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Merge pull request #104 from MariePoirierGit/dirichlet_distribution
A dedicated library for statistical distributions
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37 changes: 37 additions & 0 deletions
37
Anima/diffusion/mcm_tools/mcm_merge_anisotropic_weights/CMakeLists.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| if(BUILD_TOOLS) | ||
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| project(animaMCMMergeAnisotropicWeights) | ||
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| ## ############################################################################# | ||
| ## List Sources | ||
| ## ############################################################################# | ||
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| list_source_files(${PROJECT_NAME} | ||
| ${CMAKE_CURRENT_SOURCE_DIR} | ||
| ) | ||
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| ## ############################################################################# | ||
| ## add executable | ||
| ## ############################################################################# | ||
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| add_executable(${PROJECT_NAME} | ||
| ${${PROJECT_NAME}_CFILES} | ||
| ) | ||
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| ## ############################################################################# | ||
| ## Link | ||
| ## ############################################################################# | ||
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| target_link_libraries(${PROJECT_NAME} | ||
| ${ITKIO_LIBRARIES} | ||
| AnimaMCM | ||
| ) | ||
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| ## ############################################################################# | ||
| ## install | ||
| ## ############################################################################# | ||
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| set_exe_install_rules(${PROJECT_NAME}) | ||
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| endif() |
106 changes: 106 additions & 0 deletions
106
Anima/diffusion/mcm_tools/mcm_merge_anisotropic_weights/animaMCMMergeAnisotropicWeights.cxx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,106 @@ | ||
| #include <animaMCMFileReader.h> | ||
| #include <animaMCMImage.h> | ||
| #include <animaMultiCompartmentModel.h> | ||
| #include <animaReadWriteFunctions.h> | ||
| #include <itkImageRegionConstIterator.h> | ||
| #include <itkImageRegionIterator.h> | ||
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| #include <tclap/CmdLine.h> | ||
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| int main(int argc, char **argv) | ||
| { | ||
| TCLAP::CmdLine cmd("INRIA / IRISA - VisAGeS/Empenn Team", ' ', ANIMA_VERSION); | ||
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| TCLAP::ValueArg<std::string> inArg("i", "inputfile", "Input MCM image", true, "", "input mcm image", cmd); | ||
| TCLAP::ValueArg<std::string> outArg("o", "outputfile", "Output image with combined anisotropic weights", true, "", "output conbined weight image", cmd); | ||
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| try | ||
| { | ||
| cmd.parse(argc,argv); | ||
| } | ||
| catch (TCLAP::ArgException& e) | ||
| { | ||
| std::cerr << "Error: " << e.error() << "for argument " << e.argId() << std::endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
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| using InputImageType = anima::MCMImage <double, 3>; | ||
| using OutputImageType = itk::VectorImage <double, 3>; | ||
| using InputPixelType = InputImageType::PixelType; | ||
| using OutputPixelType = OutputImageType::PixelType; | ||
| using MCModelType = anima::MultiCompartmentModel; | ||
| using MCModelPointer = MCModelType::Pointer; | ||
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| // Read input sample | ||
| anima::MCMFileReader <double, 3> mcmReader; | ||
| mcmReader.SetFileName(inArg.getValue()); | ||
| mcmReader.Update(); | ||
| InputImageType::Pointer mcmImage = mcmReader.GetModelVectorImage(); | ||
| MCModelPointer mcmPtr = mcmImage->GetDescriptionModel()->Clone(); | ||
| InputPixelType mcmValue; | ||
| unsigned int numCompartments = mcmPtr->GetNumberOfCompartments(); | ||
| unsigned int numIsoCompartments = mcmPtr->GetNumberOfIsotropicCompartments(); | ||
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| using InputImageIteratorType = itk::ImageRegionConstIterator <InputImageType>; | ||
| using OutputImageIteratorType = itk::ImageRegionIterator <OutputImageType>; | ||
| InputImageIteratorType inItr(mcmImage, mcmImage->GetLargestPossibleRegion()); | ||
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| // Initialize output image | ||
| unsigned int nbOutputComponents = numIsoCompartments + 1; | ||
| OutputImageType::Pointer outputImage = OutputImageType::New(); | ||
| outputImage->SetRegions(mcmImage->GetLargestPossibleRegion()); | ||
| outputImage->CopyInformation(mcmImage); | ||
| outputImage->SetVectorLength(nbOutputComponents); | ||
| outputImage->Allocate(); | ||
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| OutputPixelType outputValue(nbOutputComponents); | ||
| outputValue.Fill(0.0); | ||
| outputImage->FillBuffer(outputValue); | ||
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| std::cout << "- Number of compartments in input image: " << numCompartments << std::endl; | ||
| std::cout << "- Number of compartments in output image: " << nbOutputComponents << std::endl; | ||
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| OutputImageIteratorType outItr(outputImage, outputImage->GetLargestPossibleRegion()); | ||
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| while (!outItr.IsAtEnd()) | ||
| { | ||
| mcmValue = inItr.Get(); | ||
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| bool backgroundVoxel = true; | ||
| for (unsigned int i = 0;i < mcmValue.GetNumberOfElements();++i) | ||
| { | ||
| if (mcmValue[i] != 0.0) | ||
| { | ||
| backgroundVoxel = false; | ||
| break; | ||
| } | ||
| } | ||
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| if (backgroundVoxel) | ||
| { | ||
| ++inItr; | ||
| ++outItr; | ||
| continue; | ||
| } | ||
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| mcmPtr->SetModelVector(mcmValue); | ||
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| for (unsigned int i = 0;i < numIsoCompartments;++i) | ||
| outputValue[i] = mcmPtr->GetCompartmentWeight(i); | ||
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| double anisoWeight = 0.0; | ||
| for (unsigned int i = numIsoCompartments;i < numCompartments;++i) | ||
| anisoWeight += mcmPtr->GetCompartmentWeight(i); | ||
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| outputValue[numIsoCompartments] = anisoWeight; | ||
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| outItr.Set(outputValue); | ||
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| ++inItr; | ||
| ++outItr; | ||
| } | ||
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| anima::writeImage <OutputImageType> (outArg.getValue(), outputImage); | ||
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| return EXIT_SUCCESS; | ||
| } |
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