WIP: Attempt to cross-compile PolySeg for use on the Web

web/Docker/Dockerfile

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+#FROM kitware/itk-js-vtk:latest
+FROM insighttoolkit/itk-js:latest
+MAINTAINER PerkLab
+
+WORKDIR /
+
+#2019-01-03 + Emscripten patches
+ENV VTK_GIT_TAG acd6ccd796c511acdafc9c2ff2f2135f1a8900cc
+RUN git clone https://github.com/swederik/VTK.git && \
+  cd VTK && \
+  git checkout ${VTK_GIT_TAG} && \
+  cd ../ && \
+  mkdir VTK-build && \
+  cd VTK-build && \
+  cmake \
+    -G Ninja \
+    -DCMAKE_BUILD_TYPE:STRING=Release \
+    -DBUILD_SHARED_LIBS:BOOL=OFF \
+    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE} \
+    -DCMAKE_INSTALL_PREFIX:PATH=/install-prefix \
+    -DBUILD_EXAMPLES:BOOL=OFF \
+    -DBUILD_TESTING:BOOL=OFF \
+    -DVTK_RENDERING_BACKEND:STRING=None \
+    -DModule_vtkIOExport:BOOL=ON \
+    -DVTK_NO_PLATFORM_SOCKETS:BOOL=ON \
+    -DCMAKE_USE_PTHREADS_INIT:BOOL=OFF \
+    ../VTK && \
+  ninja -j7 && \
+  find . -name '*.o' -delete && \
+  cd .. && chmod -R 777 VTK-build
+
+# 2019-01-27
+ENV ITKVtkGlue_GIT_TAG 6f3cd6fd697ec19ee12b65041537594bf295c0ca
+RUN git clone https://github.com/InsightSoftwareConsortium/ITKVtkGlue.git && \
+  cd ITKVtkGlue && \
+  git checkout ${ITKVtkGlue_GIT_TAG} && \
+  cd ../ && \
+  mkdir ITKVtkGlue-build && \
+  cd ITKVtkGlue-build && \
+  cmake \
+    -G Ninja \
+    -DCMAKE_BUILD_TYPE:STRING=Release \
+    -DBUILD_SHARED_LIBS:BOOL=OFF \
+    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE} \
+    -DCMAKE_INSTALL_PREFIX:PATH=/install-prefix \
+    -DBUILD_TESTING:BOOL=OFF \
+    -DITK_DIR:PATH=/ITK-build \
+    -DVTK_DIR:PATH=/VTK-build \
+    ../ITKVtkGlue && \
+  ninja -j7 && \
+  find . -name '*.o' -delete && \
+  cd .. && chmod -R 777 ITK-build
+
+# 2019-03-11
+ENV PolySeg_GIT_TAG 74f1665a5c2d15e22d57e3a44821ad1c15b739aa
+RUN git clone https://github.com/PerkLab/PolySeg.git && \
+  cd PolySeg && \
+  git checkout ${PolySeg_GIT_TAG} && \
+  cd ../ && \
+  mkdir PolySeg-build && \
+  cd PolySeg-build && \
+  cmake \
+    -DCMAKE_BUILD_TYPE:STRING=Release \
+    -DBUILD_SHARED_LIBS:BOOL=OFF \
+    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE} \
+    -DCMAKE_INSTALL_PREFIX:PATH=/install-prefix \
+    -DBUILD_TESTING:BOOL=OFF \
+    -DVTK_DIR:PATH=/VTK-build \
+    ../PolySeg && \
+  make && \
+  make install && \
+  cd .. && chmod -R 777 PolySeg-build
+
+COPY ITKBridgeJavaScript.cmake /usr/share/cmake-3.13/Modules/
+
+RUN ls /install-prefix/lib/PolySeg/
+
+ARG IMAGE=ohif/polyseg-web
+ARG VERSION=latest
+ENV DEFAULT_DOCKCROSS_IMAGE ${IMAGE}:${VERSION}
+WORKDIR /work

web/Docker/ITKBridgeJavaScript.cmake

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+function(web_add_executable target_name)
+  add_executable(${target_name} ${ARGN})
+  set_property(TARGET ${target_name} APPEND_STRING
+    PROPERTY LINK_FLAGS " -s WASM=0 -s ASSERTIONS=1 -s ERROR_ON_UNDEFINED_SYMBOLS=0 -s ALLOW_MEMORY_GROWTH=1 -s NO_EXIT_RUNTIME=1 -s INVOKE_RUN=0 --pre-js /ITKBridgeJavaScript/src/EmscriptenModule/itkJSPipelinePre.js --post-js /ITKBridgeJavaScript/src/EmscriptenModule/itkJSPost.js"
+    )
+  set_property(TARGET ${target_name} APPEND_STRING
+    PROPERTY LINK_FLAGS_DEBUG " -s DISABLE_EXCEPTION_CATCHING=0"
+    )
+
+  set(wasm_target_name ${target_name}Wasm)
+  add_executable(${wasm_target_name} ${ARGN})
+  set(pre_js ${CMAKE_CURRENT_BINARY_DIR}/itkJSPipelinePre${target_name}.js)
+  configure_file(/ITKBridgeJavaScript/src/EmscriptenModule/itkJSPipelinePre.js.in
+    ${pre_js} @ONLY)
+  set_property(TARGET ${wasm_target_name} APPEND_STRING
+    PROPERTY LINK_FLAGS " -s BINARYEN_ASYNC_COMPILATION=0 -s SINGLE_FILE=1 -s WASM=1 -s ASSERTIONS=1 -s ALLOW_MEMORY_GROWTH=1 -s ERROR_ON_UNDEFINED_SYMBOLS=0 -s NO_EXIT_RUNTIME=1 -s INVOKE_RUN=0 --pre-js ${pre_js} --post-js /ITKBridgeJavaScript/src/EmscriptenModule/itkJSPost.js"
+    )
+  set_property(TARGET ${wasm_target_name} APPEND_STRING
+    PROPERTY LINK_FLAGS_DEBUG " -s DISABLE_EXCEPTION_CATCHING=0"
+    )
+endfunction()
+
+function(web_target_link_libraries target_name)
+  target_link_libraries(${target_name} ${ARGN})
+
+  set(wasm_target_name ${target_name}Wasm)
+  target_link_libraries(${wasm_target_name} ${ARGN})
+endfunction()

web/README.md

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+### Build the Docker image for cross-compilation
+
+The image is based on `kitware/itk-js-vtk`
+
+```bash
+# Docker needs to be running...
+docker build -t ohif/polyseg-web .
+```
+
+### Run the build
+
+```bash
+cd helloPolySeg
+npm install
+npx itk-js build --image ohif/polyseg-web:latest .
+```
+
+#### TODO:
+- [ ] Weird that I have to clone the src into /src under helloPolySegsub

web/binaryLabelmapToClosedSurface/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.10)
+project(BinaryLabelmapToClosedSurface)
+
+if(EMSCRIPTEN)
+  find_package(VTK REQUIRED
+    COMPONENTS
+      vtkCommonCore
+      vtkCommonDataModel
+      vtkImagingCore
+      vtkImagingSources
+      vtkFiltersGeometry
+      vtkImagingStatistics
+      vtkImagingStencil
+      vtkIOExport
+    )
+else()
+  find_package(VTK REQUIRED)
+endif()
+
+include(${VTK_USE_FILE})
+
+set(io_components ITKImageIO)
+if(EMSCRIPTEN)
+  set(io_components BridgeJavaScript)
+endif()
+
+if(EMSCRIPTEN)
+  find_package(ITK REQUIRED
+    COMPONENTS
+      ITKIOMeshBase
+      ITKVtkGlue
+      ${io_components}
+    )
+else()
+  find_package(ITK REQUIRED
+    COMPONENTS
+      ${io_components}
+    )
+endif()
+
+include(${ITK_USE_FILE})
+
+set(hello_SRCS binaryLabelmapToClosedSurface.cxx)
+
+if(EMSCRIPTEN)
+  include(ITKBridgeJavaScript)
+  web_add_executable(hello ${hello_SRCS})
+  web_target_link_libraries(hello ${ITK_LIBRARIES} ${VTK_LIBRARIES} /install-prefix/lib/PolySeg/libPolySeg.a)
+else()
+  add_executable(hello ${hello_SRCS})
+  target_link_libraries(hello ${ITK_LIBRARIES} ${VTK_LIBRARIES} /install-prefix/lib/PolySeg/libPolySeg.a)
+endif()
+
+enable_testing()
+add_test(NAME binaryLabelmapToClosedSurface
+  COMMAND binaryLabelmapToClosedSurface ${CMAKE_CURRENT_BINARY_DIR}/Segmentation-label.nii 
+  ${CMAKE_CURRENT_BINARY_DIR}/Segmentation.vtk.json
+  )

web/binaryLabelmapToClosedSurface/PolySegConfigure.h

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+/*
+ * Here is where system computed values get stored.
+ * These values should only change when the target compile platform changes.
+ */
+
+/* #undef BUILD_SHARED_LIBS */
+#ifndef BUILD_SHARED_LIBS
+#define PolySeg_STATIC
+#endif
+
+#if defined(WIN32) && !defined(PolySeg_STATIC)
+#pragma warning ( disable : 4275 )
+
+#if defined(PolySeg_EXPORT)
+#define PolySeg_EXPORT __declspec( dllexport )
+#else
+#define PolySeg_EXPORT __declspec( dllimport )
+#endif
+#else
+#define PolySeg_EXPORT
+#endif

web/binaryLabelmapToClosedSurface/binaryLabelmapToClosedSurface.cxx

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+/*==============================================================================
+
+  Copyright (c) Laboratory for Percutaneous Surgery (PerkLab)
+  Queen's University, Kingston, ON, Canada. All Rights Reserved.
+
+  See https://opensource.org/licenses/BSD-2-Clause for details.
+
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License.
+
+  This file was originally developed by Csaba Pinter, PerkLab, Queen's University
+  and was supported through the Applied Cancer Research Unit program of Cancer Care
+  Ontario with funds provided by the Ontario Ministry of Health and Long-Term Care
+
+==============================================================================*/
+#include <iostream>
+#include "itkImage.h"
+#include "itkImageFileReader.h"
+#include "itkImageToVTKImageFilter.h"
+
+// VTK includes
+#include "vtkPolyData.h"
+#include "vtkImageData.h"
+#include "vtkJSONDataSetWriter.h"
+#include "vtkNew.h"
+#include "vtkSphereSource.h"
+
+// SegmentationCore includes
+#include "vtkSegmentation.h"
+#include "vtkSegment.h"
+#include "vtkSegmentationConverter.h"
+#include "vtkOrientedImageData.h"
+#include "vtkSegmentationConverterFactory.h"
+#include "vtkBinaryLabelmapToClosedSurfaceConversionRule.h"
+#include "vtkClosedSurfaceToBinaryLabelmapConversionRule.h"
+
+//----------------------------------------------------------------------------
+int main( int argc, char * argv[] )
+{
+  std::cout << __LINE__ << argv << std::endl;
+  std::cout << __LINE__ << argc << std::endl;
+  if( argc < 2 )
+  {
+    std::cerr << "Usage: " << argv[0] << " <inputImage> <outputPolyData>" << std::endl;
+    //return EXIT_FAILURE;
+  }
+  const char * inputFilename = argv[1];
+  const char * outputFilename = argv[2];
+
+  using PixelType = unsigned char;
+  constexpr unsigned int Dimension = 3;
+  using ImageType = itk::Image< PixelType, Dimension >;
+
+  using ReaderType = itk::ImageFileReader< ImageType >;
+  ReaderType::Pointer reader = ReaderType::New();
+  reader->SetFileName( inputFilename );
+
+  using FilterType = itk::ImageToVTKImageFilter< ImageType >;
+  FilterType::Pointer filter = FilterType::New();
+  filter->SetInput( reader->GetOutput() );
+
+  vtkSegmentationConverterFactory::GetInstance()->RegisterConverterRule(
+    vtkSmartPointer<vtkBinaryLabelmapToClosedSurfaceConversionRule>::New() );
+  vtkSegmentationConverterFactory::GetInstance()->RegisterConverterRule(
+    vtkSmartPointer<vtkClosedSurfaceToBinaryLabelmapConversionRule>::New() );
+
+  // Create new one because by default the direction is identity, origin is zeros and spacing is ones
+  vtkImageData * myvtkImageData = filter->GetOutput();
+  vtkNew<vtkOrientedImageData> imageData;
+  //imageData->SetExtent(vtkImageData->GetExtent);
+  imageData->AllocateScalars(VTK_UNSIGNED_CHAR, 1);
+  imageData->DeepCopy(myvtkImageData);
+  imageData->Print(std::cout);
+
+
+  //imageData->SetExtent(0,size-1,0,size,0,size-1);
+  //imageData->AllocateScalars(VTK_UNSIGNED_CHAR, 1);
+
+  // Create a segment
+  vtkNew<vtkSegment> segment;
+  segment->SetName("inputImage");
+  segment->AddRepresentation(
+    vtkSegmentationConverter::GetSegmentationBinaryLabelmapRepresentationName(), imageData.GetPointer());
+  if (!segment->GetRepresentation(vtkSegmentationConverter::GetSegmentationBinaryLabelmapRepresentationName()))
+    {
+    std::cerr << __LINE__ << ": Failed to add binary labelmap representation to segment!" << std::endl;
+    return EXIT_FAILURE;
+  }
+
+  // Create segmentation with segment
+  vtkNew<vtkSegmentation> segmentation;
+  segmentation->SetMasterRepresentationName(
+    vtkSegmentationConverter::GetSegmentationBinaryLabelmapRepresentationName() );
+  segmentation->AddSegment(segment.GetPointer());
+  if (segmentation->GetNumberOfSegments() != 1)
+  {
+    std::cerr << __LINE__ << ": Failed to add segment to segmentation!" << std::endl;
+    return EXIT_FAILURE;
+  }
+
+  // Convert to closed surface model
+  segmentation->CreateRepresentation(vtkSegmentationConverter::GetSegmentationClosedSurfaceRepresentationName());
+  vtkPolyData* closedSurfaceModel = vtkPolyData::SafeDownCast(
+    segment->GetRepresentation(vtkSegmentationConverter::GetSegmentationClosedSurfaceRepresentationName()) );
+  if (!closedSurfaceModel)
+  {
+    std::cerr << __LINE__ << ": Failed to convert binary labelmap representation to closed surface model!" << std::endl;
+    return EXIT_FAILURE;
+  }
+
+  std::cout << "ClosedSurfaceModel: " << closedSurfaceModel->GetBounds() << std::endl;
+  closedSurfaceModel->Print(std::cout);
+
+  vtkNew<vtkSphereSource> sphere;
+  sphere->SetCenter(0.0, 0.0, 0.0);
+  sphere->SetRadius(5.0);
+
+  // Create the output writer
+  vtkNew<vtkJSONDataSetWriter> writer;
+  writer->SetFileName(outputFilename);
+  //writer->SetInputData(sphere);
+  //writer->SetInputConnection(sphere->GetOutputPort());
+  writer->SetInputData(closedSurfaceModel);
+
+  try
+    {
+    writer->Update();
+    std::cout << "Written to: " << outputFilename << std::endl;
+    }
+  catch( const std::exception & error )
+    {
+    std::cerr << "Error: " << error.what() << std::endl;
+    return EXIT_FAILURE;
+    }
+
+  return EXIT_SUCCESS;
+}
+

web/binaryLabelmapToClosedSurface/example/README.md

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+itk-webpack-example
+===================
+
+This example demonstrates how to configure Webpack to build a project that
+uses [itk.js](https://insightsoftwareconsortium.github.io/itk-js/).
+More information can be found in the [example
+documentation](https://insightsoftwareconsortium.github.io/itk-js/examples/webpack.html).
+
+## Run Locally
+
+```
+npm install
+npm run start
+```
+
+And visit [http://localhost:8080/](http://localhost:8080/).
+
+## Development
+
+```
+npm install
+npm run build
+npm test
+```