /*!< pixdim[1]=dx, etc. */ - - double scl_slope ; /*!< scaling parameter - slope */ - double scl_inter ; /*!< scaling parameter - intercept */ - - double cal_min ; /*!< calibration parameter, minimum */ - double cal_max ; /*!< calibration parameter, maximum */ - - int qform_code ; /*!< codes for (x,y,z) space meaning */ - int sform_code ; /*!< codes for (x,y,z) space meaning */ - - int freq_dim ; /*!< indexes (1,2,3, or 0) for MRI */ - int phase_dim ; /*!< directions in dim[]/pixdim[] */ - int slice_dim ; /*!< directions in dim[]/pixdim[] */ - - int slice_code ; /*!< code for slice timing pattern */ - int64_t slice_start ; /*!< index for start of slices */ - int64_t slice_end ; /*!< index for end of slices */ - double slice_duration ; /*!< time between individual slices */ - - /*! quaternion transform parameters - [when writing a dataset, these are used for qform, NOT qto_xyz] */ - double quatern_b , quatern_c , quatern_d , - qoffset_x , qoffset_y , qoffset_z , - qfac ; - - nifti_dmat44 qto_xyz ; /*!< qform: transform (i,j,k) to (x,y,z) */ - nifti_dmat44 qto_ijk ; /*!< qform: transform (x,y,z) to (i,j,k) */ - - nifti_dmat44 sto_xyz ; /*!< sform: transform (i,j,k) to (x,y,z) */ - nifti_dmat44 sto_ijk ; /*!< sform: transform (x,y,z) to (i,j,k) */ - - double toffset ; /*!< time coordinate offset */ - - int xyz_units ; /*!< dx,dy,dz units: NIFTI_UNITS_* code */ - int time_units ; /*!< dt units: NIFTI_UNITS_* code */ - - int nifti_type ; /*!< see NIFTI_FTYPE_* codes, below: - 0==ANALYZE, - 1==NIFTI-1 (1 file), - 2==NIFTI-1 (2 files), - 3==NIFTI-ASCII (1 file) - 4==NIFTI-2 (1 file), - 5==NIFTI-2 (2 files) */ - - int intent_code ; /*!< statistic type (or something) */ - double intent_p1 ; /*!< intent parameters */ - double intent_p2 ; /*!< intent parameters */ - double intent_p3 ; /*!< intent parameters */ - char intent_name[16] ; /*!< optional description of intent data */ - - char descrip[80] ; /*!< optional text to describe dataset */ - char aux_file[24] ; /*!< auxiliary filename */ - - char *fname ; /*!< header filename (.hdr or .nii) */ - char *iname ; /*!< image filename (.img or .nii) */ - int64_t iname_offset ; /*!< offset into iname where data starts */ - int swapsize ; /*!< swap unit in image data (might be 0) */ - int byteorder ; /*!< byte order on disk (MSB_ or LSB_FIRST) */ - void *data ; /*!< pointer to data: nbyper*nvox bytes */ - - int num_ext ; /*!< number of extensions in ext_list */ - nifti1_extension * ext_list ; /*!< array of extension structs (with data) */ - analyze_75_orient_code analyze75_orient; /*!< for old analyze files, orient */ - -} nifti_image ; - -/* allow clarity */ -typedef nifti_image nifti2_image; - -typedef struct { - - int ndim ; /*!< last dimension greater than 1 (1..7) */ - int nx ; /*!< dimensions of grid array */ - int ny ; /*!< dimensions of grid array */ - int nz ; /*!< dimensions of grid array */ - int nt ; /*!< dimensions of grid array */ - int nu ; /*!< dimensions of grid array */ - int nv ; /*!< dimensions of grid array */ - int nw ; /*!< dimensions of grid array */ - int dim[8] ; /*!< dim[0]=ndim, dim[1]=nx, etc. */ - int64_t nvox ; /*!< number of voxels = nx*ny*nz*...*nw */ - int nbyper ; /*!< bytes per voxel, matches datatype */ - int datatype ; /*!< type of data in voxels: DT_* code */ - - float dx ; /*!< grid spacings */ - float dy ; /*!< grid spacings */ - float dz ; /*!< grid spacings */ - float dt ; /*!< grid spacings */ - float du ; /*!< grid spacings */ - float dv ; /*!< grid spacings */ - float dw ; /*!< grid spacings */ - float pixdim[8] ; /*!< pixdim[1]=dx, etc. */ - - float scl_slope ; /*!< scaling parameter - slope */ - float scl_inter ; /*!< scaling parameter - intercept */ - - float cal_min ; /*!< calibration parameter, minimum */ - float cal_max ; /*!< calibration parameter, maximum */ - - int qform_code ; /*!< codes for (x,y,z) space meaning */ - int sform_code ; /*!< codes for (x,y,z) space meaning */ - - int freq_dim ; /*!< indexes (1,2,3, or 0) for MRI */ - int phase_dim ; /*!< directions in dim[]/pixdim[] */ - int slice_dim ; /*!< directions in dim[]/pixdim[] */ - - int slice_code ; /*!< code for slice timing pattern */ - int slice_start ; /*!< index for start of slices */ - int slice_end ; /*!< index for end of slices */ - float slice_duration ; /*!< time between individual slices */ - - /*! quaternion transform parameters - [when writing a dataset, these are used for qform, NOT qto_xyz] */ - float quatern_b , quatern_c , quatern_d , - qoffset_x , qoffset_y , qoffset_z , - qfac ; - - mat44 qto_xyz ; /*!< qform: transform (i,j,k) to (x,y,z) */ - mat44 qto_ijk ; /*!< qform: transform (x,y,z) to (i,j,k) */ - - mat44 sto_xyz ; /*!< sform: transform (i,j,k) to (x,y,z) */ - mat44 sto_ijk ; /*!< sform: transform (x,y,z) to (i,j,k) */ - - float toffset ; /*!< time coordinate offset */ - - int xyz_units ; /*!< dx,dy,dz units: NIFTI_UNITS_* code */ - int time_units ; /*!< dt units: NIFTI_UNITS_* code */ - - int nifti_type ; /*!< 0==ANALYZE, 1==NIFTI-1 (1 file), - 2==NIFTI-1 (2 files), - 3==NIFTI-ASCII (1 file) */ - int intent_code ; /*!< statistic type (or something) */ - float intent_p1 ; /*!< intent parameters */ - float intent_p2 ; /*!< intent parameters */ - float intent_p3 ; /*!< intent parameters */ - char intent_name[16] ; /*!< optional description of intent data */ - - char descrip[80] ; /*!< optional text to describe dataset */ - char aux_file[24] ; /*!< auxiliary filename */ - - char *fname ; /*!< header filename (.hdr or .nii) */ - char *iname ; /*!< image filename (.img or .nii) */ - int iname_offset ; /*!< offset into iname where data starts */ - int swapsize ; /*!< swap unit in image data (might be 0) */ - int byteorder ; /*!< byte order on disk (MSB_ or LSB_FIRST) */ - void *data ; /*!< pointer to data: nbyper*nvox bytes */ - - int num_ext ; /*!< number of extensions in ext_list */ - nifti1_extension * ext_list ; /*!< array of extension structs (with data) */ - analyze_75_orient_code analyze75_orient; /*!< for old analyze files, orient */ - -} nifti1_image ; - -/* struct for return from nifti_image_read_bricks() */ -typedef struct { - int64_t nbricks; /* the number of allocated pointers in 'bricks' */ - int64_t bsize; /* the length of each data block, in bytes */ - void ** bricks; /* array of pointers to data blocks */ -} nifti_brick_list; - - -/*****************************************************************************/ -/*------------------ NIfTI version of ANALYZE 7.5 structure -----------------*/ - -/* (based on fsliolib/dbh.h, but updated for version 7.5) */ - -typedef struct { - /* header info fields - describes the header overlap with NIfTI */ - /* ------------------ */ - int sizeof_hdr; /* 0 + 4 same */ - char data_type[10]; /* 4 + 10 same */ - char db_name[18]; /* 14 + 18 same */ - int extents; /* 32 + 4 same */ - short int session_error; /* 36 + 2 same */ - char regular; /* 38 + 1 same */ - char hkey_un0; /* 39 + 1 40 bytes */ - - /* image dimension fields - describes image sizes */ - short int dim[8]; /* 0 + 16 same */ - short int unused8; /* 16 + 2 intent_p1... */ - short int unused9; /* 18 + 2 ... */ - short int unused10; /* 20 + 2 intent_p2... */ - short int unused11; /* 22 + 2 ... */ - short int unused12; /* 24 + 2 intent_p3... */ - short int unused13; /* 26 + 2 ... */ - short int unused14; /* 28 + 2 intent_code */ - short int datatype; /* 30 + 2 same */ - short int bitpix; /* 32 + 2 same */ - short int dim_un0; /* 34 + 2 slice_start */ - float pixdim[8]; /* 36 + 32 same */ - - float vox_offset; /* 68 + 4 same */ - float funused1; /* 72 + 4 scl_slope */ - float funused2; /* 76 + 4 scl_inter */ - float funused3; /* 80 + 4 slice_end, */ - /* slice_code, */ - /* xyzt_units */ - float cal_max; /* 84 + 4 same */ - float cal_min; /* 88 + 4 same */ - float compressed; /* 92 + 4 slice_duration */ - float verified; /* 96 + 4 toffset */ - int glmax,glmin; /* 100 + 8 108 bytes */ - - /* data history fields - optional */ - char descrip[80]; /* 0 + 80 same */ - char aux_file[24]; /* 80 + 24 same */ - char orient; /* 104 + 1 NO GOOD OVERLAP */ - char originator[10]; /* 105 + 10 FROM HERE DOWN... */ - char generated[10]; /* 115 + 10 */ - char scannum[10]; /* 125 + 10 */ - char patient_id[10]; /* 135 + 10 */ - char exp_date[10]; /* 145 + 10 */ - char exp_time[10]; /* 155 + 10 */ - char hist_un0[3]; /* 165 + 3 */ - int views; /* 168 + 4 */ - int vols_added; /* 172 + 4 */ - int start_field; /* 176 + 4 */ - int field_skip; /* 180 + 4 */ - int omax, omin; /* 184 + 8 */ - int smax, smin; /* 192 + 8 200 bytes */ -} nifti_analyze75; /* total: 348 bytes */ - - -/*****************************************************************************/ -/*--------------- Prototypes of functions defined in this file --------------*/ - -char const * nifti_datatype_string ( int dt ) ; -char const *nifti_units_string ( int uu ) ; -char const *nifti_intent_string ( int ii ) ; -char const *nifti_xform_string ( int xx ) ; -char const *nifti_slice_string ( int ss ) ; -char const *nifti_orientation_string( int ii ) ; - -int nifti_is_inttype( int dt ) ; - -mat44 nifti_mat44_inverse ( mat44 R ) ; -nifti_dmat44 nifti_dmat44_inverse( nifti_dmat44 R ) ; -int nifti_mat44_to_dmat44(mat44 * fm, nifti_dmat44 * dm); -int nifti_dmat44_to_mat44(nifti_dmat44 * dm, mat44 * fm); - -nifti_dmat33 nifti_dmat33_inverse( nifti_dmat33 R ) ; -nifti_dmat33 nifti_dmat33_polar ( nifti_dmat33 A ) ; -double nifti_dmat33_rownorm( nifti_dmat33 A ) ; -double nifti_dmat33_colnorm( nifti_dmat33 A ) ; -double nifti_dmat33_determ ( nifti_dmat33 R ) ; -nifti_dmat33 nifti_dmat33_mul ( nifti_dmat33 A , nifti_dmat33 B ) ; - -mat33 nifti_mat33_inverse( mat33 R ) ; -mat33 nifti_mat33_polar ( mat33 A ) ; -float nifti_mat33_rownorm( mat33 A ) ; -float nifti_mat33_colnorm( mat33 A ) ; -float nifti_mat33_determ ( mat33 R ) ; -mat33 nifti_mat33_mul ( mat33 A , mat33 B ) ; - -void nifti_swap_2bytes ( int64_t n , void *ar ) ; -void nifti_swap_4bytes ( int64_t n , void *ar ) ; -void nifti_swap_8bytes ( int64_t n , void *ar ) ; -void nifti_swap_16bytes( int64_t n , void *ar ) ; -void nifti_swap_Nbytes ( int64_t n , int siz , void *ar ) ; - -int nifti_datatype_is_valid (int dtype, int for_nifti); -int nifti_datatype_from_string (const char * name); -const char * nifti_datatype_to_string(int dtype); -int nifti_header_version (const char * buf, size_t nbytes); - -int64_t nifti_get_filesize( const char *pathname ) ; -void swap_nifti_header ( void * h , int ni_ver ) ; -void old_swap_nifti_header( struct nifti_1_header *h , int is_nifti ); -void nifti_swap_as_analyze( nifti_analyze75 *h ); -void nifti_swap_as_nifti1( nifti_1_header *h ); -void nifti_swap_as_nifti2( nifti_2_header *h ); - - -/* main read/write routines */ - -nifti_image *nifti_image_read_bricks(const char *hname , int64_t nbricks, - const int64_t *blist, nifti_brick_list * NBL); -int nifti_image_load_bricks(nifti_image *nim , int64_t nbricks, - const int64_t *blist, nifti_brick_list * NBL); -void nifti_free_NBL( nifti_brick_list * NBL ); - -nifti_image *nifti_image_read ( const char *hname , int read_data); -int nifti_image_load ( nifti_image *nim); -void nifti_image_unload ( nifti_image *nim); -void nifti_image_free ( nifti_image *nim); - -int64_t nifti_read_collapsed_image( nifti_image * nim, - const int64_t dims[8], void ** data); - -int64_t nifti_read_subregion_image(nifti_image *nim, int64_t *start_index, - int64_t *region_size, void ** data); - -void nifti_image_write ( nifti_image * nim ) ; -void nifti_image_write_bricks(nifti_image * nim, - const nifti_brick_list * NBL); -void nifti_image_infodump( const nifti_image * nim ) ; - -void nifti_disp_lib_hist( int ver ) ; /* to display library history */ -void nifti_disp_lib_version( void ) ; /* to display library version */ -int nifti_disp_matrix_orient( const char * mesg, nifti_dmat44 mat ); -int nifti_disp_type_list( int which ); - - -char * nifti_image_to_ascii ( const nifti_image * nim ) ; -nifti_image *nifti_image_from_ascii( const char * str, int * bytes_read ) ; - -int64_t nifti_get_volsize(const nifti_image *nim) ; - -/* basic file operations */ -int nifti_set_filenames(nifti_image * nim, const char * prefix, int check, - int set_byte_order); -char * nifti_makehdrname (const char * prefix, int nifti_type, int check, - int comp); -char * nifti_makeimgname (const char * prefix, int nifti_type, int check, - int comp); -int is_nifti_file (const char *hname); -char * nifti_find_file_extension(const char * name); -int nifti_is_complete_filename(const char* fname); -int nifti_validfilename(const char* fname); - - -int disp_nifti_1_header(const char * info, const nifti_1_header * hp ) ; -int disp_nifti_2_header( const char * info, const nifti_2_header * hp ) ; -void nifti_set_debug_level( int level ) ; -void nifti_set_skip_blank_ext( int skip ) ; -void nifti_set_allow_upper_fext( int allow ) ; -int nifti_get_alter_cifti( void ); -void nifti_set_alter_cifti( int alter_cifti ); - -int nifti_alter_cifti_dims(nifti_image * nim); - - -int valid_nifti_brick_list(nifti_image * nim , int64_t nbricks, - const int64_t * blist, int disp_error); - -/* znzFile operations */ -znzFile nifti_image_open(const char * hname, char * opts, nifti_image ** nim); -znzFile nifti_image_write_hdr_img(nifti_image *nim, int write_data, - const char* opts); -znzFile nifti_image_write_hdr_img2( nifti_image *nim , int write_opts , - const char* opts, znzFile imgfile, const nifti_brick_list * NBL); -int64_t nifti_read_buffer(znzFile fp, void* datatptr, int64_t ntot, - nifti_image *nim); -int nifti_write_all_data(znzFile fp, nifti_image * nim, - const nifti_brick_list * NBL); -int64_t nifti_write_buffer(znzFile fp, const void * buffer, int64_t numbytes); -nifti_image *nifti_read_ascii_image(znzFile fp, char *fname, int flen, - int read_data); -znzFile nifti_write_ascii_image(nifti_image *nim, const nifti_brick_list * NBL, - const char * opts, int write_data, int leave_open); - - -void nifti_datatype_sizes( int datatype , int *nbyper, int *swapsize ) ; - -void nifti_dmat44_to_quatern(nifti_dmat44 R , - double *qb, double *qc, double *qd, - double *qx, double *qy, double *qz, - double *dx, double *dy, double *dz, double *qfac); - -nifti_dmat44 nifti_quatern_to_dmat44( double qb, double qc, double qd, - double qx, double qy, double qz, - double dx, double dy, double dz, double qfac ); - -nifti_dmat44 nifti_make_orthog_dmat44( double r11, double r12, double r13 , - double r21, double r22, double r23 , - double r31, double r32, double r33 ) ; - -void nifti_mat44_to_quatern( mat44 R , - float *qb, float *qc, float *qd, - float *qx, float *qy, float *qz, - float *dx, float *dy, float *dz, float *qfac ) ; - -mat44 nifti_quatern_to_mat44( float qb, float qc, float qd, - float qx, float qy, float qz, - float dx, float dy, float dz, float qfac ); - -mat44 nifti_make_orthog_mat44( float r11, float r12, float r13 , - float r21, float r22, float r23 , - float r31, float r32, float r33 ) ; - -int nifti_short_order(void) ; /* CPU byte order */ - - -/* Orientation codes that might be returned from nifti_mat44_to_orientation().*/ - -#define NIFTI_L2R 1 /* Left to Right */ -#define NIFTI_R2L 2 /* Right to Left */ -#define NIFTI_P2A 3 /* Posterior to Anterior */ -#define NIFTI_A2P 4 /* Anterior to Posterior */ -#define NIFTI_I2S 5 /* Inferior to Superior */ -#define NIFTI_S2I 6 /* Superior to Inferior */ - -void nifti_mat44_to_orientation( mat44 R , int *icod, int *jcod, int *kcod ) ; -void nifti_dmat44_to_orientation( nifti_dmat44 R, - int *icod, int *jcod, int *kcod ) ; - -/*--------------------- Low level IO routines ------------------------------*/ - -char * nifti_findhdrname (const char* fname); -char * nifti_findimgname (const char* fname , int nifti_type); -int nifti_is_gzfile (const char* fname); - -char * nifti_makebasename(const char* fname); - - -/* other routines */ -int nifti_convert_nim2n1hdr(const nifti_image* nim, nifti_1_header * hdr); -int nifti_convert_nim2n2hdr(const nifti_image* nim, nifti_2_header * hdr); -nifti_1_header * nifti_make_new_n1_header(const int64_t arg_dims[], int dtype); -nifti_2_header * nifti_make_new_n2_header(const int64_t arg_dims[], int dtype); -void * nifti_read_header(const char *hname, int *nver, int check); -nifti_1_header * nifti_read_n1_hdr(const char *hname, int *swapped, int check); -nifti_2_header * nifti_read_n2_hdr(const char *hname, int *swapped, int check); -nifti_image * nifti_copy_nim_info(const nifti_image * src); -nifti_image * nifti_make_new_nim(const int64_t dims[], int datatype, - int data_fill); - - -nifti_image * nifti_simple_init_nim(void); -nifti_image * nifti_convert_n1hdr2nim(nifti_1_header nhdr,const char *fname); -nifti_image * nifti_convert_n2hdr2nim(nifti_2_header nhdr,const char *fname); - -int nifti_looks_like_cifti(nifti_image * nim); - -int nifti_hdr1_looks_good (const nifti_1_header * hdr); -int nifti_hdr2_looks_good (const nifti_2_header * hdr); -int nifti_is_valid_datatype (int dtype); -int nifti_is_valid_ecode (int ecode); -int nifti_nim_is_valid (nifti_image * nim, int complain); -int nifti_nim_has_valid_dims (nifti_image * nim, int complain); -int is_valid_nifti_type (int nifti_type); -int nifti_test_datatype_sizes (int verb); -int nifti_type_and_names_match (nifti_image * nim, int show_warn); -int nifti_update_dims_from_array(nifti_image * nim); -void nifti_set_iname_offset (nifti_image *nim); -int nifti_set_type_from_names (nifti_image * nim); -int nifti_add_extension(nifti_image * nim, const char * data, int len, - int ecode ); -int nifti_compiled_with_zlib (void); -int nifti_copy_extensions (nifti_image *nim_dest,const nifti_image *nim_src); -int nifti_free_extensions (nifti_image *nim); -int64_t * nifti_get_int64list(int64_t nvals , const char *str); -int * nifti_get_intlist (int nvals , const char *str); -char * nifti_strdup (const char *str); -int valid_nifti_extensions(const nifti_image *nim); -int nifti_valid_header_size(int ni_ver, int whine); - - -/*-------------------- Some C convenience macros ----------------------------*/ - -/* NIfTI-1.1 extension codes: - see http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q21 */ - -#define NIFTI_ECODE_IGNORE 0 /* changed from UNKNOWN, 29 June 2005 */ - -#define NIFTI_ECODE_DICOM 2 /* intended for raw DICOM attributes */ - -#define NIFTI_ECODE_AFNI 4 /* Robert W Cox: rwcox@nih.gov - https://afni.nimh.nih.gov/afni */ - -#define NIFTI_ECODE_COMMENT 6 /* plain ASCII text only */ - -#define NIFTI_ECODE_XCEDE 8 /* David B Keator: dbkeator@uci.edu - http://www.nbirn.net/Resources - /Users/Applications/ - /xcede/index.htm */ - -#define NIFTI_ECODE_JIMDIMINFO 10 /* Mark A Horsfield: - mah5@leicester.ac.uk - http://someplace/something */ - -#define NIFTI_ECODE_WORKFLOW_FWDS 12 /* Kate Fissell: fissell@pitt.edu - http://kraepelin.wpic.pitt.edu - /~fissell/NIFTI_ECODE_WORKFLOW_FWDS - /NIFTI_ECODE_WORKFLOW_FWDS.html */ - -#define NIFTI_ECODE_FREESURFER 14 /* http://surfer.nmr.mgh.harvard.edu */ - -#define NIFTI_ECODE_PYPICKLE 16 /* embedded Python objects - http://niftilib.sourceforge.net - /pynifti */ - - /* LONI MiND codes: http://www.loni.ucla.edu/twiki/bin/view/Main/MiND */ -#define NIFTI_ECODE_MIND_IDENT 18 /* Vishal Patel: vishal.patel@ucla.edu*/ -#define NIFTI_ECODE_B_VALUE 20 -#define NIFTI_ECODE_SPHERICAL_DIRECTION 22 -#define NIFTI_ECODE_DT_COMPONENT 24 -#define NIFTI_ECODE_SHC_DEGREEORDER 26 /* end LONI MiND codes */ - -#define NIFTI_ECODE_VOXBO 28 /* Dan Kimberg: www.voxbo.org */ - -#define NIFTI_ECODE_CARET 30 /* John Harwell: john@brainvis.wustl.edu - http://brainvis.wustl.edu/wiki - /index.php/Caret:Documentation - :CaretNiftiExtension */ - -#define NIFTI_ECODE_CIFTI 32 /* CIFTI-2_Main_FINAL_1March2014.pdf */ - -#define NIFTI_ECODE_VARIABLE_FRAME_TIMING 34 - -/* 36 is currently unassigned, waiting on NIFTI_ECODE_AGILENT_PROCPAR */ - -#define NIFTI_ECODE_EVAL 38 /* Munster University Hospital */ - -/* http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter */ -#define NIFTI_ECODE_MATLAB 40 /* MATLAB extension */ - - -#define NIFTI_MAX_ECODE 40 /******* maximum extension code *******/ - -/* nifti_type file codes */ -#define NIFTI_FTYPE_ANALYZE 0 /* old ANALYZE */ -#define NIFTI_FTYPE_NIFTI1_1 1 /* NIFTI-1 */ -#define NIFTI_FTYPE_NIFTI1_2 2 -#define NIFTI_FTYPE_ASCII 3 -#define NIFTI_FTYPE_NIFTI2_1 4 /* NIFTI-2 */ -#define NIFTI_FTYPE_NIFTI2_2 5 -#define NIFTI_MAX_FTYPE 5 /* this should match the maximum code */ - -/*------------------------------------------------------------------------*/ -/*-- the rest of these apply only to nifti2_io.c, check for _NIFTI2_IO_C_ */ - -#ifdef _NIFTI2_IO_C_ - -typedef struct { - int debug; /*!< debug level for status reports */ - int skip_blank_ext; /*!< skip extender if no extensions */ - int allow_upper_fext; /*!< allow uppercase file extensions */ - int alter_cifti; /*!< convert CIFTI dimensions */ -} nifti_global_options; - -typedef struct { - int type; /* should match the NIFTI_TYPE_ #define */ - int nbyper; /* bytes per value, matches nifti_image */ - int swapsize; /* bytes per swap piece, matches nifti_image */ - char const * const name; /* text string to match #define */ -} nifti_type_ele; - -#undef LNI_FERR /* local nifti file error, to be compact and repetative */ -#define LNI_FERR(func,msg,file) \ - fprintf(stderr,"** ERROR (%s): %s '%s'\n",func,msg,file) - -#undef swap_2 -#undef swap_4 -#define swap_2(s) nifti_swap_2bytes(1,&(s)) /* s: 2-byte short; swap in place */ -#define swap_4(v) nifti_swap_4bytes(1,&(v)) /* v: 4-byte value; swap in place */ - - /***** isfinite() is a C99 macro, which is - present in many C implementations already *****/ - -#undef IS_GOOD_FLOAT -#undef FIXED_FLOAT - -#ifdef isfinite /* use isfinite() to check floats/doubles for goodness */ -# define IS_GOOD_FLOAT(x) isfinite(x) /* check if x is a "good" float */ -# define FIXED_FLOAT(x) (isfinite(x) ? (x) : 0) /* fixed if bad */ -#else -# define IS_GOOD_FLOAT(x) 1 /* don't check it */ -# define FIXED_FLOAT(x) (x) /* don't fix it */ -#endif - -#undef ASSIF /* assign v to *p, if possible */ -#define ASSIF(p,v) if( (p)!=NULL ) *(p) = (v) - -#undef MSB_FIRST -#undef LSB_FIRST -#undef REVERSE_ORDER -#define LSB_FIRST 1 -#define MSB_FIRST 2 -#define REVERSE_ORDER(x) (3-(x)) /* convert MSB_FIRST <--> LSB_FIRST */ - -#define LNI_MAX_NIA_EXT_LEN 100000 /* consider a longer extension invalid */ - -#undef NIFTI_IS_16_BIT_INT -#define NIFTI_IS_16_BIT_INT(x) ((x) <= 32767 && (x) >= -32768) - -#endif /* _NIFTI2_IO_C_ section */ -/*------------------------------------------------------------------------*/ - -/*=================*/ -#ifdef __cplusplus -} -#endif -/*=================*/ - -#endif /* _NIFTI2_IO_HEADER_ */ diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/@show.diffs b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/@show.diffs deleted file mode 100755 index 0d6a53b2ae2..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/@show.diffs +++ /dev/null @@ -1,32 +0,0 @@ -#! /usr/bin/env tcsh - -set ddir = diffs -set rdirs = ( results_* ) - -# verify that there are differences to view -if ( $#rdirs < 2 ) then - echo cannot proceed, we need at least 2 result directories - exit -endif - -# make sure the output directory exists -if ( -d $ddir ) then - echo removing old diffs - \rm -f $ddir/* >& /dev/null -else - mkdir $ddir - if ( ! -d $ddir ) then - echo failed to make output directory, $ddir - exit - endif -endif - -set r1 = $rdirs[1] -set r2 = $rdirs[$#rdirs] - -cd $r2 - -foreach file (*) - echo $file... - diff ../$r1/$file $file >& ../$ddir/d.$file -end diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/@test b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/@test deleted file mode 100755 index cf59b6a3d70..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/@test +++ /dev/null @@ -1,80 +0,0 @@ -#! /usr/bin/env tcsh - -set ddir = nifti_regress_data -set prog = nifti_tool # might allow this to change - -set grind = 0 # do we run with valgrind? - -if ( $#argv > 0 ) then - if ( "$argv[1]" == "-grind" ) then - set grind = 1 - else - echo "usage: `basename $0` [-grind]" - exit - endif -endif - -# make sure $prog at least exists -# $prog -ver >& /dev/null -# if ( $status ) then -# echo "missing program '$prog' (needs to be in PATH)" -# exit -# endif - -# set date and output dir (based on grind) -set date = `date +%Y_%m_%d_%H%M` -if ( $grind ) then - set odir = vg_results_${prog}_${date} -else - set odir = results_${prog}_${date} -endif - -# note command files (in commands dir) -if ( ! -d commands ) then - echo "** failure: missing commands directory" - exit -endif - -cd commands ; set cfiles = ( c* ) ; cd .. - -if ( $#cfiles < 1 ) then - echo "** failure: no command files found in 'commands'" - exit -endif - -# create the output directory -if ( -e $odir ) then - echo "** failure: output directory '$odir' already exists" - exit -endif - -mkdir $odir - -if ( $status ) then - echo "** failure: output directory '$odir' already exists" - exit -endif - -# copy data files into output dir -cp $ddir/* $odir - -cd $odir - -# now begin the work - -echo "++ using `which $prog` ..." - -if ( $grind ) then - alias $prog "valgrind --leak-resolution=high --leak-check=full $prog" -endif - -foreach cfile ( $cfiles ) - echo -n $cfile ... - echo "--------------------------------------------------------" > e.$cfile - cat ../commands/$cfile >> e.$cfile - echo "" >> e.$cfile - echo "--------------------------" >> e.$cfile - echo "" >> e.$cfile - source ../commands/$cfile >>& e.$cfile # to keep alias - echo done -end diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/CMakeLists.txt b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/CMakeLists.txt deleted file mode 100644 index e69de29bb2d..00000000000 diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/README_regress b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/README_regress deleted file mode 100644 index 321390d780a..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/README_regress +++ /dev/null @@ -1,50 +0,0 @@ -Background: - -This is to perform regression testing, which is to say, make sure the -software works the same way that it used to. This is not to test new -features (see "modify an existing tree" for that). - -When code has been changed for a certain program that is involved in a -regression testing tree, go to that tree, run the test, and make sure -that the results have not changed (in any bad way). This is meant to -be fast and easy. - -The test consists of command scripts that were written before. The -scripts are executed, and the output is compared with the output of -an older execution. The should ususally be identical. - ---------------------------------------------------------------------------- - -To perform regression testing, one needs the data (via 'make regress_data'). -Given that, only the @test and @show_diffs are needed (sample commands are -shown with a preceeding prompt, '> '). - - 1. Run the regression testing script. It goes through the steps: - - a. Create a "results" directory, including a timestamp. - b. Copy all "data" files into it. - c. 'cd' into the "results" directory. - d. For each command script in the commands directory, execute it, - storing all output text into a file called e."command name". - - > ./@test - - - 2. To compare against an older execution, run the @show_diffs script. - It goes through the steps: - - a. Make a list of the "results" directories. - b. Create a new "diffs" directory. - c. Compare files between the newest and oldest "results" dirs: - - cd into newest "results" directory - - foreach file (*) - diff $file ../other.result/$file >& ../diffs/d.$file - - > ./@show_diffs - - - 3. Look at the sizes of the diff files, or the contents (only - expected differences should exist). - - > ls -l diffs - > cat diffs/* diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/bricks_test.sh b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/bricks_test.sh deleted file mode 100755 index 360ce0945da..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/bricks_test.sh +++ /dev/null @@ -1,35 +0,0 @@ -#!/usr/bin/env bash - -# - copy some of the sub-bricks of the default stat file, -# storing the history (command), and writing to a new 'f4.nii' -# - compare these nifti_image structs - -if [ $# -lt 2 ] -then -echo Missing nifti tool and Binary directory name -exit 1 -fi - -NT=$1 -DATA=$2 -OUT_DATA=$(dirname ${DATA}) #Need to write to separate directory -cd ${OUT_DATA} - -rm -fr ${DATA}/f4* - -if ${NT} -keep_hist -cbl -infiles ${DATA}/stat0.nii'[178..$,0,1]' -prefix ${OUT_DATA}/f4 -then -echo "" -else -echo "copy sub-bricks failed" -fi - -if ${NT} -diff_nim -infiles ${DATA}/stat0.nii ${OUT_DATA}/f4.nii -then -echo diff failed '(no diffs found' -exit 1 -else -echo diff succeeded -fi - -exit 0 diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/comment_test.sh b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/comment_test.sh deleted file mode 100755 index 1c555db0186..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/comment_test.sh +++ /dev/null @@ -1,67 +0,0 @@ -#!/bin/sh - -if [ $# -lt 2 ] -then -echo Missing nifti tool and Binary directory name -exit 1 -fi - -NT=$1 -DATA=$2 -OUT_DATA=$(dirname ${DATA}) #Need to write to separate directory -cd ${OUT_DATA} - -rm -f ${OUT_DATA}/f4.comment.nii - -# add some comment and afni extensions, then display them -if \ -${NT} -keep_hist -prefix ${OUT_DATA}/f4.comment -infiles ${DATA}/anat0.nii \ - -add_comment '4 slice time series' \ - -add_afni_ext 'and an AFNI extension' \ - -add_comment 'how about a question AND a comment?' -then -echo "" -else -echo "add comment failed" -exit 1 -fi - -if ${NT} -disp_ext -infiles ${OUT_DATA}/f4.comment.nii -then -echo "" -else -echo "failed" -exit 1 -fi - -if ${NT} -cbl -infiles ${OUT_DATA}/f4.comment.nii -prefix ${OUT_DATA}/f4.to.clear.nii -then -echo "" -else -echo "failed" -exit 1 -fi - -if ${NT} -overwrite -strip -infiles ${OUT_DATA}/f4.to.clear.nii -then -echo "" -else -echo "failed" -exit 1 -fi - -if ${NT} -disp_ext -infiles ${OUT_DATA}/f4.to.clear.nii -then -echo "" -else -echo "failed" -exit 1 -fi - -if ${NT} -diff_nim -infiles ${OUT_DATA}/f4.comment.nii ${OUT_DATA}/f4.to.clear.nii -then -echo "failed -- no changes found" -exit 1 -else -echo "diff succeed -- found changes" -fi diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/dci_test.sh b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/dci_test.sh deleted file mode 100755 index 587e842cb97..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/dci_test.sh +++ /dev/null @@ -1,48 +0,0 @@ -#!/bin/sh - -if [ $# -lt 2 ] -then -echo Missing nifti tool and Binary directory name -exit 1 -fi - -NT=$1 -DATA=$2 -OUT_DATA=$(dirname ${DATA}) #Need to write to separate directory -cd ${OUT_DATA} - -# get the time series for a slice, get the same sub-bricks, -# compare nifti_images, and display the time series again -# -# this should match the previous - -${NT} -keep_hist -cci 3 3 3 -1 -1 -1 -1 -prefix ${OUT_DATA}/r.333 -infiles ${DATA}/run.210.nii -if [ $? -ne 0 ] ; then -echo cci failed -fi - -${NT} -keep_hist -cci 3 3 3 -1 1 1 1 -prefix ${OUT_DATA}/r.333.111 -infiles ${DATA}/run.210.nii -if [ $? -ne 0 ] ; then -echo cci failed -fi - -${NT} -disp_ci -1 -1 -1 -1 -1 -1 -1 -infiles ${OUT_DATA}/r.333.111.nii -quiet \ - | tee o.10a.dci.1 -if [ $? -ne 0 ] ; then -echo disp_ci failed -fi - -${NT} -disp_ci 0 0 0 -1 1 1 1 -infiles ${OUT_DATA}/r.333.nii -quiet \ - | tee o.10a.dci.2 -if [ $? -ne 0 ] ; then -echo disp_ci failed -fi - -if diff o.10a.dci.? -then -echo "" -rm -f o.10a.dci* ${OUT_DATA}/r.333* -else -echo '** failure, o.10a.dci timeseries files differ' -exit 1 -fi diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/dsets_test.sh b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/dsets_test.sh deleted file mode 100755 index fde4a24a3c4..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/dsets_test.sh +++ /dev/null @@ -1,63 +0,0 @@ -#!/bin/sh - -if [ $# -lt 2 ] -then -echo Missing nifti tool and Binary directory name -exit 1 -fi - -NT=$1 -DATA=$2 -OUT_DATA=$(dirname ${DATA}) #Need to write to separate directory -cd ${OUT_DATA} - - -# - create datasets out of nothing -# -# - modify some fields and compare against other datasets -rm -f ${OUT_DATA}/new_epi.nii -# just test a basic make im, mostly to capture the debug output -${NT} -make_im -debug 3 -new_dim 4 64 64 21 180 0 0 0 -prefix ${OUT_DATA}/new_epi.nii -if [ $? -ne 0 ] ; then -echo failed -exit 1 -fi - -# compare hdr and nim in a fresh image to the existing one -${NT} -diff_hdr -new_dim 4 64 64 21 180 0 0 0 \ - -infiles MAKE_IM ${DATA}/stat0.nii -if [ $? = 0 ] ; then -echo unexpected 0 return code in diff -exit 1 -fi - -${NT} -diff_nim -new_dim 4 64 64 21 180 0 0 0 \ - -infiles MAKE_IM ${DATA}/stat0.nii -if [ $? = 0 ] ; then -echo unexpected 0 return code in diff -exit 1 -fi - - -rm -f ${OUT_DATA}/epi_180_pixdim.nii - -# clean up the nim by adjusting pixdim (from empty MAKE_IM) -${NT} -mod_hdr -new_dim 4 64 64 21 180 0 0 0 \ - -mod_field pixdim '0.0 4.0 4.0 6.0 3.0 1.0 1.0 1.0' \ - -prefix ${OUT_DATA}/epi_180_pixdim.nii -infiles MAKE_IM -if [ $? -ne 0 ] ; then -echo mod_hdr failed -exit 1 -fi - - -# and compare again -${NT} -diff_nim -infiles ${DATA}/stat0.nii ${OUT_DATA}/epi_180_pixdim.nii -if [ $? -ne 0 ] ; then -echo found changes -- success. -else -echo diff failed to find differences. -exit 1 -fi - -exit 0 diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/dts_test.sh b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/dts_test.sh deleted file mode 100755 index 19f301cd99f..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/dts_test.sh +++ /dev/null @@ -1,77 +0,0 @@ -#!/bin/sh - -if [ $# -lt 2 ] -then -echo Missing nifti tool and Binary directory name -exit 1 -fi - -NT=$1 -DATA=$2 -OUT_DATA=$(dirname ${DATA}) #Need to write to separate directory -cd ${OUT_DATA} - -${NT} -quiet -disp_ts 19 36 11 -infiles ${DATA}/stat0.nii | tee o.08.ts.19.36.11 - -if [ $? -ne 0 ] ; then -echo disp_ts failed -exit 1 -fi -rm -f o.08.ts.19.36.11 - -${NT} -quiet -disp_ts 19 36 11 -infiles ${DATA}/stat0.nii \ - | awk '{print $(NF-1), $NF, $1, $2}' | tee o.09.ts4.1.awk - -if [ $? -ne 0 ] ; then -echo disp_ts failed -exit 1 -fi - -${NT} -quiet -disp_ts 19 36 11 -infiles ${OUT_DATA}/f4.nii | tee o.09.ts4.2.awk - -if diff o.09.ts4.1.awk o.09.ts4.2.awk -then -echo "" -else -echo '** failure, ts4 files differ' -exit 1 -fi -rm -f 0.09.ts4.1.awk o.09.ts4.2.awk ${OUT_DATA}/f4.nii -exit 0 - -# get the time series for a slice, get the same sub-bricks, -# compare nifti_images, and display the time series again -# -# this should match the previous - -if ${NT} -keep_hist -cci 19 36 -1 -1 0 0 0 -prefix ${OUT_DATA}f.19.36 \ --infiles ${DATA}/stat0.nii -then -echo "" -else -echo cci failed -exit 1 -fi - -if ${NT} -keep_hist -cbl -prefix ${OUT_DATA}/f.19.36.t4.nii \ - -infiles ${OUT_DATA}/f.19.36.nii'[178..$,0,1]' -then -echo "" -else -echo cbi failed -exit 0 -fi - -${NT} -diff_nim -infiles ${OUT_DATA}/f.19.36.nii ${OUT_DATA}/f.19.36.t4.nii | tee o.10.diff_nim -if [ $? -ne 0 ] ; then -echo f.19.36.nii and f.19.36.t4.nii differ -else -echo f.19.36.nii and f.19.36.t4.nii do not differ -fi - -${NT} -quiet -disp_ci 0 0 11 -1 0 0 0 -infiles ${OUT_DATA}/f.19.36.t4.nii \ - | tee o.10.dci.4 -#diff o.09.ts4.1.awk o.10.dci.4 -#if( $status ) echo '** failure, o.09 and o.10 ts files differ' - -exit 0 diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/fetch_data_test.sh b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/fetch_data_test.sh deleted file mode 100755 index 5dbeb4132f4..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/fetch_data_test.sh +++ /dev/null @@ -1,54 +0,0 @@ -#!/bin/sh -# -# arg[1] is TESTING_BINARY_DIR -if [ $# -lt 1 ] -then -echo Missing Binary directory name -exit 1 -fi - -## ensure that a clean download can occur -# by preventing downloads with .1 .2 .3 suffix -# if a previous tgz file is present -rm -f nifti_regress_data.tgz* - -if cd $1 -then -echo working in `pwd` -else -echo can\'t cd to $1 -exit 1 -fi - -if wget -nd http://nifti.nimh.nih.gov/pub/dist/data/nifti_regress_data.tgz -then - echo wget succeeded -else - ## Note: On MacOSX, wget is not installed by default, but curl is - ## so use this fall back strategy when wget can not be found - if curl -O http://nifti.nimh.nih.gov/pub/dist/data/nifti_regress_data.tgz - then - echo curl succeeded - else - echo Both curl and wget failed - exit 1 - fi -fi - -if tar xzvf nifti_regress_data.tgz -then -echo "" -else -echo failed tar xzvf nifti_regress_data.tgz -exit 1 -fi - -if rm -f nifti_regress_data.tgz* -then -echo "" -else -echo can\'t remove ../nifti_regress_data.tgz -exit 1 -fi - -exit 0 diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/mod_header_test.sh b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/mod_header_test.sh deleted file mode 100755 index 672ca3789bd..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/mod_header_test.sh +++ /dev/null @@ -1,62 +0,0 @@ -#!/bin/sh - -if [ $# -lt 2 ] -then -echo Missing nifti tool and Binary directory name -exit 1 -fi - -NT=$1 -DATA=$2 -OUT_DATA=$(dirname ${DATA}) #Need to write to separate directory -cd ${OUT_DATA} - -rm -f ${OUT_DATA}/anat1* - -if ${NT} -mod_hdr -prefix ${OUT_DATA}/anat1 \ --infiles ${DATA}/anat0.nii \ --mod_field qoffset_x -17.325 -mod_field slice_start 1 \ --mod_field descrip "beer, brats and cheese, mmmmm..." -then -echo "" -else -echo mod_field failed -exit 1 -fi - -if ${NT} -diff_hdr -infiles ${DATA}/anat0.nii ${OUT_DATA}/anat1.nii -then -echo diff_hdr failed '(no difference seen)!' -exit 1 -else -echo "" -fi - -if ${NT} -add_afni_ext "wow, my first extension" \ - -add_afni_ext "look, my second.." \ - -overwrite -infiles ${OUT_DATA}/anat1.nii -then -echo "" -else -echo add_afni_ext failed -exit 1 -fi - -if ${NT} -disp_exts -infiles ${DATA}/anat0.nii ${OUT_DATA}/anat1.nii -then -echo "" -else -echo disp_exts failed -exit 1 -fi - - -if ${NT} -diff_hdr -infiles ${DATA}/anat0.nii ${OUT_DATA}/anat1.nii -then -echo diff_hdr failed '(no difference seen)!' -exit 1 -else -echo "" -fi - -exit 0 diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/newfiles_test.sh b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/newfiles_test.sh deleted file mode 100755 index 3a289e3abee..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/cmake_testscripts/newfiles_test.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh - -if [ $# -lt 2 ] -then -echo Missing nifti tool and Binary directory name -exit 1 -fi - -NT=$1 -DATA=$2 -OUT_DATA=$(dirname ${DATA}) #Need to write to separate directory -cd ${OUT_DATA} - -rm -f ${OUT_DATA}/new* ${OUT_DATA}/ncopy* - -# test writing various output file types -${NT} -make_im -prefix ${OUT_DATA}/new1.hdr -${NT} -make_im -prefix ${OUT_DATA}/new2.hdr.gz -${NT} -make_im -prefix ${OUT_DATA}/new3.img.gz -${NT} -make_im -prefix ${OUT_DATA}/new4.nii.gz -${NT} -make_im -prefix ${OUT_DATA}/new5.nia - -# test reading them -${NT} -copy_im -prefix ${OUT_DATA}/ncopy1.nii -infiles ${OUT_DATA}/new1.hdr -${NT} -copy_im -prefix ${OUT_DATA}/ncopy2.nii -infiles ${OUT_DATA}/new2.hdr.gz -${NT} -copy_im -prefix ${OUT_DATA}/ncopy3.nii -infiles ${OUT_DATA}/new3.img.gz -${NT} -copy_im -prefix ${OUT_DATA}/ncopy4.nii -infiles ${OUT_DATA}/new4.nii.gz -${NT} -copy_im -prefix ${OUT_DATA}/ncopy5.nii -infiles ${OUT_DATA}/new5.nia - -# verify that they are all the same -set count = 0 -for index in 2 3 4 5 ; do - diff ${OUT_DATA}/ncopy1.nii ${OUT_DATA}/ncopy$index.nii - if [ $? -ne 0 ] ; then - echo "-- failure on test index $index --" - exit 1 - fi -done diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c01.versions b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c01.versions deleted file mode 100644 index ed732382676..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c01.versions +++ /dev/null @@ -1,9 +0,0 @@ - -# check the version numbers for the library and tool - -nifti_tool -nifti_ver -nifti_tool -ver - -# also, check whether the library was compiled with zlib support - -nifti_tool -with_zlib diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c02.nt.help b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c02.nt.help deleted file mode 100644 index 8cdc017807b..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c02.nt.help +++ /dev/null @@ -1,4 +0,0 @@ - -nifti_tool -help -nifti_tool -help_datatypes -nifti_tool -help_datatypes T diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c03.hist b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c03.hist deleted file mode 100644 index 278b30e5fe9..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c03.hist +++ /dev/null @@ -1,5 +0,0 @@ - -# library and tool history - -nifti_tool -nifti_hist -nifti_tool -hist diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c04.disp.anat0.info b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c04.disp.anat0.info deleted file mode 100644 index fad66080913..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c04.disp.anat0.info +++ /dev/null @@ -1,7 +0,0 @@ - -# display header, nifti_image and extensions for default anat - -nifti_tool -disp_hdr -infiles anat0 -nifti_tool -disp_nim -infiles anat0 -nifti_tool -disp_ana -infiles anat0 -nifti_tool -disp_ext -infiles anat0 diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c05.mod.hdr b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c05.mod.hdr deleted file mode 100644 index c2d179a5bc1..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c05.mod.hdr +++ /dev/null @@ -1,9 +0,0 @@ - -# modify the header of default anat, creating a new anat -# -# then compare the resulting headers - -nifti_tool -mod_hdr -prefix anat1 -infiles anat0.nii \ - -mod_field qoffset_x -17.325 -mod_field slice_start 1 \ - -mod_field descrip 'beer, brats and cheese, mmmmm...' -nifti_tool -diff_hdr -infiles anat0.nii anat1.nii diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c06.add.ext b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c06.add.ext deleted file mode 100755 index e9c142405f6..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c06.add.ext +++ /dev/null @@ -1,22 +0,0 @@ -#!/bin/tcsh - -# - add junk extensions to the new anat, overwriting it -# - display extensions for the two files -# - again, compare the headers - -nifti_tool -add_afni_ext 'wow, my first extension :)' \ - -add_afni_ext 'look, my second..' \ - -overwrite -infiles anat1.nii -nifti_tool -disp_exts -infiles anat0.nii anat1.nii -nifti_tool -diff_hdr -infiles anat0.nii anat1.nii - -# add one more, via a file - -cat > my.extension << EOF -here is some formatted - extension, added via - a text file -EOF - -nifti_tool -add_comment_ext 'file:my.extension' -overwrite -infiles anat1.nii -nifti_tool -disp_exts -infiles anat1.nii diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c07.cbl.4bricks b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c07.cbl.4bricks deleted file mode 100644 index ecba78d680d..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c07.cbl.4bricks +++ /dev/null @@ -1,7 +0,0 @@ - -# - copy some of the sub-bricks of the default stat file, -# storing the history (command), and writing to a new 'f4.nii' -# - compare these nifti_image structs - -nifti_tool -keep_hist -cbl -infiles stat0.nii'[178..$,0,1]' -prefix f4 -nifti_tool -diff_nim -infiles stat0.nii f4.nii diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c08.dts.19.36.11 b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c08.dts.19.36.11 deleted file mode 100644 index 6eb797b41da..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c08.dts.19.36.11 +++ /dev/null @@ -1,4 +0,0 @@ - -# display a time series from our stat brick - -nifti_tool -quiet -disp_ts 19 36 11 -infiles stat0.nii | tee o.08.ts.19.36.11 diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c09.dts4.compare b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c09.dts4.compare deleted file mode 100644 index 48038cd0a37..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c09.dts4.compare +++ /dev/null @@ -1,9 +0,0 @@ - -# get some time series values in multiple ways, and compare - -nifti_tool -quiet -disp_ts 19 36 11 -infiles stat0.nii \ - | awk '{print $(NF-1), $NF, $1, $2}' | tee o.09.ts4.1.awk -nifti_tool -quiet -disp_ts 19 36 11 -infiles f4.nii | tee o.09.ts4.2.awk - -diff o.09.ts4.1.awk o.09.ts4.2.awk -if( $status ) echo '** failure, ts4 files differ' diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c10.dci.ts4 b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c10.dci.ts4 deleted file mode 100644 index b914947060f..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c10.dci.ts4 +++ /dev/null @@ -1,15 +0,0 @@ - -# get the time series for a slice, get the same sub-bricks, -# compare nifti_images, and display the time series again -# -# this should match the previous - -nifti_tool -keep_hist -cci 19 36 -1 -1 0 0 0 -prefix f.19.36 -infiles stat0.nii -nifti_tool -keep_hist -cbl -prefix f.19.36.t4.nii \ - -infiles f.19.36.nii'[178..$,0,1]' -nifti_tool -diff_nim -infiles f.19.36.nii f.19.36.t4.nii | tee o.10.diff_nim -nifti_tool -quiet -disp_ci 0 0 11 -1 0 0 0 -infiles f.19.36.t4.nii \ - | tee o.10.dci.4 - -diff o.09.ts4.1.awk o.10.dci.4 -if( $status ) echo '** failure, o.09 and o.10 ts files differ' diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c10a.dci.run.210 b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c10a.dci.run.210 deleted file mode 100644 index 17239f1b009..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c10a.dci.run.210 +++ /dev/null @@ -1,15 +0,0 @@ - -# get the time series for a slice, get the same sub-bricks, -# compare nifti_images, and display the time series again -# -# this should match the previous - -nifti_tool -keep_hist -cci 3 3 3 -1 -1 -1 -1 -prefix r.333 -infiles run.210.nii -nifti_tool -keep_hist -cci 3 3 3 -1 1 1 1 -prefix r.333.111 -infiles run.210.nii -nifti_tool -disp_ci -1 -1 -1 -1 -1 -1 -1 -infiles r.333.111.nii -quiet \ - | tee o.10a.dci.1 -nifti_tool -disp_ci 0 0 0 -1 1 1 1 -infiles r.333.nii -quiet \ - | tee o.10a.dci.2 - -diff o.10a.dci.? -if( $status ) echo '** failure, o.10a.dci timeseries files differ' diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c11.add.comment b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c11.add.comment deleted file mode 100644 index 04a3b00b70b..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c11.add.comment +++ /dev/null @@ -1,8 +0,0 @@ - -# add some comment and afni extensions, then display them - -nifti_tool -keep_hist -prefix f4.comment -infiles f.19.36.t4.nii \ - -add_comment '4 slice time series' \ - -add_afni_ext 'and an AFNI extension' \ - -add_comment 'how about a question AND a comment?' -nifti_tool -disp_ext -infiles f4.comment.nii diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c12.check.comments b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c12.check.comments deleted file mode 100644 index 4becb049f65..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c12.check.comments +++ /dev/null @@ -1,7 +0,0 @@ - -# duplicate a dataset, and strip the extras, then compare - -nifti_tool -cbl -infiles f4.comment.nii -prefix f4.to.clear.nii -nifti_tool -overwrite -strip -infiles f4.to.clear.nii -nifti_tool -disp_ext -infiles f4.to.clear.nii -nifti_tool -diff_nim -infiles f4.comment.nii f4.to.clear.nii diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c13.check.hdrs b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c13.check.hdrs deleted file mode 100644 index 0c61d916550..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c13.check.hdrs +++ /dev/null @@ -1,5 +0,0 @@ - -# check the nifti_1_header and nifti_image structes of the .nii files - -nifti_tool -check_hdr -infiles *.nii -nifti_tool -check_nim -infiles *.nii diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c14.make.dsets b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c14.make.dsets deleted file mode 100644 index 63d20c390bb..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c14.make.dsets +++ /dev/null @@ -1,21 +0,0 @@ - -# - create datasets out of nothing -# -# - modify some fields and compare against other datasets - -# just test a basic make im, mostly to capture the debug output -nifti_tool -make_im -debug 3 -new_dim 4 64 64 21 180 0 0 0 -prefix new_epi.nii - -# compare hdr and nim in a fresh image to the existing one -nifti_tool -diff_hdr -new_dim 4 64 64 21 180 0 0 0 \ - -infiles MAKE_IM stat0.nii -nifti_tool -diff_nim -new_dim 4 64 64 21 180 0 0 0 \ - -infiles MAKE_IM stat0.nii - -# clean up the nim by adjusting pixdim (from empty MAKE_IM) -nifti_tool -mod_hdr -new_dim 4 64 64 21 180 0 0 0 \ - -mod_field pixdim '0.0 4.0 4.0 6.0 3.0 1.0 1.0 1.0' \ - -prefix epi_180_pixdim.nii -infiles MAKE_IM - -# and compare again -nifti_tool -diff_nim -infiles stat0.nii epi_180_pixdim.nii diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c15.new.files b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c15.new.files deleted file mode 100644 index c01db54147b..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c15.new.files +++ /dev/null @@ -1,21 +0,0 @@ - -# test writing various output file types -nifti_tool -make_im -prefix new1.hdr -nifti_tool -make_im -prefix new2.hdr.gz -nifti_tool -make_im -prefix new3.img.gz -nifti_tool -make_im -prefix new4.nii.gz -nifti_tool -make_im -prefix new5.nia - -# test reading them -nifti_tool -copy_im -prefix ncopy1.nii -infiles new1.hdr -nifti_tool -copy_im -prefix ncopy2.nii -infiles new2.hdr.gz -nifti_tool -copy_im -prefix ncopy3.nii -infiles new3.img.gz -nifti_tool -copy_im -prefix ncopy4.nii -infiles new4.nii.gz -nifti_tool -copy_im -prefix ncopy5.nii -infiles new5.nia - -# verify that they are all the same -set count = 0 -foreach index ( 2 3 4 5 ) - diff ncopy1.nii ncopy$index.nii - if ( $status ) echo "-- failure on test index $index --" -end diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c16.rand.swap b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c16.rand.swap deleted file mode 100755 index a3845488072..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c16.rand.swap +++ /dev/null @@ -1,34 +0,0 @@ -#!/bin/tcsh - -echo '------------- DISP nifti_1_header -------------' -nifti_tool -disp_hdr -debug 2 -infiles rand.hdr > out.rand.hdr -echo '------------- DISP nifti_analyze75 ------------' -nifti_tool -disp_ana -debug 2 -infiles rand.hdr > out.rand.ana - -cp rand.hdr swap.ana.hdr -cp rand.hdr swap.nim.hdr -cp rand.hdr swap.old.hdr -cp rand_nifti.hdr swap.old_nifti.hdr -cp rand_nifti.hdr swap.new_nifti.hdr - -echo '------------- SWAP nifti_1_header -------------' -nifti_tool -swap_as_nifti -infiles swap.nim.hdr -overwrite -debug 2 -echo '------------- SWAP nifti_analyze75 ------------' -nifti_tool -swap_as_analyze -infiles swap.ana.hdr -overwrite -debug 2 -echo '------------- SWAP old analyze ----------------' -nifti_tool -swap_as_old -infiles swap.old.hdr -overwrite -debug 2 -echo '------------- SWAP old vs new nifti ------------------' -nifti_tool -swap_as_old -infiles swap.old_nifti.hdr -overwrite -debug 2 -nifti_tool -swap_as_nifti -infiles swap.new_nifti.hdr -overwrite -debug 2 - -echo '------------- DISP nifti_1_header swapped -------------' -nifti_tool -disp_hdr -debug 2 -infiles swap.nim.hdr > out.rand.swap.hdr -echo '------------- DISP nifti_analyze75 swapped ------------' -nifti_tool -disp_ana -debug 2 -infiles swap.ana.hdr > out.rand.swap.ana - -echo '------------- DIFF old/new analyze -----------' -nifti_tool -diff_hdr -debug 2 -infiles swap.old.hdr swap.ana.hdr \ - > out.rand.swap.compare.analyze -echo '------------- DIFF old/new nifti -------------' -nifti_tool -diff_hdr -debug 2 -infiles swap.new_nifti.hdr swap.old_nifti.hdr \ - > out.rand.swap.compare.nifti diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c17.file.case b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c17.file.case deleted file mode 100644 index f062ccddef6..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_regress_test/commands/c17.file.case +++ /dev/null @@ -1,33 +0,0 @@ - -# - test read/write of datasets with various name cases -# - .nii .hdr .img .NII .HDR .IMG -# - compressed -# - error conditions - -# start with a basic dataset -nifti_tool -make_im -new_dim 3 3 4 5 1 0 0 0 -prefix small.nii - -set prefix = t17 - -# read/write of 3 cap cases -nifti_tool -cbl -keep_hist -infiles small.nii -prefix $prefix.1.NII -nifti_tool -cbl -keep_hist -infiles $prefix.1.NII -prefix $prefix.2.HDR -nifti_tool -cbl -keep_hist -infiles $prefix.2.HDR -prefix $prefix.3.IMG - -nifti_tool -diff_hdr -infiles $prefix.2.HDR small.nii -nifti_tool -diff_nim -infiles $prefix.2.HDR $prefix.3.IMG - -# compression cases -nifti_tool -cbl -keep_hist -infiles $prefix.1.NII -prefix $prefix.4.NII.GZ -nifti_tool -cbl -keep_hist -infiles $prefix.4.NII.GZ -prefix $prefix.5.HDR.GZ -nifti_tool -cbl -keep_hist -infiles $prefix.5.HDR.GZ -prefix $prefix.6.IMG.GZ - -nifti_tool -diff_hdr -infiles $prefix.6.HDR.GZ small.nii - -# display last header -nifti_tool -disp_hdr -infiles $prefix.6.IMG.GZ - -# error cases -echo should be errors: -nifti_tool -disp_hdr -infiles small.NII -nifti_tool -disp_hdr -infiles $prefix.4.NII.gz diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_tool.c b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_tool.c deleted file mode 100644 index 07de573f47b..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_tool.c +++ /dev/null @@ -1,5115 +0,0 @@ -/*--------------------------------------------------------------------------*/ -/*! \file nifti_tool.c - * \brief a tool for nifti file perusal, manipulation and copying - * written by Rick Reynolds, SSCC, NIMH, January 2005 - * 
- *
- * usage: nifti_tool [options] -infiles files...
- *
- * Via this tool, one should be able to:
- *
- *       - copy a set of volumes (sub-bricks) from one dataset to another
- *       - copy a dataset, restricting some dimensions to given indices
- *
- *       - display the contents of a nifti_image (or various fields)
- *       - display the contents of a nifti1_header (or various fields)
- *       - display AFNI extensions (they are text)
- *       - display the time series at coordinates i,j,k
- *       - display the data from any collapsed image
- *
- *       - do a diff on two nifti_image structs (or various fields)
- *       - do a diff on two nifti1_header structs (or various fields)
- *
- *       - add an AFNI extension
- *       - remove any extension
- *
- *       - modify any field(s) of a nifti_image
- *       - modify any field(s) of a nifti1_struct
- *
- * usage forms:
- *
- *   nifti_tool -help
- *   nifti_tool -help_hdr
- *   nifti_tool -help_hdr1
- *   nifti_tool -help_hdr2
- *   nifti_tool -help_nim
- *   nifti_tool -help_nim1
- *   nifti_tool -help_nim2
- *   nifti_tool -help_ana
- *   nifti_tool -help_datatypes
- *   nifti_tool -hist
- *   nifti_tool -ver
- *   nifti_tool -nifti_hist
- *   nifti_tool -nifti_ver
- *   nifti_tool -with_zlib
- *
- *   nifti_tool -check_hdr -infiles f1 ...
- *   nifti_tool -check_nim -infiles f1 ...
-
- *   nifti_tool -disp_cext -infiles f1 ...
- *   nifti_tool -disp_exts -infiles f1 ...
- *   nifti_tool -disp_hdr  [-field fieldname] [...] -infiles f1 ...
- *   nifti_tool -disp_hdr1 [-field fieldname] [...] -infiles f1 ...
- *   nifti_tool -disp_hdr2 [-field fieldname] [...] -infiles f1 ...
- *   nifti_tool -disp_nim  [-field fieldname] [...] -infiles f1 ...
- *   nifti_tool -disp_ana  [-field fieldname] [...] -infiles f1 ...
- *   nifti_tool -disp_ts I J K [-dci_lines] -infiles f1 ...
- *   nifti_tool -disp_ci I J K T U V W [-dci_lines] -infiles f1 ...
- *
- *   nifti_tool -diff_hdr  [-field fieldname] [...] -infiles f1 f2
- *   nifti_tool -diff_hdr1 [-field fieldname] [...] -infiles f1 f2
- *   nifti_tool -diff_hdr2 [-field fieldname] [...] -infiles f1 f2
- *   nifti_tool -diff_nim  [-field fieldname] [...] -infiles f1 f2
- *
- *   nifti_tool -add_afni_ext    "extension in quotes" -infiles f1 ...
- *   nifti_tool -add_comment_ext "extension in quotes" -infiles f1 ...
- *   nifti_tool -rm_ext ext_index -infiles f1 ...
- *
- *   nifti_tool -mod_hdr  [-mod_field fieldname new_val] [...] -infiles f1 ...
- *   nifti_tool -mod_nim  [-mod_field fieldname new_val] [...] -infiles f1 ...
- *
- *
*/ -/*-------------------------------------------------------------------------*/ - -/*! module history */ -static const char * g_history[] = -{ - "----------------------------------------------------------------------\n" - "nifti_tool modification history:\n" - "\n", - "0.1 30 December 2004 [rickr]\n" - " (Rick Reynolds of the National Institutes of Health, SSCC/DIRP/NIMH)\n" - " - skeleton version: options read and printed\n" - "\n", - "1.0 07 January 2005 [rickr]\n" - " - initial release version\n" - "\n", - "1.1 14 January 2005 [rickr]\n" - " - changed all non-error/non-debug output from stderr to stdout\n" - " note: creates a mis-match between normal output and debug messages\n" - " - modified act_diff_hdrs and act_diff_nims to do the processing in\n" - " lower-level functions\n", - " - added functions diff_hdrs, diff_hdrs_list, diff_nims, diff_nims_list\n" - " - added function get_field, to return a struct pointer via a fieldname\n" - " - made 'quiet' output more quiet (no description on output)\n" - " - made hdr and nim_fields arrays global, so do not pass in main()\n" - " - return (from main()) after first act_diff() difference\n" - "\n", - "1.2 9 February 2005 [rickr] - minor\n" - " - defined a local NTL_FERR macro (so it does not come from nifti1_io.h)\n" - " - added new set_byte_order parameter to nifti_set_filenames\n" - "\n", - "1.3 23 February 2005 [rickr] - sourceforge.net merge\n" - " - moved to utils directory\n" - " - added simple casts of 3 pointers for -pedantic warnings\n" - " - added a doxygen comment for the file\n" - "\n", - "1.4 02 March 2005 [rickr] - small update\n" - " - no validation in nifti_read_header calls\n" - "\n", - "1.5 05 April 2005 [rickr] - small update\n" - " - refuse mod_hdr for gzipped files (we cannot do partial overwrites)\n" - "\n", - "1.6 08 April 2005 [rickr] - added cbl, cci and dts functionality\n" - " - added -cbl: 'copy brick list' dataset copy functionality\n" - " - added -ccd: 'copy collapsed data' dataset copy functionality\n" - " - added -disp_ts: 'disp time series' data display functionality\n" - " - moved raw data display to disp_raw_data()\n" - "\n", - "1.7 14 April 2005 [rickr] - added data display functionality\n" - " - added -dci: 'display collapsed image' functionality\n" - " - modified -dts to use -dci\n" - " - modified and updated the help in use_full()\n" - " - changed copy_collapsed_dims to copy_collapsed_image, etc.\n", - " - fixed problem in disp_raw_data() for printing NT_DT_CHAR_PTR\n" - " - modified act_disp_ci():\n" - " o was act_disp_ts(), now displays arbitrary collapsed image data\n" - " o added missed debug filename act_disp_ci()\n" - " o can now save free() of data pointer for end of file loop\n", - " - modified disp_raw_data()\n" - " o takes a flag for whether to print newline\n" - " o trailing spaces and zeros are removed from printing floats\n" - " - added clear_float_zeros(), to remove trailing zeros\n" - "\n", - "1.8 19 April 2005 [rickr] - COMMENT extensions\n" - " - added int_list struct, and keep_hist,etypes,command fields to nt_opts\n" - " - added -add_comment_ext action\n" - " - allowed for removal of multiple extensions, including option of ALL\n" - " - added -keep_hist option, to store the command as a COMMENT extension\n", - " (includes fill_cmd_string() and add_int(), is done for all actions)\n" - " - added remove_ext_list(), for removing a list of extensions by indices\n" - " - added -strip action, to strip all extensions and descrip fields\n" - "\n", - "1.9 25 Aug 2005 [rickr] - const/string cleanup for warnings\n", - "1.10 18 Nov 2005 [rickr] - added check_hdr and check_nim actions\n", - "1.11 31 Jan 2006 [rickr] - check for new vox_offset in act_mod_hdrs\n", - "1.12 02 Mar 2006 [rickr]\n" - " - in act_cbl(), check for nt = 0 because of niftilib update 1.17\n", - "1.13 24 Apr 2006 [rickr] - act_disp_ci(): remove time series length check\n", - "1.14 04 Jun 2007 [rickr] - free_opts_mem(), to appease valgrind\n", - "1.15 05 Jun 2007 [rickr] - act_check_hdrs: free(nim)->nifti_image_free()\n", - "1.16 12 Jun 2007 [rickr] - allow creation of datasets via MAKE_IM\n", - " - added nt_image_read, nt_read_header and nt_read_bricks\n" - " to wrap nifti read functions, allowing creation of new datasets\n" - " - added -make_im, -new_dim, -new_datatype and -copy_im\n" - "1.17 13 Jun 2007 [rickr] - added help for -copy_im, enumerate examples\n", - "1.18 23 Jun 2007 [rickr] - main returns 0 on -help, -hist, -ver\n" - "1.19 28 Nov 2007 [rickr] - added -help_datatypes\n", - "1.20 13 Jun 2008 [rickr]\n" - " - added -with_zlib\n" - " - added ability to create extension from text file (for J. Gunter)\n", - "1.21 03 Aug 2008 [rickr] - ANALYZE 7.5 support\n" - " - added -help_ana, -disp_ana,\n" - " -swap_as_analyze, -swap_as_nifti, -swap_as_old\n" - "1.22 08 Oct 2008 [rickr] - allow cbl with indices in 0..nt*nu*nv*nw-1\n" - "1.23 06 Jul 2010 [rickr]\n", - " - in nt_read_bricks, bsize computation should allow for large integers\n" - "1.24 26 Sep 2012 [rickr]\n", - " - changed ana originator from char to short\n" - "2.00 29 Aug 2013 [rickr] - NIFTI-2\n", - "2.01 28 Apr 2015 [rickr] - disp_hdr1/disp_hdr2 to read as those types\n" - "2.02 01 Jun 2015 [rickr]\n", - " - disp_hdr detects type\n" - " - diff_hdr detects type\n" - " - have diff_hdr1/diff_hdr2 to read as those types\n" - "2.03 23 Jul 2015 [rickr] - handle a couple of unknown version cases\n", - "2.04 05 Aug 2015 [rickr] - incorporate nifti-2 writing library change\n", - "2.05 24 Jul 2017 [rickr]\n" - " - display ANALYZE header via appropriate NIFTI-1\n" - " - apply more PRId64 for 64-bit int I/O\n" - "----------------------------------------------------------------------\n" -}; -static char g_version[] = "version 2.05 (July 24, 2017)"; -static int g_debug = 1; - -#define _NIFTI_TOOL_C_ -#include "nifti2_io.h" -#include "nifti_tool.h" - -/* local prototypes */ -static int free_opts_mem(nt_opts * nopt); -static int num_volumes(nifti_image * nim); -static char * read_file_text(const char * filename, int * length); - -#define NTL_FERR(func,msg,file) \ - fprintf(stderr,"** ERROR (%s): %s '%s'\n",func,msg,file) - -/* val may be a function call, so evalulate first, and return result */ -#define FREE_RETURN(val) \ - do{ int tval=(val); free_opts_mem(&opts); return tval; } while(0) - -/* these are effectively constant, and are built only for verification */ -field_s g_hdr1_fields[NT_HDR1_NUM_FIELDS]; /* nifti_1_header fields */ -field_s g_hdr2_fields[NT_HDR2_NUM_FIELDS]; /* nifti_2_header fields */ -field_s g_ana_fields [NT_ANA_NUM_FIELDS]; /* nifti_analyze75 */ -field_s g_nim1_fields[NT_NIM_NUM_FIELDS]; /* nifti_image fields */ -field_s g_nim2_fields[NT_NIM_NUM_FIELDS]; /* nifti2_image fields */ - -int main( int argc, char * argv[] ) -{ - nt_opts opts; - int rv; - - if( (rv = process_opts(argc, argv, &opts)) != 0) /* then return */ - { - if( rv < 0 ) FREE_RETURN(1); /* free opts memory, and return */ - else FREE_RETURN(0); /* valid usage */ - } - - if( (rv = verify_opts(&opts, argv[0])) != 0 ) - FREE_RETURN(rv); - - /* now perform the requested action(s) */ - - if( (rv = fill_hdr1_field_array(g_hdr1_fields)) != 0 ) - FREE_RETURN(rv); - - if( (rv = fill_hdr2_field_array(g_hdr2_fields)) != 0 ) - FREE_RETURN(rv); - - if( (rv = fill_nim1_field_array(g_nim1_fields)) != 0 ) - FREE_RETURN(rv); - - if( (rv = fill_nim2_field_array(g_nim2_fields)) != 0 ) - FREE_RETURN(rv); - - if( (rv = fill_ana_field_array(g_ana_fields)) != 0 ) - FREE_RETURN(rv); - - /* 'check' functions, first */ - if( opts.check_hdr || opts.check_nim ) /* allow for both */ - FREE_RETURN( act_check_hdrs(&opts) ); - - /* copy or dts functions -- do not continue after these */ - if( opts.cbl ) FREE_RETURN( act_cbl(&opts) ); - if( opts.cci ) FREE_RETURN( act_cci(&opts) ); - if( opts.dts || opts.dci ) FREE_RETURN( act_disp_ci(&opts) ); - - /* perform modifications early, in case we allow multiple actions */ - if( opts.strip && ((rv = act_strip (&opts)) != 0) ) FREE_RETURN(rv); - - if( opts.add_exts && ((rv = act_add_exts (&opts)) != 0) ) FREE_RETURN(rv); - if( opts.rm_exts && ((rv = act_rm_ext (&opts)) != 0) ) FREE_RETURN(rv); - - if( opts.mod_hdr && ((rv = act_mod_hdrs (&opts)) != 0) ) FREE_RETURN(rv); - if( opts.mod_nim && ((rv = act_mod_nims (&opts)) != 0) ) FREE_RETURN(rv); - - if((opts.swap_hdr || opts.swap_ana || opts.swap_old ) - && ((rv = act_swap_hdrs (&opts)) != 0) ) FREE_RETURN(rv); - - /* if a diff, return wither a difference exists (like the UNIX command) */ - if( opts.diff_hdr && ((rv = act_diff_hdrs (&opts)) != 0) ) FREE_RETURN(rv); - if( opts.diff_hdr1 && ((rv = act_diff_hdr1s(&opts)) != 0) ) FREE_RETURN(rv); - if( opts.diff_hdr2 && ((rv = act_diff_hdr2s(&opts)) != 0) ) FREE_RETURN(rv); - if( opts.diff_nim && ((rv = act_diff_nims(&opts)) != 0) ) FREE_RETURN(rv); - - /* last action type is display */ - if( opts.disp_exts && ((rv = act_disp_exts(&opts)) != 0) ) FREE_RETURN(rv); - if( opts.disp_cext && ((rv = act_disp_cext(&opts)) != 0) ) FREE_RETURN(rv); - if( opts.disp_hdr && ((rv = act_disp_hdr (&opts)) != 0) ) FREE_RETURN(rv); - if( opts.disp_hdr1 && ((rv = act_disp_hdr1(&opts)) != 0) ) FREE_RETURN(rv); - if( opts.disp_hdr2 && ((rv = act_disp_hdr2(&opts)) != 0) ) FREE_RETURN(rv); - if( opts.disp_nim && ((rv = act_disp_nims(&opts)) != 0) ) FREE_RETURN(rv); - if( opts.disp_ana && ((rv = act_disp_anas(&opts)) != 0) ) FREE_RETURN(rv); - - FREE_RETURN(0); -} - -/*---------------------------------------------------------------------- - * process user options, return 0 on success - *----------------------------------------------------------------------*/ -int process_opts( int argc, char * argv[], nt_opts * opts ) -{ - int ac; - - memset(opts, 0, sizeof(*opts)); - - opts->prefix = NULL; - opts->debug = 1; /* init debug level to basic output */ - - /* init options for creating a new dataset via "MAKE_IM" */ - opts->new_datatype = NIFTI_TYPE_INT16; - opts->new_dim[0] = 3; - opts->new_dim[1] = 1; opts->new_dim[2] = 1; opts->new_dim[3] = 1; - - if( argc < 2 ) return usage(argv[0], USE_FULL); - - /* terminal options are first, the rest are sorted */ - for( ac = 1; ac < argc; ac++ ) - { - if( ! strcmp(argv[ac], "-help_datatypes") ) - { - ac++; - if( ac >= argc ) - nifti_disp_type_list(3); /* show all types */ - else if( argv[ac][0] == 'd' || argv[ac][0] == 'D' ) - nifti_disp_type_list(1); /* show DT_* types */ - else if( argv[ac][0] == 't' || argv[ac][0] == 'T' ) - nifti_test_datatype_sizes(1); /* test each nbyper and swapsize */ - else - nifti_disp_type_list(2); /* show NIFTI_* types */ - return 1; - } - else if( ! strcmp(argv[ac], "-help_hdr") ) - return usage(argv[0], USE_FIELD_HDR2); - else if( ! strcmp(argv[ac], "-help_hdr1") ) - return usage(argv[0], USE_FIELD_HDR1); - else if( ! strcmp(argv[ac], "-help_hdr2") ) - return usage(argv[0], USE_FIELD_HDR2); - else if( ! strcmp(argv[ac], "-help_nim") ) - return usage(argv[0], USE_FIELD_NIM2); - else if( ! strcmp(argv[ac], "-help_nim1") ) - return usage(argv[0], USE_FIELD_NIM1); - else if( ! strcmp(argv[ac], "-help_nim2") ) - return usage(argv[0], USE_FIELD_NIM2); - else if( ! strcmp(argv[ac], "-help_ana") ) - return usage(argv[0], USE_FIELD_ANA); - else if( ! strcmp(argv[ac], "-help") ) - return usage(argv[0], USE_FULL); - else if( ! strcmp(argv[ac], "-hist") ) - return usage(argv[0], USE_HIST); - else if( ! strcmp(argv[ac], "-ver") ) - return usage(argv[0], USE_VERSION); - else if( ! strcmp(argv[ac], "-nifti_hist") ) - { - nifti_disp_lib_hist(1); - nifti_disp_lib_hist(2); - return 1; - } - else if( ! strcmp(argv[ac], "-nifti_ver") ) - { - nifti_disp_lib_version(); - return 1; - } - else if( ! strcmp(argv[ac], "-with_zlib") ) { - printf("Was NIfTI library compiled with zlib? %s\n", - nifti_compiled_with_zlib() ? "YES" : "NO"); - return 1; - } - - /* begin normal execution options... */ - else if( ! strcmp(argv[ac], "-add_ext") ) - { - int new_ecode; - ac++; - CHECK_NEXT_OPT(ac, argc, "-add_ext"); - new_ecode = atoll(argv[ac]); - if( add_int(&opts->etypes, new_ecode) ) return -1; - ac++; - CHECK_NEXT_OPT(ac, argc, "-add_ext"); - if( add_string(&opts->elist, argv[ac]) ) return -1; /* add extension */ - opts->add_exts = 1; - } - else if( ! strcmp(argv[ac], "-add_afni_ext") ) - { - ac++; - CHECK_NEXT_OPT(ac, argc, "-add_afni_ext"); - if( add_string(&opts->elist, argv[ac]) ) return -1; /* add extension */ - if( add_int(&opts->etypes, NIFTI_ECODE_AFNI) ) return -1; - opts->add_exts = 1; - } - else if( ! strncmp(argv[ac], "-add_comment_ext", 12) ) - { - ac++; - CHECK_NEXT_OPT(ac, argc, "-add_comment_ext"); - if( add_string(&opts->elist, argv[ac]) ) return -1; /* add extension */ - if( add_int(&opts->etypes, NIFTI_ECODE_COMMENT) ) return -1; - opts->add_exts = 1; - } - else if( ! strcmp(argv[ac], "-check_hdr") ) - opts->check_hdr = 1; - else if( ! strcmp(argv[ac], "-check_nim") ) - opts->check_nim = 1; - else if( ! strcmp(argv[ac], "-copy_brick_list") || - ! strcmp(argv[ac], "-copy_im") || - ! strcmp(argv[ac], "-cbl") ) - { - opts->cbl = 1; - } - else if( ! strcmp(argv[ac], "-copy_collapsed_image") || - ! strcmp(argv[ac], "-cci") ) - { - /* we need to read in the 7 dimension values */ - int index; - opts->ci_dims[0] = 0; - for( index = 1; index < 8; index++ ) - { - ac++; - CHECK_NEXT_OPT_MSG(ac,argc,"-cci","7 dimension values are requred"); - if( ! isdigit(argv[ac][0]) && strcmp(argv[ac],"-1") ){ - fprintf(stderr,"** -cci param %d (= '%s') is not a valid\n" - " consider: 'nifti_tool -help'\n",index,argv[ac]); - return -1; - } - opts->ci_dims[index] = atoll(argv[ac]); - } - - opts->cci = 1; - } - else if( ! strcmp(argv[ac], "-debug") ) - { - ac++; - CHECK_NEXT_OPT(ac, argc, "-debug"); - opts->debug = atoi(argv[ac]); - g_debug = opts->debug; - } - else if( ! strcmp(argv[ac], "-diff_hdr") ) - opts->diff_hdr = 1; - else if( ! strcmp(argv[ac], "-diff_hdr1") ) - opts->diff_hdr1 = 1; - else if( ! strcmp(argv[ac], "-diff_hdr2") ) - opts->diff_hdr2 = 1; - else if( ! strcmp(argv[ac], "-diff_nim") ) - opts->diff_nim = 1; - else if( ! strncmp(argv[ac], "-disp_exts", 9) ) - opts->disp_exts = 1; - else if( ! strncmp(argv[ac], "-disp_cext", 9) ) - opts->disp_cext = 1; - else if( ! strcmp(argv[ac], "-disp_hdr") ) - opts->disp_hdr = 1; - else if( ! strcmp(argv[ac], "-disp_hdr1") ) - opts->disp_hdr1 = 1; - else if( ! strcmp(argv[ac], "-disp_hdr2") ) - opts->disp_hdr2 = 1; - else if( ! strcmp(argv[ac], "-disp_nim") ) - opts->disp_nim = 1; - else if( ! strcmp(argv[ac], "-disp_ana") ) - opts->disp_ana = 1; - else if( ! strcmp(argv[ac], "-dci_lines") || /* before -dts */ - ! strcmp(argv[ac], "-dts_lines") ) - { - opts->dci_lines = 1; - } - else if( ! strcmp(argv[ac], "-disp_collapsed_image") || - ! strcmp(argv[ac], "-disp_ci") ) - { - /* we need to read in the 7 dimension values */ - int index; - opts->ci_dims[0] = 0; - for( index = 1; index < 8; index++ ) - { - ac++; - CHECK_NEXT_OPT_MSG(ac,argc,"-disp_ci", - "7 dimension values are requred"); - if( ! isdigit(argv[ac][0]) && strcmp(argv[ac],"-1") ){ - fprintf(stderr,"** -disp_ci param %d (= '%s') is not a valid\n" - " consider: 'nifti_tool -help'\n",index,argv[ac]); - return -1; - } - opts->ci_dims[index] = atoll(argv[ac]); - } - - opts->dci = 1; - } - else if( ! strcmp(argv[ac], "-disp_ts") || - ! strcmp(argv[ac], "-dts") ) - { - /* we need to read in the ijk indices into the ci_dims array */ - int index; - for( index = 1; index <= 3; index++ ) - { - ac++; - CHECK_NEXT_OPT_MSG(ac,argc,"-dts","i,j,k indices are requied\n"); - if( ! isdigit(argv[ac][0]) ){ - fprintf(stderr,"** -dts param %d (= '%s') is not a number\n" - " consider: 'nifti_tool -help'\n",index,argv[ac]); - return -1; - } - opts->ci_dims[index] = atoll(argv[ac]); - } - /* and fill the rest of the array */ - opts->ci_dims[0] = 0; - for( index = 4; index < 8; index++ ) opts->ci_dims[index] = -1; - - opts->dts = 1; - } - else if( ! strcmp(argv[ac], "-field") ) - { - ac++; - CHECK_NEXT_OPT(ac, argc, "-field"); - if( add_string(&opts->flist, argv[ac]) ) return -1; /* add field */ - } - else if( ! strncmp(argv[ac], "-infiles", 3) ) - { - int count; - /* for -infiles, get all next arguments until a '-' or done */ - ac++; - for( count = 0; (ac < argc) && (argv[ac][0] != '-'); ac++, count++ ) - if( add_string(&opts->infiles, argv[ac]) ) return -1;/* add field */ - if( count > 0 && ac < argc ) ac--; /* more options to process */ - if( g_debug > 2 ) fprintf(stderr,"+d have %d file names\n", count); - } - else if( ! strncmp(argv[ac], "-make_image", 8) ) - { - opts->make_im = 1; /* will setup later, as -cbl and MAKE_IM */ - } - else if( ! strcmp(argv[ac], "-mod_field") ) - { - ac++; - CHECK_NEXT_OPT(ac, argc, "-mod_field"); - if( add_string(&opts->flist, argv[ac]) ) return -1; /* add field */ - ac++; - CHECK_NEXT_OPT(ac, argc, "-mod_field (2)"); - if( add_string(&opts->vlist, argv[ac]) ) return -1; /* add value */ - } - else if( ! strcmp(argv[ac], "-mod_hdr") ) - opts->mod_hdr = 1; - else if( ! strcmp(argv[ac], "-mod_nim") ) - opts->mod_nim = 1; - else if( ! strcmp(argv[ac], "-keep_hist") ) - opts->keep_hist = 1; - else if( ! strcmp(argv[ac], "-new_dim") ) - { - /* we need to read in the 8 dimension values */ - int index; - for( index = 0; index < 8; index++ ) - { - ac++; - CHECK_NEXT_OPT_MSG(ac,argc,"-new_dim","8 dim values are requred"); - if( ! isdigit(argv[ac][0]) && strcmp(argv[ac],"-1") ){ - fprintf(stderr,"** -new_dim param %d (= '%s') is not a valid\n" - " consider: 'nifti_tool -help'\n",index,argv[ac]); - return -1; - } - opts->new_dim[index] = atoll(argv[ac]); - } - } - else if( ! strcmp(argv[ac], "-new_datatype") ) - { - ac++; - CHECK_NEXT_OPT(ac, argc, "-new_datatype"); - opts->new_datatype = atoi(argv[ac]); - } - else if( ! strcmp(argv[ac], "-overwrite") ) - opts->overwrite = 1; - else if( ! strcmp(argv[ac], "-prefix") ) - { - ac++; - CHECK_NEXT_OPT(ac, argc, "-prefix"); - opts->prefix = argv[ac]; - } - else if( ! strcmp(argv[ac], "-quiet") ) - opts->debug = 0; - else if( ! strcmp(argv[ac], "-rm_ext") ) - { - ac++; - CHECK_NEXT_OPT(ac, argc, "-rm_ext"); - if( strcmp(argv[ac],"ALL") == 0 ) /* special case, pass -1 */ - { - if( add_string(&opts->elist, "-1") ) return -1; - } - else - { - int index = atoi(argv[ac]); - if( (index != -1) && ((index > 1000) || !isdigit(*argv[ac])) ){ - fprintf(stderr, - "** '-rm_ext' requires an extension index (read '%s')\n", - argv[ac]); - return -1; - } - if( add_string(&opts->elist, argv[ac]) ) return -1; - } - opts->rm_exts = 1; - } - else if( ! strncmp(argv[ac], "-strip_extras", 6) ) - opts->strip = 1; - else if( ! strcmp(argv[ac], "-swap_as_analyze") ) - opts->swap_ana = 1; - else if( ! strcmp(argv[ac], "-swap_as_nifti") ) - opts->swap_hdr = 1; - else if( ! strcmp(argv[ac], "-swap_as_old") ) - opts->swap_old = 1; - else - { - fprintf(stderr,"** unknown option: '%s'\n", argv[ac]); - return -1; - } - } - - if( opts->make_im ) - { - if( opts->infiles.len > 0 ) - { - fprintf(stderr,"** -infiles is invalid when using -make_im\n"); - return -1; - } - /* apply -make_im via -cbl and "MAKE_IM" */ - opts->cbl = 1; - if( add_string(&opts->infiles, NT_MAKE_IM_NAME) ) return -1; - } - - /* verify for programming purposes */ - if( opts->add_exts && ( opts->elist.len != opts->etypes.len ) ) - { - fprintf(stderr,"** ext list length (%d) != etype length (%d)\n", - opts->elist.len, opts->etypes.len); - return -1; - } - - g_debug = opts->debug; - nifti_set_debug_level(g_debug); - - fill_cmd_string(opts, argc, argv); /* copy this command */ - - if( g_debug > 2 ) disp_nt_opts("options read: ", opts); - - return 0; -} - - -/*---------------------------------------------------------------------- - * verify that the options make sense - *----------------------------------------------------------------------*/ -int verify_opts( nt_opts * opts, char * prog ) -{ - int ac, errs = 0; /* number of requested action types */ - - /* check that only one of disp, diff, mod or add_*_ext is used */ - ac = (opts->check_hdr || opts->check_nim ) ? 1 : 0; - ac += (opts->diff_hdr || opts->diff_hdr1 || opts->diff_hdr2 - || opts->diff_nim ) ? 1 : 0; - ac += (opts->disp_hdr || opts->disp_hdr1 || opts->disp_hdr2 - || opts->disp_nim || opts->disp_ana - || opts->disp_exts || opts->disp_cext) ? 1 : 0; - ac += (opts->mod_hdr || opts->mod_nim ) ? 1 : 0; - ac += (opts->swap_hdr || opts->swap_ana || opts->swap_old ) ? 1 : 0; - ac += (opts->add_exts || opts->rm_exts ) ? 1 : 0; - ac += (opts->strip ) ? 1 : 0; - ac += (opts->cbl ) ? 1 : 0; - ac += (opts->cci ) ? 1 : 0; - ac += (opts->dts || opts->dci ) ? 1 : 0; - - if( ac < 1 ) - { - fprintf(stderr, - "** no action option, so nothing to do...\n" - " (try one of '-add...', '-diff...', '-disp...' or '-mod...')\n" - " (see '%s -help' for details)\n", prog); - return 1; - } - else if( ac > 1 ) - { - fprintf(stderr, - "** only one action option is allowed, please use only one of:\n" - " '-add_...', '-check_...', '-diff_...', '-disp_...',\n" - " '-mod_...', '-strip', '-dts', '-cbl' or '-cci'\n" - " (see '%s -help' for details)\n", prog); - return 1; - } - - /* can modify nifti_1_header or nifti_image, but not both */ - if( opts->mod_hdr && opts->mod_nim ) - { - fprintf(stderr,"** cannot use both '-mod_hdr' and '-mod_nim'\n"); - return 1; - } - - /* can add or remove extensions, but not both */ - if( opts->add_exts && opts->rm_exts ) - { - fprintf(stderr,"** cannot use both '-add_*_ext' and '-rm_ext'\n"); - return 1; - } - if( (opts->add_exts || opts->rm_exts) && opts->elist.len <= 0 ) - { - fprintf(stderr,"** missing extensions to add or remove\n"); - return 1; - } - - /* if modify, then we need fields and corresponding values */ - if( opts->mod_hdr || opts->mod_nim ) - { - if( opts->flist.len <= 0 ) - { - fprintf(stderr,"** missing field to modify (need '-mod_field' opt)\n"); - return 1; - } - if( opts->flist.len != opts->vlist.len ) - { - fprintf(stderr,"** error: modifying %d fields with %d values\n", - opts->flist.len, opts->vlist.len); - return 1; - } - } - - /* verify the number of files given for each of 4 action types */ - - /* -diff_... : require nfiles == 2 */ - if( opts->diff_hdr1 || opts->diff_nim ) - { - if( opts->infiles.len != 2 ) - { - fprintf(stderr,"** '-diff_XXX' options require exactly 2 inputs files\n"); - return 1; - } - } - /* if we are making changes, but not overwriting... */ - else if( (opts->elist.len > 0 || opts->mod_hdr || opts->mod_nim || - opts->swap_hdr || opts->swap_ana || opts->swap_old ) && - !opts->overwrite ) - { - if( opts->infiles.len > 1 ) - { - fprintf(stderr,"** without -overwrite, only one input file may be" - " modified at a time\n"); - errs++; - } - else if( ! opts->prefix ) - { - fprintf(stderr,"** missing -prefix for output file\n"); - errs++; - } - } - - if( opts->dci_lines && ! opts->dts && ! opts->dci ) - { - fprintf(stderr,"** option '-dci_lines' must only be used with '-dts'\n"); - errs++; - } - - if( opts->infiles.len <= 0 ) /* in any case */ - { - fprintf(stderr,"** missing input files (see -infiles option)\n"); - errs++; - } - - if ( opts->overwrite && opts->prefix ) - { - fprintf(stderr, "** please specify only one of -prefix and -overwrite\n"); - errs++; - } - - if( errs ) return 1; - - if( g_debug > 1 ) fprintf(stderr,"+d options seem valid\n"); - - return 0; -} - - -/*---------------------------------------------------------------------- - * re-assemble the command string into opts->command - *----------------------------------------------------------------------*/ -int fill_cmd_string( nt_opts * opts, int argc, char * argv[]) -{ - char * cp; - int len, remain = NT_CMD_LEN; /* NT_CMD_LEN is max command len */ - int c, ac; - int has_space; /* arguments containing space must be quoted */ - int skip = 0; /* counter to skip some of the arguments */ - - /* get the first argument separately */ - len = sprintf( opts->command, "\n command: %s", argv[0] ); - cp = opts->command + len; - remain -= len; - - /* get the rest, with special attention to input files */ - for( ac = 1; ac < argc; ac++ ) - { - if( skip ){ skip--; continue; } /* then skip these arguments */ - - len = strlen(argv[ac]); - if( len + 3 >= remain ) { /* extra 3 for space and possible '' */ - fprintf(stderr,"FCS: no space remaining for command, continuing...\n"); - return 1; - } - - /* put the argument in, possibly with '' */ - - has_space = 0; - for( c = 0; c < len-1; c++ ) - if( isspace(argv[ac][c]) ){ has_space = 1; break; } - if( has_space ) len = sprintf(cp, " '%s'", argv[ac]); - else len = sprintf(cp, " %s", argv[ac]); - - remain -= len; - - /* infiles is okay, but after the *next* argument, we may skip files */ - /* (danger, will robinson! hack alert!) */ - if( !strcmp(argv[ac-1],"-infiles") ) - { - /* if more than 4 (just to be arbitrary) input files, - include only the first and last */ - if( opts->infiles.len > 4 ) - skip = opts->infiles.len - 2; - } - - cp += len; - } - - if( g_debug > 1 ){ - fprintf(stderr,"+d filled command string, %d args, %d bytes\n", - argc, (int)(cp - opts->command)); - if( g_debug > 2 ) fprintf(stderr,"%s\n", opts->command); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * - only bother to alloc one pointer at a time (don't need efficiency here) - * - return 0 on success - *----------------------------------------------------------------------*/ -int add_int(int_list * ilist, int val) -{ - if( ilist->len == 0 ) ilist->list = NULL; /* just to be safe */ - ilist->len++; - ilist->list = (int *)realloc(ilist->list,ilist->len*sizeof(int)); - if( ! ilist->list ){ - fprintf(stderr,"** failed to alloc %d (int *) elements\n",ilist->len); - return -1; - } - - ilist->list[ilist->len-1] = val; - - return 0; -} - - -/*---------------------------------------------------------------------- - * - do not duplicate the string - * - only bother to alloc one pointer at a time (don't need efficiency here) - * - return 0 on success - *----------------------------------------------------------------------*/ -int add_string(str_list * slist, const char * str) -{ - if( slist->len == 0 ) slist->list = NULL; /* just to be safe */ - slist->len++; - slist->list = (const char **)realloc(slist->list,slist->len*sizeof(char *)); - if( ! slist->list ){ - fprintf(stderr,"** failed to alloc %d (char *) elements\n",slist->len); - return -1; - } - - slist->list[slist->len-1] = str; - - return 0; -} - - -/*---------------------------------------------------------------------- - * display information on using the program - *----------------------------------------------------------------------*/ -int usage(char * prog, int level) -{ - int c, len; - if( level == USE_SHORT ) - { - fprintf(stdout,"usage %s [options] -infiles files...\n", prog); - fprintf(stdout,"usage %s -help\n", prog); - return -1; - } - else if( level == USE_FULL ) - use_full(); /* let's not allow paths in here */ - else if( level == USE_HIST ) - { - len = sizeof(g_history)/sizeof(char *); - for( c = 0; c < len; c++) - fputs(g_history[c], stdout); - } - else if( level == USE_FIELD_HDR1 ) - { - field_s nhdr_fields[NT_HDR1_NUM_FIELDS]; /* just do it all here */ - - fill_hdr1_field_array(nhdr_fields); - disp_field_s_list("nifti_1_header: ", nhdr_fields, NT_HDR1_NUM_FIELDS); - printf(" sizeof(nifti_1_header) = %d\n", (int)sizeof(nifti_1_header)); - } - else if( level == USE_FIELD_HDR2 ) - { - field_s nhdr_fields[NT_HDR2_NUM_FIELDS]; /* just do it all here */ - - fill_hdr2_field_array(nhdr_fields); - disp_field_s_list("nifti_2_header: ", nhdr_fields, NT_HDR2_NUM_FIELDS); - printf(" sizeof(nifti_2_header) = %d\n", (int)sizeof(nifti_2_header)); - } - else if( level == USE_FIELD_ANA ) - { - field_s nhdr_fields[NT_ANA_NUM_FIELDS]; /* just do it all here */ - - fill_ana_field_array(nhdr_fields); - disp_field_s_list("nifti_analyze75: ",nhdr_fields,NT_ANA_NUM_FIELDS); - printf(" sizeof(nifti_analyze75) = %d\n", (int)sizeof(nifti_analyze75)); - } - else if( level == USE_FIELD_NIM1 ) - { - field_s nim_fields[NT_NIM_NUM_FIELDS]; - - fill_nim1_field_array(nim_fields); - disp_field_s_list("nifti1_image: ", nim_fields, NT_NIM_NUM_FIELDS); - printf(" sizeof(nifti1_image) = %d\n", (int)sizeof(nifti1_image)); - } - else if( level == USE_FIELD_NIM2 ) - { - field_s nim_fields[NT_NIM_NUM_FIELDS]; - - fill_nim2_field_array(nim_fields); - disp_field_s_list("nifti2_image: ", nim_fields, NT_NIM_NUM_FIELDS); - printf(" sizeof(nifti2_image) = %d\n", (int)sizeof(nifti2_image)); - } - else if( level == USE_VERSION ) - fprintf(stdout, "%s, %s\n", prog, g_version); - else { - fprintf(stdout,"** illegal level for usage(): %d\n", level); - return -1; - } - - return 1; -} - - -/*---------------------------------------------------------------------- - * full usage - *----------------------------------------------------------------------*/ -int use_full() -{ - printf( - "nifti_tool\n" - "\n" - " - display, modify or compare nifti structures in datasets\n" - " - copy a dataset by selecting a list of volumes from the original\n" - " - copy a dataset, collapsing any dimensions, each to a single index\n" - " - display a time series for a voxel, or more generally, the data\n" - " from any collapsed image, in ASCII text\n"); - printf( - "\n" - " This program can be used to display information from nifti datasets,\n" - " to modify information in nifti datasets, to look for differences\n" - " between two nifti datasets (like the UNIX 'diff' command), and to copy\n" - " a dataset to a new one, either by restricting any dimensions, or by\n" - " copying a list of volumes (the time dimension) from a dataset.\n" - "\n"); - printf( - " Only one action type is allowed, e.g. one cannot modify a dataset\n" - " and then take a 'diff'.\n" - "\n"); - printf( - " one can display - any or all fields in the nifti_1_header structure\n" - " - any or all fields in the nifti_image structure\n" - " - any or all fields in the nifti_analyze75 structure\n" - " - the extensions in the nifti_image structure\n" - " - the time series from a 4-D dataset, given i,j,k\n" - " - the data from any collapsed image, given dims. list\n" - "\n"); - printf( - " one can check - perform internal check on the nifti_1_header struct\n" - " (by nifti_hdr_looks_good())\n" - " - perform internal check on the nifti_image struct\n" - " (by nifti_nim_is_valid())\n" - "\n"); - printf( - " one can modify - any or all fields in the nifti_1_header structure\n" - " - any or all fields in the nifti_image structure\n" - " - swap all fields in NIFTI or ANALYZE header structure\n" - " add/rm - any or all extensions in the nifti_image structure\n" - " remove - all extensions and descriptions from the datasets\n" - "\n"); - printf( - " one can compare - any or all field pairs of nifti_1_header structures\n" - " - any or all field pairs of nifti_image structures\n" - "\n" - " one can copy - an arbitrary list of dataset volumes (time points)\n" - " - a dataset, collapsing across arbitrary dimensions\n" - " (restricting those dimensions to the given indices)\n" - "\n" - " one can create - a new dataset out of nothing\n" - "\n"); - printf( - " Note: to learn about which fields exist in either of the structures,\n" - " or to learn a field's type, size of each element, or the number\n" - " of elements in the field, use either the '-help_hdr' option, or\n" - " the '-help_nim' option. No further options are required.\n" - "\n" - " See -help_hdr, -help_hdr1, -help_hdr2, -help_ana,\n" - " -help_nim, -help_nim1, -help_nim2.\n" - "\n" - " ------------------------------\n"); - printf( - "\n" - " usage styles:\n" - "\n" - " nifti_tool -help : show this help\n" - " nifti_tool -help_hdr : show nifti_2_header field info\n" - " nifti_tool -help_hdr1 : show nifti_1_header field info\n" - " nifti_tool -help_hdr2 : show nifti_2_header field info\n" - " nifti_tool -help_nim : show nifti_image (2) field info\n" - " nifti_tool -help_nim1 : show nifti1_image field info\n" - " nifti_tool -help_nim2 : show nifti2_image field info\n" - " nifti_tool -help_ana : show nifti_analyze75 field info\n" - " nifti_tool -help_datatypes : show datatype table\n" - "\n"); - printf( - " nifti_tool -ver : show the current version\n" - " nifti_tool -hist : show the modification history\n" - " nifti_tool -nifti_ver : show the nifti library version\n" - " nifti_tool -nifti_hist : show the nifti library history\n" - " nifti_tool -with_zlib : was library compiled with zlib\n" - "\n" - "\n"); - printf( - " nifti_tool -check_hdr -infiles f1 ...\n" - " nifti_tool -check_nim -infiles f1 ...\n" - "\n"); - printf( - " nifti_tool -copy_brick_list -infiles f1'[indices...]'\n" - " nifti_tool -copy_collapsed_image I J K T U V W -infiles f1\n" - " nifti_tool -copy_im -infiles f1\n" - "\n"); - printf( - " nifti_tool -make_im -prefix new_im.nii\n" - "\n"); - printf( - " nifti_tool -disp_hdr [-field FIELDNAME] [...] -infiles f1 ...\n" - " nifti_tool -disp_hdr1 [-field FIELDNAME] [...] -infiles f1 ...\n" - " nifti_tool -disp_hdr2 [-field FIELDNAME] [...] -infiles f1 ...\n" - " nifti_tool -disp_nim [-field FIELDNAME] [...] -infiles f1 ...\n" - " nifti_tool -disp_ana [-field FIELDNAME] [...] -infiles f1 ...\n" - " nifti_tool -disp_exts -infiles f1 ...\n" - " nifti_tool -disp_cext -infiles f1 ...\n" - " nifti_tool -disp_ts I J K [-dci_lines] -infiles f1 ...\n" - " nifti_tool -disp_ci I J K T U V W [-dci_lines] -infiles f1 ...\n" - "\n"); - printf( - " nifti_tool -mod_hdr [-mod_field FIELDNAME NEW_VAL] [...] -infiles f1\n" - " nifti_tool -mod_nim [-mod_field FIELDNAME NEW_VAL] [...] -infiles f1\n" - "\n" - " nifti_tool -swap_as_nifti -overwrite -infiles f1\n" - " nifti_tool -swap_as_analyze -overwrite -infiles f1\n" - " nifti_tool -swap_as_old -overwrite -infiles f1\n" - "\n"); - printf( - " nifti_tool -add_afni_ext 'extension in quotes' [...] -infiles f1\n" - " nifti_tool -add_comment_ext 'extension in quotes' [...] -infiles f1\n" - " nifti_tool -add_comment_ext 'file:FILENAME' [...] -infiles f1\n" - " nifti_tool -rm_ext INDEX [...] -infiles f1 ...\n" - " nifti_tool -strip_extras -infiles f1 ...\n" - "\n"); - printf( - " nifti_tool -diff_hdr [-field FIELDNAME] [...] -infiles f1 f2\n" - " nifti_tool -diff_hdr1 [-field FIELDNAME] [...] -infiles f1 f2\n" - " nifti_tool -diff_hdr2 [-field FIELDNAME] [...] -infiles f1 f2\n" - " nifti_tool -diff_nim [-field FIELDNAME] [...] -infiles f1 f2\n" - "\n" - " ------------------------------\n"); - - printf( - "\n" - " selected examples:\n" - "\n" - " A. checks header (for problems):\n" - "\n" - " 1. nifti_tool -check_hdr -infiles dset0.nii dset1.nii\n" - " 2. nifti_tool -check_hdr -infiles *.nii *.hdr\n" - " 3. nifti_tool -check_hdr -quiet -infiles *.nii *.hdr\n" - "\n"); - printf( - " B. show header differences:\n" - "\n" - " 1. nifti_tool -diff_hdr -infiles dset0.nii dset1.nii \n" - " 2. nifti_tool -diff_hdr1 -infiles dset0.nii dset1.nii \n" - " 3. nifti_tool -diff_hdr2 -field dim -field intent_code \\\n" - " -infiles dset0.nii dset1.nii \n" - " 4. nifti_tool -diff_hdr1 -new_dims 3 10 20 30 0 0 0 0 \\\n" - " -infiles my_dset.nii MAKE_IM \n" - "\n" - " C. display structures or fields:\n" - "\n"); - printf( - " 1. nifti_tool -disp_hdr -infiles dset0.nii dset1.nii dset2.nii\n" - " 2. nifti_tool -disp_hdr1 -field dim -field descrip -infiles dset.nii\n" - " 3. nifti_tool -disp_hdr2 -field dim -field descrip -infiles dset.nii\n" - " 4. nifti_tool -disp_exts -infiles dset0.nii dset1.nii dset2.nii\n" - " 5. nifti_tool -disp_cext -infiles dset0.nii dset1.nii dset2.nii\n" - " 6. nifti_tool -disp_ts 23 0 172 -infiles dset1_time.nii\n" - " 7. nifti_tool -disp_ci 23 0 172 -1 0 0 0 -infiles dset1_time.nii\n" - "\n"); - printf( - " 8. nifti_tool -disp_ana -infiles analyze.hdr\n" - " 9. nifti_tool -disp_nim -infiles nifti.nii\n" - "\n"); - printf( - " D. create a new dataset from nothing:\n" - "\n" - " 1. nifti_tool -make_im -prefix new_im.nii \n" - " 2. nifti_tool -make_im -prefix float_im.nii \\\n" - " -new_dims 3 10 20 30 0 0 0 0 -new_datatype 16\n"); - printf( - " 3. nifti_tool -mod_hdr -mod_field descrip 'dataset with mods' \\\n" - " -new_dims 3 10 20 30 0 0 0 0 \\\n" - " -prefix new_desc.nii -infiles MAKE_IM\n" - "\n"); - printf( - " E. copy dataset, brick list or collapsed image:\n" - "\n" - " 1. nifti_tool -copy_im -prefix new.nii -infiles dset0.nii\n" - " 2. nifti_tool -cbl -prefix new_07.nii -infiles dset0.nii'[0,7]'\n" - " 3. nifti_tool -cbl -prefix new_partial.nii \\\n" - " -infiles dset0.nii'[3..$(2)]'\n" - "\n" - " 4. nifti_tool -cci 5 4 17 -1 -1 -1 -1 -prefix new_5_4_17.nii\n" - " 5. nifti_tool -cci 5 0 17 -1 -1 2 -1 -keep_hist \\\n" - " -prefix new_5_0_17_2.nii\n" - "\n"); - printf( - " F. modify the header (modify fields or swap entire header):\n" - "\n" - " 1. nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n" - " -mod_field dim '4 64 64 20 30 1 1 1 1'\n" - " 2. nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n" - " -mod_field descrip 'beer, brats and cheese, mmmmm...'\n" - ); - printf( - " 3. cp old_dset.hdr nifti_swap.hdr \n" - " nifti_tool -swap_as_nifti -overwrite -infiles nifti_swap.hdr\n" - " 4. cp old_dset.hdr analyze_swap.hdr \n" - " nifti_tool -swap_as_analyze -overwrite -infiles analyze_swap.hdr\n" - " 5. nifti_tool -swap_as_old -prefix old_swap.hdr -infiles old_dset.hdr\n" - " nifti_tool -diff_hdr1 -infiles nifti_swap.hdr old_swap.hdr\n" - "\n"); - printf( - " G. strip, add or remove extensions:\n" - " (in example #3, the extension is copied from a text file)\n" - "\n" - "\n" - " 1. nifti_tool -strip -overwrite -infiles *.nii\n" - " 2. nifti_tool -add_comment 'converted from MY_AFNI_DSET+orig' \\\n" - " -prefix dnew -infiles dset0.nii\n" - ); - printf( - " 3. nifti_tool -add_comment 'file:my.extension.txt' \\\n" - " -prefix dnew -infiles dset0.nii\n" - " 4. nifti_tool -rm_ext ALL -prefix dset1 -infiles dset0.nii\n" - " 5. nifti_tool -rm_ext 2 -rm_ext 3 -rm_ext 5 -overwrite \\\n" - " -infiles dset0.nii\n" - "\n" - " ------------------------------\n"); - printf( - "\n" - " options for check actions:\n" - "\n"); - printf( - " -check_hdr : check for a valid nifti_1_header struct\n" - "\n" - " This action is used to check the nifti_1_header structure for\n" - " problems. The nifti_hdr_looks_good() function is used for the\n" - " test, and currently checks:\n" - " \n" - " dim[], sizeof_hdr, magic, datatype\n" - " \n" - " More tests can be requested of the author.\n" - "\n"); - printf( - " e.g. perform checks on the headers of some datasets\n" - " nifti_tool -check_hdr -infiles dset0.nii dset1.nii\n" - " nifti_tool -check_hdr -infiles *.nii *.hdr\n" - " \n" - " e.g. add the -quiet option, so that only errors are reported\n" - " nifti_tool -check_hdr -quiet -infiles *.nii *.hdr\n" - "\n"); - printf( - " -check_nim : check for a valid nifti_image struct\n" - "\n" - " This action is used to check the nifti_image structure for\n" - " problems. This is tested via both nifti_convert_n1hdr2nim()\n" - " and nifti_nim_is_valid(), though other functions are called\n" - " below them, of course. Current checks are:\n" - "\n"); - printf( - " dim[], sizeof_hdr, datatype, fname, iname, nifti_type\n" - " \n" - " Note that creation of a nifti_image structure depends on good\n" - " header fields. So errors are terminal, meaning this check would\n" - " probably report at most one error, even if more exist. The\n" - " -check_hdr action is more complete.\n" - "\n"); - printf( - " More tests can be requested of the author.\n" - "\n"); - printf( - " e.g. nifti_tool -check_nim -infiles dset0.nii dset1.nii\n" - " e.g. nifti_tool -check_nim -infiles *.nii *.hdr\n" - "\n"); - printf( - " ------------------------------\n"); - - printf( - "\n" - " options for create action:\n" - "\n"); - printf( - " -make_im : create a new dataset from nothing\n" - "\n" - " With this the user can create a new dataset of a basic style,\n" - " which can then be modified with other options. This will create\n" - " zero-filled data of the appropriate size.\n" - " \n"); - printf( - " The default is a 1x1x1 image of shorts. These settings can be\n" - " modified with the -new_dim option, to set the 8 dimension values,\n" - " and the -new_datatype, to provide the integral type for the data.\n" - "\n"); - printf( - " See -new_dim, -new_datatype and -infiles for more information.\n" - " \n" - " Note that any -infiles dataset of the name MAKE_IM will also be\n" - " created on the fly.\n" - "\n"); - printf( - " -new_dim D0 .. D7 : specify the dim array for the a new dataset.\n" - "\n" - " e.g. -new_dim 4 64 64 27 120 0 0 0\n" - "\n" - " This dimension list will apply to any dataset created via\n" - " MAKE_IM or -make_im. All 8 values are required. Recall that\n" - " D0 is the number of dimensions, and D1 through D7 are the sizes.\n" - " \n"); - printf( - " -new_datatype TYPE : specify the dim array for the a new dataset.\n" - "\n" - " e.g. -new_datatype 16\n" - " default: -new_datatype 4 (short)\n" - "\n" - " This dimension list will apply to any dataset created via\n" - " MAKE_IM or -make_im. TYPE should be one of the NIFTI_TYPE_*\n" - " numbers, from nifti1.h.\n" - " \n"); - printf( - " ------------------------------\n"); - printf( - "\n" - " options for copy actions:\n" - "\n" - " -copy_brick_list : copy a list of volumes to a new dataset\n" - " -cbl : (a shorter, alternative form)\n" - " -copy_im : (a shorter, alternative form)\n" - "\n"); - printf( - " This action allows the user to copy a list of volumes (over time)\n" - " from one dataset to another. The listed volumes can be in any\n" - " order and contain repeats, but are of course restricted to\n" - " the set of values {1, 2, ..., nt-1}, from dimension 4.\n" - "\n"); - printf( - " This option is a flag. The index list is specified with the input\n" - " dataset, contained in square brackets. Note that square brackets\n" - " are special to most UNIX shells, so they should be contained\n" - " within single quotes. Syntax of an index list:\n" - "\n" - " notes:\n" - "\n"); - printf( - " - indices start at zero\n" - " - indices end at nt-1, which has the special symbol '$'\n" - " - single indices should be separated with commas, ','\n" - " e.g. -infiles dset0.nii'[0,3,8,5,2,2,2]'\n" - " - ranges may be specified using '..' or '-' \n"); - printf( - " e.g. -infiles dset0.nii'[2..95]'\n" - " e.g. -infiles dset0.nii'[2..$]'\n" - " - ranges may have step values, specified in ()\n" - " example: 2 through 95 with a step of 3, i.e. {2,5,8,11,...,95}\n" - " e.g. -infiles dset0.nii'[2..95(3)]'\n" - "\n"); - printf( - " This functionality applies only to 3 or 4-dimensional datasets.\n" - "\n" - " e.g. to copy a dataset:\n" - " nifti_tool -copy_im -prefix new.nii -infiles dset0.nii\n" - "\n"); - printf( - " e.g. to copy sub-bricks 0 and 7:\n" - " nifti_tool -cbl -prefix new_07.nii -infiles dset0.nii'[0,7]'\n" - "\n" - " e.g. to copy an entire dataset:\n" - " nifti_tool -cbl -prefix new_all.nii -infiles dset0.nii'[0..$]'\n" - "\n"); - printf( - " e.g. to copy every other time point, skipping the first three:\n" - " nifti_tool -cbl -prefix new_partial.nii \\\n" - " -infiles dset0.nii'[3..$(2)]'\n" - "\n" - "\n" - " -copy_collapsed_image ... : copy a list of volumes to a new dataset\n" - " -cci I J K T U V W : (a shorter, alternative form)\n" - "\n"); - printf( - " This action allows the user to copy a collapsed dataset, where\n" - " some dimensions are collapsed to a given index. For instance, the\n" - " X dimension could be collapsed to i=42, and the time dimensions\n" - " could be collapsed to t=17. To collapse a dimension, set Di to\n" - " the desired index, where i is in {0..ni-1}. Any dimension that\n" - " should not be collapsed must be listed as -1.\n" - "\n"); - printf( - " Any number (of valid) dimensions can be collapsed, even down to a\n" - " a single value, by specifying enough valid indices. The resulting\n" - " dataset will then have a reduced number of non-trivial dimensions.\n" - "\n" - " Assume dset0.nii has nim->dim[8] = { 4, 64, 64, 21, 80, 1, 1, 1 }.\n" - " Note that this is a 4-dimensional dataset.\n" - "\n"); - printf( - " e.g. copy the time series for voxel i,j,k = 5,4,17\n" - " nifti_tool -cci 5 4 17 -1 -1 -1 -1 -prefix new_5_4_17.nii\n" - "\n" - " e.g. read the single volume at time point 26\n" - " nifti_tool -cci -1 -1 -1 26 -1 -1 -1 -prefix new_t26.nii\n" - "\n"); - printf( - " Assume dset1.nii has nim->dim[8] = { 6, 64, 64, 21, 80, 4, 3, 1 }.\n" - " Note that this is a 6-dimensional dataset.\n" - "\n" - " e.g. copy all time series for voxel i,j,k = 5,0,17, with v=2\n" - " (and add the command to the history)\n" - " nifti_tool -cci 5 0 17 -1 -1 2 -1 -keep_hist \\\n" - " -prefix new_5_0_17_2.nii\n" - "\n"); - printf( - " e.g. copy all data where i=3, j=19 and v=2\n" - " (I do not claim to know a good reason to do this)\n" - " nifti_tool -cci 3 19 -1 -1 -1 2 -1 -prefix new_mess.nii\n" - "\n" - " See '-disp_ci' for more information (which displays/prints the\n" - " data, instead of copying it to a new dataset).\n" - "\n" - " ------------------------------\n"); - - printf( - "\n" - " options for display actions:\n" - "\n" - " -disp_hdr : display nifti_*_header fields for datasets\n" - "\n" - " This flag means the user wishes to see some of the nifti_*_header\n" - " fields in one or more nifti datasets. The user may want to specify\n" - " multiple '-field' options along with this. This option requires\n" - " one or more files input, via '-infiles'.\n" - "\n" - " This displays the header in its native format.\n" - "\n"); - printf( - " If no '-field' option is present, all fields will be displayed.\n" - "\n" - " e.g. to display the contents of all fields:\n" - " nifti_tool -disp_hdr -infiles dset0.nii\n" - " nifti_tool -disp_hdr -infiles dset0.nii dset1.nii dset2.nii\n" - "\n" - " e.g. to display the contents of select fields:\n" - " nifti_tool -disp_hdr -field dim -infiles dset0.nii\n" - " nifti_tool -disp_hdr -field dim -field descrip -infiles dset0.nii\n" - "\n"); - printf( - "\n" - " -disp_hdr1 : display nifti_1_header fields for datasets\n" - "\n" - " Like -disp_hdr, but only display NIFTI-1 format.\n" - "\n" - " This attempts to convert other NIFTI versions to NIFTI-1.\n" - "\n"); - printf( - "\n" - " -disp_hdr2 : display nifti_2_header fields for datasets\n" - "\n" - " Like -disp_hdr, but only display NIFTI-2 format.\n" - "\n" - " This attempts to convert other NIFTI versions to NIFTI-2.\n" - "\n"); - printf( - " -disp_nim : display nifti_image fields for datasets\n" - "\n" - " This flag option works the same way as the '-disp_hdr' option,\n" - " except that the fields in question are from the nifti_image\n" - " structure.\n" - "\n"); - printf( - " -disp_ana : display nifti_analyze75 fields for datasets\n" - "\n" - " This flag option works the same way as the '-disp_hdr' option,\n" - " except that the fields in question are from the nifti_analyze75\n" - " structure.\n" - "\n"); - printf( - " -disp_cext : display CIFTI-type extensions\n" - "\n" - " This flag option is used to display all CIFTI extension data.\n" - "\n"); - printf( - " -disp_exts : display all AFNI-type extensions\n" - "\n" - " This flag option is used to display all nifti_1_extension data,\n" - " for extensions of type AFNI (4), COMMENT (6) or CIFTI (32).\n" - "\n"); - printf( - " e.g. to display the extensions in datasets:\n" - " nifti_tool -disp_exts -infiles dset0.nii\n" - " nifti_tool -disp_exts -infiles dset0.nii dset1.nii dset2.nii\n" - "\n"); - printf( - " -disp_ts I J K : display ASCII time series at i,j,k = I,J,K\n" - "\n" - " This option is used to display the time series data for the voxel\n" - " at i,j,k indices I,J,K. The data is displayed in text, either all\n" - " on one line (the default), or as one number per line (via the\n" - " '-dci_lines' option).\n" - "\n"); - printf( - " Notes:\n" - "\n" - " o This function applies only to 4-dimensional datasets.\n" - " o The '-quiet' option can be used to suppress the text header,\n" - " leaving only the data.\n" - " o This option is short for using '-disp_ci' (display collapsed\n" - " image), restricted to 4-dimensional datasets. i.e. :\n" - " -disp_ci I J K -1 -1 -1 -1\n" - "\n"); - printf( - " e.g. to display the time series at voxel 23, 0, 172:\n" - " nifti_tool -disp_ts 23 0 172 -infiles dset1_time.nii\n" - " nifti_tool -disp_ts 23 0 172 -dci_lines -infiles dset1_time.nii\n" - " nifti_tool -disp_ts 23 0 172 -quiet -infiles dset1_time.nii\n" - "\n"); - printf( - " -disp_collapsed_image : display ASCII values for collapsed dataset\n" - " -disp_ci I J K T U V W : (a shorter, alternative form)\n" - "\n" - " This option is used to display all of the data from a collapsed\n" - " image, given the dimension list. The data is displayed in text,\n" - " either all on one line (the default), or as one number per line\n" - " (by using the '-dci_lines' flag).\n" - "\n"); - printf( - " The '-quiet' option can be used to suppress the text header.\n" - "\n" - " e.g. to display the time series at voxel 23, 0, 172:\n" - " nifti_tool -disp_ci 23 0 172 -1 0 0 0 -infiles dset1_time.nii\n" - "\n" - " e.g. to display z-slice 14, at time t=68:\n" - " nifti_tool -disp_ci -1 -1 14 68 0 0 0 -infiles dset1_time.nii\n" - "\n" - " See '-ccd' for more information, which copies such data to a new\n" - " dataset, instead of printing it to the terminal window.\n" - "\n" - " ------------------------------\n"); - printf( - "\n" - " options for modification actions:\n" - "\n" - " -mod_hdr : modify nifti_1_header fields for datasets\n" - "\n" - " This action is used to modify some of the nifti_1_header fields in\n" - " one or more datasets. The user must specify a list of fields to\n" - " modify via one or more '-mod_field' options, which include field\n" - " names, along with the new (set of) values.\n" - "\n"); - printf( - " The user can modify a dataset in place, or use '-prefix' to\n" - " produce a new dataset, to which the changes have been applied.\n" - " It is recommended to normally use the '-prefix' option, so as not\n" - " to ruin a dataset.\n" - "\n"); - printf( - " Note that some fields have a length greater than 1, meaning that\n" - " the field is an array of numbers, or a string of characters. In\n" - " order to modify an array of numbers, the user must provide the\n" - " correct number of values, and contain those values in quotes, so\n" - " that they are seen as a single option.\n" - "\n"); - printf( - " To modify a string field, put the string in quotes.\n" - "\n" - " The '-mod_field' option takes a field_name and a list of values.\n" - "\n" - " e.g. to modify the contents of various fields:\n" - "\n"); - printf( - " nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n" - " -mod_field qoffset_x -17.325\n" - " nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n" - " -mod_field dim '4 64 64 20 30 1 1 1 1'\n" - " nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n" - " -mod_field descrip 'beer, brats and cheese, mmmmm...'\n" - "\n"); - printf( - " e.g. to modify the contents of multiple fields:\n" - " nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n" - " -mod_field qoffset_x -17.325 -mod_field slice_start 1\n" - "\n" - " e.g. to modify the contents of multiple files (must overwrite):\n" - " nifti_tool -mod_hdr -overwrite -mod_field qoffset_x -17.325 \\\n" - " -infiles dset0.nii dset1.nii\n" - "\n"); - printf( - " -mod_nim : modify nifti_image fields for datasets\n" - "\n" - " This action option is used the same way that '-mod_hdr' is used,\n" - " except that the fields in question are from the nifti_image\n" - " structure.\n" - "\n"); - printf( - " -strip_extras : remove extensions and descriptions from datasets\n" - "\n" - " This action is used to attempt to 'clean' a dataset of general\n" - " text, in order to make it more anonymous. Extensions and the\n" - " nifti_image descrip field are cleared by this action.\n" - "\n"); - printf( - " e.g. to strip all *.nii datasets in this directory:\n" - " nifti_tool -strip -overwrite -infiles *.nii\n" - "\n"); - printf( - " -swap_as_nifti : swap the header according to nifti_1_header\n" - "\n" - " Perhaps a NIfTI header is mal-formed, and the user explicitly\n" - " wants to swap it before performing other operations. This action\n" - " will swap the field bytes under the assumption that the header is\n" - " in the NIfTI format.\n" - "\n"); - printf( - " ** The recommended course of action is to make a copy of the\n" - " dataset and overwrite the header via -overwrite. If the header\n" - " needs such an operation, it is likely that the data would not\n" - " otherwise be read in correctly.\n" - "\n"); - printf( - " -swap_as_analyze : swap the header according to nifti_analyze75\n" - "\n" - " Perhaps an ANALYZE header is mal-formed, and the user explicitly\n" - " wants to swap it before performing other operations. This action\n" - " will swap the field bytes under the assumption that the header is\n" - " in the ANALYZE 7.5 format.\n" - "\n"); - printf( - " ** The recommended course of action is to make a copy of the\n" - " dataset and overwrite the header via -overwrite. If the header\n" - " needs such an operation, it is likely that the data would not\n" - " otherwise be read in correctly.\n" - "\n"); - printf( - " -swap_as_old : swap the header using the old method\n" - "\n" - " As of library version 1.35 (3 Aug, 2008), nifticlib now swaps all\n" - " fields of a NIfTI dataset (including UNUSED ones), and it swaps\n" - " ANALYZE datasets according to the nifti_analyze75 structure.\n" - " This is a significant different in the case of ANALYZE datasets.\n" - "\n"); - printf( - " The -swap_as_old option was added to compare the results of the\n" - " swapping methods, or to undo one swapping method and replace it\n" - " with another (such as to undo the old method and apply the new).\n" - "\n"); - printf(" ------------------------------\n"); - printf( - "\n" - " options for adding/removing extensions:\n" - "\n" - " -add_afni_ext EXT : add an AFNI extension to the dataset\n" - "\n" - " This option is used to add AFNI-type extensions to one or more\n" - " datasets. This option may be used more than once to add more than\n" - " one extension.\n" - "\n" - " If EXT is of the form 'file:FILENAME', then the extension will\n" - " be read from the file, FILENAME.\n" - "\n"); - printf( - " The '-prefix' option is recommended, to create a new dataset.\n" - " In such a case, only a single file may be taken as input. Using\n" - " '-overwrite' allows the user to overwrite the current file, or\n" - " to add the extension(s) to multiple files, overwriting them.\n" - "\n"); - printf( - " e.g. to add a generic AFNI extension:\n" - " nifti_tool -add_afni_ext 'wow, my first extension' -prefix dnew \\\n" - " -infiles dset0.nii\n" - "\n" - " e.g. to add multiple AFNI extensions:\n" - " nifti_tool -add_afni_ext 'wow, my first extension :)' \\\n" - " -add_afni_ext 'look, my second...' \\\n" - " -prefix dnew -infiles dset0.nii\n" - "\n"); - printf( - " e.g. to add an extension, and overwrite the dataset:\n" - " nifti_tool -add_afni_ext 'some AFNI extension' -overwrite \\\n" - " -infiles dset0.nii dset1.nii \n" - "\n"); - printf( - " -add_comment_ext EXT : add a COMMENT extension to the dataset\n" - "\n" - " This option is used to add COMMENT-type extensions to one or more\n" - " datasets. This option may be used more than once to add more than\n" - " one extension. This option may also be used with '-add_afni_ext'.\n" - "\n" - " If EXT is of the form 'file:FILENAME', then the extension will\n" - " be read from the file, FILENAME.\n" - "\n"); - printf( - " The '-prefix' option is recommended, to create a new dataset.\n" - " In such a case, only a single file may be taken as input. Using\n" - " '-overwrite' allows the user to overwrite the current file, or\n" - " to add the extension(s) to multiple files, overwriting them.\n" - "\n"); - printf( - " e.g. to add a comment about the dataset:\n" - " nifti_tool -add_comment 'converted from MY_AFNI_DSET+orig' \\\n" - " -prefix dnew \\\n" - " -infiles dset0.nii\n" - "\n"); - printf( - " e.g. to add multiple extensions:\n" - " nifti_tool -add_comment 'add a comment extension' \\\n" - " -add_afni_ext 'and an AFNI XML style extension' \\\n" - " -add_comment 'dataset copied from dset0.nii' \\\n" - " -prefix dnew -infiles dset0.nii\n" - "\n"); - printf( - " -rm_ext INDEX : remove the extension given by INDEX\n" - "\n" - " This option is used to remove any single extension from the\n" - " dataset. Multiple extensions require multiple options.\n" - "\n" - " notes - extension indices begin with 0 (zero)\n" - " - to view the current extensions, see '-disp_exts'\n" - " - all extensions can be removed using ALL or -1 for INDEX\n" - "\n"); - printf( - " e.g. to remove the extension #0:\n" - " nifti_tool -rm_ext 0 -overwrite -infiles dset0.nii\n" - "\n" - " e.g. to remove ALL extensions:\n" - " nifti_tool -rm_ext ALL -prefix dset1 -infiles dset0.nii\n" - " nifti_tool -rm_ext -1 -prefix dset1 -infiles dset0.nii\n" - "\n"); - printf( - " e.g. to remove the extensions #2, #3 and #5:\n" - " nifti_tool -rm_ext 2 -rm_ext 3 -rm_ext 5 -overwrite \\\n" - " -infiles dset0.nii\n" - "\n" - " ------------------------------\n"); - - printf( - "\n" - " options for showing differences:\n" - "\n" - " -diff_hdr : display header field diffs between two datasets\n" - "\n" - " This option is used to find differences between two NIFTI-*\n" - " dataset headers. If any fields are different, the contents of\n" - " those fields are displayed (unless the '-quiet' option is used).\n" - "\n" - " The NIFTI versions must agree.\n" - "\n" - " -diff_hdr1 : display header diffs between NIFTI-1 datasets\n" - "\n" - " This option is used to find differences between two NIFTI-1\n" - " dataset headers.\n" - "\n" - " -diff_hdr2 : display header diffs between NIFTI-2 datasets\n" - "\n" - " This option is used to find differences between two NIFTI-2\n" - " dataset headers.\n" - "\n"); - printf( - " A list of fields can be specified by using multiple '-field'\n" - " options. If no '-field' option is given, all fields will be\n" - " checked.\n" - "\n" - " Exactly two dataset names must be provided via '-infiles'.\n" - "\n" - " e.g. to display all nifti_2_header field differences:\n" - " nifti_tool -diff_hdr2 -infiles dset0.nii dset1.nii\n" - "\n"); - printf( - " e.g. to display selected field differences:\n" - " nifti_tool -diff_hdr -field dim -field intent_code \\\n" - " -infiles dset0.nii dset1.nii \n" - "\n" - " -diff_nim : display nifti_image field diffs between datasets\n" - "\n" - " This option works the same as '-diff_hdr', except that the fields\n" - " in question are from the nifti_image structure.\n" - "\n" - " ------------------------------\n"); - - printf( - "\n" - " miscellaneous options:\n" - "\n" - " -debug LEVEL : set the debugging level\n" - "\n" - " Level 0 will attempt to operate with no screen output, but errors.\n" - " Level 1 is the default.\n" - " Levels 2 and 3 give progressively more information.\n" - "\n" - " e.g. -debug 2\n" - "\n"); - printf( - " -field FIELDNAME : provide a field to work with\n" - "\n" - " This option is used to provide a field to display, modify or\n" - " compare. This option can be used along with one of the action\n" - " options presented above.\n" - "\n" - " See '-disp_hdr', above, for complete examples.\n" - "\n" - " e.g. nifti_tool -field descrip\n" - " e.g. nifti_tool -field descrip -field dim\n" - "\n"); - printf( - " -infiles file0... : provide a list of files to work with\n" - "\n" - " This parameter is required for any of the actions, in order to\n" - " provide a list of files to process. If input filenames do not\n" - " have an extension, the directory we be searched for any\n" - " appropriate files (such as .nii or .hdr).\n" - "\n"); - printf( - " Note: if the filename has the form MAKE_IM, then a new dataset\n" - " will be created, without the need for file input.\n" - "\n"); - printf( - " See '-mod_hdr', above, for complete examples.\n" - "\n" - " e.g. nifti_tool -infiles file0.nii\n" - " e.g. nifti_tool -infiles file1.nii file2 file3.hdr\n" - "\n"); - printf( - " -mod_field NAME 'VALUE_LIST' : provide new values for a field\n" - "\n" - " This parameter is required for any the modification actions.\n" - " If the user wants to modify any fields of a dataset, this is\n" - " where the fields and values are specified.\n" - "\n"); - printf( - " NAME is a field name (in either the nifti_1_header structure or\n" - " the nifti_image structure). If the action option is '-mod_hdr',\n" - " then NAME must be the name of a nifti_1_header field. If the\n" - " action is '-mod_nim', NAME must be from a nifti_image structure.\n" - "\n"); - printf( - " VALUE_LIST must be one or more values, as many as are required\n" - " for the field, contained in quotes if more than one is provided.\n" - "\n" - " Use 'nifti_tool -help_hdr' to get a list of nifti_2_header fields\n" - " Use 'nifti_tool -help_hdr1' to get a list of nifti_1_header fields\n" - " Use 'nifti_tool -help_hdr2' to get a list of nifti_2_header fields\n" - " Use 'nifti_tool -help_nim' to get a list of nifti_image fields\n" - " Use 'nifti_tool -help_nim1' to get a list of nifti1_image fields\n" - " Use 'nifti_tool -help_nim2' to get a list of nifti2_image fields\n" - " Use 'nifti_tool -help_ana' to get a list of nifti_analyze75 fields\n" - "\n" - " See '-mod_hdr', above, for complete examples.\n" - "\n"); - printf( - " e.g. modifying nifti_1_header fields:\n" - " -mod_field descrip 'toga, toga, toga'\n" - " -mod_field qoffset_x 19.4 -mod_field qoffset_z -11\n" - " -mod_field pixdim '1 0.9375 0.9375 1.2 1 1 1 1'\n" - "\n"); - printf( - " -keep_hist : add the command as COMMENT (to the 'history')\n" - "\n" - " When this option is used, the current command will be added\n" - " as a NIFTI_ECODE_COMMENT type extension. This provides the\n" - " ability to keep a history of commands affecting a dataset.\n" - "\n" - " e.g. -keep_hist\n" - "\n"); - printf( - " -overwrite : any modifications will be made to input files\n" - "\n" - " This option is used so that all field modifications, including\n" - " extension additions or deletions, will be made to the files that\n" - " are input.\n" - "\n"); - printf( - " In general, the user is recommended to use the '-prefix' option\n" - " to create new files. But if overwriting the contents of the\n" - " input files is preferred, this is how to do it.\n" - "\n" - " See '-mod_hdr' or '-add_afni_ext', above, for complete examples.\n" - "\n" - " e.g. -overwrite\n" - "\n"); - printf( - " -prefix : specify an output file to write change into\n" - "\n" - " This option is used to specify an output file to write, after\n" - " modifications have been made. If modifications are being made,\n" - " then either '-prefix' or '-overwrite' is required.\n" - "\n" - " If no extension is given, the output extension will be '.nii'.\n" - "\n"); - printf( - " e.g. -prefix new_dset\n" - " e.g. -prefix new_dset.nii\n" - " e.g. -prefix new_dset.hdr\n" - "\n" - " -quiet : report only errors or requested information\n" - "\n" - " This option is equivalent to '-debug 0'.\n" - "\n" - " ------------------------------\n"); - - printf( - "\n" - " basic help options:\n" - "\n" - " -help : show this help\n" - "\n" - " e.g. nifti_tool -help\n" - "\n" - " -help_hdr : show nifti_2_header field info\n" - "\n" - " e.g. nifti_tool -help_hdr\n" - "\n" - " -help_hdr1 : show nifti_1_header field info\n" - "\n" - " e.g. nifti_tool -help_hdr1\n" - "\n" - " -help_hdr2 : show nifti_2_header field info\n" - "\n" - " e.g. nifti_tool -help_hdr2\n" - "\n" - " -help_nim : show nifti_image field info (currently NIFTI-2)\n" - "\n" - " e.g. nifti_tool -help_nim\n" - "\n" - " -help_nim1 : show nifti1_image field info\n" - "\n" - " e.g. nifti_tool -help_nim1\n" - "\n" - " -help_nim2 : show nifti2_image field info\n" - "\n" - " e.g. nifti_tool -help_nim2\n" - "\n" - " -help_ana : show nifti_analyze75 field info\n" - "\n" - " e.g. nifti_tool -help_ana\n" - ); - - printf( - "\n" - " -help_datatypes [TYPE] : display datatype table\n" - "\n" - " e.g. nifti_tool -help_datatypes\n" - " e.g. nifti_tool -help_datatypes N\n" - "\n" - " This displays the contents of the nifti_type_list table.\n" - " An additional 'D' or 'N' parameter will restrict the type\n" - " name to 'DT_' or 'NIFTI_TYPE_' names, 'T' will test.\n"); - - printf( - "\n" - " -ver : show the program version number\n" - "\n" - " e.g. nifti_tool -ver\n" - "\n" - " -hist : show the program modification history\n" - "\n" - " e.g. nifti_tool -hist\n" - "\n"); - printf( - " -nifti_ver : show the nifti library version number\n" - "\n" - " e.g. nifti_tool -nifti_ver\n" - "\n" - " -nifti_hist : show the nifti library modification history\n" - "\n" - " e.g. nifti_tool -nifti_hist\n" - "\n" - " -with_zlib : print whether library was compiled with zlib\n" - "\n" - " e.g. nifti_tool -with_zlib\n" - "\n" - " ------------------------------\n" - "\n" - " R. Reynolds\n" - " compiled: %s\n" - " %s\n\n", - __DATE__, g_version ); - - return 1; -} - - -/*---------------------------------------------------------------------- - * display the contents of the struct and all lists - *----------------------------------------------------------------------*/ -int disp_nt_opts( const char *mesg, nt_opts * opts) -{ - int c; - - if( mesg ) fputs(mesg, stderr); - if( ! opts ) - { - fprintf(stderr,"** disp_nt_opts: missing opts\n"); - return -1; - } - - fprintf(stderr,"nt_opts @ %p\n" - " check_hdr, check_nim = %d, %d\n" - " diff_hdr1, diff_hdr2 = %d, %d\n" - " diff_hdr, diff_nim = %d, %d\n" - " disp_hdr1, disp_hdr2 = %d, %d\n" - " disp_hdr, disp_nim = %d, %d\n" - " disp_ana, disp_exts = %d, %d\n" - " disp_cext = %d\n" - " add_exts, rm_exts = %d, %d\n" - " mod_hdr, mod_nim = %d, %d\n" - " swap_hdr, swap_ana = %d, %d\n" - " swap_old = %d\n" - " cbl, cci = %d, %d\n" - " dts, dci_lines = %d, %d\n" - " make_im = %d\n", - (void *)opts, - opts->check_hdr, opts->check_nim, - opts->diff_hdr1, opts->diff_hdr2, - opts->diff_hdr, opts->diff_nim, - opts->disp_hdr1, opts->disp_hdr2, opts->disp_hdr, opts->disp_nim, - opts->disp_ana, opts->disp_exts, opts->disp_cext, - opts->add_exts, opts->rm_exts, - opts->mod_hdr, opts->mod_nim, - opts->swap_hdr, opts->swap_ana, opts->swap_old, - opts->cbl, opts->cci, - opts->dts, opts->dci_lines, opts->make_im ); - - fprintf(stderr," ci_dims[8] = "); - disp_raw_data(opts->ci_dims, DT_INT64, 8, ' ', 1); - fprintf(stderr," new_dim[8] = "); - disp_raw_data(opts->new_dim, DT_INT64, 8, ' ', 1); - - fprintf(stderr,"\n" - " new_datatype = %d\n" - " debug, keep_hist = %d, %d\n" - " overwrite = %d\n" - " prefix = '%s'\n", - opts->new_datatype, opts->debug, opts->keep_hist, opts->overwrite, - opts->prefix ? opts->prefix : "(NULL)" ); - - fprintf(stderr," elist (length %d) :\n", opts->elist.len); - for( c = 0; c < opts->elist.len; c++ ) - fprintf(stderr," %d : %s\n", c, opts->elist.list[c]); - - fprintf(stderr," etypes (length %d) : ", opts->etypes.len); - disp_raw_data(opts->etypes.list, DT_INT32, opts->etypes.len, ' ', 0); - fputc('\n',stderr); - - fprintf(stderr," flist (length %d) :\n", opts->flist.len); - for( c = 0; c < opts->flist.len; c++ ) - fprintf(stderr," %d : %s\n", c, opts->flist.list[c]); - - fprintf(stderr," vlist (length %d) :\n", opts->vlist.len); - for( c = 0; c < opts->vlist.len; c++ ) - fprintf(stderr," %d : %s\n", c, opts->vlist.list[c]); - - fprintf(stderr," infiles (length %d) :\n", opts->infiles.len); - for( c = 0; c < opts->infiles.len; c++ ) - fprintf(stderr," %d : %s\n", c, opts->infiles.list[c]); - - fprintf(stderr," command len : %d\n",(int)strlen(opts->command)); - - return 0; -} - - -/*---------------------------------------------------------------------- - * For each file, add all extensions with type NIFTI_ECODE_AFNI. - * Though it should not matter, copy the trailing null characters. - *----------------------------------------------------------------------*/ -int act_add_exts( nt_opts * opts ) -{ - nifti_image * nim; - const char * ext; - char * edata = NULL; - int fc, ec, elen; - - if( g_debug > 2 ){ - fprintf(stderr,"+d adding %d extensions to %d files...\n" - " extension types are: ", - opts->elist.len, opts->infiles.len); - disp_raw_data(opts->etypes.list, DT_INT32, opts->etypes.len, ' ', 1); - } - - if( opts->prefix && opts->infiles.len != 1 ){ - fprintf(stderr,"** error: we have a prefix but %d files\n", - opts->infiles.len); - return 1; - } - - if( opts->elist.len <= 0 ) return 0; - - for( fc = 0; fc < opts->infiles.len; fc++ ) - { - nim = nt_image_read( opts, opts->infiles.list[fc], 1 ); - if( !nim ) return 1; /* errors come from the library */ - - for( ec = 0; ec < opts->elist.len; ec++ ){ - ext = opts->elist.list[ec]; - elen = strlen(ext); - if( !strncmp(ext,"file:",5) ){ - edata = read_file_text(ext+5, &elen); - if( !edata || elen <= 0 ) { - fprintf(stderr,"** failed to read extension data from '%s'\n", - ext+5); - continue; - } - ext = edata; - } - - if( ! nifti_is_valid_ecode(opts->etypes.list[ec]) ) - fprintf(stderr,"** warning: applying unknown ECODE %d\n", - opts->etypes.list[ec]); - - if( nifti_add_extension(nim, ext, elen, opts->etypes.list[ec]) ){ - nifti_image_free(nim); - return 1; - } - - /* if extension came from file, free the data */ - if( edata ){ free(edata); edata = NULL; } - } - - if( opts->keep_hist && nifti_add_extension(nim, opts->command, - strlen(opts->command), NIFTI_ECODE_COMMENT) ) - fprintf(stderr,"** failed to add command to image as extension\n"); - - if( opts->prefix && - nifti_set_filenames(nim, opts->prefix, !opts->overwrite, 1) ) - { - nifti_image_free(nim); - return 1; - } - - if( g_debug > 1 ) - fprintf(stderr,"+d writing %s with %d new extension(s)\n", - opts->infiles.list[fc], opts->elist.len); - - nifti_image_write(nim); - nifti_image_free(nim); - } - - if( g_debug > 0 ) - fprintf(stderr,"+d added %d extension(s) to %d files\n", - opts->elist.len, opts->infiles.len); - - return 0; -} - -/*---------------------------------------------------------------------- - * Return the allocated file contents. - *----------------------------------------------------------------------*/ -static char * read_file_text(const char * filename, int * length) -{ - FILE * fp; - char * text; - int len, bytes; - - if( !filename || !length ) { - fprintf(stderr,"** bad params to read_file_text\n"); - return NULL; - } - - len = nifti_get_filesize(filename); - if( len <= 0 ) { - fprintf(stderr,"** RFT: file '%s' appears empty\n", filename); - return NULL; - } - - fp = fopen(filename, "r"); - if( !fp ) { - fprintf(stderr,"** RFT: failed to open '%s' for reading\n", filename); - return NULL; - } - - /* allocate the bytes, and fill them with the file contents */ - - text = (char *)malloc(len * sizeof(char)); - if( !text ) { - fprintf(stderr,"** RFT: failed to allocate %d bytes\n", len); - fclose(fp); - return NULL; - } - - bytes = fread(text, sizeof(char), len, fp); - fclose(fp); /* in any case */ - - if( bytes != len ) { - fprintf(stderr,"** RFT: read only %d of %d bytes from %s\n", - bytes, len, filename); - free(text); - return NULL; - } - - /* success */ - - if( g_debug > 1 ) { - fprintf(stderr,"++ found extension of length %d in file %s\n", - len, filename); - if( g_debug > 2 ) - fprintf(stderr,"++ text is:\n%s\n", text); - } - - *length = len; - - return text; -} - -/*---------------------------------------------------------------------- - * For each file, strip the extra fields. - * - * Clear extensions and descrip field. No other generic strings will get - * passed to nifti_1_header struct. - * - * - this may make the datasets more anonymous - * - no history is appended here - *----------------------------------------------------------------------*/ -int act_strip( nt_opts * opts ) -{ - nifti_image * nim; - int fc; - - if( g_debug > 2 ) - fprintf(stderr,"+d stripping extras from %d files\n", opts->infiles.len); - - if( opts->prefix && opts->infiles.len != 1 ){ - fprintf(stderr,"** error: we have a prefix but %d files\n", - opts->infiles.len); - return 1; - } - - for( fc = 0; fc < opts->infiles.len; fc++ ) - { - nim = nt_image_read( opts, opts->infiles.list[fc], 1 ); - if( !nim ) return 1; /* errors come from the library */ - - /* now remove the extensions */ - nifti_free_extensions(nim); - memset(nim->descrip, 0, 80); - - if( opts->prefix && - nifti_set_filenames(nim, opts->prefix, !opts->overwrite, 1) ){ - nifti_image_free(nim); - return 1; - } - - if( g_debug > 1 ) - fprintf(stderr,"+d writing %s without extensions or 'descrip'\n", - nim->fname); - - nifti_image_write(nim); - - if( g_debug > 3 ) nifti_image_infodump(nim); - nifti_image_free(nim); - } - - if( g_debug > 0 ) - fprintf(stderr,"+d stripped extras from %d files\n", opts->infiles.len); - - return 0; -} - - -/*---------------------------------------------------------------------- - * For each file, remove the given extension for the given indices. - * - * Note that index = -1 means to remove them all. - *----------------------------------------------------------------------*/ -int act_rm_ext( nt_opts * opts ) -{ - nifti_image * nim; - int fc, ext_ind, num_ext; - - if( g_debug > 2 ) - fprintf(stderr,"+d removing %d extensions from %d files...\n", - opts->elist.len, opts->infiles.len); - - if( opts->elist.len <= 0 ) return 0; - - if( opts->prefix && opts->infiles.len != 1 ){ - fprintf(stderr,"** error: we have a prefix but %d files\n", - opts->infiles.len); - return 1; - } - else if( opts->overwrite && opts->infiles.len != 1 && - strcmp(opts->elist.list[0], "-1") ) { - fprintf(stderr,"** error: for multiple files, can only delete ALL\n"); - return 1; - } - - ext_ind = atoi(opts->elist.list[0]); - if( ext_ind < -1 ){ - fprintf(stderr,"** bad extension index to remove: %d\n", ext_ind); - return 1; - } - - if( g_debug > 1 ) fprintf(stderr,"+d removing extension index %d\n",ext_ind); - - for( fc = 0; fc < opts->infiles.len; fc++ ) - { - nim = nt_image_read( opts, opts->infiles.list[fc], 1 ); - if( !nim ) return 1; /* errors come from the library */ - - /* note the number of extensions for later */ - num_ext = nim->num_ext; - - /* now remove the extensions */ - if( remove_ext_list(nim, opts->elist.list, opts->elist.len) ) - return 1; - - if( opts->keep_hist && nifti_add_extension(nim, opts->command, - strlen(opts->command), NIFTI_ECODE_COMMENT) ) - fprintf(stderr,"** failed to add command to image as extension\n"); - - if( opts->prefix && - nifti_set_filenames(nim, opts->prefix, !opts->overwrite, 1) ){ - nifti_image_free(nim); - return 1; - } - - if( g_debug > 1 ) - fprintf(stderr,"+d writing %s with %d fewer extension(s)\n", - nim->fname, ext_ind == -1 ? num_ext : opts->elist.len); - - nifti_image_write(nim); - nifti_image_free(nim); - } - - if( g_debug > 0 ) - fprintf(stderr,"+d removed %s extension(s) from %d files\n", - ext_ind == -1 ? "ALL" : "1", opts->infiles.len); - - return 0; -} - - -/*---------------------------------------------------------------------- - * remove extensions by index - * - * return: 0 on success, -1 on failure - *----------------------------------------------------------------------*/ -int remove_ext_list( nifti_image * nim, const char ** elist, int len ) -{ - int * marks; - int c, ec, extval; - - if( len > nim->num_ext ){ - fprintf(stderr, "** cannot remove %d exts from image '%s' with only %d\n", - len, nim->fname, nim->num_ext); - return -1; - } - - if( len <= 0 ){ - fprintf(stderr,"** REL: (%d) no extensions to remove?\n",len); - return -1; - } - - extval = atoi(elist[0]); /* check the first value */ - - /* first special case, elist[0] == -1 */ - if( extval == -1 ) - { - if( g_debug > 1 ) - fprintf(stderr,"+d removing ALL (%d) extensions from '%s'\n", - nim->num_ext, nim->fname ); - nifti_free_extensions(nim); - return 0; - } - - if( g_debug > 2 ) - fprintf(stderr,"+d removing %d exts from '%s'\n", len, nim->fname ); - - if( ! (marks = (int *)calloc(nim->num_ext, sizeof(int))) ) { - fprintf(stderr,"** failed to alloc %d marks\n",nim->num_ext); - return -1; - } - - /* mark all extensions for removal */ - for( ec = 0; ec < len; ec++ ) - { - extval = atoi(elist[ec]); - - if( extval < 0 || extval >= nim->num_ext ){ - fprintf(stderr,"** ext #%d (= %d) is out of range [0,%d] for %s\n", - ec, extval, nim->num_ext-1, nim->fname); - free(marks); return -1; - } - - if( marks[extval] ){ - fprintf(stderr,"** ext #%d (= %d) is a duplicate", ec, extval); - free(marks); return -1; - } - - marks[extval]++; - } - - /* now remove them - count from top down to do lazy programming */ - for( ec = nim->num_ext-1; ec >= 0; ec-- ) - { - if( !marks[ec] ) continue; /* do not delete this one */ - - if( g_debug > 2 ) - disp_nifti1_extension("+d removing ext: ",nim->ext_list+ec,-1); - - /* delete this data, and shift the list down (yeah, inefficient) */ - if( nim->ext_list[ec].edata ) free( nim->ext_list[ec].edata ); - - /* move anything above down one */ - for( c = ec+1; c < nim->num_ext; c++ ) - nim->ext_list[c-1] = nim->ext_list[c]; - - nim->num_ext--; - } - - if( g_debug > 3 ) fprintf(stderr,"-d done removing extensions\n"); - - if( nim->num_ext == 0 ){ /* did we trash the only extension? */ - if( g_debug > 1 ) - fprintf(stderr,"-d removed ALL extensions from %s\n",nim->fname); - free(nim->ext_list); - nim->ext_list = NULL; - } - - free(marks); - return 0; -} - - -/*---------------------------------------------------------------------- - * check for diffs between all fields in opts->flist, or in the - * entire header - the 2 NIFTI versions must match - * - * if quiet mode (debug == 0) return on first diff - * - * return: 1 if diffs exist, 0 otherwise - *----------------------------------------------------------------------*/ -int act_diff_hdrs( nt_opts * opts ) -{ - void * nhdr0, * nhdr1; - int diffs = 0, nva=0, nvb=0; - - if( opts->infiles.len != 2 ){ - fprintf(stderr,"** -diff_hdr requires 2 -infiles, have %d\n", - opts->infiles.len); - return 1; - } - - if( g_debug > 2 ) - fprintf(stderr,"-d nifti_*_header diff between %s and %s...\n", - opts->infiles.list[0], opts->infiles.list[1]); - - /* get the nifiti headers (but do not validate them) */ - - /* nhdr0 = nt_read_header(opts, opts->infiles.list[0], NULL, 0); */ - nhdr0 = nt_read_header(opts->infiles.list[0], &nva, NULL, 0, - opts->new_datatype, opts->new_dim); - if( ! nhdr0 ) return 1; /* errors have been printed */ - - nhdr1 = nt_read_header(opts->infiles.list[1], &nvb, NULL, 0, - opts->new_datatype, opts->new_dim); - if( ! nhdr1 ){ free(nhdr0); return 1; } - - if( g_debug > 1 ) { - fprintf(stderr,"\n-d nifti_?_header diffs between '%s' and '%s'...\n", - opts->infiles.list[0], opts->infiles.list[1]); - fprintf(stderr," have NIFTI-%d and NIFTI-%d\n", nva, nvb); - } - - /* treat ANALYZE as NIFTI-1 */ - if( nva <= 0 || nvb <= 0 ) { - if( nva < 0 || nvb < 0 ) - fprintf(stderr,"** resetting invalid NIFTI version(s) to 1\n"); - if( nva <= 0 ) nva = 1; - if( nvb <= 0 ) nvb = 1; - } - - /* a difference is fatal */ - if( nva != nvb ) { - fprintf(stderr,"** %s is NIFTI-%d, while %s is NIFTI-%d\n" - " they must match\n", opts->infiles.list[0], nva, - opts->infiles.list[1], nvb); - free(nhdr0); free(nhdr1); return 1; - } - - if( opts->flist.len <= 0 ) { - if(nva==1) diffs = diff_hdr1s(nhdr0, nhdr1, g_debug > 0); - else diffs = diff_hdr2s(nhdr0, nhdr1, g_debug > 0); - } else { - if(nva==1) diffs = diff_hdr1s_list(nhdr0, nhdr1, &opts->flist, g_debug>0); - else diffs = diff_hdr2s_list(nhdr0, nhdr1, &opts->flist, g_debug>0); - } - - if( diffs == 0 && g_debug > 1 ) - fprintf(stderr,"+d no differences found\n"); - else if ( g_debug > 2 ) - fprintf(stderr,"+d %d differences found\n", diffs); - - free(nhdr0); - free(nhdr1); - - return (diffs > 0); -} - - -/*---------------------------------------------------------------------- - * check for diffs between all fields in opts->flist, or in the - * entire nifti_1_header - * - * if quiet mode (debug == 0) return on first diff - * - * return: 1 if diffs exist, 0 otherwise - *----------------------------------------------------------------------*/ -int act_diff_hdr1s( nt_opts * opts ) -{ - nifti_1_header * nhdr0, * nhdr1; - int diffs = 0, nv=1; - - if( opts->infiles.len != 2 ){ - fprintf(stderr,"** -diff_hdr1 requires 2 -infiles, have %d\n", - opts->infiles.len); - return 1; - } - - if( g_debug > 2 ) - fprintf(stderr,"-d nifti_1_header diff between %s and %s...\n", - opts->infiles.list[0], opts->infiles.list[1]); - - /* get the nifiti headers (but do not validate them) */ - - /* nhdr0 = nt_read_header(opts, opts->infiles.list[0], NULL, 0); */ - nhdr0 = nt_read_header(opts->infiles.list[0], &nv, NULL, 0, - opts->new_datatype, opts->new_dim); - if( ! nhdr0 ) return 1; /* errors have been printed */ - - nhdr1 = nt_read_header(opts->infiles.list[1], &nv, NULL, 0, - opts->new_datatype, opts->new_dim); - if( ! nhdr1 ){ free(nhdr0); return 1; } - - if( g_debug > 1 ) - fprintf(stderr,"\n-d nifti_1_header diffs between '%s' and '%s'...\n", - opts->infiles.list[0], opts->infiles.list[1]); - - if( opts->flist.len <= 0 ) - diffs = diff_hdr1s(nhdr0, nhdr1, g_debug > 0); - else - diffs = diff_hdr1s_list(nhdr0, nhdr1, &opts->flist, g_debug > 0); - - if( diffs == 0 && g_debug > 1 ) - fprintf(stderr,"+d no differences found\n"); - else if ( g_debug > 2 ) - fprintf(stderr,"+d %d differences found\n", diffs); - - free(nhdr0); - free(nhdr1); - - return (diffs > 0); -} - - -/*---------------------------------------------------------------------- - * check for diffs between all fields in opts->flist, or in the - * entire nifti_2_header - * - * if quiet mode (debug == 0) return on first diff - * - * return: 1 if diffs exist, 0 otherwise - *----------------------------------------------------------------------*/ -int act_diff_hdr2s( nt_opts * opts ) -{ - nifti_2_header * nhdr0, * nhdr1; - int diffs = 0, nv=2; - - if( opts->infiles.len != 2 ){ - fprintf(stderr,"** -diff_hdr2 requires 2 -infiles, have %d\n", - opts->infiles.len); - return 1; - } - - if( g_debug > 2 ) - fprintf(stderr,"-d nifti_2_header diff between %s and %s...\n", - opts->infiles.list[0], opts->infiles.list[1]); - - /* get the nifiti headers (but do not validate them) */ - - /* nhdr0 = nt_read_header(opts, opts->infiles.list[0], NULL, 0); */ - nhdr0 = nt_read_header(opts->infiles.list[0], &nv, NULL, 0, - opts->new_datatype, opts->new_dim); - if( ! nhdr0 ) return 1; /* errors have been printed */ - - nhdr1 = nt_read_header(opts->infiles.list[1], &nv, NULL, 0, - opts->new_datatype, opts->new_dim); - if( ! nhdr1 ){ free(nhdr0); return 1; } - - if( g_debug > 1 ) - fprintf(stderr,"\n-d nifti_2_header diffs between '%s' and '%s'...\n", - opts->infiles.list[0], opts->infiles.list[1]); - - if( opts->flist.len <= 0 ) - diffs = diff_hdr2s(nhdr0, nhdr1, g_debug > 0); - else - diffs = diff_hdr2s_list(nhdr0, nhdr1, &opts->flist, g_debug > 0); - - if( diffs == 0 && g_debug > 1 ) - fprintf(stderr,"+d no differences found\n"); - else if ( g_debug > 2 ) - fprintf(stderr,"+d %d differences found\n", diffs); - - free(nhdr0); - free(nhdr1); - - return (diffs > 0); -} - - -/*---------------------------------------------------------------------- - * check for diffs between all fields in opts->flist, or in the - * entire nifti_image - * - * if quiet mode (debug == 0) return on first diff - * - * return: 1 if diffs exist, 0 otherwise - *----------------------------------------------------------------------*/ -int act_diff_nims( nt_opts * opts ) -{ - nifti_image * nim0, * nim1; - int diffs = 0; - - if( opts->infiles.len != 2 ){ - fprintf(stderr,"** -diff_nim requires 2 -infiles, have %d\n", - opts->infiles.len); - return 1; - } - - if( g_debug > 2 ) - fprintf(stderr,"-d nifti_image diff between %s and %s...\n", - opts->infiles.list[0], opts->infiles.list[1]); - - /* get the nifiti images */ - - nim0 = nt_image_read(opts, opts->infiles.list[0], 0); - if( ! nim0 ) return 1; /* errors have been printed */ - - nim1 = nt_image_read(opts, opts->infiles.list[1], 0); - if( ! nim1 ){ free(nim0); return 1; } - - if( g_debug > 1 ) - fprintf(stderr,"\n-d nifti_image diffs between '%s' and '%s'...\n", - opts->infiles.list[0], opts->infiles.list[1]); - - if( opts->flist.len <= 0 ) - diffs = diff_nims(nim0, nim1, g_debug > 0); - else - diffs = diff_nims_list(nim0, nim1, &opts->flist, g_debug > 0); - - if( diffs == 0 && g_debug > 1 ) - fprintf(stderr,"+d no differences found\n"); - else if ( g_debug > 2 ) - fprintf(stderr,"+d %d differences found\n", diffs); - - nifti_image_free(nim0); - nifti_image_free(nim1); - - return (diffs > 0); -} - - -/*---------------------------------------------------------------------- - * for each file, read nifti1_header - * if checking header, check it - * if checking nifti_image, convert and check it - *----------------------------------------------------------------------*/ -int act_check_hdrs( nt_opts * opts ) -{ - nifti_1_header * nhdr; - nifti_image * nim; - int filenum, rv, nver=1; - - if( g_debug > 2 ) - fprintf(stderr,"-d checking hdrs/nims for %d nifti datasets...\n", - opts->infiles.len); - - for( filenum = 0; filenum < opts->infiles.len; filenum++ ) - { - /* do not validate the header structure */ - nhdr = nt_read_header(opts->infiles.list[filenum], &nver, NULL, 0, - opts->new_datatype, opts->new_dim); - if( !nhdr ) continue; /* errors are printed from library */ - - if( opts->check_hdr ) - { - if( g_debug > 1 ) - fprintf(stdout,"\nchecking nifti_1_header for file '%s'\n", - opts->infiles.list[filenum]); - - rv = nifti_hdr1_looks_good(nhdr); - - if( rv && g_debug > 0 ) /* if quiet, no GOOD response */ - printf("header IS GOOD for file %s\n",opts->infiles.list[filenum]); - else if( ! rv ) - printf("header FAILURE for file %s\n",opts->infiles.list[filenum]); - } - - if( opts->check_nim ) - { - nim = nifti_convert_n1hdr2nim(*nhdr, opts->infiles.list[filenum]); - if( !nim ) continue; /* errors are printed from library */ - - if( g_debug > 1 ) - fprintf(stdout,"\nchecking nifti_image for file '%s'\n", - opts->infiles.list[filenum]); - - rv = nifti_nim_is_valid(nim, 1); /* complain about errors */ - - if( rv && g_debug > 0 ) /* if quiet, no GOOD response */ - printf("nifti_image IS GOOD for file %s\n", - opts->infiles.list[filenum]); - else if( ! rv ) - printf("nifti_image FAILURE for file %s\n", - opts->infiles.list[filenum]); - - nifti_image_free(nim); - } - - free(nhdr); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * display all extensions for each dataset - *----------------------------------------------------------------------*/ -int act_disp_exts( nt_opts * opts ) -{ - nifti_image * nim; - char mesg[32], *mptr; - int ec, fc; - - if( g_debug > 2 ) - fprintf(stderr,"-d displaying all extensions for %d files...\n", - opts->infiles.len); - - for( fc = 0; fc < opts->infiles.len; fc++ ) - { - nim = nt_image_read(opts, opts->infiles.list[fc], 0); - if( !nim ) return 1; /* errors are printed from library */ - - if( g_debug > 0 ) - fprintf(stdout,"header file '%s', num_ext = %d\n", - nim->fname, nim->num_ext); - for( ec = 0; ec < nim->num_ext; ec++ ) - { - sprintf(mesg, " ext #%d : ", ec); - if( g_debug > 0 ) mptr = mesg; - else mptr = NULL; - - disp_nifti1_extension(mptr, nim->ext_list + ec, -1); - } - - nifti_image_free(nim); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * display all GIFTI extensions for each dataset - *----------------------------------------------------------------------*/ -int act_disp_cext( nt_opts * opts ) -{ - nifti_image * nim; - int ec, fc, found; - - if( g_debug > 2 ) - fprintf(stderr,"-d displaying CIFTI extensions for %d files...\n", - opts->infiles.len); - - for( fc = 0; fc < opts->infiles.len; fc++ ) - { - nim = nt_image_read(opts, opts->infiles.list[fc], 0); - if( !nim ) return 1; /* errors are printed from library */ - - if( g_debug > 1 ) - fprintf(stdout,"header file '%s', num_ext = %d\n", - nim->fname, nim->num_ext); - found = 0; - for( ec = 0; ec < nim->num_ext; ec++ ) - { - if( nim->ext_list[ec].ecode != NIFTI_ECODE_CIFTI ) continue; - found++; - - if( found == 1 && g_debug > 1 ) - fprintf(stdout,"header file '%s', ext %d of %d is CIFTI\n", - nim->fname, ec, nim->num_ext); - - disp_cifti_extension(NULL, nim->ext_list + ec, -1); - } - - if( g_debug && ! found ) - fprintf(stdout,"header file '%s': no CIFTI extension\n", nim->fname); - - nifti_image_free(nim); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * for each file, read nifti*_header and display all fields - *----------------------------------------------------------------------*/ -int act_disp_hdr( nt_opts * opts ) -{ - void * nhdr; - field_s * fnhdr; - const char ** sptr; - int nfields, filenum, fc, nver=0; - - if( g_debug > 2 ) - fprintf(stderr,"-d displaying %d fields for %d nifti datasets...\n", - opts->flist.len, opts->infiles.len); - - for( filenum = 0; filenum < opts->infiles.len; filenum++ ) - { - /* do not validate the header structure */ - nver = 0; - nhdr = nt_read_header(opts->infiles.list[filenum], &nver, NULL, g_debug>1, - opts->new_datatype, opts->new_dim); - if( !nhdr ) return 1; /* errors are printed from library */ - - if( nver < 0 ) { - fprintf(stderr,"** resetting invalid NIFTI version to 1\n"); - nver = 1; - } - - /* set the number of fields to display */ - nfields = opts->flist.len > 0 ? opts->flist.len : - nver <= 1 ? NT_HDR1_NUM_FIELDS : NT_HDR2_NUM_FIELDS; - - if( g_debug > 0 ) - fprintf(stdout,"\nN-%d header file '%s', num_fields = %d\n", - nver, opts->infiles.list[filenum], nfields); - if( g_debug > 1 ) { - if( nver <= 1 ) - fprintf(stderr,"-d header is: %s\n", - nifti_hdr1_looks_good(nhdr) ? "valid" : "invalid"); - else - fprintf(stderr,"-d header is: %s\n", - nifti_hdr2_looks_good(nhdr) ? "valid" : "invalid"); - } - - if( opts->flist.len <= 0 ) { /* then display all fields */ - if( nver <= 1 ) fnhdr = g_hdr1_fields; - else fnhdr = g_hdr2_fields; - disp_field("\nall fields:\n", fnhdr, nhdr, nfields, g_debug>0); - } else { /* print only the requested fields... */ - /* must locate each field before printing it */ - sptr = opts->flist.list; - for( fc = 0; fc < opts->flist.len; fc++ ) - { - if( nver == 1 ) fnhdr = get_hdr1_field(*sptr, filenum == 0); - else fnhdr = get_hdr2_field(*sptr, filenum == 0); - if( fnhdr ) disp_field(NULL, fnhdr, nhdr, 1, g_debug>0 && fc == 0); - sptr++; - } - } - - free(nhdr); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * for each file, read nifti1_header and display all fields - *----------------------------------------------------------------------*/ -int act_disp_hdr1( nt_opts * opts ) -{ - nifti_1_header * nhdr; - field_s * fnhdr; - const char ** sptr; - int nfields, filenum, fc, nver=-1; - - /* set the number of fields to display */ - nfields = opts->flist.len > 0 ? opts->flist.len : NT_HDR1_NUM_FIELDS; - - if( g_debug > 2 ) - fprintf(stderr,"-d displaying %d fields for %d nifti datasets...\n", - nfields, opts->infiles.len); - - for( filenum = 0; filenum < opts->infiles.len; filenum++ ) - { - /* do not validate the header structure */ - nhdr = nt_read_header(opts->infiles.list[filenum], &nver, NULL, g_debug>1, - opts->new_datatype, opts->new_dim); - if( !nhdr ) return 1; /* errors are printed from library */ - - if( g_debug > 0 ) - fprintf(stdout,"\nheader file '%s', num_fields = %d\n", - opts->infiles.list[filenum], nfields); - if( g_debug > 1 ) - fprintf(stderr,"-d header is: %s\n", - nifti_hdr1_looks_good(nhdr) ? "valid" : "invalid"); - - if( opts->flist.len <= 0 ) /* then display all fields */ - disp_field("\nall fields:\n", g_hdr1_fields, nhdr, nfields, g_debug>0); - else /* print only the requested fields... */ - { - /* must locate each field before printing it */ - sptr = opts->flist.list; - for( fc = 0; fc < opts->flist.len; fc++ ) - { - fnhdr = get_hdr1_field(*sptr, filenum == 0); - if( fnhdr ) disp_field(NULL, fnhdr, nhdr, 1, g_debug>0 && fc == 0); - sptr++; - } - } - - free(nhdr); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * for each file, read nifti1_header and display all fields - *----------------------------------------------------------------------*/ -int act_disp_hdr2( nt_opts * opts ) -{ - nifti_2_header * nhdr; - field_s * fnhdr; - const char ** sptr; - int nfields, filenum, fc, nver=-2; - - /* set the number of fields to display */ - nfields = opts->flist.len > 0 ? opts->flist.len : NT_HDR2_NUM_FIELDS; - - if( g_debug > 2 ) - fprintf(stderr,"-d displaying %d N-2 fields for %d nifti datasets...\n", - nfields, opts->infiles.len); - - for( filenum = 0; filenum < opts->infiles.len; filenum++ ) - { - /* do not validate the header structure */ - - nhdr = nt_read_header(opts->infiles.list[filenum], &nver, NULL, g_debug>1, - opts->new_datatype, opts->new_dim); - if( !nhdr ) return 1; /* errors are printed from library */ - - if( g_debug > 0 ) - fprintf(stdout,"\nNIFTI-2 header file '%s', num_fields = %d\n", - opts->infiles.list[filenum], nfields); - - if( g_debug > 1 ) - fprintf(stderr,"-d header is: %s\n", - nifti_hdr2_looks_good(nhdr) ? "valid" : "invalid"); - - - if( opts->flist.len <= 0 ) /* then display all fields */ - disp_field("\nall fields:\n", g_hdr2_fields, nhdr, nfields, g_debug>0); - else /* print only the requested fields... */ - { - /* must locate each field before printing it */ - sptr = opts->flist.list; - for( fc = 0; fc < opts->flist.len; fc++ ) - { - fnhdr = get_hdr2_field(*sptr, filenum == 0); - if( fnhdr ) disp_field(NULL, fnhdr, nhdr, 1, g_debug>0 && fc == 0); - sptr++; - } - } - - free(nhdr); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * for each file, read nifti_analyze75 and display all fields - *----------------------------------------------------------------------*/ -int act_disp_anas( nt_opts * opts ) -{ - nifti_analyze75 * nhdr; - field_s * fnhdr; - const char ** sptr; - int nfields, filenum, fc, nver=1; - - /* set the number of fields to display */ - nfields = opts->flist.len > 0 ? opts->flist.len : NT_ANA_NUM_FIELDS; - - if( g_debug > 2 ) - fprintf(stderr,"-d displaying %d fields for %d ANALYZE datasets...\n", - nfields, opts->infiles.len); - - for( filenum = 0; filenum < opts->infiles.len; filenum++ ) - { - /* do not validate the header structure */ - nhdr = nt_read_header(opts->infiles.list[filenum], &nver, NULL, 0, - opts->new_datatype, opts->new_dim); - if( !nhdr ) return 1; /* errors are printed from library */ - - if( g_debug > 0 ) - fprintf(stdout,"\nanalyze header file '%s', num_fields = %d\n", - opts->infiles.list[filenum], nfields); - if( g_debug > 1 ) - fprintf(stderr,"-d analyze header is: %s\n", - nifti_hdr1_looks_good((nifti_1_header *)nhdr) ? - "valid" : "invalid"); - - if( opts->flist.len <= 0 ) /* then display all fields */ - disp_field("\nall fields:\n", g_ana_fields, nhdr, nfields, g_debug>0); - else /* print only the requested fields... */ - { - /* must locate each field before printing it */ - sptr = opts->flist.list; - for( fc = 0; fc < opts->flist.len; fc++ ) - { - fnhdr = get_hdr1_field(*sptr, filenum == 0); - if( fnhdr ) disp_field(NULL, fnhdr, nhdr, 1, g_debug>0 && fc == 0); - sptr++; - } - } - - free(nhdr); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * for each file, get nifti_image and display all fields - *----------------------------------------------------------------------*/ -int act_disp_nims( nt_opts * opts ) -{ - nifti_image * nim; - field_s * fnim; - const char ** sptr; - int nfields, filenum, fc; - - /* set the number of fields to display */ - nfields = opts->flist.len > 0 ? opts->flist.len : NT_NIM_NUM_FIELDS; - - if( g_debug > 2 ) - fprintf(stderr,"-d displaying %d fields for %d nifti datasets...\n", - nfields, opts->infiles.len); - - for( filenum = 0; filenum < opts->infiles.len; filenum++ ) - { - nim = nt_image_read(opts, opts->infiles.list[filenum], 0); - if( !nim ) return 1; /* errors are printed from library */ - - if( g_debug > 0 ) - fprintf(stdout,"\nheader file '%s', num_fields = %d, fields:\n\n", - nim->fname, nfields); - - if( opts->flist.len <= 0 ) /* then display all fields */ - disp_field("all fields:\n", g_nim2_fields, nim, nfields, g_debug > 0); - else /* print only the requested fields... */ - { - /* must locate each field before printing it */ - sptr = opts->flist.list; - for( fc = 0; fc < opts->flist.len; fc++ ) - { - fnim = get_nim_field(*sptr, filenum == 0); - if( fnim ) disp_field(NULL, fnim, nim, 1, g_debug > 0 && fc == 0); - sptr++; - } - } - - nifti_image_free(nim); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * - read header - * - modify header - * - if -prefix duplicate file - * - else if swapped, swap back - * - overwrite file header (allows (danger-of) no evaluation of data) - *----------------------------------------------------------------------*/ -int act_mod_hdrs( nt_opts * opts ) -{ - nifti_1_header * nhdr; - nifti_image * nim; /* for reading/writing entire datasets */ - int filec, swap, nver=1; - const char * fname; - char * dupname; - char func[] = { "act_mod_hdrs" }; - - if( g_debug > 2 ) - fprintf(stderr,"-d modifying %d fields for %d nifti headers...\n", - opts->flist.len, opts->infiles.len); - if( opts->flist.len <= 0 || opts->infiles.len <= 0 ) return 0; - - for( filec = 0; filec < opts->infiles.len; filec++ ) - { - fname = opts->infiles.list[filec]; /* for convenience and mod file */ - - if( nifti_is_gzfile(fname) ){ - fprintf(stderr,"** sorry, cannot modify a gzipped file: %s\n", fname); - continue; - } - -/* rcr - this should be mod_hdr1s */ - - /* do not validate the header structure */ - nhdr = nt_read_header(fname, &nver, &swap, 0, - opts->new_datatype, opts->new_dim); - if( !nhdr ) return 1; - - if( g_debug > 1 ) - { - fprintf(stderr,"-d modifying %d fields of '%s' header\n", - opts->flist.len, fname); - fprintf(stderr,"-d header is: %s\n", - nifti_hdr1_looks_good(nhdr) ? "valid" : "invalid"); - } - - /* okay, let's actually trash the data fields */ - if( modify_all_fields(nhdr, opts, g_hdr1_fields, NT_HDR1_NUM_FIELDS) ) - { - free(nhdr); - return 1; - } - - dupname = NULL; /* unless we duplicate file */ - - /* possibly duplicate the current dataset before writing new header */ - if( opts->prefix ) - { - nim = nt_image_read(opts, fname, 1); /* get data */ - if( !nim ) { - fprintf(stderr,"** failed to dup file '%s' before modifying\n", - fname); - return 1; - } - if( opts->keep_hist && nifti_add_extension(nim, opts->command, - strlen(opts->command), NIFTI_ECODE_COMMENT) ) - fprintf(stderr,"** failed to add command to image as exten\n"); - if( nifti_set_filenames(nim, opts->prefix, 1, 1) ) - { - NTL_FERR(func,"failed to set prefix for new file: ",opts->prefix); - nifti_image_free(nim); - return 1; - } - dupname = nifti_strdup(nim->fname); /* so we know to free it */ - fname = dupname; - nifti_image_write(nim); /* create the duplicate file */ - /* if we added a history note, get the new offset into the header */ - /* mod: if the new offset is valid, use it 31 Jan 2006 [rickr] */ - if( nim->iname_offset >= 348 ) nhdr->vox_offset = nim->iname_offset; - nifti_image_free(nim); - } - else if ( swap ) - swap_nifti_header(nhdr, NIFTI_VERSION(*nhdr)); - - /* if all is well, overwrite header in fname dataset */ - (void)write_hdr_to_file(nhdr, fname); /* errors printed in function */ - - if( dupname ) free(dupname); - free(nhdr); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * - read header - * - swap header - * - if -prefix duplicate file - * - overwrite file header (allows (danger-of) no evaluation of data) - *----------------------------------------------------------------------*/ -int act_swap_hdrs( nt_opts * opts ) -{ - nifti_1_header * nhdr; - nifti_image * nim; /* for reading/writing entire datasets */ - int filec, swap, nver=1; - const char * fname; - char * dupname; - char func[] = { "act_mod_hdrs" }; - - /* count requested operations: "there can be only one", and not Sean */ - swap = opts->swap_hdr + opts->swap_ana + opts->swap_old; - if( swap > 1 ) { - fprintf(stderr,"** can perform only one swap method\n"); - return 1; - } else if( ! swap ) - return 0; /* probably shouldn't be here */ - - if( g_debug > 2 ) - fprintf(stderr,"-d swapping headers of %d files...\n",opts->infiles.len); - - for( filec = 0; filec < opts->infiles.len; filec++ ) - { - fname = opts->infiles.list[filec]; /* for convenience and mod file */ - - if( nifti_is_gzfile(fname) ){ - fprintf(stderr,"** sorry, cannot swap a gzipped header: %s\n", fname); - continue; - } - -/* rcr - this should be swap_hdr1s */ - - /* do not validate the header structure */ - nhdr = nt_read_header(fname, &nver, &swap, 0, opts->new_datatype, - opts->new_dim); - if( !nhdr ) return 1; - - if( g_debug > 1 ) { - const char * str = "NIfTI"; - if( opts->swap_ana || (opts->swap_old && !NIFTI_VERSION(*nhdr)) ) - str = "ANALYZE"; - fprintf(stderr,"-d %sswapping %s header of file %s\n", - opts->swap_old ? "OLD " : "", str, fname); - } - - if( ! swap ) { /* if not yet swapped, do as the user requested */ - - if( opts->swap_old ) old_swap_nifti_header(nhdr, NIFTI_VERSION(*nhdr)); - else swap_nifti_header(nhdr, opts->swap_ana ? 0 : 1); - - } else { /* swapped already: if not correct, need to undo */ - - /* if swapped the wrong way, undo and swap as the user requested */ - if ( opts->swap_ana && NIFTI_VERSION(*nhdr) ) { - /* want swapped as ANALYZE, but was swapped as NIFTI */ - swap_nifti_header(nhdr, 1); /* undo NIFTI */ - swap_nifti_header(nhdr, 0); /* swap ANALYZE */ - } else if( opts->swap_hdr && !NIFTI_VERSION(*nhdr) ) { - /* want swapped as NIFTI, but was swapped as ANALYZE */ - swap_nifti_header(nhdr, 0); /* undo ANALYZE */ - swap_nifti_header(nhdr, 1); /* swap NIFTI */ - } else if ( opts->swap_old ) { - /* undo whichever was done and apply the old way */ - swap_nifti_header(nhdr, NIFTI_VERSION(*nhdr)); - old_swap_nifti_header(nhdr, NIFTI_VERSION(*nhdr)); - } - - /* else it was swapped the right way to begin with */ - - } - - dupname = NULL; /* unless we duplicate file */ - - /* possibly duplicate the current dataset before writing new header */ - if( opts->prefix ) - { - nim = nt_image_read(opts, fname, 1); /* get data */ - if( !nim ) { - fprintf(stderr,"** failed to dup file '%s' before modifying\n", - fname); - return 1; - } - if( opts->keep_hist && nifti_add_extension(nim, opts->command, - strlen(opts->command), NIFTI_ECODE_COMMENT) ) - fprintf(stderr,"** failed to add command to image as exten\n"); - if( nifti_set_filenames(nim, opts->prefix, 1, 1) ) - { - NTL_FERR(func,"failed to set prefix for new file: ",opts->prefix); - nifti_image_free(nim); - return 1; - } - dupname = nifti_strdup(nim->fname); /* so we know to free it */ - fname = dupname; - nifti_image_write(nim); /* create the duplicate file */ - /* if we added a history note, get the new offset into the header */ - /* mod: if the new offset is valid, use it 31 Jan 2006 [rickr] */ - if( nim->iname_offset >= 348 ) nhdr->vox_offset = nim->iname_offset; - nifti_image_free(nim); - } - - /* if all is well, overwrite header in fname dataset */ - (void)write_hdr_to_file(nhdr, fname); /* errors printed in function */ - - if( dupname ) free(dupname); - free(nhdr); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * - read image w/data, modify and write - *----------------------------------------------------------------------*/ -int act_mod_nims( nt_opts * opts ) -{ - nifti_image * nim; /* for reading/writing entire datasets */ - int filec; - char func[] = { "act_mod_nims" }; - - if( g_debug > 2 ) - fprintf(stderr,"-d modifying %d fields for %d nifti images...\n", - opts->flist.len, opts->infiles.len); - if( opts->flist.len <= 0 || opts->infiles.len <= 0 ) return 0; - - for( filec = 0; filec < opts->infiles.len; filec++ ) - { - nim = nt_image_read(opts, opts->infiles.list[filec], 1); /* with data */ - - if( g_debug > 1 ) - fprintf(stderr,"-d modifying %d fields from '%s' image\n", - opts->flist.len, opts->infiles.list[filec]); - - /* okay, let's actually trash the data fields */ - if( modify_all_fields(nim, opts, g_nim2_fields, NT_NIM_NUM_FIELDS) ) - { - nifti_image_free(nim); - return 1; - } - - /* add command as COMMENT extension */ - if( opts->keep_hist && nifti_add_extension(nim, opts->command, - strlen(opts->command), NIFTI_ECODE_COMMENT) ) - fprintf(stderr,"** failed to add command to image as extension\n"); - - /* possibly duplicate the current dataset before writing new header */ - if( opts->prefix ) - if( nifti_set_filenames(nim, opts->prefix, 1, 1) ) - { - NTL_FERR(func,"failed to set prefix for new file: ",opts->prefix); - nifti_image_free(nim); - return 1; - } - - nifti_image_write(nim); /* and write it out, piece of cake :) */ - nifti_image_free(nim); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * overwrite nifti_1_header in the given file - *----------------------------------------------------------------------*/ -int write_hdr_to_file( nifti_1_header * nhdr, const char * fname ) -{ - znzFile fp; - size_t bytes; - char func[] = { "write_hdr_to_file" }; - int rv = 0; - - fp = znzopen(fname,"r+b",nifti_is_gzfile(fname)); - if( znz_isnull(fp) ){ - NTL_FERR(func, "failed to re-open mod file", fname); - return 1; - } - - bytes = znzwrite(nhdr, 1, sizeof(nifti_1_header), fp); - if( bytes != sizeof(nifti_1_header)){ - NTL_FERR(func, "failed to write header to file",fname); - fprintf(stderr," - wrote %d of %d bytes\n", - (int)bytes,(int)sizeof(nifti_1_header)); - rv = 1; - } - - if( g_debug > 3 ) - disp_nifti_1_header("+d writing new header to file : ", nhdr); - - znzclose(fp); - - return rv; -} - - -/*---------------------------------------------------------------------- - * modify all fields in the list - *----------------------------------------------------------------------*/ -int modify_all_fields( void * basep, nt_opts * opts, field_s * fields, int flen) -{ - field_s * fp; - int fc, lc; /* field and list counters */ - - if( opts->flist.len <= 0 ) return 0; - if( opts->flist.len != opts->vlist.len ){ - fprintf(stderr,"** have %d fields but %d new values\n", - opts->flist.len, opts->vlist.len); - return 1; - } - - for( lc = 0; lc < opts->flist.len; lc++ ) - { - /* is it in the list? */ - fp = fields; - for( fc = 0; fc < flen; fc++, fp++ ) - if( strcmp(opts->flist.list[lc], fp->name) == 0 ) break; - - if( fc == flen ) /* do no modifications on failure */ - { - fprintf(stderr,"** field '%s' not found in structure\n", - opts->flist.list[lc]); - return 1; - } - - if( modify_field( basep, fp, opts->vlist.list[lc]) ) - return 1; - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * modify a single field with the given value field - * - * pointer fields are not allowed here - *----------------------------------------------------------------------*/ -int modify_field(void * basep, field_s * field, const char * data) -{ - float fval; - const char * posn = data; - int val, max, fc, nchars; - - if( g_debug > 1 ) - fprintf(stderr,"+d modifying field '%s' with '%s'\n", field->name, data); - - if( !data || strlen(data) == 0 ) - { - fprintf(stderr,"** no data for '%s' field modification\n",field->name); - return 1; - } - - switch( field->type ) - { - case DT_UNKNOWN: - case NT_DT_POINTER: - case NT_DT_CHAR_PTR: - case NT_DT_EXT_PTR: - default: - fprintf(stderr,"** refusing to modify a pointer field, '%s'\n", - field->name); - return 1; - - case DT_INT8: - { - max = 127; - for( fc = 0; fc < field->len; fc++ ) - { - if( sscanf(posn, " %d%n", &val, &nchars) != 1 ) - { - fprintf(stderr,"** found %d of %d modify values\n", - fc,field->len); - return 1; - } - if( val > max || val < -(max+1) ) - { - fprintf(stderr, - "** mod val #%d (= %d) outside byte range [-%d,%d]\n", - fc, val, max+1, max); - return 1; - } - /* otherwise, we're good */ - (((char *)basep + field->offset))[fc] = (char)val; - if( g_debug > 1 ) - fprintf(stderr,"+d setting posn %d of '%s' to %d\n", - fc, field->name, val); - posn += nchars; - } - } - break; - - case DT_INT16: - { - max = 32767; - for( fc = 0; fc < field->len; fc++ ) - { - if( sscanf(posn, " %d%n", &val, &nchars) != 1 ) - { - fprintf(stderr,"** found %d of %d modify values\n", - fc,field->len); - return 1; - } - if( val > max || val < -(max+1) ) - { - fprintf(stderr, - "** mod val #%d (= %d) outside byte range [-%d,%d]\n", - fc, val, max+1, max); - return 1; - } - /* otherwise, we're good */ - ((short *)((char *)basep + field->offset))[fc] = (short)val; - if( g_debug > 1 ) - fprintf(stderr,"+d setting posn %d of '%s' to %d\n", - fc, field->name, val); - posn += nchars; - } - } - break; - - case DT_INT32: - { - for( fc = 0; fc < field->len; fc++ ) - { - if( sscanf(posn, " %d%n", &val, &nchars) != 1 ) - { - fprintf(stderr,"** found %d of %d modify values\n", - fc,field->len); - return 1; - } - ((int *)((char *)basep + field->offset))[fc] = val; - if( g_debug > 1 ) - fprintf(stderr,"+d setting posn %d of '%s' to %d\n", - fc, field->name, val); - posn += nchars; - } - } - break; - - case DT_INT64: - { - int64_t v64; - for( fc = 0; fc < field->len; fc++ ) - { - if( sscanf(posn, " %" PRId64 "%n", &v64, &nchars) != 1 ) - { - fprintf(stderr,"** found %d of %d modify values\n", - fc,field->len); - return 1; - } - ((int64_t *)((char *)basep + field->offset))[fc] = v64; - if( g_debug > 1 ) - fprintf(stderr,"+d setting posn %d of '%s' to %" PRId64 "\n", - fc, field->name, v64); - posn += nchars; - } - } - break; - - case DT_FLOAT32: - { - for( fc = 0; fc < field->len; fc++ ) - { - if( sscanf(posn, " %f%n", &fval, &nchars) != 1 ) - { - fprintf(stderr,"** found %d of %d modify values\n", - fc,field->len); - return 1; - } - /* otherwise, we're good */ - ((float *)((char *)basep + field->offset))[fc] = fval; - if( g_debug > 1 ) - fprintf(stderr,"+d setting posn %d of '%s' to %f\n", - fc, field->name, fval); - posn += nchars; - } - } - break; - - case DT_FLOAT64: - { - double f64; - for( fc = 0; fc < field->len; fc++ ) - { - if( sscanf(posn, " %lf%n", &f64, &nchars) != 1 ) - { - fprintf(stderr,"** found %d of %d modify values\n", - fc,field->len); - return 1; - } - /* otherwise, we're good */ - ((float *)((char *)basep + field->offset))[fc] = f64; - if( g_debug > 1 ) - fprintf(stderr,"+d setting posn %d of '%s' to %f\n", - fc, field->name, f64); - posn += nchars; - } - } - break; - - case NT_DT_STRING: - { - char * dest = (char *)basep + field->offset; - nchars = strlen(data); - strncpy(dest, data, field->len); - if( nchars < field->len ) /* clear the rest */ - memset(dest+nchars, '\0', field->len-nchars); - } - break; - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * fill the nifti_1_header field list - *----------------------------------------------------------------------*/ -int fill_hdr1_field_array( field_s * nh_fields ) -{ - nifti_1_header nhdr; - field_s * nhf = nh_fields; - int rv, errs; - - memset(nhf, 0, NT_HDR1_NUM_FIELDS*sizeof(field_s)); - - /* this macro takes (TYPE, NAME, NUM) and does: - fill_field(nhdr, TYPE, NT_OFF(nhdr,NAME), NUM, "NAME"); - nhf++; - */ - errs = 0; - NT_SFILL(nhdr, nhf, DT_INT32, sizeof_hdr, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, NT_DT_STRING, data_type, 10, rv); errs += rv; - NT_SFILL(nhdr, nhf, NT_DT_STRING, db_name, 18, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT32, extents, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT16, session_error, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, NT_DT_STRING, regular, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT8, dim_info, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_INT16, dim, 8, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, intent_p1, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, intent_p2, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, intent_p3, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT16, intent_code, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_INT16, datatype, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT16, bitpix, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT16, slice_start, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, pixdim, 8, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, vox_offset, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, scl_slope, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, scl_inter, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT16, slice_end, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_INT8, slice_code, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT8, xyzt_units, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, cal_max, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, cal_min, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, slice_duration, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, toffset, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT32, glmax, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT32, glmin, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, NT_DT_STRING, descrip, 80, rv); errs += rv; - NT_SFILL(nhdr, nhf, NT_DT_STRING, aux_file, 24, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT16, qform_code, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT16, sform_code, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_FLOAT32, quatern_b, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, quatern_c, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, quatern_d, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, qoffset_x, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, qoffset_y, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, qoffset_z, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_FLOAT32, srow_x, 4, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, srow_y, 4, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, srow_z, 4, rv); errs += rv; - NT_SFILL(nhdr, nhf, NT_DT_STRING, intent_name, 16, rv); errs += rv; - NT_SFILL(nhdr, nhf, NT_DT_STRING, magic, 4, rv); errs += rv; - - if( errs > 0 ){ - fprintf(stderr, "** %d fill_fields errors!\n", errs); - return 1; - } - - /* failure here is a serious problem */ - if( check_total_size("nifti_1_header test: ", nh_fields, - NT_HDR1_NUM_FIELDS, sizeof(nhdr)) ) - return 1; - - if( g_debug > 3 ) - disp_field_s_list("nh_fields: ", nh_fields, NT_HDR1_NUM_FIELDS); - - return 0; -} - -/*---------------------------------------------------------------------- - * fill the nifti_2_header field list - *----------------------------------------------------------------------*/ -int fill_hdr2_field_array( field_s * nh_fields ) -{ - nifti_2_header nhdr; - field_s * nhf = nh_fields; - int rv, errs; - - memset(nhf, 0, NT_HDR2_NUM_FIELDS*sizeof(field_s)); - - /* this macro takes (TYPE, NAME, NUM) and does: - fill_field(nhdr, TYPE, NT_OFF(nhdr,NAME), NUM, "NAME"); - nhf++; - */ - errs = 0; - NT_SFILL(nhdr, nhf, DT_INT32, sizeof_hdr, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, NT_DT_STRING, magic, 8, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_INT16, datatype, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT16, bitpix, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT64, dim, 8, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_FLOAT64, intent_p1, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT64, intent_p2, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT64, intent_p3, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_FLOAT64, pixdim, 8, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_INT64, vox_offset, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT64, scl_slope, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT64, scl_inter, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT64, cal_max, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT64, cal_min, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT64, slice_duration, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT64, toffset, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT64, slice_start, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT64, slice_end, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, NT_DT_STRING, descrip, 80, rv); errs += rv; - NT_SFILL(nhdr, nhf, NT_DT_STRING, aux_file, 24, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT32, qform_code, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT32, sform_code, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_FLOAT64, quatern_b, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT64, quatern_c, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT64, quatern_d, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT64, qoffset_x, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT64, qoffset_y, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT64, qoffset_z, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_FLOAT64, srow_x, 4, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT64, srow_y, 4, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT64, srow_z, 4, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_INT32, slice_code, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT32, xyzt_units, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT32, intent_code, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, NT_DT_STRING, intent_name, 16, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT8, dim_info, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, NT_DT_STRING, unused_str, 15, rv); errs += rv; - - if( errs > 0 ){ - fprintf(stderr, "** %d fill_fields errors!\n", errs); - return 1; - } - - /* failure here is a serious problem */ - if( check_total_size("nifti_2_header test: ", nh_fields, - NT_HDR2_NUM_FIELDS, sizeof(nhdr)) ) - return 1; - - if( g_debug > 3 ) - disp_field_s_list("n2h_fields: ", nh_fields, NT_HDR2_NUM_FIELDS); - - return 0; -} - - -/*---------------------------------------------------------------------- - * fill the nifti_image field list - *----------------------------------------------------------------------*/ -int fill_nim1_field_array( field_s * nim_fields ) -{ - nifti1_image nim; - field_s * nif = nim_fields; - int rv, errs; - - memset(nif, 0, NT_NIM_NUM_FIELDS*sizeof(field_s)); - - errs = 0; - - NT_SFILL(nim, nif, DT_INT32, ndim, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nx, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, ny, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nz, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nt, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nu, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nv, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nw, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, dim, 8, rv); errs += rv; - /* nvox: int32 -> size_t, 29 Jul 2007 -> int64_t, 29 Aug 2013 */ - NT_SFILL(nim, nif, DT_INT64, nvox, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nbyper, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, datatype, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, dx, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, dy, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, dz, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, dt, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, du, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, dv, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, dw, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, pixdim, 8, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, scl_slope, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, scl_inter, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, cal_min, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, cal_max, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, qform_code, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, sform_code, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, freq_dim, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, phase_dim, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, slice_dim, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, slice_code, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, slice_start, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, slice_end, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, slice_duration, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, quatern_b, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, quatern_c, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, quatern_d, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, qoffset_x, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, qoffset_y, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, qoffset_z, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, qfac, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, qto_xyz, 16, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, qto_ijk, 16, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, sto_xyz, 16, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, sto_ijk, 16, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, toffset, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, xyz_units, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, time_units, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nifti_type, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, intent_code, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, intent_p1, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, intent_p2, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, intent_p3, 1, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_STRING, intent_name, 16, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_STRING, descrip, 80, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_STRING, aux_file, 24, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_CHAR_PTR, fname, 1, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_CHAR_PTR, iname, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, iname_offset, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, swapsize, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, byteorder, 1, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_POINTER, data, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, num_ext, 1, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_EXT_PTR, ext_list, 1, rv); errs += rv; - - if( errs > 0 ){ - fprintf(stderr, "** %d fill_fields errors " - "(note that pointers get aligned)\n", errs); - return 1; - } - - if( g_debug > 3 ) /* failure here is not an error condition */ - check_total_size("nifti1_image test: ", nim_fields, - NT_NIM_NUM_FIELDS, sizeof(nim)); - - if( g_debug > 3 ) - disp_field_s_list("nim1_fields: ", nim_fields, NT_NIM_NUM_FIELDS); - - return 0; -} - - -/*---------------------------------------------------------------------- - * fill the nifti2_image field list - *----------------------------------------------------------------------*/ -int fill_nim2_field_array( field_s * nim_fields ) -{ - nifti2_image nim; - field_s * nif = nim_fields; - int rv, errs; - - memset(nif, 0, NT_NIM_NUM_FIELDS*sizeof(field_s)); - - errs = 0; - - NT_SFILL(nim, nif, DT_INT32, ndim, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT64, nx, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT64, ny, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT64, nz, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT64, nt, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT64, nu, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT64, nv, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT64, nw, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT64, dim, 8, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT64, nvox, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nbyper, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, datatype, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, dx, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, dy, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, dz, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, dt, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, du, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, dv, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, dw, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, pixdim, 8, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, scl_slope, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, scl_inter, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, cal_min, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, cal_max, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, qform_code, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, sform_code, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, freq_dim, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, phase_dim, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, slice_dim, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, slice_code, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT64, slice_start, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT64, slice_end, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, slice_duration, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, quatern_b, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, quatern_c, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, quatern_d, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, qoffset_x, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, qoffset_y, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, qoffset_z, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, qfac, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, qto_xyz, 16, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, qto_ijk, 16, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, sto_xyz, 16, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, sto_ijk, 16, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, toffset, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, xyz_units, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, time_units, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nifti_type, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, intent_code, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, intent_p1, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, intent_p2, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT64, intent_p3, 1, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_STRING, intent_name, 16, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_STRING, descrip, 80, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_STRING, aux_file, 24, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_CHAR_PTR, fname, 1, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_CHAR_PTR, iname, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT64, iname_offset, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, swapsize, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, byteorder, 1, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_POINTER, data, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, num_ext, 1, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_EXT_PTR, ext_list, 1, rv); errs += rv; - - if( errs > 0 ){ - fprintf(stderr, "** %d fill_fields errors " - "(note that pointers get aligned)\n", errs); - return 1; - } - - if( g_debug > 4 ) /* failure here is not an error condition */ - check_total_size("nifti2_image test: ", nim_fields, - NT_NIM_NUM_FIELDS, sizeof(nim)); - - if( g_debug > 3 ) - disp_field_s_list("nim2_fields: ", nim_fields, NT_NIM_NUM_FIELDS); - - return 0; -} - - -/*---------------------------------------------------------------------- - * fill the nifti_analyze75 field list - *----------------------------------------------------------------------*/ -int fill_ana_field_array( field_s * ah_fields ) -{ - nifti_analyze75 nhdr; - field_s * ahf = ah_fields; - int rv, errs; - - memset(ahf, 0, NT_ANA_NUM_FIELDS*sizeof(field_s)); - - /* this macro takes (TYPE, NAME, NUM) and does: - fill_field(nhdr, TYPE, NT_OFF(nhdr,NAME), NUM, "NAME"); - nhf++; - */ - errs = 0; - NT_SFILL(nhdr, ahf, DT_INT32, sizeof_hdr, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, data_type, 10, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, db_name, 18, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, extents, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, session_error, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, regular, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT8, hkey_un0, 1, rv); errs += rv; - - NT_SFILL(nhdr, ahf, DT_INT16, dim, 8, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, unused8, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, unused9, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, unused10, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, unused11, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, unused12, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, unused13, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, unused14, 1, rv); errs += rv; - - NT_SFILL(nhdr, ahf, DT_INT16, datatype, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, bitpix, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, dim_un0, 1, rv); errs += rv; - - NT_SFILL(nhdr, ahf, DT_FLOAT32, pixdim, 8, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_FLOAT32, vox_offset, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_FLOAT32, funused1, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_FLOAT32, funused2, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_FLOAT32, funused3, 1, rv); errs += rv; - - NT_SFILL(nhdr, ahf, DT_FLOAT32, cal_max, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_FLOAT32, cal_min, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_FLOAT32, compressed, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_FLOAT32, verified, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, glmax, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, glmin, 1, rv); errs += rv; - - NT_SFILL(nhdr, ahf, NT_DT_STRING, descrip, 80, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, aux_file, 24, rv); errs += rv; - - NT_SFILL(nhdr, ahf, DT_INT8, orient, 1, rv); errs += rv; - /* originator is 5 (3) shorts, not 10 chars 26 Sep 2012 [rickr] */ - NT_SFILL(nhdr, ahf, DT_INT16, originator, 5, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, generated, 10, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, scannum, 10, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, patient_id, 10, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, exp_date, 10, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, exp_time, 10, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, hist_un0, 3, rv); errs += rv; - - NT_SFILL(nhdr, ahf, DT_INT32, views , 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, vols_added, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, start_field, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, field_skip, 1, rv); errs += rv; - - NT_SFILL(nhdr, ahf, DT_INT32, omax, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, omin, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, smax, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, smin, 1, rv); errs += rv; - - if( errs > 0 ){ - fprintf(stderr, "** %d ana fill_fields errors!\n", errs); - return 1; - } - - /* failure here is a serious problem */ - if( check_total_size("nifti_analyze75 test: ", ah_fields, NT_ANA_NUM_FIELDS, - sizeof(nhdr)) ) - return 1; - - if( g_debug > 3 ) - disp_field_s_list("ah_fields: ", ah_fields, NT_ANA_NUM_FIELDS); - - return 0; -} - - -/*---------------------------------------------------------------------- - * compare sizes to offset, including total - *----------------------------------------------------------------------*/ -int check_total_size( const char *mesg, field_s * fields, int nfields, int tot_size ) -{ - field_s * fp; - int c, total; - int bad_offs; - - total = 0; - bad_offs = 0; - for( c = 0, fp = fields; c < nfields; c++, fp++ ){ - if( fp->offset != total ){ - if( g_debug > 3 ) - fprintf(stderr,"** bad offset for field '%s'\n" - " offset = %d, total = %d\n", - fp->name, fp->offset, total); - bad_offs++; - } - - total += fp->size * fp->len; - } - - if( g_debug > 1 || (g_debug > 0 && bad_offs > 0) ){ - fputs(mesg, stderr); c = 0; - if( bad_offs > 0 ){ - fprintf(stderr,"** found %d bad offsets\n", bad_offs); c++; } - if( total != tot_size ){ - fprintf(stderr,"** computed total %d not equal to struct size %d\n", - total, tot_size); c++; } - if( c == 0 ) fputs("... okay\n", stderr); - } - - if( bad_offs > 0 ) return 1; - - return 0; -} - - -/*---------------------------------------------------------------------- - * fill the field structure with the given data - *----------------------------------------------------------------------*/ -int fill_field( field_s * fp, int type, int offset, int num, const char * name ) -{ - fp->type = type; - fp->offset = offset; - fp->size = 1; /* init before check */ - fp->len = num; - - strncpy(fp->name, name, NT_FIELD_NAME_LEN-1); - - switch( type ){ - case DT_UNKNOWN: - case DT_INT8: - case NT_DT_STRING: - fp->size = 1; - break; - - case DT_INT16: - fp->size = 2; - break; - - case DT_INT32: - case DT_FLOAT32: - fp->size = 4; - break; - - case DT_INT64: - case DT_UINT64: - case DT_FLOAT64: - case DT_COMPLEX64: - fp->size = 8; - break; - - case NT_DT_POINTER: - case NT_DT_CHAR_PTR: - case NT_DT_EXT_PTR: - fp->size = (int)sizeof(void *); - break; - - default: - fprintf(stderr,"** fill_field: invalid type %d\n", type ); - return 1; - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * return a string matching the type - *----------------------------------------------------------------------*/ -const char * field_type_str( int type ) -{ - - - if( type == DT_INT8 ) return "DT_INT8"; - if( type == DT_INT16 ) return "DT_INT16"; - if( type == DT_INT32 ) return "DT_INT32"; - if( type == DT_INT64 ) return "DT_INT64"; - - if( type == DT_UINT8 ) return "DT_UINT8"; - if( type == DT_UINT16 ) return "DT_UINT16"; - if( type == DT_UINT32 ) return "DT_UINT32"; - if( type == DT_UINT64 ) return "DT_UINT64"; - - if( type == DT_FLOAT32 ) return "DT_FLOAT32"; - if( type == DT_FLOAT64 ) return "DT_FLOAT64"; - if( type == DT_COMPLEX64 ) return "DT_COMPLEX64"; - if( type == DT_COMPLEX128 ) return "DT_COMPLEX128"; - - if( type == DT_RGB24 ) return "DT_RGB24"; - - if( type == NT_DT_STRING ) return "NT_DT_STRING"; - if( type == NT_DT_POINTER ) return "NT_DT_POINTER"; - if( type == NT_DT_CHAR_PTR ) return "NT_DT_CHAR_PTR"; /* longest: 14 */ - if( type == NT_DT_EXT_PTR ) return "NT_DT_EXT_PTR"; - - - return "DT_UNKNOWN"; /* for DT_UNKNOWN, or as an else */ -} - -#define NT_MAX_DT_STR_LEN 14 - -/*---------------------------------------------------------------------- - * display the contents of all of the field structures - *----------------------------------------------------------------------*/ -int disp_field_s_list( const char *mesg, field_s * fp, int nfields ) -{ - int c, total=0; - - if( mesg ) fputs(mesg, stdout); - - fprintf(stdout," %d fields:\n" - " name size len offset type\n" - " ------------------- ---- --- ------ --------------\n", - nfields); - - for( c = 0; c < nfields; c++, fp++ ) { - fprintf(stdout," %-*s %4d %3d %4d %-14s\n", - NT_FIELD_NAME_LEN-1, fp->name, fp->size, fp->len, - fp->offset, field_type_str(fp->type)); - total += fp->size*fp->len; - } - - fprintf(stdout, "\n total size: %d\n\n", total); - - return 0; -} - - -/*---------------------------------------------------------------------- - * display the contents of all of the field structures - *----------------------------------------------------------------------*/ -int disp_field(const char *mesg, field_s *fieldp, void * str, int nfields, int header) -{ - field_s * fp; - int c; - - if( mesg ) fputs(mesg, stdout); - - if( header && g_debug > 0 ){ - fprintf(stdout, " name offset nvals values\n"); - fprintf(stdout, " ------------------- ------ ----- ------\n"); - } - - fp = fieldp; - for( c = 0; c < nfields; c++, fp++ ) - { - /* start by displaying the field information */ - if( g_debug > 0 ) - fprintf(stdout, " %-*.*s %4d %3d ", - NT_FIELD_NAME_LEN-1, NT_FIELD_NAME_LEN-1, fp->name, - fp->offset, fp->len); - - /* now, print the value(s), depending on the type */ - switch( fp->type ){ - case DT_UNKNOWN: - default: - fprintf(stdout,"(unknown data type)\n"); - break; - - case DT_INT8: case DT_UINT8: - case DT_INT16: case DT_UINT16: - case DT_INT32: case DT_UINT32: - case DT_INT64: - case DT_FLOAT32: case DT_FLOAT64: - disp_raw_data((char *)str+fp->offset, fp->type, fp->len, ' ', 1); - break; - - case NT_DT_POINTER: - fprintf(stdout,"(raw data of unknown type)\n"); - break; - - case NT_DT_CHAR_PTR: /* look for string of length <= 40 */ - { - char * sp; - int len; - - /* start by sucking the pointer stored here */ - sp = *(char **)((char *)str + fp->offset); - - if( ! sp ){ fprintf(stdout,"(NULL)\n"); break; } /* anything? */ - - /* see if we have a printable string here */ - for(len = 0; len <= 40 && *sp && isprint(*sp); len++, sp++ ) - ; - if( len > 40 ) - fprintf(stdout,"(apparent long string)\n"); - else if ( len == 0 ) - fprintf(stdout,"(empty string)\n"); - else if( *sp && !isprint(*sp) ) /* if no termination, it's bad */ - fprintf(stdout,"(non-printable string)\n"); - else /* woohoo! a good string */ - fprintf(stdout,"'%.40s'\n",*(char **)((char *)str + fp->offset)); - break; - } - - case NT_DT_EXT_PTR: - { - nifti1_extension * extp; - - /* yank the address sitting there into extp */ - extp = *(nifti1_extension **)((char *)str + fp->offset); - - /* the user may use -disp_exts to display all of them */ - if( extp ) disp_nifti1_extension(NULL, extp, 6); - else fprintf(stdout,"(NULL)\n"); - break; - } - - case NT_DT_STRING: - { - char * charp = (char *)str + fp->offset; - fprintf(stdout,"%.*s\n", fp->len, charp); - break; - } - } - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * no display, just return whether any fields differ - *----------------------------------------------------------------------*/ -int diff_field(field_s *fieldp, void * str0, void * str1, int nfields) -{ - field_s * fp; - char * cp0, * cp1; - int fnum, c, size; - - fp = fieldp; - for( fnum = 0; fnum < nfields; fnum++, fp++ ) - { - switch( fp->type ){ - case DT_UNKNOWN: /* all basic types are easy */ - case DT_INT8: - case DT_INT16: - case DT_INT32: - case DT_INT64: - case DT_FLOAT32: - case DT_FLOAT64: - case NT_DT_STRING: - size = fp->size * fp->len; /* total field size */ - cp0 = (char *)str0 + fp->offset; - cp1 = (char *)str1 + fp->offset; - for( c = 0; c < size; c++, cp0++, cp1++ ) - if( *cp0 != *cp1 ) break; - - if(c < size) return 1; /* found a diff */ - - break; - - case NT_DT_POINTER: /* let's pass on these - no diff */ - case NT_DT_CHAR_PTR: - - break; - - case NT_DT_EXT_PTR: - { - nifti1_extension * ext0, * ext1; - - ext0 = *(nifti1_extension **)((char *)str0 + fp->offset); - ext1 = *(nifti1_extension **)((char *)str1 + fp->offset); - - if( ! ext0 && ! ext1 ) break; /* continue on */ - - if( ext0 && ! ext1 ) return 1; /* pointer diff is diff */ - if( ! ext0 && ext1 ) return 1; - - /* just check size and type for a single extension */ - if( ext0->esize != ext1->esize ) return 1; - if( ext0->ecode != ext1->ecode ) return 1; - - break; - } - } - } - - return 0; /* no diffs found */ -} - - -/*---------------------------------------------------------------------- - * display a single extension - *----------------------------------------------------------------------*/ -int disp_cifti_extension( const char *mesg, nifti1_extension * ext, int maxlen) -{ - FILE * outfp = stdout; - int len; - if( mesg ) fputs(mesg, outfp); - - if( !ext ) { - fprintf(stderr,"** no extension to display\n"); - return 1; - } - - if( ext->ecode != NIFTI_ECODE_CIFTI ) { - fprintf(stderr,"** extension code %d is not CIFTI\n", ext->ecode); - return 1; - } - - if( g_debug > 1 ) - fprintf(outfp,"ecode = %d, esize = %d, edata = ", ext->ecode,ext->esize); - - if( !ext->edata ) - fprintf(outfp,"(NULL)\n"); - else { - len = ext->esize-8; - if( maxlen >= 0 && len > maxlen ) len = maxlen; - fprintf(outfp,"%.*s\n", len, (char *)ext->edata); - } - - fflush(outfp); - - return 0; -} - - -/*---------------------------------------------------------------------- - * display a single extension - *----------------------------------------------------------------------*/ -int disp_nifti1_extension( const char *mesg, nifti1_extension * ext, int maxlen) -{ - FILE * outfp = stdout; - int len; - if( mesg ) fputs(mesg, outfp); - - if( !ext ) - { - fprintf(stderr,"** no extension to display\n"); - return 1; - } - - if( g_debug > 0 ) - fprintf(outfp,"ecode = %d, esize = %d, edata = ", ext->ecode,ext->esize); - - if( !ext->edata ) - fprintf(outfp,"(NULL)\n"); - else if ( ext->ecode == NIFTI_ECODE_AFNI || - ext->ecode == NIFTI_ECODE_COMMENT || - ext->ecode == NIFTI_ECODE_CIFTI ) - { - len = ext->esize-8; - if( maxlen >= 0 && len > maxlen ) len = maxlen; - fprintf(outfp,"%.*s\n", len, (char *)ext->edata); - } - else - fprintf(outfp,"(unknown data type)\n"); - - fflush(outfp); - - return 0; -} - - -/*---------------------------------------------------------------------- - * return the appropritate pointer into the g_hdr1_fields struct - *----------------------------------------------------------------------*/ -field_s * get_hdr1_field( const char * fname, int show_fail ) -{ - field_s * fp; - int c; - - if( ! fname || *fname == '\0' ) return NULL; - - fp = g_hdr1_fields; - for( c = 0; c < NT_HDR1_NUM_FIELDS; c++, fp++ ) - if( strcmp(fname, fp->name) == 0 ) break; - - if( c == NT_HDR1_NUM_FIELDS ) - { - if( show_fail > 0 ) - fprintf(stderr,"** get_hdr1_field: field not found in hdr: %s\n",fname); - return NULL; - } - - return fp; -} - -/*---------------------------------------------------------------------- - * return the appropritate pointer into the g_hdr1_fields struct - *----------------------------------------------------------------------*/ -field_s * get_hdr2_field( const char * fname, int show_fail ) -{ - field_s * fp; - int c; - - if( ! fname || *fname == '\0' ) return NULL; - - fp = g_hdr2_fields; - for( c = 0; c < NT_HDR2_NUM_FIELDS; c++, fp++ ) - if( strcmp(fname, fp->name) == 0 ) break; - - if( c == NT_HDR2_NUM_FIELDS ) - { - if( show_fail > 0 ) - fprintf(stderr,"** get_hdr2_field: field not found in hdr: %s\n",fname); - return NULL; - } - - return fp; -} - - -/*---------------------------------------------------------------------- - * return the appropritate pointer into the g_hdr1_fields struct - *----------------------------------------------------------------------*/ -field_s * get_nim_field( const char * fname, int show_fail ) -{ - field_s * fp; - int c; - - if( ! fname || *fname == '\0' ) return NULL; - - fp = g_nim2_fields; - for( c = 0; c < NT_NIM_NUM_FIELDS; c++, fp++ ) - if( strcmp(fname, fp->name) == 0 ) break; - - if( c == NT_NIM_NUM_FIELDS ) - { - if( show_fail > 0 ) - fprintf(stderr,"** get_nim_field: field not found in hdr: %s\n",fname); - return NULL; - } - - return fp; -} - - -/*---------------------------------------------------------------------- - * return the number of fields that differ - *----------------------------------------------------------------------*/ -int diff_hdr1s( nifti_1_header * s0, nifti_1_header * s1, int display ) -{ - field_s * fp = g_hdr1_fields; - int c, ndiff = 0; - - for( c = 0; c < NT_HDR1_NUM_FIELDS; c++, fp++ ) - if( diff_field(fp, s0, s1, 1) ) - { - if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0); - if( display ) disp_field(NULL, fp, s1, 1, 0); - ndiff++; - } - - return ndiff; -} - - -/*---------------------------------------------------------------------- - * return the number of fields that differ - *----------------------------------------------------------------------*/ -int diff_hdr2s( nifti_2_header * s0, nifti_2_header * s1, int display ) -{ - field_s * fp = g_hdr2_fields; - int c, ndiff = 0; - - for( c = 0; c < NT_HDR2_NUM_FIELDS; c++, fp++ ) - if( diff_field(fp, s0, s1, 1) ) - { - if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0); - if( display ) disp_field(NULL, fp, s1, 1, 0); - ndiff++; - } - - return ndiff; -} - - -/*---------------------------------------------------------------------- - * return the number of fields that differ - *----------------------------------------------------------------------*/ -int diff_nims( nifti_image * s0, nifti_image * s1, int display ) -{ - field_s * fp = g_nim2_fields; - int c, ndiff = 0; - - for( c = 0; c < NT_NIM_NUM_FIELDS; c++, fp++ ) - if( diff_field(fp, s0, s1, 1) ) - { - if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0); - if( display ) disp_field(NULL, fp, s1, 1, 0); - ndiff++; - } - - return ndiff; -} - - -/*---------------------------------------------------------------------- - * return the number of fields that differ - *----------------------------------------------------------------------*/ -int diff_hdr1s_list( nifti_1_header * s0, nifti_1_header * s1, str_list * slist, - int display ) -{ - field_s * fp; - const char ** sptr; - int c, ndiff = 0; - - sptr = slist->list; - for( c = 0; c < slist->len; c++ ) - { - fp = get_hdr1_field(*sptr, 1); /* "not found" displayed in func */ - if( fp && diff_field(fp, s0, s1, 1) ) - { - if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0); - if( display ) disp_field(NULL, fp, s1, 1, 0); - ndiff++; - } - sptr++; - } - - return ndiff; -} - - -/*---------------------------------------------------------------------- - * return the number of fields that differ - *----------------------------------------------------------------------*/ -int diff_hdr2s_list( nifti_2_header * s0, nifti_2_header * s1, str_list * slist, - int display ) -{ - field_s * fp; - const char ** sptr; - int c, ndiff = 0; - - sptr = slist->list; - for( c = 0; c < slist->len; c++ ) - { - fp = get_hdr2_field(*sptr, 1); /* "not found" displayed in func */ - if( fp && diff_field(fp, s0, s1, 1) ) - { - if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0); - if( display ) disp_field(NULL, fp, s1, 1, 0); - ndiff++; - } - sptr++; - } - - return ndiff; -} - - -/*---------------------------------------------------------------------- - * return the number of fields that differ - *----------------------------------------------------------------------*/ -int diff_nims_list( nifti_image * s0, nifti_image * s1, str_list * slist, - int display ) -{ - field_s * fp; - const char ** sptr; - int c, ndiff = 0; - - sptr = slist->list; - for( c = 0; c < slist->len; c++ ) - { - fp = get_nim_field(*sptr, 1); /* "not found" displayed in func */ - if( fp && diff_field(fp, s0, s1, 1) ) - { - if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0); - if( display ) disp_field(NULL, fp, s1, 1, 0); - ndiff++; - } - sptr++; - } - - return ndiff; -} - - -/*---------------------------------------------------------------------- - * display data from collapsed_image - *----------------------------------------------------------------------*/ -int act_disp_ci( nt_opts * opts ) -{ - nifti_image * nim; - void * data = NULL; - char space = ' '; /* use space or newline */ - int filenum, len, err; - - if( opts->dci_lines ) space = '\n'; /* then use newlines as separators */ - - if( g_debug > 2 && opts->dts ) - { - fprintf(stderr,"-d displaying time series at (i,j,k) = (" - "%" PRId64 ",%" PRId64 ",%" PRId64 ")\n" - " for %d nifti datasets...\n\n", opts->ci_dims[1], - opts->ci_dims[2], opts->ci_dims[3], opts->infiles.len); - } - else if ( g_debug > 2 ) /* the general collapsed image form */ - { - fprintf(stderr,"-d displaying collapsed image for %d datasets...\n\n" - " dims = ", opts->infiles.len); - disp_raw_data(opts->ci_dims, DT_INT64, 8, ' ', 1); - } - - for( filenum = 0; filenum < opts->infiles.len; filenum++ ) - { - err = 0; - nim = nt_image_read(opts, opts->infiles.list[filenum], 0); - if( !nim ) continue; /* errors are printed from library */ - if( opts->dts && nim->ndim != 4 ) - { - fprintf(stderr,"** error: dataset '%s' is not 4-dimensional\n", - nim->fname); - err++; - } - - switch( nim->datatype ) - { - case DT_INT8: case DT_INT16: case DT_INT32: case DT_INT64: - case DT_UINT8: case DT_UINT16: case DT_UINT32: - case DT_FLOAT32: case DT_FLOAT64: - if( g_debug > 1 ) - fprintf(stderr,"-d datatype %d of size %d\n", - nim->datatype, nim->nbyper); - break; - default: - fprintf(stderr,"** dataset '%s' has unknown type %d\n", - nim->fname, nim->datatype); - err++; - break; - } - - if( err ) { nifti_image_free(nim); continue; } - - len = nifti_read_collapsed_image(nim, opts->ci_dims, &data); - if( len < 0 || !data ) - { - fprintf(stderr,"** FAILURE for dataset '%s'\n", nim->fname); - if( data ) free(data); - err++; - } - - /* remove check for length of time series 24 Apr 2006 */ - - if( err ){ nifti_image_free(nim); continue; } - - /* now just print the results */ - if( g_debug > 0 ) - { - fprintf(stdout,"\ndataset '%s' @ (", nim->fname); - if( opts->dts ) disp_raw_data(opts->ci_dims+1, DT_INT64, 3, ' ', 0); - else disp_raw_data(opts->ci_dims+1, DT_INT64, 7, ' ', 0); - fprintf(stdout,")\n"); - } - - disp_raw_data(data, nim->datatype, len / nim->nbyper, space, 1); - - nifti_image_free(nim); - } - - if( data ) free(data); - - return 0; -} - - -int disp_raw_data( void * data, int type, int nvals, char space, int newline ) -{ - char * dp, fbuf[32]; - int c, size; - - nifti_datatype_sizes( type, &size, NULL ); /* get nbyper */ - - for( c = 0, dp = (char *)data; c < nvals; c++, dp += size ) - { - switch( type ) - { - case DT_INT8: - printf("%d", *(char *)dp); - break; - case DT_INT16: - printf("%d", *(short *)dp); - break; - case DT_INT32: - printf("%d", *(int *)dp); - break; - case DT_INT64: - printf("%"PRId64, *(int64_t *)dp); - break; - case DT_UINT8: - printf("%u", *(unsigned char *)dp); - break; - case DT_UINT16: - printf("%u", *(unsigned short *)dp); - break; - case DT_UINT32: - printf("%u", *(unsigned int *)dp); - break; - case DT_FLOAT32: - { - sprintf(fbuf,"%f", *(float *)dp); - clear_float_zeros(fbuf); - printf("%s", fbuf); - break; - } - case DT_FLOAT64: - { - sprintf(fbuf,"%f", *(double *)dp); - clear_float_zeros(fbuf); - printf("%s", fbuf); - break; - } - default: - fprintf(stderr,"** disp_raw_data: unknown type %d\n", type); - return 1; - } - if( c < nvals - 1 ) fputc(space,stdout); - } - - if ( newline ) fputc('\n',stdout); - - return 0; -} - -/*---------------------------------------------------------------------- - * remove trailing zeros from string of printed float - * return 1 if something was cleared - * 0 if not - *----------------------------------------------------------------------*/ -int clear_float_zeros( char * str ) -{ - char * dp = strchr(str, '.'), * valp; - int len; - - if( !dp ) return 0; /* nothing to clear */ - - len = strlen(dp); - - /* never clear what is just to the right of '.' */ - for( valp = dp+len-1; (valp > dp+1) && (*valp==' ' || *valp=='0'); valp-- ) - *valp = '\0'; /* clear, so we don't worry about break conditions */ - - if( valp < dp + len - 1 ) return 1; - return 0; -} - -/* return the number of volumes in the nifti_image */ -static int num_volumes(nifti_image * nim) -{ - int ind, nvols = 1; - - if( nim->dim[0] < 1 ) return 0; - - for( ind = 4; ind <= nim->dim[0]; ind++ ) - nvols *= nim->dim[ind]; - - return nvols; -} - - -/*---------------------------------------------------------------------- - * create a new dataset using sub-brick selection - *----------------------------------------------------------------------*/ -int act_cbl( nt_opts * opts ) -{ - nifti_brick_list NBL; - nifti_image * nim; - char * fname, * selstr, * cp; - int64_t * blist; - int err = 0; - - if( g_debug > 2 ) - fprintf(stderr,"-d copying file info from '%s' to '%s'\n", - opts->infiles.list[0], opts->prefix); - - /* sanity checks */ - if( ! opts->prefix ) { - fprintf(stderr,"** error: -prefix is required with -cbl function\n"); - return 1; - } else if( opts->infiles.len > 1 ) { - fprintf(stderr,"** sorry, at the moment -cbl allows only 1 input\n"); - return 1; - } - - /* remove selector from fname, and copy selector string */ - fname = nifti_strdup(opts->infiles.list[0]); - cp = strchr(fname,'['); if( !cp ) cp = strchr(fname,'{'); - - if( !cp ) { - if( g_debug > 1 ) - fprintf(stderr,"-d using -cbl without brick list in '%s'\n",fname); - selstr = nifti_strdup("[0..$]"); - } else { - selstr = nifti_strdup(cp); - *cp = '\0'; /* remove selection string from fname */ - } - - if( g_debug > 1 ) - fprintf(stderr,"+d -cbl: using '%s' for selection string\n", selstr); - - nim = nt_image_read(opts, fname, 0); /* get image */ - if( !nim ) return 1; - - /* since nt can be zero now (sigh), check for it 02 Mar 2006 [rickr] */ - blist = nifti_get_int64list(nim->nt > 0 ? num_volumes(nim) : 1, selstr); - nifti_image_free(nim); /* throw away, will re-load */ - if( !blist ) { - fprintf(stderr,"** failed sub-brick selection using '%s'\n",selstr); - free(fname); free(selstr); return 1; - } - - nim = nt_read_bricks(opts, fname, blist[0], blist+1, &NBL); - free(blist); /* with this */ - if( !nim ){ free(fname); free(selstr); return 1; } - - if( g_debug > 1 ) fprintf(stderr,"+d sub-bricks loaded\n"); - - /* add command as COMMENT extension */ - if( opts->keep_hist && nifti_add_extension(nim, opts->command, - strlen(opts->command), NIFTI_ECODE_COMMENT) ) - fprintf(stderr,"** failed to add command to image as extension\n"); - - /* replace filenames using prefix */ - if( nifti_set_filenames(nim, opts->prefix, 1, 1) ) - { - fprintf(stderr,"** failed to set names, prefix = '%s'\n",opts->prefix); - err++; - } - - if(g_debug>2) disp_field("new nim:\n",g_nim2_fields,nim,NT_NIM_NUM_FIELDS,1); - - /* and finally, write out results */ - if( err == 0 && nifti_nim_is_valid(nim, g_debug) ) - nifti_image_write_bricks(nim, &NBL); - - nifti_image_free(nim); - nifti_free_NBL(&NBL); - free(fname); - free(selstr); - - return 0; -} - - -/*---------------------------------------------------------------------- - * create a new dataset using read_collapsed_image - *----------------------------------------------------------------------*/ -int act_cci( nt_opts * opts ) -{ - nifti_image * nim; - int c; - - if( g_debug > 2 ) - fprintf(stderr,"-d collapsing file info from '%s' to '%s'\n", - opts->infiles.list[0], opts->prefix); - - /* sanity checks */ - if( ! opts->prefix ) { - fprintf(stderr,"** error: -prefix is required with -cci function\n"); - return 1; - } else if( opts->infiles.len > 1 ) { - fprintf(stderr,"** sorry, at the moment -cci allows only 1 input\n"); - return 1; - } - - nim = nt_image_read(opts, opts->infiles.list[0], 0); - if( !nim ) return 1; - nim->data = NULL; /* just to be sure */ - - if( nifti_read_collapsed_image(nim, opts->ci_dims, &nim->data) < 0 ) - { - nifti_image_free(nim); - return 1; - } - - /* add command as COMMENT extension */ - if( opts->keep_hist && nifti_add_extension(nim, opts->command, - strlen(opts->command), NIFTI_ECODE_COMMENT) ) - fprintf(stderr,"** failed to add command to image as extension\n"); - - /* replace filenames using prefix */ - if( nifti_set_filenames(nim, opts->prefix, 1, 1) ) - { - fprintf(stderr,"** failed to set names, prefix = '%s'\n",opts->prefix); - nifti_image_free(nim); - return 1; - } - - for( c = 1; c < 8; c++ ) /* nuke any collapsed dimension */ - if( opts->ci_dims[c] >= 0 ) nim->dim[c] = 1; - - nifti_update_dims_from_array(nim); - - if(g_debug>2) disp_field("new nim:\n",g_nim2_fields,nim,NT_NIM_NUM_FIELDS,1); - - /* and finally, write out results */ - if( nifti_nim_is_valid(nim, g_debug) ) nifti_image_write(nim); - - nifti_image_free(nim); - - return 0; -} - - -/*---------------------------------------------------------------------- - * free all of the lists in the struct - * note: strings were not allocated - *----------------------------------------------------------------------*/ -static int free_opts_mem( nt_opts * nopt ) -{ - if( !nopt ) return 1; - - if( nopt->elist.list ) free(nopt->elist.list); - if( nopt->etypes.list ) free(nopt->etypes.list); - if( nopt->flist.list ) free(nopt->flist.list); - if( nopt->vlist.list ) free(nopt->vlist.list); - if( nopt->infiles.list ) free(nopt->infiles.list); - - return 0; -} - - -/*---------------------------------------------------------------------- - * wrapper for nifti_image_read - * - * this adds the option to generage an empty image, if the - * filename starts with "MAKE_IM" - *----------------------------------------------------------------------*/ -nifti_image * nt_image_read( nt_opts * opts, const char * fname, int doread ) -{ - if( !opts || !fname ) { - fprintf(stderr,"** nt_image_read: bad params (%p,%p)\n", - (void *)opts, (void *)fname); - return NULL; - } - - /* if the user does not want an empty image, do normal image_read */ - if( strncmp(fname,NT_MAKE_IM_NAME,strlen(NT_MAKE_IM_NAME)) ) { - if(g_debug > 1) - fprintf(stderr,"-d calling nifti_image_read(%s,%d)\n",fname,doread); - return nifti_image_read(fname, doread); - } - - /* so generate an emtpy image */ - if(g_debug > 1) { - fprintf(stderr,"+d NT_IR: generating EMPTY IMAGE from %s...\n",fname); - if(g_debug > 2) { - printf(" new_dim[8] = "); - disp_raw_data(opts->new_dim, DT_INT64, 8, ' ', 1); - printf(" new_datatype = %d\n", opts->new_datatype); - fflush(stdout); - } - } - - /* create a new nifti_image, with data depending on doread */ - return nifti_make_new_nim(opts->new_dim, opts->new_datatype, doread); -} - - -/*---------------------------------------------------------------------- - * wrapper for nifti_read_header - * - * this adds the option to generage an empty image, if the - * filename starts with "MAKE_IM" - *----------------------------------------------------------------------*/ -void * nt_read_header(const char * fname, int * nver, int * swapped, int check, - int new_datatype, int64_t new_dim[8]) -{ - nifti_image * nim = NULL; - void * nptr = NULL; - char func[] = { "nt_read_header" }; - int nv; - - /* swapped is not necessary */ - if( !fname ) { - fprintf(stderr,"** nt_read_header: missing fname\n"); - return NULL; - } - - /* if the user does not want an empty image, do normal image_read */ - if( strncmp(fname,NT_MAKE_IM_NAME,strlen(NT_MAKE_IM_NAME)) ) { - if(g_debug > 1) - fprintf(stderr,"-d calling nifti_read_n1_hdr(%s,...)\n", fname); - - /* if not set or 0, return whatever is found */ - if( ! nver || ! *nver ) return nifti_read_header(fname, nver, check); - - if( *nver < -2 || *nver > 2 ) { - fprintf(stderr,"** nt_read_header, illegal nver = %d\n", *nver); - return NULL; - } - - /* 1 or 2 means try to return only that */ - if( *nver == 1 ) return nifti_read_n1_hdr(fname, swapped, check); - if( *nver == 2 ) return nifti_read_n2_hdr(fname, swapped, check); - - /* handle negatives, start by simply reading the header */ - nptr = nifti_read_header(fname, &nv, check); - if( !nptr ) return NULL; - if( g_debug > 1 ) fprintf(stderr,"-d have NIFTI-%d header, %s\n", - nv, fname); - - /* negative means convert, if necessary */ - if( *nver == -1 ) { - nifti_1_header * hdr=NULL; - if( nv <= 1 ) return nptr; - - /* else assume 2: convert headers via nim? */ - hdr = (nifti_1_header *)malloc(sizeof(nifti_1_header)); - if( !hdr ) { - fprintf(stderr,"** %s: failed to alloc nifti_1_header\n", func); - return NULL; - } - - nim = nifti_convert_n2hdr2nim(*(nifti_2_header*)nptr, NULL); - if( !nim ) { - fprintf(stderr,"** %s: failed n2hdr2nim on %s\n", func, fname); - return NULL; - } - if( nifti_convert_nim2n1hdr(nim, hdr) ) { - fprintf(stderr,"** %s: failed convert_nim2n1hdr on %s\n", - func, fname); - return NULL; - } - return hdr; - } - else { /* assume -2 */ - nifti_2_header * hdr=NULL; - if( nv == 2 ) return nptr; - - /* else assume 2: convert headers via nim? */ - hdr = (nifti_2_header *)malloc(sizeof(nifti_2_header)); - if( !hdr ) { - fprintf(stderr,"** %s: failed to alloc nifti_2_header\n", func); - return NULL; - } - - nim = nifti_convert_n1hdr2nim(*(nifti_1_header*)nptr, NULL); - if( !nim ) { - fprintf(stderr,"** %s: failed n1hdr2nim on %s\n", func, fname); - return NULL; - } - if( nifti_convert_nim2n2hdr(nim, hdr) ) { - fprintf(stderr,"** %s: failed convert_nim2n2hdr on %s\n", - func, fname); - return NULL; - } - - return hdr; - } - } - - /* else "MAKE_IM", so generate an emtpy image */ - - if(g_debug > 1) { - fprintf(stderr,"+d NT_RH: generating EMPTY IMAGE from %s...\n",fname); - if(g_debug > 2) { - printf(" new_dim[8] = "); - disp_raw_data(new_dim, DT_INT64, 8, ' ', 1); - printf(" new_datatype = %d\n", new_datatype); - fflush(stdout); - } - } - - /* return creation of new header */ - if( (nver && *nver == 1) || (nver && *nver == -1)) - return nifti_make_new_n1_header(new_dim, new_datatype); - else { - if( nver ) *nver = 2; - return nifti_make_new_n2_header(new_dim, new_datatype); - } -} - - -/*---------------------------------------------------------------------- - * wrapper for nifti_image_read_bricks - * - * Similar to nt_read_header(), this adds the option to generage an - * empty image if the filename starts with "MAKE_IM". - * - * the returned object is a (max 4-D) nifti_image - *----------------------------------------------------------------------*/ -nifti_image * nt_read_bricks(nt_opts * opts, char * fname, int len, - int64_t * list, nifti_brick_list * NBL) -{ - nifti_image * nim; - int c; - - /* swapped is not necessary */ - if( !opts || !fname || !NBL ) { - fprintf(stderr,"** nt_read_bricks: bad params (%p,%p,%p)\n", - (void *)opts, (void *)fname, (void *)NBL); - return NULL; - } - - /* if the user does not want an empty image, do normal read_bricks */ - if( strncmp(fname,NT_MAKE_IM_NAME,strlen(NT_MAKE_IM_NAME)) ) { - if(g_debug > 1) - fprintf(stderr,"-d calling nifti_image_read_bricks(%s,...)\n",fname); - return nifti_image_read_bricks(fname, len, list, NBL); - } - - /* so generate an emtpy image */ - if(g_debug > 1) { - fprintf(stderr,"+d NT_RB: generating EMPTY IMAGE from %s...\n",fname); - if(g_debug > 2) { - printf(" new_dim[8] = "); - disp_raw_data(opts->new_dim, DT_INT64, 8, ' ', 1); - printf(" new_datatype = %d\n", opts->new_datatype); - if( list && len > 0 ) { - printf(" brick_list[%d] = ", len); - disp_raw_data(list, DT_INT64, len, ' ', 1); - } - fflush(stdout); /* disp_raw_data uses stdout */ - } - } - - /* first, get nim struct without data */ - nim = nifti_make_new_nim(opts->new_dim, opts->new_datatype, 0); - if( !nim ) { - fprintf(stderr,"** nt_read_bricks, nifti_make_new_nim failure\n"); - return NULL; - } - - /* now populate NBL (can be based only on len and nim) */ - NBL->nbricks = len; - NBL->bsize = nim->nbyper * nim->nx * nim->ny * nim->nz; - NBL->bricks = (void **)calloc(NBL->nbricks, sizeof(void *)); - if( !NBL->bricks ){ - fprintf(stderr,"** NRB: failed to alloc %" PRId64 " pointers\n", - NBL->nbricks); - nifti_image_free(nim); - return NULL; - } - - if(g_debug > 1) - fprintf(stderr,"+d NRB, allocating " - "%" PRId64 " bricks of %" PRId64 " bytes...\n", - NBL->nbricks, NBL->bsize); - - /* now allocate the data pointers */ - for( c = 0; c < len; c++ ) { - NBL->bricks[c] = calloc(1, NBL->bsize); - if( !NBL->bricks[c] ){ - fprintf(stderr, - "** NRB: failed to alloc brick %d of %" PRId64 " bytes\n", - c, NBL->bsize); - nifti_free_NBL(NBL); nifti_image_free(nim); return NULL; - } - } - - return nim; -} diff --git a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_tool.h b/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_tool.h deleted file mode 100644 index 13b6ae0b6fe..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/nifti2/nifti_tool.h +++ /dev/null @@ -1,183 +0,0 @@ -#ifndef _NIFTI_TOOL_H_ -#define _NIFTI_TOOL_H_ - -#define NT_CMD_LEN 2048 - -typedef struct{ - int len; - const char ** list; -} str_list; - -typedef struct{ - int len; - int * list; -} int_list; - -typedef struct{ - /* action options (flags) */ - int check_hdr, check_nim; - int diff_hdr, diff_hdr1, diff_hdr2, diff_nim; - int disp_hdr1, disp_hdr2, disp_hdr, disp_nim, disp_ana; - int disp_exts, add_exts, rm_exts, disp_cext; - int mod_hdr, mod_nim; - int swap_hdr, swap_ana, swap_old; - - int strip; /* strip extras from dataset(s) */ - int cbl, cci; /* -copy_XXX option flags */ - int dts, dci, dci_lines; /* display collapsed img flags */ - int make_im; /* create a new image on the fly */ - int64_t ci_dims[8]; /* user dims list (last 7 valid) */ - int64_t new_dim[8]; /* user dim list for new image */ - int new_datatype; /* datatype for new image */ - int debug, keep_hist; /* debug level and history flag */ - int overwrite; /* overwrite flag */ - char * prefix; /* for output file */ - str_list elist; /* extension strings */ - int_list etypes; /* extension type list */ - str_list flist; /* fields (to display or modify) */ - str_list vlist; /* values (to set fields to) */ - str_list infiles; /* input files */ - char command[NT_CMD_LEN]; /* for inserting the command */ -} nt_opts; - -#define USE_SHORT 1 -#define USE_FULL 2 -#define USE_HIST 3 -#define USE_FIELD_HDR1 11 -#define USE_FIELD_HDR2 12 -#define USE_FIELD_NIM1 21 -#define USE_FIELD_NIM2 22 -#define USE_FIELD_ANA 31 -#define USE_DTYPES 41 -#define USE_VERSION 51 - -#define CHECK_NEXT_OPT(n,m,str) \ - do { if ( (n) >= (m) ) { \ - fprintf(stderr,"** option '%s': missing parameter\n",str); \ - fprintf(stderr," consider: 'nifti_tool -help'\n"); \ - return 1; } \ - } while(0) - -#define CHECK_NEXT_OPT_MSG(n,m,str,msg) \ - do { if ( (n) >= (m) ) { \ - fprintf(stderr,"** option '%s': %s\n",str,msg); \ - fprintf(stderr," consider: 'nifti_tool -help'\n"); \ - return 1; } \ - } while(0) - -/*---------------------------------------------------------------------- - * this structure and definitions will be used to process the nifti_1_header - * and nifti_image structure fields (actions disp, diff, mod) - *----------------------------------------------------------------------*/ - -#define NT_FIELD_NAME_LEN 20 /* more than length of longest name */ -#define NT_HDR1_NUM_FIELDS 43 /* in the nifti_1_header struct */ -#define NT_HDR2_NUM_FIELDS 37 /* in the nifti_2_header struct */ -#define NT_ANA_NUM_FIELDS 47 /* in the nifti_analyze75 struct */ -#define NT_NIM_NUM_FIELDS 63 /* in the nifti_image struct */ -#define NT_DT_STRING -0xfff /* some strange number to abuse... */ -#define NT_DT_POINTER -0xfef /* some strange number to abuse... */ -#define NT_DT_CHAR_PTR -0xfee /* another... */ -#define NT_DT_EXT_PTR -0xfed /* and another... */ - -typedef struct { - int type; /* one of the DT_* types from nifti1.h */ - int offset; /* bytes from the start of the struct */ - int size; /* size of one element type */ - int len; /* number of elements */ - char name[NT_FIELD_NAME_LEN]; /* actual structure name used */ -} field_s; - -/* for computing the offset from the start of the struct */ -#define NT_OFF(str,field) ((int)( ((char *)&str.field) - ((char *)&str) )) -#define SHOW_STRUCT_OFFSET(str,field,mesg) do { str ss; \ - if(mesg)printf("%s ",(char*)mesg); \ - printf("%s.%s @ offset %d\n", #str, #field, NT_OFF(ss,field)); } \ - while (0) - -/* call fill_field() for a single type, name and number of elements */ -/* nstr is the base struct, and fldp is a field pointer */ -#define NT_SFILL(nstr,fldp,type,name,num,rv) do{ \ - rv=fill_field(fldp,type,NT_OFF(nstr,name),num,#name); \ - fldp++; } while (0) - -#define NT_MAKE_IM_NAME "MAKE_IM" - -/*----------------------------------------------------------------------*/ -/*----- prototypes ---------------------------------------------------*/ -/*----------------------------------------------------------------------*/ -int act_add_exts ( nt_opts * opts ); -int act_cbl ( nt_opts * opts ); /* copy brick list */ -int act_cci ( nt_opts * opts ); /* copy collapsed dimensions */ -int act_check_hdrs ( nt_opts * opts ); /* check for valid hdr or nim */ -int act_diff_hdrs ( nt_opts * opts ); -int act_diff_hdr1s ( nt_opts * opts ); -int act_diff_hdr2s ( nt_opts * opts ); -int act_diff_nims ( nt_opts * opts ); -int act_disp_ci ( nt_opts * opts ); /* display general collapsed data */ -int act_disp_exts ( nt_opts * opts ); -int act_disp_cext ( nt_opts * opts ); -int act_disp_hdr ( nt_opts * opts ); -int act_disp_hdr1 ( nt_opts * opts ); -int act_disp_hdr2 ( nt_opts * opts ); -int act_disp_nims ( nt_opts * opts ); -int act_disp_anas ( nt_opts * opts ); -int act_disp_ts ( nt_opts * opts ); /* display time series */ -int act_mod_hdrs ( nt_opts * opts ); -int act_mod_nims ( nt_opts * opts ); -int act_swap_hdrs ( nt_opts * opts ); -int act_rm_ext ( nt_opts * opts ); -int act_strip ( nt_opts * opts ); /* strip extras from datasets */ - - -field_s * get_hdr1_field( const char * fname, int show_fail ); -field_s * get_hdr2_field( const char * fname, int show_fail ); -field_s * get_nim_field( const char * fname, int show_fail ); -const char * field_type_str (int type); - -int diff_hdr1s (nifti_1_header *s0, nifti_1_header *s1, int display); -int diff_hdr1s_list(nifti_1_header *s0, nifti_1_header *s1, str_list *slist, - int display); -int diff_hdr2s (nifti_2_header *s0, nifti_2_header *s1, int display); -int diff_hdr2s_list(nifti_2_header *s0, nifti_2_header *s1, str_list *slist, - int display); -int diff_nims (nifti_image *s0,nifti_image *s1, int display); -int diff_nims_list(nifti_image *s0,nifti_image *s1,str_list *slist,int display); - -int add_int (int_list * ilist, int val); -int add_string (str_list * slist, const char * str); -int check_total_size ( const char *mesg, field_s *fields, int nfields, int tot_size); -int clear_float_zeros( char * str ); -int diff_field (field_s *fieldp, void * str0, void * str1, int nfields); -int disp_cifti_extension ( const char *mesg, nifti1_extension * ext, int maxlen); -int disp_nifti1_extension( const char *mesg, nifti1_extension * ext, int maxlen); -int disp_field (const char *mesg,field_s *fp,void *str,int nfields,int header); -int disp_field_s_list(const char * mesg, field_s *, int nfields); -int disp_nt_opts ( const char *mesg, nt_opts * opts); -int disp_raw_data (void * data, int type, int nvals, char space,int newline); -int fill_cmd_string (nt_opts * opts, int argc, char * argv[]); -int fill_field (field_s *fp, int type, int offset, int num, const char *name); -int fill_hdr1_field_array(field_s * nh_fields); -int fill_hdr2_field_array(field_s * nh_fields); -int fill_nim1_field_array(field_s * nim_fields); -int fill_nim2_field_array(field_s * nim_fields); -int fill_ana_field_array(field_s * ah_fields); -int modify_all_fields(void *basep, nt_opts *opts, field_s *fields, int flen); -int modify_field (void * basep, field_s * field, const char * data); -int process_opts (int argc, char * argv[], nt_opts * opts); -int remove_ext_list (nifti_image * nim, const char ** elist, int len); -int usage (char * prog, int level); -int use_full (); -int verify_opts (nt_opts * opts, char * prog); -int write_hdr_to_file(nifti_1_header * nhdr, const char * fname); - -/* wrappers for nifti reading functions (allow MAKE_IM) */ -nifti_image * nt_image_read (nt_opts * opts, const char * fname, int doread); -nifti_image * nt_read_bricks(nt_opts * opts, char * fname, int len, - int64_t * list, nifti_brick_list * NBL); -void * nt_read_header(const char * fname, int * nver, int * swapped, int check, - int new_datatype, int64_t new_dim[8]); - - - -#endif /* _NIFTI_TOOL_H_ */ diff --git a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/CMakeLists.txt b/Modules/ThirdParty/NIFTI/src/nifti/niftilib/CMakeLists.txt deleted file mode 100644 index ad84c4a8ca7..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/CMakeLists.txt +++ /dev/null @@ -1,110 +0,0 @@ -set(NIFTI_NIFTILIB_NAME ${NIFTI_PACKAGE_PREFIX}niftiio) -add_library(${NIFTI_NIFTILIB_NAME} nifti1_io.c ) -target_link_libraries( ${NIFTI_NIFTILIB_NAME} PUBLIC ${NIFTI_PACKAGE_PREFIX}znz) -target_include_directories(${NIFTI_NIFTILIB_NAME} PUBLIC - $ - $ - ) - -if(NIFTI_BUILD_APPLICATIONS) - add_executable(${NIFTI_PACKAGE_PREFIX}nifti1_tool nifti1_tool.c) - target_link_libraries(${NIFTI_PACKAGE_PREFIX}nifti1_tool PUBLIC ${NIFTI_NIFTILIB_NAME}) - set(NIFTI1_APPS ${NIFTI_PACKAGE_PREFIX}nifti1_tool) -endif() - -# Set library version when building shared libs. -if(BUILD_SHARED_LIBS) - set_target_properties(${NIFTI_NIFTILIB_NAME} PROPERTIES ${NIFTI_LIBRARY_PROPERTIES}) -endif() - -if(UNIX) - target_link_libraries(${NIFTI_NIFTILIB_NAME} PUBLIC m) -endif() - -if(NOT NIFTI_INSTALL_NO_LIBRARIES) - install(TARGETS ${NIFTI_NIFTILIB_NAME} ${NIFTI1_APPS} - EXPORT ${NIFTI_INSTALL_EXPORT_NAME} - RUNTIME DESTINATION ${NIFTI_INSTALL_RUNTIME_DIR} COMPONENT RuntimeLibraries - LIBRARY DESTINATION ${NIFTI_INSTALL_LIBRARY_DIR} COMPONENT RuntimeLibraries - ARCHIVE DESTINATION ${NIFTI_INSTALL_LIBRARY_DIR} COMPONENT Development - INCLUDES DESTINATION ${NIFTI_INSTALL_INCLUDE_DIR} - ) -endif() - -if(NOT NIFTI_INSTALL_NO_DEVELOPMENT) - file(GLOB __files "${CMAKE_CURRENT_SOURCE_DIR}/*.h") - install(FILES ${__files} - DESTINATION ${NIFTI_INSTALL_INCLUDE_DIR} - COMPONENT Development) -endif() - - -if(NIFTI_BUILD_TESTING AND NIFTI_BUILD_APPLICATIONS) - add_executable(${NIFTI_PACKAGE_PREFIX}nifti1_test nifti1_test.c) - target_link_libraries(${NIFTI_PACKAGE_PREFIX}nifti1_test PUBLIC ${NIFTI_NIFTILIB_NAME}) - - add_executable(nifti_first_test_program nifti_tester001.c) - target_link_libraries(nifti_first_test_program ${NIFTI_PACKAGE_PREFIX}niftiio ) - - add_executable(nifti_second_test_program nifti_tester002.c) - target_link_libraries(nifti_second_test_program ${NIFTI_PACKAGE_PREFIX}niftiio ) - - add_executable( ${NIFTI_PACKAGE_PREFIX}nifti_tester001 nifti_tester001.c) - target_link_libraries(${NIFTI_PACKAGE_PREFIX}nifti_tester001 ${NIFTI_PACKAGE_PREFIX}niftiio ) - - add_executable( ${NIFTI_PACKAGE_PREFIX}nifti_tester002 nifti_tester002.c) - target_link_libraries(${NIFTI_PACKAGE_PREFIX}nifti_tester002 ${NIFTI_PACKAGE_PREFIX}niftiio ) - - add_test( NAME nifti_first_test COMMAND $ ) - add_test( NAME nifti_second_test COMMAND $ ) - - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_test_help COMMAND $) - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_test_n1 COMMAND $ -n1 ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTI_BINARY_DIR}/niftilib/n1 ) - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_test_n2 COMMAND $ -n2 ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTI_BINARY_DIR}/niftilib/n2 ) - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_test_a2 COMMAND $ -a2 ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTI_BINARY_DIR}/niftilib/a2 ) - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_test_zn1 COMMAND $ -zn1 ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTI_BINARY_DIR}/niftilib/zn1 ) - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_test_zn2 COMMAND $ -zn2 ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTI_BINARY_DIR}/niftilib/zn2 ) - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_test_za2 COMMAND $ -za2 ${fetch_testing_data_SOURCE_DIR}/nifti_regress_data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTI_BINARY_DIR}/niftilib/za2 ) - - #The help screens always return 1; add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool1_help COMMAND $) - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool_n1 COMMAND $ -disp_hdr -infile ${NIFTI_BINARY_DIR}/niftilib/n1 ) - set_tests_properties( ${NIFTI_PACKAGE_PREFIX}nifti1_tool_n1 PROPERTIES DEPENDS ${NIFTI_PACKAGE_PREFIX}nifti1_test_n1) - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool_n2 COMMAND $ -disp_hdr -infile ${NIFTI_BINARY_DIR}/niftilib/n2 ) - set_tests_properties( ${NIFTI_PACKAGE_PREFIX}nifti1_tool_n2 PROPERTIES DEPENDS ${NIFTI_PACKAGE_PREFIX}nifti1_test_n2) - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool_a2 COMMAND $ -disp_hdr -infile ${NIFTI_BINARY_DIR}/niftilib/a2 ) - set_tests_properties( ${NIFTI_PACKAGE_PREFIX}nifti1_tool_a2 PROPERTIES DEPENDS ${NIFTI_PACKAGE_PREFIX}nifti1_test_a2) - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool_zn1 COMMAND $ -disp_hdr -infile ${NIFTI_BINARY_DIR}/niftilib/zn1 ) - set_tests_properties( ${NIFTI_PACKAGE_PREFIX}nifti1_tool_zn1 PROPERTIES DEPENDS ${NIFTI_PACKAGE_PREFIX}nifti1_test_zn1) - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool_zn2 COMMAND $ -disp_hdr -infile ${NIFTI_BINARY_DIR}/niftilib/zn2 ) - set_tests_properties( ${NIFTI_PACKAGE_PREFIX}nifti1_tool_zn2 PROPERTIES DEPENDS ${NIFTI_PACKAGE_PREFIX}nifti1_test_zn2) - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool_za2 COMMAND $ -disp_hdr -infile ${NIFTI_BINARY_DIR}/niftilib/za2 ) - set_tests_properties( ${NIFTI_PACKAGE_PREFIX}nifti1_tool_za2 PROPERTIES DEPENDS ${NIFTI_PACKAGE_PREFIX}nifti1_test_za2) - - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool_diff_hdr COMMAND $ -diff_hdr -infile ${NIFTI_BINARY_DIR}/niftilib/zn1 ${NIFTI_BINARY_DIR}/niftilib/zn1 ) - set_tests_properties( ${NIFTI_PACKAGE_PREFIX}nifti1_tool_diff_hdr PROPERTIES DEPENDS ${NIFTI_PACKAGE_PREFIX}nifti1_test_zn1) - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool_diff_nims COMMAND $ -diff_nim -infile ${NIFTI_BINARY_DIR}/niftilib/zn1 ${NIFTI_BINARY_DIR}/niftilib/zn1 ) - set_tests_properties( ${NIFTI_PACKAGE_PREFIX}nifti1_tool_diff_nims PROPERTIES DEPENDS ${NIFTI_PACKAGE_PREFIX}nifti1_test_zn1) - - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool_copy_brick_list COMMAND $ -cbl -prefix cbl_zn1.nii -infile ${NIFTI_BINARY_DIR}/niftilib/zn1.nii.gz[0,1]) - set_tests_properties( ${NIFTI_PACKAGE_PREFIX}nifti1_tool_copy_brick_list PROPERTIES DEPENDS ${NIFTI_PACKAGE_PREFIX}nifti1_test_zn1) - #add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool_copy_collapsed_image /bin/sh ${NIFTI_SOURCE_DIR}/niftilib/rmthenrun cci_zn1.nii COMMAND $ -cci 2 2 2 -1 -1 -1 -1 -prefix cci_zn1.nii -infile ${NIFTI_BINARY_DIR}/niftilib/zn1.nii.gz ) - #set_tests_properties( ${NIFTI_PACKAGE_PREFIX}nifti1_tool_copy_collapsed_image PROPERTIES DEPENDS ${NIFTI_PACKAGE_PREFIX}nifti1_test_zn1) - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool_disp_ci COMMAND $ -disp_ci 2 2 2 -1 0 0 0 -infile ${NIFTI_BINARY_DIR}/niftilib/zn1.nii.gz ) - set_tests_properties( ${NIFTI_PACKAGE_PREFIX}nifti1_tool_disp_ci PROPERTIES DEPENDS ${NIFTI_PACKAGE_PREFIX}nifti1_test_zn1) - - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool_disp_ts COMMAND $ -disp_ts 2 2 2 -infile ${NIFTI_BINARY_DIR}/niftilib/zn1.nii.gz ) - set_tests_properties( ${NIFTI_PACKAGE_PREFIX}nifti1_tool_disp_ts PROPERTIES DEPENDS ${NIFTI_PACKAGE_PREFIX}nifti1_test_zn1) - - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool_strip_extras COMMAND $ -strip_extras -infile ${NIFTI_BINARY_DIR}/niftilib/zn1.nii.gz ) - set_tests_properties( ${NIFTI_PACKAGE_PREFIX}nifti1_tool_strip_extras PROPERTIES DEPENDS ${NIFTI_PACKAGE_PREFIX}nifti1_test_zn1) - - # This test needs a file that has extensions to remove - #add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool_rm_ext /bin/sh ${NIFTI_SOURCE_DIR}/niftilib/rmthenrun rm_ext.nii COMMAND $ -rm_ext ALL -prefix rm_ext.nii -infile ${NIFTI_BINARY_DIR}/niftilib/zn1.nii.gz ) - - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool_check_hdr COMMAND $ -check_hdr -infile ${NIFTI_BINARY_DIR}/niftilib/za2 ) - set_tests_properties( ${NIFTI_PACKAGE_PREFIX}nifti1_tool_check_hdr PROPERTIES DEPENDS ${NIFTI_PACKAGE_PREFIX}nifti1_test_za2) - - add_test( NAME ${NIFTI_PACKAGE_PREFIX}nifti1_tool_check_nim COMMAND $ -check_nim -infile ${NIFTI_BINARY_DIR}/niftilib/za2 ) - set_tests_properties( ${NIFTI_PACKAGE_PREFIX}nifti1_tool_check_nim PROPERTIES DEPENDS ${NIFTI_PACKAGE_PREFIX}nifti1_test_za2) - -endif() diff --git a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/Makefile b/Modules/ThirdParty/NIFTI/src/nifti/niftilib/Makefile deleted file mode 100644 index 14e5bd29bf5..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/Makefile +++ /dev/null @@ -1,56 +0,0 @@ -include ../Makefile - -PROJNAME = niftiio - -TAR ?= /bin/tar -RM ?= /bin/rm - -INCFLAGS = $(ZLIB_INC) $(ZNZ_INC) -LIBS = $(ZLIB_LIBS) $(ZNZ_LIBS) $(NIFTI_LIBS) - -SRCS=nifti1_io.c -OBJS=nifti1_io.o -MOBJS=mjtest.o - -SCRIPTS = - -depend: - $(RM) -f depend.mk - $(MAKE) depend.mk - -depend.mk: - $(CC) $(DEPENDFLAGS) $(INCFLAGS) $(SRCS) >> depend.mk - -lib: libniftiio.a - -nifti1_io.o: nifti1_io.c nifti1_io.h - $(CC) -c $(CFLAGS) $(USEZLIB) $(INCFLAGS) $< - -libniftiio.a: $(OBJS) - $(AR) -r libniftiio.a $(OBJS) - $(RANLIB) $@ - -nifti_tool: nifti_tool.c nifti_tool.h - $(CC) $(CFLAGS) -Wall -o nifti_tool nifti_tool.c $(NIFTI_INCS) $(ZNZ_INCS) $(NIFTI_LIBS) $(ZNZ_LIBS) - -nifti1_test: nifti1_test.c - $(CC) $(CFLAGS) -o nifti1_test nifti1_test.c $(NIFTI_INCS) $(ZNZ_INCS) $(NIFTI_LIBS) $(ZNZ_LIBS) - -# get the regression testing data tree -regress_data: nifti_regress_test/nifti_regress_data - -# remove any result directories -regress_clean: - $(RM) -fr nifti_regress_test/results* - -# remove any result directories, and remove the data tree -regress_clean_all: regress_clean - $(RM) -fr nifti_regress_test/nifti_regress_data - -# download and unpack the regression data tree -nifti_regress_test/nifti_regress_data: - wget http://nifti.nimh.nih.gov/pub/dist/data/nifti_regress_data.tgz - ( cd nifti_regress_test; $(TAR) -xzf ../nifti_regress_data.tgz; ) - $(RM) nifti_regress_data.tgz - -include depend.mk diff --git a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1.h b/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1.h deleted file mode 100644 index 80066fb347c..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1.h +++ /dev/null @@ -1,1490 +0,0 @@ -/** \file nifti1.h - \brief Official definition of the nifti1 header. Written by Bob Cox, SSCC, NIMH. - - HISTORY: - - 29 Nov 2007 [rickr] - - added DT_RGBA32 and NIFTI_TYPE_RGBA32 - - added NIFTI_INTENT codes: - TIME_SERIES, NODE_INDEX, RGB_VECTOR, RGBA_VECTOR, SHAPE - */ - -#ifndef _NIFTI_HEADER_ -#define _NIFTI_HEADER_ - -/***************************************************************************** - ** This file defines the "NIFTI-1" header format. ** - ** It is derived from 2 meetings at the NIH (31 Mar 2003 and ** - ** 02 Sep 2003) of the Data Format Working Group (DFWG), ** - ** chartered by the NIfTI (Neuroimaging Informatics Technology ** - ** Initiative) at the National Institutes of Health (NIH). ** - **--------------------------------------------------------------** - ** Neither the National Institutes of Health (NIH), the DFWG, ** - ** nor any of the members or employees of these institutions ** - ** imply any warranty of usefulness of this material for any ** - ** purpose, and do not assume any liability for damages, ** - ** incidental or otherwise, caused by any use of this document. ** - ** If these conditions are not acceptable, do not use this! ** - **--------------------------------------------------------------** - ** Author: Robert W Cox (NIMH, Bethesda) ** - ** Advisors: John Ashburner (FIL, London), ** - ** Stephen Smith (FMRIB, Oxford), ** - ** Mark Jenkinson (FMRIB, Oxford) ** -******************************************************************************/ - -/*---------------------------------------------------------------------------*/ -/* Note that the ANALYZE 7.5 file header (dbh.h) is - (c) Copyright 1986-1995 - Biomedical Imaging Resource - Mayo Foundation - Incorporation of components of dbh.h are by permission of the - Mayo Foundation. - - Changes from the ANALYZE 7.5 file header in this file are released to the - public domain, including the functional comments and any amusing asides. ------------------------------------------------------------------------------*/ - -/*---------------------------------------------------------------------------*/ -/*! INTRODUCTION TO NIFTI-1: - ------------------------ - The twin (and somewhat conflicting) goals of this modified ANALYZE 7.5 - format are: - (a) To add information to the header that will be useful for functional - neuroimaging data analysis and display. These additions include: - - More basic data types. - - Two affine transformations to specify voxel coordinates. - - "Intent" codes and parameters to describe the meaning of the data. - - Affine scaling of the stored data values to their "true" values. - - Optional storage of the header and image data in one file (.nii). - (b) To maintain compatibility with non-NIFTI-aware ANALYZE 7.5 compatible - software (i.e., such a program should be able to do something useful - with a NIFTI-1 dataset -- at least, with one stored in a traditional - .img/.hdr file pair). - - Most of the unused fields in the ANALYZE 7.5 header have been taken, - and some of the lesser-used fields have been co-opted for other purposes. - Notably, most of the data_history substructure has been co-opted for - other purposes, since the ANALYZE 7.5 format describes this substructure - as "not required". - - NIFTI-1 FLAG (MAGIC STRINGS): - ---------------------------- - To flag such a struct as being conformant to the NIFTI-1 spec, the last 4 - bytes of the header must be either the C String "ni1" or "n+1"; - in hexadecimal, the 4 bytes - 6E 69 31 00 or 6E 2B 31 00 - (in any future version of this format, the '1' will be upgraded to '2', - etc.). Normally, such a "magic number" or flag goes at the start of the - file, but trying to avoid clobbering widely-used ANALYZE 7.5 fields led to - putting this marker last. However, recall that "the last shall be first" - (Matthew 20:16). - - If a NIFTI-aware program reads a header file that is NOT marked with a - NIFTI magic string, then it should treat the header as an ANALYZE 7.5 - structure. - - NIFTI-1 FILE STORAGE: - -------------------- - "ni1" means that the image data is stored in the ".img" file corresponding - to the header file (starting at file offset 0). - - "n+1" means that the image data is stored in the same file as the header - information. We recommend that the combined header+data filename suffix - be ".nii". When the dataset is stored in one file, the first byte of image - data is stored at byte location (int)vox_offset in this combined file. - The minimum allowed value of vox_offset is 352; for compatibility with - some software, vox_offset should be an integral multiple of 16. - - GRACE UNDER FIRE: - ---------------- - Most NIFTI-aware programs will only be able to handle a subset of the full - range of datasets possible with this format. All NIFTI-aware programs - should take care to check if an input dataset conforms to the program's - needs and expectations (e.g., check datatype, intent_code, etc.). If the - input dataset can't be handled by the program, the program should fail - gracefully (e.g., print a useful warning; not crash). - - SAMPLE CODES: - ------------ - The associated files nifti1_io.h and nifti1_io.c provide a sample - implementation in C of a set of functions to read, write, and manipulate - NIFTI-1 files. The file nifti1_test.c is a sample program that uses - the nifti1_io.c functions. ------------------------------------------------------------------------------*/ - -/*---------------------------------------------------------------------------*/ -/* HEADER STRUCT DECLARATION: - ------------------------- - In the comments below for each field, only NIFTI-1 specific requirements - or changes from the ANALYZE 7.5 format are described. For convenience, - the 348 byte header is described as a single struct, rather than as the - ANALYZE 7.5 group of 3 substructs. - - Further comments about the interpretation of various elements of this - header are after the data type definition itself. Fields that are - marked as ++UNUSED++ have no particular interpretation in this standard. - (Also see the UNUSED FIELDS comment section, far below.) - - The presumption below is that the various C types have particular sizes: - sizeof(int) = sizeof(float) = 4 ; sizeof(short) = 2 ------------------------------------------------------------------------------*/ - -/*=================*/ -#ifdef __cplusplus -extern "C" { -#endif -/*=================*/ - -/*! \struct nifti_1_header - \brief Data structure defining the fields in the nifti1 header. - This binary header should be found at the beginning of a valid - NIFTI-1 header file. - */ - /*************************/ /************************/ -struct nifti_1_header { /* NIFTI-1 usage */ /* ANALYZE 7.5 field(s) */ - /*************************/ /************************/ - - /*--- was header_key substruct ---*/ - int sizeof_hdr; /*!< MUST be 348 */ /* int sizeof_hdr; */ - char data_type[10]; /*!< ++UNUSED++ */ /* char data_type[10]; */ - char db_name[18]; /*!< ++UNUSED++ */ /* char db_name[18]; */ - int extents; /*!< ++UNUSED++ */ /* int extents; */ - short session_error; /*!< ++UNUSED++ */ /* short session_error; */ - char regular; /*!< ++UNUSED++ */ /* char regular; */ - char dim_info; /*!< MRI slice ordering. */ /* char hkey_un0; */ - - /*--- was image_dimension substruct ---*/ - short dim[8]; /*!< Data array dimensions.*/ /* short dim[8]; */ - float intent_p1 ; /*!< 1st intent parameter. */ /* short unused8; */ - /* short unused9; */ - float intent_p2 ; /*!< 2nd intent parameter. */ /* short unused10; */ - /* short unused11; */ - float intent_p3 ; /*!< 3rd intent parameter. */ /* short unused12; */ - /* short unused13; */ - short intent_code ; /*!< NIFTI_INTENT_* code. */ /* short unused14; */ - short datatype; /*!< Defines data type! */ /* short datatype; */ - short bitpix; /*!< Number bits/voxel. */ /* short bitpix; */ - short slice_start; /*!< First slice index. */ /* short dim_un0; */ - float pixdim[8]; /*!< Grid spacings. */ /* float pixdim[8]; */ - float vox_offset; /*!< Offset into .nii file */ /* float vox_offset; */ - float scl_slope ; /*!< Data scaling: slope. */ /* float funused1; */ - float scl_inter ; /*!< Data scaling: offset. */ /* float funused2; */ - short slice_end; /*!< Last slice index. */ /* float funused3; */ - char slice_code ; /*!< Slice timing order. */ - char xyzt_units ; /*!< Units of pixdim[1..4] */ - float cal_max; /*!< Max display intensity */ /* float cal_max; */ - float cal_min; /*!< Min display intensity */ /* float cal_min; */ - float slice_duration;/*!< Time for 1 slice. */ /* float compressed; */ - float toffset; /*!< Time axis shift. */ /* float verified; */ - int glmax; /*!< ++UNUSED++ */ /* int glmax; */ - int glmin; /*!< ++UNUSED++ */ /* int glmin; */ - - /*--- was data_history substruct ---*/ - char descrip[80]; /*!< any text you like. */ /* char descrip[80]; */ - char aux_file[24]; /*!< auxiliary filename. */ /* char aux_file[24]; */ - - short qform_code ; /*!< NIFTI_XFORM_* code. */ /*-- all ANALYZE 7.5 ---*/ - short sform_code ; /*!< NIFTI_XFORM_* code. */ /* fields below here */ - /* are replaced */ - float quatern_b ; /*!< Quaternion b param. */ - float quatern_c ; /*!< Quaternion c param. */ - float quatern_d ; /*!< Quaternion d param. */ - float qoffset_x ; /*!< Quaternion x shift. */ - float qoffset_y ; /*!< Quaternion y shift. */ - float qoffset_z ; /*!< Quaternion z shift. */ - - float srow_x[4] ; /*!< 1st row affine transform. */ - float srow_y[4] ; /*!< 2nd row affine transform. */ - float srow_z[4] ; /*!< 3rd row affine transform. */ - - char intent_name[16];/*!< 'name' or meaning of data. */ - - char magic[4] ; /*!< MUST be "ni1\0" or "n+1\0". */ - -} ; /**** 348 bytes total ****/ - -typedef struct nifti_1_header nifti_1_header ; - -/*---------------------------------------------------------------------------*/ -/* HEADER EXTENSIONS: - ----------------- - After the end of the 348 byte header (e.g., after the magic field), - the next 4 bytes are a char array field named "extension". By default, - all 4 bytes of this array should be set to zero. In a .nii file, these - 4 bytes will always be present, since the earliest start point for - the image data is byte #352. In a separate .hdr file, these bytes may - or may not be present. If not present (i.e., if the length of the .hdr - file is 348 bytes), then a NIfTI-1 compliant program should use the - default value of extension={0,0,0,0}. The first byte (extension[0]) - is the only value of this array that is specified at present. The other - 3 bytes are reserved for future use. - - If extension[0] is nonzero, it indicates that extended header information - is present in the bytes following the extension array. In a .nii file, - this extended header data is before the image data (and vox_offset - must be set correctly to allow for this). In a .hdr file, this extended - data follows extension and proceeds (potentially) to the end of the file. - - The format of extended header data is weakly specified. Each extension - must be an integer multiple of 16 bytes long. The first 8 bytes of each - extension comprise 2 integers: - int esize , ecode ; - These values may need to be byte-swapped, as indicated by dim[0] for - the rest of the header. - * esize is the number of bytes that form the extended header data - + esize must be a positive integral multiple of 16 - + this length includes the 8 bytes of esize and ecode themselves - * ecode is a non-negative integer that indicates the format of the - extended header data that follows - + different ecode values are assigned to different developer groups - + at present, the "registered" values for code are - = 0 = unknown private format (not recommended!) - = 2 = DICOM format (i.e., attribute tags and values) - = 4 = AFNI group (i.e., ASCII XML-ish elements) - In the interests of interoperability (a primary rationale for NIfTI), - groups developing software that uses this extension mechanism are - encouraged to document and publicize the format of their extensions. - To this end, the NIfTI DFWG will assign even numbered codes upon request - to groups submitting at least rudimentary documentation for the format - of their extension; at present, the contact is mailto:rwcox@nih.gov. - The assigned codes and documentation will be posted on the NIfTI - website. All odd values of ecode (and 0) will remain unassigned; - at least, until the even ones are used up, when we get to 2,147,483,646. - - Note that the other contents of the extended header data section are - totally unspecified by the NIfTI-1 standard. In particular, if binary - data is stored in such a section, its byte order is not necessarily - the same as that given by examining dim[0]; it is incumbent on the - programs dealing with such data to determine the byte order of binary - extended header data. - - Multiple extended header sections are allowed, each starting with an - esize,ecode value pair. The first esize value, as described above, - is at bytes #352-355 in the .hdr or .nii file (files start at byte #0). - If this value is positive, then the second (esize2) will be found - starting at byte #352+esize1 , the third (esize3) at byte #352+esize1+esize2, - et cetera. Of course, in a .nii file, the value of vox_offset must - be compatible with these extensions. If a malformed file indicates - that an extended header data section would run past vox_offset, then - the entire extended header section should be ignored. In a .hdr file, - if an extended header data section would run past the end-of-file, - that extended header data should also be ignored. - - With the above scheme, a program can successively examine the esize - and ecode values, and skip over each extended header section if the - program doesn't know how to interpret the data within. Of course, any - program can simply ignore all extended header sections simply by jumping - straight to the image data using vox_offset. ------------------------------------------------------------------------------*/ - -/*! \struct nifti1_extender - \brief This structure represents a 4-byte string that should follow the - binary nifti_1_header data in a NIFTI-1 header file. If the char - values are {1,0,0,0}, the file is expected to contain extensions, - values of {0,0,0,0} imply the file does not contain extensions. - Other sequences of values are not currently defined. - */ -struct nifti1_extender { char extension[4] ; } ; -typedef struct nifti1_extender nifti1_extender ; - -/*! \struct nifti1_extension - \brief Data structure defining the fields of a header extension. - */ -struct nifti1_extension { - int esize ; /*!< size of extension, in bytes (must be multiple of 16) */ - int ecode ; /*!< extension code, one of the NIFTI_ECODE_ values */ - char * edata ; /*!< raw data, with no byte swapping (length is esize-8) */ -} ; -typedef struct nifti1_extension nifti1_extension ; - -/*---------------------------------------------------------------------------*/ -/* DATA DIMENSIONALITY (as in ANALYZE 7.5): - --------------------------------------- - dim[0] = number of dimensions; - - if dim[0] is outside range 1..7, then the header information - needs to be byte swapped appropriately - - ANALYZE supports dim[0] up to 7, but NIFTI-1 reserves - dimensions 1,2,3 for space (x,y,z), 4 for time (t), and - 5,6,7 for anything else needed. - - dim[i] = length of dimension #i, for i=1..dim[0] (must be positive) - - also see the discussion of intent_code, far below - - pixdim[i] = voxel width along dimension #i, i=1..dim[0] (positive) - - cf. ORIENTATION section below for use of pixdim[0] - - the units of pixdim can be specified with the xyzt_units - field (also described far below). - - Number of bits per voxel value is in bitpix, which MUST correspond with - the datatype field. The total number of bytes in the image data is - dim[1] * ... * dim[dim[0]] * bitpix / 8 - - In NIFTI-1 files, dimensions 1,2,3 are for space, dimension 4 is for time, - and dimension 5 is for storing multiple values at each spatiotemporal - voxel. Some examples: - - A typical whole-brain FMRI experiment's time series: - - dim[0] = 4 - - dim[1] = 64 pixdim[1] = 3.75 xyzt_units = NIFTI_UNITS_MM - - dim[2] = 64 pixdim[2] = 3.75 | NIFTI_UNITS_SEC - - dim[3] = 20 pixdim[3] = 5.0 - - dim[4] = 120 pixdim[4] = 2.0 - - A typical T1-weighted anatomical volume: - - dim[0] = 3 - - dim[1] = 256 pixdim[1] = 1.0 xyzt_units = NIFTI_UNITS_MM - - dim[2] = 256 pixdim[2] = 1.0 - - dim[3] = 128 pixdim[3] = 1.1 - - A single slice EPI time series: - - dim[0] = 4 - - dim[1] = 64 pixdim[1] = 3.75 xyzt_units = NIFTI_UNITS_MM - - dim[2] = 64 pixdim[2] = 3.75 | NIFTI_UNITS_SEC - - dim[3] = 1 pixdim[3] = 5.0 - - dim[4] = 1200 pixdim[4] = 0.2 - - A 3-vector stored at each point in a 3D volume: - - dim[0] = 5 - - dim[1] = 256 pixdim[1] = 1.0 xyzt_units = NIFTI_UNITS_MM - - dim[2] = 256 pixdim[2] = 1.0 - - dim[3] = 128 pixdim[3] = 1.1 - - dim[4] = 1 pixdim[4] = 0.0 - - dim[5] = 3 intent_code = NIFTI_INTENT_VECTOR - - A single time series with a 3x3 matrix at each point: - - dim[0] = 5 - - dim[1] = 1 xyzt_units = NIFTI_UNITS_SEC - - dim[2] = 1 - - dim[3] = 1 - - dim[4] = 1200 pixdim[4] = 0.2 - - dim[5] = 9 intent_code = NIFTI_INTENT_GENMATRIX - - intent_p1 = intent_p2 = 3.0 (indicates matrix dimensions) ------------------------------------------------------------------------------*/ - -/*---------------------------------------------------------------------------*/ -/* DATA STORAGE: - ------------ - If the magic field is "n+1", then the voxel data is stored in the - same file as the header. In this case, the voxel data starts at offset - (int)vox_offset into the header file. Thus, vox_offset=352.0 means that - the data starts immediately after the NIFTI-1 header. If vox_offset is - greater than 352, the NIFTI-1 format does not say much about the - contents of the dataset file between the end of the header and the - start of the data. - - FILES: - ----- - If the magic field is "ni1", then the voxel data is stored in the - associated ".img" file, starting at offset 0 (i.e., vox_offset is not - used in this case, and should be set to 0.0). - - When storing NIFTI-1 datasets in pairs of files, it is customary to name - the files in the pattern "name.hdr" and "name.img", as in ANALYZE 7.5. - When storing in a single file ("n+1"), the file name should be in - the form "name.nii" (the ".nft" and ".nif" suffixes are already taken; - cf. http://www.icdatamaster.com/n.html ). - - BYTE ORDERING: - ------------- - The byte order of the data arrays is presumed to be the same as the byte - order of the header (which is determined by examining dim[0]). - - Floating point types are presumed to be stored in IEEE-754 format. ------------------------------------------------------------------------------*/ - -/*---------------------------------------------------------------------------*/ -/* DETAILS ABOUT vox_offset: - ------------------------ - In a .nii file, the vox_offset field value is interpreted as the start - location of the image data bytes in that file. In a .hdr/.img file pair, - the vox_offset field value is the start location of the image data - bytes in the .img file. - * If vox_offset is less than 352 in a .nii file, it is equivalent - to 352 (i.e., image data never starts before byte #352 in a .nii file). - * The default value for vox_offset in a .nii file is 352. - * In a .hdr file, the default value for vox_offset is 0. - * vox_offset should be an integer multiple of 16; otherwise, some - programs may not work properly (e.g., SPM). This is to allow - memory-mapped input to be properly byte-aligned. - Note that since vox_offset is an IEEE-754 32 bit float (for compatibility - with the ANALYZE-7.5 format), it effectively has a 24 bit mantissa. All - integers from 0 to 2^24 can be represented exactly in this format, but not - all larger integers are exactly storable as IEEE-754 32 bit floats. However, - unless you plan to have vox_offset be potentially larger than 16 MB, this - should not be an issue. (Actually, any integral multiple of 16 up to 2^27 - can be represented exactly in this format, which allows for up to 128 MB - of random information before the image data. If that isn't enough, then - perhaps this format isn't right for you.) - - In a .img file (i.e., image data stored separately from the NIfTI-1 - header), data bytes between #0 and #vox_offset-1 (inclusive) are completely - undefined and unregulated by the NIfTI-1 standard. One potential use of - having vox_offset > 0 in the .hdr/.img file pair storage method is to make - the .img file be a copy of (or link to) a pre-existing image file in some - other format, such as DICOM; then vox_offset would be set to the offset of - the image data in this file. (It may not be possible to follow the - "multiple-of-16 rule" with an arbitrary external file; using the NIfTI-1 - format in such a case may lead to a file that is incompatible with software - that relies on vox_offset being a multiple of 16.) - - In a .nii file, data bytes between #348 and #vox_offset-1 (inclusive) may - be used to store user-defined extra information; similarly, in a .hdr file, - any data bytes after byte #347 are available for user-defined extra - information. The (very weak) regulation of this extra header data is - described elsewhere. ------------------------------------------------------------------------------*/ - -/*---------------------------------------------------------------------------*/ -/* DATA SCALING: - ------------ - If the scl_slope field is nonzero, then each voxel value in the dataset - should be scaled as - y = scl_slope * x + scl_inter - where x = voxel value stored - y = "true" voxel value - Normally, we would expect this scaling to be used to store "true" floating - values in a smaller integer datatype, but that is not required. That is, - it is legal to use scaling even if the datatype is a float type (crazy, - perhaps, but legal). - - However, the scaling is to be ignored if datatype is DT_RGB24. - - If datatype is a complex type, then the scaling is to be - applied to both the real and imaginary parts. - - The cal_min and cal_max fields (if nonzero) are used for mapping (possibly - scaled) dataset values to display colors: - - Minimum display intensity (black) corresponds to dataset value cal_min. - - Maximum display intensity (white) corresponds to dataset value cal_max. - - Dataset values below cal_min should display as black also, and values - above cal_max as white. - - Colors "black" and "white", of course, may refer to any scalar display - scheme (e.g., a color lookup table specified via aux_file). - - cal_min and cal_max only make sense when applied to scalar-valued - datasets (i.e., dim[0] < 5 or dim[5] = 1). ------------------------------------------------------------------------------*/ - -/*---------------------------------------------------------------------------*/ -/* TYPE OF DATA (acceptable values for datatype field): - --------------------------------------------------- - Values of datatype smaller than 256 are ANALYZE 7.5 compatible. - Larger values are NIFTI-1 additions. These are all multiples of 256, so - that no bits below position 8 are set in datatype. But there is no need - to use only powers-of-2, as the original ANALYZE 7.5 datatype codes do. - - The additional codes are intended to include a complete list of basic - scalar types, including signed and unsigned integers from 8 to 64 bits, - floats from 32 to 128 bits, and complex (float pairs) from 64 to 256 bits. - - Note that most programs will support only a few of these datatypes! - A NIFTI-1 program should fail gracefully (e.g., print a warning message) - when it encounters a dataset with a type it doesn't like. ------------------------------------------------------------------------------*/ - -#undef DT_UNKNOWN /* defined in dirent.h on some Unix systems */ - -/*! \defgroup NIFTI1_DATATYPES - \brief nifti1 datatype codes - @{ - */ - /*--- the original ANALYZE 7.5 type codes ---*/ -#define DT_NONE 0 -#define DT_UNKNOWN 0 /* what it says, dude */ -#define DT_BINARY 1 /* binary (1 bit/voxel) */ -#define DT_UNSIGNED_CHAR 2 /* unsigned char (8 bits/voxel) */ -#define DT_SIGNED_SHORT 4 /* signed short (16 bits/voxel) */ -#define DT_SIGNED_INT 8 /* signed int (32 bits/voxel) */ -#define DT_FLOAT 16 /* float (32 bits/voxel) */ -#define DT_COMPLEX 32 /* complex (64 bits/voxel) */ -#define DT_DOUBLE 64 /* double (64 bits/voxel) */ -#define DT_RGB 128 /* RGB triple (24 bits/voxel) */ -#define DT_ALL 255 /* not very useful (?) */ - - /*----- another set of names for the same ---*/ -#define DT_UINT8 2 -#define DT_INT16 4 -#define DT_INT32 8 -#define DT_FLOAT32 16 -#define DT_COMPLEX64 32 -#define DT_FLOAT64 64 -#define DT_RGB24 128 - - /*------------------- new codes for NIFTI ---*/ -#define DT_INT8 256 /* signed char (8 bits) */ -#define DT_UINT16 512 /* unsigned short (16 bits) */ -#define DT_UINT32 768 /* unsigned int (32 bits) */ -#define DT_INT64 1024 /* long long (64 bits) */ -#define DT_UINT64 1280 /* unsigned long long (64 bits) */ -#define DT_FLOAT128 1536 /* long double (128 bits) */ -#define DT_COMPLEX128 1792 /* double pair (128 bits) */ -#define DT_COMPLEX256 2048 /* long double pair (256 bits) */ -#define DT_RGBA32 2304 /* 4 byte RGBA (32 bits/voxel) */ -/* @} */ - - - /*------- aliases for all the above codes ---*/ - -/*! \defgroup NIFTI1_DATATYPE_ALIASES - \brief aliases for the nifti1 datatype codes - @{ - */ - /*! unsigned char. */ -#define NIFTI_TYPE_UINT8 2 - /*! signed short. */ -#define NIFTI_TYPE_INT16 4 - /*! signed int. */ -#define NIFTI_TYPE_INT32 8 - /*! 32 bit float. */ -#define NIFTI_TYPE_FLOAT32 16 - /*! 64 bit complex = 2 32 bit floats. */ -#define NIFTI_TYPE_COMPLEX64 32 - /*! 64 bit float = double. */ -#define NIFTI_TYPE_FLOAT64 64 - /*! 3 8 bit bytes. */ -#define NIFTI_TYPE_RGB24 128 - /*! signed char. */ -#define NIFTI_TYPE_INT8 256 - /*! unsigned short. */ -#define NIFTI_TYPE_UINT16 512 - /*! unsigned int. */ -#define NIFTI_TYPE_UINT32 768 - /*! signed long long. */ -#define NIFTI_TYPE_INT64 1024 - /*! unsigned long long. */ -#define NIFTI_TYPE_UINT64 1280 - /*! 128 bit float = long double. */ -#define NIFTI_TYPE_FLOAT128 1536 - /*! 128 bit complex = 2 64 bit floats. */ -#define NIFTI_TYPE_COMPLEX128 1792 - /*! 256 bit complex = 2 128 bit floats */ -#define NIFTI_TYPE_COMPLEX256 2048 - /*! 4 8 bit bytes. */ -#define NIFTI_TYPE_RGBA32 2304 -/* @} */ - - /*-------- sample typedefs for complicated types ---*/ -#if 0 -typedef struct { float r,i; } complex_float ; -typedef struct { double r,i; } complex_double ; -typedef struct { long double r,i; } complex_longdouble ; -typedef struct { unsigned char r,g,b; } rgb_byte ; -#endif - -/*---------------------------------------------------------------------------*/ -/* INTERPRETATION OF VOXEL DATA: - ---------------------------- - The intent_code field can be used to indicate that the voxel data has - some particular meaning. In particular, a large number of codes is - given to indicate that the the voxel data should be interpreted as - being drawn from a given probability distribution. - - VECTOR-VALUED DATASETS: - ---------------------- - The 5th dimension of the dataset, if present (i.e., dim[0]=5 and - dim[5] > 1), contains multiple values (e.g., a vector) to be stored - at each spatiotemporal location. For example, the header values - - dim[0] = 5 - - dim[1] = 64 - - dim[2] = 64 - - dim[3] = 20 - - dim[4] = 1 (indicates no time axis) - - dim[5] = 3 - - datatype = DT_FLOAT - - intent_code = NIFTI_INTENT_VECTOR - mean that this dataset should be interpreted as a 3D volume (64x64x20), - with a 3-vector of floats defined at each point in the 3D grid. - - A program reading a dataset with a 5th dimension may want to reformat - the image data to store each voxels' set of values together in a struct - or array. This programming detail, however, is beyond the scope of the - NIFTI-1 file specification! Uses of dimensions 6 and 7 are also not - specified here. - - STATISTICAL PARAMETRIC DATASETS (i.e., SPMs): - -------------------------------------------- - Values of intent_code from NIFTI_FIRST_STATCODE to NIFTI_LAST_STATCODE - (inclusive) indicate that the numbers in the dataset should be interpreted - as being drawn from a given distribution. Most such distributions have - auxiliary parameters (e.g., NIFTI_INTENT_TTEST has 1 DOF parameter). - - If the dataset DOES NOT have a 5th dimension, then the auxiliary parameters - are the same for each voxel, and are given in header fields intent_p1, - intent_p2, and intent_p3. - - If the dataset DOES have a 5th dimension, then the auxiliary parameters - are different for each voxel. For example, the header values - - dim[0] = 5 - - dim[1] = 128 - - dim[2] = 128 - - dim[3] = 1 (indicates a single slice) - - dim[4] = 1 (indicates no time axis) - - dim[5] = 2 - - datatype = DT_FLOAT - - intent_code = NIFTI_INTENT_TTEST - mean that this is a 2D dataset (128x128) of t-statistics, with the - t-statistic being in the first "plane" of data and the degrees-of-freedom - parameter being in the second "plane" of data. - - If the dataset 5th dimension is used to store the voxel-wise statistical - parameters, then dim[5] must be 1 plus the number of parameters required - by that distribution (e.g., intent_code=NIFTI_INTENT_TTEST implies dim[5] - must be 2, as in the example just above). - - Note: intent_code values 2..10 are compatible with AFNI 1.5x (which is - why there is no code with value=1, which is obsolescent in AFNI). - - OTHER INTENTIONS: - ---------------- - The purpose of the intent_* fields is to help interpret the values - stored in the dataset. Some non-statistical values for intent_code - and conventions are provided for storing other complex data types. - - The intent_name field provides space for a 15 character (plus 0 byte) - 'name' string for the type of data stored. Examples: - - intent_code = NIFTI_INTENT_ESTIMATE; intent_name = "T1"; - could be used to signify that the voxel values are estimates of the - NMR parameter T1. - - intent_code = NIFTI_INTENT_TTEST; intent_name = "House"; - could be used to signify that the voxel values are t-statistics - for the significance of 'activation' response to a House stimulus. - - intent_code = NIFTI_INTENT_DISPVECT; intent_name = "ToMNI152"; - could be used to signify that the voxel values are a displacement - vector that transforms each voxel (x,y,z) location to the - corresponding location in the MNI152 standard brain. - - intent_code = NIFTI_INTENT_SYMMATRIX; intent_name = "DTI"; - could be used to signify that the voxel values comprise a diffusion - tensor image. - - If no data name is implied or needed, intent_name[0] should be set to 0. ------------------------------------------------------------------------------*/ - - /*! default: no intention is indicated in the header. */ - -#define NIFTI_INTENT_NONE 0 - - /*-------- These codes are for probability distributions ---------------*/ - /* Most distributions have a number of parameters, - below denoted by p1, p2, and p3, and stored in - - intent_p1, intent_p2, intent_p3 if dataset doesn't have 5th dimension - - image data array if dataset does have 5th dimension - - Functions to compute with many of the distributions below can be found - in the CDF library from U Texas. - - Formulas for and discussions of these distributions can be found in the - following books: - - [U] Univariate Discrete Distributions, - NL Johnson, S Kotz, AW Kemp. - - [C1] Continuous Univariate Distributions, vol. 1, - NL Johnson, S Kotz, N Balakrishnan. - - [C2] Continuous Univariate Distributions, vol. 2, - NL Johnson, S Kotz, N Balakrishnan. */ - /*----------------------------------------------------------------------*/ - - /*! [C2, chap 32] Correlation coefficient R (1 param): - p1 = degrees of freedom - R/sqrt(1-R*R) is t-distributed with p1 DOF. */ - -/*! \defgroup NIFTI1_INTENT_CODES - \brief nifti1 intent codes, to describe intended meaning of dataset contents - @{ - */ -#define NIFTI_INTENT_CORREL 2 - - /*! [C2, chap 28] Student t statistic (1 param): p1 = DOF. */ - -#define NIFTI_INTENT_TTEST 3 - - /*! [C2, chap 27] Fisher F statistic (2 params): - p1 = numerator DOF, p2 = denominator DOF. */ - -#define NIFTI_INTENT_FTEST 4 - - /*! [C1, chap 13] Standard normal (0 params): Density = N(0,1). */ - -#define NIFTI_INTENT_ZSCORE 5 - - /*! [C1, chap 18] Chi-squared (1 param): p1 = DOF. - Density(x) proportional to exp(-x/2) * x^(p1/2-1). */ - -#define NIFTI_INTENT_CHISQ 6 - - /*! [C2, chap 25] Beta distribution (2 params): p1=a, p2=b. - Density(x) proportional to x^(a-1) * (1-x)^(b-1). */ - -#define NIFTI_INTENT_BETA 7 - - /*! [U, chap 3] Binomial distribution (2 params): - p1 = number of trials, p2 = probability per trial. - Prob(x) = (p1 choose x) * p2^x * (1-p2)^(p1-x), for x=0,1,...,p1. */ - -#define NIFTI_INTENT_BINOM 8 - - /*! [C1, chap 17] Gamma distribution (2 params): - p1 = shape, p2 = scale. - Density(x) proportional to x^(p1-1) * exp(-p2*x). */ - -#define NIFTI_INTENT_GAMMA 9 - - /*! [U, chap 4] Poisson distribution (1 param): p1 = mean. - Prob(x) = exp(-p1) * p1^x / x! , for x=0,1,2,.... */ - -#define NIFTI_INTENT_POISSON 10 - - /*! [C1, chap 13] Normal distribution (2 params): - p1 = mean, p2 = standard deviation. */ - -#define NIFTI_INTENT_NORMAL 11 - - /*! [C2, chap 30] Noncentral F statistic (3 params): - p1 = numerator DOF, p2 = denominator DOF, - p3 = numerator noncentrality parameter. */ - -#define NIFTI_INTENT_FTEST_NONC 12 - - /*! [C2, chap 29] Noncentral chi-squared statistic (2 params): - p1 = DOF, p2 = noncentrality parameter. */ - -#define NIFTI_INTENT_CHISQ_NONC 13 - - /*! [C2, chap 23] Logistic distribution (2 params): - p1 = location, p2 = scale. - Density(x) proportional to sech^2((x-p1)/(2*p2)). */ - -#define NIFTI_INTENT_LOGISTIC 14 - - /*! [C2, chap 24] Laplace distribution (2 params): - p1 = location, p2 = scale. - Density(x) proportional to exp(-abs(x-p1)/p2). */ - -#define NIFTI_INTENT_LAPLACE 15 - - /*! [C2, chap 26] Uniform distribution: p1 = lower end, p2 = upper end. */ - -#define NIFTI_INTENT_UNIFORM 16 - - /*! [C2, chap 31] Noncentral t statistic (2 params): - p1 = DOF, p2 = noncentrality parameter. */ - -#define NIFTI_INTENT_TTEST_NONC 17 - - /*! [C1, chap 21] Weibull distribution (3 params): - p1 = location, p2 = scale, p3 = power. - Density(x) proportional to - ((x-p1)/p2)^(p3-1) * exp(-((x-p1)/p2)^p3) for x > p1. */ - -#define NIFTI_INTENT_WEIBULL 18 - - /*! [C1, chap 18] Chi distribution (1 param): p1 = DOF. - Density(x) proportional to x^(p1-1) * exp(-x^2/2) for x > 0. - p1 = 1 = 'half normal' distribution - p1 = 2 = Rayleigh distribution - p1 = 3 = Maxwell-Boltzmann distribution. */ - -#define NIFTI_INTENT_CHI 19 - - /*! [C1, chap 15] Inverse Gaussian (2 params): - p1 = mu, p2 = lambda - Density(x) proportional to - exp(-p2*(x-p1)^2/(2*p1^2*x)) / x^3 for x > 0. */ - -#define NIFTI_INTENT_INVGAUSS 20 - - /*! [C2, chap 22] Extreme value type I (2 params): - p1 = location, p2 = scale - cdf(x) = exp(-exp(-(x-p1)/p2)). */ - -#define NIFTI_INTENT_EXTVAL 21 - - /*! Data is a 'p-value' (no params). */ - -#define NIFTI_INTENT_PVAL 22 - - /*! Data is ln(p-value) (no params). - To be safe, a program should compute p = exp(-abs(this_value)). - The nifti_stats.c library returns this_value - as positive, so that this_value = -log(p). */ - - -#define NIFTI_INTENT_LOGPVAL 23 - - /*! Data is log10(p-value) (no params). - To be safe, a program should compute p = pow(10.,-abs(this_value)). - The nifti_stats.c library returns this_value - as positive, so that this_value = -log10(p). */ - -#define NIFTI_INTENT_LOG10PVAL 24 - - /*! Smallest intent_code that indicates a statistic. */ - -#define NIFTI_FIRST_STATCODE 2 - - /*! Largest intent_code that indicates a statistic. */ - -#define NIFTI_LAST_STATCODE 24 - - /*---------- these values for intent_code aren't for statistics ----------*/ - - /*! To signify that the value at each voxel is an estimate - of some parameter, set intent_code = NIFTI_INTENT_ESTIMATE. - The name of the parameter may be stored in intent_name. */ - -#define NIFTI_INTENT_ESTIMATE 1001 - - /*! To signify that the value at each voxel is an index into - some set of labels, set intent_code = NIFTI_INTENT_LABEL. - The filename with the labels may stored in aux_file. */ - -#define NIFTI_INTENT_LABEL 1002 - - /*! To signify that the value at each voxel is an index into the - NeuroNames labels set, set intent_code = NIFTI_INTENT_NEURONAME. */ - -#define NIFTI_INTENT_NEURONAME 1003 - - /*! To store an M x N matrix at each voxel: - - dataset must have a 5th dimension (dim[0]=5 and dim[5]>1) - - intent_code must be NIFTI_INTENT_GENMATRIX - - dim[5] must be M*N - - intent_p1 must be M (in float format) - - intent_p2 must be N (ditto) - - the matrix values A[i][[j] are stored in row-order: - - A[0][0] A[0][1] ... A[0][N-1] - - A[1][0] A[1][1] ... A[1][N-1] - - etc., until - - A[M-1][0] A[M-1][1] ... A[M-1][N-1] */ - -#define NIFTI_INTENT_GENMATRIX 1004 - - /*! To store an NxN symmetric matrix at each voxel: - - dataset must have a 5th dimension - - intent_code must be NIFTI_INTENT_SYMMATRIX - - dim[5] must be N*(N+1)/2 - - intent_p1 must be N (in float format) - - the matrix values A[i][[j] are stored in row-order: - - A[0][0] - - A[1][0] A[1][1] - - A[2][0] A[2][1] A[2][2] - - etc.: row-by-row */ - -#define NIFTI_INTENT_SYMMATRIX 1005 - - /*! To signify that the vector value at each voxel is to be taken - as a displacement field or vector: - - dataset must have a 5th dimension - - intent_code must be NIFTI_INTENT_DISPVECT - - dim[5] must be the dimensionality of the displacment - vector (e.g., 3 for spatial displacement, 2 for in-plane) */ - -#define NIFTI_INTENT_DISPVECT 1006 /* specifically for displacements */ -#define NIFTI_INTENT_VECTOR 1007 /* for any other type of vector */ - - /*! To signify that the vector value at each voxel is really a - spatial coordinate (e.g., the vertices or nodes of a surface mesh): - - dataset must have a 5th dimension - - intent_code must be NIFTI_INTENT_POINTSET - - dim[0] = 5 - - dim[1] = number of points - - dim[2] = dim[3] = dim[4] = 1 - - dim[5] must be the dimensionality of space (e.g., 3 => 3D space). - - intent_name may describe the object these points come from - (e.g., "pial", "gray/white" , "EEG", "MEG"). */ - -#define NIFTI_INTENT_POINTSET 1008 - - /*! To signify that the vector value at each voxel is really a triple - of indexes (e.g., forming a triangle) from a pointset dataset: - - dataset must have a 5th dimension - - intent_code must be NIFTI_INTENT_TRIANGLE - - dim[0] = 5 - - dim[1] = number of triangles - - dim[2] = dim[3] = dim[4] = 1 - - dim[5] = 3 - - datatype should be an integer type (preferably DT_INT32) - - the data values are indexes (0,1,...) into a pointset dataset. */ - -#define NIFTI_INTENT_TRIANGLE 1009 - - /*! To signify that the vector value at each voxel is a quaternion: - - dataset must have a 5th dimension - - intent_code must be NIFTI_INTENT_QUATERNION - - dim[0] = 5 - - dim[5] = 4 - - datatype should be a floating point type */ - -#define NIFTI_INTENT_QUATERNION 1010 - - /*! Dimensionless value - no params - although, as in _ESTIMATE - the name of the parameter may be stored in intent_name. */ - -#define NIFTI_INTENT_DIMLESS 1011 - - /*---------- these values apply to GIFTI datasets ----------*/ - - /*! To signify that the value at each location is from a time series. */ - -#define NIFTI_INTENT_TIME_SERIES 2001 - - /*! To signify that the value at each location is a node index, from - a complete surface dataset. */ - -#define NIFTI_INTENT_NODE_INDEX 2002 - - /*! To signify that the vector value at each location is an RGB triplet, - of whatever type. - - dataset must have a 5th dimension - - dim[0] = 5 - - dim[1] = number of nodes - - dim[2] = dim[3] = dim[4] = 1 - - dim[5] = 3 - */ - -#define NIFTI_INTENT_RGB_VECTOR 2003 - - /*! To signify that the vector value at each location is a 4 valued RGBA - vector, of whatever type. - - dataset must have a 5th dimension - - dim[0] = 5 - - dim[1] = number of nodes - - dim[2] = dim[3] = dim[4] = 1 - - dim[5] = 4 - */ - -#define NIFTI_INTENT_RGBA_VECTOR 2004 - - /*! To signify that the value at each location is a shape value, such - as the curvature. */ - -#define NIFTI_INTENT_SHAPE 2005 - -/* @} */ - -/*---------------------------------------------------------------------------*/ -/* 3D IMAGE (VOLUME) ORIENTATION AND LOCATION IN SPACE: - --------------------------------------------------- - There are 3 different methods by which continuous coordinates can - attached to voxels. The discussion below emphasizes 3D volumes, and - the continuous coordinates are referred to as (x,y,z). The voxel - index coordinates (i.e., the array indexes) are referred to as (i,j,k), - with valid ranges: - i = 0 .. dim[1]-1 - j = 0 .. dim[2]-1 (if dim[0] >= 2) - k = 0 .. dim[3]-1 (if dim[0] >= 3) - The (x,y,z) coordinates refer to the CENTER of a voxel. In methods - 2 and 3, the (x,y,z) axes refer to a subject-based coordinate system, - with - +x = Right +y = Anterior +z = Superior. - This is a right-handed coordinate system. However, the exact direction - these axes point with respect to the subject depends on qform_code - (Method 2) and sform_code (Method 3). - - N.B.: The i index varies most rapidly, j index next, k index slowest. - Thus, voxel (i,j,k) is stored starting at location - (i + j*dim[1] + k*dim[1]*dim[2]) * (bitpix/8) - into the dataset array. - - N.B.: The ANALYZE 7.5 coordinate system is - +x = Left +y = Anterior +z = Superior - which is a left-handed coordinate system. This backwardness is - too difficult to tolerate, so this NIFTI-1 standard specifies the - coordinate order which is most common in functional neuroimaging. - - N.B.: The 3 methods below all give the locations of the voxel centers - in the (x,y,z) coordinate system. In many cases, programs will wish - to display image data on some other grid. In such a case, the program - will need to convert its desired (x,y,z) values into (i,j,k) values - in order to extract (or interpolate) the image data. This operation - would be done with the inverse transformation to those described below. - - N.B.: Method 2 uses a factor 'qfac' which is either -1 or 1; qfac is - stored in the otherwise unused pixdim[0]. If pixdim[0]=0.0 (which - should not occur), we take qfac=1. Of course, pixdim[0] is only used - when reading a NIFTI-1 header, not when reading an ANALYZE 7.5 header. - - N.B.: The units of (x,y,z) can be specified using the xyzt_units field. - - METHOD 1 (the "old" way, used only when qform_code = 0): - ------------------------------------------------------- - The coordinate mapping from (i,j,k) to (x,y,z) is the ANALYZE - 7.5 way. This is a simple scaling relationship: - - x = pixdim[1] * i - y = pixdim[2] * j - z = pixdim[3] * k - - No particular spatial orientation is attached to these (x,y,z) - coordinates. (NIFTI-1 does not have the ANALYZE 7.5 orient field, - which is not general and is often not set properly.) This method - is not recommended, and is present mainly for compatibility with - ANALYZE 7.5 files. - - METHOD 2 (used when qform_code > 0, which should be the "normal" case): - --------------------------------------------------------------------- - The (x,y,z) coordinates are given by the pixdim[] scales, a rotation - matrix, and a shift. This method is intended to represent - "scanner-anatomical" coordinates, which are often embedded in the - image header (e.g., DICOM fields (0020,0032), (0020,0037), (0028,0030), - and (0018,0050)), and represent the nominal orientation and location of - the data. This method can also be used to represent "aligned" - coordinates, which would typically result from some post-acquisition - alignment of the volume to a standard orientation (e.g., the same - subject on another day, or a rigid rotation to true anatomical - orientation from the tilted position of the subject in the scanner). - The formula for (x,y,z) in terms of header parameters and (i,j,k) is: - - [ x ] [ R11 R12 R13 ] [ pixdim[1] * i ] [ qoffset_x ] - [ y ] = [ R21 R22 R23 ] [ pixdim[2] * j ] + [ qoffset_y ] - [ z ] [ R31 R32 R33 ] [ qfac * pixdim[3] * k ] [ qoffset_z ] - - The qoffset_* shifts are in the NIFTI-1 header. Note that the center - of the (i,j,k)=(0,0,0) voxel (first value in the dataset array) is - just (x,y,z)=(qoffset_x,qoffset_y,qoffset_z). - - The rotation matrix R is calculated from the quatern_* parameters. - This calculation is described below. - - The scaling factor qfac is either 1 or -1. The rotation matrix R - defined by the quaternion parameters is "proper" (has determinant 1). - This may not fit the needs of the data; for example, if the image - grid is - i increases from Left-to-Right - j increases from Anterior-to-Posterior - k increases from Inferior-to-Superior - Then (i,j,k) is a left-handed triple. In this example, if qfac=1, - the R matrix would have to be - - [ 1 0 0 ] - [ 0 -1 0 ] which is "improper" (determinant = -1). - [ 0 0 1 ] - - If we set qfac=-1, then the R matrix would be - - [ 1 0 0 ] - [ 0 -1 0 ] which is proper. - [ 0 0 -1 ] - - This R matrix is represented by quaternion [a,b,c,d] = [0,1,0,0] - (which encodes a 180 degree rotation about the x-axis). - - METHOD 3 (used when sform_code > 0): - ----------------------------------- - The (x,y,z) coordinates are given by a general affine transformation - of the (i,j,k) indexes: - - x = srow_x[0] * i + srow_x[1] * j + srow_x[2] * k + srow_x[3] - y = srow_y[0] * i + srow_y[1] * j + srow_y[2] * k + srow_y[3] - z = srow_z[0] * i + srow_z[1] * j + srow_z[2] * k + srow_z[3] - - The srow_* vectors are in the NIFTI_1 header. Note that no use is - made of pixdim[] in this method. - - WHY 3 METHODS? - -------------- - Method 1 is provided only for backwards compatibility. The intention - is that Method 2 (qform_code > 0) represents the nominal voxel locations - as reported by the scanner, or as rotated to some fiducial orientation and - location. Method 3, if present (sform_code > 0), is to be used to give - the location of the voxels in some standard space. The sform_code - indicates which standard space is present. Both methods 2 and 3 can be - present, and be useful in different contexts (method 2 for displaying the - data on its original grid; method 3 for displaying it on a standard grid). - - In this scheme, a dataset would originally be set up so that the - Method 2 coordinates represent what the scanner reported. Later, - a registration to some standard space can be computed and inserted - in the header. Image display software can use either transform, - depending on its purposes and needs. - - In Method 2, the origin of coordinates would generally be whatever - the scanner origin is; for example, in MRI, (0,0,0) is the center - of the gradient coil. - - In Method 3, the origin of coordinates would depend on the value - of sform_code; for example, for the Talairach coordinate system, - (0,0,0) corresponds to the Anterior Commissure. - - QUATERNION REPRESENTATION OF ROTATION MATRIX (METHOD 2) - ------------------------------------------------------- - The orientation of the (x,y,z) axes relative to the (i,j,k) axes - in 3D space is specified using a unit quaternion [a,b,c,d], where - a*a+b*b+c*c+d*d=1. The (b,c,d) values are all that is needed, since - we require that a = sqrt(1.0-(b*b+c*c+d*d)) be nonnegative. The (b,c,d) - values are stored in the (quatern_b,quatern_c,quatern_d) fields. - - The quaternion representation is chosen for its compactness in - representing rotations. The (proper) 3x3 rotation matrix that - corresponds to [a,b,c,d] is - - [ a*a+b*b-c*c-d*d 2*b*c-2*a*d 2*b*d+2*a*c ] - R = [ 2*b*c+2*a*d a*a+c*c-b*b-d*d 2*c*d-2*a*b ] - [ 2*b*d-2*a*c 2*c*d+2*a*b a*a+d*d-c*c-b*b ] - - [ R11 R12 R13 ] - = [ R21 R22 R23 ] - [ R31 R32 R33 ] - - If (p,q,r) is a unit 3-vector, then rotation of angle h about that - direction is represented by the quaternion - - [a,b,c,d] = [cos(h/2), p*sin(h/2), q*sin(h/2), r*sin(h/2)]. - - Requiring a >= 0 is equivalent to requiring -Pi <= h <= Pi. (Note that - [-a,-b,-c,-d] represents the same rotation as [a,b,c,d]; there are 2 - quaternions that can be used to represent a given rotation matrix R.) - To rotate a 3-vector (x,y,z) using quaternions, we compute the - quaternion product - - [0,x',y',z'] = [a,b,c,d] * [0,x,y,z] * [a,-b,-c,-d] - - which is equivalent to the matrix-vector multiply - - [ x' ] [ x ] - [ y' ] = R [ y ] (equivalence depends on a*a+b*b+c*c+d*d=1) - [ z' ] [ z ] - - Multiplication of 2 quaternions is defined by the following: - - [a,b,c,d] = a*1 + b*I + c*J + d*K - where - I*I = J*J = K*K = -1 (I,J,K are square roots of -1) - I*J = K J*K = I K*I = J - J*I = -K K*J = -I I*K = -J (not commutative!) - For example - [a,b,0,0] * [0,0,0,1] = [0,0,-b,a] - since this expands to - (a+b*I)*(K) = (a*K+b*I*K) = (a*K-b*J). - - The above formula shows how to go from quaternion (b,c,d) to - rotation matrix and direction cosines. Conversely, given R, - we can compute the fields for the NIFTI-1 header by - - a = 0.5 * sqrt(1+R11+R22+R33) (not stored) - b = 0.25 * (R32-R23) / a => quatern_b - c = 0.25 * (R13-R31) / a => quatern_c - d = 0.25 * (R21-R12) / a => quatern_d - - If a=0 (a 180 degree rotation), alternative formulas are needed. - See the nifti1_io.c function mat44_to_quatern() for an implementation - of the various cases in converting R to [a,b,c,d]. - - Note that R-transpose (= R-inverse) would lead to the quaternion - [a,-b,-c,-d]. - - The choice to specify the qoffset_x (etc.) values in the final - coordinate system is partly to make it easy to convert DICOM images to - this format. The DICOM attribute "Image Position (Patient)" (0020,0032) - stores the (Xd,Yd,Zd) coordinates of the center of the first voxel. - Here, (Xd,Yd,Zd) refer to DICOM coordinates, and Xd=-x, Yd=-y, Zd=z, - where (x,y,z) refers to the NIFTI coordinate system discussed above. - (i.e., DICOM +Xd is Left, +Yd is Posterior, +Zd is Superior, - whereas +x is Right, +y is Anterior , +z is Superior. ) - Thus, if the (0020,0032) DICOM attribute is extracted into (px,py,pz), then - qoffset_x = -px qoffset_y = -py qoffset_z = pz - is a reasonable setting when qform_code=NIFTI_XFORM_SCANNER_ANAT. - - That is, DICOM's coordinate system is 180 degrees rotated about the z-axis - from the neuroscience/NIFTI coordinate system. To transform between DICOM - and NIFTI, you just have to negate the x- and y-coordinates. - - The DICOM attribute (0020,0037) "Image Orientation (Patient)" gives the - orientation of the x- and y-axes of the image data in terms of 2 3-vectors. - The first vector is a unit vector along the x-axis, and the second is - along the y-axis. If the (0020,0037) attribute is extracted into the - value (xa,xb,xc,ya,yb,yc), then the first two columns of the R matrix - would be - [ -xa -ya ] - [ -xb -yb ] - [ xc yc ] - The negations are because DICOM's x- and y-axes are reversed relative - to NIFTI's. The third column of the R matrix gives the direction of - displacement (relative to the subject) along the slice-wise direction. - This orientation is not encoded in the DICOM standard in a simple way; - DICOM is mostly concerned with 2D images. The third column of R will be - either the cross-product of the first 2 columns or its negative. It is - possible to infer the sign of the 3rd column by examining the coordinates - in DICOM attribute (0020,0032) "Image Position (Patient)" for successive - slices. However, this method occasionally fails for reasons that I - (RW Cox) do not understand. ------------------------------------------------------------------------------*/ - - /* [qs]form_code value: */ /* x,y,z coordinate system refers to: */ - /*-----------------------*/ /*---------------------------------------*/ - -/*! \defgroup NIFTI1_XFORM_CODES - \brief nifti1 xform codes to describe the "standard" coordinate system - @{ - */ - /*! Arbitrary coordinates (Method 1). */ - -#define NIFTI_XFORM_UNKNOWN 0 - - /*! Scanner-based anatomical coordinates */ - -#define NIFTI_XFORM_SCANNER_ANAT 1 - - /*! Coordinates aligned to another file's, - or to anatomical "truth". */ - -#define NIFTI_XFORM_ALIGNED_ANAT 2 - - /*! Coordinates aligned to Talairach- - Tournoux Atlas; (0,0,0)=AC, etc. */ - -#define NIFTI_XFORM_TALAIRACH 3 - - /*! MNI 152 normalized coordinates. */ - -#define NIFTI_XFORM_MNI_152 4 -/* @} */ - -/*---------------------------------------------------------------------------*/ -/* UNITS OF SPATIAL AND TEMPORAL DIMENSIONS: - ---------------------------------------- - The codes below can be used in xyzt_units to indicate the units of pixdim. - As noted earlier, dimensions 1,2,3 are for x,y,z; dimension 4 is for - time (t). - - If dim[4]=1 or dim[0] < 4, there is no time axis. - - A single time series (no space) would be specified with - - dim[0] = 4 (for scalar data) or dim[0] = 5 (for vector data) - - dim[1] = dim[2] = dim[3] = 1 - - dim[4] = number of time points - - pixdim[4] = time step - - xyzt_units indicates units of pixdim[4] - - dim[5] = number of values stored at each time point - - Bits 0..2 of xyzt_units specify the units of pixdim[1..3] - (e.g., spatial units are values 1..7). - Bits 3..5 of xyzt_units specify the units of pixdim[4] - (e.g., temporal units are multiples of 8). - - This compression of 2 distinct concepts into 1 byte is due to the - limited space available in the 348 byte ANALYZE 7.5 header. The - macros XYZT_TO_SPACE and XYZT_TO_TIME can be used to mask off the - undesired bits from the xyzt_units fields, leaving "pure" space - and time codes. Inversely, the macro SPACE_TIME_TO_XYZT can be - used to assemble a space code (0,1,2,...,7) with a time code - (0,8,16,32,...,56) into the combined value for xyzt_units. - - Note that codes are provided to indicate the "time" axis units are - actually frequency in Hertz (_HZ), in part-per-million (_PPM) - or in radians-per-second (_RADS). - - The toffset field can be used to indicate a nonzero start point for - the time axis. That is, time point #m is at t=toffset+m*pixdim[4] - for m=0..dim[4]-1. ------------------------------------------------------------------------------*/ - -/*! \defgroup NIFTI1_UNITS - \brief nifti1 units codes to describe the unit of measurement for - each dimension of the dataset - @{ - */ - /*! NIFTI code for unspecified units. */ -#define NIFTI_UNITS_UNKNOWN 0 - - /** Space codes are multiples of 1. **/ - /*! NIFTI code for meters. */ -#define NIFTI_UNITS_METER 1 - /*! NIFTI code for millimeters. */ -#define NIFTI_UNITS_MM 2 - /*! NIFTI code for micrometers. */ -#define NIFTI_UNITS_MICRON 3 - - /** Time codes are multiples of 8. **/ - /*! NIFTI code for seconds. */ -#define NIFTI_UNITS_SEC 8 - /*! NIFTI code for milliseconds. */ -#define NIFTI_UNITS_MSEC 16 - /*! NIFTI code for microseconds. */ -#define NIFTI_UNITS_USEC 24 - - /*** These units are for spectral data: ***/ - /*! NIFTI code for Hertz. */ -#define NIFTI_UNITS_HZ 32 - /*! NIFTI code for ppm. */ -#define NIFTI_UNITS_PPM 40 - /*! NIFTI code for radians per second. */ -#define NIFTI_UNITS_RADS 48 -/* @} */ - -#undef XYZT_TO_SPACE -#undef XYZT_TO_TIME -#define XYZT_TO_SPACE(xyzt) ( (xyzt) & 0x07 ) -#define XYZT_TO_TIME(xyzt) ( (xyzt) & 0x38 ) - -#undef SPACE_TIME_TO_XYZT -#define SPACE_TIME_TO_XYZT(ss,tt) ( (((char)(ss)) & 0x07) \ - | (((char)(tt)) & 0x38) ) - -/*---------------------------------------------------------------------------*/ -/* MRI-SPECIFIC SPATIAL AND TEMPORAL INFORMATION: - --------------------------------------------- - A few fields are provided to store some extra information - that is sometimes important when storing the image data - from an FMRI time series experiment. (After processing such - data into statistical images, these fields are not likely - to be useful.) - - { freq_dim } = These fields encode which spatial dimension (1,2, or 3) - { phase_dim } = corresponds to which acquisition dimension for MRI data. - { slice_dim } = - Examples: - Rectangular scan multi-slice EPI: - freq_dim = 1 phase_dim = 2 slice_dim = 3 (or some permutation) - Spiral scan multi-slice EPI: - freq_dim = phase_dim = 0 slice_dim = 3 - since the concepts of frequency- and phase-encoding directions - don't apply to spiral scan - - slice_duration = If this is positive, AND if slice_dim is nonzero, - indicates the amount of time used to acquire 1 slice. - slice_duration*dim[slice_dim] can be less than pixdim[4] - with a clustered acquisition method, for example. - - slice_code = If this is nonzero, AND if slice_dim is nonzero, AND - if slice_duration is positive, indicates the timing - pattern of the slice acquisition. The following codes - are defined: - NIFTI_SLICE_SEQ_INC == sequential increasing - NIFTI_SLICE_SEQ_DEC == sequential decreasing - NIFTI_SLICE_ALT_INC == alternating increasing - NIFTI_SLICE_ALT_DEC == alternating decreasing - NIFTI_SLICE_ALT_INC2 == alternating increasing #2 - NIFTI_SLICE_ALT_DEC2 == alternating decreasing #2 - { slice_start } = Indicates the start and end of the slice acquisition - { slice_end } = pattern, when slice_code is nonzero. These values - are present to allow for the possible addition of - "padded" slices at either end of the volume, which - don't fit into the slice timing pattern. If there - are no padding slices, then slice_start=0 and - slice_end=dim[slice_dim]-1 are the correct values. - For these values to be meaningful, slice_start must - be non-negative and slice_end must be greater than - slice_start. Otherwise, they should be ignored. - - The following table indicates the slice timing pattern, relative to - time=0 for the first slice acquired, for some sample cases. Here, - dim[slice_dim]=7 (there are 7 slices, labeled 0..6), slice_duration=0.1, - and slice_start=1, slice_end=5 (1 padded slice on each end). - - slice - index SEQ_INC SEQ_DEC ALT_INC ALT_DEC ALT_INC2 ALT_DEC2 - 6 : n/a n/a n/a n/a n/a n/a n/a = not applicable - 5 : 0.4 0.0 0.2 0.0 0.4 0.2 (slice time offset - 4 : 0.3 0.1 0.4 0.3 0.1 0.0 doesn't apply to - 3 : 0.2 0.2 0.1 0.1 0.3 0.3 slices outside - 2 : 0.1 0.3 0.3 0.4 0.0 0.1 the range - 1 : 0.0 0.4 0.0 0.2 0.2 0.4 slice_start .. - 0 : n/a n/a n/a n/a n/a n/a slice_end) - - The SEQ slice_codes are sequential ordering (uncommon but not unknown), - either increasing in slice number or decreasing (INC or DEC), as - illustrated above. - - The ALT slice codes are alternating ordering. The 'standard' way for - these to operate (without the '2' on the end) is for the slice timing - to start at the edge of the slice_start .. slice_end group (at slice_start - for INC and at slice_end for DEC). For the 'ALT_*2' slice_codes, the - slice timing instead starts at the first slice in from the edge (at - slice_start+1 for INC2 and at slice_end-1 for DEC2). This latter - acquisition scheme is found on some Siemens scanners. - - The fields freq_dim, phase_dim, slice_dim are all squished into the single - byte field dim_info (2 bits each, since the values for each field are - limited to the range 0..3). This unpleasantness is due to lack of space - in the 348 byte allowance. - - The macros DIM_INFO_TO_FREQ_DIM, DIM_INFO_TO_PHASE_DIM, and - DIM_INFO_TO_SLICE_DIM can be used to extract these values from the - dim_info byte. - - The macro FPS_INTO_DIM_INFO can be used to put these 3 values - into the dim_info byte. ------------------------------------------------------------------------------*/ - -#undef DIM_INFO_TO_FREQ_DIM -#undef DIM_INFO_TO_PHASE_DIM -#undef DIM_INFO_TO_SLICE_DIM - -#define DIM_INFO_TO_FREQ_DIM(di) ( ((di) ) & 0x03 ) -#define DIM_INFO_TO_PHASE_DIM(di) ( ((di) >> 2) & 0x03 ) -#define DIM_INFO_TO_SLICE_DIM(di) ( ((di) >> 4) & 0x03 ) - -#undef FPS_INTO_DIM_INFO -#define FPS_INTO_DIM_INFO(fd,pd,sd) ( ( ( ((char)(fd)) & 0x03) ) | \ - ( ( ((char)(pd)) & 0x03) << 2 ) | \ - ( ( ((char)(sd)) & 0x03) << 4 ) ) - -/*! \defgroup NIFTI1_SLICE_ORDER - \brief nifti1 slice order codes, describing the acquisition order - of the slices - @{ - */ -#define NIFTI_SLICE_UNKNOWN 0 -#define NIFTI_SLICE_SEQ_INC 1 -#define NIFTI_SLICE_SEQ_DEC 2 -#define NIFTI_SLICE_ALT_INC 3 -#define NIFTI_SLICE_ALT_DEC 4 -#define NIFTI_SLICE_ALT_INC2 5 /* 05 May 2005: RWCox */ -#define NIFTI_SLICE_ALT_DEC2 6 /* 05 May 2005: RWCox */ -/* @} */ - -/*---------------------------------------------------------------------------*/ -/* UNUSED FIELDS: - ------------- - Some of the ANALYZE 7.5 fields marked as ++UNUSED++ may need to be set - to particular values for compatibility with other programs. The issue - of interoperability of ANALYZE 7.5 files is a murky one -- not all - programs require exactly the same set of fields. (Unobscuring this - murkiness is a principal motivation behind NIFTI-1.) - - Some of the fields that may need to be set for other (non-NIFTI aware) - software to be happy are: - - extents dbh.h says this should be 16384 - regular dbh.h says this should be the character 'r' - glmin, } dbh.h says these values should be the min and max voxel - glmax } values for the entire dataset - - It is best to initialize ALL fields in the NIFTI-1 header to 0 - (e.g., with calloc()), then fill in what is needed. ------------------------------------------------------------------------------*/ - -/*---------------------------------------------------------------------------*/ -/* MISCELLANEOUS C MACROS ------------------------------------------------------------------------------*/ - -/*.................*/ -/*! Given a nifti_1_header struct, check if it has a good magic number. - Returns NIFTI version number (1..9) if magic is good, 0 if it is not. */ - -#define NIFTI_VERSION(h) \ - ( ( (h).magic[0]=='n' && (h).magic[3]=='\0' && \ - ( (h).magic[1]=='i' || (h).magic[1]=='+' ) && \ - ( (h).magic[2]>='1' && (h).magic[2]<='9' ) ) \ - ? (h).magic[2]-'0' : 0 ) - -/*.................*/ -/*! Check if a nifti_1_header struct says if the data is stored in the - same file or in a separate file. Returns 1 if the data is in the same - file as the header, 0 if it is not. */ - -#define NIFTI_ONEFILE(h) ( (h).magic[1] == '+' ) - -/*.................*/ -/*! Check if a nifti_1_header struct needs to be byte swapped. - Returns 1 if it needs to be swapped, 0 if it does not. */ - -#define NIFTI_NEEDS_SWAP(h) ( (h).dim[0] < 0 || (h).dim[0] > 7 ) - -/*.................*/ -/*! Check if a nifti_1_header struct contains a 5th (vector) dimension. - Returns size of 5th dimension if > 1, returns 0 otherwise. */ - -#define NIFTI_5TH_DIM(h) ( ((h).dim[0]>4 && (h).dim[5]>1) ? (h).dim[5] : 0 ) - -/*****************************************************************************/ - -/*=================*/ -#ifdef __cplusplus -} -#endif -/*=================*/ - -#endif /* _NIFTI_HEADER_ */ diff --git a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_io.c b/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_io.c deleted file mode 100644 index 55c3553cb7f..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_io.c +++ /dev/null @@ -1,7533 +0,0 @@ -#define _NIFTI1_IO_C_ - -#include "nifti1_io.h" /* typedefs, prototypes, macros, etc. */ - -/*****===================================================================*****/ -/***** Sample functions to deal with NIFTI-1 and ANALYZE files *****/ -/*****...................................................................*****/ -/***** This code is released to the public domain. *****/ -/*****...................................................................*****/ -/***** Author: Robert W Cox, SSCC/DIRP/NIMH/NIH/DHHS/USA/EARTH *****/ -/***** Date: August 2003 *****/ -/*****...................................................................*****/ -/***** Neither the National Institutes of Health (NIH), nor any of its *****/ -/***** employees imply any warranty of usefulness of this software for *****/ -/***** any purpose, and do not assume any liability for damages, *****/ -/***** incidental or otherwise, caused by any use of this document. *****/ -/*****===================================================================*****/ - -/** \file nifti1_io.c - \brief main collection of nifti1 i/o routines - - written by Bob Cox, SSCC NIMH - - revised by Mark Jenkinson, FMRIB - - revised by Rick Reynolds, SSCC, NIMH - - revised by Kate Fissell, University of Pittsburgh - - The library history can be viewed via "nifti_tool -nifti_hist". -
The library version can be viewed via "nifti_tool -nifti_ver". - */ - -/*! global history and version strings, for printing */ -static char const * const gni_history[] = -{ - "----------------------------------------------------------------------\n" - "history (of nifti library changes):\n" - "\n", - "0.0 August, 2003 [rwcox]\n" - " (Robert W Cox of the National Institutes of Health, SSCC/DIRP/NIMH)\n" - " - initial version\n" - "\n", - "0.1 July/August, 2004 [Mark Jenkinson]\n" - " (FMRIB Centre, University of Oxford, UK)\n" - " - Mainly adding low-level IO and changing things to allow gzipped\n" - " files to be read and written\n" - " - Full backwards compatability should have been maintained\n" - "\n", - "0.2 16 Nov 2004 [rickr]\n" - " (Rick Reynolds of the National Institutes of Health, SSCC/DIRP/NIMH)\n" - " - included Mark's changes in the AFNI distribution (including znzlib/)\n" - " (HAVE_ZLIB is commented out for the standard distribution)\n" - " - modified nifti_validfilename() and nifti_makebasename()\n" - " - added nifti_find_file_extension()\n" - "\n", - "0.3 3 Dec 2004 [rickr]\n" - " - note: header extensions are not yet checked for\n" - " - added formatted history as global string, for printing\n" - " - added nifti_disp_lib_hist(), to display the nifti library history\n" - " - added nifti_disp_lib_version(), to display the nifti library history\n", - " - re-wrote nifti_findhdrname()\n" - " o used nifti_find_file_extension()\n" - " o changed order of file tests (default is .nii, depends on input)\n" - " o free hdrname on failure\n" - " - made similar changes to nifti_findimgname()\n" - " - check for NULL return from nifti_findhdrname() calls\n", - " - removed most of ERREX() macros\n" - " - modified nifti_image_read()\n" - " o added debug info and error checking (on gni_debug > 0, only)\n" - " o fail if workingname is NULL\n" - " o check for failure to open header file\n" - " o free workingname on failure\n" - " o check for failure of nifti_image_load()\n" - " o check for failure of nifti_convert_nhdr2nim()\n", - " - changed nifti_image_load() to int, and check nifti_read_buffer return\n" - " - changed nifti_read_buffer() to fail on short read, and to count float\n" - " fixes (to print on debug)\n" - " - changed nifti_image_infodump to print to stderr\n" - " - updated function header comments, or moved comments above header\n" - " - removed const keyword\n" - " - added LNI_FERR() macro for error reporting on input files\n" - "\n", - "0.4 10 Dec 2004 [rickr] - added header extensions\n" - " - in nifti1_io.h:\n" - " o added num_ext and ext_list to the definition of nifti_image\n" - " o made many functions static (more to follow)\n" - " o added LNI_MAX_NIA_EXT_LEN, for max nifti_type 3 extension length\n", - " - added __DATE__ to version output in nifti_disp_lib_version()\n" - " - added nifti_disp_matrix_orient() to print orientation information\n" - " - added '.nia' as a valid file extension in nifti_find_file_extension()\n" - " - added much more debug output\n" - " - in nifti_image_read(), in the case of an ASCII header, check for\n" - " extensions after the end of the header\n", - " - added nifti_read_extensions() function\n" - " - added nifti_read_next_extension() function\n" - " - added nifti_add_exten_to_list() function\n" - " - added nifti_check_extension() function\n" - " - added nifti_write_extensions() function\n" - " - added nifti_extension_size() function\n" - " - in nifti_set_iname_offest():\n" - " o adjust offset by the extension size and the extender size\n", - " o fixed the 'ceiling modulo 16' computation\n" - " - in nifti_image_write_hdr_img2(): \n" - " o added extension writing\n" - " o check for NULL return from nifti_findimgname()\n" - " - include number of extensions in nifti_image_to_ascii() output\n" - " - in nifti_image_from_ascii():\n" - " o return bytes_read as a parameter, computed from the final spos\n" - " o extract num_ext from ASCII header\n" - "\n", - "0.5 14 Dec 2004 [rickr] - added sub-brick reading functions\n" - " - added nifti_brick_list type to nifti1_io.h, along with new prototypes\n" - " - added main nifti_image_read_bricks() function, with description\n" - " - added nifti_image_load_bricks() - library function (requires nim)\n" - " - added valid_nifti_brick_list() - library function\n" - " - added free_NBL() - library function\n", - " - added update_nifti_image_for_brick_list() for dimension update\n" - " - added nifti_load_NBL_bricks(), nifti_alloc_NBL_mem(),\n" - " nifti_copynsort() and force_positive() (static functions)\n" - " - in nifti_image_read(), check for failed load only if read_data is set\n" - " - broke most of nifti_image_load() into nifti_image_load_prep()\n" - "\n", - "0.6 15 Dec 2004 [rickr] - added sub-brick writing functionality\n" - " - in nifti1_io.h, removed znzlib directory from include - all nifti\n" - " library files are now under the nifti directory\n" - " - nifti_read_extensions(): print no offset warning for nifti_type 3\n" - " - nifti_write_all_data():\n" - " o pass nifti_brick_list * NBL, for optional writing\n" - " o if NBL, write each sub-brick, sequentially\n", - " - nifti_set_iname_offset(): case 1 must have sizeof() cast to int\n" - " - pass NBL to nifti_image_write_hdr_img2(), and allow NBL or data\n" - " - added nifti_image_write_bricks() wrapper for ...write_hdr_img2()\n" - " - included compression abilities\n" - "\n", - "0.7 16 Dec 2004 [rickr] - minor changes to extension reading\n" - "\n", - "0.8 21 Dec 2004 [rickr] - restrict extension reading, and minor changes\n" - " - in nifti_image_read(), compute bytes for extensions (see remaining)\n" - " - in nifti_read_extensions(), pass 'remain' as space for extensions,\n" - " pass it to nifti_read_next_ext(), and update for each one read \n" - " - in nifti_check_extension(), require (size <= remain)\n", - " - in update_nifti_image_brick_list(), update nvox\n" - " - in nifti_image_load_bricks(), make explicit check for nbricks <= 0\n" - " - in int_force_positive(), check for (!list)\n" - " - in swap_nifti_header(), swap sizeof_hdr, and reorder to struct order\n" - " - change get_filesize functions to signed ( < 0 is no file or error )\n", - " - in nifti_validfilename(), lose redundant (len < 0) check\n" - " - make print_hex_vals() static\n" - " - in disp_nifti_1_header, restrict string field widths\n" - "\n", - "0.9 23 Dec 2004 [rickr] - minor changes\n" - " - broke ASCII header reading out of nifti_image_read(), into new\n" - " functions has_ascii_header() and read_ascii_image()\n", - " - check image_read failure and znzseek failure\n" - " - altered some debug output\n" - " - nifti_write_all_data() now returns an int\n" - "\n", - "0.10 29 Dec 2004 [rickr]\n" - " - renamed nifti_valid_extension() to nifti_check_extension()\n" - " - added functions nifti_makehdrname() and nifti_makeimgname()\n" - " - added function valid_nifti_extensions()\n" - " - in nifti_write_extensions(), check for validity before writing\n", - " - rewrote nifti_image_write_hdr_img2():\n" - " o set write_data and leave_open flags from write_opts\n" - " o add debug print statements\n" - " o use nifti_write_ascii_image() for the ascii case\n" - " o rewrote the logic of all cases to be easier to follow\n", - " - broke out code as nifti_write_ascii_image() function\n" - " - added debug to top-level write functions, and free the znzFile\n" - " - removed unused internal function nifti_image_open()\n" - "\n", - "0.11 30 Dec 2004 [rickr] - small mods\n" - " - moved static function prototypes from header to C file\n" - " - free extensions in nifti_image_free()\n" - "\n", - "1.0 07 Jan 2005 [rickr] - INITIAL RELEASE VERSION\n" - " - added function nifti_set_filenames()\n" - " - added function nifti_read_header()\n" - " - added static function nhdr_looks_good()\n" - " - added static function need_nhdr_swap()\n" - " - exported nifti_add_exten_to_list symbol\n", - " - fixed #bytes written in nifti_write_extensions()\n" - " - only modify offset if it is too small (nifti_set_iname_offset)\n" - " - added nifti_type 3 to nifti_makehdrname and nifti_makeimgname\n" - " - added function nifti_set_filenames()\n" - "\n", - "1.1 07 Jan 2005 [rickr]\n" - " - in nifti_read_header(), swap if needed\n" - "\n", - "1.2 07 Feb 2005 [kate fissell c/o rickr] \n" - " - nifti1.h: added doxygen comments for main struct and #define groups\n" - " - nifti1_io.h: added doxygen comments for file and nifti_image struct\n" - " - nifti1_io.h: added doxygen comments for file and some functions\n" - " - nifti1_io.c: changed nifti_copy_nim_info to use memcpy\n" - "\n", - "1.3 09 Feb 2005 [rickr]\n" - " - nifti1.h: added doxygen comments for extension structs\n" - " - nifti1_io.h: put most #defines in #ifdef _NIFTI1_IO_C_ block\n" - " - added a doxygen-style description to every exported function\n" - " - added doxygen-style comments within some functions\n" - " - re-exported many znzFile functions that I had made static\n" - " - re-added nifti_image_open (sorry, Mark)\n" - " - every exported function now has 'nifti' in the name (19 functions)\n", - " - made sure every alloc() has a failure test\n" - " - added nifti_copy_extensions function, for use in nifti_copy_nim_info\n" - " - nifti_is_gzfile: added initial strlen test\n" - " - nifti_set_filenames: added set_byte_order parameter option\n" - " (it seems appropriate to set the BO when new files are associated)\n" - " - disp_nifti_1_header: prints to stdout (a.o.t. stderr), with fflush\n" - "\n", - "1.4 23 Feb 2005 [rickr] - sourceforge merge\n" - " - merged into the nifti_io CVS directory structure at sourceforge.net\n" - " - merged in 4 changes by Mark, and re-added his const keywords\n" - " - cast some pointers to (void *) for -pedantic compile option\n" - " - added nifti_free_extensions()\n" - "\n", - "1.5 02 Mar 2005 [rickr] - started nifti global options\n" - " - gni_debug is now g_opts.debug\n" - " - added validity check parameter to nifti_read_header\n" - " - need_nhdr_swap no longer does test swaps on the stack\n" - "\n", - "1.6 05 April 2005 [rickr] - validation and collapsed_image_read\n" - " - added nifti_read_collapsed_image(), an interface for reading partial\n" - " datasets, specifying a subset of array indices\n" - " - for read_collapsed_image, added static functions: rci_read_data(),\n" - " rci_alloc_mem(), and make_pivot_list()\n", - " - added nifti_nim_is_valid() to check for consistency (more to do)\n" - " - added nifti_nim_has_valid_dims() to do many dimensions tests\n" - "\n", - "1.7 08 April 2005 [rickr]\n" - " - added nifti_update_dims_from_array() - to update dimensions\n" - " - modified nifti_makehdrname() and nifti_makeimgname():\n" - " if prefix has a valid extension, use it (else make one up)\n" - " - added nifti_get_intlist - for making an array of ints\n" - " - fixed init of NBL->bsize in nifti_alloc_NBL_mem() {thanks, Bob}\n" - "\n", - "1.8 14 April 2005 [rickr]\n" - " - added nifti_set_type_from_names(), for nifti_set_filenames()\n" - " (only updates type if number of files does not match it)\n" - " - added is_valid_nifti_type(), just to be sure\n" - " - updated description of nifti_read_collapsed_image() for *data change\n" - " (if *data is already set, assume memory exists for results)\n" - " - modified rci_alloc_mem() to allocate only if *data is NULL\n" - "\n", - "1.9 19 April 2005 [rickr]\n" - " - added extension codes NIFTI_ECODE_COMMENT and NIFTI_ECODE_XCEDE\n" - " - added nifti_type codes NIFTI_MAX_ECODE and NIFTI_MAX_FTYPE\n" - " - added nifti_add_extension() {exported}\n" - " - added nifti_fill_extension() as a static function\n" - " - added nifti_is_valid_ecode() {exported}\n", - " - nifti_type values are now NIFTI_FTYPE_* file codes\n" - " - in nifti_read_extensions(), decrement 'remain' by extender size, 4\n" - " - in nifti_set_iname_offset(), case 1, update if offset differs\n" - " - only output '-d writing nifti file' if debug > 1\n" - "\n", - "1.10 10 May 2005 [rickr]\n" - " - files are read using ZLIB only if they end in '.gz'\n" - "\n", - "1.11 12 August 2005 [kate fissell]\n" - " - Kate's 0.2 release packaging, for sourceforge\n" - "\n", - "1.12 17 August 2005 [rickr] - comment (doxygen) updates\n" - " - updated comments for most functions (2 updates from Cinly Ooi)\n" - " - added nifti_type_and_names_match()\n" - "\n", - "1.12a 24 August 2005 [rickr] - remove all tabs from Clibs/*/*.[ch]\n", - "1.12b 25 August 2005 [rickr] - changes by Hans Johnson\n", - "1.13 25 August 2005 [rickr]\n", - " - finished changes by Hans for Insight\n" - " - added const in all appropraite parameter locations (30-40)\n" - " (any pointer referencing data that will not change)\n" - " - shortened all string constants below 509 character limit\n" - "1.14 28 October 2005 [HJohnson]\n", - " - use nifti_set_filenames() in nifti_convert_nhdr2nim()\n" - "1.15 02 November 2005 [rickr]\n", - " - added skip_blank_ext to nifti_global_options\n" - " - added nifti_set_skip_blank_ext(), to set option\n" - " - if skip_blank_ext and no extensions, do not read/write extender\n" - "1.16 18 November 2005 [rickr]\n", - " - removed any test or access of dim[i], i>dim[0]\n" - " - do not set pixdim for collapsed dims to 1.0, leave them as they are\n" - " - added magic and dim[i] tests in nifti_hdr_looks_good()\n" - " - added 2 size_t casts\n" - "1.17 22 November 2005 [rickr]\n", - " - in hdr->nim, for i > dim[0], pass 0 or 1, else set to 1\n" - "1.18 02 March 2006 [rickr]\n", - " - in nifti_alloc_NBL_mem(), fixed nt=0 case from 1.17 change\n" - "1.19 23 May 2006 [HJohnson,rickr]\n", - " - nifti_write_ascii_image(): free(hstr)\n" - " - nifti_copy_extensions(): clear num_ext and ext_list\n" - "1.20 27 Jun 2006 [rickr]\n", - " - nifti_findhdrname(): fixed assign of efirst to match stated logic\n" - " (problem found by Atle Bjørnerud)\n" - "1.21 05 Sep 2006 [rickr] update for nifticlib-0.4 release\n", - " - was reminded to actually add nifti_set_skip_blank_ext()\n" - " - init g_opts.skip_blank_ext to 0\n" - "1.22 01 Jun 2007 nifticlib-0.5 release\n", - "1.23 05 Jun 2007 nifti_add_exten_to_list: revert on failure, free old list\n" - "1.24 07 Jun 2007 nifti_copy_extensions: use esize-8 for data size\n" - "1.25 12 Jun 2007 [rickr] EMPTY_IMAGE creation\n", - " - added nifti_make_new_header() - to create from dims/dtype\n" - " - added nifti_make_new_nim() - to create from dims/dtype/fill\n" - " - added nifti_is_valid_datatype(), and more debug info\n", - "1.26 27 Jul 2007 [rickr] handle single volumes > 2^31 bytes (but < 2^32)\n", - "1.27 28 Jul 2007 [rickr] nim->nvox, NBL-bsize are now type size_t\n" - "1.28 30 Jul 2007 [rickr] size_t updates\n", - "1.29 08 Aug 2007 [rickr] for list, valid_nifti_brick_list requires 3 dims\n" - "1.30 08 Nov 2007 [Yaroslav/rickr]\n" - " - fix ARM struct alignment problem in byte-swapping routines\n", - "1.31 29 Nov 2007 [rickr] for nifticlib-1.0.0\n" - " - added nifti_datatype_to/from_string routines\n" - " - added DT_RGBA32/NIFTI_TYPE_RGBA32 datatype macros (2304)\n" - " - added NIFTI_ECODE_FREESURFER (14)\n", - "1.32 08 Dec 2007 [rickr]\n" - " - nifti_hdr_looks_good() allows ANALYZE headers (req. by V. Luccio)\n" - " - added nifti_datatype_is_valid()\n", - "1.33 05 Feb 2008 [hansj,rickr] - block nia.gz use\n" - "1.34 13 Jun 2008 [rickr] - added nifti_compiled_with_zlib()\n" - "1.35 03 Aug 2008 [rickr]\n", - " - deal with swapping, so that CPU type does not affect output\n" - " (motivated by C Burns)\n" - " - added nifti_analyze75 structure and nifti_swap_as_analyze()\n" - " - previous swap_nifti_header is saved as old_swap_nifti_header\n" - " - also swap UNUSED fields in nifti_1_header struct\n", - "1.36 07 Oct 2008 [rickr]\n", - " - added nifti_NBL_matches_nim() check for write_bricks()\n" - "1.37 10 Mar 2009 [rickr]\n", - " - H Johnson cast updates (06 Feb)\n" - " - added NIFTI_ECODE_PYPICKLE for PyNIfTI (06 Feb)\n" - " - added NIFTI_ECODEs 18-28 for the LONI MiND group\n" - "1.38 28 Apr 2009 [rickr]\n", - " - uppercase extensions are now valid (requested by M. Coursolle)\n" - " - nifti_set_allow_upper_fext controls this option (req by C. Ooi)\n" - "1.39 23 Jun 2009 [rickr]: added 4 checks of alloc() returns\n", - "1.40 16 Mar 2010 [rickr]: added NIFTI_ECODE_VOXBO for D. Kimberg\n", - "1.41 28 Apr 2010 [rickr]: added NIFTI_ECODE_CARET for J. Harwell\n", - "1.42 06 Jul 2010 [rickr]: trouble with large (gz) files\n", - " - noted/investigated by M Hanke and Y Halchenko\n" - " - fixed znzread/write, noting example by M Adler\n" - " - changed nifti_swap_* routines/calls to take size_t (6)\n" - "1.43 07 Jul 2010 [rickr]: fixed znzR/W to again return nmembers\n", - "1.44 19 Jul 2013 [rickr]: ITK compatibility updates from H Johnson\n", - "----------------------------------------------------------------------\n" -}; -static const char gni_version[] = "nifti library version 1.44 (19 July, 2013)"; - -/*! global nifti options structure - init with defaults */ -static nifti_global_options g_opts = { - 1, /* debug level */ - 0, /* skip_blank_ext - skip extender if no extensions */ - 1 /* allow_upper_fext - allow uppercase file extensions */ -}; - -/*! global nifti types structure list (per type, ordered oldest to newest) */ -static const nifti_type_ele nifti_type_list[] = { - /* type nbyper swapsize name */ - { 0, 0, 0, "DT_UNKNOWN" }, - { 0, 0, 0, "DT_NONE" }, - { 1, 0, 0, "DT_BINARY" }, /* not usable */ - { 2, 1, 0, "DT_UNSIGNED_CHAR" }, - { 2, 1, 0, "DT_UINT8" }, - { 2, 1, 0, "NIFTI_TYPE_UINT8" }, - { 4, 2, 2, "DT_SIGNED_SHORT" }, - { 4, 2, 2, "DT_INT16" }, - { 4, 2, 2, "NIFTI_TYPE_INT16" }, - { 8, 4, 4, "DT_SIGNED_INT" }, - { 8, 4, 4, "DT_INT32" }, - { 8, 4, 4, "NIFTI_TYPE_INT32" }, - { 16, 4, 4, "DT_FLOAT" }, - { 16, 4, 4, "DT_FLOAT32" }, - { 16, 4, 4, "NIFTI_TYPE_FLOAT32" }, - { 32, 8, 4, "DT_COMPLEX" }, - { 32, 8, 4, "DT_COMPLEX64" }, - { 32, 8, 4, "NIFTI_TYPE_COMPLEX64" }, - { 64, 8, 8, "DT_DOUBLE" }, - { 64, 8, 8, "DT_FLOAT64" }, - { 64, 8, 8, "NIFTI_TYPE_FLOAT64" }, - { 128, 3, 0, "DT_RGB" }, - { 128, 3, 0, "DT_RGB24" }, - { 128, 3, 0, "NIFTI_TYPE_RGB24" }, - { 255, 0, 0, "DT_ALL" }, - { 256, 1, 0, "DT_INT8" }, - { 256, 1, 0, "NIFTI_TYPE_INT8" }, - { 512, 2, 2, "DT_UINT16" }, - { 512, 2, 2, "NIFTI_TYPE_UINT16" }, - { 768, 4, 4, "DT_UINT32" }, - { 768, 4, 4, "NIFTI_TYPE_UINT32" }, - { 1024, 8, 8, "DT_INT64" }, - { 1024, 8, 8, "NIFTI_TYPE_INT64" }, - { 1280, 8, 8, "DT_UINT64" }, - { 1280, 8, 8, "NIFTI_TYPE_UINT64" }, - { 1536, 16, 16, "DT_FLOAT128" }, - { 1536, 16, 16, "NIFTI_TYPE_FLOAT128" }, - { 1792, 16, 8, "DT_COMPLEX128" }, - { 1792, 16, 8, "NIFTI_TYPE_COMPLEX128" }, - { 2048, 32, 16, "DT_COMPLEX256" }, - { 2048, 32, 16, "NIFTI_TYPE_COMPLEX256" }, - { 2304, 4, 0, "DT_RGBA32" }, - { 2304, 4, 0, "NIFTI_TYPE_RGBA32" }, -}; - -/*---------------------------------------------------------------------------*/ -/* prototypes for internal functions - not part of exported library */ - -/* extension routines */ -static int nifti_read_extensions( nifti_image *nim, znzFile fp, int remain ); -static int nifti_read_next_extension( nifti1_extension * nex, nifti_image *nim, int remain, znzFile fp ); -static int nifti_check_extension(nifti_image *nim, int size,int code, int rem); -static void update_nifti_image_for_brick_list(nifti_image * nim , int nbricks); -static int nifti_add_exten_to_list(nifti1_extension * new_ext, - nifti1_extension ** list, int new_length); -static int nifti_fill_extension(nifti1_extension * ext, const char * data, - int len, int ecode); - -/* NBL routines */ -static int nifti_load_NBL_bricks(nifti_image * nim , int * slist, int * sindex, nifti_brick_list * NBL, znzFile fp ); -static int nifti_alloc_NBL_mem( nifti_image * nim, int nbricks, - nifti_brick_list * nbl); -static int nifti_copynsort(int nbricks, const int *blist, int **slist, - int **sindex); -static int nifti_NBL_matches_nim(const nifti_image *nim, - const nifti_brick_list *NBL); - -/* for nifti_read_collapsed_image: */ -static int rci_read_data(nifti_image *nim, int *pivots, int *prods, int nprods, - const int dims[], char *data, znzFile fp, size_t base_offset); -static int rci_alloc_mem(void ** data, int prods[8], int nprods, int nbyper ); -static int make_pivot_list(nifti_image * nim, const int dims[], int pivots[], - int prods[], int * nprods ); - -/* misc */ -static int compare_strlist (const char * str, char ** strlist, int len); -static int fileext_compare (const char * test_ext, const char * known_ext); -static int fileext_n_compare (const char * test_ext, - const char * known_ext, size_t maxlen); -static int is_mixedcase (const char * str); -static int is_uppercase (const char * str); -static int make_lowercase (char * str); -static int make_uppercase (char * str); -static int need_nhdr_swap (short dim0, int hdrsize); -static int print_hex_vals (const char * data, size_t nbytes, FILE * fp); -static int unescape_string (char *str); /* string utility functions */ -static char *escapize_string (const char *str); - -/* internal I/O routines */ -static znzFile nifti_image_load_prep( nifti_image *nim ); -static int has_ascii_header(znzFile fp); -/*---------------------------------------------------------------------------*/ - - -/* for calling from some main program */ - -/*----------------------------------------------------------------------*/ -/*! display the nifti library module history (via stdout) -*//*--------------------------------------------------------------------*/ -void nifti_disp_lib_hist( void ) -{ - int c, len = sizeof(gni_history)/sizeof(char *); - for( c = 0; c < len; c++ ) - fputs(gni_history[c], stdout); -} - -/*----------------------------------------------------------------------*/ -/*! display the nifti library version (via stdout) -*//*--------------------------------------------------------------------*/ -void nifti_disp_lib_version( void ) -{ - printf("%s, compiled %s\n", gni_version, __DATE__); -} - - -/*----------------------------------------------------------------------*/ -/*! nifti_image_read_bricks - read nifti data as array of bricks - * - * 13 Dec 2004 [rickr] - * - * \param hname - filename of dataset to read (must be valid) - * \param nbricks - number of sub-bricks to read - * (if blist is valid, nbricks must be > 0) - * \param blist - list of sub-bricks to read - * (can be NULL; if NULL, read complete dataset) - * \param NBL - pointer to empty nifti_brick_list struct - * (must be a valid pointer) - * - * \return - *
nim - same as nifti_image_read, but - * nim->nt = NBL->nbricks (or nt*nu*nv*nw) - * nim->nu,nv,nw = 1 - * nim->data = NULL - *
NBL - filled with data volumes - * - * By default, this function will read the nifti dataset and break the data - * into a list of nt*nu*nv*nw sub-bricks, each having size nx*ny*nz elements. - * That is to say, instead of reading the entire dataset as a single array, - * break it up into sub-bricks (volumes), each of size nx*ny*nz elements. - * - * Note: in the returned nifti_image, nu, nv and nw will always be 1. The - * intention of this function is to collapse the dataset into a single - * array of volumes (of length nbricks or nt*nu*nv*nw). - * - * If 'blist' is valid, it is taken to be a list of sub-bricks, of length - * 'nbricks'. The data will still be separated into sub-bricks of size - * nx*ny*nz elements, but now 'nbricks' sub-bricks will be returned, of the - * caller's choosing via 'blist'. - * - * E.g. consider a dataset with 12 sub-bricks (numbered 0..11), and the - * following code: - * - * 
- * { nifti_brick_list   NB_orig, NB_select;
- *   nifti_image      * nim_orig, * nim_select;
- *   int                blist[5] = { 7, 0, 5, 5, 9 };
- *
- *   nim_orig   = nifti_image_read_bricks("myfile.nii", 0, NULL,  &NB_orig);
- *   nim_select = nifti_image_read_bricks("myfile.nii", 5, blist, &NB_select);
- * }
- *
- * - * Here, nim_orig gets the entire dataset, where NB_orig.nbricks = 12. But - * nim_select has NB_select.nbricks = 5. - * - * Note that the first case is not quite the same as just calling the - * nifti_image_read function, as here the data is separated into sub-bricks. - * - * Note that valid blist elements are in [0..nt*nu*nv*nw-1], - * or written [ 0 .. (dim[4]*dim[5]*dim[6]*dim[7] - 1) ]. - * - * Note that, as is the case with all of the reading functions, the - * data will be allocated, read in, and properly byte-swapped, if - * necessary. - * - * \sa nifti_image_load_bricks, nifti_free_NBL, valid_nifti_brick_list, - nifti_image_read -*//*----------------------------------------------------------------------*/ -nifti_image *nifti_image_read_bricks(const char * hname, int nbricks, - const int * blist, nifti_brick_list * NBL) -{ - nifti_image * nim; - - if( !hname || !NBL ){ - fprintf(stderr,"** nifti_image_read_bricks: bad params (%p,%p)\n", - hname, (void *)NBL); - return NULL; - } - - if( blist && nbricks <= 0 ){ - fprintf(stderr,"** nifti_image_read_bricks: bad nbricks, %d\n", nbricks); - return NULL; - } - - nim = nifti_image_read(hname, 0); /* read header, but not data */ - - if( !nim ) return NULL; /* errors were already printed */ - - /* if we fail, free image and return */ - if( nifti_image_load_bricks(nim, nbricks, blist, NBL) <= 0 ){ - nifti_image_free(nim); - return NULL; - } - - if( blist ) update_nifti_image_for_brick_list(nim, nbricks); - - return nim; -} - - -/*---------------------------------------------------------------------- - * update_nifti_image_for_brick_list - update nifti_image - * - * When loading a specific brick list, the distinction between - * nt, nu, nv and nw is lost. So put everything in t, and set - * dim[0] = 4. - *----------------------------------------------------------------------*/ -static void update_nifti_image_for_brick_list( nifti_image * nim , int nbricks ) -{ - int ndim; - - if( g_opts.debug > 2 ){ - fprintf(stderr,"+d updating image dimensions for %d bricks in list\n", - nbricks); - fprintf(stderr," ndim = %d\n",nim->ndim); - fprintf(stderr," nx,ny,nz,nt,nu,nv,nw: (%d,%d,%d,%d,%d,%d,%d)\n", - nim->nx, nim->ny, nim->nz, nim->nt, nim->nu, nim->nv, nim->nw); - } - - nim->nt = nbricks; - nim->nu = nim->nv = nim->nw = 1; - nim->dim[4] = nbricks; - nim->dim[5] = nim->dim[6] = nim->dim[7] = 1; - - /* compute nvox */ - /* do not rely on dimensions above dim[0] 16 Nov 2005 [rickr] */ - for( nim->nvox = 1, ndim = 1; ndim <= nim->dim[0]; ndim++ ) - nim->nvox *= nim->dim[ndim]; - - /* update the dimensions to 4 or lower */ - for( ndim = 4; (ndim > 1) && (nim->dim[ndim] <= 1); ndim-- ) - ; - - if( g_opts.debug > 2 ){ - fprintf(stderr,"+d ndim = %d -> %d\n",nim->ndim, ndim); - fprintf(stderr," --> (%d,%d,%d,%d,%d,%d,%d)\n", - nim->nx, nim->ny, nim->nz, nim->nt, nim->nu, nim->nv, nim->nw); - } - - nim->dim[0] = nim->ndim = ndim; -} - - -/*----------------------------------------------------------------------*/ -/*! nifti_update_dims_from_array - update nx, ny, ... from nim->dim[] - - Fix all the dimension information, based on a new nim->dim[]. - - Note: we assume that dim[0] will not increase. - - Check for updates to pixdim[], dx,..., nx,..., nvox, ndim, dim[0]. -*//*--------------------------------------------------------------------*/ -int nifti_update_dims_from_array( nifti_image * nim ) -{ - int c, ndim; - - if( !nim ){ - fprintf(stderr,"** update_dims: missing nim\n"); - return 1; - } - - if( g_opts.debug > 2 ){ - fprintf(stderr,"+d updating image dimensions given nim->dim:"); - for( c = 0; c < 8; c++ ) fprintf(stderr," %d", nim->dim[c]); - fputc('\n',stderr); - } - - /* verify dim[0] first */ - if(nim->dim[0] < 1 || nim->dim[0] > 7){ - fprintf(stderr,"** invalid dim[0], dim[] = "); - for( c = 0; c < 8; c++ ) fprintf(stderr," %d", nim->dim[c]); - fputc('\n',stderr); - return 1; - } - - /* set nx, ny ..., dx, dy, ..., one by one */ - - /* less than 1, set to 1, else copy */ - if(nim->dim[1] < 1) nim->nx = nim->dim[1] = 1; - else nim->nx = nim->dim[1]; - nim->dx = nim->pixdim[1]; - - /* if undefined, or less than 1, set to 1 */ - if(nim->dim[0] < 2 || (nim->dim[0] >= 2 && nim->dim[2] < 1)) - nim->ny = nim->dim[2] = 1; - else - nim->ny = nim->dim[2]; - /* copy delta values, in any case */ - nim->dy = nim->pixdim[2]; - - if(nim->dim[0] < 3 || (nim->dim[0] >= 3 && nim->dim[3] < 1)) - nim->nz = nim->dim[3] = 1; - else /* just copy vals from arrays */ - nim->nz = nim->dim[3]; - nim->dz = nim->pixdim[3]; - - if(nim->dim[0] < 4 || (nim->dim[0] >= 4 && nim->dim[4] < 1)) - nim->nt = nim->dim[4] = 1; - else /* just copy vals from arrays */ - nim->nt = nim->dim[4]; - nim->dt = nim->pixdim[4]; - - if(nim->dim[0] < 5 || (nim->dim[0] >= 5 && nim->dim[5] < 1)) - nim->nu = nim->dim[5] = 1; - else /* just copy vals from arrays */ - nim->nu = nim->dim[5]; - nim->du = nim->pixdim[5]; - - if(nim->dim[0] < 6 || (nim->dim[0] >= 6 && nim->dim[6] < 1)) - nim->nv = nim->dim[6] = 1; - else /* just copy vals from arrays */ - nim->nv = nim->dim[6]; - nim->dv = nim->pixdim[6]; - - if(nim->dim[0] < 7 || (nim->dim[0] >= 7 && nim->dim[7] < 1)) - nim->nw = nim->dim[7] = 1; - else /* just copy vals from arrays */ - nim->nw = nim->dim[7]; - nim->dw = nim->pixdim[7]; - - for( c = 1, nim->nvox = 1; c <= nim->dim[0]; c++ ) - nim->nvox *= nim->dim[c]; - - /* compute ndim, assuming it can be no larger than the old one */ - for( ndim = nim->dim[0]; (ndim > 1) && (nim->dim[ndim] <= 1); ndim-- ) - ; - - if( g_opts.debug > 2 ){ - fprintf(stderr,"+d ndim = %d -> %d\n",nim->ndim, ndim); - fprintf(stderr," --> (%d,%d,%d,%d,%d,%d,%d)\n", - nim->nx, nim->ny, nim->nz, nim->nt, nim->nu, nim->nv, nim->nw); - } - - nim->dim[0] = nim->ndim = ndim; - - return 0; -} - - -/*----------------------------------------------------------------------*/ -/*! Load the image data from disk into an already-prepared image struct. - * - * \param nim - initialized nifti_image, without data - * \param nbricks - the length of blist (must be 0 if blist is NULL) - * \param blist - an array of xyz volume indices to read (can be NULL) - * \param NBL - pointer to struct where resulting data will be stored - * - * If blist is NULL, read all sub-bricks. - * - * \return the number of loaded bricks (NBL->nbricks), - * 0 on failure, < 0 on error - * - * NOTE: it is likely that another function will copy the data pointers - * out of NBL, in which case the only pointer the calling function - * will want to free is NBL->bricks (not each NBL->bricks[i]). -*//*--------------------------------------------------------------------*/ -int nifti_image_load_bricks( nifti_image * nim , int nbricks, - const int * blist, nifti_brick_list * NBL ) -{ - int * slist = NULL, * sindex = NULL, rv; - znzFile fp; - - /* we can have blist == NULL */ - if( !nim || !NBL ){ - fprintf(stderr,"** nifti_image_load_bricks, bad params (%p,%p)\n", - (void *)nim, (void *)NBL); - return -1; - } - - if( blist && nbricks <= 0 ){ - if( g_opts.debug > 1 ) - fprintf(stderr,"-d load_bricks: received blist with nbricks = %d," - "ignoring blist\n", nbricks); - blist = NULL; /* pretend nothing was passed */ - } - - if( blist && ! valid_nifti_brick_list(nim, nbricks, blist, g_opts.debug>0) ) - return -1; - - /* for efficiency, let's read the file in order */ - if( blist && nifti_copynsort( nbricks, blist, &slist, &sindex ) != 0 ) - return -1; - - /* open the file and position the FILE pointer */ - fp = nifti_image_load_prep( nim ); - if( !fp ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** nifti_image_load_bricks, failed load_prep\n"); - if( blist ){ free(slist); free(sindex); } - return -1; - } - - /* this will flag to allocate defaults */ - if( !blist ) nbricks = 0; - if( nifti_alloc_NBL_mem( nim, nbricks, NBL ) != 0 ){ - if( blist ){ free(slist); free(sindex); } - znzclose(fp); - return -1; - } - - rv = nifti_load_NBL_bricks(nim, slist, sindex, NBL, fp); - - if( rv != 0 ){ - nifti_free_NBL( NBL ); /* failure! */ - NBL->nbricks = 0; /* repetative, but clear */ - } - - if( slist ){ free(slist); free(sindex); } - - znzclose(fp); - - return NBL->nbricks; -} - - -/*----------------------------------------------------------------------*/ -/*! nifti_free_NBL - free all pointers and clear structure - * - * note: this does not presume to free the structure pointer -*//*--------------------------------------------------------------------*/ -void nifti_free_NBL( nifti_brick_list * NBL ) -{ - int c; - - if( NBL->bricks ){ - for( c = 0; c < NBL->nbricks; c++ ) - if( NBL->bricks[c] ) free(NBL->bricks[c]); - free(NBL->bricks); - NBL->bricks = NULL; - } - - NBL->bsize = NBL->nbricks = 0; -} - - -/*---------------------------------------------------------------------- - * nifti_load_NBL_bricks - read the file data into the NBL struct - * - * return 0 on success, -1 on failure - *----------------------------------------------------------------------*/ -static int nifti_load_NBL_bricks( nifti_image * nim , int * slist, int * sindex, - nifti_brick_list * NBL, znzFile fp ) -{ - size_t oposn, fposn; /* orig and current file positions */ - size_t rv; - long test; - int c; - int prev, isrc, idest; /* previous and current sub-brick, and new index */ - - test = znztell(fp); /* store current file position */ - if( test < 0 ){ - fprintf(stderr,"** load bricks: ztell failed??\n"); - return -1; - } - fposn = oposn = test; - - /* first, handle the default case, no passed blist */ - if( !slist ){ - for( c = 0; c < NBL->nbricks; c++ ) { - rv = nifti_read_buffer(fp, NBL->bricks[c], NBL->bsize, nim); - if( rv != NBL->bsize ){ - fprintf(stderr,"** load bricks: cannot read brick %d from '%s'\n", - c, nim->iname ? nim->iname : nim->fname); - return -1; - } - } - if( g_opts.debug > 1 ) - fprintf(stderr,"+d read %d default %u-byte bricks from file %s\n", - NBL->nbricks, (unsigned int)NBL->bsize, - nim->iname ? nim->iname:nim->fname ); - return 0; - } - - if( !sindex ){ - fprintf(stderr,"** load_NBL_bricks: missing index list\n"); - return -1; - } - - prev = -1; /* use prev for previous sub-brick */ - for( c = 0; c < NBL->nbricks; c++ ){ - isrc = slist[c]; /* this is original brick index (c is new one) */ - idest = sindex[c]; /* this is the destination index for this data */ - - /* if this sub-brick is not the previous, we must read from disk */ - if( isrc != prev ){ - - /* if we are not looking at the correct sub-brick, scan forward */ - if( fposn != (oposn + isrc*NBL->bsize) ){ - fposn = oposn + isrc*NBL->bsize; - if( znzseek(fp, (long)fposn, SEEK_SET) < 0 ){ - fprintf(stderr,"** failed to locate brick %d in file '%s'\n", - isrc, nim->iname ? nim->iname : nim->fname); - return -1; - } - } - - /* only 10,000 lines later and we're actually reading something! */ - rv = nifti_read_buffer(fp, NBL->bricks[idest], NBL->bsize, nim); - if( rv != NBL->bsize ){ - fprintf(stderr,"** failed to read brick %d from file '%s'\n", - isrc, nim->iname ? nim->iname : nim->fname); - if( g_opts.debug > 1 ) - fprintf(stderr," (read %u of %u bytes)\n", - (unsigned int)rv, (unsigned int)NBL->bsize); - return -1; - } - fposn += NBL->bsize; - } else { - /* we have already read this sub-brick, just copy the previous one */ - /* note that this works because they are sorted */ - memcpy(NBL->bricks[idest], NBL->bricks[sindex[c-1]], NBL->bsize); - } - - prev = isrc; /* in any case, note the now previous sub-brick */ - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * nifti_alloc_NBL_mem - allocate memory for bricks - * - * return 0 on success, -1 on failure - *----------------------------------------------------------------------*/ -static int nifti_alloc_NBL_mem(nifti_image * nim, int nbricks, - nifti_brick_list * nbl) -{ - int c; - - /* if nbricks is not specified, use the default */ - if( nbricks > 0 ) nbl->nbricks = nbricks; - else { /* I missed this one with the 1.17 change 02 Mar 2006 [rickr] */ - nbl->nbricks = 1; - for( c = 4; c <= nim->ndim; c++ ) - nbl->nbricks *= nim->dim[c]; - } - - nbl->bsize = (size_t)nim->nx * nim->ny * nim->nz * nim->nbyper;/* bytes */ - nbl->bricks = (void **)malloc(nbl->nbricks * sizeof(void *)); - - if( ! nbl->bricks ){ - fprintf(stderr,"** NANM: failed to alloc %d void ptrs\n",nbricks); - return -1; - } - - for( c = 0; c < nbl->nbricks; c++ ){ - nbl->bricks[c] = (void *)malloc(nbl->bsize); - if( ! nbl->bricks[c] ){ - fprintf(stderr,"** NANM: failed to alloc %u bytes for brick %d\n", - (unsigned int)nbl->bsize, c); - /* so free and clear everything before returning */ - while( c > 0 ){ - c--; - free(nbl->bricks[c]); - } - free(nbl->bricks); - nbl->bricks = NULL; - nbl->bsize = nbl->nbricks = 0; - return -1; - } - } - - if( g_opts.debug > 2 ) - fprintf(stderr,"+d NANM: alloc'd %d bricks of %u bytes for NBL\n", - nbl->nbricks, (unsigned int)nbl->bsize); - - return 0; -} - - -/*---------------------------------------------------------------------- - * nifti_copynsort - copy int list, and sort with indices - * - * 1. duplicate the incoming list - * 2. create an sindex list, and init with 0..nbricks-1 - * 3. do a slow insertion sort on the small slist, along with sindex list - * 4. check results, just to be positive - * - * So slist is sorted, and sindex hold original positions. - * - * return 0 on success, -1 on failure - *----------------------------------------------------------------------*/ -static int nifti_copynsort(int nbricks, const int * blist, int ** slist, - int ** sindex) -{ - int * stmp, * itmp; /* for ease of typing/reading */ - int c1, c2, spos, tmp; - - *slist = (int *)malloc(nbricks * sizeof(int)); - *sindex = (int *)malloc(nbricks * sizeof(int)); - - if( !*slist || !*sindex ){ - fprintf(stderr,"** NCS: failed to alloc %d ints for sorting\n",nbricks); - if(*slist) free(*slist); /* maybe one succeeded */ - if(*sindex) free(*sindex); - return -1; - } - - /* init the lists */ - memcpy(*slist, blist, nbricks*sizeof(int)); - for( c1 = 0; c1 < nbricks; c1++ ) (*sindex)[c1] = c1; - - /* now actually sort slist */ - stmp = *slist; - itmp = *sindex; - for( c1 = 0; c1 < nbricks-1; c1++ ) { - /* find smallest value, init to current */ - spos = c1; - for( c2 = c1+1; c2 < nbricks; c2++ ) - if( stmp[c2] < stmp[spos] ) spos = c2; - if( spos != c1 ) /* swap: fine, don't maintain sub-order, see if I care */ - { - tmp = stmp[c1]; /* first swap the sorting values */ - stmp[c1] = stmp[spos]; - stmp[spos] = tmp; - - tmp = itmp[c1]; /* then swap the index values */ - itmp[c1] = itmp[spos]; - itmp[spos] = tmp; - } - } - - if( g_opts.debug > 2 ){ - fprintf(stderr, "+d sorted indexing list:\n"); - fprintf(stderr, " orig : "); - for( c1 = 0; c1 < nbricks; c1++ ) fprintf(stderr," %d",blist[c1]); - fprintf(stderr,"\n new : "); - for( c1 = 0; c1 < nbricks; c1++ ) fprintf(stderr," %d",stmp[c1]); - fprintf(stderr,"\n indices: "); - for( c1 = 0; c1 < nbricks; c1++ ) fprintf(stderr," %d",itmp[c1]); - fputc('\n', stderr); - } - - /* check the sort (why not? I've got time...) */ - for( c1 = 0; c1 < nbricks-1; c1++ ){ - if( (stmp[c1] > stmp[c1+1]) || (blist[itmp[c1]] != stmp[c1]) ){ - fprintf(stderr,"** sorting screw-up, way to go, rick!\n"); - free(stmp); free(itmp); *slist = NULL; *sindex = NULL; - return -1; - } - } - - if( g_opts.debug > 2 ) fprintf(stderr,"-d sorting is okay\n"); - - return 0; -} - - -/*----------------------------------------------------------------------*/ -/*! valid_nifti_brick_list - check sub-brick list for image - * - * This function verifies that nbricks and blist are appropriate - * for use with this nim, based on the dimensions. - * - * \param nim nifti_image to check against - * \param nbricks number of brick indices in blist - * \param blist list of brick indices to check in nim - * \param disp_error if this flag is set, report errors to user - * - * \return 1 if valid, 0 if not -*//*--------------------------------------------------------------------*/ -int valid_nifti_brick_list(nifti_image * nim , int nbricks, - const int * blist, int disp_error) -{ - int c, nsubs; - - if( !nim ){ - if( disp_error || g_opts.debug > 0 ) - fprintf(stderr,"** valid_nifti_brick_list: missing nifti image\n"); - return 0; - } - - if( nbricks <= 0 || !blist ){ - if( disp_error || g_opts.debug > 1 ) - fprintf(stderr,"** valid_nifti_brick_list: no brick list to check\n"); - return 0; - } - - if( nim->dim[0] < 3 ){ - if( disp_error || g_opts.debug > 1 ) - fprintf(stderr,"** cannot read explict brick list from %d-D dataset\n", - nim->dim[0]); - return 0; - } - - /* nsubs sub-brick is nt*nu*nv*nw */ - for( c = 4, nsubs = 1; c <= nim->dim[0]; c++ ) - nsubs *= nim->dim[c]; - - if( nsubs <= 0 ){ - fprintf(stderr,"** VNBL warning: bad dim list (%d,%d,%d,%d)\n", - nim->dim[4], nim->dim[5], nim->dim[6], nim->dim[7]); - return 0; - } - - for( c = 0; c < nbricks; c++ ) - if( (blist[c] < 0) || (blist[c] >= nsubs) ){ - if( disp_error || g_opts.debug > 1 ) - fprintf(stderr, - "** volume index %d (#%d) is out of range [0,%d]\n", - blist[c], c, nsubs-1); - return 0; - } - - return 1; /* all is well */ -} - -/*----------------------------------------------------------------------*/ -/* verify that NBL struct is a valid data source for the image - * - * return 1 if so, 0 otherwise -*//*--------------------------------------------------------------------*/ -static int nifti_NBL_matches_nim(const nifti_image *nim, - const nifti_brick_list *NBL) -{ - size_t volbytes = 0; /* bytes per volume */ - int ind, errs = 0, nvols = 0; - - - if( !nim || !NBL ) { - if( g_opts.debug > 0 ) - fprintf(stderr,"** nifti_NBL_matches_nim: NULL pointer(s)\n"); - return 0; - } - - /* for nim, compute volbytes and nvols */ - if( nim->ndim > 0 ) { - /* first 3 indices are over a single volume */ - volbytes = (size_t)nim->nbyper; - for( ind = 1; ind <= nim->ndim && ind < 4; ind++ ) - volbytes *= (size_t)nim->dim[ind]; - - for( ind = 4, nvols = 1; ind <= nim->ndim; ind++ ) - nvols *= nim->dim[ind]; - } - - if( volbytes != NBL->bsize ) { - if( g_opts.debug > 1 ) - fprintf(stderr,"** NBL/nim mismatch, volbytes = %u, %u\n", - (unsigned)NBL->bsize, (unsigned)volbytes); - errs++; - } - - if( nvols != NBL->nbricks ) { - if( g_opts.debug > 1 ) - fprintf(stderr,"** NBL/nim mismatch, nvols = %d, %d\n", - NBL->nbricks, nvols); - errs++; - } - - if( errs ) return 0; - else if ( g_opts.debug > 2 ) - fprintf(stderr,"-- nim/NBL agree: nvols = %d, nbytes = %u\n", - nvols, (unsigned)volbytes); - - return 1; -} - -/* end of new nifti_image_read_bricks() functionality */ - -/*----------------------------------------------------------------------*/ -/*! display the orientation from the quaternian fields - * - * \param mesg if non-NULL, display this message first - * \param mat the matrix to convert to "nearest" orientation - * - * \return -1 if results cannot be determined, 0 if okay -*//*--------------------------------------------------------------------*/ -int nifti_disp_matrix_orient( const char * mesg, mat44 mat ) -{ - int i, j, k; - - if ( mesg ) fputs( mesg, stderr ); /* use stdout? */ - - nifti_mat44_to_orientation( mat, &i,&j,&k ); - if ( i <= 0 || j <= 0 || k <= 0 ) return -1; - - /* so we have good codes */ - fprintf(stderr, " i orientation = '%s'\n" - " j orientation = '%s'\n" - " k orientation = '%s'\n", - nifti_orientation_string(i), - nifti_orientation_string(j), - nifti_orientation_string(k) ); - return 0; -} - - -/*----------------------------------------------------------------------*/ -/*! duplicate the given string (alloc length+1) - * - * \return allocated pointer (or NULL on failure) -*//*--------------------------------------------------------------------*/ -char *nifti_strdup(const char *str) -{ - char *dup; - - if( !str ) return NULL; /* allow calls passing NULL */ - - dup = (char *)malloc(strlen(str) + 1); - - /* check for failure */ - if( dup ) strcpy(dup, str); - else fprintf(stderr,"** nifti_strdup: failed to alloc %u bytes\n", - (unsigned int)strlen(str)+1); - - return dup; -} - - -/*---------------------------------------------------------------------------*/ -/*! Return a pointer to a string holding the name of a NIFTI datatype. - - \param dt NIfTI-1 datatype - - \return pointer to static string holding the datatype name - - \warning Do not free() or modify this string! - It points to static storage. - - \sa NIFTI1_DATATYPES group in nifti1.h -*//*-------------------------------------------------------------------------*/ -char const * nifti_datatype_string( int dt ) -{ - switch( dt ){ - case DT_UNKNOWN: return "UNKNOWN" ; - case DT_BINARY: return "BINARY" ; - case DT_INT8: return "INT8" ; - case DT_UINT8: return "UINT8" ; - case DT_INT16: return "INT16" ; - case DT_UINT16: return "UINT16" ; - case DT_INT32: return "INT32" ; - case DT_UINT32: return "UINT32" ; - case DT_INT64: return "INT64" ; - case DT_UINT64: return "UINT64" ; - case DT_FLOAT32: return "FLOAT32" ; - case DT_FLOAT64: return "FLOAT64" ; - case DT_FLOAT128: return "FLOAT128" ; - case DT_COMPLEX64: return "COMPLEX64" ; - case DT_COMPLEX128: return "COMPLEX128" ; - case DT_COMPLEX256: return "COMPLEX256" ; - case DT_RGB24: return "RGB24" ; - case DT_RGBA32: return "RGBA32" ; - } - return "**ILLEGAL**" ; -} - -/*----------------------------------------------------------------------*/ -/*! Determine if the datatype code dt is an integer type (1=YES, 0=NO). - - \return whether the given NIfTI-1 datatype code is valid - - \sa NIFTI1_DATATYPES group in nifti1.h -*//*--------------------------------------------------------------------*/ -int nifti_is_inttype( int dt ) -{ - switch( dt ){ - case DT_UNKNOWN: return 0 ; - case DT_BINARY: return 0 ; - case DT_INT8: return 1 ; - case DT_UINT8: return 1 ; - case DT_INT16: return 1 ; - case DT_UINT16: return 1 ; - case DT_INT32: return 1 ; - case DT_UINT32: return 1 ; - case DT_INT64: return 1 ; - case DT_UINT64: return 1 ; - case DT_FLOAT32: return 0 ; - case DT_FLOAT64: return 0 ; - case DT_FLOAT128: return 0 ; - case DT_COMPLEX64: return 0 ; - case DT_COMPLEX128: return 0 ; - case DT_COMPLEX256: return 0 ; - case DT_RGB24: return 1 ; - case DT_RGBA32: return 1 ; - } - return 0 ; -} - -/*---------------------------------------------------------------------------*/ -/*! Return a pointer to a string holding the name of a NIFTI units type. - - \param uu NIfTI-1 unit code - - \return pointer to static string for the given unit type - - \warning Do not free() or modify this string! - It points to static storage. - - \sa NIFTI1_UNITS group in nifti1.h -*//*-------------------------------------------------------------------------*/ -char const *nifti_units_string( int uu ) -{ - switch( uu ){ - case NIFTI_UNITS_METER: return "m" ; - case NIFTI_UNITS_MM: return "mm" ; - case NIFTI_UNITS_MICRON: return "um" ; - case NIFTI_UNITS_SEC: return "s" ; - case NIFTI_UNITS_MSEC: return "ms" ; - case NIFTI_UNITS_USEC: return "us" ; - case NIFTI_UNITS_HZ: return "Hz" ; - case NIFTI_UNITS_PPM: return "ppm" ; - case NIFTI_UNITS_RADS: return "rad/s" ; - } - return "Unknown" ; -} - -/*---------------------------------------------------------------------------*/ -/*! Return a pointer to a string holding the name of a NIFTI transform type. - - \param xx NIfTI-1 xform code - - \return pointer to static string describing xform code - - \warning Do not free() or modify this string! - It points to static storage. - - \sa NIFTI1_XFORM_CODES group in nifti1.h -*//*-------------------------------------------------------------------------*/ -char const *nifti_xform_string( int xx ) -{ - switch( xx ){ - case NIFTI_XFORM_SCANNER_ANAT: return "Scanner Anat" ; - case NIFTI_XFORM_ALIGNED_ANAT: return "Aligned Anat" ; - case NIFTI_XFORM_TALAIRACH: return "Talairach" ; - case NIFTI_XFORM_MNI_152: return "MNI_152" ; - } - return "Unknown" ; -} - -/*---------------------------------------------------------------------------*/ -/*! Return a pointer to a string holding the name of a NIFTI intent type. - - \param ii NIfTI-1 intent code - - \return pointer to static string describing code - - \warning Do not free() or modify this string! - It points to static storage. - - \sa NIFTI1_INTENT_CODES group in nifti1.h -*//*-------------------------------------------------------------------------*/ -char const *nifti_intent_string( int ii ) -{ - switch( ii ){ - case NIFTI_INTENT_CORREL: return "Correlation statistic" ; - case NIFTI_INTENT_TTEST: return "T-statistic" ; - case NIFTI_INTENT_FTEST: return "F-statistic" ; - case NIFTI_INTENT_ZSCORE: return "Z-score" ; - case NIFTI_INTENT_CHISQ: return "Chi-squared distribution" ; - case NIFTI_INTENT_BETA: return "Beta distribution" ; - case NIFTI_INTENT_BINOM: return "Binomial distribution" ; - case NIFTI_INTENT_GAMMA: return "Gamma distribution" ; - case NIFTI_INTENT_POISSON: return "Poisson distribution" ; - case NIFTI_INTENT_NORMAL: return "Normal distribution" ; - case NIFTI_INTENT_FTEST_NONC: return "F-statistic noncentral" ; - case NIFTI_INTENT_CHISQ_NONC: return "Chi-squared noncentral" ; - case NIFTI_INTENT_LOGISTIC: return "Logistic distribution" ; - case NIFTI_INTENT_LAPLACE: return "Laplace distribution" ; - case NIFTI_INTENT_UNIFORM: return "Uniform distribition" ; - case NIFTI_INTENT_TTEST_NONC: return "T-statistic noncentral" ; - case NIFTI_INTENT_WEIBULL: return "Weibull distribution" ; - case NIFTI_INTENT_CHI: return "Chi distribution" ; - case NIFTI_INTENT_INVGAUSS: return "Inverse Gaussian distribution" ; - case NIFTI_INTENT_EXTVAL: return "Extreme Value distribution" ; - case NIFTI_INTENT_PVAL: return "P-value" ; - - case NIFTI_INTENT_LOGPVAL: return "Log P-value" ; - case NIFTI_INTENT_LOG10PVAL: return "Log10 P-value" ; - - case NIFTI_INTENT_ESTIMATE: return "Estimate" ; - case NIFTI_INTENT_LABEL: return "Label index" ; - case NIFTI_INTENT_NEURONAME: return "NeuroNames index" ; - case NIFTI_INTENT_GENMATRIX: return "General matrix" ; - case NIFTI_INTENT_SYMMATRIX: return "Symmetric matrix" ; - case NIFTI_INTENT_DISPVECT: return "Displacement vector" ; - case NIFTI_INTENT_VECTOR: return "Vector" ; - case NIFTI_INTENT_POINTSET: return "Pointset" ; - case NIFTI_INTENT_TRIANGLE: return "Triangle" ; - case NIFTI_INTENT_QUATERNION: return "Quaternion" ; - - case NIFTI_INTENT_DIMLESS: return "Dimensionless number" ; - } - return "Unknown" ; -} - -/*---------------------------------------------------------------------------*/ -/*! Return a pointer to a string holding the name of a NIFTI slice_code. - - \param ss NIfTI-1 slice order code - - \return pointer to static string describing code - - \warning Do not free() or modify this string! - It points to static storage. - - \sa NIFTI1_SLICE_ORDER group in nifti1.h -*//*-------------------------------------------------------------------------*/ -char const *nifti_slice_string( int ss ) -{ - switch( ss ){ - case NIFTI_SLICE_SEQ_INC: return "sequential_increasing" ; - case NIFTI_SLICE_SEQ_DEC: return "sequential_decreasing" ; - case NIFTI_SLICE_ALT_INC: return "alternating_increasing" ; - case NIFTI_SLICE_ALT_DEC: return "alternating_decreasing" ; - case NIFTI_SLICE_ALT_INC2: return "alternating_increasing_2" ; - case NIFTI_SLICE_ALT_DEC2: return "alternating_decreasing_2" ; - } - return "Unknown" ; -} - -/*---------------------------------------------------------------------------*/ -/*! Return a pointer to a string holding the name of a NIFTI orientation. - - \param ii orientation code - - \return pointer to static string holding the orientation information - - \warning Do not free() or modify the return string! - It points to static storage. - - \sa NIFTI_L2R in nifti1_io.h -*//*-------------------------------------------------------------------------*/ -char const *nifti_orientation_string( int ii ) -{ - switch( ii ){ - case NIFTI_L2R: return "Left-to-Right" ; - case NIFTI_R2L: return "Right-to-Left" ; - case NIFTI_P2A: return "Posterior-to-Anterior" ; - case NIFTI_A2P: return "Anterior-to-Posterior" ; - case NIFTI_I2S: return "Inferior-to-Superior" ; - case NIFTI_S2I: return "Superior-to-Inferior" ; - } - return "Unknown" ; -} - -/*--------------------------------------------------------------------------*/ -/*! Given a datatype code, set number of bytes per voxel and the swapsize. - - \param datatype nifti1 datatype code - \param nbyper pointer to return value: number of bytes per voxel - \param swapsize pointer to return value: size of swap blocks - - \return appropriate values at nbyper and swapsize - - The swapsize is set to 0 if this datatype doesn't ever need swapping. - - \sa NIFTI1_DATATYPES in nifti1.h -*//*------------------------------------------------------------------------*/ -void nifti_datatype_sizes( int datatype , int *nbyper, int *swapsize ) -{ - int nb=0, ss=0 ; - switch( datatype ){ - case DT_INT8: - case DT_UINT8: nb = 1 ; ss = 0 ; break ; - - case DT_INT16: - case DT_UINT16: nb = 2 ; ss = 2 ; break ; - - case DT_RGB24: nb = 3 ; ss = 0 ; break ; - case DT_RGBA32: nb = 4 ; ss = 0 ; break ; - - case DT_INT32: - case DT_UINT32: - case DT_FLOAT32: nb = 4 ; ss = 4 ; break ; - - case DT_COMPLEX64: nb = 8 ; ss = 4 ; break ; - - case DT_FLOAT64: - case DT_INT64: - case DT_UINT64: nb = 8 ; ss = 8 ; break ; - - case DT_FLOAT128: nb = 16 ; ss = 16 ; break ; - - case DT_COMPLEX128: nb = 16 ; ss = 8 ; break ; - - case DT_COMPLEX256: nb = 32 ; ss = 16 ; break ; - } - - ASSIF(nbyper,nb) ; ASSIF(swapsize,ss) ; return ; -} - -/*---------------------------------------------------------------------------*/ -/*! Given the quaternion parameters (etc.), compute a transformation matrix. - - See comments in nifti1.h for details. - - qb,qc,qd = quaternion parameters - - qx,qy,qz = offset parameters - - dx,dy,dz = grid stepsizes (non-negative inputs are set to 1.0) - - qfac = sign of dz step (< 0 is negative; >= 0 is positive) - - 
-   If qx=qy=qz=0, dx=dy=dz=1, then the output is a rotation matrix.
-   For qfac >= 0, the rotation is proper.
-   For qfac <  0, the rotation is improper.
-
- - \see "QUATERNION REPRESENTATION OF ROTATION MATRIX" in nifti1.h - \see nifti_mat44_to_quatern, nifti_make_orthog_mat44, - nifti_mat44_to_orientation - -*//*-------------------------------------------------------------------------*/ -mat44 nifti_quatern_to_mat44( float qb, float qc, float qd, - float qx, float qy, float qz, - float dx, float dy, float dz, float qfac ) -{ - mat44 R ; - double a,b=qb,c=qc,d=qd , xd,yd,zd ; - - /* last row is always [ 0 0 0 1 ] */ - - R.m[3][0]=R.m[3][1]=R.m[3][2] = 0.0f ; R.m[3][3]= 1.0f ; - - /* compute a parameter from b,c,d */ - - a = 1.0l - (b*b + c*c + d*d) ; - if( a < 1.e-7l ){ /* special case */ - a = 1.0l / sqrt(b*b+c*c+d*d) ; - b *= a ; c *= a ; d *= a ; /* normalize (b,c,d) vector */ - a = 0.0l ; /* a = 0 ==> 180 degree rotation */ - } else{ - a = sqrt(a) ; /* angle = 2*arccos(a) */ - } - - /* load rotation matrix, including scaling factors for voxel sizes */ - - xd = (dx > 0.0) ? dx : 1.0l ; /* make sure are positive */ - yd = (dy > 0.0) ? dy : 1.0l ; - zd = (dz > 0.0) ? dz : 1.0l ; - - if( qfac < 0.0 ) zd = -zd ; /* left handedness? */ - - R.m[0][0] = (float)( (a*a+b*b-c*c-d*d) * xd) ; - R.m[0][1] = 2.0l * (b*c-a*d ) * yd ; - R.m[0][2] = 2.0l * (b*d+a*c ) * zd ; - R.m[1][0] = 2.0l * (b*c+a*d ) * xd ; - R.m[1][1] = (float)( (a*a+c*c-b*b-d*d) * yd) ; - R.m[1][2] = 2.0l * (c*d-a*b ) * zd ; - R.m[2][0] = 2.0l * (b*d-a*c ) * xd ; - R.m[2][1] = 2.0l * (c*d+a*b ) * yd ; - R.m[2][2] = (float)( (a*a+d*d-c*c-b*b) * zd) ; - - /* load offsets */ - - R.m[0][3] = qx ; R.m[1][3] = qy ; R.m[2][3] = qz ; - - return R ; -} - -/*---------------------------------------------------------------------------*/ -/*! Given the 3x4 upper corner of the matrix R, compute the quaternion - parameters that fit it. - - - Any NULL pointer on input won't get assigned (e.g., if you don't want - dx,dy,dz, just pass NULL in for those pointers). - - If the 3 input matrix columns are NOT orthogonal, they will be - orthogonalized prior to calculating the parameters, using - the polar decomposition to find the orthogonal matrix closest - to the column-normalized input matrix. - - However, if the 3 input matrix columns are NOT orthogonal, then - the matrix produced by nifti_quatern_to_mat44 WILL have orthogonal - columns, so it won't be the same as the matrix input here. - This "feature" is because the NIFTI 'qform' transform is - deliberately not fully general -- it is intended to model a volume - with perpendicular axes. - - If the 3 input matrix columns are not even linearly independent, - you'll just have to take your luck, won't you? - - \see "QUATERNION REPRESENTATION OF ROTATION MATRIX" in nifti1.h - - \see nifti_quatern_to_mat44, nifti_make_orthog_mat44, - nifti_mat44_to_orientation -*//*-------------------------------------------------------------------------*/ -void nifti_mat44_to_quatern( mat44 R , - float *qb, float *qc, float *qd, - float *qx, float *qy, float *qz, - float *dx, float *dy, float *dz, float *qfac ) -{ - double r11,r12,r13 , r21,r22,r23 , r31,r32,r33 ; - double xd,yd,zd , a,b,c,d ; - mat33 P,Q ; - - /* offset outputs are read write out of input matrix */ - - ASSIF(qx,R.m[0][3]) ; ASSIF(qy,R.m[1][3]) ; ASSIF(qz,R.m[2][3]) ; - - /* load 3x3 matrix into local variables */ - - r11 = R.m[0][0] ; r12 = R.m[0][1] ; r13 = R.m[0][2] ; - r21 = R.m[1][0] ; r22 = R.m[1][1] ; r23 = R.m[1][2] ; - r31 = R.m[2][0] ; r32 = R.m[2][1] ; r33 = R.m[2][2] ; - - /* compute lengths of each column; these determine grid spacings */ - - xd = sqrt( r11*r11 + r21*r21 + r31*r31 ) ; - yd = sqrt( r12*r12 + r22*r22 + r32*r32 ) ; - zd = sqrt( r13*r13 + r23*r23 + r33*r33 ) ; - - /* if a column length is zero, patch the trouble */ - - if( xd == 0.0l ){ r11 = 1.0l ; r21 = r31 = 0.0l ; xd = 1.0l ; } - if( yd == 0.0l ){ r22 = 1.0l ; r12 = r32 = 0.0l ; yd = 1.0l ; } - if( zd == 0.0l ){ r33 = 1.0l ; r13 = r23 = 0.0l ; zd = 1.0l ; } - - /* assign the output lengths */ - - ASSIF(dx,(float)xd) ; ASSIF(dy,(float)yd) ; ASSIF(dz,(float)zd) ; - - /* normalize the columns */ - - r11 /= xd ; r21 /= xd ; r31 /= xd ; - r12 /= yd ; r22 /= yd ; r32 /= yd ; - r13 /= zd ; r23 /= zd ; r33 /= zd ; - - /* At this point, the matrix has normal columns, but we have to allow - for the fact that the hideous user may not have given us a matrix - with orthogonal columns. - - So, now find the orthogonal matrix closest to the current matrix. - - One reason for using the polar decomposition to get this - orthogonal matrix, rather than just directly orthogonalizing - the columns, is so that inputting the inverse matrix to R - will result in the inverse orthogonal matrix at this point. - If we just orthogonalized the columns, this wouldn't necessarily hold. */ - - Q.m[0][0] = (float)r11 ; Q.m[0][1] = (float)r12 ; Q.m[0][2] = (float)r13 ; /* load Q */ - Q.m[1][0] = (float)r21 ; Q.m[1][1] = (float)r22 ; Q.m[1][2] = (float)r23 ; - Q.m[2][0] = (float)r31 ; Q.m[2][1] = (float)r32 ; Q.m[2][2] = (float)r33 ; - - P = nifti_mat33_polar(Q) ; /* P is orthog matrix closest to Q */ - - r11 = P.m[0][0] ; r12 = P.m[0][1] ; r13 = P.m[0][2] ; /* unload */ - r21 = P.m[1][0] ; r22 = P.m[1][1] ; r23 = P.m[1][2] ; - r31 = P.m[2][0] ; r32 = P.m[2][1] ; r33 = P.m[2][2] ; - - /* [ r11 r12 r13 ] */ - /* at this point, the matrix [ r21 r22 r23 ] is orthogonal */ - /* [ r31 r32 r33 ] */ - - /* compute the determinant to determine if it is proper */ - - zd = r11*r22*r33-r11*r32*r23-r21*r12*r33 - +r21*r32*r13+r31*r12*r23-r31*r22*r13 ; /* should be -1 or 1 */ - - if( zd > 0 ){ /* proper */ - ASSIF(qfac,1.0f) ; - } else { /* improper ==> flip 3rd column */ - ASSIF(qfac,-1.0f) ; - r13 = -r13 ; r23 = -r23 ; r33 = -r33 ; - } - - /* now, compute quaternion parameters */ - - a = r11 + r22 + r33 + 1.0l ; - - if( a > 0.5l ){ /* simplest case */ - a = 0.5l * sqrt(a) ; - b = 0.25l * (r32-r23) / a ; - c = 0.25l * (r13-r31) / a ; - d = 0.25l * (r21-r12) / a ; - } else { /* trickier case */ - xd = 1.0 + r11 - (r22+r33) ; /* 4*b*b */ - yd = 1.0 + r22 - (r11+r33) ; /* 4*c*c */ - zd = 1.0 + r33 - (r11+r22) ; /* 4*d*d */ - if( xd > 1.0 ){ - b = 0.5l * sqrt(xd) ; - c = 0.25l* (r12+r21) / b ; - d = 0.25l* (r13+r31) / b ; - a = 0.25l* (r32-r23) / b ; - } else if( yd > 1.0 ){ - c = 0.5l * sqrt(yd) ; - b = 0.25l* (r12+r21) / c ; - d = 0.25l* (r23+r32) / c ; - a = 0.25l* (r13-r31) / c ; - } else { - d = 0.5l * sqrt(zd) ; - b = 0.25l* (r13+r31) / d ; - c = 0.25l* (r23+r32) / d ; - a = 0.25l* (r21-r12) / d ; - } - if( a < 0.0l ){ b=-b ; c=-c ; d=-d; a=-a; } - } - - ASSIF(qb,(float)b) ; ASSIF(qc,(float)c) ; ASSIF(qd,(float)d) ; - return ; -} - -/*---------------------------------------------------------------------------*/ -/*! Compute the inverse of a bordered 4x4 matrix. - - 
-   - Some numerical code fragments were generated by Maple 8.
-   - If a singular matrix is input, the output matrix will be all zero.
-   - You can check for this by examining the [3][3] element, which will
-     be 1.0 for the normal case and 0.0 for the bad case.
-
-     The input matrix should have the form:
-        [ r11 r12 r13 v1 ]
-        [ r21 r22 r23 v2 ]
-        [ r31 r32 r33 v3 ]
-        [  0   0   0   1 ]
-
-*//*-------------------------------------------------------------------------*/ -mat44 nifti_mat44_inverse( mat44 R ) -{ - double r11,r12,r13,r21,r22,r23,r31,r32,r33,v1,v2,v3 , deti ; - mat44 Q ; - /* INPUT MATRIX IS: */ - r11 = R.m[0][0]; r12 = R.m[0][1]; r13 = R.m[0][2]; /* [ r11 r12 r13 v1 ] */ - r21 = R.m[1][0]; r22 = R.m[1][1]; r23 = R.m[1][2]; /* [ r21 r22 r23 v2 ] */ - r31 = R.m[2][0]; r32 = R.m[2][1]; r33 = R.m[2][2]; /* [ r31 r32 r33 v3 ] */ - v1 = R.m[0][3]; v2 = R.m[1][3]; v3 = R.m[2][3]; /* [ 0 0 0 1 ] */ - - deti = r11*r22*r33-r11*r32*r23-r21*r12*r33 - +r21*r32*r13+r31*r12*r23-r31*r22*r13 ; - - if( deti != 0.0l ) deti = 1.0l / deti ; - - Q.m[0][0] = (float)( deti*( r22*r33-r32*r23) ) ; - Q.m[0][1] = (float)( deti*(-r12*r33+r32*r13) ) ; - Q.m[0][2] = (float)( deti*( r12*r23-r22*r13) ) ; - Q.m[0][3] = (float)( deti*(-r12*r23*v3+r12*v2*r33+r22*r13*v3 - -r22*v1*r33-r32*r13*v2+r32*v1*r23) ) ; - - Q.m[1][0] = (float)( deti*(-r21*r33+r31*r23) ) ; - Q.m[1][1] = (float)( deti*( r11*r33-r31*r13) ) ; - Q.m[1][2] = (float)( deti*(-r11*r23+r21*r13) ) ; - Q.m[1][3] = (float)( deti*( r11*r23*v3-r11*v2*r33-r21*r13*v3 - +r21*v1*r33+r31*r13*v2-r31*v1*r23) ) ; - - Q.m[2][0] = (float)( deti*( r21*r32-r31*r22) ) ; - Q.m[2][1] = (float)( deti*(-r11*r32+r31*r12) ) ; - Q.m[2][2] = (float)( deti*( r11*r22-r21*r12) ) ; - Q.m[2][3] = (float)( deti*(-r11*r22*v3+r11*r32*v2+r21*r12*v3 - -r21*r32*v1-r31*r12*v2+r31*r22*v1) ) ; - - Q.m[3][0] = Q.m[3][1] = Q.m[3][2] = 0.0l ; - Q.m[3][3] = (deti == 0.0l) ? 0.0l : 1.0l ; /* failure flag if deti == 0 */ - - return Q ; -} - -/*---------------------------------------------------------------------------*/ -/*! Input 9 floats and make an orthgonal mat44 out of them. - - Each row is normalized, then nifti_mat33_polar() is used to orthogonalize - them. If row #3 (r31,r32,r33) is input as zero, then it will be taken to - be the cross product of rows #1 and #2. - - This function can be used to create a rotation matrix for transforming - an oblique volume to anatomical coordinates. For this application: - - row #1 (r11,r12,r13) is the direction vector along the image i-axis - - row #2 (r21,r22,r23) is the direction vector along the image j-axis - - row #3 (r31,r32,r33) is the direction vector along the slice direction - (if available; otherwise enter it as 0's) - - The first 2 rows can be taken from the DICOM attribute (0020,0037) - "Image Orientation (Patient)". - - After forming the rotation matrix, the complete affine transformation from - (i,j,k) grid indexes to (x,y,z) spatial coordinates can be computed by - multiplying each column by the appropriate grid spacing: - - column #1 (R.m[0][0],R.m[1][0],R.m[2][0]) by delta-x - - column #2 (R.m[0][1],R.m[1][1],R.m[2][1]) by delta-y - - column #3 (R.m[0][2],R.m[1][2],R.m[2][2]) by delta-z - - and by then placing the center (x,y,z) coordinates of voxel (0,0,0) into - the column #4 (R.m[0][3],R.m[1][3],R.m[2][3]). - - \sa nifti_quatern_to_mat44, nifti_mat44_to_quatern, - nifti_mat44_to_orientation -*//*-------------------------------------------------------------------------*/ -mat44 nifti_make_orthog_mat44( float r11, float r12, float r13 , - float r21, float r22, float r23 , - float r31, float r32, float r33 ) -{ - mat44 R ; - mat33 Q , P ; - double val ; - - R.m[3][0] = R.m[3][1] = R.m[3][2] = 0.0l ; R.m[3][3] = 1.0l ; - - Q.m[0][0] = r11 ; Q.m[0][1] = r12 ; Q.m[0][2] = r13 ; /* load Q */ - Q.m[1][0] = r21 ; Q.m[1][1] = r22 ; Q.m[1][2] = r23 ; - Q.m[2][0] = r31 ; Q.m[2][1] = r32 ; Q.m[2][2] = r33 ; - - /* normalize row 1 */ - - val = Q.m[0][0]*Q.m[0][0] + Q.m[0][1]*Q.m[0][1] + Q.m[0][2]*Q.m[0][2] ; - if( val > 0.0l ){ - val = 1.0l / sqrt(val) ; - Q.m[0][0] *= (float)val ; Q.m[0][1] *= (float)val ; Q.m[0][2] *= (float)val ; - } else { - Q.m[0][0] = 1.0l ; Q.m[0][1] = 0.0l ; Q.m[0][2] = 0.0l ; - } - - /* normalize row 2 */ - - val = Q.m[1][0]*Q.m[1][0] + Q.m[1][1]*Q.m[1][1] + Q.m[1][2]*Q.m[1][2] ; - if( val > 0.0l ){ - val = 1.0l / sqrt(val) ; - Q.m[1][0] *= (float)val ; Q.m[1][1] *= (float)val ; Q.m[1][2] *= (float)val ; - } else { - Q.m[1][0] = 0.0l ; Q.m[1][1] = 1.0l ; Q.m[1][2] = 0.0l ; - } - - /* normalize row 3 */ - - val = Q.m[2][0]*Q.m[2][0] + Q.m[2][1]*Q.m[2][1] + Q.m[2][2]*Q.m[2][2] ; - if( val > 0.0l ){ - val = 1.0l / sqrt(val) ; - Q.m[2][0] *= (float)val ; Q.m[2][1] *= (float)val ; Q.m[2][2] *= (float)val ; - } else { - Q.m[2][0] = Q.m[0][1]*Q.m[1][2] - Q.m[0][2]*Q.m[1][1] ; /* cross */ - Q.m[2][1] = Q.m[0][2]*Q.m[1][0] - Q.m[0][0]*Q.m[1][2] ; /* product */ - Q.m[2][2] = Q.m[0][0]*Q.m[1][1] - Q.m[0][1]*Q.m[1][0] ; - } - - P = nifti_mat33_polar(Q) ; /* P is orthog matrix closest to Q */ - - R.m[0][0] = P.m[0][0] ; R.m[0][1] = P.m[0][1] ; R.m[0][2] = P.m[0][2] ; - R.m[1][0] = P.m[1][0] ; R.m[1][1] = P.m[1][1] ; R.m[1][2] = P.m[1][2] ; - R.m[2][0] = P.m[2][0] ; R.m[2][1] = P.m[2][1] ; R.m[2][2] = P.m[2][2] ; - - R.m[0][3] = R.m[1][3] = R.m[2][3] = 0.0f ; return R ; -} - -/*----------------------------------------------------------------------*/ -/*! compute the inverse of a 3x3 matrix -*//*--------------------------------------------------------------------*/ -mat33 nifti_mat33_inverse( mat33 R ) /* inverse of 3x3 matrix */ -{ - double r11,r12,r13,r21,r22,r23,r31,r32,r33 , deti ; - mat33 Q ; - /* INPUT MATRIX: */ - r11 = R.m[0][0]; r12 = R.m[0][1]; r13 = R.m[0][2]; /* [ r11 r12 r13 ] */ - r21 = R.m[1][0]; r22 = R.m[1][1]; r23 = R.m[1][2]; /* [ r21 r22 r23 ] */ - r31 = R.m[2][0]; r32 = R.m[2][1]; r33 = R.m[2][2]; /* [ r31 r32 r33 ] */ - - deti = r11*r22*r33-r11*r32*r23-r21*r12*r33 - +r21*r32*r13+r31*r12*r23-r31*r22*r13 ; - - if( deti != 0.0l ) deti = 1.0l / deti ; - - Q.m[0][0] = (float)( deti*( r22*r33-r32*r23) ) ; - Q.m[0][1] = (float)( deti*(-r12*r33+r32*r13) ) ; - Q.m[0][2] = (float)( deti*( r12*r23-r22*r13) ) ; - - Q.m[1][0] = (float)( deti*(-r21*r33+r31*r23) ) ; - Q.m[1][1] = (float)( deti*( r11*r33-r31*r13) ) ; - Q.m[1][2] = (float)( deti*(-r11*r23+r21*r13) ) ; - - Q.m[2][0] = (float)( deti*( r21*r32-r31*r22) ) ; - Q.m[2][1] = (float)( deti*(-r11*r32+r31*r12) ) ; - Q.m[2][2] = (float)( deti*( r11*r22-r21*r12) ) ; - - return Q ; -} - -/*----------------------------------------------------------------------*/ -/*! compute the determinant of a 3x3 matrix -*//*--------------------------------------------------------------------*/ -float nifti_mat33_determ( mat33 R ) /* determinant of 3x3 matrix */ -{ - double r11,r12,r13,r21,r22,r23,r31,r32,r33 ; - /* INPUT MATRIX: */ - r11 = R.m[0][0]; r12 = R.m[0][1]; r13 = R.m[0][2]; /* [ r11 r12 r13 ] */ - r21 = R.m[1][0]; r22 = R.m[1][1]; r23 = R.m[1][2]; /* [ r21 r22 r23 ] */ - r31 = R.m[2][0]; r32 = R.m[2][1]; r33 = R.m[2][2]; /* [ r31 r32 r33 ] */ - - return (float)(r11*r22*r33-r11*r32*r23-r21*r12*r33 - +r21*r32*r13+r31*r12*r23-r31*r22*r13) ; -} - -/*----------------------------------------------------------------------*/ -/*! compute the max row norm of a 3x3 matrix -*//*--------------------------------------------------------------------*/ -float nifti_mat33_rownorm( mat33 A ) /* max row norm of 3x3 matrix */ -{ - float r1,r2,r3 ; - - r1 = (float)( fabs(A.m[0][0])+fabs(A.m[0][1])+fabs(A.m[0][2]) ) ; - r2 = (float)( fabs(A.m[1][0])+fabs(A.m[1][1])+fabs(A.m[1][2]) ) ; - r3 = (float)( fabs(A.m[2][0])+fabs(A.m[2][1])+fabs(A.m[2][2]) ) ; - if( r1 < r2 ) r1 = r2 ; - if( r1 < r3 ) r1 = r3 ; - return r1 ; -} - -/*----------------------------------------------------------------------*/ -/*! compute the max column norm of a 3x3 matrix -*//*--------------------------------------------------------------------*/ -float nifti_mat33_colnorm( mat33 A ) /* max column norm of 3x3 matrix */ -{ - float r1,r2,r3 ; - - r1 = (float)( fabs(A.m[0][0])+fabs(A.m[1][0])+fabs(A.m[2][0]) ) ; - r2 = (float)( fabs(A.m[0][1])+fabs(A.m[1][1])+fabs(A.m[2][1]) ) ; - r3 = (float)( fabs(A.m[0][2])+fabs(A.m[1][2])+fabs(A.m[2][2]) ) ; - if( r1 < r2 ) r1 = r2 ; - if( r1 < r3 ) r1 = r3 ; - return r1 ; -} - -/*----------------------------------------------------------------------*/ -/*! multiply 2 3x3 matrices -*//*--------------------------------------------------------------------*/ -mat33 nifti_mat33_mul( mat33 A , mat33 B ) /* multiply 2 3x3 matrices */ -{ - mat33 C ; int i,j ; - for( i=0 ; i < 3 ; i++ ) - for( j=0 ; j < 3 ; j++ ) - C.m[i][j] = A.m[i][0] * B.m[0][j] - + A.m[i][1] * B.m[1][j] - + A.m[i][2] * B.m[2][j] ; - return C ; -} - -/*---------------------------------------------------------------------------*/ -/*! polar decomposition of a 3x3 matrix - - This finds the closest orthogonal matrix to input A - (in both the Frobenius and L2 norms). - - Algorithm is that from NJ Higham, SIAM J Sci Stat Comput, 7:1160-1174. -*//*-------------------------------------------------------------------------*/ -mat33 nifti_mat33_polar( mat33 A ) -{ - mat33 X , Y , Z ; - float alp,bet,gam,gmi , dif=1.0f ; - int k=0 ; - - X = A ; - - /* force matrix to be nonsingular */ - - gam = nifti_mat33_determ(X) ; - while( gam == 0.0 ){ /* perturb matrix */ - gam = (float)( 0.00001 * ( 0.001 + nifti_mat33_rownorm(X) ) ) ; - X.m[0][0] += gam ; X.m[1][1] += gam ; X.m[2][2] += gam ; - gam = nifti_mat33_determ(X) ; - } - - while(1){ - Y = nifti_mat33_inverse(X) ; - if( dif > 0.3 ){ /* far from convergence */ - alp = (float)( sqrt( nifti_mat33_rownorm(X) * nifti_mat33_colnorm(X) ) ) ; - bet = (float)( sqrt( nifti_mat33_rownorm(Y) * nifti_mat33_colnorm(Y) ) ) ; - gam = (float)( sqrt( bet / alp ) ) ; - gmi = (float)( 1.0 / gam ) ; - } else { - gam = gmi = 1.0f ; /* close to convergence */ - } - Z.m[0][0] = (float)( 0.5 * ( gam*X.m[0][0] + gmi*Y.m[0][0] ) ) ; - Z.m[0][1] = (float)( 0.5 * ( gam*X.m[0][1] + gmi*Y.m[1][0] ) ) ; - Z.m[0][2] = (float)( 0.5 * ( gam*X.m[0][2] + gmi*Y.m[2][0] ) ) ; - Z.m[1][0] = (float)( 0.5 * ( gam*X.m[1][0] + gmi*Y.m[0][1] ) ) ; - Z.m[1][1] = (float)( 0.5 * ( gam*X.m[1][1] + gmi*Y.m[1][1] ) ) ; - Z.m[1][2] = (float)( 0.5 * ( gam*X.m[1][2] + gmi*Y.m[2][1] ) ) ; - Z.m[2][0] = (float)( 0.5 * ( gam*X.m[2][0] + gmi*Y.m[0][2] ) ) ; - Z.m[2][1] = (float)( 0.5 * ( gam*X.m[2][1] + gmi*Y.m[1][2] ) ) ; - Z.m[2][2] = (float)( 0.5 * ( gam*X.m[2][2] + gmi*Y.m[2][2] ) ) ; - - dif = (float)( fabs(Z.m[0][0]-X.m[0][0])+fabs(Z.m[0][1]-X.m[0][1]) - +fabs(Z.m[0][2]-X.m[0][2])+fabs(Z.m[1][0]-X.m[1][0]) - +fabs(Z.m[1][1]-X.m[1][1])+fabs(Z.m[1][2]-X.m[1][2]) - +fabs(Z.m[2][0]-X.m[2][0])+fabs(Z.m[2][1]-X.m[2][1]) - +fabs(Z.m[2][2]-X.m[2][2]) ); - - k = k+1 ; - if( k > 100 || dif < 3.e-6 ) break ; /* convergence or exhaustion */ - X = Z ; - } - - return Z ; -} - -/*---------------------------------------------------------------------------*/ -/*! compute the (closest) orientation from a 4x4 ijk->xyz tranformation matrix - - 
-   Input:  4x4 matrix that transforms (i,j,k) indexes to (x,y,z) coordinates,
-           where +x=Right, +y=Anterior, +z=Superior.
-           (Only the upper-left 3x3 corner of R is used herein.)
-   Output: 3 orientation codes that correspond to the closest "standard"
-           anatomical orientation of the (i,j,k) axes.
-   Method: Find which permutation of (x,y,z) has the smallest angle to the
-           (i,j,k) axes directions, which are the columns of the R matrix.
-   Errors: The codes returned will be zero.
-
-   For example, an axial volume might get return values of
-     *icod = NIFTI_R2L   (i axis is mostly Right to Left)
-     *jcod = NIFTI_P2A   (j axis is mostly Posterior to Anterior)
-     *kcod = NIFTI_I2S   (k axis is mostly Inferior to Superior)
-
- - \see "QUATERNION REPRESENTATION OF ROTATION MATRIX" in nifti1.h - - \see nifti_quatern_to_mat44, nifti_mat44_to_quatern, - nifti_make_orthog_mat44 -*//*-------------------------------------------------------------------------*/ -void nifti_mat44_to_orientation( mat44 R , int *icod, int *jcod, int *kcod ) -{ - float xi,xj,xk , yi,yj,yk , zi,zj,zk , val,detQ,detP ; - mat33 P , Q , M ; - int i,j,k=0,p,q,r , ibest,jbest,kbest,pbest,qbest,rbest ; - float vbest ; - - if( icod == NULL || jcod == NULL || kcod == NULL ) return ; /* bad */ - - *icod = *jcod = *kcod = 0 ; /* error returns, if sh*t happens */ - - /* load column vectors for each (i,j,k) direction from matrix */ - - /*-- i axis --*/ /*-- j axis --*/ /*-- k axis --*/ - - xi = R.m[0][0] ; xj = R.m[0][1] ; xk = R.m[0][2] ; - yi = R.m[1][0] ; yj = R.m[1][1] ; yk = R.m[1][2] ; - zi = R.m[2][0] ; zj = R.m[2][1] ; zk = R.m[2][2] ; - - /* normalize column vectors to get unit vectors along each ijk-axis */ - - /* normalize i axis */ - - val = (float)sqrt( xi*xi + yi*yi + zi*zi ) ; - if( val == 0.0 ) return ; /* stupid input */ - xi /= val ; yi /= val ; zi /= val ; - - /* normalize j axis */ - - val = (float)sqrt( xj*xj + yj*yj + zj*zj ) ; - if( val == 0.0 ) return ; /* stupid input */ - xj /= val ; yj /= val ; zj /= val ; - - /* orthogonalize j axis to i axis, if needed */ - - val = xi*xj + yi*yj + zi*zj ; /* dot product between i and j */ - if( fabs(val) > 1.e-4 ){ - xj -= val*xi ; yj -= val*yi ; zj -= val*zi ; - val = (float)sqrt( xj*xj + yj*yj + zj*zj ) ; /* must renormalize */ - if( val == 0.0 ) return ; /* j was parallel to i? */ - xj /= val ; yj /= val ; zj /= val ; - } - - /* normalize k axis; if it is zero, make it the cross product i x j */ - - val = (float)sqrt( xk*xk + yk*yk + zk*zk ) ; - if( val == 0.0 ){ xk = yi*zj-zi*yj; yk = zi*xj-zj*xi ; zk=xi*yj-yi*xj ; } - else { xk /= val ; yk /= val ; zk /= val ; } - - /* orthogonalize k to i */ - - val = xi*xk + yi*yk + zi*zk ; /* dot product between i and k */ - if( fabs(val) > 1.e-4 ){ - xk -= val*xi ; yk -= val*yi ; zk -= val*zi ; - val = (float)sqrt( xk*xk + yk*yk + zk*zk ) ; - if( val == 0.0 ) return ; /* bad */ - xk /= val ; yk /= val ; zk /= val ; - } - - /* orthogonalize k to j */ - - val = xj*xk + yj*yk + zj*zk ; /* dot product between j and k */ - if( fabs(val) > 1.e-4 ){ - xk -= val*xj ; yk -= val*yj ; zk -= val*zj ; - val = (float)sqrt( xk*xk + yk*yk + zk*zk ) ; - if( val == 0.0 ) return ; /* bad */ - xk /= val ; yk /= val ; zk /= val ; - } - - Q.m[0][0] = xi ; Q.m[0][1] = xj ; Q.m[0][2] = xk ; - Q.m[1][0] = yi ; Q.m[1][1] = yj ; Q.m[1][2] = yk ; - Q.m[2][0] = zi ; Q.m[2][1] = zj ; Q.m[2][2] = zk ; - - /* at this point, Q is the rotation matrix from the (i,j,k) to (x,y,z) axes */ - - detQ = nifti_mat33_determ( Q ) ; - if( detQ == 0.0 ) return ; /* shouldn't happen unless user is a DUFIS */ - - /* Build and test all possible +1/-1 coordinate permutation matrices P; - then find the P such that the rotation matrix M=PQ is closest to the - identity, in the sense of M having the smallest total rotation angle. */ - - /* Despite the formidable looking 6 nested loops, there are - only 3*3*3*2*2*2 = 216 passes, which will run very quickly. */ - - vbest = -666.0f ; ibest=pbest=qbest=rbest=1 ; jbest=2 ; kbest=3 ; - for( i=1 ; i <= 3 ; i++ ){ /* i = column number to use for row #1 */ - for( j=1 ; j <= 3 ; j++ ){ /* j = column number to use for row #2 */ - if( i == j ) continue ; - for( k=1 ; k <= 3 ; k++ ){ /* k = column number to use for row #3 */ - if( i == k || j == k ) continue ; - P.m[0][0] = P.m[0][1] = P.m[0][2] = - P.m[1][0] = P.m[1][1] = P.m[1][2] = - P.m[2][0] = P.m[2][1] = P.m[2][2] = 0.0f ; - for( p=-1 ; p <= 1 ; p+=2 ){ /* p,q,r are -1 or +1 */ - for( q=-1 ; q <= 1 ; q+=2 ){ /* and go into rows #1,2,3 */ - for( r=-1 ; r <= 1 ; r+=2 ){ - P.m[0][i-1] = p ; P.m[1][j-1] = q ; P.m[2][k-1] = r ; - detP = nifti_mat33_determ(P) ; /* sign of permutation */ - if( detP * detQ <= 0.0 ) continue ; /* doesn't match sign of Q */ - M = nifti_mat33_mul(P,Q) ; - - /* angle of M rotation = 2.0*acos(0.5*sqrt(1.0+trace(M))) */ - /* we want largest trace(M) == smallest angle == M nearest to I */ - - val = M.m[0][0] + M.m[1][1] + M.m[2][2] ; /* trace */ - if( val > vbest ){ - vbest = val ; - ibest = i ; jbest = j ; kbest = k ; - pbest = p ; qbest = q ; rbest = r ; - } - }}}}}} - - /* At this point ibest is 1 or 2 or 3; pbest is -1 or +1; etc. - - The matrix P that corresponds is the best permutation approximation - to Q-inverse; that is, P (approximately) takes (x,y,z) coordinates - to the (i,j,k) axes. - - For example, the first row of P (which contains pbest in column ibest) - determines the way the i axis points relative to the anatomical - (x,y,z) axes. If ibest is 2, then the i axis is along the y axis, - which is direction P2A (if pbest > 0) or A2P (if pbest < 0). - - So, using ibest and pbest, we can assign the output code for - the i axis. Mutatis mutandis for the j and k axes, of course. */ - - switch( ibest*pbest ){ - case 1: i = NIFTI_L2R ; break ; - case -1: i = NIFTI_R2L ; break ; - case 2: i = NIFTI_P2A ; break ; - case -2: i = NIFTI_A2P ; break ; - case 3: i = NIFTI_I2S ; break ; - case -3: i = NIFTI_S2I ; break ; - } - - switch( jbest*qbest ){ - case 1: j = NIFTI_L2R ; break ; - case -1: j = NIFTI_R2L ; break ; - case 2: j = NIFTI_P2A ; break ; - case -2: j = NIFTI_A2P ; break ; - case 3: j = NIFTI_I2S ; break ; - case -3: j = NIFTI_S2I ; break ; - } - - switch( kbest*rbest ){ - case 1: k = NIFTI_L2R ; break ; - case -1: k = NIFTI_R2L ; break ; - case 2: k = NIFTI_P2A ; break ; - case -2: k = NIFTI_A2P ; break ; - case 3: k = NIFTI_I2S ; break ; - case -3: k = NIFTI_S2I ; break ; - } - - *icod = i ; *jcod = j ; *kcod = k ; return ; -} - -/*---------------------------------------------------------------------------*/ -/* Routines to swap byte arrays in various ways: - - 2 at a time: ab -> ba [short] - - 4 at a time: abcd -> dcba [int, float] - - 8 at a time: abcdDCBA -> ABCDdcba [long long, double] - - 16 at a time: abcdefghHGFEDCBA -> ABCDEFGHhgfedcba [long double] ------------------------------------------------------------------------------*/ - -/*----------------------------------------------------------------------*/ -/*! swap each byte pair from the given list of n pairs - * - * Due to alignment of structures at some architectures (e.g. on ARM), - * stick to char varaibles. - * Fixes http://bugs.debian.org/446893 Yaroslav - * -*//*--------------------------------------------------------------------*/ -void nifti_swap_2bytes( size_t n , void *ar ) /* 2 bytes at a time */ -{ - size_t ii ; - unsigned char * cp1 = (unsigned char *)ar, * cp2 ; - unsigned char tval; - - for( ii=0 ; ii < n ; ii++ ){ - cp2 = cp1 + 1; - tval = *cp1; *cp1 = *cp2; *cp2 = tval; - cp1 += 2; - } - return ; -} - -/*----------------------------------------------------------------------*/ -/*! swap 4 bytes at a time from the given list of n sets of 4 bytes -*//*--------------------------------------------------------------------*/ -void nifti_swap_4bytes( size_t n , void *ar ) /* 4 bytes at a time */ -{ - size_t ii ; - unsigned char * cp0 = (unsigned char *)ar, * cp1, * cp2 ; - unsigned char tval ; - - for( ii=0 ; ii < n ; ii++ ){ - cp1 = cp0; cp2 = cp0+3; - tval = *cp1; *cp1 = *cp2; *cp2 = tval; - cp1++; cp2--; - tval = *cp1; *cp1 = *cp2; *cp2 = tval; - cp0 += 4; - } - return ; -} - -/*----------------------------------------------------------------------*/ -/*! swap 8 bytes at a time from the given list of n sets of 8 bytes - * - * perhaps use this style for the general Nbytes, as Yaroslav suggests -*//*--------------------------------------------------------------------*/ -void nifti_swap_8bytes( size_t n , void *ar ) /* 8 bytes at a time */ -{ - size_t ii ; - unsigned char * cp0 = (unsigned char *)ar, * cp1, * cp2 ; - unsigned char tval ; - - for( ii=0 ; ii < n ; ii++ ){ - cp1 = cp0; cp2 = cp0+7; - while ( cp2 > cp1 ) /* unroll? */ - { - tval = *cp1 ; *cp1 = *cp2 ; *cp2 = tval ; - cp1++; cp2--; - } - cp0 += 8; - } - return ; -} - -/*----------------------------------------------------------------------*/ -/*! swap 16 bytes at a time from the given list of n sets of 16 bytes -*//*--------------------------------------------------------------------*/ -void nifti_swap_16bytes( size_t n , void *ar ) /* 16 bytes at a time */ -{ - size_t ii ; - unsigned char * cp0 = (unsigned char *)ar, * cp1, * cp2 ; - unsigned char tval ; - - for( ii=0 ; ii < n ; ii++ ){ - cp1 = cp0; cp2 = cp0+15; - while ( cp2 > cp1 ) - { - tval = *cp1 ; *cp1 = *cp2 ; *cp2 = tval ; - cp1++; cp2--; - } - cp0 += 16; - } - return ; -} - -#if 0 /* not important: save for version update 6 Jul 2010 [rickr] */ - -/*----------------------------------------------------------------------*/ -/*! generic: swap siz bytes at a time from the given list of n sets -*//*--------------------------------------------------------------------*/ -void nifti_swap_bytes( size_t n , int siz , void *ar ) -{ - size_t ii ; - unsigned char * cp0 = (unsigned char *)ar, * cp1, * cp2 ; - unsigned char tval ; - - for( ii=0 ; ii < n ; ii++ ){ - cp1 = cp0; cp2 = cp0+(siz-1); - while ( cp2 > cp1 ) - { - tval = *cp1 ; *cp1 = *cp2 ; *cp2 = tval ; - cp1++; cp2--; - } - cp0 += siz; - } - return ; -} -#endif - -/*---------------------------------------------------------------------------*/ - -/*----------------------------------------------------------------------*/ -/*! based on siz, call the appropriate nifti_swap_Nbytes() function -*//*--------------------------------------------------------------------*/ -void nifti_swap_Nbytes( size_t n , int siz , void *ar ) /* subsuming case */ -{ - switch( siz ){ - case 2: nifti_swap_2bytes ( n , ar ) ; break ; - case 4: nifti_swap_4bytes ( n , ar ) ; break ; - case 8: nifti_swap_8bytes ( n , ar ) ; break ; - case 16: nifti_swap_16bytes( n , ar ) ; break ; - default: /* nifti_swap_bytes ( n , siz, ar ) ; */ - fprintf(stderr,"** NIfTI: cannot swap in %d byte blocks\n", siz); - break ; - } - return ; -} - - -/*-------------------------------------------------------------------------*/ -/*! Byte swap NIFTI-1 file header in various places and ways. - - If is_nifti, swap all (even UNUSED) fields of NIfTI header. - Else, swap as a nifti_analyze75 struct. -*//*---------------------------------------------------------------------- */ -void swap_nifti_header( struct nifti_1_header *h , int is_nifti ) -{ - - /* if ANALYZE, swap as such and return */ - if( ! is_nifti ) { - nifti_swap_as_analyze((nifti_analyze75 *)h); - return; - } - - /* otherwise, swap all NIFTI fields */ - - nifti_swap_4bytes(1, &h->sizeof_hdr); - nifti_swap_4bytes(1, &h->extents); - nifti_swap_2bytes(1, &h->session_error); - - nifti_swap_2bytes(8, h->dim); - nifti_swap_4bytes(1, &h->intent_p1); - nifti_swap_4bytes(1, &h->intent_p2); - nifti_swap_4bytes(1, &h->intent_p3); - - nifti_swap_2bytes(1, &h->intent_code); - nifti_swap_2bytes(1, &h->datatype); - nifti_swap_2bytes(1, &h->bitpix); - nifti_swap_2bytes(1, &h->slice_start); - - nifti_swap_4bytes(8, h->pixdim); - - nifti_swap_4bytes(1, &h->vox_offset); - nifti_swap_4bytes(1, &h->scl_slope); - nifti_swap_4bytes(1, &h->scl_inter); - nifti_swap_2bytes(1, &h->slice_end); - - nifti_swap_4bytes(1, &h->cal_max); - nifti_swap_4bytes(1, &h->cal_min); - nifti_swap_4bytes(1, &h->slice_duration); - nifti_swap_4bytes(1, &h->toffset); - nifti_swap_4bytes(1, &h->glmax); - nifti_swap_4bytes(1, &h->glmin); - - nifti_swap_2bytes(1, &h->qform_code); - nifti_swap_2bytes(1, &h->sform_code); - - nifti_swap_4bytes(1, &h->quatern_b); - nifti_swap_4bytes(1, &h->quatern_c); - nifti_swap_4bytes(1, &h->quatern_d); - nifti_swap_4bytes(1, &h->qoffset_x); - nifti_swap_4bytes(1, &h->qoffset_y); - nifti_swap_4bytes(1, &h->qoffset_z); - - nifti_swap_4bytes(4, h->srow_x); - nifti_swap_4bytes(4, h->srow_y); - nifti_swap_4bytes(4, h->srow_z); - - return ; -} - -/*-------------------------------------------------------------------------*/ -/*! Byte swap as an ANALYZE 7.5 header - * - * return non-zero on failure -*//*---------------------------------------------------------------------- */ -int nifti_swap_as_analyze( nifti_analyze75 * h ) -{ - if( !h ) return 1; - - nifti_swap_4bytes(1, &h->sizeof_hdr); - nifti_swap_4bytes(1, &h->extents); - nifti_swap_2bytes(1, &h->session_error); - - nifti_swap_2bytes(8, h->dim); - nifti_swap_2bytes(1, &h->unused8); - nifti_swap_2bytes(1, &h->unused9); - nifti_swap_2bytes(1, &h->unused10); - nifti_swap_2bytes(1, &h->unused11); - nifti_swap_2bytes(1, &h->unused12); - nifti_swap_2bytes(1, &h->unused13); - nifti_swap_2bytes(1, &h->unused14); - - nifti_swap_2bytes(1, &h->datatype); - nifti_swap_2bytes(1, &h->bitpix); - nifti_swap_2bytes(1, &h->dim_un0); - - nifti_swap_4bytes(8, h->pixdim); - - nifti_swap_4bytes(1, &h->vox_offset); - nifti_swap_4bytes(1, &h->funused1); - nifti_swap_4bytes(1, &h->funused2); - nifti_swap_4bytes(1, &h->funused3); - - nifti_swap_4bytes(1, &h->cal_max); - nifti_swap_4bytes(1, &h->cal_min); - nifti_swap_4bytes(1, &h->compressed); - nifti_swap_4bytes(1, &h->verified); - - nifti_swap_4bytes(1, &h->glmax); - nifti_swap_4bytes(1, &h->glmin); - - nifti_swap_4bytes(1, &h->views); - nifti_swap_4bytes(1, &h->vols_added); - nifti_swap_4bytes(1, &h->start_field); - nifti_swap_4bytes(1, &h->field_skip); - - nifti_swap_4bytes(1, &h->omax); - nifti_swap_4bytes(1, &h->omin); - nifti_swap_4bytes(1, &h->smax); - nifti_swap_4bytes(1, &h->smin); - - return 0; -} - -/*-------------------------------------------------------------------------*/ -/*! OLD VERSION of swap_nifti_header (left for undo/compare operations) - - Byte swap NIFTI-1 file header in various places and ways. - - If is_nifti is nonzero, will also swap the NIFTI-specific - components of the header; otherwise, only the components - common to NIFTI and ANALYZE will be swapped. -*//*---------------------------------------------------------------------- */ -void old_swap_nifti_header( struct nifti_1_header *h , int is_nifti ) -{ - /* this stuff is always present, for ANALYZE and NIFTI */ - - swap_4(h->sizeof_hdr) ; - nifti_swap_2bytes( 8 , h->dim ) ; - nifti_swap_4bytes( 8 , h->pixdim ) ; - - swap_2(h->datatype) ; - swap_2(h->bitpix) ; - - swap_4(h->vox_offset); swap_4(h->cal_max); swap_4(h->cal_min); - - /* this stuff is NIFTI specific */ - - if( is_nifti ){ - swap_4(h->intent_p1); swap_4(h->intent_p2); swap_4(h->intent_p3); - swap_2(h->intent_code); - - swap_2(h->slice_start); swap_2(h->slice_end); - swap_4(h->scl_slope); swap_4(h->scl_inter); - swap_4(h->slice_duration); swap_4(h->toffset); - - swap_2(h->qform_code); swap_2(h->sform_code); - swap_4(h->quatern_b); swap_4(h->quatern_c); swap_4(h->quatern_d); - swap_4(h->qoffset_x); swap_4(h->qoffset_y); swap_4(h->qoffset_z); - nifti_swap_4bytes(4,h->srow_x); - nifti_swap_4bytes(4,h->srow_y); - nifti_swap_4bytes(4,h->srow_z); - } - return ; -} - - -#define USE_STAT -#ifdef USE_STAT -/*---------------------------------------------------------------------------*/ -/* Return the file length (0 if file not found or has no contents). - This is a Unix-specific function, since it uses stat(). ------------------------------------------------------------------------------*/ -#include -#include - -/*---------------------------------------------------------------------------*/ -/*! return the size of a file, in bytes - - \return size of file on success, -1 on error or no file - - changed to return int, -1 means no file or error 20 Dec 2004 [rickr] -*//*-------------------------------------------------------------------------*/ -int nifti_get_filesize( const char *pathname ) -{ - struct stat buf ; int ii ; - - if( pathname == NULL || *pathname == '\0' ) return -1 ; - ii = stat( pathname , &buf ); if( ii != 0 ) return -1 ; - return (unsigned int)buf.st_size ; -} - -#else /*---------- non-Unix version of the above, less efficient -----------*/ - -int nifti_get_filesize( const char *pathname ) -{ - znzFile fp ; int len ; - - if( pathname == NULL || *pathname == '\0' ) return -1 ; - fp = znzopen(pathname,"rb",0); if( znz_isnull(fp) ) return -1 ; - znzseek(fp,0L,SEEK_END) ; len = znztell(fp) ; - znzclose(fp) ; return len ; -} - -#endif /* USE_STAT */ - - -/*----------------------------------------------------------------------*/ -/*! return the total volume size, in bytes - - This is computed as nvox * nbyper. -*//*--------------------------------------------------------------------*/ -size_t nifti_get_volsize(const nifti_image *nim) -{ - return (size_t)(nim->nbyper) * (size_t)(nim->nvox) ; /* total bytes */ -} - - -/*--------------------------------------------------------------------------*/ -/* Support functions for filenames in read and write - - allows for gzipped files -*/ - - -/*----------------------------------------------------------------------*/ -/*! simple check for file existence - - \return 1 on existence, 0 otherwise -*//*--------------------------------------------------------------------*/ -int nifti_fileexists(const char* fname) -{ - znzFile fp; - fp = znzopen( fname , "rb" , 1 ) ; - if( !znz_isnull(fp) ) { znzclose(fp); return 1; } - return 0; /* fp is NULL */ -} - -/*----------------------------------------------------------------------*/ -/*! return whether the filename is valid - - Note: uppercase extensions are now valid. 27 Apr 2009 [rickr] - - The name is considered valid if the file basename has length greater than - zero, AND one of the valid nifti extensions is provided. - fname input | return | - =============================== - "myimage" | 0 | - "myimage.tif" | 0 | - "myimage.tif.gz" | 0 | - "myimage.nii" | 1 | - ".nii" | 0 | - ".myhiddenimage" | 0 | - ".myhiddenimage.nii" | 1 | -*//*--------------------------------------------------------------------*/ -int nifti_is_complete_filename(const char* fname) -{ - const char * ext; - - /* check input file(s) for sanity */ - if( fname == NULL || *fname == '\0' ){ - if ( g_opts.debug > 1 ) - fprintf(stderr,"-- empty filename in nifti_validfilename()\n"); - return 0; - } - - ext = nifti_find_file_extension(fname); - if ( ext == NULL ) { /*Invalid extension given */ - if ( g_opts.debug > 0 ) - fprintf(stderr,"-- no nifti valid extension for filename '%s'\n", fname); - return 0; - } - - if ( ext && ext == fname ) { /* then no filename prefix */ - if ( g_opts.debug > 0 ) - fprintf(stderr,"-- no prefix for filename '%s'\n", fname); - return 0; - } - return 1; -} - -/*----------------------------------------------------------------------*/ -/*! return whether the filename is valid - - Allow uppercase extensions as valid. 27 Apr 2009 [rickr] - Any .gz extension case must match the base extension case. - - The name is considered valid if its length is positive, excluding - any nifti filename extension. - fname input | return | result of nifti_makebasename - ==================================================================== - "myimage" | 1 | "myimage" - "myimage.tif" | 1 | "myimage.tif" - "myimage.tif.gz" | 1 | "myimage.tif" - "myimage.nii" | 1 | "myimage" - ".nii" | 0 | - ".myhiddenimage" | 1 | ".myhiddenimage" - ".myhiddenimage.nii | 1 | ".myhiddenimage" -*//*--------------------------------------------------------------------*/ -int nifti_validfilename(const char* fname) -{ - const char * ext; - - /* check input file(s) for sanity */ - if( fname == NULL || *fname == '\0' ){ - if ( g_opts.debug > 1 ) - fprintf(stderr,"-- empty filename in nifti_validfilename()\n"); - return 0; - } - - ext = nifti_find_file_extension(fname); - - if ( ext && ext == fname ) { /* then no filename prefix */ - if ( g_opts.debug > 0 ) - fprintf(stderr,"-- no prefix for filename '%s'\n", fname); - return 0; - } - - return 1; -} - -/*----------------------------------------------------------------------*/ -/*! check the end of the filename for a valid nifti extension - - Valid extensions are currently .nii, .hdr, .img, .nia, - or any of them followed by .gz. Note that '.' is part of - the extension. - - Uppercase extensions are also valid, but not mixed case. - - \return a pointer to the extension substring within the original - function input parameter name, or NULL if not found. - \caution Note that if the input parameter is is immutabale - (i.e. a const char *) then this function performs an - implicit casting away of the mutability constraint and - the return parameter will appear as a mutable - even though it is part of the immuttable string. -*//*--------------------------------------------------------------------*/ -char * nifti_find_file_extension( const char * name ) -{ - const char * ext; - char extcopy[8]; - int len; - char extnii[8] = ".nii"; /* modifiable, for possible uppercase */ - char exthdr[8] = ".hdr"; /* (leave space for .gz) */ - char extimg[8] = ".img"; - char extnia[8] = ".nia"; - char extgz[4] = ".gz"; - char * elist[4] = { NULL, NULL, NULL, NULL}; - - /* stupid compiler... */ - elist[0] = extnii; elist[1] = exthdr; elist[2] = extimg; elist[3] = extnia; - - if ( ! name ) return NULL; - - len = (int)strlen(name); - if ( len < 4 ) return NULL; - - ext = name + len - 4; - - /* make manipulation copy, and possibly convert to lowercase */ - strcpy(extcopy, ext); - if( g_opts.allow_upper_fext ) make_lowercase(extcopy); - - /* if it look like a basic extension, fail or return it */ - if( compare_strlist(extcopy, elist, 4) >= 0 ) { - if( is_mixedcase(ext) ) { - fprintf(stderr,"** mixed case extension '%s' is not valid\n", ext); - return NULL; - } - else return (char *)ext; /* Cast away the constness of the input parameter */ - } - -#ifdef HAVE_ZLIB - if ( len < 7 ) return NULL; - - ext = name + len - 7; - - /* make manipulation copy, and possibly convert to lowercase */ - strcpy(extcopy, ext); - if( g_opts.allow_upper_fext ) make_lowercase(extcopy); - - /* go after .gz extensions using the modifiable strings */ - strcat(elist[0], extgz); strcat(elist[1], extgz); strcat(elist[2], extgz); - - if( compare_strlist(extcopy, elist, 3) >= 0 ) { - if( is_mixedcase(ext) ) { - fprintf(stderr,"** mixed case extension '%s' is not valid\n", ext); - return NULL; - } - else return (char *)ext; /* Cast away the constness of the input parameter */ - } - -#endif - - if( g_opts.debug > 1 ) - fprintf(stderr,"** find_file_ext: failed for name '%s'\n", name); - - return NULL; -} - -/*----------------------------------------------------------------------*/ -/*! return whether the filename ends in ".gz" -*//*--------------------------------------------------------------------*/ -int nifti_is_gzfile(const char* fname) -{ - /* return true if the filename ends with .gz */ - if (fname == NULL) { return 0; } -#ifdef HAVE_ZLIB - { /* just so len doesn't generate compile warning */ - int len; - len = (int)strlen(fname); - if (len < 3) return 0; /* so we don't search before the name */ - if (fileext_compare(fname + strlen(fname) - 3,".gz")==0) { return 1; } - } -#endif - return 0; -} - -/*----------------------------------------------------------------------*/ -/*! return whether the given library was compiled with HAVE_ZLIB set -*//*--------------------------------------------------------------------*/ -int nifti_compiled_with_zlib(void) -{ -#ifdef HAVE_ZLIB - return 1; -#else - return 0; -#endif -} - -/*----------------------------------------------------------------------*/ -/*! duplicate the filename, while clearing any extension - - This allocates memory for basename which should eventually be freed. -*//*--------------------------------------------------------------------*/ -char * nifti_makebasename(const char* fname) -{ - char *basename; - const char *ext; - - basename=nifti_strdup(fname); - - ext = nifti_find_file_extension(basename); - if ( ext ) - { - basename[strlen(basename)-strlen(ext)] = '\0'; /* clear out extension */ - } - - return basename; /* in either case */ -} - -/*----------------------------------------------------------------------*/ -/*! set nifti's global debug level, for status reporting - - - 0 : quiet, nothing is printed to the terminal, but errors - - 1 : normal execution (the default) - - 2, 3 : more details -*//*--------------------------------------------------------------------*/ -void nifti_set_debug_level( int level ) -{ - g_opts.debug = level; -} - -/*----------------------------------------------------------------------*/ -/*! set nifti's global skip_blank_ext flag 5 Sep 2006 [rickr] - - explicitly set to 0 or 1 -*//*--------------------------------------------------------------------*/ -void nifti_set_skip_blank_ext( int skip ) -{ - g_opts.skip_blank_ext = skip ? 1 : 0; -} - -/*----------------------------------------------------------------------*/ -/*! set nifti's global allow_upper_fext flag 28 Apr 2009 [rickr] - - explicitly set to 0 or 1 -*//*--------------------------------------------------------------------*/ -void nifti_set_allow_upper_fext( int allow ) -{ - g_opts.allow_upper_fext = allow ? 1 : 0; -} - -/*----------------------------------------------------------------------*/ -/*! check current directory for existing header file - - \return filename of header on success and NULL if no appropriate file - could be found - - If fname has an uppercase extension, check for uppercase files. - - NB: it allocates memory for hdrname which should be freed - when no longer required -*//*-------------------------------------------------------------------*/ -char * nifti_findhdrname(const char* fname) -{ - char *basename, *hdrname; - const char *ext; - char elist[2][5] = { ".hdr", ".nii" }; - char extzip[4] = ".gz"; - int efirst = 1; /* init to .nii extension */ - int eisupper = 0; /* init to lowercase extensions */ - - /**- check input file(s) for sanity */ - if( !nifti_validfilename(fname) ) return NULL; - - basename = nifti_makebasename(fname); - if( !basename ) return NULL; /* only on string alloc failure */ - - /**- return filename if it has a valid extension and exists - (except if it is an .img file (and maybe .gz)) */ - ext = nifti_find_file_extension(fname); - - if( ext ) eisupper = is_uppercase(ext); /* do we look for uppercase? */ - - /* if the file exists and is a valid header name (not .img), return it */ - if ( ext && nifti_fileexists(fname) ) { - /* allow for uppercase extension */ - if ( fileext_n_compare(ext,".img",4) != 0 ){ - hdrname = nifti_strdup(fname); - free(basename); - return hdrname; - } else - efirst = 0; /* note for below */ - } - - /* So the requested name is a basename, contains .img, or does not exist. */ - /* In any case, use basename. */ - - /**- if .img, look for .hdr, .hdr.gz, .nii, .nii.gz, in that order */ - /**- else, look for .nii, .nii.gz, .hdr, .hdr.gz, in that order */ - - /* if we get more extension choices, this could be a loop */ - - /* note: efirst is 0 in the case of ".img" */ - - /* if the user passed an uppercase entension (.IMG), search for uppercase */ - if( eisupper ) { - make_uppercase(elist[0]); - make_uppercase(elist[1]); - make_uppercase(extzip); - } - - hdrname = (char *)calloc(sizeof(char),strlen(basename)+8); - if( !hdrname ){ - fprintf(stderr,"** nifti_findhdrname: failed to alloc hdrname\n"); - free(basename); - return NULL; - } - - strcpy(hdrname,basename); - strcat(hdrname,elist[efirst]); - if (nifti_fileexists(hdrname)) { free(basename); return hdrname; } -#ifdef HAVE_ZLIB - strcat(hdrname,extzip); - if (nifti_fileexists(hdrname)) { free(basename); return hdrname; } -#endif - - /* okay, try the other possibility */ - - efirst = 1 - efirst; - - strcpy(hdrname,basename); - strcat(hdrname,elist[efirst]); - if (nifti_fileexists(hdrname)) { free(basename); return hdrname; } -#ifdef HAVE_ZLIB - strcat(hdrname,extzip); - if (nifti_fileexists(hdrname)) { free(basename); return hdrname; } -#endif - - /**- if nothing has been found, return NULL */ - free(basename); - free(hdrname); - return NULL; -} - - -/*------------------------------------------------------------------------*/ -/*! check current directory for existing image file - - \param fname filename to check for - \nifti_type nifti_type for dataset - this determines whether to - first check for ".nii" or ".img" (since both may exist) - - \return filename of data/img file on success and NULL if no appropriate - file could be found - - If fname has a valid, uppercase extension, apply all extensions as - uppercase. - - NB: it allocates memory for the image filename, which should be freed - when no longer required -*//*---------------------------------------------------------------------*/ -char * nifti_findimgname(const char* fname , int nifti_type) -{ - /* store all extensions as strings, in case we need to go uppercase */ - char *basename, *imgname, elist[2][5] = { ".nii", ".img" }; - char extzip[4] = ".gz"; - char extnia[5] = ".nia"; - const char *ext; - int first; /* first extension to use */ - - /* check input file(s) for sanity */ - if( !nifti_validfilename(fname) ) return NULL; - - basename = nifti_makebasename(fname); - imgname = (char *)calloc(sizeof(char),strlen(basename)+8); - if( !imgname ){ - fprintf(stderr,"** nifti_findimgname: failed to alloc imgname\n"); - free(basename); - return NULL; - } - - /* if we are looking for uppercase, apply the fact now */ - ext = nifti_find_file_extension(fname); - if( ext && is_uppercase(ext) ) { - make_uppercase(elist[0]); - make_uppercase(elist[1]); - make_uppercase(extzip); - make_uppercase(extnia); - } - - /* only valid extension for ASCII type is .nia, handle first */ - if( nifti_type == NIFTI_FTYPE_ASCII ){ - strcpy(imgname,basename); - strcat(imgname,extnia); - if (nifti_fileexists(imgname)) { free(basename); return imgname; } - - } else { - - /**- test for .nii and .img (don't assume input type from image type) */ - /**- if nifti_type = 1, check for .nii first, else .img first */ - - /* if we get 3 or more extensions, can make a loop here... */ - - if (nifti_type == NIFTI_FTYPE_NIFTI1_1) first = 0; /* should match .nii */ - else first = 1; /* should match .img */ - - strcpy(imgname,basename); - strcat(imgname,elist[first]); - if (nifti_fileexists(imgname)) { free(basename); return imgname; } -#ifdef HAVE_ZLIB /* then also check for .gz */ - strcat(imgname,extzip); - if (nifti_fileexists(imgname)) { free(basename); return imgname; } -#endif - - /* failed to find image file with expected extension, try the other */ - - strcpy(imgname,basename); - strcat(imgname,elist[1-first]); /* can do this with only 2 choices */ - if (nifti_fileexists(imgname)) { free(basename); return imgname; } -#ifdef HAVE_ZLIB /* then also check for .gz */ - strcat(imgname,extzip); - if (nifti_fileexists(imgname)) { free(basename); return imgname; } -#endif - } - - /**- if nothing has been found, return NULL */ - free(basename); - free(imgname); - return NULL; -} - - -/*----------------------------------------------------------------------*/ -/*! creates a filename for storing the header, based on nifti_type - - \param prefix - this will be copied before the suffix is added - \param nifti_type - determines the extension, unless one is in prefix - \param check - check for existence (fail condition) - \param comp - add .gz for compressed name - - Note that if prefix provides a file suffix, nifti_type is not used. - - NB: this allocates memory which should be freed - - \sa nifti_set_filenames -*//*-------------------------------------------------------------------*/ -char * nifti_makehdrname(const char * prefix, int nifti_type, int check, - int comp) -{ - char * iname; - const char * ext; - char extnii[5] = ".nii"; /* modifiable, for possible uppercase */ - char exthdr[5] = ".hdr"; - char extimg[5] = ".img"; - char extnia[5] = ".nia"; - char extgz[5] = ".gz"; - - if( !nifti_validfilename(prefix) ) return NULL; - - /* add space for extension, optional ".gz", and null char */ - iname = (char *)calloc(sizeof(char),strlen(prefix)+8); - if( !iname ){ fprintf(stderr,"** small malloc failure!\n"); return NULL; } - strcpy(iname, prefix); - - /* use any valid extension */ - if( (ext = nifti_find_file_extension(iname)) != NULL ){ - /* if uppercase, convert all extensions */ - if( is_uppercase(ext) ) { - make_uppercase(extnii); - make_uppercase(exthdr); - make_uppercase(extimg); - make_uppercase(extnia); - make_uppercase(extgz); - } - - if( strncmp(ext,extimg,4) == 0 ) - { - memcpy(&(iname[strlen(iname)-strlen(ext)]),exthdr,4); /* then convert img name to hdr */ - } - } - /* otherwise, make one up */ - else if( nifti_type == NIFTI_FTYPE_NIFTI1_1 ) strcat(iname, extnii); - else if( nifti_type == NIFTI_FTYPE_ASCII ) strcat(iname, extnia); - else strcat(iname, exthdr); - -#ifdef HAVE_ZLIB /* if compression is requested, make sure of suffix */ - if( comp && (!ext || !strstr(iname,extgz)) ) strcat(iname,extgz); -#endif - - /* check for existence failure */ - if( check && nifti_fileexists(iname) ){ - fprintf(stderr,"** failure: header file '%s' already exists\n",iname); - free(iname); - return NULL; - } - - if(g_opts.debug > 2) fprintf(stderr,"+d made header filename '%s'\n", iname); - - return iname; -} - - -/*----------------------------------------------------------------------*/ -/*! creates a filename for storing the image, based on nifti_type - - \param prefix - this will be copied before the suffix is added - \param nifti_type - determines the extension, unless provided by prefix - \param check - check for existence (fail condition) - \param comp - add .gz for compressed name - - Note that if prefix provides a file suffix, nifti_type is not used. - - NB: it allocates memory which should be freed - - \sa nifti_set_filenames -*//*-------------------------------------------------------------------*/ -char * nifti_makeimgname(const char * prefix, int nifti_type, int check, - int comp) -{ - char * iname; - const char * ext; - char extnii[5] = ".nii"; /* modifiable, for possible uppercase */ - char exthdr[5] = ".hdr"; - char extimg[5] = ".img"; - char extnia[5] = ".nia"; - char extgz[5] = ".gz"; - - if( !nifti_validfilename(prefix) ) return NULL; - - /* add space for extension, optional ".gz", and null char */ - iname = (char *)calloc(sizeof(char),strlen(prefix)+8); - if( !iname ){ fprintf(stderr,"** small malloc failure!\n"); return NULL; } - strcpy(iname, prefix); - - /* use any valid extension */ - if( (ext = nifti_find_file_extension(iname)) != NULL ){ - /* if uppercase, convert all extensions */ - if( is_uppercase(ext) ) { - make_uppercase(extnii); - make_uppercase(exthdr); - make_uppercase(extimg); - make_uppercase(extnia); - make_uppercase(extgz); - } - - if( strncmp(ext,exthdr,4) == 0 ) - { - memcpy(&(iname[strlen(iname)-strlen(ext)]),extimg,4); /* then convert hdr name to img */ - } - } - /* otherwise, make one up */ - else if( nifti_type == NIFTI_FTYPE_NIFTI1_1 ) strcat(iname, extnii); - else if( nifti_type == NIFTI_FTYPE_ASCII ) strcat(iname, extnia); - else strcat(iname, extimg); - -#ifdef HAVE_ZLIB /* if compression is requested, make sure of suffix */ - if( comp && (!ext || !strstr(iname,extgz)) ) strcat(iname,extgz); -#endif - - /* check for existence failure */ - if( check && nifti_fileexists(iname) ){ - fprintf(stderr,"** failure: image file '%s' already exists\n",iname); - free(iname); - return NULL; - } - - if( g_opts.debug > 2 ) fprintf(stderr,"+d made image filename '%s'\n",iname); - - return iname; -} - - -/*----------------------------------------------------------------------*/ -/*! create and set new filenames, based on prefix and image type - - \param nim pointer to nifti_image in which to set filenames - \param prefix (required) prefix for output filenames - \param check check for previous existence of filename - (existence is an error condition) - \param set_byte_order flag to set nim->byteorder here - (this is probably a logical place to do so) - - \return 0 on successful update - - \warning this will free() any existing names and create new ones - - \sa nifti_makeimgname, nifti_makehdrname, nifti_type_and_names_match -*//*--------------------------------------------------------------------*/ -int nifti_set_filenames( nifti_image * nim, const char * prefix, int check, - int set_byte_order ) -{ - int comp = nifti_is_gzfile(prefix); - - if( !nim || !prefix ){ - fprintf(stderr,"** nifti_set_filenames, bad params %p, %p\n", - (void *)nim,prefix); - return -1; - } - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d modifying output filenames using prefix %s\n", prefix); - - if( nim->fname ) free(nim->fname); - if( nim->iname ) free(nim->iname); - nim->fname = nifti_makehdrname(prefix, nim->nifti_type, check, comp); - nim->iname = nifti_makeimgname(prefix, nim->nifti_type, check, comp); - if( !nim->fname || !nim->iname ){ - LNI_FERR("nifti_set_filename","failed to set prefix for",prefix); - return -1; - } - - if( set_byte_order ) nim->byteorder = nifti_short_order() ; - - if( nifti_set_type_from_names(nim) < 0 ) - return -1; - - if( g_opts.debug > 2 ) - fprintf(stderr,"+d have new filenames %s and %s\n",nim->fname,nim->iname); - - return 0; -} - - -/*--------------------------------------------------------------------------*/ -/*! check whether nifti_type matches fname and iname for the nifti_image - - - if type 0 or 2, expect .hdr/.img pair - - if type 1, expect .nii (and names must match) - - \param nim given nifti_image - \param show_warn if set, print a warning message for any mis-match - - \return - - 1 if the values seem to match - - 0 if there is a mis-match - - -1 if there is not sufficient information to create file(s) - - \sa NIFTI_FTYPE_* codes in nifti1_io.h - \sa nifti_set_type_from_names, is_valid_nifti_type -*//*------------------------------------------------------------------------*/ -int nifti_type_and_names_match( nifti_image * nim, int show_warn ) -{ - char func[] = "nifti_type_and_names_match"; - const char * ext_h; /* header filename extension */ - const char * ext_i; /* image filename extension */ - int errs = 0; /* error counter */ - - /* sanity checks */ - if( !nim ){ - if( show_warn ) fprintf(stderr,"** %s: missing nifti_image\n", func); - return -1; - } - if( !nim->fname ){ - if( show_warn ) fprintf(stderr,"** %s: missing header filename\n", func); - errs++; - } - if( !nim->iname ){ - if( show_warn ) fprintf(stderr,"** %s: missing image filename\n", func); - errs++; - } - if( !is_valid_nifti_type(nim->nifti_type) ){ - if( show_warn ) - fprintf(stderr,"** %s: bad nifti_type %d\n", func, nim->nifti_type); - errs++; - } - - if( errs ) return -1; /* then do not proceed */ - - /* get pointers to extensions */ - ext_h = nifti_find_file_extension( nim->fname ); - ext_i = nifti_find_file_extension( nim->iname ); - - /* check for filename extensions */ - if( !ext_h ){ - if( show_warn ) - fprintf(stderr,"-d missing NIFTI extension in header filename, %s\n", - nim->fname); - errs++; - } - if( !ext_i ){ - if( show_warn ) - fprintf(stderr,"-d missing NIFTI extension in image filename, %s\n", - nim->iname); - errs++; - } - - if( errs ) return 0; /* do not proceed, but this is just a mis-match */ - - /* general tests */ - if( nim->nifti_type == NIFTI_FTYPE_NIFTI1_1 ){ /* .nii */ - if( fileext_n_compare(ext_h,".nii",4) ) { - if( show_warn ) - fprintf(stderr, - "-d NIFTI_FTYPE 1, but no .nii extension in header filename, %s\n", - nim->fname); - errs++; - } - if( fileext_n_compare(ext_i,".nii",4) ) { - if( show_warn ) - fprintf(stderr, - "-d NIFTI_FTYPE 1, but no .nii extension in image filename, %s\n", - nim->iname); - errs++; - } - if( strcmp(nim->fname, nim->iname) != 0 ){ - if( show_warn ) - fprintf(stderr, - "-d NIFTI_FTYPE 1, but header and image filenames differ: %s, %s\n", - nim->fname, nim->iname); - errs++; - } - } - else if( (nim->nifti_type == NIFTI_FTYPE_NIFTI1_2) || /* .hdr/.img */ - (nim->nifti_type == NIFTI_FTYPE_ANALYZE) ) - { - if( fileext_n_compare(ext_h,".hdr",4) != 0 ){ - if( show_warn ) - fprintf(stderr,"-d no '.hdr' extension, but NIFTI type is %d, %s\n", - nim->nifti_type, nim->fname); - errs++; - } - if( fileext_n_compare(ext_i,".img",4) != 0 ){ - if( show_warn ) - fprintf(stderr,"-d no '.img' extension, but NIFTI type is %d, %s\n", - nim->nifti_type, nim->iname); - errs++; - } - } - /* ignore any other nifti_type */ - - return 1; -} - -/* like strcmp, but also check against capitalization of known_ext - * (test as local string, with max length 7) */ -static int fileext_compare(const char * test_ext, const char * known_ext) -{ - char caps[8] = ""; - size_t c,len; - /* if equal, don't need to check case (store to avoid multiple calls) */ - const int cmp = strcmp(test_ext, known_ext); - if( cmp == 0 ) return cmp; - - /* if anything odd, use default */ - if( !test_ext || !known_ext ) return cmp; - - len = strlen(known_ext); - if( len > 7 ) return cmp; - - /* if here, strings are different but need to check upper-case */ - - for(c = 0; c < len; c++ ) caps[c] = toupper((int) known_ext[c]); - caps[c] = '\0'; - - return strcmp(test_ext, caps); -} - -/* like strncmp, but also check against capitalization of known_ext - * (test as local string, with max length 7) */ -static int fileext_n_compare(const char * test_ext, - const char * known_ext, size_t maxlen) -{ - char caps[8] = ""; - size_t c,len; - /* if equal, don't need to check case (store to avoid multiple calls) */ - const int cmp = strncmp(test_ext, known_ext, maxlen); - if( cmp == 0 ) return cmp; - - /* if anything odd, use default */ - if( !test_ext || !known_ext ) return cmp; - - len = strlen(known_ext); - if( len > maxlen ) len = maxlen; /* ignore anything past maxlen */ - if( len > 7 ) return cmp; - - /* if here, strings are different but need to check upper-case */ - for(c = 0; c < len; c++ ) caps[c] = toupper((int) known_ext[c]); - caps[c] = '\0'; - - return strncmp(test_ext, caps, maxlen); -} - -/* return 1 if there are uppercase but no lowercase */ -static int is_uppercase(const char * str) -{ - size_t c; - int hasupper = 0; - - if( !str || !*str ) return 0; - - for(c = 0; c < strlen(str); c++ ) { - if( islower((int) str[c]) ) return 0; - if( !hasupper && isupper((int) str[c]) ) hasupper = 1; - } - - return hasupper; -} - -/* return 1 if there are both uppercase and lowercase characters */ -static int is_mixedcase(const char * str) -{ - size_t c; - int hasupper = 0, haslower = 0; - - if( !str || !*str ) return 0; - - for(c = 0; c < strlen(str); c++ ) { - if( !haslower && islower((int) str[c]) ) haslower = 1; - if( !hasupper && isupper((int) str[c]) ) hasupper = 1; - - if( haslower && hasupper ) return 1; - } - - return 0; -} - -/* convert any lowercase chars to uppercase */ -static int make_uppercase(char * str) -{ - size_t c; - - if( !str || !*str ) return 0; - - for(c = 0; c < strlen(str); c++ ) - if( islower((int) str[c]) ) str[c] = toupper((int) str[c]); - - return 0; -} - -/* convert any uppercase chars to lowercase */ -static int make_lowercase(char * str) -{ - size_t c; - if( !str || !*str ) return 0; - - for(c = 0; c < strlen(str); c++ ) - if( isupper((int) str[c]) ) str[c] = tolower((int) str[c]); - - return 0; -} - -/* run strcmp against of list of strings - * return index of equality, if found - * else return -1 */ -static int compare_strlist(const char * str, char ** strlist, int len) -{ - int c; - if( len <= 0 || !str || !strlist ) return -1; - for( c = 0; c < len; c++ ) - if( strlist[c] && !strcmp(str, strlist[c]) ) return c; - return -1; -} - -/*--------------------------------------------------------------------------*/ -/*! check whether the given type is on the "approved" list - - The code is valid if it is non-negative, and does not exceed - NIFTI_MAX_FTYPE. - - \return 1 if nifti_type is valid, 0 otherwise - \sa NIFTI_FTYPE_* codes in nifti1_io.h -*//*------------------------------------------------------------------------*/ -int is_valid_nifti_type( int nifti_type ) -{ - if( nifti_type >= NIFTI_FTYPE_ANALYZE && /* smallest type, 0 */ - nifti_type <= NIFTI_MAX_FTYPE ) - return 1; - return 0; -} - - -/*--------------------------------------------------------------------------*/ -/*! check whether the given type is on the "approved" list - - The type is explicitly checked against the NIFTI_TYPE_* list - in nifti1.h. - - \return 1 if dtype is valid, 0 otherwise - \sa NIFTI_TYPE_* codes in nifti1.h -*//*------------------------------------------------------------------------*/ -int nifti_is_valid_datatype( int dtype ) -{ - if( dtype == NIFTI_TYPE_UINT8 || - dtype == NIFTI_TYPE_INT16 || - dtype == NIFTI_TYPE_INT32 || - dtype == NIFTI_TYPE_FLOAT32 || - dtype == NIFTI_TYPE_COMPLEX64 || - dtype == NIFTI_TYPE_FLOAT64 || - dtype == NIFTI_TYPE_RGB24 || - dtype == NIFTI_TYPE_RGBA32 || - dtype == NIFTI_TYPE_INT8 || - dtype == NIFTI_TYPE_UINT16 || - dtype == NIFTI_TYPE_UINT32 || - dtype == NIFTI_TYPE_INT64 || - dtype == NIFTI_TYPE_UINT64 || - dtype == NIFTI_TYPE_FLOAT128 || - dtype == NIFTI_TYPE_COMPLEX128 || - dtype == NIFTI_TYPE_COMPLEX256 ) return 1; - return 0; -} - - -/*--------------------------------------------------------------------------*/ -/*! set the nifti_type field based on fname and iname - - Note that nifti_type is changed only when it does not match - the filenames. - - \return 0 on success, -1 on error - - \sa is_valid_nifti_type, nifti_type_and_names_match -*//*------------------------------------------------------------------------*/ -int nifti_set_type_from_names( nifti_image * nim ) -{ - /* error checking first */ - if( !nim ){ fprintf(stderr,"** NSTFN: no nifti_image\n"); return -1; } - - if( !nim->fname || !nim->iname ){ - fprintf(stderr,"** NSTFN: missing filename(s) fname @ %p, iname @ %p\n", - nim->fname, nim->iname); - return -1; - } - - if( ! nifti_validfilename ( nim->fname ) || - ! nifti_validfilename ( nim->iname ) || - ! nifti_find_file_extension( nim->fname ) || - ! nifti_find_file_extension( nim->iname ) - ) { - fprintf(stderr,"** NSTFN: invalid filename(s) fname='%s', iname='%s'\n", - nim->fname, nim->iname); - return -1; - } - - if( g_opts.debug > 2 ) - fprintf(stderr,"-d verify nifti_type from filenames: %d",nim->nifti_type); - - /* type should be NIFTI_FTYPE_ASCII if extension is .nia */ - if( (fileext_compare(nifti_find_file_extension(nim->fname),".nia")==0)){ - nim->nifti_type = NIFTI_FTYPE_ASCII; - } else { - /* not too picky here, do what must be done, and then verify */ - if( strcmp(nim->fname, nim->iname) == 0 ) /* one file, type 1 */ - nim->nifti_type = NIFTI_FTYPE_NIFTI1_1; - else if( nim->nifti_type == NIFTI_FTYPE_NIFTI1_1 ) /* cannot be type 1 */ - nim->nifti_type = NIFTI_FTYPE_NIFTI1_2; - } - - if( g_opts.debug > 2 ) fprintf(stderr," -> %d\n",nim->nifti_type); - - if( g_opts.debug > 1 ) /* warn user about anything strange */ - nifti_type_and_names_match(nim, 1); - - if( is_valid_nifti_type(nim->nifti_type) ) return 0; /* success! */ - - fprintf(stderr,"** NSTFN: bad nifti_type %d, for '%s' and '%s'\n", - nim->nifti_type, nim->fname, nim->iname); - - return -1; -} - - -/*--------------------------------------------------------------------------*/ -/*! Determine if this is a NIFTI-formatted file. - - 
-   \return  0 if file looks like ANALYZE 7.5 [checks sizeof_hdr field == 348]
-            1 if file marked as NIFTI (header+data in 1 file)
-            2 if file marked as NIFTI (header+data in 2 files)
-           -1 if it can't tell, file doesn't exist, etc.
-
-*//*------------------------------------------------------------------------*/ -int is_nifti_file( const char *hname ) -{ - struct nifti_1_header nhdr ; - znzFile fp ; - int ii ; - char *tmpname; - - /* bad input name? */ - - if( !nifti_validfilename(hname) ) return -1 ; - - /* open file */ - - tmpname = nifti_findhdrname(hname); - if( tmpname == NULL ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** no header file found for '%s'\n",hname); - return -1; - } - fp = znzopen( tmpname , "rb" , nifti_is_gzfile(tmpname) ) ; - free(tmpname); - if (znz_isnull(fp)) return -1 ; /* bad open? */ - - /* read header, close file */ - - ii = (int)znzread( &nhdr , 1 , sizeof(nhdr) , fp ) ; - znzclose( fp ) ; - if( ii < (int) sizeof(nhdr) ) return -1 ; /* bad read? */ - - /* check for NIFTI-ness */ - - if( NIFTI_VERSION(nhdr) != 0 ){ - return ( NIFTI_ONEFILE(nhdr) ) ? 1 : 2 ; - } - - /* check for ANALYZE-ness (sizeof_hdr field == 348) */ - - ii = nhdr.sizeof_hdr ; - if( ii == (int)sizeof(nhdr) ) return 0 ; /* matches */ - - /* try byte-swapping header */ - - swap_4(ii) ; - if( ii == (int)sizeof(nhdr) ) return 0 ; /* matches */ - - return -1 ; /* not good */ -} - -static int print_hex_vals( const char * data, size_t nbytes, FILE * fp ) -{ - size_t c; - - if ( !data || nbytes < 1 || !fp ) return -1; - - fputs("0x", fp); - for ( c = 0; c < nbytes; c++ ) - fprintf(fp, " %x", data[c]); - - return 0; -} - -/*----------------------------------------------------------------------*/ -/*! display the contents of the nifti_1_header (send to stdout) - - \param info if non-NULL, print this character string - \param hp pointer to nifti_1_header -*//*--------------------------------------------------------------------*/ -int disp_nifti_1_header( const char * info, const nifti_1_header * hp ) -{ - int c; - - fputs( "-------------------------------------------------------\n", stdout ); - if ( info ) fputs( info, stdout ); - if ( !hp ){ fputs(" ** no nifti_1_header to display!\n",stdout); return 1; } - - fprintf(stdout," nifti_1_header :\n" - " sizeof_hdr = %d\n" - " data_type[10] = ", hp->sizeof_hdr); - print_hex_vals(hp->data_type, 10, stdout); - fprintf(stdout, "\n" - " db_name[18] = "); - print_hex_vals(hp->db_name, 18, stdout); - fprintf(stdout, "\n" - " extents = %d\n" - " session_error = %d\n" - " regular = 0x%x\n" - " dim_info = 0x%x\n", - hp->extents, hp->session_error, hp->regular, hp->dim_info ); - fprintf(stdout, " dim[8] ="); - for ( c = 0; c < 8; c++ ) fprintf(stdout," %d", hp->dim[c]); - fprintf(stdout, "\n" - " intent_p1 = %f\n" - " intent_p2 = %f\n" - " intent_p3 = %f\n" - " intent_code = %d\n" - " datatype = %d\n" - " bitpix = %d\n" - " slice_start = %d\n" - " pixdim[8] =", - hp->intent_p1, hp->intent_p2, hp->intent_p3, hp->intent_code, - hp->datatype, hp->bitpix, hp->slice_start); - /* break pixdim over 2 lines */ - for ( c = 0; c < 4; c++ ) fprintf(stdout," %f", hp->pixdim[c]); - fprintf(stdout, "\n "); - for ( c = 4; c < 8; c++ ) fprintf(stdout," %f", hp->pixdim[c]); - fprintf(stdout, "\n" - " vox_offset = %f\n" - " scl_slope = %f\n" - " scl_inter = %f\n" - " slice_end = %d\n" - " slice_code = %d\n" - " xyzt_units = 0x%x\n" - " cal_max = %f\n" - " cal_min = %f\n" - " slice_duration = %f\n" - " toffset = %f\n" - " glmax = %d\n" - " glmin = %d\n", - hp->vox_offset, hp->scl_slope, hp->scl_inter, hp->slice_end, - hp->slice_code, hp->xyzt_units, hp->cal_max, hp->cal_min, - hp->slice_duration, hp->toffset, hp->glmax, hp->glmin); - fprintf(stdout, - " descrip = '%.80s'\n" - " aux_file = '%.24s'\n" - " qform_code = %d\n" - " sform_code = %d\n" - " quatern_b = %f\n" - " quatern_c = %f\n" - " quatern_d = %f\n" - " qoffset_x = %f\n" - " qoffset_y = %f\n" - " qoffset_z = %f\n" - " srow_x[4] = %f, %f, %f, %f\n" - " srow_y[4] = %f, %f, %f, %f\n" - " srow_z[4] = %f, %f, %f, %f\n" - " intent_name = '%-.16s'\n" - " magic = '%-.4s'\n", - hp->descrip, hp->aux_file, hp->qform_code, hp->sform_code, - hp->quatern_b, hp->quatern_c, hp->quatern_d, - hp->qoffset_x, hp->qoffset_y, hp->qoffset_z, - hp->srow_x[0], hp->srow_x[1], hp->srow_x[2], hp->srow_x[3], - hp->srow_y[0], hp->srow_y[1], hp->srow_y[2], hp->srow_y[3], - hp->srow_z[0], hp->srow_z[1], hp->srow_z[2], hp->srow_z[3], - hp->intent_name, hp->magic); - fputs( "-------------------------------------------------------\n", stdout ); - fflush(stdout); - - return 0; -} - - -#undef ERREX -#define ERREX(msg) \ - do{ fprintf(stderr,"** ERROR: nifti_convert_nhdr2nim: %s\n", (msg) ) ; \ - return NULL ; } while(0) - -/*----------------------------------------------------------------------*/ -/*! convert a nifti_1_header into a nift1_image - - \return an allocated nifti_image, or NULL on failure -*//*--------------------------------------------------------------------*/ -nifti_image* nifti_convert_nhdr2nim(struct nifti_1_header nhdr, - const char * fname) -{ - int ii , doswap , ioff ; - int is_nifti , is_onefile ; - nifti_image *nim; - - nim = (nifti_image *)calloc( 1 , sizeof(nifti_image) ) ; - if( !nim ) ERREX("failed to allocate nifti image"); - - /* be explicit with pointers */ - nim->fname = NULL; - nim->iname = NULL; - nim->data = NULL; - - /**- check if we must swap bytes */ - - doswap = need_nhdr_swap(nhdr.dim[0], nhdr.sizeof_hdr); /* swap data flag */ - - if( doswap < 0 ){ - free(nim); - if( doswap == -1 ) ERREX("bad dim[0]") ; - ERREX("bad sizeof_hdr") ; /* else */ - } - - /**- determine if this is a NIFTI-1 compliant header */ - - is_nifti = NIFTI_VERSION(nhdr) ; - /* - * before swapping header, record the Analyze75 orient code - */ - if(!is_nifti) - { - /**- in analyze75, the orient code is at the same address as - * qform_code, but it's just one byte - * the qform_code will be zero, at which point you can check - * analyze75_orient if you care to. - */ - unsigned char c = *((char *)(&nhdr.qform_code)); - nim->analyze75_orient = (analyze_75_orient_code)c; - } - if( doswap ) { - if ( g_opts.debug > 3 ) disp_nifti_1_header("-d ni1 pre-swap: ", &nhdr); - swap_nifti_header( &nhdr , is_nifti ) ; - } - - if ( g_opts.debug > 2 ) disp_nifti_1_header("-d nhdr2nim : ", &nhdr); - - if( nhdr.datatype == DT_BINARY || nhdr.datatype == DT_UNKNOWN ) - { - free(nim); - ERREX("bad datatype") ; - } - - if( nhdr.dim[1] <= 0 ) - { - free(nim); - ERREX("bad dim[1]") ; - } - - /* fix bad dim[] values in the defined dimension range */ - for( ii=2 ; ii <= nhdr.dim[0] ; ii++ ) - if( nhdr.dim[ii] <= 0 ) nhdr.dim[ii] = 1 ; - - /* fix any remaining bad dim[] values, so garbage does not propagate */ - /* (only values 0 or 1 seem rational, otherwise set to arbirary 1) */ - for( ii=nhdr.dim[0]+1 ; ii <= 7 ; ii++ ) - if( nhdr.dim[ii] != 1 && nhdr.dim[ii] != 0) nhdr.dim[ii] = 1 ; - -#if 0 /* rely on dim[0], do not attempt to modify it 16 Nov 2005 [rickr] */ - - /**- get number of dimensions (ignoring dim[0] now) */ - for( ii=7 ; ii >= 2 ; ii-- ) /* loop backwards until we */ - if( nhdr.dim[ii] > 1 ) break ; /* find a dim bigger than 1 */ - ndim = ii ; -#endif - - /**- set bad grid spacings to 1.0 */ - - for( ii=1 ; ii <= nhdr.dim[0] ; ii++ ){ - if( nhdr.pixdim[ii] == 0.0 || - !IS_GOOD_FLOAT(nhdr.pixdim[ii]) ) nhdr.pixdim[ii] = 1.0f ; - } - - is_onefile = is_nifti && NIFTI_ONEFILE(nhdr) ; - - if( is_nifti ) nim->nifti_type = (is_onefile) ? NIFTI_FTYPE_NIFTI1_1 - : NIFTI_FTYPE_NIFTI1_2 ; - else nim->nifti_type = NIFTI_FTYPE_ANALYZE ; - - ii = nifti_short_order() ; - if( doswap ) nim->byteorder = REVERSE_ORDER(ii) ; - else nim->byteorder = ii ; - - - /**- set dimensions of data array */ - - nim->ndim = nim->dim[0] = nhdr.dim[0]; - nim->nx = nim->dim[1] = nhdr.dim[1]; - nim->ny = nim->dim[2] = nhdr.dim[2]; - nim->nz = nim->dim[3] = nhdr.dim[3]; - nim->nt = nim->dim[4] = nhdr.dim[4]; - nim->nu = nim->dim[5] = nhdr.dim[5]; - nim->nv = nim->dim[6] = nhdr.dim[6]; - nim->nw = nim->dim[7] = nhdr.dim[7]; - - for( ii=1, nim->nvox=1; ii <= nhdr.dim[0]; ii++ ) - nim->nvox *= nhdr.dim[ii]; - - /**- set the type of data in voxels and how many bytes per voxel */ - - nim->datatype = nhdr.datatype ; - - nifti_datatype_sizes( nim->datatype , &(nim->nbyper) , &(nim->swapsize) ) ; - if( nim->nbyper == 0 ){ free(nim); ERREX("bad datatype"); } - - /**- set the grid spacings */ - - nim->dx = nim->pixdim[1] = nhdr.pixdim[1] ; - nim->dy = nim->pixdim[2] = nhdr.pixdim[2] ; - nim->dz = nim->pixdim[3] = nhdr.pixdim[3] ; - nim->dt = nim->pixdim[4] = nhdr.pixdim[4] ; - nim->du = nim->pixdim[5] = nhdr.pixdim[5] ; - nim->dv = nim->pixdim[6] = nhdr.pixdim[6] ; - nim->dw = nim->pixdim[7] = nhdr.pixdim[7] ; - - /**- compute qto_xyz transformation from pixel indexes (i,j,k) to (x,y,z) */ - - if( !is_nifti || nhdr.qform_code <= 0 ){ - /**- if not nifti or qform_code <= 0, use grid spacing for qto_xyz */ - - nim->qto_xyz.m[0][0] = nim->dx ; /* grid spacings */ - nim->qto_xyz.m[1][1] = nim->dy ; /* along diagonal */ - nim->qto_xyz.m[2][2] = nim->dz ; - - /* off diagonal is zero */ - - nim->qto_xyz.m[0][1]=nim->qto_xyz.m[0][2]=nim->qto_xyz.m[0][3] = 0.0f; - nim->qto_xyz.m[1][0]=nim->qto_xyz.m[1][2]=nim->qto_xyz.m[1][3] = 0.0f; - nim->qto_xyz.m[2][0]=nim->qto_xyz.m[2][1]=nim->qto_xyz.m[2][3] = 0.0f; - - /* last row is always [ 0 0 0 1 ] */ - - nim->qto_xyz.m[3][0]=nim->qto_xyz.m[3][1]=nim->qto_xyz.m[3][2] = 0.0f; - nim->qto_xyz.m[3][3]= 1.0f ; - - nim->qform_code = NIFTI_XFORM_UNKNOWN ; - - if( g_opts.debug > 1 ) fprintf(stderr,"-d no qform provided\n"); - } else { - /**- else NIFTI: use the quaternion-specified transformation */ - - nim->quatern_b = FIXED_FLOAT( nhdr.quatern_b ) ; - nim->quatern_c = FIXED_FLOAT( nhdr.quatern_c ) ; - nim->quatern_d = FIXED_FLOAT( nhdr.quatern_d ) ; - - nim->qoffset_x = FIXED_FLOAT(nhdr.qoffset_x) ; - nim->qoffset_y = FIXED_FLOAT(nhdr.qoffset_y) ; - nim->qoffset_z = FIXED_FLOAT(nhdr.qoffset_z) ; - - nim->qfac = (nhdr.pixdim[0] < 0.0) ? -1.0f : 1.0f ; /* left-handedness? */ - - nim->qto_xyz = nifti_quatern_to_mat44( - nim->quatern_b, nim->quatern_c, nim->quatern_d, - nim->qoffset_x, nim->qoffset_y, nim->qoffset_z, - nim->dx , nim->dy , nim->dz , - nim->qfac ) ; - - nim->qform_code = nhdr.qform_code ; - - if( g_opts.debug > 1 ) - nifti_disp_matrix_orient("-d qform orientations:\n", nim->qto_xyz); - } - - /**- load inverse transformation (x,y,z) -> (i,j,k) */ - - nim->qto_ijk = nifti_mat44_inverse( nim->qto_xyz ) ; - - /**- load sto_xyz affine transformation, if present */ - - if( !is_nifti || nhdr.sform_code <= 0 ){ - /**- if not nifti or sform_code <= 0, then no sto transformation */ - - nim->sform_code = NIFTI_XFORM_UNKNOWN ; - - if( g_opts.debug > 1 ) fprintf(stderr,"-d no sform provided\n"); - - } else { - /**- else set the sto transformation from srow_*[] */ - - nim->sto_xyz.m[0][0] = nhdr.srow_x[0] ; - nim->sto_xyz.m[0][1] = nhdr.srow_x[1] ; - nim->sto_xyz.m[0][2] = nhdr.srow_x[2] ; - nim->sto_xyz.m[0][3] = nhdr.srow_x[3] ; - - nim->sto_xyz.m[1][0] = nhdr.srow_y[0] ; - nim->sto_xyz.m[1][1] = nhdr.srow_y[1] ; - nim->sto_xyz.m[1][2] = nhdr.srow_y[2] ; - nim->sto_xyz.m[1][3] = nhdr.srow_y[3] ; - - nim->sto_xyz.m[2][0] = nhdr.srow_z[0] ; - nim->sto_xyz.m[2][1] = nhdr.srow_z[1] ; - nim->sto_xyz.m[2][2] = nhdr.srow_z[2] ; - nim->sto_xyz.m[2][3] = nhdr.srow_z[3] ; - - /* last row is always [ 0 0 0 1 ] */ - - nim->sto_xyz.m[3][0]=nim->sto_xyz.m[3][1]=nim->sto_xyz.m[3][2] = 0.0f; - nim->sto_xyz.m[3][3]= 1.0f ; - - nim->sto_ijk = nifti_mat44_inverse( nim->sto_xyz ) ; - - nim->sform_code = nhdr.sform_code ; - - if( g_opts.debug > 1 ) - nifti_disp_matrix_orient("-d sform orientations:\n", nim->sto_xyz); - } - - /**- set miscellaneous NIFTI stuff */ - - if( is_nifti ){ - nim->scl_slope = FIXED_FLOAT( nhdr.scl_slope ) ; - nim->scl_inter = FIXED_FLOAT( nhdr.scl_inter ) ; - - nim->intent_code = nhdr.intent_code ; - - nim->intent_p1 = FIXED_FLOAT( nhdr.intent_p1 ) ; - nim->intent_p2 = FIXED_FLOAT( nhdr.intent_p2 ) ; - nim->intent_p3 = FIXED_FLOAT( nhdr.intent_p3 ) ; - - nim->toffset = FIXED_FLOAT( nhdr.toffset ) ; - - memcpy(nim->intent_name,nhdr.intent_name,15); nim->intent_name[15] = '\0'; - - nim->xyz_units = XYZT_TO_SPACE(nhdr.xyzt_units) ; - nim->time_units = XYZT_TO_TIME (nhdr.xyzt_units) ; - - nim->freq_dim = DIM_INFO_TO_FREQ_DIM ( nhdr.dim_info ) ; - nim->phase_dim = DIM_INFO_TO_PHASE_DIM( nhdr.dim_info ) ; - nim->slice_dim = DIM_INFO_TO_SLICE_DIM( nhdr.dim_info ) ; - - nim->slice_code = nhdr.slice_code ; - nim->slice_start = nhdr.slice_start ; - nim->slice_end = nhdr.slice_end ; - nim->slice_duration = FIXED_FLOAT(nhdr.slice_duration) ; - } - - /**- set Miscellaneous ANALYZE stuff */ - - nim->cal_min = FIXED_FLOAT(nhdr.cal_min) ; - nim->cal_max = FIXED_FLOAT(nhdr.cal_max) ; - - memcpy(nim->descrip ,nhdr.descrip ,79) ; nim->descrip [79] = '\0' ; - memcpy(nim->aux_file,nhdr.aux_file,23) ; nim->aux_file[23] = '\0' ; - - /**- set ioff from vox_offset (but at least sizeof(header)) */ - - is_onefile = is_nifti && NIFTI_ONEFILE(nhdr) ; - - if( is_onefile ){ - ioff = (int)nhdr.vox_offset ; - if( ioff < (int) sizeof(nhdr) ) ioff = (int) sizeof(nhdr) ; - } else { - ioff = (int)nhdr.vox_offset ; - } - nim->iname_offset = ioff ; - - - /**- deal with file names if set */ - if (fname!=NULL) { - nifti_set_filenames(nim,fname,0,0); - if (nim->iname==NULL) { ERREX("bad filename"); } - } else { - nim->fname = NULL; - nim->iname = NULL; - } - - /* clear extension fields */ - nim->num_ext = 0; - nim->ext_list = NULL; - - return nim; -} - -#undef ERREX -#define ERREX(msg) \ - do{ fprintf(stderr,"** ERROR: nifti_image_open(%s): %s\n", \ - (hname != NULL) ? hname : "(null)" , (msg) ) ; \ - return fptr ; } while(0) - -/*************************************************************** - * nifti_image_open - ***************************************************************/ -/*! znzFile nifti_image_open( char *hname, char *opts , nifti_image **nim) - \brief Read in NIFTI-1 or ANALYZE-7.5 file (pair) header information into a nifti_image struct. - - - The image data is not read from disk (it may be read later using - nifti_image_load(), for example). - - The image data will be stored in whatever data format the - input data is; no scaling will be applied. - - DT_BINARY data is not supported. - - nifti_image_free() can be used to delete the returned struct, - when you are done with it. - - \param hname filename of dataset .hdr or .nii file - \param opts options string for opening the header file - \param nim pointer to pointer to nifti_image struct - (this routine allocates the nifti_image struct) - \return file pointer (gzippable) to the file with the image data, - ready for reading. -
NULL if something fails badly. - \sa nifti_image_load, nifti_image_free - */ -znzFile nifti_image_open(const char * hname, const char * opts, nifti_image ** nim) -{ - znzFile fptr=NULL; - /* open the hdr and reading it in, but do not load the data */ - *nim = nifti_image_read(hname,0); - /* open the image file, ready for reading (compressed works for all reads) */ - if( ((*nim) == NULL) || ((*nim)->iname == NULL) || - ((*nim)->nbyper <= 0) || ((*nim)->nvox <= 0) ) - ERREX("bad header info") ; - - /* open image data file */ - fptr = znzopen( (*nim)->iname, opts, nifti_is_gzfile((*nim)->iname) ); - if( znz_isnull(fptr) ) ERREX("Can't open data file") ; - - return fptr; -} - - -/*----------------------------------------------------------------------*/ -/*! return an allocated and filled nifti_1_header struct - - Read the binary header from disk, and swap bytes if necessary. - - \return an allocated nifti_1_header struct, or NULL on failure - - \param hname name of file containing header - \param swapped if not NULL, return whether header bytes were swapped - \param check flag to check for invalid nifti_1_header - - \warning ASCII header type is not supported - - \sa nifti_image_read, nifti_image_free, nifti_image_read_bricks -*//*--------------------------------------------------------------------*/ -nifti_1_header * nifti_read_header(const char * hname, int * swapped, int check) -{ - nifti_1_header nhdr, * hptr; - znzFile fp; - int bytes, lswap; - char * hfile; - char fname[] = { "nifti_read_header" }; - - /* determine file name to use for header */ - hfile = nifti_findhdrname(hname); - if( hfile == NULL ){ - if( g_opts.debug > 0 ) - LNI_FERR(fname,"failed to find header file for", hname); - return NULL; - } else if( g_opts.debug > 1 ) - fprintf(stderr,"-d %s: found header filename '%s'\n",fname,hfile); - - fp = znzopen( hfile, "rb", nifti_is_gzfile(hfile) ); - if( znz_isnull(fp) ){ - if( g_opts.debug > 0 ) LNI_FERR(fname,"failed to open header file",hfile); - free(hfile); - return NULL; - } - - free(hfile); /* done with filename */ - - if( has_ascii_header(fp) == 1 ){ - znzclose( fp ); - if( g_opts.debug > 0 ) - LNI_FERR(fname,"ASCII header type not supported",hname); - return NULL; - } - - /* read the binary header */ - bytes = (int)znzread( &nhdr, 1, sizeof(nhdr), fp ); - znzclose( fp ); /* we are done with the file now */ - - if( bytes < (int)sizeof(nhdr) ){ - if( g_opts.debug > 0 ){ - LNI_FERR(fname,"bad binary header read for file", hname); - fprintf(stderr," - read %d of %d bytes\n",bytes, (int)sizeof(nhdr)); - } - return NULL; - } - - /* now just decide on byte swapping */ - lswap = need_nhdr_swap(nhdr.dim[0], nhdr.sizeof_hdr); /* swap data flag */ - if( check && lswap < 0 ){ - LNI_FERR(fname,"bad nifti_1_header for file", hname); - return NULL; - } else if ( lswap < 0 ) { - lswap = 0; /* if swapping does not help, don't do it */ - if(g_opts.debug > 1) fprintf(stderr,"-- swap failure, none applied\n"); - } - - if( lswap ) { - if ( g_opts.debug > 3 ) disp_nifti_1_header("-d nhdr pre-swap: ", &nhdr); - swap_nifti_header( &nhdr , NIFTI_VERSION(nhdr) ) ; - } - - if ( g_opts.debug > 2 ) disp_nifti_1_header("-d nhdr post-swap: ", &nhdr); - - if ( check && ! nifti_hdr_looks_good(&nhdr) ){ - LNI_FERR(fname,"nifti_1_header looks bad for file", hname); - return NULL; - } - - /* all looks good, so allocate memory for and return the header */ - hptr = (nifti_1_header *)malloc(sizeof(nifti_1_header)); - if( ! hptr ){ - fprintf(stderr,"** nifti_read_hdr: failed to alloc nifti_1_header\n"); - return NULL; - } - - if( swapped ) *swapped = lswap; /* only if they care */ - - memcpy(hptr, &nhdr, sizeof(nifti_1_header)); - - return hptr; -} - - -/*----------------------------------------------------------------------*/ -/*! decide if this nifti_1_header structure looks reasonable - - Check dim[0], dim[1], sizeof_hdr, and datatype. - Check magic string for "n+1". - Maybe more tests will follow. - - \return 1 if the header seems valid, 0 otherwise - - \sa nifti_nim_is_valid, valid_nifti_extensions -*//*--------------------------------------------------------------------*/ -int nifti_hdr_looks_good(const nifti_1_header * hdr) -{ - int is_nifti, c, errs = 0; - - /* check dim[0] and sizeof_hdr */ - if( need_nhdr_swap(hdr->dim[0], hdr->sizeof_hdr) < 0 ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** bad nhdr fields: dim0, sizeof_hdr = %d, %d\n", - hdr->dim[0], hdr->sizeof_hdr); - errs++; - } - - /* check the valid dimension sizes (maybe dim[0] is bad) */ - for( c = 1; c <= hdr->dim[0] && c <= 7; c++ ) - if( hdr->dim[c] <= 0 ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** bad nhdr field: dim[%d] = %d\n",c,hdr->dim[c]); - errs++; - } - - is_nifti = NIFTI_VERSION(*hdr); /* determine header type */ - - if( is_nifti ){ /* NIFTI */ - - if( ! nifti_datatype_is_valid(hdr->datatype, 1) ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** bad NIFTI datatype in hdr, %d\n",hdr->datatype); - errs++; - } - - } else { /* ANALYZE 7.5 */ - - if( g_opts.debug > 1 ) /* maybe tell user it's an ANALYZE hdr */ - fprintf(stderr, - "-- nhdr magic field implies ANALYZE: magic = '%.4s'\n",hdr->magic); - - if( ! nifti_datatype_is_valid(hdr->datatype, 0) ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** bad ANALYZE datatype in hdr, %d\n",hdr->datatype); - errs++; - } - } - - if( errs ) return 0; /* problems */ - - if( g_opts.debug > 2 ) fprintf(stderr,"-d nifti header looks good\n"); - - return 1; /* looks good */ -} - - -/*---------------------------------------------------------------------- - * check whether byte swapping is needed - * - * dim[0] should be in [0,7], and sizeof_hdr should be accurate - * - * \returns > 0 : needs swap - * 0 : does not need swap - * < 0 : error condition - *----------------------------------------------------------------------*/ -static int need_nhdr_swap( short dim0, int hdrsize ) -{ - short d0 = dim0; /* so we won't have to swap them on the stack */ - int hsize = hdrsize; - - if( d0 != 0 ){ /* then use it for the check */ - if( d0 > 0 && d0 <= 7 ) return 0; - - nifti_swap_2bytes(1, &d0); /* swap? */ - if( d0 > 0 && d0 <= 7 ) return 1; - - if( g_opts.debug > 1 ){ - fprintf(stderr,"** NIFTI: bad swapped d0 = %d, unswapped = ", d0); - nifti_swap_2bytes(1, &d0); /* swap? */ - fprintf(stderr,"%d\n", d0); - } - - return -1; /* bad, naughty d0 */ - } - - /* dim[0] == 0 should not happen, but could, so try hdrsize */ - if( hsize == sizeof(nifti_1_header) ) return 0; - - nifti_swap_4bytes(1, &hsize); /* swap? */ - if( hsize == sizeof(nifti_1_header) ) return 1; - - if( g_opts.debug > 1 ){ - fprintf(stderr,"** NIFTI: bad swapped hsize = %d, unswapped = ", hsize); - nifti_swap_4bytes(1, &hsize); /* swap? */ - fprintf(stderr,"%d\n", hsize); - } - - return -2; /* bad, naughty hsize */ -} - - -/* use macro LNI_FILE_ERROR instead of ERREX() -#undef ERREX -#define ERREX(msg) \ - do{ fprintf(stderr,"** ERROR: nifti_image_read(%s): %s\n", \ - (hname != NULL) ? hname : "(null)" , (msg) ) ; \ - return NULL ; } while(0) -*/ - - -/*************************************************************** - * nifti_image_read - ***************************************************************/ -/*! \brief Read a nifti header and optionally the data, creating a nifti_image. - - - The data buffer will be byteswapped if necessary. - - The data buffer will not be scaled. - - The data buffer is allocated with calloc(). - - \param hname filename of the nifti dataset - \param read_data Flag, true=read data blob, false=don't read blob. - \return A pointer to the nifti_image data structure. - - \sa nifti_image_free, nifti_free_extensions, nifti_image_read_bricks -*/ -nifti_image *nifti_image_read( const char *hname , int read_data ) -{ - struct nifti_1_header nhdr ; - nifti_image *nim ; - znzFile fp ; - int rv, ii , filesize, remaining; - char fname[] = { "nifti_image_read" }; - char *hfile=NULL; - - if( g_opts.debug > 1 ){ - fprintf(stderr,"-d image_read from '%s', read_data = %d",hname,read_data); -#ifdef HAVE_ZLIB - fprintf(stderr,", HAVE_ZLIB = 1\n"); -#else - fprintf(stderr,", HAVE_ZLIB = 0\n"); -#endif - } - - /**- determine filename to use for header */ - hfile = nifti_findhdrname(hname); - if( hfile == NULL ){ - if(g_opts.debug > 0) - LNI_FERR(fname,"failed to find header file for", hname); - return NULL; /* check return */ - } else if( g_opts.debug > 1 ) - fprintf(stderr,"-d %s: found header filename '%s'\n",fname,hfile); - - if( nifti_is_gzfile(hfile) ) filesize = -1; /* unknown */ - else filesize = nifti_get_filesize(hfile); - - fp = znzopen(hfile, "rb", nifti_is_gzfile(hfile)); - if( znz_isnull(fp) ){ - if( g_opts.debug > 0 ) LNI_FERR(fname,"failed to open header file",hfile); - free(hfile); - return NULL; - } - - rv = has_ascii_header( fp ); - if( rv < 0 ){ - if( g_opts.debug > 0 ) LNI_FERR(fname,"short header read",hfile); - znzclose( fp ); - free(hfile); - return NULL; - } - else if ( rv == 1 ) /* process special file type */ - return nifti_read_ascii_image( fp, hfile, filesize, read_data ); - - /* else, just process normally */ - - /**- read binary header */ - - ii = (int)znzread( &nhdr , 1 , sizeof(nhdr) , fp ) ; /* read the thing */ - - /* keep file open so we can check for exts. after nifti_convert_nhdr2nim() */ - - if( ii < (int) sizeof(nhdr) ){ - if( g_opts.debug > 0 ){ - LNI_FERR(fname,"bad binary header read for file", hfile); - fprintf(stderr," - read %d of %d bytes\n",ii, (int)sizeof(nhdr)); - } - znzclose(fp) ; - free(hfile); - return NULL; - } - - /* create output image struct and set it up */ - - /**- convert all nhdr fields to nifti_image fields */ - nim = nifti_convert_nhdr2nim(nhdr,hfile); - - if( nim == NULL ){ - znzclose( fp ) ; /* close the file */ - if( g_opts.debug > 0 ) - LNI_FERR(fname,"cannot create nifti image from header",hfile); - free(hfile); /* had to save this for debug message */ - return NULL; - } - - if( g_opts.debug > 3 ){ - fprintf(stderr,"+d nifti_image_read(), have nifti image:\n"); - if( g_opts.debug > 2 ) nifti_image_infodump(nim); - } - - /**- check for extensions (any errors here means no extensions) */ - if( NIFTI_ONEFILE(nhdr) ) remaining = nim->iname_offset - sizeof(nhdr); - else remaining = filesize - sizeof(nhdr); - - (void)nifti_read_extensions(nim, fp, remaining); - - znzclose( fp ) ; /* close the file */ - free(hfile); - - /**- read the data if desired, then bug out */ - if( read_data ){ - if( nifti_image_load( nim ) < 0 ){ - nifti_image_free(nim); /* take ball, go home. */ - return NULL; - } - } - else nim->data = NULL ; - - return nim ; -} - - -/*---------------------------------------------------------------------- - * has_ascii_header - see if the NIFTI header is an ASCII format - * - * If the file starts with the ASCII string " 1 ) - fprintf(stderr,"-d %s: have ASCII NIFTI file of size %d\n",fname,slen); - - if( slen > 65530 ) slen = 65530 ; - sbuf = (char *)calloc(sizeof(char),slen+1) ; - if( !sbuf ){ - fprintf(stderr,"** %s: failed to alloc %d bytes for sbuf",lfunc,65530); - free(fname); znzclose(fp); return NULL; - } - znzread( sbuf , 1 , slen , fp ) ; - nim = nifti_image_from_ascii( sbuf, &txt_size ) ; free( sbuf ) ; - if( nim == NULL ){ - LNI_FERR(lfunc,"failed nifti_image_from_ascii()",fname); - free(fname); znzclose(fp); return NULL; - } - nim->nifti_type = NIFTI_FTYPE_ASCII ; - - /* compute remaining space for extensions */ - remain = flen - txt_size - (int)nifti_get_volsize(nim); - if( remain > 4 ){ - /* read extensions (reposition file pointer, first) */ - znzseek(fp, txt_size, SEEK_SET); - (void) nifti_read_extensions(nim, fp, remain); - } - - free(fname); - znzclose( fp ) ; - - nim->iname_offset = -1 ; /* check from the end of the file */ - - if( read_data ) rv = nifti_image_load( nim ) ; - else nim->data = NULL ; - - /* check for nifti_image_load() failure, maybe bail out */ - if( read_data && rv != 0 ){ - if( g_opts.debug > 1 ) - fprintf(stderr,"-d failed image_load, free nifti image struct\n"); - free(nim); - return NULL; - } - - return nim ; -} - - -/*---------------------------------------------------------------------- - * Read the extensions into the nifti_image struct 08 Dec 2004 [rickr] - * - * This function is called just after the header struct is read in, and - * it is assumed the file pointer has not moved. The value in remain - * is assumed to be accurate, reflecting the bytes of space for potential - * extensions. - * - * return the number of extensions read in, or < 0 on error - *----------------------------------------------------------------------*/ -static int nifti_read_extensions( nifti_image *nim, znzFile fp, int remain ) -{ - nifti1_extender extdr; /* defines extension existence */ - nifti1_extension extn; /* single extension to process */ - nifti1_extension * Elist; /* list of processed extensions */ - int posn, count; - - if( !nim || znz_isnull(fp) ) { - if( g_opts.debug > 0 ) - fprintf(stderr,"** nifti_read_extensions: bad inputs (%p,%p)\n", - (void *)nim, (void *)fp); - return -1; - } - - posn = znztell(fp); - - if( (posn != sizeof(nifti_1_header)) && - (nim->nifti_type != NIFTI_FTYPE_ASCII) ) - fprintf(stderr,"** WARNING: posn not header size (%d, %d)\n", - posn, (int)sizeof(nifti_1_header)); - - if( g_opts.debug > 2 ) - fprintf(stderr,"-d nre: posn = %d, offset = %d, type = %d, remain = %d\n", - posn, nim->iname_offset, nim->nifti_type, remain); - - if( remain < 16 ){ - if( g_opts.debug > 2 ){ - if( g_opts.skip_blank_ext ) - fprintf(stderr,"-d no extender in '%s' is okay, as " - "skip_blank_ext is set\n",nim->fname); - else - fprintf(stderr,"-d remain=%d, no space for extensions\n",remain); - } - return 0; - } - - count = (int)znzread( extdr.extension, 1, 4, fp ); /* get extender */ - - if( count < 4 ){ - if( g_opts.debug > 1 ) - fprintf(stderr,"-d file '%s' is too short for an extender\n", - nim->fname); - return 0; - } - - if( extdr.extension[0] != 1 ){ - if( g_opts.debug > 2 ) - fprintf(stderr,"-d extender[0] (%d) shows no extensions for '%s'\n", - extdr.extension[0], nim->fname); - return 0; - } - - remain -= 4; - if( g_opts.debug > 2 ) - fprintf(stderr,"-d found valid 4-byte extender, remain = %d\n", remain); - - /* so we expect extensions, but have no idea of how many there may be */ - - count = 0; - Elist = NULL; - while (nifti_read_next_extension(&extn, nim, remain, fp) > 0) - { - if( nifti_add_exten_to_list(&extn, &Elist, count+1) < 0 ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** failed adding ext %d to list\n", count); - return -1; - } - - /* we have a new extension */ - if( g_opts.debug > 1 ){ - fprintf(stderr,"+d found extension #%d, code = 0x%x, size = %d\n", - count, extn.ecode, extn.esize); - if( extn.ecode == NIFTI_ECODE_AFNI && g_opts.debug > 2 ) /* ~XML */ - fprintf(stderr," AFNI extension: %.*s\n", - extn.esize-8,extn.edata); - else if( extn.ecode == NIFTI_ECODE_COMMENT && g_opts.debug > 2 ) - fprintf(stderr," COMMENT extension: %.*s\n", /* TEXT */ - extn.esize-8,extn.edata); - } - remain -= extn.esize; - count++; - } - - if( g_opts.debug > 2 ) fprintf(stderr,"+d found %d extension(s)\n", count); - - nim->num_ext = count; - nim->ext_list = Elist; - - return count; -} - - -/*----------------------------------------------------------------------*/ -/*! nifti_add_extension - add an extension, with a copy of the data - - Add an extension to the nim->ext_list array. - Fill this extension with a copy of the data, noting the - length and extension code. - - \param nim - nifti_image to add extension to - \param data - raw extension data - \param length - length of raw extension data - \param ecode - extension code - - \sa extension codes NIFTI_ECODE_* in nifti1_io.h - \sa nifti_free_extensions, valid_nifti_extensions, nifti_copy_extensions - - \return 0 on success, -1 on error (and free the entire list) -*//*--------------------------------------------------------------------*/ -int nifti_add_extension(nifti_image *nim, const char * data, int len, int ecode) -{ - nifti1_extension ext; - - /* error are printed in functions */ - if( nifti_fill_extension(&ext, data, len, ecode) ) return -1; - if( nifti_add_exten_to_list(&ext, &nim->ext_list, nim->num_ext+1)) return -1; - - nim->num_ext++; /* success, so increment */ - - return 0; -} - - -/*----------------------------------------------------------------------*/ -/* nifti_add_exten_to_list - add a new nifti1_extension to the list - - We will append via "malloc, copy and free", because on an error, - the list will revert to the previous one (sorry realloc(), only - quality dolphins get to become part of St@rk!st brand tunafish). - - return 0 on success, -1 on error (and free the entire list) -*//*--------------------------------------------------------------------*/ -static int nifti_add_exten_to_list( nifti1_extension * new_ext, - nifti1_extension ** list, int new_length ) -{ - nifti1_extension * tmplist; - - tmplist = *list; - *list = (nifti1_extension *)malloc(new_length * sizeof(nifti1_extension)); - - /* check for failure first */ - if( ! *list ){ - fprintf(stderr,"** failed to alloc %d extension structs (%d bytes)\n", - new_length, new_length*(int)sizeof(nifti1_extension)); - if( !tmplist ) return -1; /* no old list to lose */ - - *list = tmplist; /* reset list to old one */ - return -1; - } - - /* if an old list exists, copy the pointers and free the list */ - if( tmplist ){ - memcpy(*list, tmplist, (new_length-1)*sizeof(nifti1_extension)); - free(tmplist); - } - - /* for some reason, I just don't like struct copy... */ - (*list)[new_length-1].esize = new_ext->esize; - (*list)[new_length-1].ecode = new_ext->ecode; - (*list)[new_length-1].edata = new_ext->edata; - - if( g_opts.debug > 2 ) - fprintf(stderr,"+d allocated and appended extension #%d to list\n", - new_length); - - return 0; -} - - -/*----------------------------------------------------------------------*/ -/* nifti_fill_extension - given data and length, fill an extension struct - - Allocate memory for data, copy data, set the size and code. - - return 0 on success, -1 on error (and free the entire list) -*//*--------------------------------------------------------------------*/ -static int nifti_fill_extension( nifti1_extension *ext, const char * data, - int len, int ecode) -{ - int esize; - - if( !ext || !data || len < 0 ){ - fprintf(stderr,"** fill_ext: bad params (%p,%p,%d)\n", - (void *)ext, data, len); - return -1; - } else if( ! nifti_is_valid_ecode(ecode) ){ - fprintf(stderr,"** warning: writing unknown ecode %d\n", ecode); - /* should not be fatal 29 Apr 2015 [rickr] */ - } - - /* compute esize, first : len+8, and take ceiling up to a mult of 16 */ - esize = len+8; - if( esize & 0xf ) esize = (esize + 0xf) & ~0xf; - ext->esize = esize; - - /* allocate esize-8 (maybe more than len), using calloc for fill */ - ext->edata = (char *)calloc(esize-8, sizeof(char)); - if( !ext->edata ){ - fprintf(stderr,"** NFE: failed to alloc %d bytes for extension\n",len); - return -1; - } - - memcpy(ext->edata, data, len); /* copy the data, using len */ - ext->ecode = ecode; /* set the ecode */ - - if( g_opts.debug > 2 ) - fprintf(stderr,"+d alloc %d bytes for ext len %d, ecode %d, esize %d\n", - esize-8, len, ecode, esize); - - return 0; -} - - -/*---------------------------------------------------------------------- - * nifti_read_next_extension - read a single extension from the file - * - * return (>= 0 is okay): - * - * success : esize - * no extension : 0 - * error : -1 - *----------------------------------------------------------------------*/ -static int nifti_read_next_extension( nifti1_extension * nex, nifti_image *nim, - int remain, znzFile fp ) -{ - int swap = nim->byteorder != nifti_short_order(); - int count, size, code; - - /* first clear nex */ - nex->esize = nex->ecode = 0; - nex->edata = NULL; - - if( remain < 16 ){ - if( g_opts.debug > 2 ) - fprintf(stderr,"-d only %d bytes remain, so no extension\n", remain); - return 0; - } - - /* must start with 4-byte size and code */ - count = (int)znzread( &size, 4, 1, fp ); - if( count == 1 ) count += (int)znzread( &code, 4, 1, fp ); - - if( count != 2 ){ - if( g_opts.debug > 2 ) - fprintf(stderr,"-d current extension read failed\n"); - znzseek(fp, -4*count, SEEK_CUR); /* back up past any read */ - return 0; /* no extension, no error condition */ - } - - if( swap ){ - if( g_opts.debug > 2 ) - fprintf(stderr,"-d pre-swap exts: code %d, size %d\n", code, size); - - nifti_swap_4bytes(1, &size); - nifti_swap_4bytes(1, &code); - } - - if( g_opts.debug > 2 ) - fprintf(stderr,"-d potential extension: code %d, size %d\n", code, size); - - if( !nifti_check_extension(nim, size, code, remain) ){ - if( znzseek(fp, -8, SEEK_CUR) < 0 ){ /* back up past any read */ - fprintf(stderr,"** failure to back out of extension read!\n"); - return -1; - } - return 0; - } - - /* now get the actual data */ - nex->esize = size; - nex->ecode = code; - - size -= 8; /* subtract space for size and code in extension */ - nex->edata = (char *)malloc(size * sizeof(char)); - if( !nex->edata ){ - fprintf(stderr,"** failed to allocate %d bytes for extension\n",size); - return -1; - } - - count = (int)znzread(nex->edata, 1, size, fp); - if( count < size ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"-d read only %d (of %d) bytes for extension\n", - count, size); - free(nex->edata); - nex->edata = NULL; - return -1; - } - - /* success! */ - if( g_opts.debug > 2 ) - fprintf(stderr,"+d successfully read extension, code %d, size %d\n", - nex->ecode, nex->esize); - - return nex->esize; -} - - -/*----------------------------------------------------------------------*/ -/*! for each extension, check code, size and data pointer -*//*--------------------------------------------------------------------*/ -int valid_nifti_extensions(const nifti_image * nim) -{ - nifti1_extension * ext; - int c, errs; - - if( nim->num_ext <= 0 || nim->ext_list == NULL ){ - if( g_opts.debug > 2 ) fprintf(stderr,"-d empty extension list\n"); - return 0; - } - - /* for each extension, check code, size and data pointer */ - ext = nim->ext_list; - errs = 0; - for ( c = 0; c < nim->num_ext; c++ ){ - if( ! nifti_is_valid_ecode(ext->ecode) ) { - if( g_opts.debug > 1 ) - fprintf(stderr,"-d ext %d, unknown code %d\n", c, ext->ecode); - /* should not be fatal 29 Apr 2015 [rickr] */ - } - - if( ext->esize <= 0 ){ - if( g_opts.debug > 1 ) - fprintf(stderr,"-d ext %d, bad size = %d\n", c, ext->esize); - errs++; - } else if( ext->esize & 0xf ){ - if( g_opts.debug > 1 ) - fprintf(stderr,"-d ext %d, size %d not multiple of 16\n", - c, ext->esize); - errs++; - } - - if( ext->edata == NULL ){ - if( g_opts.debug > 1 ) fprintf(stderr,"-d ext %d, missing data\n", c); - errs++; - } - - ext++; - } - - if( errs > 0 ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"-d had %d extension errors, none will be written\n", - errs); - return 0; - } - - /* if we're here, we're good */ - return 1; -} - - -/*----------------------------------------------------------------------*/ -/*! check whether the extension code is valid - - \return 1 if valid, 0 otherwise -*//*--------------------------------------------------------------------*/ -int nifti_is_valid_ecode( int ecode ) -{ - if( ecode < NIFTI_ECODE_IGNORE || /* minimum code number (0) */ - ecode > NIFTI_MAX_ECODE || /* maximum code number */ - ecode & 1 ) /* cannot be odd */ - return 0; - - return 1; -} - - -/*---------------------------------------------------------------------- - * check for valid size and code, as well as can be done - *----------------------------------------------------------------------*/ -static int nifti_check_extension(nifti_image *nim, int size, int code, int rem) -{ - /* check for bad code before bad size */ - if( ! nifti_is_valid_ecode(code) ) { - if( g_opts.debug > 2 ) - fprintf(stderr,"-d invalid extension code %d\n",code); - /* should not be fatal 29 Apr 2015 [rickr] */ - } - - if( size < 16 ){ - if( g_opts.debug > 2 ) - fprintf(stderr,"-d ext size %d, no extension\n",size); - return 0; - } - - if( size > rem ){ - if( g_opts.debug > 2 ) - fprintf(stderr,"-d ext size %d, space %d, no extension\n", size, rem); - return 0; - } - - if( size & 0xf ){ - if( g_opts.debug > 2 ) - fprintf(stderr,"-d nifti extension size %d not multiple of 16\n",size); - return 0; - } - - if( nim->nifti_type == NIFTI_FTYPE_ASCII && size > LNI_MAX_NIA_EXT_LEN ){ - if( g_opts.debug > 2 ) - fprintf(stderr,"-d NVE, bad nifti_type 3 size %d\n", size); - return 0; - } - - return 1; -} - - -/*---------------------------------------------------------------------- - * nifti_image_load_prep - prepare to read data - * - * Check nifti_image fields, open the file and seek to the appropriate - * offset for reading. - * - * return NULL on failure - *----------------------------------------------------------------------*/ -static znzFile nifti_image_load_prep( nifti_image *nim ) -{ - /* set up data space, open data file and seek, then call nifti_read_buffer */ - size_t ntot , ii , ioff; - znzFile fp; - char *tmpimgname; - char fname[] = { "nifti_image_load_prep" }; - - /**- perform sanity checks */ - if( nim == NULL || nim->iname == NULL || - nim->nbyper <= 0 || nim->nvox <= 0 ) - { - if ( g_opts.debug > 0 ){ - if( !nim ) fprintf(stderr,"** ERROR: N_image_load: no nifti image\n"); - else fprintf(stderr,"** ERROR: N_image_load: bad params (%p,%d,%u)\n", - nim->iname, nim->nbyper, (unsigned)nim->nvox); - } - return NULL; - } - - ntot = nifti_get_volsize(nim) ; /* total bytes to read */ - - /**- open image data file */ - - tmpimgname = nifti_findimgname(nim->iname , nim->nifti_type); - if( tmpimgname == NULL ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** no image file found for '%s'\n",nim->iname); - return NULL; - } - - fp = znzopen(tmpimgname, "rb", nifti_is_gzfile(tmpimgname)); - if (znz_isnull(fp)){ - if(g_opts.debug > 0) LNI_FERR(fname,"cannot open data file",tmpimgname); - free(tmpimgname); - return NULL; /* bad open? */ - } - free(tmpimgname); - - /**- get image offset: a negative offset means to figure from end of file */ - if( nim->iname_offset < 0 ){ - if( nifti_is_gzfile(nim->iname) ){ - if( g_opts.debug > 0 ) - LNI_FERR(fname,"negative offset for compressed file",nim->iname); - znzclose(fp); - return NULL; - } - ii = nifti_get_filesize( nim->iname ) ; - if( ii <= 0 ){ - if( g_opts.debug > 0 ) LNI_FERR(fname,"empty data file",nim->iname); - znzclose(fp); - return NULL; - } - ioff = (ii > ntot) ? ii-ntot : 0 ; - } else { /* non-negative offset */ - ioff = nim->iname_offset ; /* means use it directly */ - } - - /**- seek to the appropriate read position */ - if( znzseek(fp , (long)ioff , SEEK_SET) < 0 ){ - fprintf(stderr,"** could not seek to offset %u in file '%s'\n", - (unsigned)ioff, nim->iname); - znzclose(fp); - return NULL; - } - - /**- and return the File pointer */ - return fp; -} - - -/*---------------------------------------------------------------------- - * nifti_image_load - *----------------------------------------------------------------------*/ -/*! \fn int nifti_image_load( nifti_image *nim ) - \brief Load the image blob into a previously initialized nifti_image. - - - If not yet set, the data buffer is allocated with calloc(). - - The data buffer will be byteswapped if necessary. - - The data buffer will not be scaled. - - This function is used to read the image from disk. It should be used - after a function such as nifti_image_read(), so that the nifti_image - structure is already initialized. - - \param nim pointer to a nifti_image (previously initialized) - \return 0 on success, -1 on failure - \sa nifti_image_read, nifti_image_free, nifti_image_unload -*/ -int nifti_image_load( nifti_image *nim ) -{ - /* set up data space, open data file and seek, then call nifti_read_buffer */ - size_t ntot , ii ; - znzFile fp ; - - /**- open the file and position the FILE pointer */ - fp = nifti_image_load_prep( nim ); - - if( fp == NULL ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** nifti_image_load, failed load_prep\n"); - return -1; - } - - ntot = nifti_get_volsize(nim); - - /**- if the data pointer is not yet set, get memory space for the image */ - - if( nim->data == NULL ) - { - nim->data = (void *)calloc(1,ntot) ; /* create image memory */ - if( nim->data == NULL ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** failed to alloc %d bytes for image data\n", - (int)ntot); - znzclose(fp); - return -1; - } - } - - /**- now that everything is set up, do the reading */ - ii = nifti_read_buffer(fp,nim->data,ntot,nim); - if( ii < ntot ){ - znzclose(fp) ; - free(nim->data) ; - nim->data = NULL ; - return -1 ; /* errors were printed in nifti_read_buffer() */ - } - - /**- close the file */ - znzclose( fp ) ; - - return 0 ; -} - - -/* 30 Nov 2004 [rickr] -#undef ERREX -#define ERREX(msg) \ - do{ fprintf(stderr,"** ERROR: nifti_read_buffer: %s\n",(msg)) ; \ - return 0; } while(0) -*/ - -/*----------------------------------------------------------------------*/ -/*! read ntot bytes of data from an open file and byte swaps if necessary - - note that nifti_image is required for information on datatype, bsize - (for any needed byte swapping), etc. - - This function does not allocate memory, so dataptr must be valid. -*//*--------------------------------------------------------------------*/ -size_t nifti_read_buffer(znzFile fp, void* dataptr, size_t ntot, - nifti_image *nim) -{ - size_t ii; - - if( dataptr == NULL ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** ERROR: nifti_read_buffer: NULL dataptr\n"); - return -1; - } - - ii = znzread( dataptr , 1 , ntot , fp ) ; /* data input */ - - /* if read was short, fail */ - if( ii < ntot ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"++ WARNING: nifti_read_buffer(%s):\n" - " data bytes needed = %u\n" - " data bytes input = %u\n" - " number missing = %u (set to 0)\n", - nim->iname , (unsigned int)ntot , - (unsigned int)ii , (unsigned int)(ntot-ii) ) ; - /* memset( (char *)(dataptr)+ii , 0 , ntot-ii ) ; now failure [rickr] */ - return -1 ; - } - - if( g_opts.debug > 2 ) - fprintf(stderr,"+d nifti_read_buffer: read %u bytes\n", (unsigned)ii); - - /* byte swap array if needed */ - - /* ntot/swapsize might not fit as int, use size_t 6 Jul 2010 [rickr] */ - if( nim->swapsize > 1 && nim->byteorder != nifti_short_order() ) { - if( g_opts.debug > 1 ) - fprintf(stderr,"+d nifti_read_buffer: swapping data bytes...\n"); - nifti_swap_Nbytes( (int)(ntot / nim->swapsize), nim->swapsize , dataptr ) ; - } - -#ifdef isfinite -{ - /* check input float arrays for goodness, and fix bad floats */ - int fix_count = 0 ; - - switch( nim->datatype ){ - - case NIFTI_TYPE_FLOAT32: - case NIFTI_TYPE_COMPLEX64:{ - float *far = (float *)dataptr ; size_t jj,nj ; - nj = ntot / sizeof(float) ; - for( jj=0 ; jj < nj ; jj++ ) /* count fixes 30 Nov 2004 [rickr] */ - if( !IS_GOOD_FLOAT(far[jj]) ){ - far[jj] = 0 ; - fix_count++ ; - } - } - break ; - - case NIFTI_TYPE_FLOAT64: - case NIFTI_TYPE_COMPLEX128:{ - double *far = (double *)dataptr ; size_t jj,nj ; - nj = ntot / sizeof(double) ; - for( jj=0 ; jj < nj ; jj++ ) /* count fixes 30 Nov 2004 [rickr] */ - if( !IS_GOOD_FLOAT(far[jj]) ){ - far[jj] = 0 ; - fix_count++ ; - } - } - break ; - - } - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d in image, %d bad floats were set to 0\n", fix_count); -} -#endif - - return ii; -} - -/*--------------------------------------------------------------------------*/ -/*! Unload the data in a nifti_image struct, but keep the metadata. -*//*------------------------------------------------------------------------*/ -void nifti_image_unload( nifti_image *nim ) -{ - if( nim != NULL && nim->data != NULL ){ - free(nim->data) ; nim->data = NULL ; - } - return ; -} - -/*--------------------------------------------------------------------------*/ -/*! free 'everything' about a nifti_image struct (including the passed struct) - - free (only fields which are not NULL): - - fname and iname - - data - - any ext_list[i].edata - - ext_list - - nim -*//*------------------------------------------------------------------------*/ -void nifti_image_free( nifti_image *nim ) -{ - if( nim == NULL ) return ; - if( nim->fname != NULL ) free(nim->fname) ; - if( nim->iname != NULL ) free(nim->iname) ; - if( nim->data != NULL ) free(nim->data ) ; - (void)nifti_free_extensions( nim ) ; - free(nim) ; return ; -} - - -/*--------------------------------------------------------------------------*/ -/*! free the nifti extensions - - - If any edata pointer is set in the extension list, free() it. - - Free ext_list, if it is set. - - Clear num_ext and ext_list from nim. - - \return 0 on success, -1 on error - - \sa nifti_add_extension, nifti_copy_extensions -*//*------------------------------------------------------------------------*/ -int nifti_free_extensions( nifti_image *nim ) -{ - int c ; - if( nim == NULL ) return -1; - if( nim->num_ext > 0 && nim->ext_list ){ - for( c = 0; c < nim->num_ext; c++ ) - if ( nim->ext_list[c].edata ) free(nim->ext_list[c].edata); - free(nim->ext_list); - } - /* or if it is inconsistent, warn the user (if we are not in quiet mode) */ - else if ( (nim->num_ext > 0 || nim->ext_list != NULL) && (g_opts.debug > 0) ) - fprintf(stderr,"** warning: nifti extension num/ptr mismatch (%d,%p)\n", - nim->num_ext, (void *)nim->ext_list); - - if( g_opts.debug > 2 ) - fprintf(stderr,"+d free'd %d extension(s)\n", nim->num_ext); - - nim->num_ext = 0; - nim->ext_list = NULL; - - return 0; -} - - -/*--------------------------------------------------------------------------*/ -/*! Print to stdout some info about a nifti_image struct. -*//*------------------------------------------------------------------------*/ -void nifti_image_infodump( const nifti_image *nim ) -{ - char *str = nifti_image_to_ascii( nim ) ; - /* stdout -> stderr 2 Dec 2004 [rickr] */ - if( str != NULL ){ fputs(str,stderr) ; free(str) ; } - return ; -} - - -/*-------------------------------------------------------------------------- - * nifti_write_buffer just check for a null znzFile and call znzwrite - *--------------------------------------------------------------------------*/ -/*! \fn size_t nifti_write_buffer(znzFile fp, void *buffer, size_t numbytes) - \brief write numbytes of buffer to file, fp - - \param fp File pointer (from znzopen) to gzippable nifti datafile - \param buffer data buffer to be written - \param numbytes number of bytes in buffer to write - \return number of bytes successfully written -*/ -size_t nifti_write_buffer(znzFile fp, const void *buffer, size_t numbytes) -{ - /* Write all the image data at once (no swapping here) */ - size_t ss; - if (znz_isnull(fp)){ - fprintf(stderr,"** ERROR: nifti_write_buffer: null file pointer\n"); - return 0; - } - ss = znzwrite( (const void*)buffer , 1 , numbytes , fp ) ; - return ss; -} - - -/*----------------------------------------------------------------------*/ -/*! write the nifti_image data to file (from nim->data or from NBL) - - If NBL is not NULL, write the data from that structure. Otherwise, - write it out from nim->data. No swapping is done here. - - \param fp : File pointer - \param nim : nifti_image corresponding to the data - \param NBL : optional source of write data (if NULL use nim->data) - - \return 0 on success, -1 on failure - - Note: the nifti_image byte_order is set as that of the current CPU. - This is because such a conversion was made to the data upon - reading, while byte_order was not set (so the programs would - know what format the data was on disk). Effectively, since - byte_order should match what is on disk, it should bet set to - that of the current CPU whenever new filenames are assigned. -*//*--------------------------------------------------------------------*/ -int nifti_write_all_data(znzFile fp, nifti_image * nim, - const nifti_brick_list * NBL) -{ - size_t ss; - int bnum; - - if( !NBL ){ /* just write one buffer and get out of here */ - if( nim->data == NULL ){ - fprintf(stderr,"** NWAD: no image data to write\n"); - return -1; - } - - ss = nifti_write_buffer(fp,nim->data,nim->nbyper * nim->nvox); - if (ss < nim->nbyper * nim->nvox){ - fprintf(stderr, - "** ERROR: NWAD: wrote only %u of %u bytes to file\n", - (unsigned)ss, (unsigned)(nim->nbyper * nim->nvox)); - return -1; - } - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d wrote single image of %u bytes\n", (unsigned)ss); - } else { - if( ! NBL->bricks || NBL->nbricks <= 0 || NBL->bsize <= 0 ){ - fprintf(stderr,"** NWAD: no brick data to write (%p,%d,%u)\n", - (void *)NBL->bricks, NBL->nbricks, (unsigned)NBL->bsize); - return -1; - } - - for( bnum = 0; bnum < NBL->nbricks; bnum++ ){ - ss = nifti_write_buffer(fp, NBL->bricks[bnum], NBL->bsize); - if( ss < NBL->bsize ){ - fprintf(stderr, - "** NWAD ERROR: wrote %u of %u bytes of brick %d of %d to file", - (unsigned)ss, (unsigned)NBL->bsize, bnum+1, NBL->nbricks); - return -1; - } - } - if( g_opts.debug > 1 ) - fprintf(stderr,"+d wrote image of %d brick(s), each of %u bytes\n", - NBL->nbricks, (unsigned int)NBL->bsize); - } - - /* mark as being in this CPU byte order */ - nim->byteorder = nifti_short_order() ; - - return 0; -} - -/* return number of extensions written, or -1 on error */ -static int nifti_write_extensions(znzFile fp, nifti_image *nim) -{ - nifti1_extension * list; - char extdr[4] = { 0, 0, 0, 0 }; - int c, size, ok = 1; - - if( znz_isnull(fp) || !nim || nim->num_ext < 0 ){ - if( g_opts.debug > 0 ) - fprintf(stderr,"** nifti_write_extensions, bad params\n"); - return -1; - } - - /* if no extensions and user requests it, skip extender */ - if( g_opts.skip_blank_ext && (nim->num_ext == 0 || ! nim->ext_list ) ){ - if( g_opts.debug > 1 ) - fprintf(stderr,"-d no exts and skip_blank_ext set, " - "so skipping 4-byte extender\n"); - return 0; - } - - /* if invalid extension list, clear num_ext */ - if( ! valid_nifti_extensions(nim) ) nim->num_ext = 0; - - /* write out extender block */ - if( nim->num_ext > 0 ) extdr[0] = 1; - if( nifti_write_buffer(fp, extdr, 4) != 4 ){ - fprintf(stderr,"** failed to write extender\n"); - return -1; - } - - list = nim->ext_list; - for ( c = 0; c < nim->num_ext; c++ ){ - size = (int)nifti_write_buffer(fp, &list->esize, sizeof(int)); - ok = (size == (int)sizeof(int)); - if( ok ){ - size = (int)nifti_write_buffer(fp, &list->ecode, sizeof(int)); - ok = (size == (int)sizeof(int)); - } - if( ok ){ - size = (int)nifti_write_buffer(fp, list->edata, list->esize - 8); - ok = (size == list->esize - 8); - } - - if( !ok ){ - fprintf(stderr,"** failed while writing extension #%d\n",c); - return -1; - } else if ( g_opts.debug > 2 ) - fprintf(stderr,"+d wrote extension %d of %d bytes\n", c, size); - - list++; - } - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d wrote out %d extension(s)\n", nim->num_ext); - - return nim->num_ext; -} - - -/*----------------------------------------------------------------------*/ -/*! basic initialization of a nifti_image struct (to a 1x1x1 image) -*//*--------------------------------------------------------------------*/ -nifti_image* nifti_simple_init_nim(void) -{ - nifti_image *nim; - struct nifti_1_header nhdr; - int nbyper, swapsize; - - memset(&nhdr,0,sizeof(nhdr)) ; /* zero out header, to be safe */ - - nhdr.sizeof_hdr = sizeof(nhdr) ; - nhdr.regular = 'r' ; /* for some stupid reason */ - - nhdr.dim[0] = 3 ; - nhdr.dim[1] = 1 ; nhdr.dim[2] = 1 ; nhdr.dim[3] = 1 ; - nhdr.dim[4] = 0 ; - - nhdr.pixdim[0] = 0.0f ; - nhdr.pixdim[1] = 1.0f ; nhdr.pixdim[2] = 1.0f ; - nhdr.pixdim[3] = 1.0f ; - - nhdr.datatype = DT_FLOAT32 ; - nifti_datatype_sizes( nhdr.datatype , &nbyper, &swapsize ); - nhdr.bitpix = 8 * nbyper ; - - strcpy(nhdr.magic, "n+1"); /* init to single file */ - - nim = nifti_convert_nhdr2nim(nhdr,NULL); - nim->fname = NULL; - nim->iname = NULL; - return nim; -} - - -/*----------------------------------------------------------------------*/ -/*! basic initialization of a nifti_1_header struct (with given dimensions) - - Return an allocated nifti_1_header struct, based on the given - dimensions and datatype. - - \param arg_dims : optional dim[8] array (default {3,1,1,1,0,0,0,0}) - \param arg_dtype : optional datatype (default DT_FLOAT32) - - \return pointer to allocated nifti_1_header struct -*//*--------------------------------------------------------------------*/ -nifti_1_header * nifti_make_new_header(const int arg_dims[], int arg_dtype) -{ - nifti_1_header * nhdr; - const int default_dims[8] = { 3, 1, 1, 1, 0, 0, 0, 0 }; - const int * dim; /* either passed or default dims */ - int dtype; /* either passed or default dtype */ - int c, nbyper, swapsize; - - /* if arg_dims is passed, apply it */ - if( arg_dims ) dim = arg_dims; - else dim = default_dims; - - /* validate dim: if there is any problem, apply default_dims */ - if( dim[0] < 1 || dim[0] > 7 ) { - fprintf(stderr,"** nifti_simple_hdr_with_dims: bad dim[0]=%d\n",dim[0]); - dim = default_dims; - } else { - for( c = 1; c <= dim[0]; c++ ) - if( dim[c] < 1 ) - { - fprintf(stderr, - "** nifti_simple_hdr_with_dims: bad dim[%d]=%d\n",c,dim[c]); - dim = default_dims; - break; - } - } - - /* validate dtype, too */ - dtype = arg_dtype; - if( ! nifti_is_valid_datatype(dtype) ) { - fprintf(stderr,"** nifti_simple_hdr_with_dims: bad dtype %d\n",dtype); - dtype = DT_FLOAT32; - } - - /* now populate the header struct */ - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d nifti_make_new_header, dim[0] = %d, datatype = %d\n", - dim[0], dtype); - - nhdr = (nifti_1_header *)calloc(1,sizeof(nifti_1_header)); - if( !nhdr ){ - fprintf(stderr,"** nifti_make_new_header: failed to alloc hdr\n"); - return NULL; - } - - nhdr->sizeof_hdr = sizeof(nifti_1_header) ; - nhdr->regular = 'r' ; /* for some stupid reason */ - - /* init dim and pixdim */ - nhdr->dim[0] = dim[0] ; - nhdr->pixdim[0] = 0.0f; - for( c = 1; c <= dim[0]; c++ ) { - nhdr->dim[c] = dim[c]; - nhdr->pixdim[c] = 1.0f; - } - - nhdr->datatype = dtype ; - nifti_datatype_sizes( nhdr->datatype , &nbyper, &swapsize ); - nhdr->bitpix = 8 * nbyper ; - - strcpy(nhdr->magic, "n+1"); /* init to single file */ - - return nhdr; -} - - -/*----------------------------------------------------------------------*/ -/*! basic creation of a nifti_image struct - - Create a nifti_image from the given dimensions and data type. - Optinally, allocate zero-filled data. - - \param dims : optional dim[8] (default {3,1,1,1,0,0,0,0}) - \param datatype : optional datatype (default DT_FLOAT32) - \param data_fill : if flag is set, allocate zero-filled data for image - - \return pointer to allocated nifti_image struct -*//*--------------------------------------------------------------------*/ -nifti_image * nifti_make_new_nim(const int dims[], int datatype, int data_fill) -{ - nifti_image * nim; - nifti_1_header * nhdr; - - nhdr = nifti_make_new_header(dims, datatype); - if( !nhdr ) return NULL; /* error already printed */ - - nim = nifti_convert_nhdr2nim(*nhdr,NULL); - free(nhdr); /* in any case, we are done with this */ - if( !nim ){ - fprintf(stderr,"** NMNN: nifti_convert_nhdr2nim failure\n"); - return NULL; - } - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d nifti_make_new_nim, data_fill = %d\n",data_fill); - - if( data_fill ) { - nim->data = calloc(nim->nvox, nim->nbyper); - - /* if we cannot allocate data, take ball and go home */ - if( !nim->data ) { - fprintf(stderr,"** NMNN: failed to alloc %u bytes for data\n", - (unsigned)(nim->nvox*nim->nbyper)); - nifti_image_free(nim); - nim = NULL; - } - } - - return nim; -} - - -/*----------------------------------------------------------------------*/ -/*! convert a nifti_image structure to a nifti_1_header struct - - No allocation is done, this should be used via structure copy. - As in: - 
-    nifti_1_header my_header;
-    my_header = nifti_convert_nim2nhdr(my_nim_pointer);
-
-*//*--------------------------------------------------------------------*/ -struct nifti_1_header nifti_convert_nim2nhdr(const nifti_image * nim) -{ - struct nifti_1_header nhdr; - - memset(&nhdr,0,sizeof(nhdr)) ; /* zero out header, to be safe */ - - - /**- load the ANALYZE-7.5 generic parts of the header struct */ - - nhdr.sizeof_hdr = sizeof(nhdr) ; - nhdr.regular = 'r' ; /* for some stupid reason */ - - nhdr.dim[0] = nim->ndim ; - nhdr.dim[1] = nim->nx ; nhdr.dim[2] = nim->ny ; nhdr.dim[3] = nim->nz ; - nhdr.dim[4] = nim->nt ; nhdr.dim[5] = nim->nu ; nhdr.dim[6] = nim->nv ; - nhdr.dim[7] = nim->nw ; - - nhdr.pixdim[0] = 0.0f ; - nhdr.pixdim[1] = nim->dx ; nhdr.pixdim[2] = nim->dy ; - nhdr.pixdim[3] = nim->dz ; nhdr.pixdim[4] = nim->dt ; - nhdr.pixdim[5] = nim->du ; nhdr.pixdim[6] = nim->dv ; - nhdr.pixdim[7] = nim->dw ; - - nhdr.datatype = nim->datatype ; - nhdr.bitpix = 8 * nim->nbyper ; - - if( nim->cal_max > nim->cal_min ){ - nhdr.cal_max = nim->cal_max ; - nhdr.cal_min = nim->cal_min ; - } - - if( nim->scl_slope != 0.0 ){ - nhdr.scl_slope = nim->scl_slope ; - nhdr.scl_inter = nim->scl_inter ; - } - - if( nim->descrip[0] != '\0' ){ - memcpy(nhdr.descrip ,nim->descrip ,79) ; nhdr.descrip[79] = '\0' ; - } - if( nim->aux_file[0] != '\0' ){ - memcpy(nhdr.aux_file ,nim->aux_file ,23) ; nhdr.aux_file[23] = '\0' ; - } - - /**- Load NIFTI specific stuff into the header */ - - if( nim->nifti_type > NIFTI_FTYPE_ANALYZE ){ /* then not ANALYZE */ - - if( nim->nifti_type == NIFTI_FTYPE_NIFTI1_1 ) strcpy(nhdr.magic,"n+1") ; - else strcpy(nhdr.magic,"ni1") ; - - nhdr.pixdim[1] = (float)fabs(nhdr.pixdim[1]) ; nhdr.pixdim[2] = (float)fabs(nhdr.pixdim[2]) ; - nhdr.pixdim[3] = (float)fabs(nhdr.pixdim[3]) ; nhdr.pixdim[4] = (float)fabs(nhdr.pixdim[4]) ; - nhdr.pixdim[5] = (float)fabs(nhdr.pixdim[5]) ; nhdr.pixdim[6] = (float)fabs(nhdr.pixdim[6]) ; - nhdr.pixdim[7] = (float)fabs(nhdr.pixdim[7]) ; - - nhdr.intent_code = nim->intent_code ; - nhdr.intent_p1 = nim->intent_p1 ; - nhdr.intent_p2 = nim->intent_p2 ; - nhdr.intent_p3 = nim->intent_p3 ; - if( nim->intent_name[0] != '\0' ){ - memcpy(nhdr.intent_name,nim->intent_name,15) ; - nhdr.intent_name[15] = '\0' ; - } - - nhdr.vox_offset = (float) nim->iname_offset ; - nhdr.xyzt_units = SPACE_TIME_TO_XYZT( nim->xyz_units, nim->time_units ) ; - nhdr.toffset = nim->toffset ; - - if( nim->qform_code > 0 ){ - nhdr.qform_code = nim->qform_code ; - nhdr.quatern_b = nim->quatern_b ; - nhdr.quatern_c = nim->quatern_c ; - nhdr.quatern_d = nim->quatern_d ; - nhdr.qoffset_x = nim->qoffset_x ; - nhdr.qoffset_y = nim->qoffset_y ; - nhdr.qoffset_z = nim->qoffset_z ; - nhdr.pixdim[0] = (nim->qfac >= 0.0) ? 1.0f : -1.0f ; - } - - if( nim->sform_code > 0 ){ - nhdr.sform_code = nim->sform_code ; - nhdr.srow_x[0] = nim->sto_xyz.m[0][0] ; - nhdr.srow_x[1] = nim->sto_xyz.m[0][1] ; - nhdr.srow_x[2] = nim->sto_xyz.m[0][2] ; - nhdr.srow_x[3] = nim->sto_xyz.m[0][3] ; - nhdr.srow_y[0] = nim->sto_xyz.m[1][0] ; - nhdr.srow_y[1] = nim->sto_xyz.m[1][1] ; - nhdr.srow_y[2] = nim->sto_xyz.m[1][2] ; - nhdr.srow_y[3] = nim->sto_xyz.m[1][3] ; - nhdr.srow_z[0] = nim->sto_xyz.m[2][0] ; - nhdr.srow_z[1] = nim->sto_xyz.m[2][1] ; - nhdr.srow_z[2] = nim->sto_xyz.m[2][2] ; - nhdr.srow_z[3] = nim->sto_xyz.m[2][3] ; - } - - nhdr.dim_info = FPS_INTO_DIM_INFO( nim->freq_dim , - nim->phase_dim , nim->slice_dim ) ; - nhdr.slice_code = nim->slice_code ; - nhdr.slice_start = nim->slice_start ; - nhdr.slice_end = nim->slice_end ; - nhdr.slice_duration = nim->slice_duration ; - } - - return nhdr; -} - - -/*----------------------------------------------------------------------*/ -/*! \fn int nifti_copy_extensions(nifti_image * nim_dest, nifti_image * nim_src) - \brief copy the nifti1_extension list from src to dest - - Duplicate the list of nifti1_extensions. The dest structure must - be clear of extensions. - \return 0 on success, -1 on failure - - \sa nifti_add_extension, nifti_free_extensions -*/ -int nifti_copy_extensions(nifti_image * nim_dest, const nifti_image * nim_src) -{ - char * data; - size_t bytes; - int c, size, old_size; - - if( nim_dest->num_ext > 0 || nim_dest->ext_list != NULL ){ - fprintf(stderr,"** will not copy extensions over existing ones\n"); - return -1; - } - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d duplicating %d extension(s)\n", nim_src->num_ext); - - if( nim_src->num_ext <= 0 ) return 0; - - bytes = nim_src->num_ext * sizeof(nifti1_extension); /* I'm lazy */ - nim_dest->ext_list = (nifti1_extension *)malloc(bytes); - if( !nim_dest->ext_list ){ - fprintf(stderr,"** failed to allocate %d nifti1_extension structs\n", - nim_src->num_ext); - return -1; - } - - /* copy the extension data */ - nim_dest->num_ext = 0; - for( c = 0; c < nim_src->num_ext; c++ ){ - size = old_size = nim_src->ext_list[c].esize; - if( size & 0xf ) size = (size + 0xf) & ~0xf; /* make multiple of 16 */ - if( g_opts.debug > 2 ) - fprintf(stderr,"+d dup'ing ext #%d of size %d (from size %d)\n", - c, size, old_size); - /* data length is size-8, as esize includes space for esize and ecode */ - data = (char *)calloc(size-8,sizeof(char)); /* maybe size > old */ - if( !data ){ - fprintf(stderr,"** failed to alloc %d bytes for extention\n", size); - if( c == 0 ) { free(nim_dest->ext_list); nim_dest->ext_list = NULL; } - /* otherwise, keep what we have (a.o.t. deleting them all) */ - return -1; - } - /* finally, fill the new structure */ - nim_dest->ext_list[c].esize = size; - nim_dest->ext_list[c].ecode = nim_src->ext_list[c].ecode; - nim_dest->ext_list[c].edata = data; - memcpy(data, nim_src->ext_list[c].edata, old_size-8); - - nim_dest->num_ext++; - } - - return 0; -} - - -/*----------------------------------------------------------------------*/ -/*! compute the total size of all extensions - - \return the total of all esize fields - - Note that each esize includes 4 bytes for ecode, 4 bytes for esize, - and the bytes used for the data. Each esize also needs to be a - multiple of 16, so it may be greater than the sum of its 3 parts. -*//*--------------------------------------------------------------------*/ -int nifti_extension_size(nifti_image *nim) -{ - int c, size = 0; - - if( !nim || nim->num_ext <= 0 ) return 0; - - if( g_opts.debug > 2 ) fprintf(stderr,"-d ext sizes:"); - - for ( c = 0; c < nim->num_ext; c++ ){ - size += nim->ext_list[c].esize; - if( g_opts.debug > 2 ) fprintf(stderr," %d",nim->ext_list[c].esize); - } - - if( g_opts.debug > 2 ) fprintf(stderr," (total = %d)\n",size); - - return size; -} - - -/*----------------------------------------------------------------------*/ -/*! set the nifti_image iname_offset field, based on nifti_type - - - if writing to 2 files, set offset to 0 - - if writing to a single NIFTI-1 file, set the offset to - 352 + total extension size, then align to 16-byte boundary - - if writing an ASCII header, set offset to -1 -*//*--------------------------------------------------------------------*/ -void nifti_set_iname_offset(nifti_image *nim) -{ - int offset; - - switch( nim->nifti_type ){ - - default: /* writing into 2 files */ - /* we only write files with 0 offset in the 2 file format */ - nim->iname_offset = 0 ; - break ; - - /* NIFTI-1 single binary file - always update */ - case NIFTI_FTYPE_NIFTI1_1: - offset = nifti_extension_size(nim)+sizeof(struct nifti_1_header)+4; - /* be sure offset is aligned to a 16 byte boundary */ - if ( ( offset % 16 ) != 0 ) offset = ((offset + 0xf) & ~0xf); - if( nim->iname_offset != offset ){ - if( g_opts.debug > 1 ) - fprintf(stderr,"+d changing offset from %d to %d\n", - nim->iname_offset, offset); - nim->iname_offset = offset; - } - break ; - - /* non-standard case: NIFTI-1 ASCII header + binary data (single file) */ - case NIFTI_FTYPE_ASCII: - nim->iname_offset = -1 ; /* compute offset from filesize */ - break ; - } -} - - -/*----------------------------------------------------------------------*/ -/*! write the nifti_image dataset to disk, optionally including data - - This is just a front-end for nifti_image_write_hdr_img2. - - \param nim nifti_image to write to disk - \param write_data write options (see nifti_image_write_hdr_img2) - \param opts file open options ("wb" from nifti_image_write) - - \sa nifti_image_write, nifti_image_write_hdr_img2, nifti_image_free, - nifti_set_filenames -*//*--------------------------------------------------------------------*/ -znzFile nifti_image_write_hdr_img( nifti_image *nim , int write_data , - const char* opts ) -{ - return nifti_image_write_hdr_img2(nim,write_data,opts,NULL,NULL); -} - - -#undef ERREX -#define ERREX(msg) \ - do{ fprintf(stderr,"** ERROR: nifti_image_write_hdr_img: %s\n",(msg)) ; \ - return fp ; } while(0) - - -/* ----------------------------------------------------------------------*/ -/*! This writes the header (and optionally the image data) to file - * - * If the image data file is left open it returns a valid znzFile handle. - * It also uses imgfile as the open image file is not null, and modifies - * it inside. - * - * \param nim nifti_image to write to disk - * \param write_opts flags whether to write data and/or close file (see below) - * \param opts file-open options, probably "wb" from nifti_image_write() - * \param imgfile optional open znzFile struct, for writing image data - (may be NULL) - * \param NBL optional nifti_brick_list, containing the image data - (may be NULL) - * - * Values for write_opts mode are based on two binary flags - * ( 0/1 for no-write/write data, and 0/2 for close/leave-open files ) : - * - 0 = do not write data and close (do not open data file) - * - 1 = write data and close - * - 2 = do not write data and leave data file open - * - 3 = write data and leave data file open - * - * \sa nifti_image_write, nifti_image_write_hdr_img, nifti_image_free, - * nifti_set_filenames -*//*---------------------------------------------------------------------*/ -znzFile nifti_image_write_hdr_img2(nifti_image *nim, int write_opts, - const char * opts, znzFile imgfile, const nifti_brick_list * NBL) -{ - struct nifti_1_header nhdr ; - znzFile fp=NULL; - size_t ss ; - int write_data, leave_open; - char func[] = { "nifti_image_write_hdr_img2" }; - - write_data = write_opts & 1; /* just separate the bits now */ - leave_open = write_opts & 2; - - if( ! nim ) ERREX("NULL input") ; - if( ! nifti_validfilename(nim->fname) ) ERREX("bad fname input") ; - if( write_data && ! nim->data && ! NBL ) ERREX("no image data") ; - - if( write_data && NBL && ! nifti_NBL_matches_nim(nim, NBL) ) - ERREX("NBL does not match nim"); - - nifti_set_iname_offset(nim); - - if( g_opts.debug > 1 ){ - fprintf(stderr,"-d writing nifti file '%s'...\n", nim->fname); - if( g_opts.debug > 2 ) - fprintf(stderr,"-d nifti type %d, offset %d\n", - nim->nifti_type, nim->iname_offset); - } - - if( nim->nifti_type == NIFTI_FTYPE_ASCII ) /* non-standard case */ - return nifti_write_ascii_image(nim,NBL,opts,write_data,leave_open); - - nhdr = nifti_convert_nim2nhdr(nim); /* create the nifti1_header struct */ - - /* if writing to 2 files, make sure iname is set and different from fname */ - if( nim->nifti_type != NIFTI_FTYPE_NIFTI1_1 ){ - if( nim->iname && strcmp(nim->iname,nim->fname) == 0 ){ - free(nim->iname) ; nim->iname = NULL ; - } - if( nim->iname == NULL ){ /* then make a new one */ - nim->iname = nifti_makeimgname(nim->fname,nim->nifti_type,0,0); - if( nim->iname == NULL ) return NULL; - } - } - - /* if we have an imgfile and will write the header there, use it */ - if( ! znz_isnull(imgfile) && nim->nifti_type == NIFTI_FTYPE_NIFTI1_1 ){ - if( g_opts.debug > 2 ) fprintf(stderr,"+d using passed file for hdr\n"); - fp = imgfile; - } - else { - if( g_opts.debug > 2 ) - fprintf(stderr,"+d opening output file %s [%s]\n",nim->fname,opts); - fp = znzopen( nim->fname , opts , nifti_is_gzfile(nim->fname) ) ; - if( znz_isnull(fp) ){ - LNI_FERR(func,"cannot open output file",nim->fname); - return fp; - } - } - - /* write the header and extensions */ - - ss = znzwrite(&nhdr , 1 , sizeof(nhdr) , fp); /* write header */ - if( ss < sizeof(nhdr) ){ - LNI_FERR(func,"bad header write to output file",nim->fname); - znzclose(fp); return fp; - } - - /* partial file exists, and errors have been printed, so ignore return */ - if( nim->nifti_type != NIFTI_FTYPE_ANALYZE ) - (void)nifti_write_extensions(fp,nim); - - /* if the header is all we want, we are done */ - if( ! write_data && ! leave_open ){ - if( g_opts.debug > 2 ) fprintf(stderr,"-d header is all we want: done\n"); - znzclose(fp); return(fp); - } - - if( nim->nifti_type != NIFTI_FTYPE_NIFTI1_1 ){ /* get a new file pointer */ - znzclose(fp); /* first, close header file */ - if( ! znz_isnull(imgfile) ){ - if(g_opts.debug > 2) fprintf(stderr,"+d using passed file for img\n"); - fp = imgfile; - } - else { - if( g_opts.debug > 2 ) - fprintf(stderr,"+d opening img file '%s'\n", nim->iname); - fp = znzopen( nim->iname , opts , nifti_is_gzfile(nim->iname) ) ; - if( znz_isnull(fp) ) ERREX("cannot open image file") ; - } - } - - znzseek(fp, nim->iname_offset, SEEK_SET); /* in any case, seek to offset */ - - if( write_data ) nifti_write_all_data(fp,nim,NBL); - if( ! leave_open ) znzclose(fp); - - return fp; -} - - -/*----------------------------------------------------------------------*/ -/*! write a nifti_image to disk in ASCII format -*//*--------------------------------------------------------------------*/ -znzFile nifti_write_ascii_image(nifti_image *nim, const nifti_brick_list * NBL, - const char *opts, int write_data, int leave_open) -{ - znzFile fp; - char * hstr; - - hstr = nifti_image_to_ascii( nim ) ; /* get header in ASCII form */ - if( ! hstr ){ fprintf(stderr,"** failed image_to_ascii()\n"); return NULL; } - - fp = znzopen( nim->fname , opts , nifti_is_gzfile(nim->fname) ) ; - if( znz_isnull(fp) ){ - free(hstr); - fprintf(stderr,"** failed to open '%s' for ascii write\n",nim->fname); - return fp; - } - - znzputs(hstr,fp); /* header */ - nifti_write_extensions(fp,nim); /* extensions */ - - if ( write_data ) { nifti_write_all_data(fp,nim,NBL); } /* data */ - if ( ! leave_open ) { znzclose(fp); } - free(hstr); - return fp; /* returned but may be closed */ -} - - -/*--------------------------------------------------------------------------*/ -/*! Write a nifti_image to disk. - - Since data is properly byte-swapped upon reading, it is assumed - to be in the byte-order of the current CPU at write time. Thus, - nim->byte_order should match that of the current CPU. Note that - the nifti_set_filenames() function takes the flag, set_byte_order. - - The following fields of nim affect how the output appears: - - nifti_type = 0 ==> ANALYZE-7.5 format file pair will be written - - nifti_type = 1 ==> NIFTI-1 format single file will be written - (data offset will be 352+extensions) - - nifti_type = 2 ==> NIFTI_1 format file pair will be written - - nifti_type = 3 ==> NIFTI_1 ASCII single file will be written - - fname is the name of the output file (header or header+data) - - if a file pair is being written, iname is the name of the data file - - existing files WILL be overwritten with extreme prejudice - - if qform_code > 0, the quatern_*, qoffset_*, and qfac fields determine - the qform output, NOT the qto_xyz matrix; if you want to compute these - fields from the qto_xyz matrix, you can use the utility function - nifti_mat44_to_quatern() - - \sa nifti_image_write_bricks, nifti_image_free, nifti_set_filenames, - nifti_image_write_hdr_img -*//*------------------------------------------------------------------------*/ -void nifti_image_write( nifti_image *nim ) -{ - znzFile fp = nifti_image_write_hdr_img(nim,1,"wb"); - if( fp ){ - if( g_opts.debug > 2 ) fprintf(stderr,"-d niw: done with znzFile\n"); - free(fp); - } - if( g_opts.debug > 1 ) fprintf(stderr,"-d nifti_image_write: done\n"); -} - - -/*----------------------------------------------------------------------*/ -/*! similar to nifti_image_write, but data is in NBL struct, not nim->data - - \sa nifti_image_write, nifti_image_free, nifti_set_filenames, nifti_free_NBL -*//*--------------------------------------------------------------------*/ -void nifti_image_write_bricks( nifti_image *nim, const nifti_brick_list * NBL ) -{ - znzFile fp = nifti_image_write_hdr_img2(nim,1,"wb",NULL,NBL); - if( fp ){ - if( g_opts.debug > 2 ) fprintf(stderr,"-d niwb: done with znzFile\n"); - free(fp); - } - if( g_opts.debug > 1 ) fprintf(stderr,"-d niwb: done writing bricks\n"); -} - - -/*----------------------------------------------------------------------*/ -/*! copy the nifti_image structure, without data - - Duplicate the structure, including fname, iname and extensions. - Leave the data pointer as NULL. -*//*--------------------------------------------------------------------*/ -nifti_image * nifti_copy_nim_info(const nifti_image * src) -{ - nifti_image *dest; - dest = (nifti_image *)calloc(1,sizeof(nifti_image)); - if( !dest ){ - fprintf(stderr,"** NCNI: failed to alloc nifti_image\n"); - return NULL; - } - memcpy(dest, src, sizeof(nifti_image)); - if( src->fname ) dest->fname = nifti_strdup(src->fname); - if( src->iname ) dest->iname = nifti_strdup(src->iname); - dest->num_ext = 0; - dest->ext_list = NULL; - /* errors will be printed in NCE(), continue in either case */ - (void)nifti_copy_extensions(dest, src); - - dest->data = NULL; - - return dest; -} - - -/*------------------------------------------------------------------------*/ -/* Un-escape a C string in place -- that is, convert XML escape sequences - back into their characters. (This can be done in place since the - replacement is always smaller than the input.) Escapes recognized are: - - < -> < - - > -> > - - " -> " - - ' -> ' - - & -> & - Also replace CR LF pair (Microsoft), or CR alone (Macintosh) with - LF (Unix), per the XML standard. - Return value is number of replacements made (if you care). ---------------------------------------------------------------------------*/ - -#undef CR -#undef LF -#define CR 0x0D -#define LF 0x0A - -static int unescape_string( char *str ) -{ - int ii,jj , nn,ll ; - - if( str == NULL ) return 0 ; /* no string? */ - ll = (int)strlen(str) ; if( ll == 0 ) return 0 ; - - /* scan for escapes: &something; */ - - for( ii=jj=nn=0 ; ii': lout += 4 ; break ; /* replace '<' with "<" */ - - case '"' : - case '\'': lout += 6 ; break ; /* replace '"' with """ */ - - case CR: - case LF: lout += 6 ; break ; /* replace CR with " " - LF with " " */ - - default: lout++ ; break ; /* copy all other chars */ - } - } - out = (char *)calloc(1,lout) ; /* allocate output string */ - if( !out ){ - fprintf(stderr,"** escapize_string: failed to alloc %d bytes\n",lout); - return NULL; - } - out[0] = '\'' ; /* opening quote mark */ - for( ii=0,jj=1 ; ii < lstr ; ii++ ){ - switch( str[ii] ){ - default: out[jj++] = str[ii] ; break ; /* normal characters */ - - case '&': memcpy(out+jj,"&",5) ; jj+=5 ; break ; - - case '<': memcpy(out+jj,"<",4) ; jj+=4 ; break ; - case '>': memcpy(out+jj,">",4) ; jj+=4 ; break ; - - case '"' : memcpy(out+jj,""",6) ; jj+=6 ; break ; - - case '\'': memcpy(out+jj,"'",6) ; jj+=6 ; break ; - - case CR: memcpy(out+jj," ",6) ; jj+=6 ; break ; - case LF: memcpy(out+jj," ",6) ; jj+=6 ; break ; - } - } - out[jj++] = '\'' ; /* closing quote mark */ - out[jj] = '\0' ; /* terminate the string */ - return out ; -} - -/*---------------------------------------------------------------------------*/ -/*! Dump the information in a NIFTI image header to an XML-ish ASCII string - that can later be converted back into a NIFTI header in - nifti_image_from_ascii(). - - The resulting string can be free()-ed when you are done with it. -*//*-------------------------------------------------------------------------*/ -char *nifti_image_to_ascii( const nifti_image *nim ) -{ - char *buf , *ebuf ; int nbuf ; - - if( nim == NULL ) return NULL ; /* stupid caller */ - - buf = (char *)calloc(1,65534); nbuf = 0; /* longer than needed, to be safe */ - if( !buf ){ - fprintf(stderr,"** NITA: failed to alloc %d bytes\n",65534); - return NULL; - } - - sprintf( buf , "nifti_type == NIFTI_FTYPE_NIFTI1_1) ? "NIFTI-1+" - :(nim->nifti_type == NIFTI_FTYPE_NIFTI1_2) ? "NIFTI-1" - :(nim->nifti_type == NIFTI_FTYPE_ASCII ) ? "NIFTI-1A" - : "ANALYZE-7.5" ) ; - - /** Strings that we don't control (filenames, etc.) that might - contain "weird" characters (like quotes) are "escaped": - - A few special characters are replaced by XML-style escapes, using - the function escapize_string(). - - On input, function unescape_string() reverses this process. - - The result is that the NIFTI ASCII-format header is XML-compliant. */ - - ebuf = escapize_string(nim->fname) ; - sprintf( buf+strlen(buf) , " header_filename = %s\n",ebuf); free(ebuf); - - ebuf = escapize_string(nim->iname) ; - sprintf( buf+strlen(buf) , " image_filename = %s\n", ebuf); free(ebuf); - - sprintf( buf+strlen(buf) , " image_offset = '%d'\n" , nim->iname_offset ); - - sprintf( buf+strlen(buf), " ndim = '%d'\n", nim->ndim); - sprintf( buf+strlen(buf), " nx = '%d'\n", nim->nx ); - if( nim->ndim > 1 ) sprintf( buf+strlen(buf), " ny = '%d'\n", nim->ny ); - if( nim->ndim > 2 ) sprintf( buf+strlen(buf), " nz = '%d'\n", nim->nz ); - if( nim->ndim > 3 ) sprintf( buf+strlen(buf), " nt = '%d'\n", nim->nt ); - if( nim->ndim > 4 ) sprintf( buf+strlen(buf), " nu = '%d'\n", nim->nu ); - if( nim->ndim > 5 ) sprintf( buf+strlen(buf), " nv = '%d'\n", nim->nv ); - if( nim->ndim > 6 ) sprintf( buf+strlen(buf), " nw = '%d'\n", nim->nw ); - sprintf( buf+strlen(buf), " dx = '%g'\n", nim->dx ); - if( nim->ndim > 1 ) sprintf( buf+strlen(buf), " dy = '%g'\n", nim->dy ); - if( nim->ndim > 2 ) sprintf( buf+strlen(buf), " dz = '%g'\n", nim->dz ); - if( nim->ndim > 3 ) sprintf( buf+strlen(buf), " dt = '%g'\n", nim->dt ); - if( nim->ndim > 4 ) sprintf( buf+strlen(buf), " du = '%g'\n", nim->du ); - if( nim->ndim > 5 ) sprintf( buf+strlen(buf), " dv = '%g'\n", nim->dv ); - if( nim->ndim > 6 ) sprintf( buf+strlen(buf), " dw = '%g'\n", nim->dw ); - - sprintf( buf+strlen(buf) , " datatype = '%d'\n" , nim->datatype ) ; - sprintf( buf+strlen(buf) , " datatype_name = '%s'\n" , - nifti_datatype_string(nim->datatype) ) ; - - sprintf( buf+strlen(buf) , " nvox = '%u'\n" , (unsigned)nim->nvox ) ; - sprintf( buf+strlen(buf) , " nbyper = '%d'\n" , nim->nbyper ) ; - - sprintf( buf+strlen(buf) , " byteorder = '%s'\n" , - (nim->byteorder==MSB_FIRST) ? "MSB_FIRST" : "LSB_FIRST" ) ; - - if( nim->cal_min < nim->cal_max ){ - sprintf( buf+strlen(buf) , " cal_min = '%g'\n", nim->cal_min ) ; - sprintf( buf+strlen(buf) , " cal_max = '%g'\n", nim->cal_max ) ; - } - - if( nim->scl_slope != 0.0 ){ - sprintf( buf+strlen(buf) , " scl_slope = '%g'\n" , nim->scl_slope ) ; - sprintf( buf+strlen(buf) , " scl_inter = '%g'\n" , nim->scl_inter ) ; - } - - if( nim->intent_code > 0 ){ - sprintf( buf+strlen(buf) , " intent_code = '%d'\n", nim->intent_code ) ; - sprintf( buf+strlen(buf) , " intent_code_name = '%s'\n" , - nifti_intent_string(nim->intent_code) ) ; - sprintf( buf+strlen(buf) , " intent_p1 = '%g'\n" , nim->intent_p1 ) ; - sprintf( buf+strlen(buf) , " intent_p2 = '%g'\n" , nim->intent_p2 ) ; - sprintf( buf+strlen(buf) , " intent_p3 = '%g'\n" , nim->intent_p3 ) ; - - if( nim->intent_name[0] != '\0' ){ - ebuf = escapize_string(nim->intent_name) ; - sprintf( buf+strlen(buf) , " intent_name = %s\n",ebuf) ; - free(ebuf) ; - } - } - - if( nim->toffset != 0.0 ) - sprintf( buf+strlen(buf) , " toffset = '%g'\n",nim->toffset ) ; - - if( nim->xyz_units > 0 ) - sprintf( buf+strlen(buf) , - " xyz_units = '%d'\n" - " xyz_units_name = '%s'\n" , - nim->xyz_units , nifti_units_string(nim->xyz_units) ) ; - - if( nim->time_units > 0 ) - sprintf( buf+strlen(buf) , - " time_units = '%d'\n" - " time_units_name = '%s'\n" , - nim->time_units , nifti_units_string(nim->time_units) ) ; - - if( nim->freq_dim > 0 ) - sprintf( buf+strlen(buf) , " freq_dim = '%d'\n",nim->freq_dim ) ; - if( nim->phase_dim > 0 ) - sprintf( buf+strlen(buf) , " phase_dim = '%d'\n",nim->phase_dim ) ; - if( nim->slice_dim > 0 ) - sprintf( buf+strlen(buf) , " slice_dim = '%d'\n",nim->slice_dim ) ; - if( nim->slice_code > 0 ) - sprintf( buf+strlen(buf) , - " slice_code = '%d'\n" - " slice_code_name = '%s'\n" , - nim->slice_code , nifti_slice_string(nim->slice_code) ) ; - if( nim->slice_start >= 0 && nim->slice_end > nim->slice_start ) - sprintf( buf+strlen(buf) , - " slice_start = '%d'\n" - " slice_end = '%d'\n" , nim->slice_start , nim->slice_end ) ; - if( nim->slice_duration != 0.0 ) - sprintf( buf+strlen(buf) , " slice_duration = '%g'\n", - nim->slice_duration ) ; - - if( nim->descrip[0] != '\0' ){ - ebuf = escapize_string(nim->descrip) ; - sprintf( buf+strlen(buf) , " descrip = %s\n",ebuf) ; - free(ebuf) ; - } - - if( nim->aux_file[0] != '\0' ){ - ebuf = escapize_string(nim->aux_file) ; - sprintf( buf+strlen(buf) , " aux_file = %s\n",ebuf) ; - free(ebuf) ; - } - - if( nim->qform_code > 0 ){ - int i,j,k ; - - sprintf( buf+strlen(buf) , - " qform_code = '%d'\n" - " qform_code_name = '%s'\n" - " qto_xyz_matrix = '%g %g %g %g %g %g %g %g %g %g %g %g %g %g %g %g'\n" , - nim->qform_code , nifti_xform_string(nim->qform_code) , - nim->qto_xyz.m[0][0] , nim->qto_xyz.m[0][1] , - nim->qto_xyz.m[0][2] , nim->qto_xyz.m[0][3] , - nim->qto_xyz.m[1][0] , nim->qto_xyz.m[1][1] , - nim->qto_xyz.m[1][2] , nim->qto_xyz.m[1][3] , - nim->qto_xyz.m[2][0] , nim->qto_xyz.m[2][1] , - nim->qto_xyz.m[2][2] , nim->qto_xyz.m[2][3] , - nim->qto_xyz.m[3][0] , nim->qto_xyz.m[3][1] , - nim->qto_xyz.m[3][2] , nim->qto_xyz.m[3][3] ) ; - - sprintf( buf+strlen(buf) , - " qto_ijk_matrix = '%g %g %g %g %g %g %g %g %g %g %g %g %g %g %g %g'\n" , - nim->qto_ijk.m[0][0] , nim->qto_ijk.m[0][1] , - nim->qto_ijk.m[0][2] , nim->qto_ijk.m[0][3] , - nim->qto_ijk.m[1][0] , nim->qto_ijk.m[1][1] , - nim->qto_ijk.m[1][2] , nim->qto_ijk.m[1][3] , - nim->qto_ijk.m[2][0] , nim->qto_ijk.m[2][1] , - nim->qto_ijk.m[2][2] , nim->qto_ijk.m[2][3] , - nim->qto_ijk.m[3][0] , nim->qto_ijk.m[3][1] , - nim->qto_ijk.m[3][2] , nim->qto_ijk.m[3][3] ) ; - - sprintf( buf+strlen(buf) , - " quatern_b = '%g'\n" - " quatern_c = '%g'\n" - " quatern_d = '%g'\n" - " qoffset_x = '%g'\n" - " qoffset_y = '%g'\n" - " qoffset_z = '%g'\n" - " qfac = '%g'\n" , - nim->quatern_b , nim->quatern_c , nim->quatern_d , - nim->qoffset_x , nim->qoffset_y , nim->qoffset_z , nim->qfac ) ; - - nifti_mat44_to_orientation( nim->qto_xyz , &i,&j,&k ) ; - if( i > 0 && j > 0 && k > 0 ) - sprintf( buf+strlen(buf) , - " qform_i_orientation = '%s'\n" - " qform_j_orientation = '%s'\n" - " qform_k_orientation = '%s'\n" , - nifti_orientation_string(i) , - nifti_orientation_string(j) , - nifti_orientation_string(k) ) ; - } - - if( nim->sform_code > 0 ){ - int i,j,k ; - - sprintf( buf+strlen(buf) , - " sform_code = '%d'\n" - " sform_code_name = '%s'\n" - " sto_xyz_matrix = '%g %g %g %g %g %g %g %g %g %g %g %g %g %g %g %g'\n" , - nim->sform_code , nifti_xform_string(nim->sform_code) , - nim->sto_xyz.m[0][0] , nim->sto_xyz.m[0][1] , - nim->sto_xyz.m[0][2] , nim->sto_xyz.m[0][3] , - nim->sto_xyz.m[1][0] , nim->sto_xyz.m[1][1] , - nim->sto_xyz.m[1][2] , nim->sto_xyz.m[1][3] , - nim->sto_xyz.m[2][0] , nim->sto_xyz.m[2][1] , - nim->sto_xyz.m[2][2] , nim->sto_xyz.m[2][3] , - nim->sto_xyz.m[3][0] , nim->sto_xyz.m[3][1] , - nim->sto_xyz.m[3][2] , nim->sto_xyz.m[3][3] ) ; - - sprintf( buf+strlen(buf) , - " sto_ijk matrix = '%g %g %g %g %g %g %g %g %g %g %g %g %g %g %g %g'\n" , - nim->sto_ijk.m[0][0] , nim->sto_ijk.m[0][1] , - nim->sto_ijk.m[0][2] , nim->sto_ijk.m[0][3] , - nim->sto_ijk.m[1][0] , nim->sto_ijk.m[1][1] , - nim->sto_ijk.m[1][2] , nim->sto_ijk.m[1][3] , - nim->sto_ijk.m[2][0] , nim->sto_ijk.m[2][1] , - nim->sto_ijk.m[2][2] , nim->sto_ijk.m[2][3] , - nim->sto_ijk.m[3][0] , nim->sto_ijk.m[3][1] , - nim->sto_ijk.m[3][2] , nim->sto_ijk.m[3][3] ) ; - - nifti_mat44_to_orientation( nim->sto_xyz , &i,&j,&k ) ; - if( i > 0 && j > 0 && k > 0 ) - sprintf( buf+strlen(buf) , - " sform_i_orientation = '%s'\n" - " sform_j_orientation = '%s'\n" - " sform_k_orientation = '%s'\n" , - nifti_orientation_string(i) , - nifti_orientation_string(j) , - nifti_orientation_string(k) ) ; - } - - sprintf( buf+strlen(buf) , " num_ext = '%d'\n", nim->num_ext ) ; - - sprintf( buf+strlen(buf) , "/>\n" ) ; /* XML-ish closer */ - - nbuf = (int)strlen(buf) ; - buf = (char *)realloc((void *)buf, nbuf+1); /* cut back to proper length */ - if( !buf ) fprintf(stderr,"** NITA: failed to realloc %d bytes\n",nbuf+1); - return buf ; -} - -/*---------------------------------------------------------------------------*/ - -/*----------------------------------------------------------------------*/ -/*! get the byte order for this CPU - - - LSB_FIRST means least significant byte, first (little endian) - - MSB_FIRST means most significant byte, first (big endian) -*//*--------------------------------------------------------------------*/ -int nifti_short_order(void) /* determine this CPU's byte order */ -{ - union { unsigned char bb[2] ; - short ss ; } fred ; - - fred.bb[0] = 1 ; fred.bb[1] = 0 ; - - return (fred.ss == 1) ? LSB_FIRST : MSB_FIRST ; -} - -/*---------------------------------------------------------------------------*/ - -#undef QQNUM -#undef QNUM -#undef QSTR - -/* macro to check lhs string against "n1"; if it matches, - interpret rhs string as a number, and put it into nim->"n2" */ - -#define QQNUM(n1,n2,tt) if( strcmp(lhs,#n1)==0 ) nim->n2=(tt)strtod(rhs,NULL) - -/* same, but where "n1" == "n2" */ - -#define QNUM(nam,tt) QQNUM(nam,nam,tt) - -/* macro to check lhs string against "nam"; if it matches, - put rhs string into nim->"nam" string, with max length = "ml" */ - -#define QSTR(nam,ml) if( strcmp(lhs,#nam) == 0 ) \ - strncpy(nim->nam,rhs,ml), nim->nam[ml]='\0' - -/*---------------------------------------------------------------------------*/ -/*! Take an XML-ish ASCII string and create a NIFTI image header to match. - - NULL is returned if enough information isn't present in the input string. - - The image data can later be loaded with nifti_image_load(). - - The struct returned here can be liberated with nifti_image_free(). - - Not a lot of error checking is done here to make sure that the - input values are reasonable! -*//*-------------------------------------------------------------------------*/ -nifti_image *nifti_image_from_ascii( const char *str, int * bytes_read ) -{ - char lhs[1024] , rhs[1024] ; - int ii , spos, nn ; - nifti_image *nim ; /* will be output */ - - if( str == NULL || *str == '\0' ) return NULL ; /* bad input!? */ - - /* scan for opening string */ - - spos = 0 ; - ii = sscanf( str+spos , "%1023s%n" , lhs , &nn ) ; spos += nn ; - if( ii == 0 || strcmp(lhs,"nx = nim->ny = nim->nz = nim->nt - = nim->nu = nim->nv = nim->nw = 1 ; - nim->dx = nim->dy = nim->dz = nim->dt - = nim->du = nim->dv = nim->dw = 0 ; - nim->qfac = 1.0f ; - - nim->byteorder = nifti_short_order() ; - - /* starting at str[spos], scan for "equations" of the form - lhs = 'rhs' - and assign rhs values into the struct component named by lhs */ - - while(1){ - - while( isspace((int) str[spos]) ) spos++ ; /* skip whitespace */ - if( str[spos] == '\0' ) break ; /* end of string? */ - - /* get lhs string */ - - ii = sscanf( str+spos , "%1023s%n" , lhs , &nn ) ; spos += nn ; - if( ii == 0 || strcmp(lhs,"/>") == 0 ) break ; /* end of input? */ - - /* skip whitespace and the '=' marker */ - - while( isspace((int) str[spos]) || str[spos] == '=' ) spos++ ; - if( str[spos] == '\0' ) break ; /* end of string? */ - - /* if next character is a quote ', copy everything up to next ' - otherwise, copy everything up to next nonblank */ - - if( str[spos] == '\'' ){ - ii = spos+1 ; - while( str[ii] != '\0' && str[ii] != '\'' ) ii++ ; - nn = ii-spos-1 ; if( nn > 1023 ) nn = 1023 ; - memcpy(rhs,str+spos+1,nn) ; rhs[nn] = '\0' ; - spos = (str[ii] == '\'') ? ii+1 : ii ; - } else { - ii = sscanf( str+spos , "%1023s%n" , rhs , &nn ) ; spos += nn ; - if( ii == 0 ) break ; /* nothing found? */ - } - unescape_string(rhs) ; /* remove any XML escape sequences */ - - /* Now can do the assignment, based on lhs string. - Start with special cases that don't fit the QNUM/QSTR macros. */ - - if( strcmp(lhs,"nifti_type") == 0 ){ - if( strcmp(rhs,"ANALYZE-7.5") == 0 ) - nim->nifti_type = NIFTI_FTYPE_ANALYZE ; - else if( strcmp(rhs,"NIFTI-1+") == 0 ) - nim->nifti_type = NIFTI_FTYPE_NIFTI1_1 ; - else if( strcmp(rhs,"NIFTI-1") == 0 ) - nim->nifti_type = NIFTI_FTYPE_NIFTI1_2 ; - else if( strcmp(rhs,"NIFTI-1A") == 0 ) - nim->nifti_type = NIFTI_FTYPE_ASCII ; - } - else if( strcmp(lhs,"header_filename") == 0 ){ - nim->fname = nifti_strdup(rhs) ; - } - else if( strcmp(lhs,"image_filename") == 0 ){ - nim->iname = nifti_strdup(rhs) ; - } - else if( strcmp(lhs,"sto_xyz_matrix") == 0 ){ - sscanf( rhs , "%f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f" , - &(nim->sto_xyz.m[0][0]) , &(nim->sto_xyz.m[0][1]) , - &(nim->sto_xyz.m[0][2]) , &(nim->sto_xyz.m[0][3]) , - &(nim->sto_xyz.m[1][0]) , &(nim->sto_xyz.m[1][1]) , - &(nim->sto_xyz.m[1][2]) , &(nim->sto_xyz.m[1][3]) , - &(nim->sto_xyz.m[2][0]) , &(nim->sto_xyz.m[2][1]) , - &(nim->sto_xyz.m[2][2]) , &(nim->sto_xyz.m[2][3]) , - &(nim->sto_xyz.m[3][0]) , &(nim->sto_xyz.m[3][1]) , - &(nim->sto_xyz.m[3][2]) , &(nim->sto_xyz.m[3][3]) ) ; - } - else if( strcmp(lhs,"byteorder") == 0 ){ - if( strcmp(rhs,"MSB_FIRST") == 0 ) nim->byteorder = MSB_FIRST ; - if( strcmp(rhs,"LSB_FIRST") == 0 ) nim->byteorder = LSB_FIRST ; - } - else QQNUM(image_offset,iname_offset,int) ; - else QNUM(datatype,short int) ; - else QNUM(ndim,int) ; - else QNUM(nx,int) ; - else QNUM(ny,int) ; - else QNUM(nz,int) ; - else QNUM(nt,int) ; - else QNUM(nu,int) ; - else QNUM(nv,int) ; - else QNUM(nw,int) ; - else QNUM(dx,float) ; - else QNUM(dy,float) ; - else QNUM(dz,float) ; - else QNUM(dt,float) ; - else QNUM(du,float) ; - else QNUM(dv,float) ; - else QNUM(dw,float) ; - else QNUM(cal_min,float) ; - else QNUM(cal_max,float) ; - else QNUM(scl_slope,float) ; - else QNUM(scl_inter,float) ; - else QNUM(intent_code,short) ; - else QNUM(intent_p1,float) ; - else QNUM(intent_p2,float) ; - else QNUM(intent_p3,float) ; - else QSTR(intent_name,15) ; - else QNUM(toffset,float) ; - else QNUM(xyz_units,int) ; - else QNUM(time_units,int) ; - else QSTR(descrip,79) ; - else QSTR(aux_file,23) ; - else QNUM(qform_code,int) ; - else QNUM(quatern_b,float) ; - else QNUM(quatern_c,float) ; - else QNUM(quatern_d,float) ; - else QNUM(qoffset_x,float) ; - else QNUM(qoffset_y,float) ; - else QNUM(qoffset_z,float) ; - else QNUM(qfac,float) ; - else QNUM(sform_code,int) ; - else QNUM(freq_dim,int) ; - else QNUM(phase_dim,int) ; - else QNUM(slice_dim,int) ; - else QNUM(slice_code,int) ; - else QNUM(slice_start,int) ; - else QNUM(slice_end,int) ; - else QNUM(slice_duration,float) ; - else QNUM(num_ext,int) ; - - } /* end of while loop */ - - if( bytes_read ) *bytes_read = spos+1; /* "process" last '\n' */ - - /* do miscellaneous checking and cleanup */ - - if( nim->ndim <= 0 ){ nifti_image_free(nim); return NULL; } /* bad! */ - - nifti_datatype_sizes( nim->datatype, &(nim->nbyper), &(nim->swapsize) ); - if( nim->nbyper == 0 ){ nifti_image_free(nim); return NULL; } /* bad! */ - - nim->dim[0] = nim->ndim ; - nim->dim[1] = nim->nx ; nim->pixdim[1] = nim->dx ; - nim->dim[2] = nim->ny ; nim->pixdim[2] = nim->dy ; - nim->dim[3] = nim->nz ; nim->pixdim[3] = nim->dz ; - nim->dim[4] = nim->nt ; nim->pixdim[4] = nim->dt ; - nim->dim[5] = nim->nu ; nim->pixdim[5] = nim->du ; - nim->dim[6] = nim->nv ; nim->pixdim[6] = nim->dv ; - nim->dim[7] = nim->nw ; nim->pixdim[7] = nim->dw ; - - nim->nvox = (size_t)nim->nx * nim->ny * nim->nz - * nim->nt * nim->nu * nim->nv * nim->nw ; - - if( nim->qform_code > 0 ) - nim->qto_xyz = nifti_quatern_to_mat44( - nim->quatern_b, nim->quatern_c, nim->quatern_d, - nim->qoffset_x, nim->qoffset_y, nim->qoffset_z, - nim->dx , nim->dy , nim->dz , - nim->qfac ) ; - else - nim->qto_xyz = nifti_quatern_to_mat44( - 0.0f , 0.0f , 0.0f , 0.0f , 0.0f , 0.0f , - nim->dx , nim->dy , nim->dz , 0.0f ) ; - - - nim->qto_ijk = nifti_mat44_inverse( nim->qto_xyz ) ; - - if( nim->sform_code > 0 ) - nim->sto_ijk = nifti_mat44_inverse( nim->sto_xyz ) ; - - return nim ; -} - - -/*---------------------------------------------------------------------------*/ -/*! validate the nifti_image - - \return 1 if the structure seems valid, otherwise 0 - - \sa nifti_nim_has_valid_dims, nifti_hdr_looks_good -*//*-------------------------------------------------------------------------*/ -int nifti_nim_is_valid(nifti_image * nim, int complain) -{ - int errs = 0; - - if( !nim ){ - fprintf(stderr,"** is_valid_nim: nim is NULL\n"); - return 0; - } - - if( g_opts.debug > 2 ) fprintf(stderr,"-d nim_is_valid check...\n"); - - /**- check that dim[] matches the individual values ndim, nx, ny, ... */ - if( ! nifti_nim_has_valid_dims(nim,complain) ){ - if( !complain ) return 0; - errs++; - } - - /* might check nbyper, pixdim, q/sforms, swapsize, nifti_type, ... */ - - /**- be explicit in return of 0 or 1 */ - if( errs > 0 ) return 0; - else return 1; -} - -/*---------------------------------------------------------------------------*/ -/*! validate nifti dimensions - - \return 1 if valid, 0 if not - - \sa nifti_nim_is_valid, nifti_hdr_looks_good - - rely on dim[] as the master -*//*-------------------------------------------------------------------------*/ -int nifti_nim_has_valid_dims(nifti_image * nim, int complain) -{ - size_t prod; - int c, errs = 0; - - /**- start with dim[0]: failure here is considered terminal */ - if( nim->dim[0] <= 0 || nim->dim[0] > 7 ){ - errs++; - if( complain ) - fprintf(stderr,"** NVd: dim[0] (%d) out of range [1,7]\n",nim->dim[0]); - return 0; - } - - /**- check whether ndim equals dim[0] */ - if( nim->ndim != nim->dim[0] ){ - errs++; - if( ! complain ) return 0; - fprintf(stderr,"** NVd: ndim != dim[0] (%d,%d)\n",nim->ndim,nim->dim[0]); - } - - /**- compare each dim[i] to the proper nx, ny, ... */ - if( ( (nim->dim[0] >= 1) && (nim->dim[1] != nim->nx) ) || - ( (nim->dim[0] >= 2) && (nim->dim[2] != nim->ny) ) || - ( (nim->dim[0] >= 3) && (nim->dim[3] != nim->nz) ) || - ( (nim->dim[0] >= 4) && (nim->dim[4] != nim->nt) ) || - ( (nim->dim[0] >= 5) && (nim->dim[5] != nim->nu) ) || - ( (nim->dim[0] >= 6) && (nim->dim[6] != nim->nv) ) || - ( (nim->dim[0] >= 7) && (nim->dim[7] != nim->nw) ) ){ - errs++; - if( !complain ) return 0; - fprintf(stderr,"** NVd mismatch: dims = %d,%d,%d,%d,%d,%d,%d\n" - " nxyz... = %d,%d,%d,%d,%d,%d,%d\n", - nim->dim[1], nim->dim[2], nim->dim[3], - nim->dim[4], nim->dim[5], nim->dim[6], nim->dim[7], - nim->nx, nim->ny, nim->nz, - nim->nt, nim->nu, nim->nv, nim->nw ); - } - - if( g_opts.debug > 2 ){ - fprintf(stderr,"-d check dim[%d] =", nim->dim[0]); - for( c = 0; c < 7; c++ ) fprintf(stderr," %d", nim->dim[c]); - fputc('\n', stderr); - } - - /**- check the dimensions, and that their product matches nvox */ - prod = 1; - for( c = 1; c <= nim->dim[0]; c++ ){ - if( nim->dim[c] > 0) - prod *= nim->dim[c]; - else if( nim->dim[c] <= 0 ){ - if( !complain ) return 0; - fprintf(stderr,"** NVd: dim[%d] (=%d) <= 0\n",c, nim->dim[c]); - errs++; - } - } - if( prod != nim->nvox ){ - if( ! complain ) return 0; - fprintf(stderr,"** NVd: nvox does not match %d-dim product (%u, %u)\n", - nim->dim[0], (unsigned)nim->nvox, (unsigned)prod); - errs++; - } - - /**- if debug, warn about any remaining dim that is neither 0, nor 1 */ - /* (values in dims above dim[0] are undefined, as reminded by Cinly - Ooi and Alle Meije Wink) 16 Nov 2005 [rickr] */ - if( g_opts.debug > 1 ) - for( c = nim->dim[0]+1; c <= 7; c++ ) - if( nim->dim[c] != 0 && nim->dim[c] != 1 ) - fprintf(stderr,"** NVd warning: dim[%d] = %d, but ndim = %d\n", - c, nim->dim[c], nim->dim[0]); - - if( g_opts.debug > 2 ) - fprintf(stderr,"-d nim_has_valid_dims check, errs = %d\n", errs); - - /**- return invalid or valid */ - if( errs > 0 ) return 0; - else return 1; -} - - -/*---------------------------------------------------------------------------*/ -/*! read a nifti image, collapsed across dimensions according to dims[8] 
-
-    This function may be used to read parts of a nifti dataset, such as
-    the time series for a single voxel, or perhaps a slice.  It is similar
-    to nifti_image_load(), though the passed 'data' parameter is used for
-    returning the image, not nim->data.
-
-    \param nim  given nifti_image struct, corresponding to the data file
-    \param dims given list of dimensions (see below)
-    \param data pointer to data pointer (if *data is NULL, data will be
-                allocated, otherwise not)
-
-    Here, dims is an array of 8 ints, similar to nim->dim[8].  While dims[0]
-    is unused at this point, the other indices specify which dimensions to
-    collapse (and at which index), and which not to collapse.  If dims[i] is
-    set to -1, then that entire dimension will be read in, from index 0 to
-    index (nim->dim[i] - 1).  If dims[i] >= 0, then only that index will be
-    read in (so dims[i] must also be < nim->dim[i]).
-
-    Example: given  nim->dim[8] = { 4, 64, 64, 21, 80, 1, 1, 1 } (4-D dataset)
-
-      if dims[8] = { 0,  5,  4, 17, -1, -1, -1, -1 }
-         -> read time series for voxel i,j,k = 5,4,17
-
-      if dims[8] = { 0, -1, -1, -1, 17, -1, -1, -1 }
-         -> read single volume at time point 17
-
-    Example: given  nim->dim[8] = { 6, 64, 64, 21, 80, 4, 3, 1 } (6-D dataset)
-
-      if dims[8] = { 0, 5, 4, 17, -1, 2, 1, 0 }
-         -> read time series for the voxel i,j,k = 5,4,17, and dim 5,6 = 2,1
-
-      if dims[8] = { 0, 5, 4, -1, -1, 0, 0, 0 }
-         -> read time series for slice at i,j = 5,4, and dim 5,6,7 = 0,0,0
-            (note that dims[7] is not relevant, but must be 0 or -1)
-
-    If *data is NULL, then *data will be set as a pointer to new memory,
-    allocated here for the resulting collapsed image data.
-
-      e.g. { int    dims[8] = { 0,  5,  4, 17, -1, -1, -1, -1 };
-             void * data    = NULL;
-             ret_val = nifti_read_collapsed_image(nim, dims, &data);
-             if( ret_val > 0 ){
-                process_time_series(data);
-                if( data != NULL ) free(data);
-             }
-           }
-
-    NOTE: If *data is not NULL, then it will be assumed that it points to
-          valid memory, sufficient to hold the results.  This is done for
-          speed and possibly repeated calls to this function.
-
-      e.g. { int    dims[8] = { 0,  -1, -1, -1, -1, -1, -1, -1 };
-             void * data    = NULL;
-             for( zslice = 0; zslice < nzslices; zslice++ ){
-                dims[3] = zslice;
-                ret_val = nifti_read_collapsed_image(nim, dims, &data);
-                if( ret_val > 0 ) process_slice(zslice, data);
-             }
-             if( data != NULL ) free(data);
-           }
-
-    \return
-        -  the total number of bytes read, or < 0 on failure
-        -  the read and byte-swapped data, in 'data'
- - \sa nifti_image_read, nifti_image_free, nifti_image_read_bricks - nifti_image_load -*//*-------------------------------------------------------------------------*/ -int nifti_read_collapsed_image( nifti_image * nim, const int dims [8], - void ** data ) -{ - znzFile fp; - int pivots[8], prods[8], nprods; /* sizes are bounded by dims[], so 8 */ - int c, bytes; - - /** - check pointers for sanity */ - if( !nim || !dims || !data ){ - fprintf(stderr,"** nifti_RCI: bad params %p, %p, %p\n", - (void *)nim, (const void *)dims, (void *)data); - return -1; - } - - if( g_opts.debug > 2 ){ - fprintf(stderr,"-d read_collapsed_image:\n dims ="); - for(c = 0; c < 8; c++) fprintf(stderr," %3d", dims[c]); - fprintf(stderr,"\n nim->dims ="); - for(c = 0; c < 8; c++) fprintf(stderr," %3d", nim->dim[c]); - fputc('\n', stderr); - } - - /** - verify that dim[] makes sense */ - if( ! nifti_nim_is_valid(nim, g_opts.debug > 0) ){ - fprintf(stderr,"** invalid nim (file is '%s')\n", nim->fname ); - return -1; - } - - /** - verify that dims[] makes sense for this dataset */ - for( c = 1; c <= nim->dim[0]; c++ ){ - if( dims[c] >= nim->dim[c] ){ - fprintf(stderr,"** nifti_RCI: dims[%d] >= nim->dim[%d] (%d,%d)\n", - c, c, dims[c], nim->dim[c]); - return -1; - } - } - - /** - prepare pivot list - pivots are fixed indices */ - if( make_pivot_list(nim, dims, pivots, prods, &nprods) < 0 ) return -1; - - bytes = rci_alloc_mem(data, prods, nprods, nim->nbyper); - if( bytes < 0 ) return -1; - - /** - open the image file for reading at the appropriate offset */ - fp = nifti_image_load_prep( nim ); - if( ! fp ){ free(*data); *data = NULL; return -1; } /* failure */ - - /** - call the recursive reading function, passing nim, the pivot info, - location to store memory, and file pointer and position */ - c = rci_read_data(nim, pivots,prods,nprods,dims, - (char *)*data, fp, znztell(fp)); - znzclose(fp); /* in any case, close the file */ - if( c < 0 ){ free(*data); *data = NULL; return -1; } /* failure */ - - if( g_opts.debug > 1 ) - fprintf(stderr,"+d read %d bytes of collapsed image from %s\n", - bytes, nim->fname); - - return bytes; -} - - -/* local function to find strides per dimension. assumes 7D size and -** stride array. -*/ -static void -compute_strides(int *strides,const int *size,int nbyper) -{ - int i; - strides[0] = nbyper; - for(i = 1; i < 7; i++) - { - strides[i] = size[i-1] * strides[i-1]; - } -} - -/*---------------------------------------------------------------------------*/ -/*! read an arbitrary subregion from a nifti image - - This function may be used to read a single arbitary subregion of any - rectangular size from a nifti dataset, such as a small 5x5x5 subregion - around the center of a 3D image. - - \param nim given nifti_image struct, corresponding to the data file - \param start_index the index location of the first voxel that will be returned - \param region_size the size of the subregion to be returned - \param data pointer to data pointer (if *data is NULL, data will be - allocated, otherwise not) - - Example: given nim->dim[8] = {3, 64, 64, 64, 1, 1, 1, 1 } (3-D dataset) - - if start_index[7] = { 29, 29, 29, 0, 0, 0, 0 } and - region_size[7] = { 5, 5, 5, 1, 1, 1, 1 } - -> read 5x5x5 region starting with the first voxel location at (29,29,29) - - NOTE: If *data is not NULL, then it will be assumed that it points to - valid memory, sufficient to hold the results. This is done for - speed and possibly repeated calls to this function. - \return - - the total number of bytes read, or < 0 on failure - - the read and byte-swapped data, in 'data' - - \sa nifti_image_read, nifti_image_free, nifti_image_read_bricks - nifti_image_load, nifti_read_collapsed_image -*//*-------------------------------------------------------------------------*/ -int nifti_read_subregion_image( nifti_image * nim, - int *start_index, - int *region_size, - void ** data ) -{ - znzFile fp; /* file to read */ - int i,j,k,l,m,n; /* indices for dims */ - long int bytes = 0; /* total # bytes read */ - int total_alloc_size; /* size of buffer allocation */ - char *readptr; /* where in *data to read next */ - int strides[7]; /* strides between dimensions */ - int collapsed_dims[8]; /* for read_collapsed_image */ - int *image_size; /* pointer to dimensions in header */ - long int initial_offset; - long int offset; /* seek offset for reading current row */ - - /* probably ignored, but set to ndim for consistency*/ - collapsed_dims[0] = nim->ndim; - - /* build a dims array for collapsed image read */ - for(i = 0; i < nim->ndim; i++) - { - /* if you take the whole extent in this dimension */ - if(start_index[i] == 0 && - region_size[i] == nim->dim[i+1]) - { - collapsed_dims[i+1] = -1; - } - /* if you specify a single element in this dimension */ - else if(region_size[i] == 1) - { - collapsed_dims[i+1] = start_index[i]; - } - else - { - collapsed_dims[i+1] = -2; /* sentinel value */ - } - } - /* fill out end of collapsed_dims */ - for(i = nim->ndim ; i < 7; i++) - { - collapsed_dims[i+1] = -1; - } - - /* check to see whether collapsed read is possible */ - for(i = 1; i <= nim->ndim; i++) - { - if(collapsed_dims[i] == -2) - { - break; - } - } - - /* if you get through all the dimensions without hitting - ** a subrange of size > 1, a collapsed read is possible - */ - if(i > nim->ndim) - { - return nifti_read_collapsed_image(nim, collapsed_dims, data); - } - - /* point past first element of dim, which holds nim->ndim */ - image_size = &(nim->dim[1]); - - /* check region sizes for sanity */ - for(i = 0; i < nim->ndim; i++) - { - if(start_index[i] + region_size[i] > image_size[i]) - { - if(g_opts.debug > 1) - { - fprintf(stderr,"region doesn't fit within image size\n"); - } - return -1; - } - } - - /* get the file open */ - fp = nifti_image_load_prep( nim ); - /* the current offset is just past the nifti header, save - * location so that SEEK_SET can be used below - */ - initial_offset = znztell(fp); - /* get strides*/ - compute_strides(strides,image_size,nim->nbyper); - - total_alloc_size = nim->nbyper; /* size of pixel */ - - /* find alloc size */ - for(i = 0; i < nim->ndim; i++) - { - total_alloc_size *= region_size[i]; - } - /* allocate buffer, if necessary */ - if(*data == 0) - { - *data = (void *)malloc(total_alloc_size); - } - - if(*data == 0) - { - if(g_opts.debug > 1) - { - fprintf(stderr,"allocation of %d bytes failed\n",total_alloc_size); - return -1; - } - } - - /* point to start of data buffer as char * */ - readptr = *((char **)data); - { - /* can't assume that start_index and region_size have any more than - ** nim->ndim elements so make local copies, filled out to seven elements - */ - int si[7], rs[7]; - for(i = 0; i < nim->ndim; i++) - { - si[i] = start_index[i]; - rs[i] = region_size[i]; - } - for(i = nim->ndim; i < 7; i++) - { - si[i] = 0; - rs[i] = 1; - } - /* loop through subregion and read a row at a time */ - for(i = si[6]; i < (si[6] + rs[6]); i++) - { - for(j = si[5]; j < (si[5] + rs[5]); j++) - { - for(k = si[4]; k < (si[4] + rs[4]); k++) - { - for(l = si[3]; l < (si[3] + rs[3]); l++) - { - for(m = si[2]; m < (si[2] + rs[2]); m++) - { - for(n = si[1]; n < (si[1] + rs[1]); n++) - { - int nread,read_amount; - offset = initial_offset + - (i * strides[6]) + - (j * strides[5]) + - (k * strides[4]) + - (l * strides[3]) + - (m * strides[2]) + - (n * strides[1]) + - (si[0] * strides[0]); - znzseek(fp, offset, SEEK_SET); /* seek to current row */ - read_amount = rs[0] * nim->nbyper; /* read a row of the subregion*/ - nread = (int)nifti_read_buffer(fp, readptr, read_amount, nim); - if(nread != read_amount) - { - if(g_opts.debug > 1) - { - fprintf(stderr,"read of %d bytes failed\n",read_amount); - return -1; - } - } - bytes += nread; - readptr += read_amount; - } - } - } - } - } - } - } - return bytes; -} - - -/* read the data from the file pointed to by fp - - - this a recursive function, so start with the base case - - data is now (char *) for easy incrementing - - return 0 on success, < 0 on failure -*/ -static int rci_read_data(nifti_image * nim, int * pivots, int * prods, - int nprods, const int dims[], char * data, znzFile fp, size_t base_offset) -{ - size_t sublen, offset, read_size; - int c; - - /* bad check first - base_offset may not have been checked */ - if( nprods <= 0 ){ - fprintf(stderr,"** rci_read_data, bad prods, %d\n", nprods); - return -1; - } - - /* base case: actually read the data */ - if( nprods == 1 ){ - size_t nread, bytes; - - /* make sure things look good here */ - if( *pivots != 0 ){ - fprintf(stderr,"** rciRD: final pivot == %d!\n", *pivots); - return -1; - } - - /* so just seek and read (prods[0] * nbyper) bytes from the file */ - znzseek(fp, (long)base_offset, SEEK_SET); - bytes = (size_t)prods[0] * nim->nbyper; - nread = nifti_read_buffer(fp, data, bytes, nim); - if( nread != bytes ){ - fprintf(stderr,"** rciRD: read only %u of %u bytes from '%s'\n", - (unsigned)nread, (unsigned)bytes, nim->fname); - return -1; - } else if( g_opts.debug > 3 ) - fprintf(stderr,"+d successful read of %u bytes at offset %u\n", - (unsigned)bytes, (unsigned)base_offset); - - return 0; /* done with base case - return success */ - } - - /* not the base case, so do a set of reduced reads */ - - /* compute size of sub-brick: all dimensions below pivot */ - for( c = 1, sublen = 1; c < *pivots; c++ ) sublen *= nim->dim[c]; - - /* compute number of values to read, i.e. remaining prods */ - for( c = 1, read_size = 1; c < nprods; c++ ) read_size *= prods[c]; - read_size *= nim->nbyper; /* and multiply by bytes per voxel */ - - /* now repeatedly compute offsets, and recursively read */ - for( c = 0; c < prods[0]; c++ ){ - /* offset is (c * sub-block size (including pivot dim)) */ - /* + (dims[] index into pivot sub-block) */ - /* the unneeded multiplication is to make this more clear */ - offset = (size_t)c * sublen * nim->dim[*pivots] + - (size_t)sublen * dims[*pivots]; - offset *= nim->nbyper; - - if( g_opts.debug > 3 ) - fprintf(stderr,"-d reading %u bytes, foff %u + %u, doff %u\n", - (unsigned)read_size, (unsigned)base_offset, (unsigned)offset, - (unsigned)(c*read_size)); - - /* now read the next level down, adding this offset */ - if( rci_read_data(nim, pivots+1, prods+1, nprods-1, dims, - data + c * read_size, fp, base_offset + offset) < 0 ) - return -1; - } - - return 0; -} - - -/* allocate memory for all collapsed image data - - If *data is already set, do not allocate, but still calculate - size for debug report. - - return total size on success, and < 0 on failure -*/ -static int rci_alloc_mem(void ** data, int prods[8], int nprods, int nbyper ) -{ - int size, memindex; - - if( nbyper < 0 || nprods < 1 || nprods > 8 ){ - fprintf(stderr,"** rci_am: bad params, %d, %d\n", nbyper, nprods); - return -1; - } - - for( memindex = 0, size = 1; memindex < nprods; memindex++ ) - size *= prods[memindex]; - - size *= nbyper; - - if( ! *data ){ /* then allocate what is needed */ - if( g_opts.debug > 1 ) - fprintf(stderr,"+d alloc %d (= %d x %d) bytes for collapsed image\n", - size, size/nbyper, nbyper); - - *data = malloc(size); /* actually allocate the memory */ - if( ! *data ){ - fprintf(stderr,"** rci_am: failed to alloc %d bytes for data\n", size); - return -1; - } - } else if( g_opts.debug > 1 ) - fprintf(stderr,"-d rci_am: *data already set, need %d (%d x %d) bytes\n", - size, size/nbyper, nbyper); - - return size; -} - - -/* prepare a pivot list for reading - - The pivot points are the indices into dims where the calling function - wants to collapse a dimension. The last pivot should always be zero - (note that we have space for that in the lists). -*/ -static int make_pivot_list(nifti_image * nim, const int dims[], int pivots[], - int prods[], int * nprods ) -{ - int len, dim_index; - - len = 0; - dim_index = nim->dim[0]; - while( dim_index > 0 ){ - prods[len] = 1; - while( dim_index > 0 && (nim->dim[dim_index] == 1 || dims[dim_index] == -1) ){ - prods[len] *= nim->dim[dim_index]; - dim_index--; - } - pivots[len] = dim_index; - len++; - dim_index--; /* fine, let it drop out at -1 */ - } - - /* make sure to include 0 as a pivot (instead of just 1, if it is) */ - if( pivots[len-1] != 0 ){ - pivots[len] = 0; - prods[len] = 1; - len++; - } - - *nprods = len; - - if( g_opts.debug > 2 ){ - fprintf(stderr,"+d pivot list created, pivots :"); - for(dim_index = 0; dim_index < len; dim_index++) fprintf(stderr," %d", pivots[dim_index]); - fprintf(stderr,", prods :"); - for(dim_index = 0; dim_index < len; dim_index++) fprintf(stderr," %d", prods[dim_index]); - fputc('\n',stderr); - } - - return 0; -} - - -#undef ISEND -#define ISEND(c) ( (c)==']' || (c)=='}' || (c)=='\0' ) - -/*---------------------------------------------------------------------*/ -/*! Get an integer list in the range 0..(nvals-1), from the - character string str. If we call the output pointer fred, - then fred[0] = number of integers in the list (> 0), and - fred[i] = i-th integer in the list for i=1..fred[0]. - If on return, fred == NULL or fred[0] == 0, then something is - wrong, and the caller must deal with that. - - Syntax of input string: - - initial '{' or '[' is skipped, if present - - ends when '}' or ']' or end of string is found - - contains entries separated by commas - - entries have one of these forms: - - a single number - - a dollar sign '$', which means nvals-1 - - a sequence of consecutive numbers in the form "a..b" or - "a-b", where "a" and "b" are single numbers (or '$') - - a sequence of evenly spaced numbers in the form - "a..b(c)" or "a-b(c)", where "c" encodes the step - - Example: "[2,7..4,3..9(2)]" decodes to the list - 2 7 6 5 4 3 5 7 9 - - entries should be in the range 0..nvals-1 - - (borrowed, with permission, from thd_intlist.c) -*//*-------------------------------------------------------------------*/ -int * nifti_get_intlist( int nvals , const char * str ) -{ - int *subv = NULL ; - int ii , ipos , nout , slen ; - int ibot,itop,istep , nused ; - char *cpt ; - - /* Meaningless input? */ - if( nvals < 1 ) return NULL ; - - /* No selection list? */ - if( str == NULL || str[0] == '\0' ) return NULL ; - - /* skip initial '[' or '{' */ - subv = (int *)malloc( sizeof(int) * 2 ) ; - if( !subv ) { - fprintf(stderr,"** nifti_get_intlist: failed alloc of 2 ints\n"); - return NULL; - } - subv[0] = nout = 0 ; - - ipos = 0 ; - if( str[ipos] == '[' || str[ipos] == '{' ) ipos++ ; - - if( g_opts.debug > 1 ) - fprintf(stderr,"-d making int_list (vals = %d) from '%s'\n", nvals, str); - - /**- for each sub-selector until end of input... */ - - slen = (int)strlen(str) ; - while( ipos < slen && !ISEND(str[ipos]) ){ - - while( isspace((int) str[ipos]) ) ipos++ ; /* skip blanks */ - if( ISEND(str[ipos]) ) break ; /* done */ - - /**- get starting value */ - - if( str[ipos] == '$' ){ /* special case */ - ibot = nvals-1 ; ipos++ ; - } else { /* decode an integer */ - ibot = strtol( str+ipos , &cpt , 10 ) ; - if( ibot < 0 ){ - fprintf(stderr,"** ERROR: list index %d is out of range 0..%d\n", - ibot,nvals-1) ; - free(subv) ; return NULL ; - } - if( ibot >= nvals ){ - fprintf(stderr,"** ERROR: list index %d is out of range 0..%d\n", - ibot,nvals-1) ; - free(subv) ; return NULL ; - } - nused = (cpt-(str+ipos)) ; - if( ibot == 0 && nused == 0 ){ - fprintf(stderr,"** ERROR: list syntax error '%s'\n",str+ipos) ; - free(subv) ; return NULL ; - } - ipos += nused ; - } - - while( isspace((int) str[ipos]) ) ipos++ ; /* skip blanks */ - - /**- if that's it for this sub-selector, add one value to list */ - - if( str[ipos] == ',' || ISEND(str[ipos]) ){ - nout++ ; - subv = (int *)realloc( (char *)subv , sizeof(int) * (nout+1) ) ; - if( !subv ) { - fprintf(stderr,"** nifti_get_intlist: failed realloc of %d ints\n", - nout+1); - return NULL; - } - subv[0] = nout ; - subv[nout] = ibot ; - if( ISEND(str[ipos]) ) break ; /* done */ - ipos++ ; continue ; /* re-start loop at next sub-selector */ - } - - /**- otherwise, must have '..' or '-' as next inputs */ - - if( str[ipos] == '-' ){ - ipos++ ; - } else if( str[ipos] == '.' && str[ipos+1] == '.' ){ - ipos++ ; ipos++ ; - } else { - fprintf(stderr,"** ERROR: index list syntax is bad: '%s'\n", - str+ipos) ; - free(subv) ; return NULL ; - } - - /**- get ending value for loop now */ - - if( str[ipos] == '$' ){ /* special case */ - itop = nvals-1 ; ipos++ ; - } else { /* decode an integer */ - itop = strtol( str+ipos , &cpt , 10 ) ; - if( itop < 0 ){ - fprintf(stderr,"** ERROR: index %d is out of range 0..%d\n", - itop,nvals-1) ; - free(subv) ; return NULL ; - } - if( itop >= nvals ){ - fprintf(stderr,"** ERROR: index %d is out of range 0..%d\n", - itop,nvals-1) ; - free(subv) ; return NULL ; - } - nused = (cpt-(str+ipos)) ; - if( itop == 0 && nused == 0 ){ - fprintf(stderr,"** ERROR: index list syntax error '%s'\n",str+ipos) ; - free(subv) ; return NULL ; - } - ipos += nused ; - } - - /**- set default loop step */ - - istep = (ibot <= itop) ? 1 : -1 ; - - while( isspace((int) str[ipos]) ) ipos++ ; /* skip blanks */ - - /**- check if we have a non-default loop step */ - - if( str[ipos] == '(' ){ /* decode an integer */ - ipos++ ; - istep = strtol( str+ipos , &cpt , 10 ) ; - if( istep == 0 ){ - fprintf(stderr,"** ERROR: index loop step is 0!\n") ; - free(subv) ; return NULL ; - } - nused = (cpt-(str+ipos)) ; - ipos += nused ; - if( str[ipos] == ')' ) ipos++ ; - if( (ibot-itop)*istep > 0 ){ - fprintf(stderr,"** WARNING: index list '%d..%d(%d)' means nothing\n", - ibot,itop,istep ) ; - } - } - - /**- add values to output */ - - for( ii=ibot ; (ii-itop)*istep <= 0 ; ii += istep ){ - nout++ ; - subv = (int *)realloc( (char *)subv , sizeof(int) * (nout+1) ) ; - if( !subv ) { - fprintf(stderr,"** nifti_get_intlist: failed realloc of %d ints\n", - nout+1); - return NULL; - } - subv[0] = nout ; - subv[nout] = ii ; - } - - /**- check if we have a comma to skip over */ - - while( isspace((int) str[ipos]) ) ipos++ ; /* skip blanks */ - if( str[ipos] == ',' ) ipos++ ; /* skip commas */ - - } /* end of loop through selector string */ - - if( g_opts.debug > 1 ) { - fprintf(stderr,"+d int_list (vals = %d): ", subv[0]); - for( ii = 1; ii <= subv[0]; ii++ ) fprintf(stderr,"%d ", subv[ii]); - fputc('\n',stderr); - } - - if( subv[0] == 0 ){ free(subv); subv = NULL; } - return subv ; -} - -/*---------------------------------------------------------------------*/ -/*! Given a NIFTI_TYPE string, such as "NIFTI_TYPE_INT16", return the - * corresponding integral type code. The type code is the macro - * value defined in nifti1.h. -*//*-------------------------------------------------------------------*/ -int nifti_datatype_from_string( const char * name ) -{ - int tablen = sizeof(nifti_type_list)/sizeof(nifti_type_ele); - int c; - - if( !name ) return DT_UNKNOWN; - - for( c = tablen-1; c > 0; c-- ) - if( !strcmp(name, nifti_type_list[c].name) ) - break; - - return nifti_type_list[c].type; -} - - -/*---------------------------------------------------------------------*/ -/*! Given a NIFTI_TYPE value, such as NIFTI_TYPE_INT16, return the - * corresponding macro label as a string. The dtype code is the - * macro value defined in nifti1.h. -*//*-------------------------------------------------------------------*/ -const char * nifti_datatype_to_string( int dtype ) -{ - int tablen = sizeof(nifti_type_list)/sizeof(nifti_type_ele); - int c; - - for( c = tablen-1; c > 0; c-- ) - if( nifti_type_list[c].type == dtype ) - break; - - return nifti_type_list[c].name; -} - - -/*---------------------------------------------------------------------*/ -/*! Determine whether dtype is a valid NIFTI_TYPE. - * - * DT_UNKNOWN is considered invalid - * - * The only difference 'for_nifti' makes is that DT_BINARY - * should be invalid for a NIfTI dataset. -*//*-------------------------------------------------------------------*/ -int nifti_datatype_is_valid( int dtype, int for_nifti ) -{ - int tablen = sizeof(nifti_type_list)/sizeof(nifti_type_ele); - int c; - - /* special case */ - if( for_nifti && dtype == DT_BINARY ) return 0; - - for( c = tablen-1; c > 0; c-- ) - if( nifti_type_list[c].type == dtype ) - return 1; - - return 0; -} - - -/*---------------------------------------------------------------------*/ -/*! Only as a test, verify that the new nifti_type_list table matches - * the the usage of nifti_datatype_sizes (which could be changed to - * use the table, if there were interest). - * - * return the number of errors (so 0 is success, as usual) -*//*-------------------------------------------------------------------*/ -int nifti_test_datatype_sizes(int verb) -{ - int tablen = sizeof(nifti_type_list)/sizeof(nifti_type_ele); - int nbyper, ssize; - int c, errs = 0; - - for( c = 0; c < tablen; c++ ) - { - nbyper = ssize = -1; - nifti_datatype_sizes(nifti_type_list[c].type, &nbyper, &ssize); - if( nbyper < 0 || ssize < 0 || - nbyper != nifti_type_list[c].nbyper || - ssize != nifti_type_list[c].swapsize ) - { - if( verb || g_opts.debug > 2 ) - fprintf(stderr, "** type mismatch: %s, %d, %d, %d : %d, %d\n", - nifti_type_list[c].name, nifti_type_list[c].type, - nifti_type_list[c].nbyper, nifti_type_list[c].swapsize, - nbyper, ssize); - errs++; - } - } - - if( errs ) - fprintf(stderr,"** nifti_test_datatype_sizes: found %d errors\n",errs); - else if( verb || g_opts.debug > 1 ) - fprintf(stderr,"-- nifti_test_datatype_sizes: all OK\n"); - - return errs; -} - - -/*---------------------------------------------------------------------*/ -/*! Display the nifti_type_list table. - * - * if which == 1 : display DT_* - * if which == 2 : display NIFTI_TYPE* - * else : display all -*//*-------------------------------------------------------------------*/ -int nifti_disp_type_list( int which ) -{ - const char * style; - int tablen = sizeof(nifti_type_list)/sizeof(nifti_type_ele); - int lwhich, c; - - if ( which == 1 ){ lwhich = 1; style = "DT_"; } - else if( which == 2 ){ lwhich = 2; style = "NIFTI_TYPE_"; } - else { lwhich = 3; style = "ALL"; } - - printf("nifti_type_list entries (%s) :\n" - " name type nbyper swapsize\n" - " --------------------- ---- ------ --------\n", style); - - for( c = 0; c < tablen; c++ ) - if( (lwhich & 1 && nifti_type_list[c].name[0] == 'D') || - (lwhich & 2 && nifti_type_list[c].name[0] == 'N') ) - printf(" %-22s %5d %3d %5d\n", - nifti_type_list[c].name, - nifti_type_list[c].type, - nifti_type_list[c].nbyper, - nifti_type_list[c].swapsize); - - return 0; -} diff --git a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_io.h b/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_io.h deleted file mode 100644 index 23a6b71b34f..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_io.h +++ /dev/null @@ -1,555 +0,0 @@ -/** \file nifti1_io.h - \brief Data structures for using nifti1_io API. - - Written by Bob Cox, SSCC NIMH - - Revisions by Rick Reynolds, SSCC NIMH - */ -#ifndef _NIFTI_IO_HEADER_ -#define _NIFTI_IO_HEADER_ - -#include -#include -#include -#include -#include - -#ifndef DONT_INCLUDE_ANALYZE_STRUCT -#define DONT_INCLUDE_ANALYZE_STRUCT /*** not needed herein ***/ -#endif -#include "nifti1.h" /*** NIFTI-1 header specification ***/ - -#include - -/*=================*/ -#ifdef __cplusplus -extern "C" { -#endif -/*=================*/ - -/*****===================================================================*****/ -/***** File nifti1_io.h == Declarations for nifti1_io.c *****/ -/*****...................................................................*****/ -/***** This code is released to the public domain. *****/ -/*****...................................................................*****/ -/***** Author: Robert W Cox, SSCC/DIRP/NIMH/NIH/DHHS/USA/EARTH *****/ -/***** Date: August 2003 *****/ -/*****...................................................................*****/ -/***** Neither the National Institutes of Health (NIH), nor any of its *****/ -/***** employees imply any warranty of usefulness of this software for *****/ -/***** any purpose, and do not assume any liability for damages, *****/ -/***** incidental or otherwise, caused by any use of this document. *****/ -/*****===================================================================*****/ - -/* - Modified by: Mark Jenkinson (FMRIB Centre, University of Oxford, UK) - Date: July/August 2004 - - Mainly adding low-level IO and changing things to allow gzipped files - to be read and written - Full backwards compatability should have been maintained - - Modified by: Rick Reynolds (SSCC/DIRP/NIMH, National Institutes of Health) - Date: December 2004 - - Modified and added many routines for I/O. -*/ - -/********************** Some sample data structures **************************/ - -typedef struct { /** 4x4 matrix struct **/ - float m[4][4] ; -} mat44 ; - -typedef struct { /** 3x3 matrix struct **/ - float m[3][3] ; -} mat33 ; - -/*...........................................................................*/ - -/*! \enum analyze_75_orient_code - * \brief Old-style analyze75 orientation - * codes. - */ -typedef enum _analyze75_orient_code { - a75_transverse_unflipped = 0, - a75_coronal_unflipped = 1, - a75_sagittal_unflipped = 2, - a75_transverse_flipped = 3, - a75_coronal_flipped = 4, - a75_sagittal_flipped = 5, - a75_orient_unknown = 6 -} analyze_75_orient_code; - -/*! \struct nifti_image - \brief High level data structure for open nifti datasets in the - nifti1_io API. Note that this structure is not part of the - nifti1 format definition; it is used to implement one API - for reading/writing formats in the nifti1 format. - */ -typedef struct { /*!< Image storage struct **/ - - int ndim ; /*!< last dimension greater than 1 (1..7) */ - int nx ; /*!< dimensions of grid array */ - int ny ; /*!< dimensions of grid array */ - int nz ; /*!< dimensions of grid array */ - int nt ; /*!< dimensions of grid array */ - int nu ; /*!< dimensions of grid array */ - int nv ; /*!< dimensions of grid array */ - int nw ; /*!< dimensions of grid array */ - int dim[8] ; /*!< dim[0]=ndim, dim[1]=nx, etc. */ - size_t nvox ; /*!< number of voxels = nx*ny*nz*...*nw */ - int nbyper ; /*!< bytes per voxel, matches datatype */ - int datatype ; /*!< type of data in voxels: DT_* code */ - - float dx ; /*!< grid spacings */ - float dy ; /*!< grid spacings */ - float dz ; /*!< grid spacings */ - float dt ; /*!< grid spacings */ - float du ; /*!< grid spacings */ - float dv ; /*!< grid spacings */ - float dw ; /*!< grid spacings */ - float pixdim[8] ; /*!< pixdim[1]=dx, etc. */ - - float scl_slope ; /*!< scaling parameter - slope */ - float scl_inter ; /*!< scaling parameter - intercept */ - - float cal_min ; /*!< calibration parameter, minimum */ - float cal_max ; /*!< calibration parameter, maximum */ - - int qform_code ; /*!< codes for (x,y,z) space meaning */ - int sform_code ; /*!< codes for (x,y,z) space meaning */ - - int freq_dim ; /*!< indexes (1,2,3, or 0) for MRI */ - int phase_dim ; /*!< directions in dim[]/pixdim[] */ - int slice_dim ; /*!< directions in dim[]/pixdim[] */ - - int slice_code ; /*!< code for slice timing pattern */ - int slice_start ; /*!< index for start of slices */ - int slice_end ; /*!< index for end of slices */ - float slice_duration ; /*!< time between individual slices */ - - /*! quaternion transform parameters - [when writing a dataset, these are used for qform, NOT qto_xyz] */ - float quatern_b , quatern_c , quatern_d , - qoffset_x , qoffset_y , qoffset_z , - qfac ; - - mat44 qto_xyz ; /*!< qform: transform (i,j,k) to (x,y,z) */ - mat44 qto_ijk ; /*!< qform: transform (x,y,z) to (i,j,k) */ - - mat44 sto_xyz ; /*!< sform: transform (i,j,k) to (x,y,z) */ - mat44 sto_ijk ; /*!< sform: transform (x,y,z) to (i,j,k) */ - - float toffset ; /*!< time coordinate offset */ - - int xyz_units ; /*!< dx,dy,dz units: NIFTI_UNITS_* code */ - int time_units ; /*!< dt units: NIFTI_UNITS_* code */ - - int nifti_type ; /*!< 0==ANALYZE, 1==NIFTI-1 (1 file), - 2==NIFTI-1 (2 files), - 3==NIFTI-ASCII (1 file) */ - int intent_code ; /*!< statistic type (or something) */ - float intent_p1 ; /*!< intent parameters */ - float intent_p2 ; /*!< intent parameters */ - float intent_p3 ; /*!< intent parameters */ - char intent_name[16] ; /*!< optional description of intent data */ - - char descrip[80] ; /*!< optional text to describe dataset */ - char aux_file[24] ; /*!< auxiliary filename */ - - char *fname ; /*!< header filename (.hdr or .nii) */ - char *iname ; /*!< image filename (.img or .nii) */ - int iname_offset ; /*!< offset into iname where data starts */ - int swapsize ; /*!< swap unit in image data (might be 0) */ - int byteorder ; /*!< byte order on disk (MSB_ or LSB_FIRST) */ - void *data ; /*!< pointer to data: nbyper*nvox bytes */ - - int num_ext ; /*!< number of extensions in ext_list */ - nifti1_extension * ext_list ; /*!< array of extension structs (with data) */ - analyze_75_orient_code analyze75_orient; /*!< for old analyze files, orient */ - -} nifti_image ; - - - -/* struct for return from nifti_image_read_bricks() */ -typedef struct { - int nbricks; /* the number of allocated pointers in 'bricks' */ - size_t bsize; /* the length of each data block, in bytes */ - void ** bricks; /* array of pointers to data blocks */ -} nifti_brick_list; - - -/*****************************************************************************/ -/*------------------ NIfTI version of ANALYZE 7.5 structure -----------------*/ - -/* (based on fsliolib/dbh.h, but updated for version 7.5) */ - -typedef struct { - /* header info fields - describes the header overlap with NIfTI */ - /* ------------------ */ - int sizeof_hdr; /* 0 + 4 same */ - char data_type[10]; /* 4 + 10 same */ - char db_name[18]; /* 14 + 18 same */ - int extents; /* 32 + 4 same */ - short int session_error; /* 36 + 2 same */ - char regular; /* 38 + 1 same */ - char hkey_un0; /* 39 + 1 40 bytes */ - - /* image dimension fields - describes image sizes */ - short int dim[8]; /* 0 + 16 same */ - short int unused8; /* 16 + 2 intent_p1... */ - short int unused9; /* 18 + 2 ... */ - short int unused10; /* 20 + 2 intent_p2... */ - short int unused11; /* 22 + 2 ... */ - short int unused12; /* 24 + 2 intent_p3... */ - short int unused13; /* 26 + 2 ... */ - short int unused14; /* 28 + 2 intent_code */ - short int datatype; /* 30 + 2 same */ - short int bitpix; /* 32 + 2 same */ - short int dim_un0; /* 34 + 2 slice_start */ - float pixdim[8]; /* 36 + 32 same */ - - float vox_offset; /* 68 + 4 same */ - float funused1; /* 72 + 4 scl_slope */ - float funused2; /* 76 + 4 scl_inter */ - float funused3; /* 80 + 4 slice_end, */ - /* slice_code, */ - /* xyzt_units */ - float cal_max; /* 84 + 4 same */ - float cal_min; /* 88 + 4 same */ - float compressed; /* 92 + 4 slice_duration */ - float verified; /* 96 + 4 toffset */ - int glmax,glmin; /* 100 + 8 108 bytes */ - - /* data history fields - optional */ - char descrip[80]; /* 0 + 80 same */ - char aux_file[24]; /* 80 + 24 same */ - char orient; /* 104 + 1 NO GOOD OVERLAP */ - char originator[10]; /* 105 + 10 FROM HERE DOWN... */ - char generated[10]; /* 115 + 10 */ - char scannum[10]; /* 125 + 10 */ - char patient_id[10]; /* 135 + 10 */ - char exp_date[10]; /* 145 + 10 */ - char exp_time[10]; /* 155 + 10 */ - char hist_un0[3]; /* 165 + 3 */ - int views; /* 168 + 4 */ - int vols_added; /* 172 + 4 */ - int start_field; /* 176 + 4 */ - int field_skip; /* 180 + 4 */ - int omax, omin; /* 184 + 8 */ - int smax, smin; /* 192 + 8 200 bytes */ -} nifti_analyze75; /* total: 348 bytes */ - - -/*****************************************************************************/ -/*--------------- Prototypes of functions defined in this file --------------*/ - -char const * nifti_datatype_string ( int dt ) ; -char const *nifti_units_string ( int uu ) ; -char const *nifti_intent_string ( int ii ) ; -char const *nifti_xform_string ( int xx ) ; -char const *nifti_slice_string ( int ss ) ; -char const *nifti_orientation_string( int ii ) ; - -int nifti_is_inttype( int dt ) ; - -mat44 nifti_mat44_inverse( mat44 R ) ; - -mat33 nifti_mat33_inverse( mat33 R ) ; -mat33 nifti_mat33_polar ( mat33 A ) ; -float nifti_mat33_rownorm( mat33 A ) ; -float nifti_mat33_colnorm( mat33 A ) ; -float nifti_mat33_determ ( mat33 R ) ; -mat33 nifti_mat33_mul ( mat33 A , mat33 B ) ; - -void nifti_swap_2bytes ( size_t n , void *ar ) ; -void nifti_swap_4bytes ( size_t n , void *ar ) ; -void nifti_swap_8bytes ( size_t n , void *ar ) ; -void nifti_swap_16bytes( size_t n , void *ar ) ; -void nifti_swap_Nbytes ( size_t n , int siz , void *ar ) ; - -int nifti_datatype_is_valid (int dtype, int for_nifti); -int nifti_datatype_from_string(const char * name); -const char * nifti_datatype_to_string (int dtype); - -int nifti_get_filesize( const char *pathname ) ; -void swap_nifti_header ( struct nifti_1_header *h , int is_nifti ) ; -void old_swap_nifti_header( struct nifti_1_header *h , int is_nifti ); -int nifti_swap_as_analyze( nifti_analyze75 *h ); - - -/* main read/write routines */ - -nifti_image *nifti_image_read_bricks(const char *hname , int nbricks, - const int *blist, nifti_brick_list * NBL); -int nifti_image_load_bricks(nifti_image *nim , int nbricks, - const int *blist, nifti_brick_list * NBL); -void nifti_free_NBL( nifti_brick_list * NBL ); - -nifti_image *nifti_image_read ( const char *hname , int read_data ) ; -int nifti_image_load ( nifti_image *nim ) ; -void nifti_image_unload ( nifti_image *nim ) ; -void nifti_image_free ( nifti_image *nim ) ; - -int nifti_read_collapsed_image( nifti_image * nim, const int dims [8], - void ** data ); - -int nifti_read_subregion_image( nifti_image * nim, - int *start_index, int *region_size, - void ** data ); - -void nifti_image_write ( nifti_image * nim ) ; -void nifti_image_write_bricks(nifti_image * nim, - const nifti_brick_list * NBL); -void nifti_image_infodump( const nifti_image * nim ) ; - -void nifti_disp_lib_hist( void ) ; /* to display library history */ -void nifti_disp_lib_version( void ) ; /* to display library version */ -int nifti_disp_matrix_orient( const char * mesg, mat44 mat ); -int nifti_disp_type_list( int which ); - - -char * nifti_image_to_ascii ( const nifti_image * nim ) ; -nifti_image *nifti_image_from_ascii( const char * str, int * bytes_read ) ; - -size_t nifti_get_volsize(const nifti_image *nim) ; - -/* basic file operations */ -int nifti_set_filenames(nifti_image * nim, const char * prefix, int check, - int set_byte_order); -char * nifti_makehdrname (const char * prefix, int nifti_type, int check, - int comp); -char * nifti_makeimgname (const char * prefix, int nifti_type, int check, - int comp); -int is_nifti_file (const char *hname); -char * nifti_find_file_extension(const char * name); -int nifti_is_complete_filename(const char* fname); -int nifti_validfilename(const char* fname); - -int disp_nifti_1_header(const char * info, const nifti_1_header * hp ) ; -void nifti_set_debug_level( int level ) ; -void nifti_set_skip_blank_ext( int skip ) ; -void nifti_set_allow_upper_fext( int allow ) ; - -int valid_nifti_brick_list(nifti_image * nim , int nbricks, - const int * blist, int disp_error); - -/* znzFile operations */ -znzFile nifti_image_open(const char * hname, const char * opts, nifti_image ** nim); -znzFile nifti_image_write_hdr_img(nifti_image *nim, int write_data, - const char* opts); -znzFile nifti_image_write_hdr_img2( nifti_image *nim , int write_opts , - const char* opts, znzFile imgfile, const nifti_brick_list * NBL); -size_t nifti_read_buffer(znzFile fp, void* datatptr, size_t ntot, - nifti_image *nim); -int nifti_write_all_data(znzFile fp, nifti_image * nim, - const nifti_brick_list * NBL); -size_t nifti_write_buffer(znzFile fp, const void * buffer, size_t numbytes); -nifti_image *nifti_read_ascii_image(znzFile fp, char *fname, int flen, - int read_data); -znzFile nifti_write_ascii_image(nifti_image *nim, const nifti_brick_list * NBL, - const char * opts, int write_data, int leave_open); - - -void nifti_datatype_sizes( int datatype , int *nbyper, int *swapsize ) ; - -void nifti_mat44_to_quatern( mat44 R , - float *qb, float *qc, float *qd, - float *qx, float *qy, float *qz, - float *dx, float *dy, float *dz, float *qfac ) ; - -mat44 nifti_quatern_to_mat44( float qb, float qc, float qd, - float qx, float qy, float qz, - float dx, float dy, float dz, float qfac ); - -mat44 nifti_make_orthog_mat44( float r11, float r12, float r13 , - float r21, float r22, float r23 , - float r31, float r32, float r33 ) ; - -int nifti_short_order(void) ; /* CPU byte order */ - - -/* Orientation codes that might be returned from nifti_mat44_to_orientation().*/ - -#define NIFTI_L2R 1 /* Left to Right */ -#define NIFTI_R2L 2 /* Right to Left */ -#define NIFTI_P2A 3 /* Posterior to Anterior */ -#define NIFTI_A2P 4 /* Anterior to Posterior */ -#define NIFTI_I2S 5 /* Inferior to Superior */ -#define NIFTI_S2I 6 /* Superior to Inferior */ - -void nifti_mat44_to_orientation( mat44 R , int *icod, int *jcod, int *kcod ) ; - -/*--------------------- Low level IO routines ------------------------------*/ - -char * nifti_findhdrname (const char* fname); -char * nifti_findimgname (const char* fname , int nifti_type); -int nifti_is_gzfile (const char* fname); - -char * nifti_makebasename(const char* fname); - - -/* other routines */ -struct nifti_1_header nifti_convert_nim2nhdr(const nifti_image* nim); -nifti_1_header * nifti_make_new_header(const int arg_dims[], int arg_dtype); -nifti_1_header * nifti_read_header(const char *hname, int *swapped, int check); -nifti_image * nifti_copy_nim_info(const nifti_image * src); -nifti_image * nifti_make_new_nim(const int dims[], int datatype, - int data_fill); -nifti_image * nifti_simple_init_nim(void); -nifti_image * nifti_convert_nhdr2nim(struct nifti_1_header nhdr, - const char * fname); - -int nifti_hdr_looks_good (const nifti_1_header * hdr); -int nifti_is_valid_datatype (int dtype); -int nifti_is_valid_ecode (int ecode); -int nifti_nim_is_valid (nifti_image * nim, int complain); -int nifti_nim_has_valid_dims (nifti_image * nim, int complain); -int is_valid_nifti_type (int nifti_type); -int nifti_test_datatype_sizes (int verb); -int nifti_type_and_names_match (nifti_image * nim, int show_warn); -int nifti_update_dims_from_array(nifti_image * nim); -void nifti_set_iname_offset (nifti_image *nim); -int nifti_set_type_from_names (nifti_image * nim); -int nifti_add_extension(nifti_image * nim, const char * data, int len, - int ecode ); -int nifti_compiled_with_zlib (void); -int nifti_copy_extensions (nifti_image *nim_dest,const nifti_image *nim_src); -int nifti_free_extensions (nifti_image *nim); -int * nifti_get_intlist (int nvals , const char *str); -char * nifti_strdup (const char *str); -int valid_nifti_extensions(const nifti_image *nim); - - -/*-------------------- Some C convenience macros ----------------------------*/ - -/* NIfTI-1.1 extension codes: - see http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q21 */ - -#define NIFTI_ECODE_IGNORE 0 /* changed from UNKNOWN, 29 June 2005 */ - -#define NIFTI_ECODE_DICOM 2 /* intended for raw DICOM attributes */ - -#define NIFTI_ECODE_AFNI 4 /* Robert W Cox: rwcox@nih.gov - https://afni.nimh.nih.gov/afni */ - -#define NIFTI_ECODE_COMMENT 6 /* plain ASCII text only */ - -#define NIFTI_ECODE_XCEDE 8 /* David B Keator: dbkeator@uci.edu - http://www.nbirn.net/Resources - /Users/Applications/ - /xcede/index.htm */ - -#define NIFTI_ECODE_JIMDIMINFO 10 /* Mark A Horsfield: - mah5@leicester.ac.uk - http://someplace/something */ - -#define NIFTI_ECODE_WORKFLOW_FWDS 12 /* Kate Fissell: fissell@pitt.edu - http://kraepelin.wpic.pitt.edu - /~fissell/NIFTI_ECODE_WORKFLOW_FWDS - /NIFTI_ECODE_WORKFLOW_FWDS.html */ - -#define NIFTI_ECODE_FREESURFER 14 /* http://surfer.nmr.mgh.harvard.edu */ - -#define NIFTI_ECODE_PYPICKLE 16 /* embedded Python objects - http://niftilib.sourceforge.net - /pynifti */ - - /* LONI MiND codes: http://www.loni.ucla.edu/twiki/bin/view/Main/MiND */ -#define NIFTI_ECODE_MIND_IDENT 18 /* Vishal Patel: vishal.patel@ucla.edu*/ -#define NIFTI_ECODE_B_VALUE 20 -#define NIFTI_ECODE_SPHERICAL_DIRECTION 22 -#define NIFTI_ECODE_DT_COMPONENT 24 -#define NIFTI_ECODE_SHC_DEGREEORDER 26 /* end LONI MiND codes */ - -#define NIFTI_ECODE_VOXBO 28 /* Dan Kimberg: www.voxbo.org */ - -#define NIFTI_ECODE_CARET 30 /* John Harwell: john@brainvis.wustl.edu - http://brainvis.wustl.edu/wiki - /index.php/Caret:Documentation - :CaretNiftiExtension */ - -#define NIFTI_ECODE_CIFTI 32 /* CIFTI-2_Main_FINAL_1March2014.pdf */ - -#define NIFTI_ECODE_VARIABLE_FRAME_TIMING 34 - -/* 36 is currently unassigned, waiting on NIFTI_ECODE_AGILENT_PROCPAR */ - -#define NIFTI_ECODE_EVAL 38 /* Munster University Hospital */ - -/* http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter */ -#define NIFTI_ECODE_MATLAB 40 /* MATLAB extension */ - - -#define NIFTI_MAX_ECODE 40 /******* maximum extension code *******/ - -/* nifti_type file codes */ -#define NIFTI_FTYPE_ANALYZE 0 -#define NIFTI_FTYPE_NIFTI1_1 1 -#define NIFTI_FTYPE_NIFTI1_2 2 -#define NIFTI_FTYPE_ASCII 3 -#define NIFTI_MAX_FTYPE 3 /* this should match the maximum code */ - -/*------------------------------------------------------------------------*/ -/*-- the rest of these apply only to nifti1_io.c, check for _NIFTI1_IO_C_ */ -/* Feb 9, 2005 [rickr] */ -#ifdef _NIFTI1_IO_C_ - -typedef struct { - int debug; /*!< debug level for status reports */ - int skip_blank_ext; /*!< skip extender if no extensions */ - int allow_upper_fext; /*!< allow uppercase file extensions */ -} nifti_global_options; - -typedef struct { - int type; /* should match the NIFTI_TYPE_ #define */ - int nbyper; /* bytes per value, matches nifti_image */ - int swapsize; /* bytes per swap piece, matches nifti_image */ - char const * const name; /* text string to match #define */ -} nifti_type_ele; - -#undef LNI_FERR /* local nifti file error, to be compact and repetative */ -#define LNI_FERR(func,msg,file) \ - fprintf(stderr,"** ERROR (%s): %s '%s'\n",func,msg,file) - -#undef swap_2 -#undef swap_4 -#define swap_2(s) nifti_swap_2bytes(1,&(s)) /* s: 2-byte short; swap in place */ -#define swap_4(v) nifti_swap_4bytes(1,&(v)) /* v: 4-byte value; swap in place */ - - /***** isfinite() is a C99 macro, which is - present in many C implementations already *****/ - -#undef IS_GOOD_FLOAT -#undef FIXED_FLOAT - -#ifdef isfinite /* use isfinite() to check floats/doubles for goodness */ -# define IS_GOOD_FLOAT(x) isfinite(x) /* check if x is a "good" float */ -# define FIXED_FLOAT(x) (isfinite(x) ? (x) : 0) /* fixed if bad */ -#else -# define IS_GOOD_FLOAT(x) 1 /* don't check it */ -# define FIXED_FLOAT(x) (x) /* don't fix it */ -#endif - -#undef ASSIF /* assign v to *p, if possible */ -#define ASSIF(p,v) if( (p)!=NULL ) *(p) = (v) - -#undef MSB_FIRST -#undef LSB_FIRST -#undef REVERSE_ORDER -#define LSB_FIRST 1 -#define MSB_FIRST 2 -#define REVERSE_ORDER(x) (3-(x)) /* convert MSB_FIRST <--> LSB_FIRST */ - -#define LNI_MAX_NIA_EXT_LEN 100000 /* consider a longer extension invalid */ - -#endif /* _NIFTI1_IO_C_ section */ -/*------------------------------------------------------------------------*/ - -/*=================*/ -#ifdef __cplusplus -} -#endif -/*=================*/ - -#endif /* _NIFTI_IO_HEADER_ */ diff --git a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_test.c b/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_test.c deleted file mode 100644 index 515dad8e382..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_test.c +++ /dev/null @@ -1,107 +0,0 @@ -#include /* directly include I/O library functions */ - - -static int local_fileexists(const char* fname) -{ - znzFile fp = znzopen( fname , "rb" , 1 ) ; - if( !znz_isnull(fp) ) { znzclose(fp); return 1; } - return 0; /* fp is NULL */ -} - -/*-----------------------------------------------*/ -/* cc -o nifti1_test -O2 nifti1_test.c -lm */ -/*-----------------------------------------------*/ - -/****************************************************************************/ - -int main( int argc , char *argv[] ) -{ - nifti_image *nim ; - int iarg=1 , outmode=1 , ll , argn=1, usegzip=0; - char *tmpstr; - - if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ - printf("Usage: nifti1_test [-n2|-n1|-na|-a2] infile [prefix]\n" - "\n" - " If prefix is given, then the options mean:\n" - " -a2 ==> write an ANALYZE 7.5 file pair: prefix.hdr/prefix.img\n" - " -n2 ==> write a NIFTI-1 file pair: prefix.hdr/prefix.img\n" - " -n1 ==> write a NIFTI-1 single file: prefix.nii\n" - " -na ==> write a NIFTI-1 ASCII+binary file: prefix.nia\n"); - printf(" -za2 => write an ANALYZE 7.5 file pair:\n" - " prefix.hdr.gz/prefix.img.gz\n" - " -zn2 => write a NIFTI-1 file pair: prefix.hdr.gz/prefix.img.gz\n" - " -zn1 => write a NIFTI-1 single file: prefix.nii.gz\n"); - printf(" The default is '-n1'.\n" - "\n" - " If prefix is not given, then the header info from infile\n" - " file is printed to stdout.\n" - "\n" - " Please note that the '.nia' format is NOT part of the\n" - " NIFTI-1 specification, but is provided mostly for ease\n" - " of visualization (e.g., you can edit a .nia file and\n" - " change some header fields, then rewrite it as .nii)\n" - ) ; - printf("\nsizeof(nifti_1_header)=%u\n", - (unsigned int)sizeof(nifti_1_header)) ; - exit(0) ; - } - - if( argv[1][0] == '-' ){ - argn=1; - if (argv[1][1] == 'z' ) { - usegzip = 1; - argn=2; - } - if( argv[1][argn] == 'a' ){ - outmode = 0 ; - } else if( argv[1][argn] == 'n' ){ - switch( argv[1][argn+1] ){ - case '1': outmode = 1 ; break ; - default: outmode = 2 ; break ; - case 'a': outmode = 3 ; break ; - } - } - iarg++ ; - } - - if( iarg >= argc ){ - fprintf(stderr,"** ERROR: no input file on command line!?\n"); exit(1); - } - - nim = nifti_image_read( argv[iarg++] , 1 ) ; - if( nim == NULL ) exit(1) ; - - if( iarg >= argc ){ nifti_image_infodump(nim); exit(0); } - - nim->nifti_type = outmode ; - if( nim->fname != NULL ) free(nim->fname) ; - if( nim->iname != NULL ) free(nim->iname) ; - - ll = strlen(argv[iarg]) ; - tmpstr = nifti_makebasename(argv[iarg]); - nim->fname = (char *)calloc(1,ll+8) ; strcpy(nim->fname,tmpstr) ; - nim->iname = (char *)calloc(1,ll+8) ; strcpy(nim->iname,tmpstr) ; - free(tmpstr); - if( nim->nifti_type == 1 ){ - strcat(nim->fname,".nii") ; - strcat(nim->iname,".nii") ; - } else if ( nim->nifti_type == 3 ){ - strcat(nim->fname,".nia") ; - strcat(nim->iname,".nia") ; - } else { - strcat(nim->fname,".hdr") ; - strcat(nim->iname,".img") ; - } - if (usegzip) { - strcat(nim->fname,".gz"); - strcat(nim->iname,".gz"); - } - nifti_image_write( nim ) ; - if ( ! local_fileexists( nim->fname ) ) - { - return EXIT_FAILURE; - } - nifti_image_free( nim ) ; - return EXIT_SUCCESS; -} diff --git a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_tool.c b/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_tool.c deleted file mode 100644 index fc46c123f83..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_tool.c +++ /dev/null @@ -1,4199 +0,0 @@ -/*--------------------------------------------------------------------------*/ -/*! \file nifti_tool.c - * \brief a tool for nifti file perusal, manipulation and copying - * written by Rick Reynolds, SSCC, NIMH, January 2005 - * 
- *
- * usage: nifti_tool [options] -infiles files...
- *
- * Via this tool, one should be able to:
- *
- *       - copy a set of volumes (sub-bricks) from one dataset to another
- *       - copy a dataset, restricting some dimensions to given indices
- *
- *       - display the contents of a nifti_image (or various fields)
- *       - display the contents of a nifti1_header (or various fields)
- *       - display AFNI extensions (they are text)
- *       - display the time series at coordinates i,j,k
- *       - display the data from any collapsed image
- *
- *       - do a diff on two nifti_image structs (or various fields)
- *       - do a diff on two nifti1_header structs (or various fields)
- *
- *       - add an AFNI extension
- *       - remove any extension
- *
- *       - modify any field(s) of a nifti_image
- *       - modify any field(s) of a nifti1_struct
- *
- * usage forms:
- *
- *   nifti_tool -help
- *   nifti_tool -help_hdr
- *   nifti_tool -help_nim
- *   nifti_tool -help_ana
- *   nifti_tool -help_datatypes
- *   nifti_tool -hist
- *   nifti_tool -ver
- *   nifti_tool -nifti_hist
- *   nifti_tool -nifti_ver
- *   nifti_tool -with_zlib
- *
- *   nifti_tool -check_hdr -infiles f1 ...
- *   nifti_tool -check_nim -infiles f1 ...
-
- *   nifti_tool -disp_exts -infiles f1 ...
- *   nifti_tool -disp_hdr [-field fieldname] [...] -infiles f1 ...
- *   nifti_tool -disp_nim [-field fieldname] [...] -infiles f1 ...
- *   nifti_tool -disp_ana [-field fieldname] [...] -infiles f1 ...
- *   nifti_tool -disp_ts I J K [-dci_lines] -infiles f1 ...
- *   nifti_tool -disp_ci I J K T U V W [-dci_lines] -infiles f1 ...
- *
- *   nifti_tool -diff_hdr [-field fieldname] [...] -infiles f1 f2
- *   nifti_tool -diff_nim [-field fieldname] [...] -infiles f1 f2
- *
- *   nifti_tool -add_afni_ext    "extension in quotes" -infiles f1 ...
- *   nifti_tool -add_comment_ext "extension in quotes" -infiles f1 ...
- *   nifti_tool -rm_ext ext_index -infiles f1 ...
- *
- *   nifti_tool -mod_hdr  [-mod_field fieldname new_val] [...] -infiles f1 ...
- *   nifti_tool -mod_nim  [-mod_field fieldname new_val] [...] -infiles f1 ...
- *
- *
*/ -/*-------------------------------------------------------------------------*/ - -/*! module history */ -static const char * g_history[] = -{ - "----------------------------------------------------------------------\n" - "nifti_tool modification history:\n" - "\n", - "0.1 30 December 2004 [rickr]\n" - " (Rick Reynolds of the National Institutes of Health, SSCC/DIRP/NIMH)\n" - " - skeleton version: options read and printed\n" - "\n", - "1.0 07 January 2005 [rickr]\n" - " - initial release version\n" - "\n", - "1.1 14 January 2005 [rickr]\n" - " - changed all non-error/non-debug output from stderr to stdout\n" - " note: creates a mis-match between normal output and debug messages\n" - " - modified act_diff_hdrs and act_diff_nims to do the processing in\n" - " lower-level functions\n", - " - added functions diff_hdrs, diff_hdrs_list, diff_nims, diff_nims_list\n" - " - added function get_field, to return a struct pointer via a fieldname\n" - " - made 'quiet' output more quiet (no description on output)\n" - " - made hdr and nim_fields arrays global, so do not pass in main()\n" - " - return (from main()) after first act_diff() difference\n" - "\n", - "1.2 9 February 2005 [rickr] - minor\n" - " - defined a local NTL_FERR macro (so it does not come from nifti1_io.h)\n" - " - added new set_byte_order parameter to nifti_set_filenames\n" - "\n", - "1.3 23 February 2005 [rickr] - sourceforge.net merge\n" - " - moved to utils directory\n" - " - added simple casts of 3 pointers for -pedantic warnings\n" - " - added a doxygen comment for the file\n" - "\n", - "1.4 02 March 2005 [rickr] - small update\n" - " - no validation in nifti_read_header calls\n" - "\n", - "1.5 05 April 2005 [rickr] - small update\n" - " - refuse mod_hdr for gzipped files (we cannot do partial overwrites)\n" - "\n", - "1.6 08 April 2005 [rickr] - added cbl, cci and dts functionality\n" - " - added -cbl: 'copy brick list' dataset copy functionality\n" - " - added -ccd: 'copy collapsed data' dataset copy functionality\n" - " - added -disp_ts: 'disp time series' data display functionality\n" - " - moved raw data display to disp_raw_data()\n" - "\n", - "1.7 14 April 2005 [rickr] - added data display functionality\n" - " - added -dci: 'display collapsed image' functionality\n" - " - modified -dts to use -dci\n" - " - modified and updated the help in use_full()\n" - " - changed copy_collapsed_dims to copy_collapsed_image, etc.\n", - " - fixed problem in disp_raw_data() for printing NT_DT_CHAR_PTR\n" - " - modified act_disp_ci():\n" - " o was act_disp_ts(), now displays arbitrary collapsed image data\n" - " o added missed debug filename act_disp_ci()\n" - " o can now save free() of data pointer for end of file loop\n", - " - modified disp_raw_data()\n" - " o takes a flag for whether to print newline\n" - " o trailing spaces and zeros are removed from printing floats\n" - " - added clear_float_zeros(), to remove trailing zeros\n" - "\n", - "1.8 19 April 2005 [rickr] - COMMENT extensions\n" - " - added int_list struct, and keep_hist,etypes,command fields to nt_opts\n" - " - added -add_comment_ext action\n" - " - allowed for removal of multiple extensions, including option of ALL\n" - " - added -keep_hist option, to store the command as a COMMENT extension\n", - " (includes fill_cmd_string() and add_int(), is done for all actions)\n" - " - added remove_ext_list(), for removing a list of extensions by indices\n" - " - added -strip action, to strip all extensions and descrip fields\n" - "\n", - "1.9 25 Aug 2005 [rickr] - const/string cleanup for warnings\n", - "1.10 18 Nov 2005 [rickr] - added check_hdr and check_nim actions\n", - "1.11 31 Jan 2006 [rickr] - check for new vox_offset in act_mod_hdrs\n", - "1.12 02 Mar 2006 [rickr]\n" - " - in act_cbl(), check for nt = 0 because of niftilib update 1.17\n", - "1.13 24 Apr 2006 [rickr] - act_disp_ci(): remove time series length check\n", - "1.14 04 Jun 2007 [rickr] - free_opts_mem(), to appease valgrind\n", - "1.15 05 Jun 2007 [rickr] - act_check_hdrs: free(nim)->nifti_image_free()\n", - "1.16 12 Jun 2007 [rickr] - allow creation of datasets via MAKE_IM\n", - " - added nt_image_read, nt_read_header and nt_read_bricks\n" - " to wrap nifti read functions, allowing creation of new datasets\n" - " - added -make_im, -new_dim, -new_datatype and -copy_im\n" - "1.17 13 Jun 2007 [rickr] - added help for -copy_im, enumerate examples\n", - "1.18 23 Jun 2007 [rickr] - main returns 0 on -help, -hist, -ver\n" - "1.19 28 Nov 2007 [rickr] - added -help_datatypes\n", - "1.20 13 Jun 2008 [rickr]\n" - " - added -with_zlib\n" - " - added ability to create extension from text file (for J. Gunter)\n", - "1.21 03 Aug 2008 [rickr] - ANALYZE 7.5 support\n" - " - added -help_ana, -disp_ana,\n" - " -swap_as_analyze, -swap_as_nifti, -swap_as_old\n" - "1.22 08 Oct 2008 [rickr] - allow cbl with indices in 0..nt*nu*nv*nw-1\n" - "1.23 06 Jul 2010 [rickr]\n", - " - in nt_read_bricks, bsize computation should allow for large integers\n" - "1.24 26 Sep 2012 [rickr]\n", - " - changed ana originator from char to short\n" - "----------------------------------------------------------------------\n" -}; -static char g_version[] = "version 1.24 (September 26, 2012)"; -static int g_debug = 1; - -#define _NIFTI_TOOL_C_ -#include "nifti1_io.h" -#include "nifti1_tool.h" - -/* local prototypes */ -static int free_opts_mem(nt_opts * nopt); -static int num_volumes(nifti_image * nim); -static char * read_file_text(const char * filename, int * length); - -#define NTL_FERR(func,msg,file) \ - fprintf(stderr,"** ERROR (%s): %s '%s'\n",func,msg,file) - -/* val may be a function call, so evalulate first, and return result */ -#define FREE_RETURN(val) \ - do{ int tval=(val); free_opts_mem(&opts); return tval; } while(0) - -/* these are effectively constant, and are built only for verification */ -field_s g_hdr_fields[NT_HDR_NUM_FIELDS]; /* nifti_1_header fields */ -field_s g_ana_fields[NT_ANA_NUM_FIELDS]; /* nifti_analyze75 */ -field_s g_nim_fields[NT_NIM_NUM_FIELDS]; /* nifti_image fields */ - -int main( int argc, char * argv[] ) -{ - nt_opts opts; - int rv; - - if( (rv = process_opts(argc, argv, &opts)) != 0) /* then return */ - { - if( rv < 0 ) FREE_RETURN(1); /* free opts memory, and return */ - else FREE_RETURN(0); /* valid usage */ - } - - if( (rv = verify_opts(&opts, argv[0])) != 0 ) - FREE_RETURN(rv); - - /* now perform the requested action(s) */ - - if( (rv = fill_hdr_field_array(g_hdr_fields)) != 0 ) - FREE_RETURN(rv); - - if( (rv = fill_nim_field_array(g_nim_fields)) != 0 ) - FREE_RETURN(rv); - - if( (rv = fill_ana_field_array(g_ana_fields)) != 0 ) - FREE_RETURN(rv); - - /* 'check' functions, first */ - if( opts.check_hdr || opts.check_nim ) /* allow for both */ - FREE_RETURN( act_check_hdrs(&opts) ); - - /* copy or dts functions -- do not continue after these */ - if( opts.cbl ) FREE_RETURN( act_cbl(&opts) ); - if( opts.cci ) FREE_RETURN( act_cci(&opts) ); - if( opts.dts || opts.dci ) FREE_RETURN( act_disp_ci(&opts) ); - - /* perform modifications early, in case we allow multiple actions */ - if( opts.strip && ((rv = act_strip (&opts)) != 0) ) FREE_RETURN(rv); - - if( opts.add_exts && ((rv = act_add_exts (&opts)) != 0) ) FREE_RETURN(rv); - if( opts.rm_exts && ((rv = act_rm_ext (&opts)) != 0) ) FREE_RETURN(rv); - - if( opts.mod_hdr && ((rv = act_mod_hdrs (&opts)) != 0) ) FREE_RETURN(rv); - if( opts.mod_nim && ((rv = act_mod_nims (&opts)) != 0) ) FREE_RETURN(rv); - - if((opts.swap_hdr || opts.swap_ana || opts.swap_old ) - && ((rv = act_swap_hdrs (&opts)) != 0) ) FREE_RETURN(rv); - - /* if a diff, return wither a difference exists (like the UNIX command) */ - if( opts.diff_hdr && ((rv = act_diff_hdrs(&opts)) != 0) ) FREE_RETURN(rv); - if( opts.diff_nim && ((rv = act_diff_nims(&opts)) != 0) ) FREE_RETURN(rv); - - /* last action type is display */ - if( opts.disp_exts && ((rv = act_disp_exts(&opts)) != 0) ) FREE_RETURN(rv); - if( opts.disp_hdr && ((rv = act_disp_hdrs(&opts)) != 0) ) FREE_RETURN(rv); - if( opts.disp_nim && ((rv = act_disp_nims(&opts)) != 0) ) FREE_RETURN(rv); - if( opts.disp_ana && ((rv = act_disp_anas(&opts)) != 0) ) FREE_RETURN(rv); - - FREE_RETURN(0); -} - -/*---------------------------------------------------------------------- - * process user options, return 0 on success - *----------------------------------------------------------------------*/ -int process_opts( int argc, char * argv[], nt_opts * opts ) -{ - int ac; - - memset(opts, 0, sizeof(*opts)); - - opts->prefix = NULL; - opts->debug = 1; /* init debug level to basic output */ - - /* init options for creating a new dataset via "MAKE_IM" */ - opts->new_datatype = NIFTI_TYPE_INT16; - opts->new_dim[0] = 3; - opts->new_dim[1] = 1; opts->new_dim[2] = 1; opts->new_dim[3] = 1; - - if( argc < 2 ) return usage(argv[0], USE_FULL); - - /* terminal options are first, the rest are sorted */ - for( ac = 1; ac < argc; ac++ ) - { - if( ! strncmp(argv[ac], "-help_datatypes", 9) ) - { - ac++; - if( ac >= argc ) - nifti_disp_type_list(3); /* show all types */ - else if( argv[ac][0] == 'd' || argv[ac][0] == 'D' ) - nifti_disp_type_list(1); /* show DT_* types */ - else if( argv[ac][0] == 't' || argv[ac][0] == 'T' ) - nifti_test_datatype_sizes(1); /* test each nbyper and swapsize */ - else - nifti_disp_type_list(2); /* show NIFTI_* types */ - return 1; - } - else if( ! strncmp(argv[ac], "-help_hdr", 9) ) - return usage(argv[0], USE_FIELD_HDR); - else if( ! strncmp(argv[ac], "-help_nim", 9) ) - return usage(argv[0], USE_FIELD_NIM); - else if( ! strncmp(argv[ac], "-help_ana", 9) ) - return usage(argv[0], USE_FIELD_ANA); - else if( ! strncmp(argv[ac], "-help", 5) ) - return usage(argv[0], USE_FULL); - else if( ! strncmp(argv[ac], "-hist", 5) ) - return usage(argv[0], USE_HIST); - else if( ! strncmp(argv[ac], "-ver", 2) ) - return usage(argv[0], USE_VERSION); - else if( ! strncmp(argv[ac], "-nifti_hist", 11) ) - { - nifti_disp_lib_hist(); - return 1; - } - else if( ! strncmp(argv[ac], "-nifti_ver", 10) ) - { - nifti_disp_lib_version(); - return 1; - } - else if( ! strncmp(argv[ac], "-with_zlib", 5) ) { - printf("Was NIfTI library compiled with zlib? %s\n", - nifti_compiled_with_zlib() ? "YES" : "NO"); - return 1; - } - - /* begin normal execution options... */ - else if( ! strncmp(argv[ac], "-add_afni_ext", 9) ) - { - ac++; - CHECK_NEXT_OPT(ac, argc, "-add_afni_ext"); - if( add_string(&opts->elist, argv[ac]) ) return -1; /* add extension */ - if( add_int(&opts->etypes, NIFTI_ECODE_AFNI) ) return -1; - opts->add_exts = 1; - } - else if( ! strncmp(argv[ac], "-add_comment_ext", 9) ) - { - ac++; - CHECK_NEXT_OPT(ac, argc, "-add_comment_ext"); - if( add_string(&opts->elist, argv[ac]) ) return -1; /* add extension */ - if( add_int(&opts->etypes, NIFTI_ECODE_COMMENT) ) return -1; - opts->add_exts = 1; - } - else if( ! strncmp(argv[ac], "-check_hdr", 10) ) - opts->check_hdr = 1; - else if( ! strncmp(argv[ac], "-check_nim", 10) ) - opts->check_nim = 1; - else if( ! strncmp(argv[ac], "-copy_brick_list", 11) || - ! strncmp(argv[ac], "-copy_im", 10) || - ! strncmp(argv[ac], "-cbl", 4) ) - { - opts->cbl = 1; - } - else if( ! strncmp(argv[ac], "-copy_collapsed_image", 10) || - ! strncmp(argv[ac], "-cci", 4) ) - { - /* we need to read in the 7 dimension values */ - int index; - opts->ci_dims[0] = 0; - for( index = 1; index < 8; index++ ) - { - ac++; - CHECK_NEXT_OPT_MSG(ac,argc,"-cci","7 dimension values are requred"); - if( ! isdigit(argv[ac][0]) && strcmp(argv[ac],"-1") ){ - fprintf(stderr,"** -cci param %d (= '%s') is not a valid\n" - " consider: 'nifti_tool -help'\n",index,argv[ac]); - return -1; - } - opts->ci_dims[index] = atoi(argv[ac]); - } - - opts->cci = 1; - } - else if( ! strncmp(argv[ac], "-debug", 6) ) - { - ac++; - CHECK_NEXT_OPT(ac, argc, "-debug"); - opts->debug = atoi(argv[ac]); - } - else if( ! strncmp(argv[ac], "-diff_hdr", 8) ) - opts->diff_hdr = 1; - else if( ! strncmp(argv[ac], "-diff_nim", 8) ) - opts->diff_nim = 1; - else if( ! strncmp(argv[ac], "-disp_exts", 7) ) - opts->disp_exts = 1; - else if( ! strncmp(argv[ac], "-disp_hdr", 8) ) - opts->disp_hdr = 1; - else if( ! strncmp(argv[ac], "-disp_nim", 8) ) - opts->disp_nim = 1; - else if( ! strncmp(argv[ac], "-disp_ana", 8) ) - opts->disp_ana = 1; - else if( ! strncmp(argv[ac], "-dci_lines", 6) || /* before -dts */ - ! strncmp(argv[ac], "-dts_lines", 6) ) - { - opts->dci_lines = 1; - } - else if( ! strncmp(argv[ac], "-disp_collapsed_image", 10) || - ! strncmp(argv[ac], "-disp_ci", 8) ) - { - /* we need to read in the 7 dimension values */ - int index; - opts->ci_dims[0] = 0; - for( index = 1; index < 8; index++ ) - { - ac++; - CHECK_NEXT_OPT_MSG(ac,argc,"-disp_ci", - "7 dimension values are requred"); - if( ! isdigit(argv[ac][0]) && strcmp(argv[ac],"-1") ){ - fprintf(stderr,"** -disp_ci param %d (= '%s') is not a valid\n" - " consider: 'nifti_tool -help'\n",index,argv[ac]); - return -1; - } - opts->ci_dims[index] = atoi(argv[ac]); - } - - opts->dci = 1; - } - else if( ! strncmp(argv[ac], "-disp_ts", 10) || - ! strncmp(argv[ac], "-dts", 4) ) - { - /* we need to read in the ijk indices into the ci_dims array */ - int index; - for( index = 1; index <= 3; index++ ) - { - ac++; - CHECK_NEXT_OPT_MSG(ac,argc,"-dts","i,j,k indices are requied\n"); - if( ! isdigit(argv[ac][0]) ){ - fprintf(stderr,"** -dts param %d (= '%s') is not a number\n" - " consider: 'nifti_tool -help'\n",index,argv[ac]); - return -1; - } - opts->ci_dims[index] = atoi(argv[ac]); - } - /* and fill the rest of the array */ - opts->ci_dims[0] = 0; - for( index = 4; index < 8; index++ ) opts->ci_dims[index] = -1; - - opts->dts = 1; - } - else if( ! strncmp(argv[ac], "-field", 2) ) - { - ac++; - CHECK_NEXT_OPT(ac, argc, "-field"); - if( add_string(&opts->flist, argv[ac]) ) return -1; /* add field */ - } - else if( ! strncmp(argv[ac], "-infiles", 3) ) - { - int count; - /* for -infiles, get all next arguments until a '-' or done */ - ac++; - for( count = 0; (ac < argc) && (argv[ac][0] != '-'); ac++, count++ ) - if( add_string(&opts->infiles, argv[ac]) ) return -1;/* add field */ - if( count > 0 && ac < argc ) ac--; /* more options to process */ - if( g_debug > 2 ) fprintf(stderr,"+d have %d file names\n", count); - } - else if( ! strncmp(argv[ac], "-make_image", 8) ) - { - opts->make_im = 1; /* will setup later, as -cbl and MAKE_IM */ - } - else if( ! strncmp(argv[ac], "-mod_field", 6) ) - { - ac++; - CHECK_NEXT_OPT(ac, argc, "-mod_field"); - if( add_string(&opts->flist, argv[ac]) ) return -1; /* add field */ - ac++; - CHECK_NEXT_OPT(ac, argc, "-mod_field (2)"); - if( add_string(&opts->vlist, argv[ac]) ) return -1; /* add value */ - } - else if( ! strncmp(argv[ac], "-mod_hdr", 7) ) - opts->mod_hdr = 1; - else if( ! strncmp(argv[ac], "-mod_nim", 7) ) - opts->mod_nim = 1; - else if( ! strncmp(argv[ac], "-keep_hist", 5) ) - opts->keep_hist = 1; - else if( ! strncmp(argv[ac], "-new_dim", 8) ) - { - /* we need to read in the 8 dimension values */ - int index; - for( index = 0; index < 8; index++ ) - { - ac++; - CHECK_NEXT_OPT_MSG(ac,argc,"-new_dim","8 dim values are requred"); - if( ! isdigit(argv[ac][0]) && strcmp(argv[ac],"-1") ){ - fprintf(stderr,"** -new_dim param %d (= '%s') is not a valid\n" - " consider: 'nifti_tool -help'\n",index,argv[ac]); - return -1; - } - opts->new_dim[index] = atoi(argv[ac]); - } - } - else if( ! strncmp(argv[ac], "-new_datatype", 10) ) - { - ac++; - CHECK_NEXT_OPT(ac, argc, "-new_datatype"); - opts->new_datatype = atoi(argv[ac]); - } - else if( ! strncmp(argv[ac], "-overwrite", 6) ) - opts->overwrite = 1; - else if( ! strncmp(argv[ac], "-prefix", 4) ) - { - ac++; - CHECK_NEXT_OPT(ac, argc, "-prefix"); - opts->prefix = argv[ac]; - } - else if( ! strncmp(argv[ac], "-quiet", 3) ) - opts->debug = 0; - else if( ! strncmp(argv[ac], "-rm_ext", 7) ) - { - ac++; - CHECK_NEXT_OPT(ac, argc, "-rm_ext"); - if( strcmp(argv[ac],"ALL") == 0 ) /* special case, pass -1 */ - { - if( add_string(&opts->elist, "-1") ) return -1; - } - else - { - int index = atoi(argv[ac]); - if( (index != -1) && ((index > 1000) || !isdigit(*argv[ac])) ){ - fprintf(stderr, - "** '-rm_ext' requires an extension index (read '%s')\n", - argv[ac]); - return -1; - } - if( add_string(&opts->elist, argv[ac]) ) return -1; - } - opts->rm_exts = 1; - } - else if( ! strncmp(argv[ac], "-strip_extras", 6) ) - opts->strip = 1; - else if( ! strncmp(argv[ac], "-swap_as_analyze", 12) ) - opts->swap_ana = 1; - else if( ! strncmp(argv[ac], "-swap_as_nifti", 12) ) - opts->swap_hdr = 1; - else if( ! strncmp(argv[ac], "-swap_as_old", 12) ) - opts->swap_old = 1; - else - { - fprintf(stderr,"** unknown option: '%s'\n", argv[ac]); - return -1; - } - } - - if( opts->make_im ) - { - if( opts->infiles.len > 0 ) - { - fprintf(stderr,"** -infiles is invalid when using -make_im\n"); - return -1; - } - /* apply -make_im via -cbl and "MAKE_IM" */ - opts->cbl = 1; - if( add_string(&opts->infiles, NT_MAKE_IM_NAME) ) return -1; - } - - /* verify for programming purposes */ - if( opts->add_exts && ( opts->elist.len != opts->etypes.len ) ) - { - fprintf(stderr,"** ext list length (%d) != etype length (%d)\n", - opts->elist.len, opts->etypes.len); - return -1; - } - - g_debug = opts->debug; - nifti_set_debug_level(g_debug); - - fill_cmd_string(opts, argc, argv); /* copy this command */ - - if( g_debug > 2 ) disp_nt_opts("options read: ", opts); - - return 0; -} - - -/*---------------------------------------------------------------------- - * verify that the options make sense - *----------------------------------------------------------------------*/ -int verify_opts( nt_opts * opts, char * prog ) -{ - int ac, errs = 0; /* number of requested action types */ - - /* check that only one of disp, diff, mod or add_*_ext is used */ - ac = (opts->check_hdr || opts->check_nim ) ? 1 : 0; - ac += (opts->diff_hdr || opts->diff_nim ) ? 1 : 0; - ac += (opts->disp_hdr || opts->disp_nim || - opts->disp_ana || opts->disp_exts ) ? 1 : 0; - ac += (opts->mod_hdr || opts->mod_nim ) ? 1 : 0; - ac += (opts->swap_hdr || opts->swap_ana || opts->swap_old ) ? 1 : 0; - ac += (opts->add_exts || opts->rm_exts ) ? 1 : 0; - ac += (opts->strip ) ? 1 : 0; - ac += (opts->cbl ) ? 1 : 0; - ac += (opts->cci ) ? 1 : 0; - ac += (opts->dts || opts->dci ) ? 1 : 0; - - if( ac < 1 ) - { - fprintf(stderr, - "** no action option, so nothing to do...\n" - " (try one of '-add...', '-diff...', '-disp...' or '-mod...')\n" - " (see '%s -help' for details)\n", prog); - return 1; - } - else if( ac > 1 ) - { - fprintf(stderr, - "** only one action option is allowed, please use only one of:\n" - " '-add_...', '-check_...', '-diff_...', '-disp_...',\n" - " '-mod_...', '-strip', '-dts', '-cbl' or '-cci'\n" - " (see '%s -help' for details)\n", prog); - return 1; - } - - /* can modify nifti_1_header or nifti_image, but not both */ - if( opts->mod_hdr && opts->mod_nim ) - { - fprintf(stderr,"** cannot use both '-mod_hdr' and '-mod_nim'\n"); - return 1; - } - - /* can add or remove extensions, but not both */ - if( opts->add_exts && opts->rm_exts ) - { - fprintf(stderr,"** cannot use both '-add_*_ext' and '-rm_ext'\n"); - return 1; - } - if( (opts->add_exts || opts->rm_exts) && opts->elist.len <= 0 ) - { - fprintf(stderr,"** missing extensions to add or remove\n"); - return 1; - } - - /* if modify, then we need fields and corresponding values */ - if( opts->mod_hdr || opts->mod_nim ) - { - if( opts->flist.len <= 0 ) - { - fprintf(stderr,"** missing field to modify (need '-mod_field' opt)\n"); - return 1; - } - if( opts->flist.len != opts->vlist.len ) - { - fprintf(stderr,"** error: modifying %d fields with %d values\n", - opts->flist.len, opts->vlist.len); - return 1; - } - } - - /* verify the number of files given for each of 4 action types */ - - /* -diff_... : require nfiles == 2 */ - if( opts->diff_hdr || opts->diff_nim ) - { - if( opts->infiles.len != 2 ) - { - fprintf(stderr,"** '-diff_XXX' options require exactly 2 inputs files\n"); - return 1; - } - } - /* if we are making changes, but not overwriting... */ - else if( (opts->elist.len > 0 || opts->mod_hdr || opts->mod_nim || - opts->swap_hdr || opts->swap_ana || opts->swap_old ) && - !opts->overwrite ) - { - if( opts->infiles.len > 1 ) - { - fprintf(stderr,"** without -overwrite, only one input file may be" - " modified at a time\n"); - errs++; - } - else if( ! opts->prefix ) - { - fprintf(stderr,"** missing -prefix for output file\n"); - errs++; - } - } - - if( opts->dci_lines && ! opts->dts && ! opts->dci ) - { - fprintf(stderr,"** option '-dci_lines' must only be used with '-dts'\n"); - errs++; - } - - if( opts->infiles.len <= 0 ) /* in any case */ - { - fprintf(stderr,"** missing input files (see -infiles option)\n"); - errs++; - } - - if ( opts->overwrite && opts->prefix ) - { - fprintf(stderr, "** please specify only one of -prefix and -overwrite\n"); - errs++; - } - - if( errs ) return 1; - - if( g_debug > 1 ) fprintf(stderr,"+d options seem valid\n"); - - return 0; -} - - -/*---------------------------------------------------------------------- - * re-assemble the command string into opts->command - *----------------------------------------------------------------------*/ -int fill_cmd_string( nt_opts * opts, int argc, char * argv[]) -{ - char * cp; - int len, remain = NT_CMD_LEN; /* NT_CMD_LEN is max command len */ - int c, ac; - int has_space; /* arguments containing space must be quoted */ - int skip = 0; /* counter to skip some of the arguments */ - - /* get the first argument separately */ - len = sprintf( opts->command, "\n command: %s", argv[0] ); - cp = opts->command + len; - remain -= len; - - /* get the rest, with special attention to input files */ - for( ac = 1; ac < argc; ac++ ) - { - if( skip ){ skip--; continue; } /* then skip these arguments */ - - len = strlen(argv[ac]); - if( len + 3 >= remain ) { /* extra 3 for space and possible '' */ - fprintf(stderr,"FCS: no space remaining for command, continuing...\n"); - return 1; - } - - /* put the argument in, possibly with '' */ - - has_space = 0; - for( c = 0; c < len-1; c++ ) - if( isspace(argv[ac][c]) ){ has_space = 1; break; } - if( has_space ) len = sprintf(cp, " '%s'", argv[ac]); - else len = sprintf(cp, " %s", argv[ac]); - - remain -= len; - - /* infiles is okay, but after the *next* argument, we may skip files */ - /* (danger, will robinson! hack alert!) */ - if( !strncmp(argv[ac-1],"-infiles",3) ) - { - /* if more than 4 (just to be arbitrary) input files, - include only the first and last */ - if( opts->infiles.len > 4 ) - skip = opts->infiles.len - 2; - } - - cp += len; - } - - if( g_debug > 1 ){ - fprintf(stderr,"+d filled command string, %d args, %d bytes\n", - argc, (int)(cp - opts->command)); - if( g_debug > 2 ) fprintf(stderr,"%s\n", opts->command); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * - only bother to alloc one pointer at a time (don't need efficiency here) - * - return 0 on success - *----------------------------------------------------------------------*/ -int add_int(int_list * ilist, int val) -{ - if( ilist->len == 0 ) ilist->list = NULL; /* just to be safe */ - ilist->len++; - ilist->list = (int *)realloc(ilist->list,ilist->len*sizeof(int)); - if( ! ilist->list ){ - fprintf(stderr,"** failed to alloc %d (int *) elements\n",ilist->len); - return -1; - } - - ilist->list[ilist->len-1] = val; - - return 0; -} - - -/*---------------------------------------------------------------------- - * - do not duplicate the string - * - only bother to alloc one pointer at a time (don't need efficiency here) - * - return 0 on success - *----------------------------------------------------------------------*/ -int add_string(str_list * slist, const char * str) -{ - if( slist->len == 0 ) slist->list = NULL; /* just to be safe */ - slist->len++; - slist->list = (const char **)realloc(slist->list,slist->len*sizeof(char *)); - if( ! slist->list ){ - fprintf(stderr,"** failed to alloc %d (char *) elements\n",slist->len); - return -1; - } - - slist->list[slist->len-1] = str; - - return 0; -} - - -/*---------------------------------------------------------------------- - * display information on using the program - *----------------------------------------------------------------------*/ -int usage(const char * prog, int level) -{ - int c, len; - if( level == USE_SHORT ) - { - fprintf(stdout,"usage %s [options] -infiles files...\n", prog); - fprintf(stdout,"usage %s -help\n", prog); - return -1; - } - else if( level == USE_FULL ) - use_full("nifti_tool"); /* let's not allow paths in here */ - else if( level == USE_HIST ) - { - len = sizeof(g_history)/sizeof(char *); - for( c = 0; c < len; c++) - fputs(g_history[c], stdout); - } - else if( level == USE_FIELD_HDR ) - { - field_s nhdr_fields[NT_HDR_NUM_FIELDS]; /* just do it all here */ - - fill_hdr_field_array(nhdr_fields); - disp_field_s_list("nifti_1_header: ", nhdr_fields, NT_HDR_NUM_FIELDS); - } - else if( level == USE_FIELD_ANA ) - { - field_s nhdr_fields[NT_ANA_NUM_FIELDS]; /* just do it all here */ - - fill_ana_field_array(nhdr_fields); - disp_field_s_list("nifti_analyze75: ",nhdr_fields,NT_ANA_NUM_FIELDS); - } - else if( level == USE_FIELD_NIM ) - { - field_s nim_fields[NT_NIM_NUM_FIELDS]; - - fill_nim_field_array(nim_fields); - disp_field_s_list("nifti_image: ", nim_fields, NT_NIM_NUM_FIELDS); - } - else if( level == USE_VERSION ) - fprintf(stdout, "%s, %s\n", prog, g_version); - else { - fprintf(stdout,"** illegal level for usage(): %d\n", level); - return -1; - } - - return 1; -} - - -/*---------------------------------------------------------------------- - * full usage - *----------------------------------------------------------------------*/ -int use_full(const char * prog ) -{ - printf( - "%s\n" - "\n" - " - display, modify or compare nifti structures in datasets\n" - " - copy a dataset by selecting a list of volumes from the original\n" - " - copy a dataset, collapsing any dimensions, each to a single index\n" - " - display a time series for a voxel, or more generally, the data\n" - " from any collapsed image, in ASCII text\n", prog); - printf( - "\n" - " This program can be used to display information from nifti datasets,\n" - " to modify information in nifti datasets, to look for differences\n" - " between two nifti datasets (like the UNIX 'diff' command), and to copy\n" - " a dataset to a new one, either by restricting any dimensions, or by\n" - " copying a list of volumes (the time dimension) from a dataset.\n" - "\n"); - printf( - " Only one action type is allowed, e.g. one cannot modify a dataset\n" - " and then take a 'diff'.\n" - "\n"); - printf( - " one can display - any or all fields in the nifti_1_header structure\n" - " - any or all fields in the nifti_image structure\n" - " - any or all fields in the nifti_analyze75 structure\n" - " - the extensions in the nifti_image structure\n" - " - the time series from a 4-D dataset, given i,j,k\n" - " - the data from any collapsed image, given dims. list\n" - "\n"); - printf( - " one can check - perform internal check on the nifti_1_header struct\n" - " (by nifti_hdr_looks_good())\n" - " - perform internal check on the nifti_image struct\n" - " (by nifti_nim_is_valid())\n" - "\n"); - printf( - " one can modify - any or all fields in the nifti_1_header structure\n" - " - any or all fields in the nifti_image structure\n" - " - swap all fields in NIFTI or ANALYZE header structure\n" - " add/rm - any or all extensions in the nifti_image structure\n" - " remove - all extensions and descriptions from the datasets\n" - "\n"); - printf( - " one can compare - any or all field pairs of nifti_1_header structures\n" - " - any or all field pairs of nifti_image structures\n" - "\n" - " one can copy - an arbitrary list of dataset volumes (time points)\n" - " - a dataset, collapsing across arbitrary dimensions\n" - " (restricting those dimensions to the given indices)\n" - "\n" - " one can create - a new dataset out of nothing\n" - "\n"); - printf( - " Note: to learn about which fields exist in either of the structures,\n" - " or to learn a field's type, size of each element, or the number\n" - " of elements in the field, use either the '-help_hdr' option, or\n" - " the '-help_nim' option. No further options are required.\n" - " ------------------------------\n"); - printf( - "\n" - " usage styles:\n" - "\n" - " nifti_tool -help : show this help\n" - " nifti_tool -help_hdr : show nifti_1_header field info\n" - " nifti_tool -help_nim : show nifti_image field info\n" - " nifti_tool -help_ana : show nifti_analyze75 field info\n" - " nifti_tool -help_datatypes : show datatype table\n" - "\n"); - printf( - " nifti_tool -ver : show the current version\n" - " nifti_tool -hist : show the modification history\n" - " nifti_tool -nifti_ver : show the nifti library version\n" - " nifti_tool -nifti_hist : show the nifti library history\n" - " nifti_tool -with_zlib : was library compiled with zlib\n" - "\n" - "\n"); - printf( - " nifti_tool -check_hdr -infiles f1 ...\n" - " nifti_tool -check_nim -infiles f1 ...\n" - "\n"); - printf( - " nifti_tool -copy_brick_list -infiles f1'[indices...]'\n" - " nifti_tool -copy_collapsed_image I J K T U V W -infiles f1\n" - " nifti_tool -copy_im -infiles f1\n" - "\n"); - printf( - " nifti_tool -make_im -prefix new_im.nii\n" - "\n"); - printf( - " nifti_tool -disp_hdr [-field FIELDNAME] [...] -infiles f1 ...\n" - " nifti_tool -disp_nim [-field FIELDNAME] [...] -infiles f1 ...\n" - " nifti_tool -disp_ana [-field FIELDNAME] [...] -infiles f1 ...\n" - " nifti_tool -disp_exts -infiles f1 ...\n" - " nifti_tool -disp_ts I J K [-dci_lines] -infiles f1 ...\n" - " nifti_tool -disp_ci I J K T U V W [-dci_lines] -infiles f1 ...\n" - "\n"); - printf( - " nifti_tool -mod_hdr [-mod_field FIELDNAME NEW_VAL] [...] -infiles f1\n" - " nifti_tool -mod_nim [-mod_field FIELDNAME NEW_VAL] [...] -infiles f1\n" - "\n" - " nifti_tool -swap_as_nifti -overwrite -infiles f1\n" - " nifti_tool -swap_as_analyze -overwrite -infiles f1\n" - " nifti_tool -swap_as_old -overwrite -infiles f1\n" - "\n"); - printf( - " nifti_tool -add_afni_ext 'extension in quotes' [...] -infiles f1\n" - " nifti_tool -add_comment_ext 'extension in quotes' [...] -infiles f1\n" - " nifti_tool -add_comment_ext 'file:FILENAME' [...] -infiles f1\n" - " nifti_tool -rm_ext INDEX [...] -infiles f1 ...\n" - " nifti_tool -strip_extras -infiles f1 ...\n" - "\n"); - printf( - " nifti_tool -diff_hdr [-field FIELDNAME] [...] -infiles f1 f2\n" - " nifti_tool -diff_nim [-field FIELDNAME] [...] -infiles f1 f2\n" - "\n" - " ------------------------------\n"); - - printf( - "\n" - " selected examples:\n" - "\n" - " A. checks header (for problems):\n" - "\n" - " 1. nifti_tool -check_hdr -infiles dset0.nii dset1.nii\n" - " 2. nifti_tool -check_hdr -infiles *.nii *.hdr\n" - " 3. nifti_tool -check_hdr -quiet -infiles *.nii *.hdr\n" - "\n"); - printf( - " B. show header differences:\n" - "\n" - " 1. nifti_tool -diff_hdr -field dim -field intent_code \\\n" - " -infiles dset0.nii dset1.nii \n" - " 2. nifti_tool -diff_hdr -new_dims 3 10 20 30 0 0 0 0 \\\n" - " -infiles my_dset.nii MAKE_IM \n" - "\n" - " C. display structures or fields:\n" - "\n"); - printf( - " 1. nifti_tool -disp_hdr -infiles dset0.nii dset1.nii dset2.nii\n" - " 2. nifti_tool -disp_hdr -field dim -field descrip -infiles dset.nii\n" - " 3. nifti_tool -disp_exts -infiles dset0.nii dset1.nii dset2.nii\n" - " 4. nifti_tool -disp_ts 23 0 172 -infiles dset1_time.nii\n" - " 5. nifti_tool -disp_ci 23 0 172 -1 0 0 0 -infiles dset1_time.nii\n" - "\n"); - printf( - " 6. nifti_tool -disp_ana -infiles analyze.hdr\n" - " 7. nifti_tool -disp_nim -infiles nifti.nii\n" - "\n"); - printf( - " D. create a new dataset from nothing:\n" - "\n" - " 1. nifti_tool -make_im -prefix new_im.nii \n" - " 2. nifti_tool -make_im -prefix float_im.nii \\\n" - " -new_dims 3 10 20 30 0 0 0 0 -new_datatype 16\n"); - printf( - " 3. nifti_tool -mod_hdr -mod_field descrip 'dataset with mods' \\\n" - " -new_dims 3 10 20 30 0 0 0 0 \\\n" - " -prefix new_desc.nii -infiles MAKE_IM\n" - "\n"); - printf( - " E. copy dataset, brick list or collapsed image:\n" - "\n" - " 1. nifti_tool -copy_im -prefix new.nii -infiles dset0.nii\n" - " 2. nifti_tool -cbl -prefix new_07.nii -infiles dset0.nii'[0,7]'\n" - " 3. nifti_tool -cbl -prefix new_partial.nii \\\n" - " -infiles dset0.nii'[3..$(2)]'\n" - "\n" - " 4. nifti_tool -cci 5 4 17 -1 -1 -1 -1 -prefix new_5_4_17.nii\n" - " 5. nifti_tool -cci 5 0 17 -1 -1 2 -1 -keep_hist \\\n" - " -prefix new_5_0_17_2.nii\n" - "\n"); - printf( - " F. modify the header (modify fields or swap entire header):\n" - "\n" - " 1. nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n" - " -mod_field dim '4 64 64 20 30 1 1 1 1'\n" - " 2. nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n" - " -mod_field descrip 'beer, brats and cheese, mmmmm...'\n" - ); - printf( - " 3. cp old_dset.hdr nifti_swap.hdr \n" - " nifti_tool -swap_as_nifti -overwrite -infiles nifti_swap.hdr\n" - " 4. cp old_dset.hdr analyze_swap.hdr \n" - " nifti_tool -swap_as_analyze -overwrite -infiles analyze_swap.hdr\n" - " 5. nifti_tool -swap_as_old -prefix old_swap.hdr -infiles old_dset.hdr\n" - " nifti_tool -diff_hdr -infiles nifti_swap.hdr old_swap.hdr\n" - "\n"); - printf( - " G. strip, add or remove extensions:\n" - " (in example #3, the extension is copied from a text file)\n" - "\n" - "\n" - " 1. nifti_tool -strip -overwrite -infiles *.nii\n" - " 2. nifti_tool -add_comment 'converted from MY_AFNI_DSET+orig' \\\n" - " -prefix dnew -infiles dset0.nii\n" - ); - printf( - " 3. nifti_tool -add_comment 'file:my.extension.txt' \\\n" - " -prefix dnew -infiles dset0.nii\n" - " 4. nifti_tool -rm_ext ALL -prefix dset1 -infiles dset0.nii\n" - " 5. nifti_tool -rm_ext 2 -rm_ext 3 -rm_ext 5 -overwrite \\\n" - " -infiles dset0.nii\n" - "\n" - " ------------------------------\n"); - printf( - "\n" - " options for check actions:\n" - "\n"); - printf( - " -check_hdr : check for a valid nifti_1_header struct\n" - "\n" - " This action is used to check the nifti_1_header structure for\n" - " problems. The nifti_hdr_looks_good() function is used for the\n" - " test, and currently checks:\n" - " \n" - " dim[], sizeof_hdr, magic, datatype\n" - " \n" - " More tests can be requested of the author.\n" - "\n"); - printf( - " e.g. perform checks on the headers of some datasets\n" - " nifti_tool -check_hdr -infiles dset0.nii dset1.nii\n" - " nifti_tool -check_hdr -infiles *.nii *.hdr\n" - " \n" - " e.g. add the -quiet option, so that only errros are reported\n" - " nifti_tool -check_hdr -quiet -infiles *.nii *.hdr\n" - "\n"); - printf( - " -check_nim : check for a valid nifti_image struct\n" - "\n" - " This action is used to check the nifti_image structure for\n" - " problems. This is tested via both nifti_convert_nhdr2nim()\n" - " and nifti_nim_is_valid(), though other functions are called\n" - " below them, of course. Current checks are:\n" - "\n"); - printf( - " dim[], sizeof_hdr, datatype, fname, iname, nifti_type\n" - " \n" - " Note that creation of a nifti_image structure depends on good\n" - " header fields. So errors are terminal, meaning this check would\n" - " probably report at most one error, even if more exist. The\n" - " -check_hdr action is more complete.\n" - "\n"); - printf( - " More tests can be requested of the author.\n" - "\n"); - printf( - " e.g. nifti_tool -check_nim -infiles dset0.nii dset1.nii\n" - " e.g. nifti_tool -check_nim -infiles *.nii *.hdr\n" - "\n"); - printf( - " ------------------------------\n"); - - printf( - "\n" - " options for create action:\n" - "\n"); - printf( - " -make_im : create a new dataset from nothing\n" - "\n" - " With this the user can create a new dataset of a basic style,\n" - " which can then be modified with other options. This will create\n" - " zero-filled data of the appropriate size.\n" - " \n"); - printf( - " The default is a 1x1x1 image of shorts. These settings can be\n" - " modified with the -new_dim option, to set the 8 dimension values,\n" - " and the -new_datatype, to provide the integral type for the data.\n" - "\n"); - printf( - " See -new_dim, -new_datatype and -infiles for more information.\n" - " \n" - " Note that any -infiles dataset of the name MAKE_IM will also be\n" - " created on the fly.\n" - "\n"); - printf( - " -new_dim D0 .. D7 : specify the dim array for the a new dataset.\n" - "\n" - " e.g. -new_dim 4 64 64 27 120 0 0 0\n" - "\n" - " This dimension list will apply to any dataset created via\n" - " MAKE_IM or -make_im. All 8 values are required. Recall that\n" - " D0 is the number of dimensions, and D1 through D7 are the sizes.\n" - " \n"); - printf( - " -new_datatype TYPE : specify the dim array for the a new dataset.\n" - "\n" - " e.g. -new_datatype 16\n" - " default: -new_datatype 4 (short)\n" - "\n" - " This dimension list will apply to any dataset created via\n" - " MAKE_IM or -make_im. TYPE should be one of the NIFTI_TYPE_*\n" - " numbers, from nifti1.h.\n" - " \n"); - printf( - " ------------------------------\n"); - printf( - "\n" - " options for copy actions:\n" - "\n" - " -copy_brick_list : copy a list of volumes to a new dataset\n" - " -cbl : (a shorter, alternative form)\n" - " -copy_im : (a shorter, alternative form)\n" - "\n"); - printf( - " This action allows the user to copy a list of volumes (over time)\n" - " from one dataset to another. The listed volumes can be in any\n" - " order and contain repeats, but are of course restricted to\n" - " the set of values {1, 2, ..., nt-1}, from dimension 4.\n" - "\n"); - printf( - " This option is a flag. The index list is specified with the input\n" - " dataset, contained in square brackets. Note that square brackets\n" - " are special to most UNIX shells, so they should be contained\n" - " within single quotes. Syntax of an index list:\n" - "\n" - " notes:\n" - "\n"); - printf( - " - indices start at zero\n" - " - indices end at nt-1, which has the special symbol '$'\n" - " - single indices should be separated with commas, ','\n" - " e.g. -infiles dset0.nii'[0,3,8,5,2,2,2]'\n" - " - ranges may be specified using '..' or '-' \n"); - printf( - " e.g. -infiles dset0.nii'[2..95]'\n" - " e.g. -infiles dset0.nii'[2..$]'\n" - " - ranges may have step values, specified in ()\n" - " example: 2 through 95 with a step of 3, i.e. {2,5,8,11,...,95}\n" - " e.g. -infiles dset0.nii'[2..95(3)]'\n" - "\n"); - printf( - " This functionality applies only to 3 or 4-dimensional datasets.\n" - "\n" - " e.g. to copy a dataset:\n" - " nifti_tool -copy_im -prefix new.nii -infiles dset0.nii\n" - "\n"); - printf( - " e.g. to copy sub-bricks 0 and 7:\n" - " nifti_tool -cbl -prefix new_07.nii -infiles dset0.nii'[0,7]'\n" - "\n" - " e.g. to copy an entire dataset:\n" - " nifti_tool -cbl -prefix new_all.nii -infiles dset0.nii'[0..$]'\n" - "\n"); - printf( - " e.g. to copy every other time point, skipping the first three:\n" - " nifti_tool -cbl -prefix new_partial.nii \\\n" - " -infiles dset0.nii'[3..$(2)]'\n" - "\n" - "\n" - " -copy_collapsed_image ... : copy a list of volumes to a new dataset\n" - " -cci I J K T U V W : (a shorter, alternative form)\n" - "\n"); - printf( - " This action allows the user to copy a collapsed dataset, where\n" - " some dimensions are collapsed to a given index. For instance, the\n" - " X dimension could be collapsed to i=42, and the time dimensions\n" - " could be collapsed to t=17. To collapse a dimension, set Di to\n" - " the desired index, where i is in {0..ni-1}. Any dimension that\n" - " should not be collapsed must be listed as -1.\n" - "\n"); - printf( - " Any number (of valid) dimensions can be collapsed, even down to a\n" - " a single value, by specifying enough valid indices. The resulting\n" - " dataset will then have a reduced number of non-trivial dimensions.\n" - "\n" - " Assume dset0.nii has nim->dim[8] = { 4, 64, 64, 21, 80, 1, 1, 1 }.\n" - " Note that this is a 4-dimensional dataset.\n" - "\n"); - printf( - " e.g. copy the time series for voxel i,j,k = 5,4,17\n" - " nifti_tool -cci 5 4 17 -1 -1 -1 -1 -prefix new_5_4_17.nii\n" - "\n" - " e.g. read the single volume at time point 26\n" - " nifti_tool -cci -1 -1 -1 26 -1 -1 -1 -prefix new_t26.nii\n" - "\n"); - printf( - " Assume dset1.nii has nim->dim[8] = { 6, 64, 64, 21, 80, 4, 3, 1 }.\n" - " Note that this is a 6-dimensional dataset.\n" - "\n" - " e.g. copy all time series for voxel i,j,k = 5,0,17, with v=2\n" - " (and add the command to the history)\n" - " nifti_tool -cci 5 0 17 -1 -1 2 -1 -keep_hist \\\n" - " -prefix new_5_0_17_2.nii\n" - "\n"); - printf( - " e.g. copy all data where i=3, j=19 and v=2\n" - " (I do not claim to know a good reason to do this)\n" - " nifti_tool -cci 3 19 -1 -1 -1 2 -1 -prefix new_mess.nii\n" - "\n" - " See '-disp_ci' for more information (which displays/prints the\n" - " data, instead of copying it to a new dataset).\n" - "\n" - " ------------------------------\n"); - - printf( - "\n" - " options for display actions:\n" - "\n" - " -disp_hdr : display nifti_1_header fields for datasets\n" - "\n" - " This flag means the user wishes to see some of the nifti_1_header\n" - " fields in one or more nifti datasets. The user may want to specify\n" - " multiple '-field' options along with this. This option requires\n" - " one or more files input, via '-infiles'.\n" - "\n"); - printf( - " If no '-field' option is present, all fields will be displayed.\n" - "\n" - " e.g. to display the contents of all fields:\n" - " nifti_tool -disp_hdr -infiles dset0.nii\n" - " nifti_tool -disp_hdr -infiles dset0.nii dset1.nii dset2.nii\n" - "\n" - " e.g. to display the contents of select fields:\n" - " nifti_tool -disp_hdr -field dim -infiles dset0.nii\n" - " nifti_tool -disp_hdr -field dim -field descrip -infiles dset0.nii\n" - "\n"); - printf( - " -disp_nim : display nifti_image fields for datasets\n" - "\n" - " This flag option works the same way as the '-disp_hdr' option,\n" - " except that the fields in question are from the nifti_image\n" - " structure.\n" - "\n"); - printf( - " -disp_ana : display nifti_analyze75 fields for datasets\n" - "\n" - " This flag option works the same way as the '-disp_hdr' option,\n" - " except that the fields in question are from the nifti_analyze75\n" - " structure.\n" - "\n"); - printf( - " -disp_exts : display all AFNI-type extensions\n" - "\n" - " This flag option is used to display all nifti_1_extension data,\n" - " for only those extensions of type AFNI (code = 4). The only\n" - " other option used will be '-infiles'.\n" - "\n"); - printf( - " e.g. to display the extensions in datasets:\n" - " nifti_tool -disp_exts -infiles dset0.nii\n" - " nifti_tool -disp_exts -infiles dset0.nii dset1.nii dset2.nii\n" - "\n"); - printf( - " -disp_ts I J K : display ASCII time series at i,j,k = I,J,K\n" - "\n" - " This option is used to display the time series data for the voxel\n" - " at i,j,k indices I,J,K. The data is displayed in text, either all\n" - " on one line (the default), or as one number per line (via the\n" - " '-dci_lines' option).\n" - "\n"); - printf( - " Notes:\n" - "\n" - " o This function applies only to 4-dimensional datasets.\n" - " o The '-quiet' option can be used to suppress the text header,\n" - " leaving only the data.\n" - " o This option is short for using '-disp_ci' (display collapsed\n" - " image), restricted to 4-dimensional datasets. i.e. :\n" - " -disp_ci I J K -1 -1 -1 -1\n" - "\n"); - printf( - " e.g. to display the time series at voxel 23, 0, 172:\n" - " nifti_tool -disp_ts 23 0 172 -infiles dset1_time.nii\n" - " nifti_tool -disp_ts 23 0 172 -dci_lines -infiles dset1_time.nii\n" - " nifti_tool -disp_ts 23 0 172 -quiet -infiles dset1_time.nii\n" - "\n"); - printf( - " -disp_collapsed_image : display ASCII values for collapsed dataset\n" - " -disp_ci I J K T U V W : (a shorter, alternative form)\n" - "\n" - " This option is used to display all of the data from a collapsed\n" - " image, given the dimension list. The data is displayed in text,\n" - " either all on one line (the default), or as one number per line\n" - " (by using the '-dci_lines' flag).\n" - "\n"); - printf( - " The '-quiet' option can be used to suppress the text header.\n" - "\n" - " e.g. to display the time series at voxel 23, 0, 172:\n" - " nifti_tool -disp_ci 23 0 172 -1 0 0 0 -infiles dset1_time.nii\n" - "\n" - " e.g. to display z-slice 14, at time t=68:\n" - " nifti_tool -disp_ci -1 -1 14 68 0 0 0 -infiles dset1_time.nii\n" - "\n" - " See '-ccd' for more information, which copies such data to a new\n" - " dataset, instead of printing it to the terminal window.\n" - "\n" - " ------------------------------\n"); - printf( - "\n" - " options for modification actions:\n" - "\n" - " -mod_hdr : modify nifti_1_header fields for datasets\n" - "\n" - " This action is used to modify some of the nifti_1_header fields in\n" - " one or more datasets. The user must specify a list of fields to\n" - " modify via one or more '-mod_field' options, which include field\n" - " names, along with the new (set of) values.\n" - "\n"); - printf( - " The user can modify a dataset in place, or use '-prefix' to\n" - " produce a new dataset, to which the changes have been applied.\n" - " It is recommended to normally use the '-prefix' option, so as not\n" - " to ruin a dataset.\n" - "\n"); - printf( - " Note that some fields have a length greater than 1, meaning that\n" - " the field is an array of numbers, or a string of characters. In\n" - " order to modify an array of numbers, the user must provide the\n" - " correct number of values, and contain those values in quotes, so\n" - " that they are seen as a single option.\n" - "\n"); - printf( - " To modify a string field, put the string in quotes.\n" - "\n" - " The '-mod_field' option takes a field_name and a list of values.\n" - "\n" - " e.g. to modify the contents of various fields:\n" - "\n"); - printf( - " nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n" - " -mod_field qoffset_x -17.325\n" - " nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n" - " -mod_field dim '4 64 64 20 30 1 1 1 1'\n" - " nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n" - " -mod_field descrip 'beer, brats and cheese, mmmmm...'\n" - "\n"); - printf( - " e.g. to modify the contents of multiple fields:\n" - " nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n" - " -mod_field qoffset_x -17.325 -mod_field slice_start 1\n" - "\n" - " e.g. to modify the contents of multiple files (must overwrite):\n" - " nifti_tool -mod_hdr -overwrite -mod_field qoffset_x -17.325 \\\n" - " -infiles dset0.nii dset1.nii\n" - "\n"); - printf( - " -mod_nim : modify nifti_image fields for datasets\n" - "\n" - " This action option is used the same way that '-mod_hdr' is used,\n" - " except that the fields in question are from the nifti_image\n" - " structure.\n" - "\n"); - printf( - " -strip_extras : remove extensions and descriptions from datasets\n" - "\n" - " This action is used to attempt to 'clean' a dataset of general\n" - " text, in order to make it more anonymous. Extensions and the\n" - " nifti_image descrip field are cleared by this action.\n" - "\n"); - printf( - " e.g. to strip all *.nii datasets in this directory:\n" - " nifti_tool -strip -overwrite -infiles *.nii\n" - "\n"); - printf( - " -swap_as_nifti : swap the header according to nifti_1_header\n" - "\n" - " Perhaps a NIfTI header is mal-formed, and the user explicitly\n" - " wants to swap it before performing other operations. This action\n" - " will swap the field bytes under the assumption that the header is\n" - " in the NIfTI format.\n" - "\n"); - printf( - " ** The recommended course of action is to make a copy of the\n" - " dataset and overwrite the header via -overwrite. If the header\n" - " needs such an operation, it is likely that the data would not\n" - " otherwise be read in correctly.\n" - "\n"); - printf( - " -swap_as_analyze : swap the header according to nifti_analyze75\n" - "\n" - " Perhaps an ANALYZE header is mal-formed, and the user explicitly\n" - " wants to swap it before performing other operations. This action\n" - " will swap the field bytes under the assumption that the header is\n" - " in the ANALYZE 7.5 format.\n" - "\n"); - printf( - " ** The recommended course of action is to make a copy of the\n" - " dataset and overwrite the header via -overwrite. If the header\n" - " needs such an operation, it is likely that the data would not\n" - " otherwise be read in correctly.\n" - "\n"); - printf( - " -swap_as_old : swap the header using the old method\n" - "\n" - " As of library version 1.35 (3 Aug, 2008), nifticlib now swaps all\n" - " fields of a NIfTI dataset (including UNUSED ones), and it swaps\n" - " ANALYZE datasets according to the nifti_analyze75 structure.\n" - " This is a significant different in the case of ANALYZE datasets.\n" - "\n"); - printf( - " The -swap_as_old option was added to compare the results of the\n" - " swapping methods, or to undo one swapping method and replace it\n" - " with another (such as to undo the old method and apply the new).\n" - "\n"); - printf(" ------------------------------\n"); - printf( - "\n" - " options for adding/removing extensions:\n" - "\n" - " -add_afni_ext EXT : add an AFNI extension to the dataset\n" - "\n" - " This option is used to add AFNI-type extensions to one or more\n" - " datasets. This option may be used more than once to add more than\n" - " one extension.\n" - "\n" - " If EXT is of the form 'file:FILENAME', then the extension will\n" - " be read from the file, FILENAME.\n" - "\n"); - printf( - " The '-prefix' option is recommended, to create a new dataset.\n" - " In such a case, only a single file may be taken as input. Using\n" - " '-overwrite' allows the user to overwrite the current file, or\n" - " to add the extension(s) to multiple files, overwriting them.\n" - "\n"); - printf( - " e.g. to add a generic AFNI extension:\n" - " nifti_tool -add_afni_ext 'wow, my first extension' -prefix dnew \\\n" - " -infiles dset0.nii\n" - "\n" - " e.g. to add multiple AFNI extensions:\n" - " nifti_tool -add_afni_ext 'wow, my first extension :)' \\\n" - " -add_afni_ext 'look, my second...' \\\n" - " -prefix dnew -infiles dset0.nii\n" - "\n"); - printf( - " e.g. to add an extension, and overwrite the dataset:\n" - " nifti_tool -add_afni_ext 'some AFNI extension' -overwrite \\\n" - " -infiles dset0.nii dset1.nii \n" - "\n"); - printf( - " -add_comment_ext EXT : add a COMMENT extension to the dataset\n" - "\n" - " This option is used to add COMMENT-type extensions to one or more\n" - " datasets. This option may be used more than once to add more than\n" - " one extension. This option may also be used with '-add_afni_ext'.\n" - "\n" - " If EXT is of the form 'file:FILENAME', then the extension will\n" - " be read from the file, FILENAME.\n" - "\n"); - printf( - " The '-prefix' option is recommended, to create a new dataset.\n" - " In such a case, only a single file may be taken as input. Using\n" - " '-overwrite' allows the user to overwrite the current file, or\n" - " to add the extension(s) to multiple files, overwriting them.\n" - "\n"); - printf( - " e.g. to add a comment about the dataset:\n" - " nifti_tool -add_comment 'converted from MY_AFNI_DSET+orig' \\\n" - " -prefix dnew \\\n" - " -infiles dset0.nii\n" - "\n"); - printf( - " e.g. to add multiple extensions:\n" - " nifti_tool -add_comment 'add a comment extension' \\\n" - " -add_afni_ext 'and an AFNI XML style extension' \\\n" - " -add_comment 'dataset copied from dset0.nii' \\\n" - " -prefix dnew -infiles dset0.nii\n" - "\n"); - printf( - " -rm_ext INDEX : remove the extension given by INDEX\n" - "\n" - " This option is used to remove any single extension from the\n" - " dataset. Multiple extensions require multiple options.\n" - "\n" - " notes - extension indices begin with 0 (zero)\n" - " - to view the current extensions, see '-disp_exts'\n" - " - all extensions can be removed using ALL or -1 for INDEX\n" - "\n"); - printf( - " e.g. to remove the extension #0:\n" - " nifti_tool -rm_ext 0 -overwrite -infiles dset0.nii\n" - "\n" - " e.g. to remove ALL extensions:\n" - " nifti_tool -rm_ext ALL -prefix dset1 -infiles dset0.nii\n" - " nifti_tool -rm_ext -1 -prefix dset1 -infiles dset0.nii\n" - "\n"); - printf( - " e.g. to remove the extensions #2, #3 and #5:\n" - " nifti_tool -rm_ext 2 -rm_ext 3 -rm_ext 5 -overwrite \\\n" - " -infiles dset0.nii\n" - "\n" - " ------------------------------\n"); - - printf( - "\n" - " options for showing differences:\n" - "\n" - " -diff_hdr : display header field diffs between two datasets\n" - "\n" - " This option is used to find differences between two datasets.\n" - " If any fields are different, the contents of those fields is\n" - " displayed (unless the '-quiet' option is used).\n" - "\n"); - printf( - " A list of fields can be specified by using multiple '-field'\n" - " options. If no '-field' option is given, all fields will be\n" - " checked.\n" - "\n" - " Exactly two dataset names must be provided via '-infiles'.\n" - "\n" - " e.g. to display all nifti_1_header field differences:\n" - " nifti_tool -diff_hdr -infiles dset0.nii dset1.nii\n" - "\n"); - printf( - " e.g. to display selected nifti_1_header field differences:\n" - " nifti_tool -diff_hdr -field dim -field intent_code \\\n" - " -infiles dset0.nii dset1.nii \n" - "\n" - " -diff_nim : display nifti_image field diffs between datasets\n" - "\n" - " This option works the same as '-diff_hdr', except that the fields\n" - " in question are from the nifti_image structure.\n" - "\n" - " ------------------------------\n"); - - printf( - "\n" - " miscellaneous options:\n" - "\n" - " -debug LEVEL : set the debugging level\n" - "\n" - " Level 0 will attempt to operate with no screen output, but errors.\n" - " Level 1 is the default.\n" - " Levels 2 and 3 give progressively more information.\n" - "\n" - " e.g. -debug 2\n" - "\n"); - printf( - " -field FIELDNAME : provide a field to work with\n" - "\n" - " This option is used to provide a field to display, modify or\n" - " compare. This option can be used along with one of the action\n" - " options presented above.\n" - "\n" - " See '-disp_hdr', above, for complete examples.\n" - "\n" - " e.g. nifti_tool -field descrip\n" - " e.g. nifti_tool -field descrip -field dim\n" - "\n"); - printf( - " -infiles file0... : provide a list of files to work with\n" - "\n" - " This parameter is required for any of the actions, in order to\n" - " provide a list of files to process. If input filenames do not\n" - " have an extension, the directory we be searched for any\n" - " appropriate files (such as .nii or .hdr).\n" - "\n"); - printf( - " Note: if the filename has the form MAKE_IM, then a new dataset\n" - " will be created, without the need for file input.\n" - "\n"); - printf( - " See '-mod_hdr', above, for complete examples.\n" - "\n" - " e.g. nifti_tool -infiles file0.nii\n" - " e.g. nifti_tool -infiles file1.nii file2 file3.hdr\n" - "\n"); - printf( - " -mod_field NAME 'VALUE_LIST' : provide new values for a field\n" - "\n" - " This parameter is required for any the modification actions.\n" - " If the user wants to modify any fields of a dataset, this is\n" - " where the fields and values are specified.\n" - "\n"); - printf( - " NAME is a field name (in either the nifti_1_header structure or\n" - " the nifti_image structure). If the action option is '-mod_hdr',\n" - " then NAME must be the name of a nifti_1_header field. If the\n" - " action is '-mod_nim', NAME must be from a nifti_image structure.\n" - "\n"); - printf( - " VALUE_LIST must be one or more values, as many as are required\n" - " for the field, contained in quotes if more than one is provided.\n" - "\n" - " Use 'nifti_tool -help_hdr' to get a list of nifti_1_header fields\n" - " Use 'nifti_tool -help_nim' to get a list of nifti_image fields\n" - "\n" - " See '-mod_hdr', above, for complete examples.\n" - "\n"); - printf( - " e.g. modifying nifti_1_header fields:\n" - " -mod_field descrip 'toga, toga, toga'\n" - " -mod_field qoffset_x 19.4 -mod_field qoffset_z -11\n" - " -mod_field pixdim '1 0.9375 0.9375 1.2 1 1 1 1'\n" - "\n"); - printf( - " -keep_hist : add the command as COMMENT (to the 'history')\n" - "\n" - " When this option is used, the current command will be added\n" - " as a NIFTI_ECODE_COMMENT type extension. This provides the\n" - " ability to keep a history of commands affecting a dataset.\n" - "\n" - " e.g. -keep_hist\n" - "\n"); - printf( - " -overwrite : any modifications will be made to input files\n" - "\n" - " This option is used so that all field modifications, including\n" - " extension additions or deletions, will be made to the files that\n" - " are input.\n" - "\n"); - printf( - " In general, the user is recommended to use the '-prefix' option\n" - " to create new files. But if overwriting the contents of the\n" - " input files is preferred, this is how to do it.\n" - "\n" - " See '-mod_hdr' or '-add_afni_ext', above, for complete examples.\n" - "\n" - " e.g. -overwrite\n" - "\n"); - printf( - " -prefix : specify an output file to write change into\n" - "\n" - " This option is used to specify an output file to write, after\n" - " modifications have been made. If modifications are being made,\n" - " then either '-prefix' or '-overwrite' is required.\n" - "\n" - " If no extension is given, the output extension will be '.nii'.\n" - "\n"); - printf( - " e.g. -prefix new_dset\n" - " e.g. -prefix new_dset.nii\n" - " e.g. -prefix new_dset.hdr\n" - "\n" - " -quiet : report only errors or requested information\n" - "\n" - " This option is equivalent to '-debug 0'.\n" - "\n" - " ------------------------------\n"); - - printf( - "\n" - " basic help options:\n" - "\n" - " -help : show this help\n" - "\n" - " e.g. nifti_tool -help\n" - "\n" - " -help_hdr : show nifti_1_header field info\n" - "\n" - " e.g. nifti_tool -help_hdr\n" - "\n" - " -help_nim : show nifti_image field info\n" - "\n" - " e.g. nifti_tool -help_nim\n" - "\n" - " -help_ana : show nifti_analyze75 field info\n" - "\n" - " e.g. nifti_tool -help_ana\n" - ); - - printf( - "\n" - " -help_datatypes [TYPE] : display datatype table\n" - "\n" - " e.g. nifti_tool -help_datatypes\n" - " e.g. nifti_tool -help_datatypes N\n" - "\n" - " This displays the contents of the nifti_type_list table.\n" - " An additional 'D' or 'N' parameter will restrict the type\n" - " name to 'DT_' or 'NIFTI_TYPE_' names, 'T' will test.\n"); - - printf( - "\n" - " -ver : show the program version number\n" - "\n" - " e.g. nifti_tool -ver\n" - "\n" - " -hist : show the program modification history\n" - "\n" - " e.g. nifti_tool -hist\n" - "\n"); - printf( - " -nifti_ver : show the nifti library version number\n" - "\n" - " e.g. nifti_tool -nifti_ver\n" - "\n" - " -nifti_hist : show the nifti library modification history\n" - "\n" - " e.g. nifti_tool -nifti_hist\n" - "\n" - " -with_zlib : print whether library was compiled with zlib\n" - "\n" - " e.g. nifti_tool -with_zlib\n" - "\n" - " ------------------------------\n" - "\n" - " R. Reynolds\n" - " compiled: %s\n" - " %s\n\n", - __DATE__, g_version ); - - return 1; -} - - -/*---------------------------------------------------------------------- - * display the contents of the struct and all lists - *----------------------------------------------------------------------*/ -int disp_nt_opts( const char *mesg, nt_opts * opts) -{ - int c; - - if( mesg ) fputs(mesg, stderr); - if( ! opts ) - { - fprintf(stderr,"** disp_nt_opts: missing opts\n"); - return -1; - } - - fprintf(stderr,"nt_opts @ %p\n" - " check_hdr, check_nim = %d, %d\n" - " diff_hdr, diff_nim = %d, %d\n" - " disp_hdr, disp_nim = %d, %d\n" - " disp_ana, disp_exts = %d, %d\n" - " add_exts, rm_exts = %d, %d\n" - " mod_hdr, mod_nim = %d, %d\n" - " swap_hdr, swap_ana = %d, %d\n" - " swap_old = %d\n" - " cbl, cci = %d, %d\n" - " dts, dci_lines = %d, %d\n" - " make_im = %d\n", - (void *)opts, - opts->check_hdr, opts->check_nim, - opts->diff_hdr, opts->diff_nim, opts->disp_hdr, opts->disp_nim, - opts->disp_ana, opts->disp_exts, opts->add_exts, opts->rm_exts, - opts->mod_hdr, opts->mod_nim, - opts->swap_hdr, opts->swap_ana, opts->swap_old, - opts->cbl, opts->cci, - opts->dts, opts->dci_lines, opts->make_im ); - - fprintf(stderr," ci_dims[8] = "); - disp_raw_data(opts->ci_dims, DT_INT32, 8, ' ', 1); - fprintf(stderr," new_dim[8] = "); - disp_raw_data(opts->new_dim, DT_INT32, 8, ' ', 1); - - fprintf(stderr,"\n" - " new_datatype = %d\n" - " debug, keep_hist = %d, %d\n" - " overwrite = %d\n" - " prefix = '%s'\n", - opts->new_datatype, opts->debug, opts->keep_hist, opts->overwrite, - opts->prefix ? opts->prefix : "(NULL)" ); - - fprintf(stderr," elist (length %d) :\n", opts->elist.len); - for( c = 0; c < opts->elist.len; c++ ) - fprintf(stderr," %d : %s\n", c, opts->elist.list[c]); - - fprintf(stderr," etypes (length %d) : ", opts->etypes.len); - disp_raw_data(opts->etypes.list, DT_INT32, opts->etypes.len, ' ', 0); - fputc('\n',stderr); - - fprintf(stderr," flist (length %d) :\n", opts->flist.len); - for( c = 0; c < opts->flist.len; c++ ) - fprintf(stderr," %d : %s\n", c, opts->flist.list[c]); - - fprintf(stderr," vlist (length %d) :\n", opts->vlist.len); - for( c = 0; c < opts->vlist.len; c++ ) - fprintf(stderr," %d : %s\n", c, opts->vlist.list[c]); - - fprintf(stderr," infiles (length %d) :\n", opts->infiles.len); - for( c = 0; c < opts->infiles.len; c++ ) - fprintf(stderr," %d : %s\n", c, opts->infiles.list[c]); - - fprintf(stderr," command len : %d\n",(int)strlen(opts->command)); - - return 0; -} - - -/*---------------------------------------------------------------------- - * For each file, add all extensions with type NIFTI_ECODE_AFNI. - * Though it should not matter, copy the trailing null characters. - *----------------------------------------------------------------------*/ -int act_add_exts( nt_opts * opts ) -{ - nifti_image * nim; - const char * ext; - char * edata = NULL; - int fc, ec, elen; - - if( g_debug > 2 ){ - fprintf(stderr,"+d adding %d extensions to %d files...\n" - " extension types are: ", - opts->elist.len, opts->infiles.len); - disp_raw_data(opts->etypes.list, DT_INT32, opts->etypes.len, ' ', 1); - } - - if( opts->prefix && opts->infiles.len != 1 ){ - fprintf(stderr,"** error: we have a prefix but %d files\n", - opts->infiles.len); - return 1; - } - - if( opts->elist.len <= 0 ) return 0; - - for( fc = 0; fc < opts->infiles.len; fc++ ) - { - nim = nt_image_read( opts, opts->infiles.list[fc], 1 ); - if( !nim ) return 1; /* errors come from the library */ - - for( ec = 0; ec < opts->elist.len; ec++ ){ - ext = opts->elist.list[ec]; - elen = strlen(ext); - if( !strncmp(ext,"file:",5) ){ - edata = read_file_text(ext+5, &elen); - if( !edata || elen <= 0 ) { - fprintf(stderr,"** failed to read extension data from '%s'\n", - ext+5); - continue; - } - ext = edata; - } - - if( nifti_add_extension(nim, ext, elen, opts->etypes.list[ec]) ){ - nifti_image_free(nim); - return 1; - } - - /* if extension came from file, free the data */ - if( edata ){ free(edata); edata = NULL; } - } - - if( opts->keep_hist && nifti_add_extension(nim, opts->command, - strlen(opts->command), NIFTI_ECODE_COMMENT) ) - fprintf(stderr,"** failed to add command to image as extension\n"); - - if( opts->prefix && - nifti_set_filenames(nim, opts->prefix, !opts->overwrite, 1) ) - { - nifti_image_free(nim); - return 1; - } - - if( g_debug > 1 ) - fprintf(stderr,"+d writing %s with %d new extension(s)\n", - opts->infiles.list[fc], opts->elist.len); - - nifti_image_write(nim); - nifti_image_free(nim); - } - - if( g_debug > 0 ) - fprintf(stderr,"+d added %d extension(s) to %d files\n", - opts->elist.len, opts->infiles.len); - - return 0; -} - -/*---------------------------------------------------------------------- - * Return the allocated file contents. - *----------------------------------------------------------------------*/ -static char * read_file_text(const char * filename, int * length) -{ - FILE * fp; - char * text; - int len, bytes; - - if( !filename || !length ) { - fprintf(stderr,"** bad params to read_file_text\n"); - return NULL; - } - - len = nifti_get_filesize(filename); - if( len <= 0 ) { - fprintf(stderr,"** RFT: file '%s' appears empty\n", filename); - return NULL; - } - - fp = fopen(filename, "r"); - if( !fp ) { - fprintf(stderr,"** RFT: failed to open '%s' for reading\n", filename); - return NULL; - } - - /* allocate the bytes, and fill them with the file contents */ - - text = (char *)malloc(len * sizeof(char)); - if( !text ) { - fprintf(stderr,"** RFT: failed to allocate %d bytes\n", len); - fclose(fp); - return NULL; - } - - bytes = fread(text, sizeof(char), len, fp); - fclose(fp); /* in any case */ - - if( bytes != len ) { - fprintf(stderr,"** RFT: read only %d of %d bytes from %s\n", - bytes, len, filename); - free(text); - return NULL; - } - - /* success */ - - if( g_debug > 1 ) { - fprintf(stderr,"++ found extension of length %d in file %s\n", - len, filename); - if( g_debug > 2 ) - fprintf(stderr,"++ text is:\n%s\n", text); - } - - *length = len; - - return text; -} - -/*---------------------------------------------------------------------- - * For each file, strip the extra fields. - * - * Clear extensions and descrip field. No other generic strings will get - * passed to nifti_1_header struct. - * - * - this may make the datasets more anonymous - * - no history is appended here - *----------------------------------------------------------------------*/ -int act_strip( nt_opts * opts ) -{ - nifti_image * nim; - int fc; - - if( g_debug > 2 ) - fprintf(stderr,"+d stripping extras from %d files\n", opts->infiles.len); - - if( opts->prefix && opts->infiles.len != 1 ){ - fprintf(stderr,"** error: we have a prefix but %d files\n", - opts->infiles.len); - return 1; - } - - for( fc = 0; fc < opts->infiles.len; fc++ ) - { - nim = nt_image_read( opts, opts->infiles.list[fc], 1 ); - if( !nim ) return 1; /* errors come from the library */ - - /* now remove the extensions */ - nifti_free_extensions(nim); - memset(nim->descrip, 0, 80); - - if( opts->prefix && - nifti_set_filenames(nim, opts->prefix, !opts->overwrite, 1) ){ - nifti_image_free(nim); - return 1; - } - - if( g_debug > 1 ) - fprintf(stderr,"+d writing %s without extensions or 'descrip'\n", - nim->fname); - - nifti_image_write(nim); - - if( g_debug > 3 ) nifti_image_infodump(nim); - nifti_image_free(nim); - } - - if( g_debug > 0 ) - fprintf(stderr,"+d stripped extras from %d files\n", opts->infiles.len); - - return 0; -} - - -/*---------------------------------------------------------------------- - * For each file, remove the given extension for the given indices. - * - * Note that index = -1 means to remove them all. - *----------------------------------------------------------------------*/ -int act_rm_ext( nt_opts * opts ) -{ - nifti_image * nim; - int fc, ext_ind, num_ext; - - if( g_debug > 2 ) - fprintf(stderr,"+d removing %d extensions from %d files...\n", - opts->elist.len, opts->infiles.len); - - if( opts->elist.len <= 0 ) return 0; - - if( opts->prefix && opts->infiles.len != 1 ){ - fprintf(stderr,"** error: we have a prefix but %d files\n", - opts->infiles.len); - return 1; - } - else if( opts->overwrite && opts->infiles.len != 1 && - strcmp(opts->elist.list[0], "-1") ) { - fprintf(stderr,"** error: for multiple files, can only delete ALL\n"); - return 1; - } - - ext_ind = atoi(opts->elist.list[0]); - if( ext_ind < -1 ){ - fprintf(stderr,"** bad extension index to remove: %d\n", ext_ind); - return 1; - } - - if( g_debug > 1 ) fprintf(stderr,"+d removing extension index %d\n",ext_ind); - - for( fc = 0; fc < opts->infiles.len; fc++ ) - { - nim = nt_image_read( opts, opts->infiles.list[fc], 1 ); - if( !nim ) return 1; /* errors come from the library */ - - /* note the number of extensions for later */ - num_ext = nim->num_ext; - - /* now remove the extensions */ - if( remove_ext_list(nim, opts->elist.list, opts->elist.len) ) - return 1; - - if( opts->keep_hist && nifti_add_extension(nim, opts->command, - strlen(opts->command), NIFTI_ECODE_COMMENT) ) - fprintf(stderr,"** failed to add command to image as extension\n"); - - if( opts->prefix && - nifti_set_filenames(nim, opts->prefix, !opts->overwrite, 1) ){ - nifti_image_free(nim); - return 1; - } - - if( g_debug > 1 ) - fprintf(stderr,"+d writing %s with %d fewer extension(s)\n", - nim->fname, ext_ind == -1 ? num_ext : opts->elist.len); - - nifti_image_write(nim); - nifti_image_free(nim); - } - - if( g_debug > 0 ) - fprintf(stderr,"+d removed %s extension(s) from %d files\n", - ext_ind == -1 ? "ALL" : "1", opts->infiles.len); - - return 0; -} - - -/*---------------------------------------------------------------------- - * remove extensions by index - * - * return: 0 on success, -1 on failure - *----------------------------------------------------------------------*/ -int remove_ext_list( nifti_image * nim, const char ** elist, int len ) -{ - int * marks; - int c, ec, extval; - - if( len > nim->num_ext ){ - fprintf(stderr, "** cannot remove %d exts from image '%s' with only %d\n", - len, nim->fname, nim->num_ext); - return -1; - } - - if( len <= 0 ){ - fprintf(stderr,"** REL: (%d) no extensions to remove?\n",len); - return -1; - } - - extval = atoi(elist[0]); /* check the first value */ - - /* first special case, elist[0] == -1 */ - if( extval == -1 ) - { - if( g_debug > 1 ) - fprintf(stderr,"+d removing ALL (%d) extensions from '%s'\n", - nim->num_ext, nim->fname ); - nifti_free_extensions(nim); - return 0; - } - - if( g_debug > 2 ) - fprintf(stderr,"+d removing %d exts from '%s'\n", len, nim->fname ); - - if( ! (marks = (int *)calloc(nim->num_ext, sizeof(int))) ) { - fprintf(stderr,"** failed to alloc %d marks\n",nim->num_ext); - return -1; - } - - /* mark all extensions for removal */ - for( ec = 0; ec < len; ec++ ) - { - extval = atoi(elist[ec]); - - if( extval < 0 || extval >= nim->num_ext ){ - fprintf(stderr,"** ext #%d (= %d) is out of range [0,%d] for %s\n", - ec, extval, nim->num_ext-1, nim->fname); - free(marks); return -1; - } - - if( marks[extval] ){ - fprintf(stderr,"** ext #%d (= %d) is a duplicate", ec, extval); - free(marks); return -1; - } - - marks[extval]++; - } - - /* now remove them - count from top down to do lazy programming */ - for( ec = nim->num_ext-1; ec >= 0; ec-- ) - { - if( !marks[ec] ) continue; /* do not delete this one */ - - if( g_debug > 2 ) - disp_nifti1_extension("+d removing ext: ",nim->ext_list+ec,-1); - - /* delete this data, and shift the list down (yeah, inefficient) */ - if( nim->ext_list[ec].edata ) free( nim->ext_list[ec].edata ); - - /* move anything above down one */ - for( c = ec+1; c < nim->num_ext; c++ ) - nim->ext_list[c-1] = nim->ext_list[c]; - - nim->num_ext--; - } - - if( g_debug > 3 ) fprintf(stderr,"-d done removing extensions\n"); - - if( nim->num_ext == 0 ){ /* did we trash the only extension? */ - if( g_debug > 1 ) - fprintf(stderr,"-d removed ALL extensions from %s\n",nim->fname); - free(nim->ext_list); - nim->ext_list = NULL; - } - - free(marks); - return 0; -} - - -/*---------------------------------------------------------------------- - * check for diffs between all fields in opts->flist, or in the - * entire nifti_1_header - * - * if quiet mode (debug == 0) return on first diff - * - * return: 1 if diffs exist, 0 otherwise - *----------------------------------------------------------------------*/ -int act_diff_hdrs( nt_opts * opts ) -{ - nifti_1_header * nhdr0, * nhdr1; - int diffs = 0; - - if( opts->infiles.len != 2 ){ - fprintf(stderr,"** -diff_hdr requires 2 -infiles, have %d\n", - opts->infiles.len); - return 1; - } - - if( g_debug > 2 ) - fprintf(stderr,"-d nifti_1_header diff between %s and %s...\n", - opts->infiles.list[0], opts->infiles.list[1]); - - /* get the nifiti headers (but do not validate them) */ - - nhdr0 = nt_read_header(opts, opts->infiles.list[0], NULL, 0); - if( ! nhdr0 ) return 1; /* errors have been printed */ - - nhdr1 = nt_read_header(opts, opts->infiles.list[1], NULL, 0); - if( ! nhdr1 ){ free(nhdr0); return 1; } - - if( g_debug > 1 ) - fprintf(stderr,"\n-d nifti_1_header diffs between '%s' and '%s'...\n", - opts->infiles.list[0], opts->infiles.list[1]); - - if( opts->flist.len <= 0 ) - diffs = diff_hdrs(nhdr0, nhdr1, g_debug > 0); - else - diffs = diff_hdrs_list(nhdr0, nhdr1, &opts->flist, g_debug > 0); - - if( diffs == 0 && g_debug > 1 ) - fprintf(stderr,"+d no differences found\n"); - else if ( g_debug > 2 ) - fprintf(stderr,"+d %d differences found\n", diffs); - - free(nhdr0); - free(nhdr1); - - return (diffs > 0); -} - - -/*---------------------------------------------------------------------- - * check for diffs between all fields in opts->flist, or in the - * entire nifti_image - * - * if quiet mode (debug == 0) return on first diff - * - * return: 1 if diffs exist, 0 otherwise - *----------------------------------------------------------------------*/ -int act_diff_nims( nt_opts * opts ) -{ - nifti_image * nim0, * nim1; - int diffs = 0; - - if( opts->infiles.len != 2 ){ - fprintf(stderr,"** -diff_nim requires 2 -infiles, have %d\n", - opts->infiles.len); - return 1; - } - - if( g_debug > 2 ) - fprintf(stderr,"-d nifti_image diff between %s and %s...\n", - opts->infiles.list[0], opts->infiles.list[1]); - - /* get the nifiti images */ - - nim0 = nt_image_read(opts, opts->infiles.list[0], 0); - if( ! nim0 ) return 1; /* errors have been printed */ - - nim1 = nt_image_read(opts, opts->infiles.list[1], 0); - if( ! nim1 ){ free(nim0); return 1; } - - if( g_debug > 1 ) - fprintf(stderr,"\n-d nifti_image diffs between '%s' and '%s'...\n", - opts->infiles.list[0], opts->infiles.list[1]); - - if( opts->flist.len <= 0 ) - diffs = diff_nims(nim0, nim1, g_debug > 0); - else - diffs = diff_nims_list(nim0, nim1, &opts->flist, g_debug > 0); - - if( diffs == 0 && g_debug > 1 ) - fprintf(stderr,"+d no differences found\n"); - else if ( g_debug > 2 ) - fprintf(stderr,"+d %d differences found\n", diffs); - - nifti_image_free(nim0); - nifti_image_free(nim1); - - return (diffs > 0); -} - - -/*---------------------------------------------------------------------- - * for each file, read nifti1_header - * if checking header, check it - * if checking nifti_image, convert and check it - *----------------------------------------------------------------------*/ -int act_check_hdrs( nt_opts * opts ) -{ - nifti_1_header * nhdr; - nifti_image * nim; - int filenum, rv; - - if( g_debug > 2 ) - fprintf(stderr,"-d checking hdrs/nims for %d nifti datasets...\n", - opts->infiles.len); - - for( filenum = 0; filenum < opts->infiles.len; filenum++ ) - { - /* do not validate the header structure */ - nhdr = nt_read_header(opts, opts->infiles.list[filenum], NULL, 0); - if( !nhdr ) continue; /* errors are printed from library */ - - if( opts->check_hdr ) - { - if( g_debug > 1 ) - fprintf(stdout,"\nchecking nifti_1_header for file '%s'\n", - opts->infiles.list[filenum]); - - rv = nifti_hdr_looks_good(nhdr); - - if( rv && g_debug > 0 ) /* if quiet, no GOOD response */ - printf("header IS GOOD for file %s\n",opts->infiles.list[filenum]); - else if( ! rv ) - printf("header FAILURE for file %s\n",opts->infiles.list[filenum]); - } - - if( opts->check_nim ) - { - nim = nifti_convert_nhdr2nim(*nhdr, opts->infiles.list[filenum]); - if( !nim ) continue; /* errors are printed from library */ - - if( g_debug > 1 ) - fprintf(stdout,"\nchecking nifti_image for file '%s'\n", - opts->infiles.list[filenum]); - - rv = nifti_nim_is_valid(nim, 1); /* complain about errors */ - - if( rv && g_debug > 0 ) /* if quiet, no GOOD response */ - printf("nifti_image IS GOOD for file %s\n", - opts->infiles.list[filenum]); - else if( ! rv ) - printf("nifti_image FAILURE for file %s\n", - opts->infiles.list[filenum]); - - nifti_image_free(nim); - } - - free(nhdr); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * display all extensions for each dataset - *----------------------------------------------------------------------*/ -int act_disp_exts( nt_opts * opts ) -{ - nifti_image * nim; - char mesg[32]; - int ec, fc; - - if( g_debug > 2 ) - fprintf(stderr,"-d displaying all extensions for %d files...\n", - opts->infiles.len); - - for( fc = 0; fc < opts->infiles.len; fc++ ) - { - nim = nt_image_read(opts, opts->infiles.list[fc], 0); - if( !nim ) return 1; /* errors are printed from library */ - - if( g_debug > 0 ) - fprintf(stdout,"header file '%s', num_ext = %d\n", - nim->fname, nim->num_ext); - for( ec = 0; ec < nim->num_ext; ec++ ) - { - sprintf(mesg, " ext #%d : ", ec); - disp_nifti1_extension(mesg, nim->ext_list + ec, -1); - } - - nifti_image_free(nim); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * for each file, read nifti1_header and display all fields - *----------------------------------------------------------------------*/ -int act_disp_hdrs( nt_opts * opts ) -{ - nifti_1_header * nhdr; - field_s * fnhdr; - const char ** sptr; - int nfields, filenum, fc; - - /* set the number of fields to display */ - nfields = opts->flist.len > 0 ? opts->flist.len : NT_HDR_NUM_FIELDS; - - if( g_debug > 2 ) - fprintf(stderr,"-d displaying %d fields for %d nifti datasets...\n", - nfields, opts->infiles.len); - - for( filenum = 0; filenum < opts->infiles.len; filenum++ ) - { - /* do not validate the header structure */ - nhdr = nt_read_header(opts, opts->infiles.list[filenum], NULL, 0); - if( !nhdr ) return 1; /* errors are printed from library */ - - if( g_debug > 0 ) - fprintf(stdout,"\nheader file '%s', num_fields = %d\n", - opts->infiles.list[filenum], nfields); - if( g_debug > 1 ) - fprintf(stderr,"-d header is: %s\n", - nifti_hdr_looks_good(nhdr) ? "valid" : "invalid"); - - if( opts->flist.len <= 0 ) /* then display all fields */ - disp_field("\nall fields:\n", g_hdr_fields, nhdr, nfields, g_debug>0); - else /* print only the requested fields... */ - { - /* must locate each field before printing it */ - sptr = opts->flist.list; - for( fc = 0; fc < opts->flist.len; fc++ ) - { - fnhdr = get_hdr_field(*sptr, filenum == 0); - if( fnhdr ) disp_field(NULL, fnhdr, nhdr, 1, g_debug>0 && fc == 0); - sptr++; - } - } - - free(nhdr); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * for each file, read nifti_analyze75 and display all fields - *----------------------------------------------------------------------*/ -int act_disp_anas( nt_opts * opts ) -{ - nifti_analyze75 * nhdr; - field_s * fnhdr; - const char ** sptr; - int nfields, filenum, fc; - - /* set the number of fields to display */ - nfields = opts->flist.len > 0 ? opts->flist.len : NT_ANA_NUM_FIELDS; - - if( g_debug > 2 ) - fprintf(stderr,"-d displaying %d fields for %d ANALYZE datasets...\n", - nfields, opts->infiles.len); - - for( filenum = 0; filenum < opts->infiles.len; filenum++ ) - { - /* do not validate the header structure */ - nhdr = (nifti_analyze75 *)nt_read_header(opts, - opts->infiles.list[filenum], NULL, 0); - if( !nhdr ) return 1; /* errors are printed from library */ - - if( g_debug > 0 ) - fprintf(stdout,"\nanalyze header file '%s', num_fields = %d\n", - opts->infiles.list[filenum], nfields); - if( g_debug > 1 ) - fprintf(stderr,"-d analyze header is: %s\n", - nifti_hdr_looks_good((nifti_1_header *)nhdr) ? - "valid" : "invalid"); - - if( opts->flist.len <= 0 ) /* then display all fields */ - disp_field("\nall fields:\n", g_ana_fields, nhdr, nfields, g_debug>0); - else /* print only the requested fields... */ - { - /* must locate each field before printing it */ - sptr = opts->flist.list; - for( fc = 0; fc < opts->flist.len; fc++ ) - { - fnhdr = get_hdr_field(*sptr, filenum == 0); - if( fnhdr ) disp_field(NULL, fnhdr, nhdr, 1, g_debug>0 && fc == 0); - sptr++; - } - } - - free(nhdr); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * for each file, get nifti_image and display all fields - *----------------------------------------------------------------------*/ -int act_disp_nims( nt_opts * opts ) -{ - nifti_image * nim; - field_s * fnim; - const char ** sptr; - int nfields, filenum, fc; - - /* set the number of fields to display */ - nfields = opts->flist.len > 0 ? opts->flist.len : NT_NIM_NUM_FIELDS; - - if( g_debug > 2 ) - fprintf(stderr,"-d displaying %d fields for %d nifti datasets...\n", - nfields, opts->infiles.len); - - for( filenum = 0; filenum < opts->infiles.len; filenum++ ) - { - nim = nt_image_read(opts, opts->infiles.list[filenum], 0); - if( !nim ) return 1; /* errors are printed from library */ - - if( g_debug > 0 ) - fprintf(stdout,"\nheader file '%s', num_fields = %d, fields:\n\n", - nim->fname, nfields); - - if( opts->flist.len <= 0 ) /* then display all fields */ - disp_field("all fields:\n", g_nim_fields, nim, nfields, g_debug > 0); - else /* print only the requested fields... */ - { - /* must locate each field before printing it */ - sptr = opts->flist.list; - for( fc = 0; fc < opts->flist.len; fc++ ) - { - fnim = get_nim_field(*sptr, filenum == 0); - if( fnim ) disp_field(NULL, fnim, nim, 1, g_debug > 0 && fc == 0); - sptr++; - } - } - - nifti_image_free(nim); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * - read header - * - modify header - * - if -prefix duplicate file - * - else if swapped, swap back - * - overwrite file header (allows (danger-of) no evaluation of data) - *----------------------------------------------------------------------*/ -int act_mod_hdrs( nt_opts * opts ) -{ - nifti_1_header * nhdr; - nifti_image * nim; /* for reading/writing entire datasets */ - int filec, swap; - const char * fname; - char * dupname; - char func[] = { "act_mod_hdrs" }; - - if( g_debug > 2 ) - fprintf(stderr,"-d modifying %d fields for %d nifti headers...\n", - opts->flist.len, opts->infiles.len); - if( opts->flist.len <= 0 || opts->infiles.len <= 0 ) return 0; - - for( filec = 0; filec < opts->infiles.len; filec++ ) - { - fname = opts->infiles.list[filec]; /* for convenience and mod file */ - - if( nifti_is_gzfile(fname) ){ - fprintf(stderr,"** sorry, cannot modify a gzipped file: %s\n", fname); - continue; - } - - /* do not validate the header structure */ - nhdr = nt_read_header(opts, fname, &swap, 0); - if( !nhdr ) return 1; - - if( g_debug > 1 ) - { - fprintf(stderr,"-d modifying %d fields of '%s' header\n", - opts->flist.len, fname); - fprintf(stderr,"-d header is: %s\n", - nifti_hdr_looks_good(nhdr) ? "valid" : "invalid"); - } - - /* okay, let's actually trash the data fields */ - if( modify_all_fields(nhdr, opts, g_hdr_fields, NT_HDR_NUM_FIELDS) ) - { - free(nhdr); - return 1; - } - - dupname = NULL; /* unless we duplicate file */ - - /* possibly duplicate the current dataset before writing new header */ - if( opts->prefix ) - { - nim = nt_image_read(opts, fname, 1); /* get data */ - if( !nim ) { - fprintf(stderr,"** failed to dup file '%s' before modifying\n", - fname); - return 1; - } - if( opts->keep_hist && nifti_add_extension(nim, opts->command, - strlen(opts->command), NIFTI_ECODE_COMMENT) ) - fprintf(stderr,"** failed to add command to image as exten\n"); - if( nifti_set_filenames(nim, opts->prefix, 1, 1) ) - { - NTL_FERR(func,"failed to set prefix for new file: ",opts->prefix); - nifti_image_free(nim); - return 1; - } - dupname = nifti_strdup(nim->fname); /* so we know to free it */ - fname = dupname; - nifti_image_write(nim); /* create the duplicate file */ - /* if we added a history note, get the new offset into the header */ - /* mod: if the new offset is valid, use it 31 Jan 2006 [rickr] */ - if( nim->iname_offset >= 348 ) nhdr->vox_offset = nim->iname_offset; - nifti_image_free(nim); - } - else if ( swap ) - swap_nifti_header(nhdr, NIFTI_VERSION(*nhdr)); - - /* if all is well, overwrite header in fname dataset */ - (void)write_hdr_to_file(nhdr, fname); /* errors printed in function */ - - if( dupname ) free(dupname); - free(nhdr); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * - read header - * - swap header - * - if -prefix duplicate file - * - overwrite file header (allows (danger-of) no evaluation of data) - *----------------------------------------------------------------------*/ -int act_swap_hdrs( nt_opts * opts ) -{ - nifti_1_header * nhdr; - nifti_image * nim; /* for reading/writing entire datasets */ - int filec, swap; - const char * fname; - char * dupname; - char func[] = { "act_mod_hdrs" }; - - /* count requested operations: "there can be only one", and not Sean */ - swap = opts->swap_hdr + opts->swap_ana + opts->swap_old; - if( swap > 1 ) { - fprintf(stderr,"** can perform only one swap method\n"); - return 1; - } else if( ! swap ) - return 0; /* probably shouldn't be here */ - - if( g_debug > 2 ) - fprintf(stderr,"-d swapping headers of %d files...\n",opts->infiles.len); - - for( filec = 0; filec < opts->infiles.len; filec++ ) - { - fname = opts->infiles.list[filec]; /* for convenience and mod file */ - - if( nifti_is_gzfile(fname) ){ - fprintf(stderr,"** sorry, cannot swap a gzipped header: %s\n", fname); - continue; - } - - /* do not validate the header structure */ - nhdr = nt_read_header(opts, fname, &swap, 0); - if( !nhdr ) return 1; - - if( g_debug > 1 ) { - const char * str = "NIfTI"; - if( opts->swap_ana || (opts->swap_old && !NIFTI_VERSION(*nhdr)) ) - str = "ANALYZE"; - fprintf(stderr,"-d %sswapping %s header of file %s\n", - opts->swap_old ? "OLD " : "", str, fname); - } - - if( ! swap ) { /* if not yet swapped, do as the user requested */ - - if( opts->swap_old ) old_swap_nifti_header(nhdr, NIFTI_VERSION(*nhdr)); - else swap_nifti_header(nhdr, opts->swap_ana ? 0 : 1); - - } else { /* swapped already: if not correct, need to undo */ - - /* if swapped the wrong way, undo and swap as the user requested */ - if ( opts->swap_ana && NIFTI_VERSION(*nhdr) ) { - /* want swapped as ANALYZE, but was swapped as NIFTI */ - swap_nifti_header(nhdr, 1); /* undo NIFTI */ - swap_nifti_header(nhdr, 0); /* swap ANALYZE */ - } else if( opts->swap_hdr && !NIFTI_VERSION(*nhdr) ) { - /* want swapped as NIFTI, but was swapped as ANALYZE */ - swap_nifti_header(nhdr, 0); /* undo ANALYZE */ - swap_nifti_header(nhdr, 1); /* swap NIFTI */ - } else if ( opts->swap_old ) { - /* undo whichever was done and apply the old way */ - swap_nifti_header(nhdr, NIFTI_VERSION(*nhdr)); - old_swap_nifti_header(nhdr, NIFTI_VERSION(*nhdr)); - } - - /* else it was swapped the right way to begin with */ - - } - - dupname = NULL; /* unless we duplicate file */ - - /* possibly duplicate the current dataset before writing new header */ - if( opts->prefix ) - { - nim = nt_image_read(opts, fname, 1); /* get data */ - if( !nim ) { - fprintf(stderr,"** failed to dup file '%s' before modifying\n", - fname); - return 1; - } - if( opts->keep_hist && nifti_add_extension(nim, opts->command, - strlen(opts->command), NIFTI_ECODE_COMMENT) ) - fprintf(stderr,"** failed to add command to image as exten\n"); - if( nifti_set_filenames(nim, opts->prefix, 1, 1) ) - { - NTL_FERR(func,"failed to set prefix for new file: ",opts->prefix); - nifti_image_free(nim); - return 1; - } - dupname = nifti_strdup(nim->fname); /* so we know to free it */ - fname = dupname; - nifti_image_write(nim); /* create the duplicate file */ - /* if we added a history note, get the new offset into the header */ - /* mod: if the new offset is valid, use it 31 Jan 2006 [rickr] */ - if( nim->iname_offset >= 348 ) nhdr->vox_offset = nim->iname_offset; - nifti_image_free(nim); - } - - /* if all is well, overwrite header in fname dataset */ - (void)write_hdr_to_file(nhdr, fname); /* errors printed in function */ - - if( dupname ) free(dupname); - free(nhdr); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * - read image w/data, modify and write - *----------------------------------------------------------------------*/ -int act_mod_nims( nt_opts * opts ) -{ - nifti_image * nim; /* for reading/writing entire datasets */ - int filec; - char func[] = { "act_mod_nims" }; - - if( g_debug > 2 ) - fprintf(stderr,"-d modifying %d fields for %d nifti images...\n", - opts->flist.len, opts->infiles.len); - if( opts->flist.len <= 0 || opts->infiles.len <= 0 ) return 0; - - for( filec = 0; filec < opts->infiles.len; filec++ ) - { - nim = nt_image_read(opts, opts->infiles.list[filec], 1); /* with data */ - - if( g_debug > 1 ) - fprintf(stderr,"-d modifying %d fields from '%s' image\n", - opts->flist.len, opts->infiles.list[filec]); - - /* okay, let's actually trash the data fields */ - if( modify_all_fields(nim, opts, g_nim_fields, NT_NIM_NUM_FIELDS) ) - { - nifti_image_free(nim); - return 1; - } - - /* add command as COMMENT extension */ - if( opts->keep_hist && nifti_add_extension(nim, opts->command, - strlen(opts->command), NIFTI_ECODE_COMMENT) ) - fprintf(stderr,"** failed to add command to image as extension\n"); - - /* possibly duplicate the current dataset before writing new header */ - if( opts->prefix ) - if( nifti_set_filenames(nim, opts->prefix, 1, 1) ) - { - NTL_FERR(func,"failed to set prefix for new file: ",opts->prefix); - nifti_image_free(nim); - return 1; - } - - nifti_image_write(nim); /* and write it out, piece of cake :) */ - nifti_image_free(nim); - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * overwrite nifti_1_header in the given file - *----------------------------------------------------------------------*/ -int write_hdr_to_file( nifti_1_header * nhdr, const char * fname ) -{ - znzFile fp; - size_t bytes; - char func[] = { "write_hdr_to_file" }; - int rv = 0; - - fp = znzopen(fname,"r+b",nifti_is_gzfile(fname)); - if( znz_isnull(fp) ){ - NTL_FERR(func, "failed to re-open mod file", fname); - return 1; - } - - bytes = znzwrite(nhdr, 1, sizeof(nifti_1_header), fp); - if( bytes != sizeof(nifti_1_header)){ - NTL_FERR(func, "failed to write header to file",fname); - fprintf(stderr," - wrote %d of %d bytes\n", - (int)bytes,(int)sizeof(nifti_1_header)); - rv = 1; - } - - if( g_debug > 3 ) - disp_nifti_1_header("+d writing new header to file : ", nhdr); - - znzclose(fp); - - return rv; -} - - -/*---------------------------------------------------------------------- - * modify all fields in the list - *----------------------------------------------------------------------*/ -int modify_all_fields( void * basep, nt_opts * opts, field_s * fields, int flen) -{ - field_s * fp; - int fc, lc; /* field and list counters */ - - if( opts->flist.len <= 0 ) return 0; - if( opts->flist.len != opts->vlist.len ){ - fprintf(stderr,"** have %d fields but %d new values\n", - opts->flist.len, opts->vlist.len); - return 1; - } - - for( lc = 0; lc < opts->flist.len; lc++ ) - { - /* is it in the list? */ - fp = fields; - for( fc = 0; fc < flen; fc++, fp++ ) - if( strcmp(opts->flist.list[lc], fp->name) == 0 ) break; - - if( fc == flen ) /* do no modifications on failure */ - { - fprintf(stderr,"** field '%s' not found in structure\n", - opts->flist.list[lc]); - return 1; - } - - if( modify_field( basep, fp, opts->vlist.list[lc]) ) - return 1; - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * modify a single field with the given value field - * - * pointer fields are not allowed here - *----------------------------------------------------------------------*/ -int modify_field(void * basep, field_s * field, const char * data) -{ - float fval; - const char * posn = data; - int val, max, fc, nchars; - - if( g_debug > 1 ) - fprintf(stderr,"+d modifying field '%s' with '%s'\n", field->name, data); - - if( !data || strlen(data) == 0 ) - { - fprintf(stderr,"** no data for '%s' field modification\n",field->name); - return 1; - } - - switch( field->type ) - { - case DT_UNKNOWN: - case NT_DT_POINTER: - case NT_DT_CHAR_PTR: - case NT_DT_EXT_PTR: - default: - fprintf(stderr,"** refusing to modify a pointer field, '%s'\n", - field->name); - return 1; - - case DT_INT8: - { - max = 127; - for( fc = 0; fc < field->len; fc++ ) - { - if( sscanf(posn, " %d%n", &val, &nchars) != 1 ) - { - fprintf(stderr,"** found %d of %d modify values\n", - fc,field->len); - return 1; - } - if( val > max || val < -(max+1) ) - { - fprintf(stderr, - "** mod val #%d (= %d) outside byte range [-%d,%d]\n", - fc, val, max+1, max); - return 1; - } - /* otherwise, we're good */ - (((char *)basep + field->offset))[fc] = (char)val; - if( g_debug > 1 ) - fprintf(stderr,"+d setting posn %d of '%s' to %d\n", - fc, field->name, val); - posn += nchars; - } - } - break; - - case DT_INT16: - { - max = 32767; - for( fc = 0; fc < field->len; fc++ ) - { - if( sscanf(posn, " %d%n", &val, &nchars) != 1 ) - { - fprintf(stderr,"** found %d of %d modify values\n", - fc,field->len); - return 1; - } - if( val > max || val < -(max+1) ) - { - fprintf(stderr, - "** mod val #%d (= %d) outside byte range [-%d,%d]\n", - fc, val, max+1, max); - return 1; - } - /* otherwise, we're good */ - ((short *)((char *)basep + field->offset))[fc] = (short)val; - if( g_debug > 1 ) - fprintf(stderr,"+d setting posn %d of '%s' to %d\n", - fc, field->name, val); - posn += nchars; - } - } - break; - - case DT_INT32: - { - for( fc = 0; fc < field->len; fc++ ) - { - if( sscanf(posn, " %d%n", &val, &nchars) != 1 ) - { - fprintf(stderr,"** found %d of %d modify values\n", - fc,field->len); - return 1; - } - ((int *)((char *)basep + field->offset))[fc] = val; - if( g_debug > 1 ) - fprintf(stderr,"+d setting posn %d of '%s' to %d\n", - fc, field->name, val); - posn += nchars; - } - } - break; - - case DT_FLOAT32: - { - for( fc = 0; fc < field->len; fc++ ) - { - if( sscanf(posn, " %f%n", &fval, &nchars) != 1 ) - { - fprintf(stderr,"** found %d of %d modify values\n", - fc,field->len); - return 1; - } - /* otherwise, we're good */ - ((float *)((char *)basep + field->offset))[fc] = fval; - if( g_debug > 1 ) - fprintf(stderr,"+d setting posn %d of '%s' to %f\n", - fc, field->name, fval); - posn += nchars; - } - } - break; - - case NT_DT_STRING: - { - char * dest = (char *)basep + field->offset; - nchars = strlen(data); - strncpy(dest, data, field->len); - if( nchars < field->len ) /* clear the rest */ - memset(dest+nchars, '\0', field->len-nchars); - } - break; - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * fill the nifti_1_header field list - *----------------------------------------------------------------------*/ -int fill_hdr_field_array( field_s * nh_fields ) -{ - nifti_1_header nhdr; - field_s * nhf = nh_fields; - int rv, errs; - - memset(nhf, 0, NT_HDR_NUM_FIELDS*sizeof(field_s)); - - /* this macro takes (TYPE, NAME, NUM) and does: - fill_field(nhdr, TYPE, NT_OFF(nhdr,NAME), NUM, "NAME"); - nhf++; - */ - errs = 0; - NT_SFILL(nhdr, nhf, DT_INT32, sizeof_hdr, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, NT_DT_STRING, data_type, 10, rv); errs += rv; - NT_SFILL(nhdr, nhf, NT_DT_STRING, db_name, 18, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT32, extents, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT16, session_error, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, NT_DT_STRING, regular, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT8, dim_info, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_INT16, dim, 8, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, intent_p1, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, intent_p2, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, intent_p3, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT16, intent_code, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_INT16, datatype, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT16, bitpix, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT16, slice_start, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, pixdim, 8, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, vox_offset, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, scl_slope, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, scl_inter, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT16, slice_end, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_INT8, slice_code, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT8, xyzt_units, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, cal_max, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, cal_min, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, slice_duration, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, toffset, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT32, glmax, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT32, glmin, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, NT_DT_STRING, descrip, 80, rv); errs += rv; - NT_SFILL(nhdr, nhf, NT_DT_STRING, aux_file, 24, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT16, qform_code, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_INT16, sform_code, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_FLOAT32, quatern_b, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, quatern_c, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, quatern_d, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, qoffset_x, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, qoffset_y, 1, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, qoffset_z, 1, rv); errs += rv; - - NT_SFILL(nhdr, nhf, DT_FLOAT32, srow_x, 4, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, srow_y, 4, rv); errs += rv; - NT_SFILL(nhdr, nhf, DT_FLOAT32, srow_z, 4, rv); errs += rv; - NT_SFILL(nhdr, nhf, NT_DT_STRING, intent_name, 16, rv); errs += rv; - NT_SFILL(nhdr, nhf, NT_DT_STRING, magic, 4, rv); errs += rv; - - if( errs > 0 ){ - fprintf(stderr, "** %d fill_fields errors!\n", errs); - return 1; - } - - /* failure here is a serious problem */ - if( check_total_size("nifti_1_header test: ", nh_fields, - NT_HDR_NUM_FIELDS, sizeof(nhdr)) ) - return 1; - - if( g_debug > 3 ) - disp_field_s_list("nh_fields: ", nh_fields, NT_HDR_NUM_FIELDS); - - return 0; -} - - -/*---------------------------------------------------------------------- - * fill the nifti_image field list - *----------------------------------------------------------------------*/ -int fill_nim_field_array( field_s * nim_fields ) -{ - nifti_image nim; - field_s * nif = nim_fields; - int rv, errs; - - memset(nif, 0, NT_NIM_NUM_FIELDS*sizeof(field_s)); - - errs = 0; - - NT_SFILL(nim, nif, DT_INT32, ndim, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nx, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, ny, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nz, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nt, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nu, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nv, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nw, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, dim, 8, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nvox, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nbyper, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, datatype, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, dx, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, dy, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, dz, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, dt, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, du, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, dv, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, dw, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, pixdim, 8, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, scl_slope, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, scl_inter, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, cal_min, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, cal_max, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, qform_code, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, sform_code, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, freq_dim, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, phase_dim, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, slice_dim, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, slice_code, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, slice_start, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, slice_end, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, slice_duration, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, quatern_b, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, quatern_c, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, quatern_d, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, qoffset_x, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, qoffset_y, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, qoffset_z, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, qfac, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, qto_xyz, 16, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, qto_ijk, 16, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, sto_xyz, 16, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, sto_ijk, 16, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, toffset, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, xyz_units, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, time_units, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, nifti_type, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, intent_code, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, intent_p1, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, intent_p2, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_FLOAT32, intent_p3, 1, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_STRING, intent_name, 16, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_STRING, descrip, 80, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_STRING, aux_file, 24, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_CHAR_PTR, fname, 1, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_CHAR_PTR, iname, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, iname_offset, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, swapsize, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, byteorder, 1, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_POINTER, data, 1, rv); errs += rv; - NT_SFILL(nim, nif, DT_INT32, num_ext, 1, rv); errs += rv; - NT_SFILL(nim, nif, NT_DT_EXT_PTR, ext_list, 1, rv); errs += rv; - - if( errs > 0 ){ - fprintf(stderr, "** %d fill_fields errors " - "(note that pointers get aligned)\n", errs); - return 1; - } - - if( g_debug > 3 ) /* failure here is not an error condition */ - check_total_size("nifti_image test: ", nim_fields, - NT_NIM_NUM_FIELDS, sizeof(nim)); - - if( g_debug > 3 ) - disp_field_s_list("nim_fields: ", nim_fields, NT_NIM_NUM_FIELDS); - - return 0; -} - - -/*---------------------------------------------------------------------- - * fill the nifti_analyze75 field list - *----------------------------------------------------------------------*/ -int fill_ana_field_array( field_s * ah_fields ) -{ - nifti_analyze75 nhdr; - field_s * ahf = ah_fields; - int rv, errs; - - memset(ahf, 0, NT_ANA_NUM_FIELDS*sizeof(field_s)); - - /* this macro takes (TYPE, NAME, NUM) and does: - fill_field(nhdr, TYPE, NT_OFF(nhdr,NAME), NUM, "NAME"); - nhf++; - */ - errs = 0; - NT_SFILL(nhdr, ahf, DT_INT32, sizeof_hdr, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, data_type, 10, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, db_name, 18, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, extents, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, session_error, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, regular, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT8, hkey_un0, 1, rv); errs += rv; - - NT_SFILL(nhdr, ahf, DT_INT16, dim, 8, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, unused8, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, unused9, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, unused10, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, unused11, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, unused12, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, unused13, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, unused14, 1, rv); errs += rv; - - NT_SFILL(nhdr, ahf, DT_INT16, datatype, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, bitpix, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT16, dim_un0, 1, rv); errs += rv; - - NT_SFILL(nhdr, ahf, DT_FLOAT32, pixdim, 8, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_FLOAT32, vox_offset, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_FLOAT32, funused1, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_FLOAT32, funused2, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_FLOAT32, funused3, 1, rv); errs += rv; - - NT_SFILL(nhdr, ahf, DT_FLOAT32, cal_max, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_FLOAT32, cal_min, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_FLOAT32, compressed, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_FLOAT32, verified, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, glmax, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, glmin, 1, rv); errs += rv; - - NT_SFILL(nhdr, ahf, NT_DT_STRING, descrip, 80, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, aux_file, 24, rv); errs += rv; - - NT_SFILL(nhdr, ahf, DT_INT8, orient, 1, rv); errs += rv; - /* originator is 5 (3) shorts, not 10 chars 26 Sep 2012 [rickr] */ - NT_SFILL(nhdr, ahf, DT_INT16, originator, 5, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, generated, 10, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, scannum, 10, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, patient_id, 10, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, exp_date, 10, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, exp_time, 10, rv); errs += rv; - NT_SFILL(nhdr, ahf, NT_DT_STRING, hist_un0, 3, rv); errs += rv; - - NT_SFILL(nhdr, ahf, DT_INT32, views , 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, vols_added, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, start_field, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, field_skip, 1, rv); errs += rv; - - NT_SFILL(nhdr, ahf, DT_INT32, omax, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, omin, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, smax, 1, rv); errs += rv; - NT_SFILL(nhdr, ahf, DT_INT32, smin, 1, rv); errs += rv; - - if( errs > 0 ){ - fprintf(stderr, "** %d ana fill_fields errors!\n", errs); - return 1; - } - - /* failure here is a serious problem */ - if( check_total_size("nifti_analyze75 test: ", ah_fields, NT_ANA_NUM_FIELDS, - sizeof(nhdr)) ) - return 1; - - if( g_debug > 3 ) - disp_field_s_list("ah_fields: ", ah_fields, NT_ANA_NUM_FIELDS); - - return 0; -} - - -/*---------------------------------------------------------------------- - * compare sizes to offset, including total - *----------------------------------------------------------------------*/ -int check_total_size( const char *mesg, field_s * fields, int nfields, int tot_size ) -{ - field_s * fp; - int c, total; - int bad_offs; - - total = 0; - bad_offs = 0; - for( c = 0, fp = fields; c < nfields; c++, fp++ ){ - if( fp->offset != total ){ - if( g_debug > 2 ) - fprintf(stderr,"** bad offset for field '%s'\n" - " offset = %d, total = %d\n", - fp->name, fp->offset, total); - bad_offs++; - } - - total += fp->size * fp->len; - } - - if( g_debug > 1 || (g_debug > 0 && bad_offs > 0) ){ - fputs(mesg, stderr); c = 0; - if( bad_offs > 0 ){ - fprintf(stderr,"** found %d bad offsets\n", bad_offs); c++; } - if( total != tot_size ){ - fprintf(stderr,"** computed total %d not equal to struct size %d\n", - total, tot_size); c++; } - if( c == 0 ) fputs("... okay\n", stderr); - } - - if( bad_offs > 0 ) return 1; - - return 0; -} - - -/*---------------------------------------------------------------------- - * fill the field structure with the given data - *----------------------------------------------------------------------*/ -int fill_field( field_s * fp, int type, int offset, int num, const char * name ) -{ - fp->type = type; - fp->offset = offset; - fp->size = 1; /* init before check */ - fp->len = num; - - strncpy(fp->name, name, NT_FIELD_NAME_LEN-1); - - switch( type ){ - case DT_UNKNOWN: - case DT_INT8: - case NT_DT_STRING: - fp->size = 1; - break; - - case DT_INT16: - fp->size = 2; - break; - - case DT_INT32: - case DT_FLOAT32: - fp->size = 4; - break; - - case NT_DT_POINTER: - case NT_DT_CHAR_PTR: - case NT_DT_EXT_PTR: - fp->size = (int)sizeof(void *); - break; - - default: - fprintf(stderr,"** fill_field: invalid type %d\n", type ); - return 1; - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * display the contents of all of the field structures - *----------------------------------------------------------------------*/ -const char * field_type_str( int type ) -{ - if( type == DT_INT8 ) return "DT_INT8"; - if( type == DT_INT16 ) return "DT_INT16"; - if( type == DT_INT32 ) return "DT_INT32"; - if( type == DT_FLOAT32 ) return "DT_FLOAT32"; - if( type == NT_DT_STRING ) return "NT_DT_STRING"; - if( type == NT_DT_POINTER ) return "NT_DT_POINTER"; - if( type == NT_DT_CHAR_PTR ) return "NT_DT_CHAR_PTR"; /* longest: 14 */ - if( type == NT_DT_EXT_PTR ) return "NT_DT_EXT_PTR"; - - return "DT_UNKNOWN"; /* for DT_UNKNOWN, or as an else */ -} - -#define NT_MAX_DT_STR_LEN 14 - -/*---------------------------------------------------------------------- - * display the contents of all of the field structures - *----------------------------------------------------------------------*/ -int disp_field_s_list( const char *mesg, field_s * fp, int nfields ) -{ - int c; - - if( mesg ) fputs(mesg, stdout); - - fprintf(stdout," %d fields:\n" - " name size len offset type\n" - " ------------------- ---- --- ------ --------------\n", - nfields); - - for( c = 0; c < nfields; c++, fp++ ) - fprintf(stdout," %-*s %4d %3d %4d %-14s\n", - NT_FIELD_NAME_LEN-1, fp->name, fp->size, fp->len, - fp->offset, field_type_str(fp->type)); - - return 0; -} - - -/*---------------------------------------------------------------------- - * display the contents of all of the field structures - *----------------------------------------------------------------------*/ -int disp_field( const char *mesg, field_s *fieldp, void * str, int nfields, int header) -{ - field_s * fp; - int c; - - if( mesg ) fputs(mesg, stdout); - - if( header && g_debug > 0 ){ - fprintf(stdout, " name offset nvals values\n"); - fprintf(stdout, " ------------------- ------ ----- ------\n"); - } - - fp = fieldp; - for( c = 0; c < nfields; c++, fp++ ) - { - /* start by displaying the field information */ - if( g_debug > 0 ) - fprintf(stdout, " %-*.*s %4d %3d ", - NT_FIELD_NAME_LEN-1, NT_FIELD_NAME_LEN-1, fp->name, - fp->offset, fp->len); - - /* now, print the value(s), depending on the type */ - switch( fp->type ){ - case DT_UNKNOWN: - default: - fprintf(stdout,"(unknown data type)\n"); - break; - - case DT_INT8: case DT_UINT8: - case DT_INT16: case DT_UINT16: - case DT_INT32: case DT_UINT32: - case DT_FLOAT32: case DT_FLOAT64: - disp_raw_data((char *)str+fp->offset, fp->type, fp->len, ' ', 1); - break; - - case NT_DT_POINTER: - fprintf(stdout,"(raw data of unknown type)\n"); - break; - - case NT_DT_CHAR_PTR: /* look for string of length <= 40 */ - { - char * sp; - int len; - - /* start by sucking the pointer stored here */ - sp = *(char **)((char *)str + fp->offset); - - if( ! sp ){ fprintf(stdout,"(NULL)\n"); break; } /* anything? */ - - /* see if we have a printable string here */ - for(len = 0; len <= 40 && *sp && isprint(*sp); len++, sp++ ) - ; - if( len > 40 ) - fprintf(stdout,"(apparent long string)\n"); - else if ( len == 0 ) - fprintf(stdout,"(empty string)\n"); - else if( *sp && !isprint(*sp) ) /* if no termination, it's bad */ - fprintf(stdout,"(non-printable string)\n"); - else /* woohoo! a good string */ - fprintf(stdout,"'%.40s'\n",*(char **)((char *)str + fp->offset)); - break; - } - - case NT_DT_EXT_PTR: - { - nifti1_extension * extp; - - /* yank the address sitting there into extp */ - extp = *(nifti1_extension **)((char *)str + fp->offset); - - /* the user may use -disp_exts to display all of them */ - if( extp ) disp_nifti1_extension(NULL, extp, 6); - else fprintf(stdout,"(NULL)\n"); - break; - } - - case NT_DT_STRING: - { - char * charp = (char *)str + fp->offset; - fprintf(stdout,"%.*s\n", fp->len, charp); - break; - } - } - } - - return 0; -} - - -/*---------------------------------------------------------------------- - * no display, just return whether any fields differ - *----------------------------------------------------------------------*/ -int diff_field(field_s *fieldp, void * str0, void * str1, int nfields) -{ - field_s * fp; - char * cp0, * cp1; - int fnum, c, size; - - fp = fieldp; - for( fnum = 0; fnum < nfields; fnum++, fp++ ) - { - switch( fp->type ){ - case DT_UNKNOWN: /* all basic types are easy */ - case DT_INT8: - case DT_INT16: - case DT_INT32: - case DT_FLOAT32: - case NT_DT_STRING: - size = fp->size * fp->len; /* total field size */ - cp0 = (char *)str0 + fp->offset; - cp1 = (char *)str1 + fp->offset; - for( c = 0; c < size; c++, cp0++, cp1++ ) - if( *cp0 != *cp1 ) break; - - if(c < size) return 1; /* found a diff */ - - break; - - case NT_DT_POINTER: /* let's pass on these - no diff */ - case NT_DT_CHAR_PTR: - - break; - - case NT_DT_EXT_PTR: - { - nifti1_extension * ext0, * ext1; - - ext0 = *(nifti1_extension **)((char *)str0 + fp->offset); - ext1 = *(nifti1_extension **)((char *)str1 + fp->offset); - - if( ! ext0 && ! ext1 ) break; /* continue on */ - - if( ext0 && ! ext1 ) return 1; /* pointer diff is diff */ - if( ! ext0 && ext1 ) return 1; - - /* just check size and type for a single extension */ - if( ext0->esize != ext1->esize ) return 1; - if( ext0->ecode != ext1->ecode ) return 1; - - break; - } - } - } - - return 0; /* no diffs found */ -} - - -/*---------------------------------------------------------------------- - * display a single extension - *----------------------------------------------------------------------*/ -int disp_nifti1_extension( const char *mesg, nifti1_extension * ext, int maxlen) -{ - int len; - if( mesg ) fputs(mesg, stdout); - - if( !ext ) - { - fprintf(stderr,"** no extension to display\n"); - return 1; - } - - fprintf(stdout,"ecode = %d, esize = %d, edata = ", - ext->ecode, ext->esize); - - if( !ext->edata ) - fprintf(stdout,"(NULL)\n"); - else if ( ext->ecode == NIFTI_ECODE_AFNI || - ext->ecode == NIFTI_ECODE_COMMENT ) - { - len = ext->esize-8; - if( maxlen >= 0 && len > maxlen ) len = maxlen; - fprintf(stdout,"%.*s\n", len, (char *)ext->edata); - } - else - fprintf(stdout,"(unknown data type)\n"); - - fflush(stdout); - - return 0; -} - - -/*---------------------------------------------------------------------- - * return the appropritate pointer into the g_hdr_fields struct - *----------------------------------------------------------------------*/ -field_s * get_hdr_field( const char * fname, int show_fail ) -{ - field_s * fp; - int c; - - if( ! fname || *fname == '\0' ) return NULL; - - fp = g_hdr_fields; - for( c = 0; c < NT_HDR_NUM_FIELDS; c++, fp++ ) - if( strcmp(fname, fp->name) == 0 ) break; - - if( c == NT_HDR_NUM_FIELDS ) - { - if( show_fail > 0 ) - fprintf(stderr,"** get_hdr_field: field not found in hdr: %s\n",fname); - return NULL; - } - - return fp; -} - - -/*---------------------------------------------------------------------- - * return the appropritate pointer into the g_hdr_fields struct - *----------------------------------------------------------------------*/ -field_s * get_nim_field( const char * fname, int show_fail ) -{ - field_s * fp; - int c; - - if( ! fname || *fname == '\0' ) return NULL; - - fp = g_nim_fields; - for( c = 0; c < NT_NIM_NUM_FIELDS; c++, fp++ ) - if( strcmp(fname, fp->name) == 0 ) break; - - if( c == NT_NIM_NUM_FIELDS ) - { - if( show_fail > 0 ) - fprintf(stderr,"** get_nim_field: field not found in hdr: %s\n",fname); - return NULL; - } - - return fp; -} - - -/*---------------------------------------------------------------------- - * return the number of fields that differ - *----------------------------------------------------------------------*/ -int diff_hdrs( nifti_1_header * s0, nifti_1_header * s1, int display ) -{ - field_s * fp = g_hdr_fields; - int c, ndiff = 0; - - for( c = 0; c < NT_HDR_NUM_FIELDS; c++, fp++ ) - if( diff_field(fp, s0, s1, 1) ) - { - if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0); - if( display ) disp_field(NULL, fp, s1, 1, 0); - ndiff++; - } - - return ndiff; -} - - -/*---------------------------------------------------------------------- - * return the number of fields that differ - *----------------------------------------------------------------------*/ -int diff_nims( nifti_image * s0, nifti_image * s1, int display ) -{ - field_s * fp = g_nim_fields; - int c, ndiff = 0; - - for( c = 0; c < NT_NIM_NUM_FIELDS; c++, fp++ ) - if( diff_field(fp, s0, s1, 1) ) - { - if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0); - if( display ) disp_field(NULL, fp, s1, 1, 0); - ndiff++; - } - - return ndiff; -} - - -/*---------------------------------------------------------------------- - * return the number of fields that differ - *----------------------------------------------------------------------*/ -int diff_hdrs_list( nifti_1_header * s0, nifti_1_header * s1, str_list * slist, - int display ) -{ - field_s * fp; - const char ** sptr; - int c, ndiff = 0; - - sptr = slist->list; - for( c = 0; c < slist->len; c++ ) - { - fp = get_hdr_field(*sptr, 1); /* "not found" displayed in func */ - if( fp && diff_field(fp, s0, s1, 1) ) - { - if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0); - if( display ) disp_field(NULL, fp, s1, 1, 0); - ndiff++; - } - sptr++; - } - - return ndiff; -} - - -/*---------------------------------------------------------------------- - * return the number of fields that differ - *----------------------------------------------------------------------*/ -int diff_nims_list( nifti_image * s0, nifti_image * s1, str_list * slist, - int display ) -{ - field_s * fp; - const char ** sptr; - int c, ndiff = 0; - - sptr = slist->list; - for( c = 0; c < slist->len; c++ ) - { - fp = get_nim_field(*sptr, 1); /* "not found" displayed in func */ - if( fp && diff_field(fp, s0, s1, 1) ) - { - if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0); - if( display ) disp_field(NULL, fp, s1, 1, 0); - ndiff++; - } - sptr++; - } - - return ndiff; -} - - -/*---------------------------------------------------------------------- - * display data from collapsed_image - *----------------------------------------------------------------------*/ -int act_disp_ci( nt_opts * opts ) -{ - nifti_image * nim; - void * data = NULL; - char space = ' '; /* use space or newline */ - int filenum, len, err; - - if( opts->dci_lines ) space = '\n'; /* then use newlines as separators */ - - if( g_debug > 2 && opts->dts ) - { - fprintf(stderr,"-d displaying time series at (i,j,k) = (%d,%d,%d)\n" - " for %d nifti datasets...\n\n", opts->ci_dims[1], - opts->ci_dims[2], opts->ci_dims[3], opts->infiles.len); - } - else if ( g_debug > 2 ) /* the general collapsed image form */ - { - fprintf(stderr,"-d displaying collapsed image for %d datasets...\n\n" - " dims = ", opts->infiles.len); - disp_raw_data(opts->ci_dims, DT_INT32, 8, ' ', 1); - } - - for( filenum = 0; filenum < opts->infiles.len; filenum++ ) - { - err = 0; - nim = nt_image_read(opts, opts->infiles.list[filenum], 0); - if( !nim ) continue; /* errors are printed from library */ - if( opts->dts && nim->ndim != 4 ) - { - fprintf(stderr,"** error: dataset '%s' is not 4-dimensional\n", - nim->fname); - err++; - } - - switch( nim->datatype ) - { - case DT_INT8: case DT_INT16: case DT_INT32: - case DT_UINT8: case DT_UINT16: case DT_UINT32: - case DT_FLOAT32: case DT_FLOAT64: - if( g_debug > 1 ) - fprintf(stderr,"-d datatype %d of size %d\n", - nim->datatype, nim->nbyper); - break; - default: - fprintf(stderr,"** dataset '%s' has unknown type %d\n", - nim->fname, nim->datatype); - err++; - break; - } - - if( err ) { nifti_image_free(nim); continue; } - - len = nifti_read_collapsed_image(nim, opts->ci_dims, &data); - if( len < 0 || !data ) - { - fprintf(stderr,"** FAILURE for dataset '%s'\n", nim->fname); - if( data ) free(data); - err++; - } - - /* remove check for length of time series 24 Apr 2006 */ - - if( err ){ nifti_image_free(nim); continue; } - - /* now just print the results */ - if( g_debug > 0 ) - { - fprintf(stdout,"\ndataset '%s' @ (", nim->fname); - if( opts->dts ) disp_raw_data(opts->ci_dims+1, DT_INT32, 3, ' ', 0); - else disp_raw_data(opts->ci_dims+1, DT_INT32, 7, ' ', 0); - fprintf(stdout,")\n"); - } - - disp_raw_data(data, nim->datatype, len / nim->nbyper, space, 1); - - nifti_image_free(nim); - } - - if( data ) free(data); - - return 0; -} - - -int disp_raw_data( void * data, int type, int nvals, char space, int newline ) -{ - char * dp, fbuf[32]; - int c, size; - - nifti_datatype_sizes( type, &size, NULL ); /* get nbyper */ - - for( c = 0, dp = (char *)data; c < nvals; c++, dp += size ) - { - switch( type ) - { - case DT_INT8: - printf("%d", *(char *)dp); - break; - case DT_INT16: - printf("%d", *(short *)dp); - break; - case DT_INT32: - printf("%d", *(int *)dp); - break; - case DT_UINT8: - printf("%u", *(unsigned char *)dp); - break; - case DT_UINT16: - printf("%u", *(unsigned short *)dp); - break; - case DT_UINT32: - printf("%u", *(unsigned int *)dp); - break; - case DT_FLOAT32: - { - sprintf(fbuf,"%f", *(float *)dp); - clear_float_zeros(fbuf); - printf("%s", fbuf); - break; - } - case DT_FLOAT64: - { - sprintf(fbuf,"%f", *(double *)dp); - clear_float_zeros(fbuf); - printf("%s", fbuf); - break; - } - default: - fprintf(stderr,"** disp_raw_data: unknown type %d\n", type); - return 1; - } - if( c < nvals - 1 ) fputc(space,stdout); - } - - if ( newline ) fputc('\n',stdout); - - return 0; -} - -/*---------------------------------------------------------------------- - * remove trailing zeros from string of printed float - * return 1 if something was cleared - * 0 if not - *----------------------------------------------------------------------*/ -int clear_float_zeros( char * str ) -{ - char * dp = strchr(str, '.'), * valp; - int len; - - if( !dp ) return 0; /* nothing to clear */ - - len = strlen(dp); - - /* never clear what is just to the right of '.' */ - for( valp = dp+len-1; (valp > dp+1) && (*valp==' ' || *valp=='0'); valp-- ) - *valp = '\0'; /* clear, so we don't worry about break conditions */ - - if( valp < dp + len - 1 ) return 1; - return 0; -} - -/* return the number of volumes in the nifti_image */ -static int num_volumes(nifti_image * nim) -{ - int ind, nvols = 1; - - if( nim->dim[0] < 1 ) return 0; - - for( ind = 4; ind <= nim->dim[0]; ind++ ) - nvols *= nim->dim[ind]; - - return nvols; -} - - -/*---------------------------------------------------------------------- - * create a new dataset using sub-brick selection - *----------------------------------------------------------------------*/ -int act_cbl( nt_opts * opts ) -{ - nifti_brick_list NBL; - nifti_image * nim; - char * fname, * selstr, * cp; - int * blist; - int err = 0; - - if( g_debug > 2 ) - fprintf(stderr,"-d copying file info from '%s' to '%s'\n", - opts->infiles.list[0], opts->prefix); - - /* sanity checks */ - if( ! opts->prefix ) { - fprintf(stderr,"** error: -prefix is required with -cbl function\n"); - return 1; - } else if( opts->infiles.len > 1 ) { - fprintf(stderr,"** sorry, at the moment -cbl allows only 1 input\n"); - return 1; - } - - /* remove selector from fname, and copy selector string */ - fname = nifti_strdup(opts->infiles.list[0]); - cp = strchr(fname,'['); if( !cp ) cp = strchr(fname,'{'); - - if( !cp ) { - if( g_debug > 1 ) - fprintf(stderr,"-d using -cbl without brick list in '%s'\n",fname); - selstr = nifti_strdup("[0..$]"); - } else { - selstr = nifti_strdup(cp); - *cp = '\0'; /* remove selection string from fname */ - } - - if( g_debug > 1 ) - fprintf(stderr,"+d -cbl: using '%s' for selection string\n", selstr); - - nim = nt_image_read(opts, fname, 0); /* get image */ - if( !nim ) return 1; - - /* since nt can be zero now (sigh), check for it 02 Mar 2006 [rickr] */ - blist = nifti_get_intlist(nim->nt > 0 ? num_volumes(nim) : 1, selstr); - nifti_image_free(nim); /* throw away, will re-load */ - if( !blist ){ - fprintf(stderr,"** failed sub-brick selection using '%s'\n",selstr); - free(fname); free(selstr); return 1; - } - - nim = nt_read_bricks(opts, fname, blist[0], blist+1, &NBL); - free(blist); /* with this */ - if( !nim ){ free(fname); free(selstr); return 1; } - - if( g_debug > 1 ) fprintf(stderr,"+d sub-bricks loaded\n"); - - /* add command as COMMENT extension */ - if( opts->keep_hist && nifti_add_extension(nim, opts->command, - strlen(opts->command), NIFTI_ECODE_COMMENT) ) - fprintf(stderr,"** failed to add command to image as extension\n"); - - /* replace filenames using prefix */ - if( nifti_set_filenames(nim, opts->prefix, 1, 1) ) - { - fprintf(stderr,"** failed to set names, prefix = '%s'\n",opts->prefix); - err++; - } - - if(g_debug>2) disp_field("new nim:\n",g_nim_fields,nim,NT_NIM_NUM_FIELDS,1); - - /* and finally, write out results */ - if( err == 0 && nifti_nim_is_valid(nim, g_debug) ) - nifti_image_write_bricks(nim, &NBL); - - nifti_image_free(nim); - nifti_free_NBL(&NBL); - free(fname); - free(selstr); - - return 0; -} - - -/*---------------------------------------------------------------------- - * create a new dataset using read_collapsed_image - *----------------------------------------------------------------------*/ -int act_cci( nt_opts * opts ) -{ - nifti_image * nim; - int c; - - if( g_debug > 2 ) - fprintf(stderr,"-d collapsing file info from '%s' to '%s'\n", - opts->infiles.list[0], opts->prefix); - - /* sanity checks */ - if( ! opts->prefix ) { - fprintf(stderr,"** error: -prefix is required with -cci function\n"); - return 1; - } else if( opts->infiles.len > 1 ) { - fprintf(stderr,"** sorry, at the moment -cci allows only 1 input\n"); - return 1; - } - - nim = nt_image_read(opts, opts->infiles.list[0], 0); - if( !nim ) return 1; - nim->data = NULL; /* just to be sure */ - - if( nifti_read_collapsed_image(nim, opts->ci_dims, &nim->data) < 0 ) - { - nifti_image_free(nim); - return 1; - } - - /* add command as COMMENT extension */ - if( opts->keep_hist && nifti_add_extension(nim, opts->command, - strlen(opts->command), NIFTI_ECODE_COMMENT) ) - fprintf(stderr,"** failed to add command to image as extension\n"); - - /* replace filenames using prefix */ - if( nifti_set_filenames(nim, opts->prefix, 1, 1) ) - { - fprintf(stderr,"** failed to set names, prefix = '%s'\n",opts->prefix); - nifti_image_free(nim); - return 1; - } - - for( c = 1; c < 8; c++ ) /* nuke any collapsed dimension */ - if( opts->ci_dims[c] >= 0 ) nim->dim[c] = 1; - - nifti_update_dims_from_array(nim); - - if(g_debug>2) disp_field("new nim:\n",g_nim_fields,nim,NT_NIM_NUM_FIELDS,1); - - /* and finally, write out results */ - if( nifti_nim_is_valid(nim, g_debug) ) nifti_image_write(nim); - - nifti_image_free(nim); - - return 0; -} - - -/*---------------------------------------------------------------------- - * free all of the lists in the struct - * note: strings were not allocated - *----------------------------------------------------------------------*/ -static int free_opts_mem( nt_opts * nopt ) -{ - if( !nopt ) return 1; - - if( nopt->elist.list ) free(nopt->elist.list); - if( nopt->etypes.list ) free(nopt->etypes.list); - if( nopt->flist.list ) free(nopt->flist.list); - if( nopt->vlist.list ) free(nopt->vlist.list); - if( nopt->infiles.list ) free(nopt->infiles.list); - - return 0; -} - - -/*---------------------------------------------------------------------- - * wrapper for nifti_image_read - * - * this adds the option to generage an empty image, if the - * filename starts with "MAKE_IM" - *----------------------------------------------------------------------*/ -nifti_image * nt_image_read( nt_opts * opts, const char * fname, int doread ) -{ - if( !opts || !fname ) { - fprintf(stderr,"** nt_image_read: bad params (%p,%p)\n", - (void *)opts, (void *)fname); - return NULL; - } - - /* if the user does not want an empty image, do normal image_read */ - if( strncmp(fname,NT_MAKE_IM_NAME,strlen(NT_MAKE_IM_NAME)) ) { - if(g_debug > 1) - fprintf(stderr,"-d calling nifti_image_read(%s,%d)\n",fname,doread); - return nifti_image_read(fname, doread); - } - - /* so generate an emtpy image */ - if(g_debug > 1) { - fprintf(stderr,"+d NT_IR: generating EMPTY IMAGE from %s...\n",fname); - if(g_debug > 2) { - printf(" new_dim[8] = "); - disp_raw_data(opts->new_dim, DT_INT32, 8, ' ', 1); - printf(" new_datatype = %d\n", opts->new_datatype); - fflush(stdout); - } - } - - /* create a new nifti_image, with data depending on doread */ - return nifti_make_new_nim(opts->new_dim, opts->new_datatype, doread); -} - - -/*---------------------------------------------------------------------- - * wrapper for nifti_read_header - * - * this adds the option to generage an empty image, if the - * filename starts with "MAKE_IM" - *----------------------------------------------------------------------*/ -nifti_1_header * nt_read_header(nt_opts * opts, const char * fname, int * swapped, - int check) -{ - /* swapped is not necessary */ - if( !opts || !fname ) { - fprintf(stderr,"** nt_read_header: bad params (%p,%p)\n", - (void *)opts,(void *)fname); - return NULL; - } - - /* if the user does not want an empty image, do normal image_read */ - if( strncmp(fname,NT_MAKE_IM_NAME,strlen(NT_MAKE_IM_NAME)) ) { - if(g_debug > 1) - fprintf(stderr,"-d calling nifti_read_header(%s,...)\n", fname); - return nifti_read_header(fname, swapped, check); - } - - /* so generate an emtpy image */ - if(g_debug > 1) { - fprintf(stderr,"+d NT_RH: generating EMPTY IMAGE from %s...\n",fname); - if(g_debug > 2) { - printf(" new_dim[8] = "); - disp_raw_data(opts->new_dim, DT_INT32, 8, ' ', 1); - printf(" new_datatype = %d\n", opts->new_datatype); - fflush(stdout); - } - } - - /* return creation of new header */ - return nifti_make_new_header(opts->new_dim, opts->new_datatype); -} - - - -/*---------------------------------------------------------------------- - * wrapper for nifti_read_header - * - * this adds the option to generage an empty image, if the - * filename starts with "MAKE_IM" - *----------------------------------------------------------------------*/ -nifti_image * nt_read_bricks(nt_opts * opts, const char * fname, int len, int * list, - nifti_brick_list * NBL) -{ - nifti_image * nim; - int c; - - /* swapped is not necessary */ - if( !opts || !fname || !NBL ) { - fprintf(stderr,"** nt_read_bricks: bad params (%p,%p,%p)\n", - (void *)opts, (void *)fname, (void *)NBL); - return NULL; - } - - /* if the user does not want an empty image, do normal read_bricks */ - if( strncmp(fname,NT_MAKE_IM_NAME,strlen(NT_MAKE_IM_NAME)) ) { - if(g_debug > 1) - fprintf(stderr,"-d calling nifti_image_read_bricks(%s,...)\n",fname); - return nifti_image_read_bricks(fname, len, list, NBL); - } - - /* so generate an emtpy image */ - if(g_debug > 1) { - fprintf(stderr,"+d NT_RB: generating EMPTY IMAGE from %s...\n",fname); - if(g_debug > 2) { - printf(" new_dim[8] = "); - disp_raw_data(opts->new_dim, DT_INT32, 8, ' ', 1); - printf(" new_datatype = %d\n", opts->new_datatype); - if( list && len > 0 ) { - printf(" brick_list[%d] = ", len); - disp_raw_data(list, DT_INT32, len, ' ', 1); - } - fflush(stdout); /* disp_raw_data uses stdout */ - } - } - - /* first, get nim struct without data */ - nim = nifti_make_new_nim(opts->new_dim, opts->new_datatype, 0); - if( !nim ) { - fprintf(stderr,"** nt_read_bricks, nifti_make_new_nim failure\n"); - return NULL; - } - - /* now populate NBL (can be based only on len and nim) */ - NBL->nbricks = len; - NBL->bsize = (size_t)nim->nbyper * nim->nx * nim->ny * nim->nz; - NBL->bricks = (void **)calloc(NBL->nbricks, sizeof(void *)); - if( !NBL->bricks ){ - fprintf(stderr,"** NRB: failed to alloc %d pointers\n",NBL->nbricks); - nifti_image_free(nim); - return NULL; - } - - if(g_debug > 1) - fprintf(stderr,"+d NRB, allocating %d bricks of %u bytes...\n", - NBL->nbricks, (unsigned)NBL->bsize); - - /* now allocate the data pointers */ - for( c = 0; c < len; c++ ) { - NBL->bricks[c] = calloc(1, NBL->bsize); - if( !NBL->bricks[c] ){ - fprintf(stderr,"** NRB: failed to alloc brick %d of %u bytes\n", - c, (unsigned)NBL->bsize); - nifti_free_NBL(NBL); nifti_image_free(nim); return NULL; - } - } - - return nim; -} diff --git a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_tool.h b/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_tool.h deleted file mode 100644 index b0f658df0fe..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_tool.h +++ /dev/null @@ -1,163 +0,0 @@ -#ifndef _NIFTI_TOOL_H_ -#define _NIFTI_TOOL_H_ - -#define NT_CMD_LEN 2048 - -typedef struct{ - int len; - const char ** list; -} str_list; - -typedef struct{ - int len; - int * list; -} int_list; - -typedef struct{ - /* action options (flags) */ - int check_hdr, check_nim; - int diff_hdr, diff_nim; - int disp_hdr, disp_nim, disp_ana; - int disp_exts, add_exts, rm_exts; - int mod_hdr, mod_nim; - int swap_hdr, swap_ana, swap_old; - - int strip; /* strip extras from dataset(s) */ - int cbl, cci; /* -copy_XXX option flags */ - int dts, dci, dci_lines; /* display collapsed img flags */ - int make_im; /* create a new image on the fly */ - int ci_dims[8]; /* user dims list (last 7 valid) */ - int new_dim[8]; /* user dim list for new image */ - int new_datatype; /* datatype for new image */ - int debug, keep_hist; /* debug level and history flag */ - int overwrite; /* overwrite flag */ - char * prefix; /* for output file */ - str_list elist; /* extension strings */ - int_list etypes; /* extension type list */ - str_list flist; /* fields (to display or modify) */ - str_list vlist; /* values (to set fields to) */ - str_list infiles; /* input files */ - char command[NT_CMD_LEN]; /* for inserting the command */ -} nt_opts; - -#define USE_SHORT 1 -#define USE_FULL 2 -#define USE_HIST 3 -#define USE_FIELD_HDR 4 -#define USE_FIELD_NIM 5 -#define USE_FIELD_ANA 6 -#define USE_DTYPES 7 -#define USE_VERSION 8 - -#define CHECK_NEXT_OPT(n,m,str) \ - do { if ( (n) >= (m) ) { \ - fprintf(stderr,"** option '%s': missing parameter\n",str); \ - fprintf(stderr," consider: 'nifti_tool -help'\n"); \ - return 1; } \ - } while(0) - -#define CHECK_NEXT_OPT_MSG(n,m,str,msg) \ - do { if ( (n) >= (m) ) { \ - fprintf(stderr,"** option '%s': %s\n",str,msg); \ - fprintf(stderr," consider: 'nifti_tool -help'\n"); \ - return 1; } \ - } while(0) - -/*---------------------------------------------------------------------- - * this structure and definitions will be used to process the nifti_1_header - * and nifti_image structure fields (actions disp, diff, mod) - *----------------------------------------------------------------------*/ - -#define NT_FIELD_NAME_LEN 20 /* more than length of longest name */ -#define NT_HDR_NUM_FIELDS 43 /* in the nifti_1_header struct */ -#define NT_ANA_NUM_FIELDS 47 /* in the nifti_analyze75 struct */ -#define NT_NIM_NUM_FIELDS 63 /* in the nifti_image struct */ -#define NT_DT_STRING -0xfff /* some strange number to abuse... */ -#define NT_DT_POINTER -0xfef /* some strange number to abuse... */ -#define NT_DT_CHAR_PTR -0xfee /* another... */ -#define NT_DT_EXT_PTR -0xfed /* and another... */ - -typedef struct { - int type; /* one of the DT_* types from nifti1.h */ - int offset; /* bytes from the start of the struct */ - int size; /* size of one element type */ - int len; /* number of elements */ - char name[NT_FIELD_NAME_LEN]; /* actual structure name used */ -} field_s; - -/* for computing the offset from the start of the struct */ -#define NT_OFF(str,field) ((int)( ((char *)&str.field) - ((char *)&str) )) - -/* call fill_field() for a single type, name and number of elements */ -/* nstr is the base struct, and fldp is a field pointer */ -#define NT_SFILL(nstr,fldp,type,name,num,rv) do{ \ - rv=fill_field(fldp,type,NT_OFF(nstr,name),num,#name); \ - fldp++; } while (0) - -#define NT_MAKE_IM_NAME "MAKE_IM" - -/*----------------------------------------------------------------------*/ -/*----- prototypes ---------------------------------------------------*/ -/*----------------------------------------------------------------------*/ -int act_add_exts ( nt_opts * opts ); -int act_cbl ( nt_opts * opts ); /* copy brick list */ -int act_cci ( nt_opts * opts ); /* copy collapsed dimensions */ -int act_check_hdrs ( nt_opts * opts ); /* check for valid hdr or nim */ -int act_diff_hdrs ( nt_opts * opts ); -int act_diff_nims ( nt_opts * opts ); -int act_disp_ci ( nt_opts * opts ); /* display general collapsed data */ -int act_disp_exts ( nt_opts * opts ); -int act_disp_hdrs ( nt_opts * opts ); -int act_disp_nims ( nt_opts * opts ); -int act_disp_anas ( nt_opts * opts ); -int act_disp_ts ( nt_opts * opts ); /* display time series */ -int act_mod_hdrs ( nt_opts * opts ); -int act_mod_nims ( nt_opts * opts ); -int act_swap_hdrs ( nt_opts * opts ); -int act_rm_ext ( nt_opts * opts ); -int act_strip ( nt_opts * opts ); /* strip extras from datasets */ - - -field_s * get_hdr_field( const char * fname, int show_fail ); -field_s * get_nim_field( const char * fname, int show_fail ); -const char * field_type_str (int type); - -int diff_hdrs (nifti_1_header *s0, nifti_1_header *s1, int display); -int diff_hdrs_list(nifti_1_header *s0, nifti_1_header *s1, str_list *slist, - int display); -int diff_nims (nifti_image *s0,nifti_image *s1, int display); -int diff_nims_list(nifti_image *s0,nifti_image *s1,str_list *slist,int display); - -int add_int (int_list * ilist, int val); -int add_string (str_list * slist, const char * str); -int check_total_size ( const char *mesg, field_s *fields, int nfields, int tot_size); -int clear_float_zeros( char * str ); -int diff_field (field_s *fieldp, void * str0, void * str1, int nfields); -int disp_nifti1_extension( const char *mesg, nifti1_extension * ext, int maxlen); -int disp_field ( const char *mesg,field_s *fp,void *str,int nfields,int header); -int disp_field_s_list( const char *mesg, field_s *, int nfields); -int disp_nt_opts ( const char *mesg, nt_opts * opts); -int disp_raw_data (void * data, int type, int nvals, char space,int newline); -int fill_cmd_string (nt_opts * opts, int argc, char * argv[]); -int fill_field (field_s *fp, int type, int offset, int num, const char *name); -int fill_hdr_field_array(field_s * nh_fields); -int fill_nim_field_array(field_s * nim_fields); -int fill_ana_field_array(field_s * ah_fields); -int modify_all_fields(void *basep, nt_opts *opts, field_s *fields, int flen); -int modify_field (void * basep, field_s * field, const char * data); -int process_opts (int argc, char * argv[], nt_opts * opts); -int remove_ext_list (nifti_image * nim, const char ** elist, int len); -int usage (const char * prog, int level); -int use_full (const char * prog); -int verify_opts (nt_opts * opts, char * prog); -int write_hdr_to_file(nifti_1_header * nhdr, const char * fname); - -/* wrappers for nifti reading functions (allow MAKE_IM) */ -nifti_image * nt_image_read (nt_opts * opts, const char * fname, int doread); -nifti_image * nt_read_bricks(nt_opts * opts, const char * fname, int len, - int * list, nifti_brick_list * NBL); -nifti_1_header * nt_read_header(nt_opts * opts, const char * fname, int * swapped, - int check); - - -#endif /* _NIFTI_TOOL_H_ */ diff --git a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti_tester001.c b/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti_tester001.c deleted file mode 100644 index b9644f4ed61..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti_tester001.c +++ /dev/null @@ -1,695 +0,0 @@ -/* - * test program for NIFTI lib. - */ -#include -enum NIFTITEST_BOOL { - NIFTITEST_TRUE=1, - NIFTITEST_FALSE=0 -}; - -void _PrintTest(const int line,const char * message,const int FailureOccured, const enum NIFTITEST_BOOL isFatal,int *ErrorAccum) -{ - if(FailureOccured==NIFTITEST_TRUE) /* This line can be commented out for a more verbose output */ - { - char const * const PREFIX= (FailureOccured)?"==========ERROR":"..........SUCCESS"; - char const * const ISFATALPREFIX= (isFatal && FailureOccured)?" FATAL":""; - printf("%s%s (LINE %d): %s\n",PREFIX,ISFATALPREFIX,line,message); - fflush(stdout); - *ErrorAccum+=FailureOccured; - if(isFatal==NIFTITEST_TRUE && FailureOccured==NIFTITEST_TRUE) - { - printf("\n\nTOTAL ERRORS=%d\n",*ErrorAccum); - exit( *ErrorAccum); - } - } - return; -} -#define PrintTest(message,failure,isfailure,errorcount) \ - _PrintTest(__LINE__,message,failure,isfailure,errorcount) - -nifti_image * generate_reference_image( const char * write_image_filename , int * const Errors) -{ - nifti_1_header reference_header; - memset(&reference_header,0,sizeof(reference_header)); - reference_header.sizeof_hdr=sizeof(reference_header); - reference_header.regular='r'; - reference_header.extents=16384; - - reference_header.dim[0]=5; - reference_header.dim[1]=23; - reference_header.dim[2]=17; - reference_header.dim[3]=11; - reference_header.dim[4]=7; - reference_header.dim[5]=3; - reference_header.dim[6]=1; //This MUST be 1 anything else is invalid due to code that usees huristics to fix other possible problems; - reference_header.dim[7]=1; //This MUST be 1 anything else is invalid due to code that usees huristics to fix other possible problems; - reference_header.intent_p1=10101010.101F; - reference_header.intent_p2=987654321.0F; - reference_header.intent_p3=-1234.0F; - reference_header.intent_code=NIFTI_INTENT_ESTIMATE; - reference_header.datatype=DT_INT32; - reference_header.pixdim[0]=-1.0F; /* this is really qfac */ - reference_header.pixdim[1]=0.25F; - reference_header.pixdim[2]=0.5F; - reference_header.pixdim[3]=1.0F; - reference_header.pixdim[4]=2.0F; - reference_header.pixdim[5]=4.0F; - reference_header.pixdim[6]=-2.0e10F; - reference_header.pixdim[7]=-2.0e10F; - reference_header.vox_offset=0; - reference_header.scl_slope=0.25; - reference_header.scl_inter=128; - reference_header.qform_code=NIFTI_XFORM_SCANNER_ANAT; - reference_header.quatern_b=-0.5F; - reference_header.quatern_c= 0.5F; - reference_header.quatern_d=-0.5F; - reference_header.qoffset_x=reference_header.dim[1]/2.0F; - reference_header.qoffset_y=reference_header.dim[2]/2.0F; - reference_header.qoffset_z=reference_header.dim[3]/2.0F; - reference_header.sform_code=NIFTI_XFORM_SCANNER_ANAT; - reference_header.srow_x[0]=0.5; - reference_header.srow_x[1]=0.0; - reference_header.srow_x[2]=0.0; - reference_header.srow_x[3]=0.0; - reference_header.srow_y[0]=0.0; - reference_header.srow_y[1]=1.0; - reference_header.srow_y[2]=0.0; - reference_header.srow_y[3]=0.0; - reference_header.srow_z[0]=0.0; - reference_header.srow_z[1]=0.0; - reference_header.srow_z[2]=2.0; - reference_header.srow_z[3]=0.0; - reference_header.magic[0]='n'; - reference_header.magic[1]='+'; - reference_header.magic[2]='1'; - reference_header.magic[3]='\0'; - /* String is purposfully too long */ - strncpy(reference_header.intent_name,"PHANTOM_DATA to be used for regression testing the nifti reader/writer",16); - strncpy(reference_header.descrip,"This is a very long dialog here to use up more than 80 characters of space to test to see if the code is robust enough to deal appropriatly with very long and obnoxious lines.",80); - - { - int nbyper; - int swapsize; - nifti_datatype_sizes(reference_header.datatype ,&nbyper,&swapsize); - reference_header.bitpix=nbyper*8; - } - - nifti_image * reference_image=nifti_convert_nhdr2nim(reference_header,write_image_filename); - { - const unsigned int NumVoxels=reference_image->nx*reference_image->ny*reference_image->nz*reference_image->nt*reference_image->nu; - reference_image->data=(signed int *)calloc(NumVoxels,sizeof(signed int)) ; /*!< pointer to data: nbyper*nvox bytes */ - PrintTest("Checking memory allocation",reference_image->data ==0 ,NIFTITEST_TRUE,Errors); - { - signed int i=0; - for(; i < (signed int)NumVoxels ; i++) - { - ((signed int *)(reference_image->data))[i]=i; - } - } - } - PrintTest("Setting filenames",nifti_set_filenames( reference_image,write_image_filename, 0, 0 ) != 0, NIFTITEST_TRUE,Errors); - PrintTest("Setting type from names",nifti_set_type_from_names( reference_image ) != 0, NIFTITEST_TRUE,Errors); - /* PrintTest("Checking type and names",nifti_type_and_names_match( reference_image , 1 ) != 1, NIFTITEST_TRUE,Errors); */ - PrintTest("Check reference_image data is non null",(reference_image->data==0),NIFTITEST_TRUE,Errors); - return reference_image; -} - - -void compare_reference_image_values(nifti_image const * const reference_image, nifti_image const * const reloaded_image, int * const Errors) -{ - PrintTest("Checking nifti_type",(reference_image->nifti_type!=reloaded_image->nifti_type),NIFTITEST_FALSE,Errors); - PrintTest("Checking fname",(strcmp(reference_image->fname,reloaded_image->fname)),NIFTITEST_FALSE,Errors); - PrintTest("Checking iname",(strcmp(reference_image->iname,reloaded_image->iname)),NIFTITEST_FALSE,Errors); - PrintTest("Checking ndim",(reference_image->ndim!=reloaded_image->ndim),NIFTITEST_FALSE,Errors); - PrintTest("Checking nx",(reference_image->nx!=reloaded_image->nx),NIFTITEST_FALSE,Errors); - PrintTest("Checking ny",(reference_image->ny!=reloaded_image->ny),NIFTITEST_FALSE,Errors); - PrintTest("Checking nz",(reference_image->nz!=reloaded_image->nz),NIFTITEST_FALSE,Errors); - PrintTest("Checking nt",(reference_image->nt!=reloaded_image->nt),NIFTITEST_FALSE,Errors); - PrintTest("Checking nu",(reference_image->nu!=reloaded_image->nu),NIFTITEST_FALSE,Errors); - PrintTest("Checking dx",(reference_image->dx!=reloaded_image->dx),NIFTITEST_FALSE,Errors); - PrintTest("Checking dy",(reference_image->dy!=reloaded_image->dy),NIFTITEST_FALSE,Errors); - PrintTest("Checking dz",(reference_image->dz!=reloaded_image->dz),NIFTITEST_FALSE,Errors); - PrintTest("Checking dt",(reference_image->dt!=reloaded_image->dt),NIFTITEST_FALSE,Errors); - PrintTest("Checking du",(reference_image->du!=reloaded_image->du),NIFTITEST_FALSE,Errors); - PrintTest("Checking datatype",(reference_image->datatype!=reloaded_image->datatype),NIFTITEST_FALSE,Errors); - { - const unsigned int NumVoxels=reference_image->nx*reference_image->ny*reference_image->nz*reference_image->nt*reference_image->nu; - PrintTest("Check loaded data is non null",(reloaded_image->data==0),NIFTITEST_TRUE,Errors); - PrintTest("Check reference_image data is non null",(reference_image->data==0),NIFTITEST_TRUE,Errors); - { - unsigned int CurrVoxel=0; - for(; CurrVoxel < NumVoxels ; CurrVoxel++) - { - /*printf("%d ",CurrVoxel); fflush(stdout);*/ - if( ((int *)(reference_image->data))[CurrVoxel] != ((int *)(reloaded_image->data))[CurrVoxel]) - { - PrintTest("Incorrect Pixel Value Found",0,NIFTITEST_FALSE,Errors); - } - } - } - } - PrintTest("Checking xyz_units",(reference_image->xyz_units!=reloaded_image->xyz_units),NIFTITEST_FALSE,Errors); - PrintTest("Checking time_units",(reference_image->time_units!=reloaded_image->time_units),NIFTITEST_FALSE,Errors); - PrintTest("Checking intent_code",(reference_image->intent_code!=reloaded_image->intent_code),NIFTITEST_FALSE,Errors); - PrintTest("Checking intent_name",(strncmp(reference_image->intent_name,reloaded_image->intent_name,16) )!=0,NIFTITEST_FALSE,Errors); - PrintTest("Checking description",(strncmp(reference_image->descrip,reloaded_image->descrip,80))!=0,NIFTITEST_FALSE,Errors); - return ; -} - -int main (int argc, char *argv[]) -{ - if (argc > 1) - { - printf("The test program takes no arguments: %s", argv[0]); - return EXIT_FAILURE; - } - char TEMP_STR[256]; - nifti_set_debug_level(3); - int Errors=0; - { - PrintTest("NOT REALLY AN ERROR, JUST TESTING THE ERROR TEST REPORTING MECHANISM",1,NIFTITEST_FALSE,&Errors); - PrintTest("NOT REALLY AN ERROR, JUST TESTING THE ERROR COUNTING MECHANISM",Errors==1,NIFTITEST_FALSE,&Errors); - Errors=0; - } - { - const char write_image_filename[6][64]={ - "ATestReferenceImageForReadingAndWriting.nii", - "ATestReferenceImageForReadingAndWriting.hdr", - "ATestReferenceImageForReadingAndWriting.img", - "ATestReferenceImageForReadingAndWriting.nii.gz", - "ATestReferenceImageForReadingAndWriting.hdr.gz", - "ATestReferenceImageForReadingAndWriting.img.gz" - }; - printf("======= Testing All Nifti Valid Names ======\n"); - fflush(stdout); - unsigned int filenameindex; - for(filenameindex=0;filenameindex<6; filenameindex++) - { - char buf[512]; - int CompressedTwoFile = strstr(write_image_filename[filenameindex],".img.gz") != 0 || - strstr(write_image_filename[filenameindex],".hdr.gz") != 0; - - printf("======= Testing with filename: %s ======\n",write_image_filename[filenameindex]); - fflush(stdout); - nifti_image * reference_image = generate_reference_image(write_image_filename[filenameindex],&Errors); - /* - * Add an extension to test extension reading - */ - { - static char ext[] = "THIS IS A TEST"; - sprintf(buf,"nifti_add_extension %s",write_image_filename[filenameindex]); - PrintTest(buf, - nifti_add_extension(reference_image, - ext,sizeof(ext), - NIFTI_ECODE_COMMENT) == -1, - NIFTITEST_FALSE,&Errors); - sprintf(buf,"valid_nifti_extension %s",write_image_filename[filenameindex]); - PrintTest("valid_nifti_extensions", - valid_nifti_extensions(reference_image) == 0, - NIFTITEST_FALSE,&Errors); - } - PrintTest("Create reference image",reference_image==0,NIFTITEST_TRUE,&Errors); - nifti_image_write ( reference_image ) ; - /* - * test nifti_copy_extension - */ - { - nifti_image *nim = nifti_simple_init_nim(); - PrintTest("nifti_copy_extension", - nifti_copy_extensions(nim,reference_image), - NIFTITEST_FALSE,&Errors); - - nifti_image_free(nim); - nim = nifti_copy_nim_info(reference_image); - PrintTest("nifti_copy_nim_info", - nim == 0, - NIFTITEST_FALSE,&Errors); - PrintTest("nifti_nim_is_valid", - nifti_nim_is_valid(nim,0) == 0, - NIFTITEST_FALSE,&Errors); - - - nifti_image_free(nim); - - } - { - nifti_image * reloaded_image = nifti_image_read(reference_image->fname,1); - PrintTest("Reload of image ",reloaded_image==0,NIFTITEST_TRUE,&Errors); - - { - /* - * if the file is named '.img', '.hdr', '.img.gz', or '.hdr.gz', then - * the header extensions won't be saved with the file. - * The test will fail if it finds an extension in a 2-file NIfTI, or - * fails to find one in a '.nii' or '.nii.gz' file. - */ - int result = valid_nifti_extensions(reloaded_image); - sprintf(buf,"reload valid_nifti_extensions %s",write_image_filename[filenameindex]); - PrintTest(buf, - CompressedTwoFile ? result != 0 : result == 0, - NIFTITEST_FALSE,&Errors); - } - nifti_image_infodump(reloaded_image); - compare_reference_image_values(reference_image,reloaded_image,&Errors); - nifti_image_free(reloaded_image); - } - - { - nifti_brick_list NB_orig, NB_select; - - nifti_image * nim_orig, * nim_select; - - int blist[5] = { 7, 0, 5, 5, 9 }; - - /* - * test some error paths in the nifti_image_read_bricks - */ - nim_orig = nifti_image_read_bricks(reference_image->fname,0,blist, &NB_orig); - PrintTest("invalid arg bricked image read 1",nim_orig != 0,NIFTITEST_FALSE,&Errors); - - nim_orig = nifti_image_read_bricks(reference_image->fname, 0, NULL, &NB_orig); - PrintTest("Reload of bricked image",nim_orig == 0,NIFTITEST_FALSE,&Errors); - nifti_free_NBL(&NB_orig); - nifti_image_free(nim_orig); - - nim_select = nifti_image_read_bricks(reference_image->fname, 5, blist, &NB_select); - PrintTest("Reload of bricked image with blist",nim_orig == 0,NIFTITEST_FALSE,&Errors); - nifti_free_NBL(&NB_select); - nifti_image_free(nim_select); - - } - /* - * test nifti_update_dims_from_array - */ - PrintTest("nifti_update_dims_from_array -- valid dims", - nifti_update_dims_from_array(reference_image) != 0, - NIFTITEST_FALSE,&Errors); - reference_image->dim[0] = 8; - PrintTest("nifti_update_dims_from_array -- invalid dims", - nifti_update_dims_from_array(reference_image) == 0, - NIFTITEST_FALSE,&Errors); - { - nifti_1_header x = nifti_convert_nim2nhdr(reference_image); - char local_buffer[512]; - sprintf(local_buffer,"nifti_hdr_looks_good %s",reference_image->fname); - PrintTest(local_buffer, - !nifti_hdr_looks_good(&x), - NIFTITEST_FALSE,&Errors); - } - - nifti_image_free(reference_image); - } - /* - * check nifti_findimgname - */ - { - char *imgname = nifti_findimgname("ATestReferenceImageForReadingAndWriting.hdr",2); - PrintTest("nifti_findimgname", - imgname == 0 || - strcmp(imgname,"ATestReferenceImageForReadingAndWriting.img") != 0, - NIFTITEST_FALSE,&Errors); - free(imgname); - } - { - int IsNiftiFile; - IsNiftiFile = is_nifti_file(write_image_filename[0]); - PrintTest("is_nifti_file0", - IsNiftiFile != 1,NIFTITEST_FALSE,&Errors); - IsNiftiFile = is_nifti_file(write_image_filename[1]); - PrintTest("is_nifti_file1", - IsNiftiFile != 2,NIFTITEST_FALSE,&Errors); - IsNiftiFile = is_nifti_file(write_image_filename[3]); - PrintTest("is_nifti_file2", - IsNiftiFile != 1,NIFTITEST_FALSE,&Errors); - IsNiftiFile = is_nifti_file(write_image_filename[4]); - PrintTest("is_nifti_file2", - IsNiftiFile != 2,NIFTITEST_FALSE,&Errors); - } - - } - { - /* - * test writing and reading an ascii file - */ - nifti_image * reference_image = - generate_reference_image("TestAsciiImage.nia",&Errors); - reference_image->nifti_type = 3; - nifti_image_write(reference_image); - nifti_image * reloaded_image = nifti_image_read("TestAsciiImage.nia",1); - PrintTest("Read/Write Ascii image", - reloaded_image == 0,NIFTITEST_FALSE,&Errors); - nifti_image_free(reference_image); - nifti_image_free(reloaded_image); - } - - { - enum { NUM_FILE_NAMES=8 }; - const char * FILE_NAMES[NUM_FILE_NAMES]={ - "myimage", - "myimage.tif", - "myimage.tif.gz", - "myimage.nii", - "myimage.img.gz", - ".nii", - ".myhiddenimage", - ".myhiddenimage.nii" - }; - const char * KNOWN_FILE_BASENAMES[NUM_FILE_NAMES]={ - "myimage", - "myimage.tif", - "myimage.tif.gz", - "myimage", - "myimage", - "", - ".myhiddenimage", - ".myhiddenimage" - }; - const int KNOWN_nifti_validfilename[NUM_FILE_NAMES]={ - 1, - 1, - 1, - 1, - 1, - 0, - 1, - 1 - }; - const int KNOWN_nifti_is_complete_filename[NUM_FILE_NAMES]={ - 0, - 0, - 0, - 1, - 1, - 0, - 0, - 1 - }; - unsigned int fni; - for(fni=0;fnidata != 0, - NIFTITEST_FALSE,&Errors); - - znzclose(f); - nifti_image_free(nim); - } - /* - * call various functions from nifti_stats - */ - printf("\n\nTOTAL ERRORS=%d\n",Errors); - return Errors; -} diff --git a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti_tester002.c b/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti_tester002.c deleted file mode 100644 index c72cf2a2ed2..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti_tester002.c +++ /dev/null @@ -1,38 +0,0 @@ -/* - * nifti_test2 -- this exercises a particular bug, whereby nifti_copy_nim_info was - * not working correctly, which left the copy of an image pointing to the same - * extension list, which could cause all sorts of grief. - */ -#include -int main (int argc, char *argv[]) -{ - if (argc > 1) - { - printf("The test program takes no arguments: %s", argv[0]); - return EXIT_FAILURE; - } - - /* - * create a 'dummy' image - */ - nifti_image *i1 = nifti_simple_init_nim(); - nifti_image *i2; - - /* - * add an extension to the dummy - */ - static char ext[] = "THIS IS A TEST"; - nifti_add_extension(i1,ext,sizeof(ext),NIFTI_ECODE_COMMENT); - /* - * make a new nim from the dummy - */ - i2 = nifti_copy_nim_info(i1); - /* - * if the bug isn't fixed in niftilib, the second nifti_image_free - * will fail because both nims point to the same extensions. With gcc - * this will abort inside the standard library - */ - nifti_image_free(i1); - nifti_image_free(i2); - return 0; -} diff --git a/Modules/ThirdParty/NIFTI/src/nifti/znzlib/CMakeLists.txt b/Modules/ThirdParty/NIFTI/src/nifti/znzlib/CMakeLists.txt deleted file mode 100644 index 427f98e09be..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/znzlib/CMakeLists.txt +++ /dev/null @@ -1,31 +0,0 @@ -set(NIFTI_ZNZLIB_NAME ${NIFTI_PACKAGE_PREFIX}znz) - -add_library(${NIFTI_ZNZLIB_NAME} znzlib.c ) -target_link_libraries( ${NIFTI_ZNZLIB_NAME} PUBLIC ${NIFTI_ZLIB_LIBRARIES} ) -target_include_directories(${NIFTI_ZNZLIB_NAME} PUBLIC - $ - $ - ) - -# Set library version if building shared libs. -if(BUILD_SHARED_LIBS) - set_target_properties(${NIFTI_ZNZLIB_NAME} PROPERTIES ${NIFTI_LIBRARY_PROPERTIES}) -endif() - - -if(NOT NIFTI_INSTALL_NO_LIBRARIES) - install(TARGETS ${NIFTI_ZNZLIB_NAME} - EXPORT ${NIFTI_INSTALL_EXPORT_NAME} - RUNTIME DESTINATION ${NIFTI_INSTALL_RUNTIME_DIR} COMPONENT RuntimeLibraries - LIBRARY DESTINATION ${NIFTI_INSTALL_LIBRARY_DIR} COMPONENT RuntimeLibraries - ARCHIVE DESTINATION ${NIFTI_INSTALL_LIBRARY_DIR} COMPONENT Development - INCLUDES DESTINATION ${NIFTI_INSTALL_INCLUDE_DIR} - ) -endif() - -if(NOT NIFTI_INSTALL_NO_DEVELOPMENT) - file(GLOB __files "${CMAKE_CURRENT_SOURCE_DIR}/*.h") - install(FILES ${__files} - DESTINATION ${NIFTI_INSTALL_INCLUDE_DIR} - COMPONENT Development) -endif() diff --git a/Modules/ThirdParty/NIFTI/src/nifti/znzlib/Makefile b/Modules/ThirdParty/NIFTI/src/nifti/znzlib/Makefile deleted file mode 100644 index 2560c995b87..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/znzlib/Makefile +++ /dev/null @@ -1,26 +0,0 @@ -include ../Makefile - -PROJNAME = znzlib - -INCFLAGS = $(ZLIB_INC) - -SRCS=znzlib.c -OBJS=znzlib.o - -depend: - $(RM) -f depend.mk - $(MAKE) depend.mk - -depend.mk: - $(CC) $(DEPENDFLAGS) $(INCFLAGS) $(SRCS) >> depend.mk - -lib: libznz.a - -znzlib.o: znzlib.c znzlib.h - $(CC) -c $(CFLAGS) $(USEZLIB) $(INCFLAGS) $< - -libznz.a: $(OBJS) - $(AR) -r libznz.a $(OBJS) - $(RANLIB) $@ - -include depend.mk diff --git a/Modules/ThirdParty/NIFTI/src/nifti/znzlib/znzlib.c b/Modules/ThirdParty/NIFTI/src/nifti/znzlib/znzlib.c deleted file mode 100644 index 2fe34125e77..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/znzlib/znzlib.c +++ /dev/null @@ -1,321 +0,0 @@ -/** \file znzlib.c - \brief Low level i/o interface to compressed and noncompressed files. - Written by Mark Jenkinson, FMRIB - -This library provides an interface to both compressed (gzip/zlib) and -uncompressed (normal) file IO. The functions are written to have the -same interface as the standard file IO functions. - -To use this library instead of normal file IO, the following changes -are required: - - replace all instances of FILE* with znzFile - - change the name of all function calls, replacing the initial character - f with the znz (e.g. fseek becomes znzseek) - one exception is rewind() -> znzrewind() - - add a third parameter to all calls to znzopen (previously fopen) - that specifies whether to use compression (1) or not (0) - - use znz_isnull rather than any (pointer == NULL) comparisons in the code - for znzfile types (normally done after a return from znzopen) - -NB: seeks for writable files with compression are quite restricted - - */ - -#include "znzlib.h" - -/* -znzlib.c (zipped or non-zipped library) - -***** This code is released to the public domain. ***** - -***** Author: Mark Jenkinson, FMRIB Centre, University of Oxford ***** -***** Date: September 2004 ***** - -***** Neither the FMRIB Centre, the University of Oxford, nor any of ***** -***** its employees imply any warranty of usefulness of this software ***** -***** for any purpose, and do not assume any liability for damages, ***** -***** incidental or otherwise, caused by any use of this document. ***** - -*/ - - -/* Note extra argument (use_compression) where - use_compression==0 is no compression - use_compression!=0 uses zlib (gzip) compression -*/ - -znzFile znzopen(const char *path, const char *mode, int use_compression) -{ - znzFile file; - file = (znzFile) calloc(1,sizeof(struct znzptr)); - if( file == NULL ){ - fprintf(stderr,"** ERROR: znzopen failed to alloc znzptr\n"); - return NULL; - } - - file->nzfptr = NULL; - -#ifdef HAVE_ZLIB - file->zfptr = NULL; - - if (use_compression) { - file->withz = 1; - if((file->zfptr = gzopen(path,mode)) == NULL) { - free(file); - file = NULL; - } - } else { -#endif - - file->withz = 0; - if((file->nzfptr = fopen(path,mode)) == NULL) { - free(file); - file = NULL; - } - -#ifdef HAVE_ZLIB - } -#endif - - return file; -} - - -znzFile znzdopen(int fd, const char *mode, int use_compression) -{ - znzFile file; - file = (znzFile) calloc(1,sizeof(struct znzptr)); - if( file == NULL ){ - fprintf(stderr,"** ERROR: znzdopen failed to alloc znzptr\n"); - return NULL; - } -#ifdef HAVE_ZLIB - if (use_compression) { - file->withz = 1; - file->zfptr = gzdopen(fd,mode); - file->nzfptr = NULL; - } else { -#endif - file->withz = 0; -#ifdef HAVE_FDOPEN - file->nzfptr = fdopen(fd,mode); -#endif -#ifdef HAVE_ZLIB - file->zfptr = NULL; - }; -#endif - return file; -} - - -int Xznzclose(znzFile * file) -{ - int retval = 0; - if (*file!=NULL) { -#ifdef HAVE_ZLIB - if ((*file)->zfptr!=NULL) { retval = gzclose((*file)->zfptr); } -#endif - if ((*file)->nzfptr!=NULL) { retval = fclose((*file)->nzfptr); } - - free(*file); - *file = NULL; - } - return retval; -} - - -/* we already assume ints are 4 bytes */ -#undef ZNZ_MAX_BLOCK_SIZE -#define ZNZ_MAX_BLOCK_SIZE (1<<30) - -size_t znzread(void* buf, size_t size, size_t nmemb, znzFile file) -{ - size_t remain = size*nmemb; - char * cbuf = (char *)buf; - unsigned n2read; - int nread; - - if (file==NULL) { return 0; } -#ifdef HAVE_ZLIB - if (file->zfptr!=NULL) { - /* gzread/write take unsigned int length, so maybe read in int pieces - (noted by M Hanke, example given by M Adler) 6 July 2010 [rickr] */ - while( remain > 0 ) { - n2read = (remain < ZNZ_MAX_BLOCK_SIZE) ? remain : ZNZ_MAX_BLOCK_SIZE; - nread = gzread(file->zfptr, (void *)cbuf, n2read); - if( nread < 0 ) return nread; /* returns -1 on error */ - - remain -= nread; - cbuf += nread; - - /* require reading n2read bytes, so we don't get stuck */ - if( nread < (int)n2read ) break; /* return will be short */ - } - - /* warn of a short read that will seem complete */ - if( remain > 0 && remain < size ) - fprintf(stderr,"** znzread: read short by %u bytes\n",(unsigned)remain); - - return nmemb - remain/size; /* return number of members processed */ - } -#endif - return fread(buf,size,nmemb,file->nzfptr); -} - -size_t znzwrite(const void* buf, size_t size, size_t nmemb, znzFile file) -{ - size_t remain = size*nmemb; - const char * cbuf = (const char *)buf; - unsigned n2write; - int nwritten; - - if (file==NULL) { return 0; } -#ifdef HAVE_ZLIB - if (file->zfptr!=NULL) { - while( remain > 0 ) { - n2write = (remain < ZNZ_MAX_BLOCK_SIZE) ? remain : ZNZ_MAX_BLOCK_SIZE; - nwritten = gzwrite(file->zfptr, (const void *)cbuf, n2write); - - /* gzread returns 0 on error, but in case that ever changes... */ - if( nwritten < 0 ) return nwritten; - - remain -= nwritten; - cbuf += nwritten; - - /* require writing n2write bytes, so we don't get stuck */ - if( nwritten < (int)n2write ) break; - } - - /* warn of a short write that will seem complete */ - if( remain > 0 && remain < size ) - fprintf(stderr,"** znzwrite: write short by %u bytes\n",(unsigned)remain); - - return nmemb - remain/size; /* return number of members processed */ - } -#endif - return fwrite(buf,size,nmemb,file->nzfptr); -} - -long znzseek(znzFile file, long offset, int whence) -{ - if (file==NULL) { return 0; } -#ifdef HAVE_ZLIB - if (file->zfptr!=NULL) return (long) gzseek(file->zfptr,offset,whence); -#endif - return fseek(file->nzfptr,offset,whence); -} - -int znzrewind(znzFile stream) -{ - if (stream==NULL) { return 0; } -#ifdef HAVE_ZLIB - /* On some systems, gzrewind() fails for uncompressed files. - Use gzseek(), instead. 10, May 2005 [rickr] - - if (stream->zfptr!=NULL) return gzrewind(stream->zfptr); - */ - - if (stream->zfptr!=NULL) return (int)gzseek(stream->zfptr, 0L, SEEK_SET); -#endif - rewind(stream->nzfptr); - return 0; -} - -long znztell(znzFile file) -{ - if (file==NULL) { return 0; } -#ifdef HAVE_ZLIB - if (file->zfptr!=NULL) return (long) gztell(file->zfptr); -#endif - return ftell(file->nzfptr); -} - -int znzputs(const char * str, znzFile file) -{ - if (file==NULL) { return 0; } -#ifdef HAVE_ZLIB - if (file->zfptr!=NULL) return gzputs(file->zfptr,str); -#endif - return fputs(str,file->nzfptr); -} - - -char * znzgets(char* str, int size, znzFile file) -{ - if (file==NULL) { return NULL; } -#ifdef HAVE_ZLIB - if (file->zfptr!=NULL) return gzgets(file->zfptr,str,size); -#endif - return fgets(str,size,file->nzfptr); -} - - -int znzflush(znzFile file) -{ - if (file==NULL) { return 0; } -#ifdef HAVE_ZLIB - if (file->zfptr!=NULL) return gzflush(file->zfptr,Z_SYNC_FLUSH); -#endif - return fflush(file->nzfptr); -} - - -int znzeof(znzFile file) -{ - if (file==NULL) { return 0; } -#ifdef HAVE_ZLIB - if (file->zfptr!=NULL) return gzeof(file->zfptr); -#endif - return feof(file->nzfptr); -} - - -int znzputc(int c, znzFile file) -{ - if (file==NULL) { return 0; } -#ifdef HAVE_ZLIB - if (file->zfptr!=NULL) return gzputc(file->zfptr,c); -#endif - return fputc(c,file->nzfptr); -} - - -int znzgetc(znzFile file) -{ - if (file==NULL) { return 0; } -#ifdef HAVE_ZLIB - if (file->zfptr!=NULL) return gzgetc(file->zfptr); -#endif - return fgetc(file->nzfptr); -} - -#if !defined (WIN32) -int znzprintf(znzFile stream, const char *format, ...) -{ - int retval=0; - char *tmpstr; - va_list va; - if (stream==NULL) { return 0; } - va_start(va, format); -#ifdef HAVE_ZLIB - if (stream->zfptr!=NULL) { - int size; /* local to HAVE_ZLIB block */ - size = strlen(format) + 1000000; /* overkill I hope */ - tmpstr = (char *)calloc(1, size); - if( tmpstr == NULL ){ - fprintf(stderr,"** ERROR: znzprintf failed to alloc %d bytes\n", size); - return retval; - } - vsprintf(tmpstr,format,va); - retval=gzprintf(stream->zfptr,"%s",tmpstr); - free(tmpstr); - } else -#endif - { - retval=vfprintf(stream->nzfptr,format,va); - } - va_end(va); - return retval; -} - -#endif diff --git a/Modules/ThirdParty/NIFTI/src/nifti/znzlib/znzlib.h b/Modules/ThirdParty/NIFTI/src/nifti/znzlib/znzlib.h deleted file mode 100644 index fb10ed94a7b..00000000000 --- a/Modules/ThirdParty/NIFTI/src/nifti/znzlib/znzlib.h +++ /dev/null @@ -1,122 +0,0 @@ -#ifndef _ZNZLIB_H_ -#define _ZNZLIB_H_ - -/* -znzlib.h (zipped or non-zipped library) - -***** This code is released to the public domain. ***** - -***** Author: Mark Jenkinson, FMRIB Centre, University of Oxford ***** -***** Date: September 2004 ***** - -***** Neither the FMRIB Centre, the University of Oxford, nor any of ***** -***** its employees imply any warranty of usefulness of this software ***** -***** for any purpose, and do not assume any liability for damages, ***** -***** incidental or otherwise, caused by any use of this document. ***** - -*/ - -/* - -This library provides an interface to both compressed (gzip/zlib) and -uncompressed (normal) file IO. The functions are written to have the -same interface as the standard file IO functions. - -To use this library instead of normal file IO, the following changes -are required: - - replace all instances of FILE* with znzFile - - change the name of all function calls, replacing the initial character - f with the znz (e.g. fseek becomes znzseek) - - add a third parameter to all calls to znzopen (previously fopen) - that specifies whether to use compression (1) or not (0) - - use znz_isnull rather than any (pointer == NULL) comparisons in the code - -NB: seeks for writable files with compression are quite restricted - -*/ - - -/*=================*/ -#ifdef __cplusplus -extern "C" { -#endif -/*=================*/ - -#include -#include -#include -#include - -/* include optional check for HAVE_FDOPEN here, from deleted config.h: - - uncomment the following line if fdopen() exists for your compiler and - compiler options -*/ -/* #define HAVE_FDOPEN */ - - -#ifdef HAVE_ZLIB -#if defined(ITKZLIB) && !defined(ITK_USE_SYSTEM_ZLIB) -#include "itk_zlib.h" -#else -#include "zlib.h" -#endif -#endif - -struct znzptr { - int withz; - FILE* nzfptr; -#ifdef HAVE_ZLIB - gzFile zfptr; -#endif -} ; - -/* the type for all file pointers */ -typedef struct znzptr * znzFile; - - -/* int znz_isnull(znzFile f); */ -/* int znzclose(znzFile f); */ -#define znz_isnull(f) ((f) == NULL) -#define znzclose(f) Xznzclose(&(f)) - -/* Note extra argument (use_compression) where - use_compression==0 is no compression - use_compression!=0 uses zlib (gzip) compression -*/ - -znzFile znzopen(const char *path, const char *mode, int use_compression); - -znzFile znzdopen(int fd, const char *mode, int use_compression); - -int Xznzclose(znzFile * file); - -size_t znzread(void* buf, size_t size, size_t nmemb, znzFile file); - -size_t znzwrite(const void* buf, size_t size, size_t nmemb, znzFile file); - -long znzseek(znzFile file, long offset, int whence); - -int znzrewind(znzFile stream); - -long znztell(znzFile file); - -int znzputs(const char *str, znzFile file); - -char * znzgets(char* str, int size, znzFile file); - -int znzputc(int c, znzFile file); - -int znzgetc(znzFile file); - -#if !defined(WIN32) -int znzprintf(znzFile stream, const char *format, ...); -#endif - -/*=================*/ -#ifdef __cplusplus -} -#endif -/*=================*/ - -#endif