diff --git a/Anima/diffusion/odf/tod_estimator/animaTODEstimatorImageFilter.hxx b/Anima/diffusion/odf/tod_estimator/animaTODEstimatorImageFilter.hxx index edfd168f6..47bd8692c 100644 --- a/Anima/diffusion/odf/tod_estimator/animaTODEstimatorImageFilter.hxx +++ b/Anima/diffusion/odf/tod_estimator/animaTODEstimatorImageFilter.hxx @@ -84,6 +84,20 @@ namespace anima for (int i = 0; i < nbPoints; i++) { DirType dir = GetFiberDirection(i, fiber); + if(output->GetDirection()[0][0] > 0) + { + dir[0] *= -1; + } + if(output->GetDirection()[1][1] < 0) + { + dir[1] *= -1; + } + if(output->GetDirection()[2][2] < 0) + { + dir[2] *= -1; + } + + PointType point = GetCenterVoxel(i, fiber); itk::Index<3> index; diff --git a/Anima/math-tools/common_tools/CMakeLists.txt b/Anima/math-tools/common_tools/CMakeLists.txt index 5b64b5c1b..63f091afb 100644 --- a/Anima/math-tools/common_tools/CMakeLists.txt +++ b/Anima/math-tools/common_tools/CMakeLists.txt @@ -8,4 +8,5 @@ add_subdirectory(convert_shape) add_subdirectory(merge_block_images) add_subdirectory(shapes_to_density) add_subdirectory(vectorize_images) +add_subdirectory(image_to_mask) diff --git a/Anima/math-tools/common_tools/image_to_mask/CMakeLists.txt b/Anima/math-tools/common_tools/image_to_mask/CMakeLists.txt new file mode 100644 index 000000000..29d3b7f66 --- /dev/null +++ b/Anima/math-tools/common_tools/image_to_mask/CMakeLists.txt @@ -0,0 +1,35 @@ +if(BUILD_TOOLS) + +project(animaImageToMask) + +## ############################################################################# +## List Sources +## ############################################################################# + +list_source_files(${PROJECT_NAME} + ${CMAKE_CURRENT_SOURCE_DIR} + ) + +## add executable +## ############################################################################# + +add_executable(${PROJECT_NAME} + ${${PROJECT_NAME}_CFILES} + ) + + +## ############################################################################# +## Link +## ############################################################################# + +target_link_libraries(${PROJECT_NAME} + ${ITKIO_LIBRARIES} + ) + +## ############################################################################# +## install +## ############################################################################# + +set_exe_install_rules(${PROJECT_NAME}) + +endif() diff --git a/Anima/math-tools/common_tools/image_to_mask/animaImageToMask.cxx b/Anima/math-tools/common_tools/image_to_mask/animaImageToMask.cxx new file mode 100644 index 000000000..dd2fc78b6 --- /dev/null +++ b/Anima/math-tools/common_tools/image_to_mask/animaImageToMask.cxx @@ -0,0 +1,143 @@ +#include +#include +#include + +#include +#include +#include + +#include + +/** + * @brief Converts an input image (either vectorial or not) into a mask + * The output mask will be 0 in the voxels where the input image is 0 (or a null vector) and 1 elsewhere + */ +int main(int argc, char **argv) +{ + TCLAP::CmdLine cmd("INRIA / IRISA - VisAGeS/Empenn Team", ' ',ANIMA_VERSION); + + //Define arguments + TCLAP::ValueArg inArg("i","inputfile","input image",true,"","input image",cmd); + TCLAP::ValueArg outArg("o","outputfile","output mask",true,"","output mask",cmd); + + //Try to parse + try + { + cmd.parse(argc,argv); + } + catch (TCLAP::ArgException& e) + { + std::cerr << "Error: " << e.error() << "for argument " << e.argId() << std::endl; + return(1); + } + + //Define types + typedef itk::Image ImageType; + typedef itk::Image Image4DType; + typedef itk::VectorImage VectorImageType; + + //Read input image + itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(inArg.getValue().c_str(), + itk::IOFileModeEnum::ReadMode); + + imageIO->SetFileName(inArg.getValue()); + imageIO->ReadImageInformation(); + + //Initialize the output image (which is a mask) and allocate memory + ImageType::Pointer outImage = ImageType::New(); + + //Determine if the input image is a vector image (each voxel value is a vector) or not + bool vectorImage = (imageIO->GetNumberOfComponents() > 1); + + if (vectorImage) + { + //Case of a vector image + + //Read input image and store in the correct format + VectorImageType::Pointer image = anima::readImage (inArg.getValue()); + + //Set the output image with the same properties as the input image + outImage->Initialize(); + outImage->SetDirection(image->GetDirection()); + outImage->SetSpacing(image->GetSpacing()); + outImage->SetOrigin(image->GetOrigin()); + + //Allocate the correct size for output image. region (image->GetLargestPossibleRegion()) is the whole image + VectorImageType::RegionType region = image->GetLargestPossibleRegion(); + outImage->SetRegions(region); + outImage->Allocate(); + + //Create a vector with as many components as there are for each voxel, and with each component equal to 0 + VectorImageType::PixelType zeroVec(image->GetNumberOfComponentsPerPixel()); + zeroVec.Fill(0); + + //Create iterators on input and output images + itk::ImageRegionIterator inItr(image,region); + itk::ImageRegionIterator outItr(outImage,outImage->GetLargestPossibleRegion()); + + //Main algorithm + while (!outItr.IsAtEnd()) + { + if(inItr.Get() == zeroVec) + { + //The voxel in the input image is a constant vector equal to 0, so this voxel in the output mask will be 0. + outItr.Set(0); + } + else + { + //The voxel in the input image is not a constant vector equal to 0, so this voxel in the output mask will be 1. + outItr.Set(1); + } + + //Move to following voxel + ++inItr; + ++outItr; + } + } + else + { + //Case of a non-vector image + + //Read input image and store in the correct format + ImageType::Pointer image = anima::readImage (inArg.getValue()); + + //Set the output image with the same properties as the input image + outImage->Initialize(); + outImage->SetDirection(image->GetDirection()); + outImage->SetSpacing(image->GetSpacing()); + outImage->SetOrigin(image->GetOrigin()); + + //Allocate the correct size for output image. largestRegion (image->GetLargestPossibleRegion()) is the whole image + ImageType::RegionType largestRegion = image->GetLargestPossibleRegion(); + outImage->SetRegions(largestRegion); + outImage->Allocate(); + outImage->FillBuffer(0.0); + + //Create iterators on input and output images + itk::ImageRegionIterator inItr(image,image->GetLargestPossibleRegion()); + itk::ImageRegionIterator outItr(outImage,outImage->GetLargestPossibleRegion()); + + //Main algorithm + while (!outItr.IsAtEnd()) + { + if(inItr.Get() == 0.0) + { + //The voxel in the input image is 0, so this voxel in the output mask will be 0. + outItr.Set(0); + } + else + { + //The voxel in the input image is not 0, so this voxel in the output mask will be 1. + outItr.Set(1); + } + + //Move to following voxel + ++inItr; + ++outItr; + } + } + + //Write output image and exit + anima::writeImage (outArg.getValue(),outImage); + return EXIT_SUCCESS; +} diff --git a/superbuild/TCLAP.cmake b/superbuild/TCLAP.cmake index 340021552..a665dafa5 100644 --- a/superbuild/TCLAP.cmake +++ b/superbuild/TCLAP.cmake @@ -2,7 +2,7 @@ set (proj TCLAP) set (location "") if (NOT DEFINED ${proj}_SRC_DIR) - set(location URL https://netix.dl.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz) + set(location URL https://sourceforge.net/projects/tclap/files/tclap-1.2.1.tar.gz/download) endif() ExternalProject_Add(${proj}