diff --git a/Anima/math-tools/common_tools/CMakeLists.txt b/Anima/math-tools/common_tools/CMakeLists.txt index 4a0a3b040..34de43f19 100644 --- a/Anima/math-tools/common_tools/CMakeLists.txt +++ b/Anima/math-tools/common_tools/CMakeLists.txt @@ -7,4 +7,5 @@ add_subdirectory(convert_image) add_subdirectory(convert_shape) add_subdirectory(merge_block_images) 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..6de93ddeb --- /dev/null +++ b/Anima/math-tools/common_tools/image_to_mask/animaImageToMask.cxx @@ -0,0 +1,108 @@ +#include +#include +#include + +#include +#include +#include + +#include + +int main(int argc, char **argv) +{ + TCLAP::CmdLine cmd("INRIA / IRISA - VisAGeS/Empenn Team", ' ',ANIMA_VERSION); + + TCLAP::ValueArg inArg("i","inputfile","input image",true,"","input image",cmd); + TCLAP::ValueArg outArg("o","outputfile","output mask",true,"","output mask",cmd); + + try + { + cmd.parse(argc,argv); + } + catch (TCLAP::ArgException& e) + { + std::cerr << "Error: " << e.error() << "for argument " << e.argId() << std::endl; + return(1); + } + + typedef itk::Image ImageType; + typedef itk::Image Image4DType; + typedef itk::VectorImage VectorImageType; + + itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(inArg.getValue().c_str(), + itk::IOFileModeEnum::ReadMode); + + imageIO->SetFileName(inArg.getValue()); + imageIO->ReadImageInformation(); + + bool vectorImage = (imageIO->GetNumberOfComponents() > 1); + + if (vectorImage) + { + // Vectorial case + VectorImageType::Pointer image = anima::readImage (inArg.getValue()); + + ImageType::Pointer outImage = ImageType::New(); + outImage->Initialize(); +// outImage->SetNumberOfComponentsPerPixel(image->GetNumberOfComponentsPerPixel()); + outImage->SetDirection(image->GetDirection()); + outImage->SetSpacing(image->GetSpacing()); + outImage->SetOrigin(image->GetOrigin()); + + VectorImageType::RegionType region = image->GetLargestPossibleRegion(); + outImage->SetRegions(region); + outImage->Allocate(); + + VectorImageType::PixelType zeroVec(image->GetNumberOfComponentsPerPixel()); + zeroVec.Fill(0); + + itk::ImageRegionIterator inItr(image,region); + itk::ImageRegionIterator outItr(outImage,outImage->GetLargestPossibleRegion()); + + while (!outItr.IsAtEnd()) + { + if(inItr.Get() == zeroVec) + outItr.Set(0); + else + outItr.Set(1); + + ++inItr; + ++outItr; + } + + anima::writeImage (outArg.getValue(),outImage); + + return EXIT_SUCCESS; + } + + ImageType::Pointer image = anima::readImage (inArg.getValue()); + + ImageType::Pointer outImage = ImageType::New(); + outImage->Initialize(); + outImage->SetDirection(image->GetDirection()); + outImage->SetSpacing(image->GetSpacing()); + outImage->SetOrigin(image->GetOrigin()); + + ImageType::RegionType largestRegion = image->GetLargestPossibleRegion(); + outImage->SetRegions(largestRegion); + outImage->Allocate(); + outImage->FillBuffer(0.0); + + itk::ImageRegionIterator inItr(image,image->GetLargestPossibleRegion()); + itk::ImageRegionIterator outItr(outImage,outImage->GetLargestPossibleRegion()); + + while (!outItr.IsAtEnd()) + { + if(inItr.Get() == 0.0) + outItr.Set(0); + else + outItr.Set(1); + + ++inItr; + ++outItr; + } + + anima::writeImage (outArg.getValue(),outImage); + + return EXIT_SUCCESS; +}