Merge branch 'develop' into master

.travis.yml

@@ -0,0 +1,51 @@
+language: cpp
+
+env:
+  global:
+    HOME_DIR=${TRAVIS_BUILD_DIR}/..
+    ELASTIX_SOURCE_DIR=${TRAVIS_BUILD_DIR}
+    ELASTIX_BUILD_DIR=${HOME_DIR}/elastix-build
+    ITK_URL=https://github.com/InsightSoftwareConsortium/ITK
+    ITK_SOURCE_DIR=${HOME_DIR}/ITK-source
+    ITK_BUILD_DIR=${HOME_DIR}/ITK-build
+    OMP_NUM_THREADS=2
+
+cache:
+  directories:
+    - ${ITK_SOURCE_DIR}
+    - ${ITK_BUILD_DIR}
+
+matrix:
+  include:
+    - os: linux
+      dist: trusty
+      sudo: required
+      compiler: clang
+    - os: linux
+      dist: trusty
+      sudo: required
+      compiler: gcc
+    - os: osx
+      compiler: clang
+    - os: osx
+      compiler: gcc
+
+before_script:
+  - mkdir -p ${ELASTIX_BUILD_DIR}
+
+script:
+  - if [[ ! -e ${ITK_BUILD_DIR}/ITKConfig.cmake ]]; then
+      rm -rf ${ITK_SOURCE_DIR} {ITK_BUILD_DIR} &&
+      git clone ${ITK_URL} ${ITK_SOURCE_DIR} &&
+      cd ${ITK_SOURCE_DIR} &&
+      git checkout v4.11.1 &&
+      mkdir -p ${ITK_BUILD_DIR} &&
+      cd ${ITK_BUILD_DIR} &&
+      cmake -DBUILD_EXAMPLES=OFF -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF -DITKGroup_IO:BOOL=ON -DModule_ITKDistanceMap:BOOL=ON -DModule_ITKImageFusion:BOOL=ON -DModule_ITKLabelMap:BOOL:=ON -DModule_ITKMathematicalMorphology:BOOL=ON -DModule_ITKOptimizers:BOOL=ON -DModule_ITKOptimizersv4:BOOL=ON -DModule_ITKRegistrationCommon:BOOL=ON -DModule_ITKVideoIO:BOOL=ON-DCMAKE_BUILD_TYPE=Release ${ITK_SOURCE_DIR} &&
+      make --jobs=4 && 
+      touch ${HOME}/built_cache; fi
+  - if [[ ! -e ${HOME_DIR}/built_cache ]]; then
+      cd ${ELASTIX_BUILD_DIR} &&
+      cmake -DITK_DIR=${ITK_BUILD_DIR} -DCMAKE_BUILD_TYPE=Release ${ELASTIX_SOURCE_DIR} &&
+      make --jobs=4 && 
+      ctest --jobs=4; fi

src/Common/CostFunctions/itkAdvancedImageToImageMetric.hxx

@@ -85,6 +85,7 @@ AdvancedImageToImageMetric< TFixedImage, TMovingImage >
 
   /** Threading related variables. */
   this->m_UseMetricSingleThreaded = true;
+  this->m_UseMultiThread = false;
   this->m_Threader->SetUseThreadPool( false ); // setting to true makes elastix hang
                                                // at a WaitForSingleMethodThread()
 

src/Common/itkImageMaskSpatialObject2.hxx

@@ -166,6 +166,13 @@ ImageMaskSpatialObject2< TDimension >
   ImagePointer image        = this->GetImage();
   PixelType    outsideValue = NumericTraits< PixelType >::Zero;
 
+  // Initialize index and size in case image only consists of background values.
+  for( unsigned int axis = 0; axis < ImageType::ImageDimension; ++axis )
+  {
+    index[ axis ] = 0;
+    size[ axis ] = 0;
+  }
+
   /** For 3D a smart implementation existed in the ITK already. */
   if( ImageType::ImageDimension == 3 )
   {

src/Core/Main/elastixlib.cxx

@@ -48,7 +48,8 @@ namespace elastix
 
 ELASTIX::ELASTIX() :
   m_ResultImage( 0 )
-{} // end Constructor
+{
+} // end Constructor
 
 
 /**
@@ -135,7 +136,8 @@ ELASTIX::RegisterImages(
   bool performLogging,
   bool performCout,
   ImagePointer fixedMask,
-  ImagePointer movingMask )
+  ImagePointer movingMask,
+  ObjectPointer transform)
 {
   /** Some typedef's. */
   typedef elx::ElastixMain                            ElastixMainType;
@@ -159,7 +161,7 @@ ELASTIX::RegisterImages(
   /** Some declarations and initialisations. */
   ElastixMainVectorType elastices;
 
-  ObjectPointer              transform            = 0;
+  //ObjectPointer              transform = 0;
   DataObjectContainerPointer fixedImageContainer  = 0;
   DataObjectContainerPointer movingImageContainer = 0;
   DataObjectContainerPointer fixedMaskContainer   = 0;

src/Core/Main/elastixlib.h

@@ -24,6 +24,8 @@
 #include <itkDataObject.h>
 #include "itkParameterFileParser.h"
 #include "elxMacro.h"
+#include "elxElastixMain.h"
+
 
 /********************************************************************************
  *                          *
@@ -47,6 +49,9 @@ class ELASTIXLIB_API ELASTIX
   typedef itk::ParameterFileParser::ParameterMapType                ParameterMapType;
   typedef std::vector< itk::ParameterFileParser::ParameterMapType > ParameterMapListType;
 
+  //typedefs for ObjectPointer
+  typedef elastix::ElastixMain::ObjectPointer              ObjectPointer;
+
   /**
    *  Constructor and destructor
    */
@@ -94,7 +99,8 @@ class ELASTIXLIB_API ELASTIX
     bool performLogging,
     bool performCout,
     ImagePointer fixedMask = 0,
-    ImagePointer movingMask = 0 );
+    ImagePointer movingMask = 0,
+    ObjectPointer transform = 0);
 
   /** Getter for result image. */
   ImagePointer GetResultImage( void );