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ocommowiocommowi
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Merge pull request #54 from ocommowi/lesion-evolution
Add lesion evolution detection tool
2 parents 96779d3 + bad4e34 commit 870558c

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‎Anima/segmentation/validation_tools/CMakeLists.txt‎

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add_subdirectory(detected_components)
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add_subdirectory(dice_measure)
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add_subdirectory(lesion_evolution_detection)
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add_subdirectory(segmentation_performance_analyzer)

‎Anima/segmentation/validation_tools/lesion_evolution_detection/CMakeLists.txt‎

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if(BUILD_TOOLS)
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project(animaLesionEvolutionDetection)
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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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## #############################################################################
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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/segmentation/validation_tools/lesion_evolution_detection/animaLesionEvolutionDetection.cxx‎

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#include <animaReadWriteFunctions.h>
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#include <itkConnectedComponentImageFilter.h>
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#include <itkRelabelComponentImageFilter.h>
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#include <itkImageRegionIterator.h>
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#include <itkMultiThreader.h>
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#include <vnl/vnl_matrix.h>
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#include <tclap/CmdLine.h>
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#include <fstream>
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#include <algorithm>
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int main(int argc, char **argv)
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{
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TCLAP::CmdLine cmd("Computes from two segmentations the connected components that grew (L=3), were already there (L=1), or are new (L=2).\n INRIA / IRISA - VisAGeS/Empenn Team", ' ', ANIMA_VERSION);
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TCLAP::ValueArg <std::string> refArg("r", "ref", "Reference binary segmentation", true, "", "reference segmentation", cmd);
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TCLAP::ValueArg <std::string> testArg("t", "test", "Test binary segmentation", true, "", "test segmentation", cmd);
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TCLAP::ValueArg <std::string> outArg("o", "out", "output image with labeled lesions", true, "", "output labeled lesions", cmd);
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TCLAP::ValueArg <double> alphaArg("a", "alpha", "Alpha threshold (in between 0 and 1, default: 0)", false, 0, "alpha threshold", cmd);
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TCLAP::ValueArg <double> gammaArg("g", "gamma", "Gamma threshold (*100 %, default: 0.5)", false, 0.5, "gamma threshold", cmd);
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TCLAP::ValueArg <double> betaArg("b", "beta", "Beta threshold (in between 0 and 1, default: 0.05)", false, 0.05, "beta threshold", cmd);
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TCLAP::ValueArg <unsigned int> minVolumeArg("m", "min-vol", "Minimal volume for the component to be considered (default: 3 mm3)", false, 3, "minimal volume", cmd);
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TCLAP::ValueArg <unsigned int> nbpArg("T","numberofthreads","Number of threads to run on (default : all cores)",false,itk::MultiThreader::GetGlobalDefaultNumberOfThreads(),"number of threads",cmd);
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TCLAP::SwitchArg fullConnectArg("F","full-connect","Use 26-connectivity instead of 6-connectivity",cmd,false);
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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 EXIT_FAILURE;
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}
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typedef itk::Image <unsigned short, 3> ImageType;
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typedef itk::ImageRegionIterator <ImageType> ImageIteratorType;
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ImageType::Pointer refSegmentation = anima::readImage <ImageType> (refArg.getValue());
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ImageType::Pointer testSegmentation = anima::readImage <ImageType> (testArg.getValue());
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typedef itk::ConnectedComponentImageFilter <ImageType, ImageType> CCFilterType;
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typedef itk::RelabelComponentImageFilter <ImageType, ImageType> RelabelComponentFilterType;
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CCFilterType::Pointer refCCFilter = CCFilterType::New();
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refCCFilter->SetInput(refSegmentation);
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refCCFilter->SetFullyConnected(fullConnectArg.isSet());
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refCCFilter->SetNumberOfThreads(nbpArg.getValue());
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refCCFilter->Update();
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ImageType::SpacingType spacing = refSegmentation->GetSpacing();
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ImageType::SpacingValueType spacingTot = spacing[0];
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for (unsigned int i = 1;i < 3;++i)
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spacingTot *= spacing[i];
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// Compute minsize in voxels
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unsigned int minSizeInVoxel = static_cast <unsigned int> (std::ceil(minVolumeArg.getValue() / spacingTot));
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// Remove too small reference objects
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RelabelComponentFilterType::Pointer relabelRefFilter = RelabelComponentFilterType::New();
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relabelRefFilter->SetInput(refCCFilter->GetOutput());
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relabelRefFilter->SetMinimumObjectSize(minSizeInVoxel);
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relabelRefFilter->SetNumberOfThreads(nbpArg.getValue());
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relabelRefFilter->Update();
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// Reference segmentation is now labeled per connected objects
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refSegmentation = relabelRefFilter->GetOutput();
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refSegmentation->DisconnectPipeline();
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CCFilterType::Pointer testCCFilter = CCFilterType::New();
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testCCFilter->SetInput(testSegmentation);
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testCCFilter->SetFullyConnected(fullConnectArg.isSet());
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testCCFilter->SetNumberOfThreads(nbpArg.getValue());
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testCCFilter->Update();
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// Remove too small test objects
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RelabelComponentFilterType::Pointer relabelTestFilter = RelabelComponentFilterType::New();
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relabelTestFilter->SetInput(testCCFilter->GetOutput());
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relabelTestFilter->SetMinimumObjectSize(minSizeInVoxel);
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relabelTestFilter->SetNumberOfThreads(nbpArg.getValue());
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relabelTestFilter->Update();
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// Test segmentation is now labeled per connected objects
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testSegmentation = relabelTestFilter->GetOutput();
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testSegmentation->DisconnectPipeline();
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ImageIteratorType testItr(testSegmentation, testSegmentation->GetLargestPossibleRegion());
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unsigned short maxTestLabel = 0;
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while (!testItr.IsAtEnd())
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{
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if (testItr.Get() > maxTestLabel)
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maxTestLabel = testItr.Get();
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++testItr;
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}
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++maxTestLabel;
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ImageIteratorType refItr(refSegmentation, refSegmentation->GetLargestPossibleRegion());
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std::vector <unsigned int> labelsOverlap(maxTestLabel,0);
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std::vector <unsigned int> labelsNonOverlapping(maxTestLabel,0);
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std::vector <unsigned int> labelsSizes(maxTestLabel,0);
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ImageType::Pointer subImage = ImageType::New();
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subImage->Initialize();
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subImage->SetRegions(testSegmentation->GetLargestPossibleRegion());
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subImage->SetSpacing (testSegmentation->GetSpacing());
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subImage->SetOrigin (testSegmentation->GetOrigin());
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subImage->SetDirection (testSegmentation->GetDirection());
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subImage->Allocate();
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ImageIteratorType subItr(subImage,testSegmentation->GetLargestPossibleRegion());
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testItr.GoToBegin();
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while (!refItr.IsAtEnd())
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{
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if (refItr.Get() != 0)
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labelsOverlap[testItr.Get()]++;
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else
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labelsNonOverlapping[testItr.Get()]++;
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labelsSizes[testItr.Get()]++;
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++refItr;
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++testItr;
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}
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std::cout << "Processing " << maxTestLabel << " lesions in second timepoint..." << std::endl;
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for (unsigned int i = 1;i < maxTestLabel;++i)
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{
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testItr.GoToBegin();
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double ratioNonOverlapOverlap = static_cast <double> (labelsNonOverlapping[i]) / labelsOverlap[i];
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// Shrinking or not enough change -> label = maxTestLabel + 1
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if ((labelsNonOverlapping[i] <= minSizeInVoxel) || (ratioNonOverlapOverlap <= betaArg.getValue()))
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{
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while (!testItr.IsAtEnd())
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{
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if (testItr.Get() == i)
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testItr.Set(maxTestLabel + 1);
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++testItr;
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}
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continue;
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}
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// New lesion -> put it all as new -> label = maxTestLabel + 2
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double ratioOverlapSizes = static_cast <double> (labelsOverlap[i]) / labelsSizes[i];
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if (ratioOverlapSizes <= alphaArg.getValue())
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{
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while (!testItr.IsAtEnd())
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{
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if (testItr.Get() == i)
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testItr.Set(maxTestLabel + 2);
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++testItr;
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}
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continue;
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}
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// Test for growing lesion too large
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if (ratioNonOverlapOverlap > gammaArg.getValue())
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{
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// New lesion -> label = maxTestLabel + 2
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while (!testItr.IsAtEnd())
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{
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if (testItr.Get() == i)
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testItr.Set(maxTestLabel + 2);
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++testItr;
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}
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continue;
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}
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// We are looking at a growing lesion -> label = maxTestLabel + 3
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subImage->FillBuffer(0);
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refItr.GoToBegin();
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subItr.GoToBegin();
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while (!testItr.IsAtEnd())
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{
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if ((testItr.Get() == i)&&(refItr.Get() == 0))
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subItr.Set(1);
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++testItr;
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++refItr;
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++subItr;
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}
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CCFilterType::Pointer tmpCCFilter = CCFilterType::New();
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tmpCCFilter->SetInput(subImage);
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tmpCCFilter->SetFullyConnected(fullConnectArg.isSet());
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tmpCCFilter->SetNumberOfThreads(nbpArg.getValue());
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tmpCCFilter->Update();
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// Remove too small test objects
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RelabelComponentFilterType::Pointer relabelTmpCCFilter = RelabelComponentFilterType::New();
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relabelTmpCCFilter->SetInput(tmpCCFilter->GetOutput());
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relabelTmpCCFilter->SetMinimumObjectSize(0);
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relabelTmpCCFilter->SetNumberOfThreads(nbpArg.getValue());
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relabelTmpCCFilter->Update();
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ImageIteratorType subCCItr(relabelTmpCCFilter->GetOutput(),testSegmentation->GetLargestPossibleRegion());
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std::vector <unsigned int> numVoxelsCCSub(1);
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while (!subCCItr.IsAtEnd())
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{
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unsigned int currentSize = numVoxelsCCSub.size();
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unsigned int value = subCCItr.Get();
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if (value >= currentSize)
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{
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numVoxelsCCSub.resize(value + 1);
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for (unsigned int j = currentSize;j <= value;++j)
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numVoxelsCCSub[j] = 0;
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}
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numVoxelsCCSub[value]++;
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++subCCItr;
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}
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unsigned int numSubLabels = numVoxelsCCSub.size() - 1;
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double ratioOverlap = static_cast <double> (numVoxelsCCSub[numSubLabels]) / labelsOverlap[i];
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bool okGrowing = (ratioOverlap > betaArg.getValue());
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refItr.GoToBegin();
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testItr.GoToBegin();
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if (okGrowing)
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{
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while (!refItr.IsAtEnd())
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{
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if (testItr.Get() == i)
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{
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if (refItr.Get() == 0)
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testItr.Set(maxTestLabel + 3);
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else
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testItr.Set(maxTestLabel + 1);
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}
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++refItr;
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++testItr;
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}
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}
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else
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{
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// Non growing lesion, setting to
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while (!testItr.IsAtEnd())
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{
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if (testItr.Get() == i)
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testItr.Set(maxTestLabel + 1);
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++testItr;
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}
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}
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}
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testItr.GoToBegin();
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while (!testItr.IsAtEnd())
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{
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unsigned int value = testItr.Get();
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if (value > 0)
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testItr.Set(value - maxTestLabel);
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++testItr;
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}
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std::cout << "Writing output to " << outArg.getValue() << std::endl;
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anima::writeImage <ImageType> (outArg.getValue(),testSegmentation);
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return EXIT_SUCCESS;
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}
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‎superbuild/BinariesPackaging.cmake.in‎

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@@ -41,6 +41,7 @@ set(BINARY_TOOLS_LIST
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animaInfluenceZones
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animaIsosurface
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animaKMeansClustering
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animaLesionEvolutionDetection
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animaLinearTransformArithmetic
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animaLinearTransformToSVF
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animaLocalPatchCovarianceDistance

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