Merge pull request #106 from astamm/statistical_distributions

Statistical distributions

Anima/diffusion/mcm_tools/CMakeLists.txt

@@ -7,4 +7,4 @@ add_subdirectory(mcm_merge_block_images)
 add_subdirectory(mcm_orientation_priors)
 add_subdirectory(mcm_scalar_maps)
 add_subdirectory(mt_estimation_validation)
-add_subdirectory(test_averaging)
+add_subdirectory(test_averaging)

Anima/diffusion/mcm_tools/mcm_merge_anisotropic_weights/animaMCMMergeAnisotropicWeights.cxx

@@ -2,6 +2,7 @@
 #include <animaMCMImage.h>
 #include <animaMultiCompartmentModel.h>
 #include <animaReadWriteFunctions.h>
+
 #include <itkImageRegionConstIterator.h>
 #include <itkImageRegionIterator.h>
 
@@ -10,41 +11,47 @@
 int main(int argc, char **argv)
 {
     TCLAP::CmdLine cmd("INRIA / IRISA - VisAGeS/Empenn Team", ' ', ANIMA_VERSION);
-
-    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);
-
+
+    TCLAP::ValueArg<std::string> inArg(
+        "i", "inputfile",
+        "A string specifying the name of the file that stores the input MCM image.",
+        true, "", "input mcm image", cmd);
+    TCLAP::ValueArg<std::string> outArg(
+        "o", "outputfile",
+        "A string specifying the name of the file that stores the output image with combined anisotropic weights.",
+        true, "", "output combined weight image", cmd);
+
     try
     {
-        cmd.parse(argc,argv);
+        cmd.parse(argc, argv);
     }
-    catch (TCLAP::ArgException& e)
+    catch (TCLAP::ArgException &e)
     {
         std::cerr << "Error: " << e.error() << "for argument " << e.argId() << std::endl;
         return EXIT_FAILURE;
     }
 
-    using InputImageType = anima::MCMImage <double, 3>;
-    using OutputImageType = itk::VectorImage <double, 3>;
+    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;
 
     // Read input sample
-    anima::MCMFileReader <double, 3> mcmReader;
+    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();
-    
-    using InputImageIteratorType = itk::ImageRegionConstIterator <InputImageType>;
-    using OutputImageIteratorType = itk::ImageRegionIterator <OutputImageType>;
+
+    using InputImageIteratorType = itk::ImageRegionConstIterator<InputImageType>;
+    using OutputImageIteratorType = itk::ImageRegionIterator<OutputImageType>;
     InputImageIteratorType inItr(mcmImage, mcmImage->GetLargestPossibleRegion());
-    
+
     // Initialize output image
     unsigned int nbOutputComponents = numIsoCompartments + 1;
     OutputImageType::Pointer outputImage = OutputImageType::New();
@@ -59,15 +66,15 @@ int main(int argc, char **argv)
 
     std::cout << "- Number of compartments in input image: " << numCompartments << std::endl;
     std::cout << "- Number of compartments in output image: " << nbOutputComponents << std::endl;
-    
+
     OutputImageIteratorType outItr(outputImage, outputImage->GetLargestPossibleRegion());
 
-	while (!outItr.IsAtEnd())
-	{
+    while (!outItr.IsAtEnd())
+    {
         mcmValue = inItr.Get();
 
         bool backgroundVoxel = true;
-        for (unsigned int i = 0;i < mcmValue.GetNumberOfElements();++i)
+        for (unsigned int i = 0; i < mcmValue.GetNumberOfElements(); ++i)
         {
             if (mcmValue[i] != 0.0)
             {
@@ -85,22 +92,22 @@ int main(int argc, char **argv)
 
         mcmPtr->SetModelVector(mcmValue);
 
-        for (unsigned int i = 0;i < numIsoCompartments;++i)
+        for (unsigned int i = 0; i < numIsoCompartments; ++i)
             outputValue[i] = mcmPtr->GetCompartmentWeight(i);
-        
+
         double anisoWeight = 0.0;
-        for (unsigned int i = numIsoCompartments;i < numCompartments;++i)
+        for (unsigned int i = numIsoCompartments; i < numCompartments; ++i)
             anisoWeight += mcmPtr->GetCompartmentWeight(i);
-        
+
         outputValue[numIsoCompartments] = anisoWeight;
-        
+
         outItr.Set(outputValue);
 
         ++inItr;
         ++outItr;
-	}
-    
-    anima::writeImage <OutputImageType> (outArg.getValue(), outputImage);
-	
-	return EXIT_SUCCESS;
+    }
+
+    anima::writeImage<OutputImageType>(outArg.getValue(), outputImage);
+
+    return EXIT_SUCCESS;
 }

Anima/diffusion/mcm_tools/mcm_orientation_priors/CMakeLists.txt

@@ -1,38 +1,30 @@
 if(BUILD_TOOLS)
 
-project(animaMCMOrientationPriors)
+  project(animaMCMOrientationPriors)
 
-## #############################################################################
-## List Sources
-## #############################################################################
+  # ############################################################################
+  # List Sources
+  # ############################################################################
 
-list_source_files(${PROJECT_NAME}
-  ${CMAKE_CURRENT_SOURCE_DIR}
-  )
+  list_source_files(${PROJECT_NAME} ${CMAKE_CURRENT_SOURCE_DIR})
 
-## #############################################################################
-## add executable
-## #############################################################################
+  # ############################################################################
+  # add executable
+  # ############################################################################
 
-add_executable(${PROJECT_NAME}
-  ${${PROJECT_NAME}_CFILES}
-  )
+  add_executable(${PROJECT_NAME} ${${PROJECT_NAME}_CFILES})
 
-## #############################################################################
-## Link
-## #############################################################################
+  # ############################################################################
+  # Link
+  # ############################################################################
 
-target_link_libraries(${PROJECT_NAME}
-  ${ITKIO_LIBRARIES}
-  ${TinyXML2_LIBRARY}
-  AnimaMCM
-  AnimaStatisticalDistributions
-  )
+  target_link_libraries(${PROJECT_NAME} ${ITKIO_LIBRARIES} ${TinyXML2_LIBRARY}
+                        AnimaMCM AnimaStatisticalDistributions)
 
-## #############################################################################
-## install
-## #############################################################################
+  # ############################################################################
+  # install
+  # ############################################################################
 
-set_exe_install_rules(${PROJECT_NAME})
+  set_exe_install_rules(${PROJECT_NAME})
 
 endif()

Anima/diffusion/mcm_tools/mcm_orientation_priors/animaMCMOrientationPriors.cxx

@@ -1,55 +1,59 @@
 #include <animaMCMFileReader.h>
-#include <animaReadWriteFunctions.h>
 #include <animaMCMOrientationPriorsImageFilter.h>
+#include <animaReadWriteFunctions.h>
 
 #include <itkTimeProbe.h>
+
 #include <tclap/CmdLine.h>
 
-int main(int argc,  char **argv)
+int main(int argc, char **argv)
 {
-    TCLAP::CmdLine cmd("INRIA / IRISA - VisAGeS Team", ' ',ANIMA_VERSION);
+    TCLAP::CmdLine cmd("INRIA / IRISA - VisAGeS Team", ' ', ANIMA_VERSION);
 
     TCLAP::ValueArg<std::string> inArg(
-        "i", "input-mcms", 
-        "A text file specifying a list of MCM images in a common geometry.", 
-        true, "", "input MCM images", cmd
-    );
+        "i", "input-mcms",
+        "A text file specifying a list of MCM images in a common geometry.",
+        true, "", "input MCM images", cmd);
     TCLAP::ValueArg<std::string> outOrientationArg(
-        "o", "output-orientation", 
-        "A string specifying the basename for the output vector images that will store priors on the orientations.", 
-        true, "", "output orientation priors",cmd
-    );
+        "o", "output-orientation",
+        "A string specifying the basename for the output vector images that will store priors on the orientations.",
+        true, "", "output orientation priors", cmd);
     TCLAP::ValueArg<std::string> outWeightsArg(
-        "w", "output-weights", 
-        "A string specifying the filename for the output vector image that will store priors on the weights.", 
-        true, "", "output weights priors", cmd
-    );
-
+        "w", "output-weights",
+        "A string specifying the filename for the output vector image that will store fractions prior.",
+        true, "", "output weights priors", cmd);
+
     TCLAP::ValueArg<std::string> maskArg(
-        "m", "input-masks", 
-        "A text file specifying a list of mask images in the same common geometry as the input MCM images (default: none).", 
-        false, "", "input mask images", cmd
-    );
+        "m", "input-masks",
+        "A text file specifying a list of mask images in the same common geometry as the input MCM images (default: none).",
+        false, "", "input mask images", cmd);
+    TCLAP::ValueArg<std::string> meanOrientationsArg(
+        "", "mean-orientations",
+        "A string specifying the basename for the output vector images that will store mean orientations.",
+        false, "", "output mean orientation images", cmd);
+    TCLAP::ValueArg<std::string> meanFractionsArg(
+        "", "mean-fractions",
+        "A string specifying the filename for the output vector image that will store fractions mean.",
+        false, "", "output mean fractions image", cmd);
     TCLAP::ValueArg<unsigned int> nbThreadsArg(
-        "T", "nthreads", 
-        "An integer value specifying the number of threads to run on (default: all cores).", 
-        false, itk::MultiThreaderBase::GetGlobalDefaultNumberOfThreads(), "number of threads", cmd
-    );
+        "T", "nthreads",
+        "An integer value specifying the number of threads to run on (default: all cores).",
+        false, itk::MultiThreaderBase::GetGlobalDefaultNumberOfThreads(), "number of threads", cmd);
 
     try
     {
-        cmd.parse(argc,argv);
+        cmd.parse(argc, argv);
     }
-    catch (TCLAP::ArgException& e)
+    catch (TCLAP::ArgException &e)
     {
         std::cerr << "Error: " << e.error() << "for argument " << e.argId() << std::endl;
         return EXIT_FAILURE;
     }
 
-    using MainFilterType = anima::MCMOrientationPriorsImageFilter <double>;
+    using MainFilterType = anima::MCMOrientationPriorsImageFilter<double>;
     MainFilterType::Pointer mainFilter = MainFilterType::New();
 
-    using MCMReaderType = anima::MCMFileReader <double,3>;
+    using MCMReaderType = anima::MCMFileReader<double, 3>;
     using MaskImageType = MainFilterType::MaskImageType;
     using OutputImageType = MainFilterType::OutputImageType;
 
@@ -67,9 +71,9 @@ int main(int argc,  char **argv)
     while (!inputFile.eof())
     {
         char tmpStr[2048];
-        inputFile.getline(tmpStr,2048);
+        inputFile.getline(tmpStr, 2048);
 
-        if (strcmp(tmpStr,"") == 0)
+        if (strcmp(tmpStr, "") == 0)
             continue;
 
         std::cout << "Loading image " << nbOfImages + 1 << ": " << tmpStr << std::endl;
@@ -92,26 +96,38 @@ int main(int argc,  char **argv)
         char tmpStr[2048];
         while (!masksIn.eof())
         {
-            masksIn.getline(tmpStr,2048);
+            masksIn.getline(tmpStr, 2048);
 
-            if (strcmp(tmpStr,"") == 0)
+            if (strcmp(tmpStr, "") == 0)
                 continue;
 
-            mainFilter->AddMaskImage(anima::readImage <MaskImageType> (tmpStr));
+            mainFilter->AddMaskImage(anima::readImage<MaskImageType>(tmpStr));
         }
     }
 
     mainFilter->SetNumberOfWorkUnits(nbThreadsArg.getValue());
     mainFilter->Update();
 
     unsigned int numberOfAnisotropicCompartments = mainFilter->GetNumberOfAnisotropicCompartments();
-    for (unsigned int i = 0;i < numberOfAnisotropicCompartments;++i)
+    for (unsigned int i = 0; i < numberOfAnisotropicCompartments; ++i)
     {
         std::string fileName = outOrientationArg.getValue() + "_" + std::to_string(i) + ".nrrd";
-        anima::writeImage <OutputImageType> (fileName, mainFilter->GetOutput(i));
+        anima::writeImage<OutputImageType>(fileName, mainFilter->GetOutput(i));
     }
-
-    anima::writeImage <OutputImageType> (outWeightsArg.getValue(), mainFilter->GetOutput(numberOfAnisotropicCompartments));
+
+    anima::writeImage<OutputImageType>(outWeightsArg.getValue(), mainFilter->GetOutput(numberOfAnisotropicCompartments));
+
+    if (meanOrientationsArg.getValue() != "")
+    {
+        for (unsigned int i = 0; i < numberOfAnisotropicCompartments; ++i)
+        {
+            std::string fileName = meanOrientationsArg.getValue() + "_" + std::to_string(i) + ".nrrd";
+            anima::writeImage<OutputImageType>(fileName, mainFilter->GetMeanOrientationImage(i));
+        }
+    }
+
+    if (meanFractionsArg.getValue() != "")
+        anima::writeImage<OutputImageType>(meanFractionsArg.getValue(), mainFilter->GetMeanFractionsImage());
 
     return EXIT_SUCCESS;
 }