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Gregoire-VGregoire-V
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Merge remote-tracking branch 'origin/master' into ShapeToDensityFeature
This merge to put image_to_mask feature inside ShapeToDensityFeature branch, to avoid conflicts later on.
2 parents 8cb68d0 + 9625d03 commit 6f16368

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‎Anima/diffusion/odf/tod_estimator/animaTODEstimatorImageFilter.hxx‎

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@@ -84,6 +84,20 @@ namespace anima
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for (int i = 0; i < nbPoints; i++)
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{
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DirType dir = GetFiberDirection(i, fiber);
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if(output->GetDirection()[0][0] > 0)
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{
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dir[0] *= -1;
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}
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if(output->GetDirection()[1][1] < 0)
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{
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dir[1] *= -1;
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}
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if(output->GetDirection()[2][2] < 0)
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{
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dir[2] *= -1;
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}
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PointType point = GetCenterVoxel(i, fiber);
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itk::Index<3> index;
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‎Anima/math-tools/common_tools/CMakeLists.txt‎

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Original file line numberDiff line numberDiff line change
@@ -8,4 +8,5 @@ add_subdirectory(convert_shape)
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add_subdirectory(merge_block_images)
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add_subdirectory(shapes_to_density)
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add_subdirectory(vectorize_images)
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add_subdirectory(image_to_mask)
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‎Anima/math-tools/common_tools/image_to_mask/CMakeLists.txt‎

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@@ -0,0 +1,35 @@
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if(BUILD_TOOLS)
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project(animaImageToMask)
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## #############################################################################
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## List Sources
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## #############################################################################
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list_source_files(${PROJECT_NAME}
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${CMAKE_CURRENT_SOURCE_DIR}
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)
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## add executable
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## #############################################################################
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add_executable(${PROJECT_NAME}
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${${PROJECT_NAME}_CFILES}
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)
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## #############################################################################
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## Link
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## #############################################################################
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target_link_libraries(${PROJECT_NAME}
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${ITKIO_LIBRARIES}
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)
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## #############################################################################
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## install
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## #############################################################################
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set_exe_install_rules(${PROJECT_NAME})
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endif()

‎Anima/math-tools/common_tools/image_to_mask/animaImageToMask.cxx‎

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@@ -0,0 +1,143 @@
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#include <tclap/CmdLine.h>
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#include <iostream>
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#include <string>
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#include <itkImage.h>
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#include <itkVectorImage.h>
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#include <itkImageRegionIterator.h>
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#include <animaReadWriteFunctions.h>
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/**
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* @brief Converts an input image (either vectorial or not) into a mask
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* The output mask will be 0 in the voxels where the input image is 0 (or a null vector) and 1 elsewhere
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*/
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int main(int argc, char **argv)
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{
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TCLAP::CmdLine cmd("INRIA / IRISA - VisAGeS/Empenn Team", ' ',ANIMA_VERSION);
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//Define arguments
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TCLAP::ValueArg<std::string> inArg("i","inputfile","input image",true,"","input image",cmd);
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TCLAP::ValueArg<std::string> outArg("o","outputfile","output mask",true,"","output mask",cmd);
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//Try to parse
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try
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{
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cmd.parse(argc,argv);
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}
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catch (TCLAP::ArgException& e)
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{
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std::cerr << "Error: " << e.error() << "for argument " << e.argId() << std::endl;
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return(1);
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}
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//Define types
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typedef itk::Image <double,3> ImageType;
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typedef itk::Image <double,4> Image4DType;
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typedef itk::VectorImage <double,3> VectorImageType;
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//Read input image
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itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(inArg.getValue().c_str(),
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itk::IOFileModeEnum::ReadMode);
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imageIO->SetFileName(inArg.getValue());
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imageIO->ReadImageInformation();
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//Initialize the output image (which is a mask) and allocate memory
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ImageType::Pointer outImage = ImageType::New();
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//Determine if the input image is a vector image (each voxel value is a vector) or not
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bool vectorImage = (imageIO->GetNumberOfComponents() > 1);
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if (vectorImage)
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{
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//Case of a vector image
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//Read input image and store in the correct format
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VectorImageType::Pointer image = anima::readImage <VectorImageType> (inArg.getValue());
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//Set the output image with the same properties as the input image
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outImage->Initialize();
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outImage->SetDirection(image->GetDirection());
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outImage->SetSpacing(image->GetSpacing());
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outImage->SetOrigin(image->GetOrigin());
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//Allocate the correct size for output image. region (image->GetLargestPossibleRegion()) is the whole image
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VectorImageType::RegionType region = image->GetLargestPossibleRegion();
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outImage->SetRegions(region);
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outImage->Allocate();
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//Create a vector with as many components as there are for each voxel, and with each component equal to 0
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VectorImageType::PixelType zeroVec(image->GetNumberOfComponentsPerPixel());
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zeroVec.Fill(0);
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//Create iterators on input and output images
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itk::ImageRegionIterator <VectorImageType> inItr(image,region);
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itk::ImageRegionIterator <ImageType> outItr(outImage,outImage->GetLargestPossibleRegion());
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//Main algorithm
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while (!outItr.IsAtEnd())
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{
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if(inItr.Get() == zeroVec)
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{
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//The voxel in the input image is a constant vector equal to 0, so this voxel in the output mask will be 0.
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outItr.Set(0);
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}
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else
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{
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//The voxel in the input image is not a constant vector equal to 0, so this voxel in the output mask will be 1.
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outItr.Set(1);
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}
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//Move to following voxel
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++inItr;
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++outItr;
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}
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}
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else
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{
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//Case of a non-vector image
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//Read input image and store in the correct format
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ImageType::Pointer image = anima::readImage <ImageType> (inArg.getValue());
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//Set the output image with the same properties as the input image
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outImage->Initialize();
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outImage->SetDirection(image->GetDirection());
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outImage->SetSpacing(image->GetSpacing());
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outImage->SetOrigin(image->GetOrigin());
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//Allocate the correct size for output image. largestRegion (image->GetLargestPossibleRegion()) is the whole image
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ImageType::RegionType largestRegion = image->GetLargestPossibleRegion();
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outImage->SetRegions(largestRegion);
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outImage->Allocate();
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outImage->FillBuffer(0.0);
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//Create iterators on input and output images
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itk::ImageRegionIterator <ImageType> inItr(image,image->GetLargestPossibleRegion());
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itk::ImageRegionIterator <ImageType> outItr(outImage,outImage->GetLargestPossibleRegion());
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//Main algorithm
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while (!outItr.IsAtEnd())
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{
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if(inItr.Get() == 0.0)
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{
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//The voxel in the input image is 0, so this voxel in the output mask will be 0.
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outItr.Set(0);
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}
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else
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{
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//The voxel in the input image is not 0, so this voxel in the output mask will be 1.
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outItr.Set(1);
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}
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//Move to following voxel
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++inItr;
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++outItr;
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}
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}
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//Write output image and exit
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anima::writeImage <ImageType> (outArg.getValue(),outImage);
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return EXIT_SUCCESS;
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}

‎superbuild/TCLAP.cmake‎

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@@ -2,7 +2,7 @@ set (proj TCLAP)
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set (location "")
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if (NOT DEFINED ${proj}_SRC_DIR)
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set(location URL https://netix.dl.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz)
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set(location URL https://sourceforge.net/projects/tclap/files/tclap-1.2.1.tar.gz/download)
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endif()
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ExternalProject_Add(${proj}

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