├── .gitignore ├── .travis.yml ├── Applications ├── CMakeLists.txt ├── DWIProcessing │ ├── CMakeLists.txt │ ├── CorrectBValues.cxx │ ├── CorrectBValues.xml │ ├── DWIMultipleShellSplit.cxx │ ├── DWIMultipleShellSplit.xml │ ├── DWINoiseGenerator.cxx │ ├── DWINoiseGenerator.xml │ ├── DWIPreprocess.cxx │ ├── DWIPreprocess.xml │ ├── DWISimulator.cxx │ ├── DWISimulator.xml │ ├── DWISingleVoxelSimulator.cxx │ └── DWISingleVoxelSimulator.xml ├── DiffusionModels │ ├── CMakeLists.txt │ ├── ComputeSHCoefficientsOfDWIFromSymmetricTensor.cxx │ ├── ComputeSHCoefficientsOfDWIFromSymmetricTensor.xml │ ├── MeanDiffusivityEstimator.cxx │ ├── MeanDiffusivityEstimator.xml │ ├── ODFNormalization.cxx │ ├── ODFNormalization.xml │ ├── SHCoefficientsFit.cxx │ ├── SHCoefficientsFit.xml │ ├── SHCoefficientsPower.cxx │ ├── SHCoefficientsPower.xml │ ├── SHCoefficientsRotate.cxx │ ├── SHCoefficientsRotate.xml │ ├── SHCoefficientsToGFA.cxx │ ├── SHCoefficientsToGFA.xml │ ├── SHCoefficientsToSphericalFunctionSamples.cxx │ ├── SHCoefficientsToSphericalFunctionSamples.xml │ ├── SPFToODF.cxx │ ├── SPFToODF.xml │ ├── SPFToProfile.cxx │ ├── SPFToProfile.xml │ ├── SPFToScalarMap.cxx │ ├── SPFToScalarMap.xml │ ├── SphereTessellator.cxx │ ├── SphereTessellator.xml │ ├── SphericalPolarFourierImaging.cxx │ ├── SphericalPolarFourierImaging.xml │ ├── TensorFormatConverter.cxx │ └── TensorFormatConverter.xml ├── SamplingScheme │ ├── CMakeLists.txt │ ├── OrientationStatistics.cxx │ ├── OrientationStatistics.xml │ ├── SamplingSchemeDistance.cxx │ ├── SamplingSchemeDistance.xml │ ├── SamplingSchemeQSpace1OptEstimation.cxx │ ├── SamplingSchemeQSpace1OptEstimation.xml │ ├── SamplingSchemeQSpaceIMOCEstimation.cxx │ ├── SamplingSchemeQSpaceIMOCEstimation.xml │ ├── SamplingSchemeQSpaceIncrementalEstimation.cxx │ ├── SamplingSchemeQSpaceIncrementalEstimation.xml │ ├── SamplingSchemeQSpaceRandomEstimation.cxx │ └── SamplingSchemeQSpaceRandomEstimation.xml ├── Scripts │ ├── CMakeLists.txt │ ├── CombineVTKPolyData.py │ ├── ConvertGurobiSolToIndex.py │ ├── README.md │ ├── VTKPolyData.py │ ├── VTKPolyData_gui.py │ ├── __init__.py │ ├── utlDMRITool.py │ └── utlVTK.py ├── Utilities │ ├── 4DImageMath.cxx │ ├── 4DImageMath.xml │ ├── 4DToVectorImageConverter.cxx │ ├── 4DToVectorImageConverter.xml │ ├── CMakeLists.txt │ ├── ImageInfo.cxx │ ├── ImageInfo.xml │ ├── ImageMultiplication.cxx │ ├── ImageMultiplication.xml │ ├── PrintImage.cxx │ ├── PrintImage.xml │ ├── TextFileOperator.cxx │ ├── TextFileOperator.xml │ ├── VectorImageNormalization.cxx │ ├── VectorImageNormalization.xml │ ├── VectorTo4DImageConverter.cxx │ └── VectorTo4DImageConverter.xml └── Visualization │ ├── CMakeLists.txt │ ├── MeshFromDiscreteFiberODF.cxx │ ├── MeshFromDiscreteFiberODF.xml │ ├── MeshFromPeaks.cxx │ ├── MeshFromPeaks.xml │ ├── MeshFromSHCoefficients.cxx │ ├── MeshFromSHCoefficients.xml │ ├── MeshFromSphericalFunctionTessellatedSamples.cxx │ ├── MeshFromSphericalFunctionTessellatedSamples.xml │ ├── MeshFromTensors.cxx │ ├── MeshFromTensors.xml │ ├── MeshFromTracts.cxx │ ├── MeshFromTracts.xml │ ├── OrientationsViewer.cxx │ ├── OrientationsViewer.xml │ ├── RGBImageToVTKXMLImageConverter.cxx │ ├── RGBImageToVTKXMLImageConverter.xml │ ├── VTKXMLImageToVectorImageConverter.cxx │ ├── VTKXMLImageToVectorImageConverter.xml │ ├── VectorImageToVTKXMLImageConverter.cxx │ └── VectorImageToVTKXMLImageConverter.xml ├── CMake ├── DMRITOOLConfig.cmake.in ├── DMRITOOLConfigure.h.in ├── DownloadDoxygenTAG.cmake ├── ExternalDoxygenTAG.cmake ├── FindGSL.cmake ├── FindLAPACK.cmake ├── FindMKL.cmake ├── FindOpenBLAS.cmake ├── PreventInBuildInstalls.cmake ├── PreventInSourceBuilds.cmake ├── ProjectCMakeFunctions.cmake └── UseDMRITOOL.cmake.in ├── CMakeLists.txt ├── Data ├── ElectricRepulsion │ ├── Elec003.txt │ ├── Elec004.txt │ ├── Elec005.txt │ ├── Elec006.txt │ ├── Elec007.txt │ ├── Elec008.txt │ ├── Elec009.txt │ ├── Elec010.txt │ ├── Elec011.txt │ ├── Elec012.txt │ ├── Elec013.txt │ ├── Elec014.txt │ ├── Elec015.txt │ ├── Elec016.txt │ ├── Elec017.txt │ ├── Elec018.txt │ ├── Elec019.txt │ ├── Elec020.txt │ ├── Elec021.txt │ ├── Elec022.txt │ ├── Elec023.txt │ ├── Elec024.txt │ ├── Elec025.txt │ ├── Elec026.txt │ ├── Elec027.txt │ ├── Elec028.txt │ ├── Elec029.txt │ ├── Elec030.txt │ ├── Elec031.txt │ ├── Elec032.txt │ ├── Elec033.txt │ ├── Elec034.txt │ ├── Elec035.txt │ ├── Elec036.txt │ ├── Elec037.txt │ ├── Elec038.txt │ ├── Elec039.txt │ ├── Elec040.txt │ ├── Elec041.txt │ ├── Elec042.txt │ ├── Elec043.txt │ ├── Elec044.txt │ ├── Elec045.txt │ ├── Elec046.txt │ ├── Elec047.txt │ ├── Elec048.txt │ ├── Elec049.txt │ ├── Elec050.txt │ ├── Elec051.txt │ ├── Elec052.txt │ ├── Elec053.txt │ ├── Elec054.txt │ ├── Elec055.txt │ ├── Elec056.txt │ ├── Elec057.txt │ ├── Elec058.txt │ ├── Elec059.txt │ ├── Elec060.txt │ ├── Elec061.txt │ ├── Elec062.txt │ ├── Elec063.txt │ ├── Elec064.txt │ ├── Elec065.txt │ ├── Elec066.txt │ ├── Elec067.txt │ ├── Elec068.txt │ ├── Elec069.txt │ ├── Elec070.txt │ ├── Elec071.txt │ ├── Elec072.txt │ ├── Elec073.txt │ ├── Elec074.txt │ ├── Elec075.txt │ ├── Elec076.txt │ ├── Elec077.txt │ ├── Elec078.txt │ ├── Elec079.txt │ ├── Elec080.txt │ ├── Elec081.txt │ ├── Elec082.txt │ ├── Elec083.txt │ ├── Elec084.txt │ ├── Elec085.txt │ ├── Elec086.txt │ ├── Elec087.txt │ ├── Elec088.txt │ ├── Elec089.txt │ ├── Elec090.txt │ ├── Elec091.txt │ ├── Elec092.txt │ ├── Elec093.txt │ ├── Elec094.txt │ ├── Elec095.txt │ ├── Elec096.txt │ ├── Elec097.txt │ ├── Elec098.txt │ ├── Elec099.txt │ ├── Elec100.txt │ ├── Elec101.txt │ ├── Elec102.txt │ ├── Elec103.txt │ ├── Elec104.txt │ ├── Elec105.txt │ ├── Elec106.txt │ ├── Elec107.txt │ ├── Elec108.txt │ ├── Elec109.txt │ ├── Elec110.txt │ ├── Elec111.txt │ ├── Elec112.txt │ ├── Elec113.txt │ ├── Elec114.txt │ ├── Elec115.txt │ ├── Elec116.txt │ ├── Elec117.txt │ ├── Elec118.txt │ ├── Elec119.txt │ ├── Elec120.txt │ ├── Elec121.txt │ ├── Elec122.txt │ ├── Elec123.txt │ ├── Elec124.txt │ ├── Elec125.txt │ ├── Elec126.txt │ ├── Elec127.txt │ ├── Elec128.txt │ ├── Elec129.txt │ ├── Elec130.txt │ ├── Elec131.txt │ ├── Elec132.txt │ ├── Elec133.txt │ ├── Elec134.txt │ ├── Elec135.txt │ ├── Elec136.txt │ ├── Elec137.txt │ ├── Elec138.txt │ ├── Elec139.txt │ ├── Elec140.txt │ ├── Elec141.txt │ ├── Elec142.txt │ ├── Elec143.txt │ ├── Elec144.txt │ ├── Elec145.txt │ ├── Elec146.txt │ ├── Elec147.txt │ ├── Elec148.txt │ ├── Elec149.txt │ ├── Elec150.txt │ ├── Elec151.txt │ ├── Elec152.txt │ ├── Elec153.txt │ ├── Elec154.txt │ ├── Elec155.txt │ ├── Elec156.txt │ ├── Elec157.txt │ ├── Elec158.txt │ ├── Elec159.txt │ ├── Elec160.txt │ ├── Elec161.txt │ ├── Elec162.txt │ ├── Elec163.txt │ ├── Elec164.txt │ ├── Elec165.txt │ ├── Elec166.txt │ ├── Elec167.txt │ ├── Elec168.txt │ ├── Elec169.txt │ ├── Elec170.txt │ ├── Elec171.txt │ ├── Elec172.txt │ ├── Elec173.txt │ ├── Elec174.txt │ ├── Elec175.txt │ ├── Elec176.txt │ ├── Elec177.txt │ ├── Elec178.txt │ ├── Elec179.txt │ ├── Elec180.txt │ ├── Elec181.txt │ ├── Elec182.txt │ ├── Elec183.txt │ ├── Elec184.txt │ ├── Elec185.txt │ ├── Elec186.txt │ ├── Elec187.txt │ ├── Elec188.txt │ ├── Elec189.txt │ ├── Elec190.txt │ ├── Elec191.txt │ ├── Elec192.txt │ ├── Elec193.txt │ ├── Elec194.txt │ ├── Elec195.txt │ ├── Elec196.txt │ ├── Elec197.txt │ ├── Elec198.txt │ ├── Elec199.txt │ ├── Elec200.txt │ ├── Elec201.txt │ ├── Elec202.txt │ ├── Elec203.txt │ ├── Elec204.txt │ ├── Elec205.txt │ ├── Elec206.txt │ ├── Elec207.txt │ ├── Elec208.txt │ ├── Elec209.txt │ ├── Elec210.txt │ ├── Elec211.txt │ ├── Elec212.txt │ ├── Elec213.txt │ ├── Elec214.txt │ ├── Elec215.txt │ ├── Elec216.txt │ ├── Elec217.txt │ ├── Elec218.txt │ ├── Elec219.txt │ ├── Elec220.txt │ ├── Elec221.txt │ ├── Elec222.txt │ ├── Elec223.txt │ ├── Elec224.txt │ ├── Elec225.txt │ ├── Elec226.txt │ ├── Elec227.txt │ ├── Elec228.txt │ ├── Elec229.txt │ ├── Elec230.txt │ ├── Elec231.txt │ ├── Elec232.txt │ ├── Elec233.txt │ ├── Elec234.txt │ ├── Elec235.txt │ ├── Elec236.txt │ ├── Elec237.txt │ ├── Elec238.txt │ ├── Elec239.txt │ ├── Elec240.txt │ ├── Elec241.txt │ ├── Elec242.txt │ ├── Elec243.txt │ ├── Elec244.txt │ ├── Elec245.txt │ ├── Elec246.txt │ ├── Elec247.txt │ ├── Elec248.txt │ ├── Elec249.txt │ ├── Elec250.txt │ ├── Elec251.txt │ ├── Elec252.txt │ ├── Elec253.txt │ ├── Elec254.txt │ ├── Elec255.txt │ ├── Elec256.txt │ └── Elec755.txt ├── Packing │ ├── Pack003.txt │ ├── Pack004.txt │ ├── Pack005.txt │ ├── Pack006.txt │ ├── Pack007.txt │ ├── Pack008.txt │ ├── Pack009.txt │ ├── Pack010.txt │ ├── Pack011.txt │ ├── Pack012.txt │ ├── Pack013.txt │ ├── Pack014.txt │ ├── Pack015.txt │ ├── Pack016.txt │ ├── Pack017.txt │ ├── Pack018.txt │ ├── Pack019.txt │ ├── Pack020.txt │ ├── Pack021.txt │ ├── Pack022.txt │ ├── Pack023.txt │ ├── Pack024.txt │ ├── Pack025.txt │ ├── Pack026.txt │ ├── Pack027.txt │ ├── Pack028.txt │ ├── Pack029.txt │ ├── Pack030.txt │ ├── Pack031.txt │ ├── Pack032.txt │ ├── Pack033.txt │ ├── Pack034.txt │ ├── Pack035.txt │ ├── Pack036.txt │ ├── Pack037.txt │ ├── Pack038.txt │ ├── Pack039.txt │ ├── Pack040.txt │ ├── Pack041.txt │ ├── Pack042.txt │ ├── Pack043.txt │ ├── Pack044.txt │ ├── Pack045.txt │ ├── Pack046.txt │ ├── Pack047.txt │ ├── Pack048.txt │ ├── Pack049.txt │ ├── Pack050.txt │ ├── Pack051.txt │ ├── Pack052.txt │ ├── Pack053.txt │ ├── Pack054.txt │ ├── Pack055.txt │ ├── Pack056.txt │ ├── Pack057.txt │ ├── Pack058.txt │ ├── Pack059.txt │ ├── Pack060.txt │ ├── Pack061.txt │ ├── Pack062.txt │ ├── Pack063.txt │ ├── Pack064.txt │ ├── Pack065.txt │ ├── Pack066.txt │ ├── Pack067.txt │ ├── Pack068.txt │ ├── Pack069.txt │ ├── Pack070.txt │ ├── Pack071.txt │ ├── Pack072.txt │ ├── Pack073.txt │ ├── Pack074.txt │ ├── Pack075.txt │ ├── Pack076.txt │ ├── Pack077.txt │ ├── Pack078.txt │ ├── Pack079.txt │ ├── Pack080.txt │ ├── Pack081.txt │ ├── Pack082.txt │ ├── Pack083.txt │ ├── Pack084.txt │ ├── Pack085.txt │ ├── Pack086.txt │ ├── Pack087.txt │ ├── Pack088.txt │ ├── Pack089.txt │ ├── Pack090.txt │ ├── Pack091.txt │ ├── Pack092.txt │ ├── Pack093.txt │ ├── Pack094.txt │ ├── Pack095.txt │ ├── Pack096.txt │ ├── Pack097.txt │ ├── Pack098.txt │ ├── Pack099.txt │ └── Pack100.txt ├── PreComputedTables │ ├── SPFDictionary_sh8_ra4_eps0.0001_iter10000_online_iso2_k250_md5_fa10_mdiso10x321.txt │ ├── SPFEnergy_sh8_ra4_eps0.0001_iter10000_online_iso2_k250_md5_fa10_mdiso10x321.txt │ ├── sh3integral.hdr │ └── sh3integral.img └── Tessellation │ ├── directions_t1.txt │ ├── directions_t2.txt │ ├── directions_t3.txt │ ├── directions_t4.txt │ ├── directions_t5.txt │ ├── directions_t6.txt │ └── directions_t7.txt ├── Documentation ├── Doxygen │ ├── DoxygenLayout.xml │ ├── Modules.dox │ └── doxygen.in └── Sphinx │ ├── HelperFunctions.rst │ ├── Makefile │ ├── _static │ ├── GitHub.png │ ├── linux-icon.png │ ├── theme_overrides.css │ └── tutorials │ │ └── spfi │ │ ├── HCP_DL-SPFI_1e-6_MSD.png │ │ ├── HCP_DL-SPFI_1e-6_PFA.png │ │ ├── HCP_DL-SPFI_1e-6_RTO.png │ │ ├── HCP_DL-SPFI_1e-6_eap_r0.015_ROI.png │ │ └── HCP_DL-SPFI_1e-6_eap_r0.015_whole.png │ ├── _templates │ └── layout.html │ ├── building.rst │ ├── citation.rst │ ├── codemodules.rst │ ├── conf.py │ ├── developers.rst │ ├── index.rst │ ├── license.rst │ ├── links.inc │ ├── meta_keywords.txt │ ├── newCommands.tex │ ├── news.rst │ ├── support.rst │ ├── tools │ ├── extract_bash_from_rst.py │ ├── generate_doc_for_commands.py │ ├── generate_doc_for_matlabfunctions.py │ ├── make_tutorial_outputs.py │ ├── publish_matlabdemos.sh │ ├── upload_doxygen.sh │ └── upload_ghpages.sh │ ├── tutorial_dwisimulation.rst │ ├── tutorial_qspacesampling.rst │ ├── tutorial_spfi.rst │ ├── tutoriallist.txt │ ├── tutorials.rst │ └── userguide.rst ├── Examples ├── Elec060.txt ├── directions_t3.txt ├── directions_t4.txt ├── dwi_circle_crossing.txt ├── dwi_crossing.txt ├── dwi_crossingCylinder_3x3.txt ├── dwi_diagonal_spherical.txt └── test.sh ├── LICENSE.txt ├── Matlab ├── Demos │ ├── demo_mutishell_IMOC_1Opt_CNLO.m │ ├── demo_separate_HCPQ390x3_30x3.m │ ├── demo_separate_HCPQ390x3_45x3.m │ ├── demo_separate_sets.m │ ├── demo_separate_t4_1shell.m │ ├── demo_separate_t4_28x3.m │ └── demo_singleshell_IMOC_1Opt_CNLO.m ├── README.md ├── SamplingScheme │ ├── CartesianToSpherical.m │ ├── CoveringRadius.m │ ├── CoveringRadiusUpperBound.m │ ├── GetGradAllShells.m │ ├── OptimalSamplingMultiShellCNLO.m │ ├── OptimalSamplingMultiShellCNLO_singleRun.m │ ├── OptimalSamplingMultiSubsetsFromDifferentSets.m │ ├── OptimalSamplingMultiSubsetsFromSameSet.m │ ├── OptimalSamplingSingleShellCNLO.m │ ├── OptimalSamplingSingleSubset.m │ ├── ReadDirections.m │ ├── VisualizeMultiShellScheme.m │ └── WriteDirections.m └── Utils │ └── CopyDefaultStructParams.m ├── Modules ├── Common │ ├── include │ │ ├── itkCastImageFileWriter.h │ │ ├── itkCastImageFileWriter.hxx │ │ ├── itkCastVectorImageFileWriter.h │ │ ├── itkCastVectorImageFileWriter.hxx │ │ ├── itkComposeVectorImageFilter.h │ │ ├── itkComposeVectorImageFilter.hxx │ │ ├── itkFunctorBaseVectorImageFilter.h │ │ ├── itkFunctorFromStringImageFilter.h │ │ ├── itkFunctorFromStringImageFilter.hxx │ │ ├── itkMaskedImageToImageFilter.h │ │ ├── itkMaskedImageToImageFilter.hxx │ │ ├── itkMultiVariableFunctorVectorImageFilter.h │ │ ├── itkMultiVariableFunctorVectorImageFilter.hxx │ │ ├── itkMultiVolumeImageToVectorImageFilter.h │ │ ├── itkMultiVolumeImageToVectorImageFilter.hxx │ │ ├── itkMultiplyByConstantMatrixVectorImageFilter.h │ │ ├── itkMultiplyByConstantVectorImageFilter.h │ │ ├── itkNormalizeVectorImageFilter.h │ │ ├── itkOuterProductVectorImageFilter.h │ │ ├── itkSlowPolyLineParametricPath.h │ │ ├── itkSlowPolyLineParametricPath.hxx │ │ ├── itkStructureTensorImageFilter.h │ │ ├── itkStructureTensorImageFilter.hxx │ │ ├── itkUnaryFunctorVectorImageFilter.h │ │ ├── itkUnaryFunctorVectorImageFilter.hxx │ │ ├── itkVectorImageChannelFilter.h │ │ ├── itkVectorImageChannelFilter.hxx │ │ ├── itkVectorImageRegionIterator.h │ │ ├── itkVectorImageRegionIteratorWithIndex.h │ │ ├── itkVectorImageRegionIteratorWithIndexSpecial.h │ │ ├── itkVectorImageToMultiVolumeImageFilter.h │ │ └── itkVectorImageToMultiVolumeImageFilter.hxx │ └── test │ │ ├── CMakeLists.txt │ │ ├── itkUnaryFunctorVectorImageFilterTest.cxx │ │ ├── itkUnaryFunctorVectorImageFilterTest.xml │ │ └── itkVectorImageRegionIteratorWithIndexTest.cxx ├── DWIProcessing │ ├── include │ │ ├── itkAddNoiseToDWIImageFilter.h │ │ ├── itkAddNoiseToDWIImageFilter.hxx │ │ ├── itkDWIGenerator.h │ │ ├── itkDWIGenerator.hxx │ │ ├── itkDWIGeneratorBase.h │ │ ├── itkDWIGeneratorBase.hxx │ │ ├── itkDWIReader.h │ │ ├── itkDWIReader.hxx │ │ ├── itkDWISingleVoxelGenerator.h │ │ ├── itkDWISingleVoxelGenerator.hxx │ │ ├── itkDWIWriter.h │ │ └── itkDWIWriter.hxx │ └── test │ │ ├── CMakeLists.txt │ │ ├── itkDWIReaderTest.cxx │ │ └── itkDWIReaderTest.xml ├── DiffusionModels │ ├── include │ │ ├── itkBasisMatrixGenerator.h │ │ ├── itkBasisMatrixGenerator.hxx │ │ ├── itkCylinderModelGenerator.h │ │ ├── itkCylinderModelGenerator.hxx │ │ ├── itkDiffusionModelEstimationImageFilter.h │ │ ├── itkDiffusionModelEstimationImageFilter.hxx │ │ ├── itkDiffusionModelEstimationInSphericalCoordinateImageFilter.h │ │ ├── itkDiffusionModelEstimationInSphericalCoordinateImageFilter.hxx │ │ ├── itkDiffusionModelGenerator.h │ │ ├── itkDiffusionTensor.h │ │ ├── itkDiffusionTensor.hxx │ │ ├── itkDiscreteBasisMatrixGenerator.h │ │ ├── itkDiscreteBasisMatrixGenerator.hxx │ │ ├── itkFeaturesFromSPFImageFilter.h │ │ ├── itkFeaturesFromSPFImageFilter.hxx │ │ ├── itkGeneralizedHighOrderTensorImageFilter.h │ │ ├── itkGeneralizedHighOrderTensorImageFilter.hxx │ │ ├── itkMeanDiffusivityFromGHOTImageFilter.h │ │ ├── itkNormalizeODFImageFilter.h │ │ ├── itkODFFromSPFImageFilter.h │ │ ├── itkODFFromSPFImageFilter.hxx │ │ ├── itkPeakContainerHelper.h │ │ ├── itkProfileFromSPFImageFilter.h │ │ ├── itkProfileFromSPFImageFilter.hxx │ │ ├── itkRotateSHCoefficientsImageFilter.h │ │ ├── itkSHCoefficientsPowerImageFilter.h │ │ ├── itkSHCoefficientsToGFAImageFilter.h │ │ ├── itkSPFScaleFromMeanDiffusivityImageFilter.h │ │ ├── itkScalarMapFromSPFImageFilter.h │ │ ├── itkScalarMapFromSPFImageFilter.hxx │ │ ├── itkSphericalPolarFourierEstimationImageFilter.h │ │ ├── itkSphericalPolarFourierEstimationImageFilter.hxx │ │ ├── itkSphericalPolarFourierImageFilter.h │ │ ├── itkSphericalPolarFourierImageFilter.hxx │ │ ├── itkTensorBasisMatrixGenerator.h │ │ └── itkTensorBasisMatrixGenerator.hxx │ └── test │ │ ├── CMakeLists.txt │ │ ├── itkDiffusionTensorTest.cxx │ │ ├── itkSHBasisGeneratorTest.cxx │ │ └── itkSHBasisGeneratorTest.xml ├── HelperFunctions │ ├── README.rst │ ├── include │ │ ├── utl.h │ │ ├── utl4thOrderTensor.h │ │ ├── utlBlas.h │ │ ├── utlCommandLineParser.h │ │ ├── utlConstants.h │ │ ├── utlCore.h │ │ ├── utlCore11.h │ │ ├── utlCoreMKL.h │ │ ├── utlCoreMacro.h │ │ ├── utlDMRI.h │ │ ├── utlDMRIStoredTables.h │ │ ├── utlExpression.h │ │ ├── utlExprtk.h │ │ ├── utlFunctors.h │ │ ├── utlGTest.h │ │ ├── utlITK.h │ │ ├── utlITKConceptChecking.h │ │ ├── utlITKMacro.h │ │ ├── utlLapack.h │ │ ├── utlMKL.h │ │ ├── utlMath.h │ │ ├── utlMatrix.h │ │ ├── utlNDArray.h │ │ ├── utlNDArrayFunctions.h │ │ ├── utlOpenMP.h │ │ ├── utlRotationMatrixFromVectors.h │ │ ├── utlSTDHeaders.h │ │ ├── utlSmartAssert.h │ │ ├── utlTypeinfo.h │ │ ├── utlVNL.h │ │ ├── utlVNLBlas.h │ │ ├── utlVNLIO.h │ │ ├── utlVNLLapack.h │ │ ├── utlVTK.h │ │ ├── utlVTKMacro.h │ │ ├── utlVector.h │ │ └── utl_cblas.h │ └── test │ │ ├── CMakeLists.txt │ │ ├── utl4thOrderTensorGTest.cxx │ │ ├── utlCoreGTest.cxx │ │ ├── utlCoreMKLGTest.cxx │ │ ├── utlDMRIGTest.cxx │ │ ├── utlGTest.cxx │ │ ├── utlGradientTest.cxx │ │ ├── utlMathGTest.cxx │ │ ├── utlMatrixGTest.cxx │ │ ├── utlNDArrayGTest.cxx │ │ ├── utlVNLBlasGTest.cxx │ │ ├── utlVNLBlasTest.cxx │ │ ├── utlVNLLapackGTest.cxx │ │ └── utlVectorGTest.cxx ├── Math │ ├── include │ │ ├── itkFunctorHashTable.h │ │ ├── itkFunctorTableBase.h │ │ ├── itkFunctors.h │ │ ├── itkSHCoefficientsFit.h │ │ ├── itkSHCoefficientsRotation.h │ │ ├── itkSpecialFunctionGenerator.h │ │ ├── itkSpecialFunctionGenerator.hxx │ │ ├── itkSphericalHarmonicsGenerator.h │ │ ├── itkSphericalHarmonicsGenerator.hxx │ │ ├── itkSphericalPolarFourierGenerator.h │ │ ├── itkSphericalPolarFourierGenerator.hxx │ │ └── itkUnaryFunctorLookUpTable.h │ └── test │ │ ├── CMakeLists.txt │ │ ├── itkFunctorHashTableTest.cxx │ │ ├── itkSHCoefficientsRotationGTest.cxx │ │ ├── itkSpecialFunctionGeneratorGTest.cxx │ │ ├── itkSphericalHarmonicsGeneratorGTest.cxx │ │ ├── itkSphericalHarmonicsGeneratorTest.cxx │ │ ├── itkSphericalPolarFourierGeneratorTest.cxx │ │ ├── itkUnaryFunctorLookUpTableGTest.cxx │ │ └── itkUnaryFunctorLookUpTableTest.cxx ├── Observers │ └── include │ │ └── itkCommandProgressUpdate.h ├── SamplingScheme │ └── include │ │ ├── itkSamplingScheme3D.h │ │ ├── itkSamplingScheme3D.hxx │ │ ├── itkSamplingSchemeQSpace.h │ │ ├── itkSamplingSchemeQSpace.hxx │ │ ├── itkSamplingSchemeQSpace1OptEstimationFilter.h │ │ ├── itkSamplingSchemeQSpace1OptEstimationFilter.hxx │ │ ├── itkSamplingSchemeQSpaceEstimationFilter.h │ │ ├── itkSamplingSchemeQSpaceIMOCEstimationFilter.h │ │ ├── itkSamplingSchemeQSpaceIMOCEstimationFilter.hxx │ │ ├── itkSamplingSchemeQSpaceIncrementalEstimationFilter.h │ │ ├── itkSamplingSchemeQSpaceIncrementalEstimationFilter.hxx │ │ ├── itkSamplingSchemeQSpaceWriter.h │ │ ├── itkSamplingSchemeQSpaceWriter.hxx │ │ ├── itkSphereTessellator.h │ │ └── itkSphereTessellator.hxx ├── Solvers │ ├── include │ │ ├── itkIterativeSolverBase.h │ │ ├── itkIterativeSolverBase.hxx │ │ ├── itkL1RegularizedLeastSquaresFISTASolver.h │ │ ├── itkL1RegularizedLeastSquaresFISTASolver.hxx │ │ ├── itkL2RegularizedLeastSquaresSolver.h │ │ ├── itkL2RegularizedLeastSquaresSolver.hxx │ │ ├── itkSolverBase.h │ │ ├── itkSolverBase.hxx │ │ ├── itkSpamsWeightedLassoSolver.h │ │ └── itkSpamsWeightedLassoSolver.hxx │ └── test │ │ ├── CMakeLists.txt │ │ ├── itkL1RegularizedLeastSquaresFISTASolverTest.cxx │ │ └── itkSpamsWeightedLassoSolverTest.cxx ├── Tractography │ ├── include │ │ ├── itkFiber.h │ │ ├── itkFiber.hxx │ │ ├── itkFiberTracts.h │ │ ├── itkFiberTracts.hxx │ │ ├── itkFiberTractsReader.h │ │ ├── itkFiberTractsReader.hxx │ │ ├── itkFiberTractsWriter.h │ │ ├── itkFiberTractsWriter.hxx │ │ └── itkTrackvisHeader.h │ └── test │ │ ├── CMakeLists.txt │ │ └── test_fibertTacksReaderWriter.cxx └── Visualization │ └── include │ ├── itkImageToVTKImageDataFilter.h │ ├── itkImageToVTKImageDataFilter.hxx │ ├── itkMeshFromContinuousSphericalFunctionImageFilter.h │ ├── itkMeshFromContinuousSphericalFunctionImageFilter.hxx │ ├── itkMeshFromDiscreteFiberODFImageFilter.h │ ├── itkMeshFromFiberTractsFilter.h │ ├── itkMeshFromFiberTractsFilter.hxx │ ├── itkMeshFromImageImageFilter.h │ ├── itkMeshFromPeaksImageFilter.h │ ├── itkMeshFromPeaksImageFilter.hxx │ ├── itkMeshFromSHCoefficientsImageFilter.h │ ├── itkMeshFromSphericalFunctionImageFilter.h │ ├── itkMeshFromSphericalFunctionTessellatedSamplesImageFilter.h │ ├── itkMeshFromTensorImageFilter.h │ ├── itkMeshFromTensorImageFilter.hxx │ ├── itkRGBImageToVTKImageDataFilter.h │ ├── itkRGBImageToVTKImageDataFilter.hxx │ ├── itkVTKImageDataToImageFilter.h │ ├── itkVTKImageDataToImageFilter.hxx │ ├── vtkPolyDataViewer.h │ └── vtkPolyDataViewer.hxx ├── QTApplications ├── CMakeLists.txt └── vtkviewer │ ├── CMakeLists.txt │ ├── README.txt │ ├── VTKViewer.cxx │ ├── VTKViewer.h │ └── main.cxx ├── README.md ├── Testing └── CMakeLists.txt ├── ThirdParty ├── Spams │ ├── COPYING │ ├── README │ ├── include │ │ ├── cblas_alt_template.h │ │ ├── cblas_defvar.h │ │ ├── cblas_template.h │ │ ├── dag.h │ │ ├── decomp.h │ │ ├── dicts.h │ │ ├── fista.h │ │ ├── linalg.h │ │ ├── list.h │ │ ├── misc.h │ │ ├── project.h │ │ ├── utils.h │ │ ├── utlITKSpams.h │ │ └── utlSpams.h │ └── test │ │ ├── CMakeLists.txt │ │ ├── cppLasso.cpp │ │ ├── spamsLassoTest.cxx │ │ └── spamsMatrixTest.cxx ├── SpatiallyDenseSparseVectorImage │ ├── CMakeLists.txt │ ├── README.md │ ├── include │ │ ├── itkSparseVector.h │ │ ├── itkSpatiallyDenseSparseVectorImage.h │ │ ├── itkSpatiallyDenseSparseVectorImage.hxx │ │ ├── itkSpatiallyDenseSparseVectorImageFileReader.h │ │ ├── itkSpatiallyDenseSparseVectorImageFileReader.hxx │ │ ├── itkSpatiallyDenseSparseVectorImageFileWriter.h │ │ ├── itkSpatiallyDenseSparseVectorImageFileWriter.hxx │ │ ├── itkSpatiallyDenseSparseVectorImageNeighborhoodAccessorFunctor.h │ │ ├── itkSpatiallyDenseSparseVectorImagePixelAccessor.h │ │ └── itkSpatiallyDenseSparseVectorImagePixelAccessorFunctor.h │ ├── itk-module.cmake │ ├── src │ │ └── CMakeLists.txt │ └── test │ │ ├── Baseline │ │ ├── itkSpatiallyDenseSparseVectorImageTestBaseline_Dense.nii.gz.md5 │ │ ├── itkSpatiallyDenseSparseVectorImageTestBaseline_Sparse.spr.md5 │ │ ├── itkSpatiallyDenseSparseVectorImageTestBaseline_Sparse_key.nrrd.md5 │ │ └── itkSpatiallyDenseSparseVectorImageTestBaseline_Sparse_value.nrrd.md5 │ │ ├── CMakeLists.txt │ │ ├── itkSparseVectorToVectorImageTest.cxx │ │ └── itkVectorToSparseVectorImageTest.cxx ├── VariableLengthVectorImage │ ├── include │ │ ├── itkVariableLengthVectorImageFileReader.h │ │ ├── itkVariableLengthVectorImageFileReader.hxx │ │ ├── itkVariableLengthVectorImageFileWriter.h │ │ └── itkVariableLengthVectorImageFileWriter.hxx │ ├── src │ │ └── CMakeLists.txt │ └── test │ │ ├── CMakeLists.txt │ │ └── test_VariableLengthVectorImage.cxx ├── exprtk │ ├── CMakeLists.txt │ ├── README.md │ ├── include │ │ └── exprtk_lib.h │ ├── src │ │ ├── CMakeLists.txt │ │ └── exprtk_lib.cxx │ └── test │ │ ├── CMakeLists.txt │ │ └── test_exprtk.cxx └── gtest │ ├── CMakeLists.txt │ └── test │ ├── CMakeLists.txt │ └── gtest_test.cxx ├── ThirdPartyApplications ├── CMakeLists.txt └── SpatiallyDenseSparseImage │ ├── CMakeLists.txt │ ├── SparseToVectorImageConverter.cxx │ ├── SparseToVectorImageConverter.xml │ ├── VectorToSparseImageConverter.cxx │ └── VectorToSparseImageConverter.xml ├── Utilities ├── CMakeLists.txt └── GUnzip.py └── Wrapping ├── CMakeLists.txt └── Matlab ├── CMake ├── FindGSL.cmake ├── FindLAPACK.cmake ├── FindMKL.cmake ├── FindMatlab.cmake ├── FindOpenBLAS.cmake ├── MatlabMakeMacros.cmake └── ProjectCMakeFunctions.cmake ├── CMakeLists.txt ├── Common ├── CMakeLists.txt ├── mexITKImageRead.cxx ├── mexITKImageRead.m ├── mexITKImageWrite.cxx └── mexITKImageWrite.m ├── DWIProcessing ├── CMakeLists.txt ├── mexReadDWIList.cxx └── mexReadDWIList.m ├── DiffusionModels ├── CMakeLists.txt ├── mexGetSHBasisMatrix.cxx ├── mexGetSHBasisMatrix.m ├── mexGetSPFBasisMatrix.cxx ├── mexGetSPFBasisMatrix.m ├── mexGetSamplesFromSPFCoefficients.cxx ├── mexGetSamplesFromSPFCoefficients.m ├── mexSphericalPolarFourierImaging.cxx └── mexSphericalPolarFourierImaging.m ├── MEXHelperFunctions ├── mexITK.h ├── mexSTD.h ├── mexVNL.h ├── mexutils.h └── utlMEX.h ├── README.md ├── SamplingScheme ├── CMakeLists.txt ├── mexReadGrad.cxx └── mexReadGrad.m └── Tests ├── CMakeLists.txt ├── test_GetSPFBaissMatrix.m ├── test_Spams.cxx ├── test_Spams2.cxx ├── test_purecpp.cxx ├── test_puremex.cxx ├── test_puremexOpenmp.cxx └── test_puremexitk.cxx /.gitignore: -------------------------------------------------------------------------------- 1 | 2 | build 3 | _build 4 | 5 | Examples/temp 6 | 7 | Documentation/Sphinx/commands/ 8 | Documentation/Sphinx/matlabfiles/ 9 | Documentation/Sphinx/.tutorial* 10 | 11 | Matlab/Demos/html 12 | Matlab/Demos/*.txt 13 | Matlab/Demos/*.mps 14 | 15 | -------------------------------------------------------------------------------- /Applications/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | ADD_SUBDIRECTORY(Utilities) 3 | ADD_SUBDIRECTORY(DiffusionModels) 4 | ADD_SUBDIRECTORY(DWIProcessing) 5 | ADD_SUBDIRECTORY(SamplingScheme) 6 | ADD_SUBDIRECTORY(Visualization) 7 | add_subdirectory(Scripts) 8 | -------------------------------------------------------------------------------- /Applications/DWIProcessing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_clp_application(DWISimulator DWISimulator ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES} ${GSL_LIBRARIES}) 3 | add_clp_application(DWISingleVoxelSimulator DWISingleVoxelSimulator ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES} ${GSL_LIBRARIES}) 4 | add_clp_application(DWINoiseGenerator DWINoiseGenerator ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES}) 5 | add_clp_application(DWIMultipleShellSplit DWIMultipleShellSplit ${ITK_LIBRARIES}) 6 | add_clp_application(CorrectBValues CorrectBValues ) 7 | add_clp_application(DWIPreprocess DWIPreprocess ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES}) 8 | 9 | -------------------------------------------------------------------------------- /Applications/DWIProcessing/CorrectBValues.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | DWI Processing 4 | Correct b values 5 | group similar b values into several shells. 6 | 7 | Jian Cheng (jian.cheng.1983@gmail.com) 8 | 9 | 10 | 11 | 12 | _InputFile 13 | 14 | Text file that contains b values. 15 | 0 16 | input 17 | 18 | 19 | 20 | _OutputFile 21 | 22 | Output file with b values. 23 | 1 24 | output 25 | 26 | 27 | 28 | _BThreshold 29 | 15 30 | b values whose distance is smallter the threshold will be considered in the same shell. 31 | t 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | -------------------------------------------------------------------------------- /Applications/DiffusionModels/ODFNormalization.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file ODFNormalization.cxx 3 | * @brief 4 | * 5 | * 6 | * @author Dr. Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * @internal 9 | * Created "04-21-2014 10 | * Revision 1.0 11 | * Compiler gcc/g++ 12 | * Company IDEA@UNC-CH 13 | * Copyright Copyright (c) 2014, Jian Cheng 14 | * 15 | * ===================================================================================== 16 | */ 17 | #include "utlITK.h" 18 | 19 | #include "itkMultiplyByConstantVectorImageFilter.h" 20 | #include "ODFNormalizationCLP.h" 21 | 22 | #include "itkNormalizeODFImageFilter.h" 23 | 24 | /** 25 | * \brief Normalize ODF represented by SH basis or uniform spherical samples 26 | * 27 | * \author Jian Cheng (jian.cheng.1983@gmail.com) 28 | */ 29 | int 30 | main (int argc, char const* argv[]) 31 | { 32 | // GenerateCLP 33 | PARSE_ARGS; 34 | 35 | typedef double FloatType; 36 | 37 | typedef itk::VectorImage InputImageType; 38 | typedef itk::VectorImage OutputImageType; 39 | 40 | InputImageType::Pointer input = InputImageType::New(); 41 | itk::ReadImage(_InputFile, input); 42 | 43 | 44 | typedef itk::NormalizeODFImageFilter FilterType; 45 | FilterType::Pointer filter = FilterType::New(); 46 | 47 | filter->SetInput(input); 48 | 49 | if (_Type=="SH") 50 | filter->SetODFType(FilterType::FunctorType::SH); 51 | else if (_Type=="SAMPLE") 52 | filter->SetODFType(FilterType::FunctorType::SAMPLE); 53 | 54 | filter->Update(); 55 | 56 | OutputImageType::Pointer output = filter->GetOutput(); 57 | itk::SaveImage(output, _OutputFile); 58 | 59 | return 0; 60 | } 61 | -------------------------------------------------------------------------------- /Applications/DiffusionModels/ODFNormalization.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Diffusion Models 4 | Normalize ODF (VectorImage) 5 | Normalize ODF (VectorImage) represented by SH basis or uniform spherical samples. 6 | 7 | Jian Cheng (jian.cheng.1983@gmail.com) 8 | 9 | 10 | 11 | 12 | _InputFile 13 | 14 | Input image file. 15 | 0 16 | input 17 | 18 | 19 | 20 | _OutputFile 21 | 22 | Input output file. 23 | 1 24 | input 25 | 26 | 27 | 28 | _Type 29 | 30 | Type of input ODF. SH: spherical harmonic coefficients. SAMPLE: uniform spherical samples. 31 | SH 32 | SH 33 | SAMPLE 34 | type 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | -------------------------------------------------------------------------------- /Applications/DiffusionModels/SHCoefficientsToGFA.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file SHCoefficientsTOGFA.cxx 3 | * @brief 4 | * Created "02-11-2013 5 | * 6 | * @author Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * ===================================================================================== 9 | */ 10 | 11 | #include "SHCoefficientsToGFACLP.h" 12 | 13 | #include "utl.h" 14 | #include "itkSHCoefficientsToGFAImageFilter.h" 15 | #include "itkSHCoefficientsPowerImageFilter.h" 16 | 17 | /** 18 | * \brief Calculate GFA from SH coefficients. 19 | */ 20 | int 21 | main (int argc, char const* argv[]) 22 | { 23 | // GenerateCLP 24 | PARSE_ARGS; 25 | 26 | typedef double TScalarType; 27 | typedef itk::VectorImage VectorImageType; 28 | typedef itk::Image ImageType; 29 | 30 | VectorImageType::Pointer shImage = VectorImageType::New(); 31 | itk::ReadVectorImage(_InputSHFile, shImage); 32 | 33 | typedef itk::SHCoefficientsToGFAImageFilter FilterType; 34 | FilterType::Pointer filter = FilterType::New(); 35 | 36 | if (_Power==1) 37 | { 38 | filter->SetInput(shImage); 39 | } 40 | else 41 | { 42 | typedef itk::SHCoefficientsPowerImageFilter FilterType; 43 | FilterType::Pointer shFilter = FilterType::New(); 44 | 45 | 46 | shFilter->SetInput(shImage); 47 | shFilter->SetPower(_Power); 48 | shFilter->SetSHRank(utl::DimToRankSH(shImage->GetNumberOfComponentsPerPixel())); 49 | 50 | shFilter->Update(); 51 | 52 | VectorImageType::Pointer shPowerImage = shFilter->GetOutput(); 53 | filter->SetInput(shPowerImage); 54 | } 55 | 56 | filter->Update(); 57 | ImageType::Pointer gfaImage = filter->GetOutput(); 58 | 59 | itk::SaveImage(gfaImage, _OutputFile); 60 | 61 | return 0; 62 | } 63 | -------------------------------------------------------------------------------- /Applications/DiffusionModels/SHCoefficientsToSphericalFunctionSamples.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Diffusion Models 4 | Spherical Harmonic coefficients To Spherical Function Samples 5 | conversion from SH coefficients to spherical function samples. 6 | 7 | Jian Cheng (jian.cheng.1983@gmail.com) 8 | 9 | 10 | 11 | 12 | _InputSHFile 13 | Input image file where each voxel contains a vector of SH coefficients. 14 | 0 15 | input 16 | 17 | 18 | 19 | _OutputFile 20 | Output image file where each voxel contains a vector of spherical function samples. 21 | 1 22 | input 23 | 24 | 25 | 26 | _dataOrientationsFile 27 | 28 | Text file that contains the gradient orientations of the data 29 | 2 30 | input 31 | 32 | 33 | 34 | _Power 35 | Power argument. 1.0: original value on mesh, 2.0: pow 2, 0.5: sqrt. 36 | pow 37 | 1.0 38 | 39 | 40 | 41 | _Debug 42 | 43 | debug 44 | --debug 45 | false 46 | 47 | 48 | 49 | 50 | 51 | 52 | -------------------------------------------------------------------------------- /Applications/SamplingScheme/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_clp_application(OrientationStatistics OrientationStatistics ${ITK_LIBRARIES} ${BLAS_LIBRARIES}) 3 | add_clp_application(SamplingSchemeQSpaceIncrementalEstimation SamplingSchemeQSpaceIncrementalEstimation ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES}) 4 | add_clp_application(SamplingSchemeQSpaceIMOCEstimation SamplingSchemeQSpaceIMOCEstimation ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES}) 5 | add_clp_application(SamplingSchemeQSpace1OptEstimation SamplingSchemeQSpace1OptEstimation ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES}) 6 | add_clp_application(SamplingSchemeQSpaceRandomEstimation SamplingSchemeQSpaceRandomEstimation ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES}) 7 | 8 | add_clp_application(SamplingSchemeDistance SamplingSchemeDistance ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES}) 9 | -------------------------------------------------------------------------------- /Applications/SamplingScheme/SamplingSchemeDistance.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Sampling Scheme 4 | Distance between Two Single Sampling Schemes 5 | Calculate the distance (maximum of the minimal angles) between two single shell sampling schemes. \n\ 6 | Examples: \n\ 7 | SamplingSchemeDistance grad1.txt grad2.txt 8 | 9 | 10 | Jian Cheng (jian.cheng.1983@gmail.com) 11 | 12 | 13 | 14 | Input/Output Parameters 15 | 16 | 17 | _InputFile1 18 | Input gradient File 1. 19 | 0 20 | 21 | 22 | 23 | _InputFile2 24 | Input gradient File 2. 25 | 1 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | _Debug 34 | debug 35 | debug 36 | false 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | -------------------------------------------------------------------------------- /Applications/SamplingScheme/SamplingSchemeQSpaceRandomEstimation.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file SamplingSchemeQSpaceRandomEstimation.cxx 3 | * @brief 4 | * Created "01-17-2017 5 | * 6 | * @author Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * ===================================================================================== 9 | */ 10 | 11 | 12 | 13 | #include "utl.h" 14 | #include "itkSamplingSchemeQSpaceWriter.h" 15 | #include "itkSamplingSchemeQSpace.h" 16 | 17 | #include "SamplingSchemeQSpaceRandomEstimationCLP.h" 18 | 19 | /** 20 | * \brief randome generator for single and multiple shell sampling scheme 21 | * \author Jian Cheng (jian.cheng.1983@gmail.com) 22 | */ 23 | int 24 | main (int argc, char const* argv[]) 25 | { 26 | 27 | PARSE_ARGS; 28 | 29 | typedef itk::SamplingSchemeQSpace SamplingType; 30 | typedef SamplingType::Pointer SamplingPointer; 31 | 32 | utlGlobalException(_NumberOfSamples.size()==0, "should give the numbers of samples in shells"); 33 | 34 | SamplingPointer scheme = SamplingType::New(); 35 | scheme->GenerateFromRandomPoints(_NumberOfSamples); 36 | 37 | typedef itk::SamplingSchemeQSpaceWriter WriterType; 38 | WriterType::Pointer writer = WriterType::New(); 39 | writer->SetSampling(scheme); 40 | writer->SetOrientationFile(_OutputOrientations); 41 | writer->SaveSingleShellOn(); 42 | writer->SaveAllShellsInOneFileOff(); 43 | writer->Update(); 44 | 45 | return 0; 46 | } 47 | 48 | -------------------------------------------------------------------------------- /Applications/SamplingScheme/SamplingSchemeQSpaceRandomEstimation.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Sampling Scheme 4 | Random generator for schemes 5 | Random generator for multi-shell schemes.\n\ 6 | Examples: \n\ 7 | SamplingSchemeQSpaceRandomEstimation grad.txt --numberOfSamples 60 \n\ 8 | SamplingSchemeQSpaceRandomEstimation grad.txt --numberOfSamples 28,28,28 \n\ 9 | Reference: \n\ 10 | Jian Cheng, Dinggang Shen, Pew-Thian Yap, Peter J. Basser, "Single- and Multiple-Shell Uniform Sampling Schemes for Diffusion MRI Using Spherical Codes", IEEE Transactions on Medical Imaging (TMI), 2017. 11 | 12 | 13 | Jian Cheng (jian.cheng.1983@gmail.com) 14 | 15 | 16 | 17 | Input/Output Parameters 18 | 19 | 20 | _OutputOrientations 21 | Output orientation file(s), single shell or multiple shells. 22 | 0 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | _NumberOfSamples 31 | 32 | number of samples in single/multiple shells. 33 | numberOfSamples 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | -------------------------------------------------------------------------------- /Applications/Scripts/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | file(GLOB pyfiles *.py) 3 | file(GLOB shfiles *.sh) 4 | 5 | set(copy_files ${pyfiles} ${shfiles}) 6 | # message("copy_files=${copy_files}") 7 | 8 | file(MAKE_DIRECTORY ${DMRITOOL_BINARY_DIR}/bin) 9 | file(COPY ${copy_files} DESTINATION ${DMRITOOL_BINARY_DIR}/bin) 10 | 11 | 12 | -------------------------------------------------------------------------------- /Applications/Scripts/CombineVTKPolyData.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | """ 3 | Description: Combine several vtk files into one vtk file. 4 | 5 | Usage: 6 | CombineVTKPolyData.py ... -o [-v] 7 | CombineVTKPolyData.py (-h | --help) 8 | 9 | Options: 10 | -h --help Show this screen. 11 | -v --verbose Verbose 12 | -o --output Output file 13 | 14 | Examples: 15 | CombineVTKPolyData.py file1.vtk file2.vtk -o file_combine.vtk 16 | CombineVTKPolyData.py file1.vtk -o file_combine.vtp 17 | 18 | Author(s): Jian Cheng (jian.cheng.1983@gmail.com) 19 | """ 20 | 21 | import vtk 22 | from docopt import docopt 23 | 24 | import utlVTK 25 | import utlDMRITool as utl 26 | 27 | 28 | def main(): 29 | 30 | args = docopt(utl.app_doc(__doc__), version='1.0') 31 | 32 | if (args['--verbose']): 33 | print(args) 34 | 35 | append = vtk.vtkAppendPolyData() 36 | 37 | for inputFile in args['']: 38 | polyData = utlVTK.readPolydata(inputFile) 39 | append.AddInputData(polyData) 40 | 41 | append.Update() 42 | utlVTK.savePolydata(append.GetOutput(), args['--output']) 43 | 44 | 45 | if __name__ == '__main__': 46 | main() 47 | -------------------------------------------------------------------------------- /Applications/Scripts/README.md: -------------------------------------------------------------------------------- 1 | Scripts 2 | ======= 3 | 4 | This folder contains some scripts in python and bash. 5 | 6 | 7 | -------------------------------------------------------------------------------- /Applications/Scripts/VTKPolyData_gui.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | ''' 4 | Description: GUI for VTKPolyData.py. 5 | ''' 6 | 7 | import sys 8 | 9 | import utlDMRITool as utl 10 | import VTKPolyData 11 | 12 | from gooey import Gooey 13 | 14 | @Gooey(program_name='VTKPolyData @ dmritool',default_size=(1000, 800)) 15 | def main(): 16 | VTKPolyData.main() 17 | 18 | if __name__ == '__main__': 19 | if '-h' in sys.argv or '--help' in sys.argv: 20 | print(utl.app_doc(__doc__)) 21 | else: 22 | main() 23 | -------------------------------------------------------------------------------- /Applications/Scripts/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | """ 3 | Python Scripts for DMRITool 4 | """ 5 | -------------------------------------------------------------------------------- /Applications/Utilities/4DToVectorImageConverter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Converter 4 | 4D Image to Vector Image Converter 5 | Convert a 4D image to a vector image. \n\ 6 | Examples: \n\ 7 | 4DToVectorImageConverter 4dImage.nii.gz vectorImage.nii.gz 8 | 9 | 10 | http://www.unc.edu/~ptyap 11 | 12 | Pew-Thian Yap (ptyap@med.unc.edu) 13 | 14 | 15 | http://www.unc.edu/~ptyap 16 | 17 | 18 | 19 | 20 | _InputFile 21 | 22 | Input file. 23 | 0 24 | input 25 | 26 | 27 | 28 | _OutputFile 29 | 30 | Output file. 31 | 1 32 | output 33 | 34 | 35 | 36 | 37 | 38 | -------------------------------------------------------------------------------- /Applications/Utilities/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_clp_application(ImageInfo ImageInfo ${ITK_LIBRARIES}) 3 | add_clp_application(PrintImage PrintImage ${ITK_LIBRARIES} ${BLAS_LIBRARIES} ${GSL_LIBRARIES}) 4 | add_clp_application(4DImageMath 4DImageMath ${ITK_LIBRARIES} ${BLAS_LIBRARIES} ${EXPRTK_LIBRARY}) 5 | add_clp_application(VectorImageNormalization VectorImageNormalization ${ITK_LIBRARIES}) 6 | # add_clp_application(ImageMultiplication ImageMultiplication ${ITK_LIBRARIES}) 7 | 8 | add_clp_application(4DToVectorImageConverter 4DToVectorImageConverter ${ITK_LIBRARIES}) 9 | add_clp_application(VectorTo4DImageConverter VectorTo4DImageConverter ${ITK_LIBRARIES}) 10 | 11 | add_clp_application(TextFileOperator TextFileOperator) -------------------------------------------------------------------------------- /Applications/Utilities/ImageMultiplication.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Image Operator 4 | Multiply a scale value to Image 5 | Scale each voxel in a 3D vector image or 4D image. 6 | 7 | Jian Cheng (jian.cheng.1983@gmail.com) 8 | 9 | 10 | 11 | 12 | _InputFile 13 | 14 | Input image file. 15 | 0 16 | input 17 | 18 | 19 | 20 | _OutputFile 21 | 22 | Output image file. 23 | 1 24 | output 25 | 26 | 27 | 28 | _Scale 29 | 30 | a scale value for multiplication. 31 | --scale 32 | 1.0 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | -------------------------------------------------------------------------------- /Applications/Utilities/VectorImageNormalization.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | VectorImage Operator 4 | Normalize Vector Image 5 | Normalize each voxel in a VectorImage or SparseVectorImage. 6 | 7 | Jian Cheng (jian.cheng.1983@gmail.com) 8 | 9 | 10 | 11 | 12 | _InputFile 13 | 14 | Input image file. 15 | 0 16 | input 17 | 18 | 19 | 20 | _OutputFile 21 | 22 | Input output file. 23 | 1 24 | input 25 | 26 | 27 | 28 | 29 | _NormalizationType 30 | 31 | Type of normalization. 32 | NONE 33 | SUM 34 | L1NORM 35 | L2NORM 36 | type 37 | 38 | 39 | 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /Applications/Utilities/VectorTo4DImageConverter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Converter 5 | Vector Image to 4D Image Converter 6 | Convert a vector image to a 4D image.\n\ 7 | Examples: \n\ 8 | VectorTo4DImageConverter vectorImage.nii.gz 4dImage.nii.gz 9 | 10 | 11 | http://www.unc.edu/~ptyap 12 | 13 | Pew-Thian Yap (ptyap@med.unc.edu) 14 | 15 | 16 | http://www.unc.edu/~ptyap 17 | 18 | 19 | 20 | 21 | _InputFile 22 | 23 | Input file. 24 | 0 25 | input 26 | 27 | 28 | 29 | _OutputFile 30 | 31 | Output file. 32 | 1 33 | output 34 | 35 | 36 | 37 | 38 | 39 | -------------------------------------------------------------------------------- /Applications/Visualization/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_clp_application(OrientationsViewer OrientationsViewer ${ITK_LIBRARIES} ${VTK_LIBRARIES}) 3 | 4 | add_clp_application(MeshFromSHCoefficients MeshFromSHCoefficients ${BLAS_LIBRARIES} ${ITK_LIBRARIES} ${VTK_LIBRARIES} ${GSL_LIBRARIES}) 5 | add_clp_application(MeshFromDiscreteFiberODF MeshFromDiscreteFiberODF ${BLAS_LIBRARIES} ${ITK_LIBRARIES} ${VTK_LIBRARIES} ${GSL_LIBRARIES}) 6 | add_clp_application(MeshFromSphericalFunctionTessellatedSamples MeshFromSphericalFunctionTessellatedSamples ${BLAS_LIBRARIES} ${ITK_LIBRARIES} ${VTK_LIBRARIES} ${GSL_LIBRARIES}) 7 | add_clp_application(MeshFromPeaks MeshFromPeaks ${BLAS_LIBRARIES} ${ITK_LIBRARIES} ${VTK_LIBRARIES} ${GSL_LIBRARIES}) 8 | add_clp_application(MeshFromTensors MeshFromTensors ${BLAS_LIBRARIES} ${ITK_LIBRARIES} ${VTK_LIBRARIES}) 9 | add_clp_application(MeshFromTracts MeshFromTracts ${BLAS_LIBRARIES} ${ITK_LIBRARIES} ${VTK_LIBRARIES}) 10 | 11 | # add_clp_application(VectorImageToVTK VectorImageToVTK ${ITK_LIBRARIES} ${BLAS_LIBRARIES}) 12 | add_clp_application(VectorImageToVTKXMLImageConverter VectorImageToVTKXMLImageConverter ${ITK_LIBRARIES} ${VTK_LIBRARIES}) 13 | add_clp_application(RGBImageToVTKXMLImageConverter RGBImageToVTKXMLImageConverter ${ITK_LIBRARIES} ${VTK_LIBRARIES}) 14 | add_clp_application(VTKXMLImageToVectorImageConverter VTKXMLImageToVectorImageConverter ${ITK_LIBRARIES} ${VTK_LIBRARIES}) 15 | -------------------------------------------------------------------------------- /Applications/Visualization/RGBImageToVTKXMLImageConverter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Visualization 5 | RGB ITK Image to VTK XML Image Converter 6 | Convert an ITK image to a VTK XML image. 7 | 8 | http://www.unc.edu/~ptyap 9 | 10 | Pew-Thian Yap (ptyap@med.unc.edu) 11 | 12 | 13 | http://www.unc.edu/~ptyap 14 | 15 | 16 | 17 | 18 | _InputFile 19 | 20 | Input image file. 21 | 0 22 | input 23 | 24 | 25 | 26 | _OutputFile 27 | 28 | Output image data (.vti) file. 29 | 1 30 | output 31 | 32 | 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /Applications/Visualization/VTKXMLImageToVectorImageConverter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Visualization 5 | VTK XML Image to Image Converter 6 | Convert a VTK XML image to an ITK image. 7 | 8 | http://www.unc.edu/~ptyap 9 | 10 | Pew-Thian Yap (ptyap@med.unc.edu) 11 | 12 | 13 | http://www.unc.edu/~ptyap 14 | 15 | 16 | 17 | 18 | _InputFile 19 | 20 | Input image data (.vti) file. 21 | 0 22 | input 23 | 24 | 25 | 26 | _OutputFile 27 | 28 | Output file. 29 | 1 30 | output 31 | 32 | 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /Applications/Visualization/VectorImageToVTKXMLImageConverter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Visualization 5 | ITK Image to VTK XML Image Converter 6 | Convert an ITK image to a VTK XML image. 7 | 8 | http://www.unc.edu/~ptyap 9 | 10 | Pew-Thian Yap (ptyap@med.unc.edu) 11 | 12 | 13 | http://www.unc.edu/~ptyap 14 | 15 | 16 | 17 | 18 | _InputFile 19 | 20 | Input image file. 21 | 0 22 | input 23 | 24 | 25 | 26 | _OutputFile 27 | 28 | Output image data (.vti) file. 29 | 1 30 | output 31 | 32 | 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /CMake/DMRITOOLConfig.cmake.in: -------------------------------------------------------------------------------- 1 | #----------------------------------------------------------------------------- 2 | # 3 | # DMRITOOLConfig.cmake - 4 | # DMRITOOL CMake configuration file for external projects. 5 | # 6 | # This file is configured by DMRITOOL and used by the UseDMRITOOL.cmake module 7 | # to load DMRITOOL's settings for an external project. 8 | 9 | # # The DMRITOOL source tree. 10 | # SET(DMRITOOL_SOURCE_DIR "@PROJECT_SOURCE_DIRECTORIES@") 11 | 12 | # SET(DMRITOOL_BINARY_DIR "@PROJECT_BINARY_DIRECTORIES@") 13 | 14 | # The DMRITOOL include file directories. 15 | SET(DMRITOOL_INCLUDE_DIRS "@DMRITOOL_INCLUDE_DIRECTORIES@") 16 | 17 | # The DMRITOOL library directories. 18 | # Includes DMRITOOL libs directory and OTHER libs directories 19 | SET(DMRITOOL_LIBRARY_DIRS "@DMRITOOL_LIBRARY_DIRECTORIES@") 20 | 21 | # This includes all libraries that DMRITOOL generates. 22 | # SET(DMRITOOL_LIBRARIES "@DMRITOOL_LIBRARIES@") 23 | 24 | # The location of the UseDMRITOOL.cmake file. 25 | SET(DMRITOOL_USE_FILE "@DMRITOOL_USE_FILE@") 26 | 27 | 28 | SET(DMRITOOL_SETTINGS_DIR "${DMRITOOL_SETTINGS_DIRECTORY}") 29 | 30 | SET(DMRITOOL_USE_OPENMP "@DMRITOOL_USE_OPENMP@") 31 | SET(DMRITOOL_USE_MKL "@DMRITOOL_USE_MKL@") 32 | SET(DMRITOOL_USE_FASTLAPACK "@DMRITOOL_USE_FASTLAPACK@") 33 | 34 | 35 | -------------------------------------------------------------------------------- /CMake/DownloadDoxygenTAG.cmake: -------------------------------------------------------------------------------- 1 | file( DOWNLOAD http://public.kitware.com/pub/itk/NightlyDoxygen/InsightDoxygenDocTag.gz 2 | ${ITKTAG_DIR}/InsightDoxygen.tag.gz SHOW_PROGRESS 3 | ) 4 | 5 | file( DOWNLOAD http://www.vtk.org/files/nightly/vtkNightlyDoc.tag.gz 6 | ${VTKTAG_DIR}/vtkNightlyDoc.tag.gz SHOW_PROGRESS 7 | ) 8 | -------------------------------------------------------------------------------- /CMake/ExternalDoxygenTAG.cmake: -------------------------------------------------------------------------------- 1 | 2 | set(ExternalTAG_DIR ${DMRITOOL_DOXYGEN_OUTPUT_DIR}) 3 | 4 | find_package(PythonInterp REQUIRED) 5 | 6 | add_custom_command( OUTPUT ${ExternalTAG_DIR}/InsightDoxygen.tag ${ExternalTAG_DIR}/vtkNightlyDoc.tag 7 | COMMAND ${CMAKE_COMMAND} -DITKTAG_DIR="${ExternalTAG_DIR}" -DVTKTAG_DIR="${ExternalTAG_DIR}" -P ${PROJECT_SOURCE_DIR}/CMake/DownloadDoxygenTAG.cmake 8 | COMMAND ${PYTHON_EXECUTABLE} "${PROJECT_SOURCE_DIR}/Utilities/GUnzip.py" "${ExternalTAG_DIR}/InsightDoxygen.tag.gz" 9 | COMMAND ${PYTHON_EXECUTABLE} "${PROJECT_SOURCE_DIR}/Utilities/GUnzip.py" "${ExternalTAG_DIR}/vtkNightlyDoc.tag.gz" 10 | COMMENT "Downloading and unpacking the Doxygen TAG" 11 | ) 12 | add_custom_target( ExternalDoxygenTAG ${CMAKE_COMMAND} -E echo "Finished obtaining external Doxygen TAG" 13 | DEPENDS 14 | ${ExternalTAG_DIR}/InsightDoxygen.tag 15 | ${ExternalTAG_DIR}/vtkNightlyDoc.tag 16 | ) 17 | -------------------------------------------------------------------------------- /CMake/FindOpenBLAS.cmake: -------------------------------------------------------------------------------- 1 | # - Find the OpenBLAS library (no includes) 2 | # This module defines 3 | # OpenBLAS_LIBRARIES, the libraries needed to use OpenBLAS. 4 | # OpenBLAS_FOUND, If false, do not try to use OpenBLAS. 5 | # also defined, but not for general use are 6 | # OpenBLAS_LIBRARY, where to find the OpenBLAS library. 7 | 8 | SET(OpenBLAS_NAMES ${OpenBLAS_NAMES} openblas) 9 | FIND_LIBRARY(OpenBLAS_LIBRARY 10 | NAMES ${OpenBLAS_NAMES} 11 | PATHS /opt/OpenBLAS/lib /usr/local/lib64 /usr/local/lib/openblas-base /lib64 /usr/lib64 /lib /usr/lib /usr/local/lib /usr/lib/openblas-base 12 | ) 13 | 14 | IF (OpenBLAS_LIBRARY) 15 | SET(OpenBLAS_LIBRARIES ${OpenBLAS_LIBRARY}) 16 | SET(OpenBLAS_FOUND "YES") 17 | ELSE (OpenBLAS_LIBRARY) 18 | SET(OpenBLAS_FOUND "NO") 19 | ENDIF (OpenBLAS_LIBRARY) 20 | 21 | 22 | IF (OpenBLAS_FOUND) 23 | IF (NOT OpenBLAS_FIND_QUIETLY) 24 | MESSAGE(STATUS "Found the OpenBLAS library: ${OpenBLAS_LIBRARIES}") 25 | ENDIF (NOT OpenBLAS_FIND_QUIETLY) 26 | ELSE (OpenBLAS_FOUND) 27 | IF (OpenBLAS_FIND_REQUIRED) 28 | MESSAGE(FATAL_ERROR "Could not find the OpenBLAS library") 29 | ENDIF (OpenBLAS_FIND_REQUIRED) 30 | ENDIF (OpenBLAS_FOUND) 31 | 32 | # Deprecated declarations. 33 | GET_FILENAME_COMPONENT (NATIVE_OpenBLAS_LIB_PATH ${OpenBLAS_LIBRARY} PATH) 34 | 35 | MARK_AS_ADVANCED( 36 | OpenBLAS_LIBRARY 37 | ) 38 | 39 | -------------------------------------------------------------------------------- /CMake/PreventInBuildInstalls.cmake: -------------------------------------------------------------------------------- 1 | string(TOLOWER "${CMAKE_INSTALL_PREFIX}" _PREFIX) 2 | string(TOLOWER "${ITK_BINARY_DIR}" _BUILD) 3 | if("${_PREFIX}" STREQUAL "${_BUILD}") 4 | message(FATAL_ERROR 5 | "The current CMAKE_INSTALL_PREFIX points at the build tree:\n" 6 | " ${CMAKE_INSTALL_PREFIX}\n" 7 | "This is not supported." 8 | ) 9 | endif() 10 | -------------------------------------------------------------------------------- /CMake/PreventInSourceBuilds.cmake: -------------------------------------------------------------------------------- 1 | # 2 | # This function will prevent in-source builds 3 | function(AssureOutOfSourceBuilds) 4 | # make sure the user doesn't play dirty with symlinks 5 | get_filename_component(srcdir "${CMAKE_SOURCE_DIR}" REALPATH) 6 | get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH) 7 | 8 | # disallow in-source builds 9 | if("${srcdir}" STREQUAL "${bindir}") 10 | message("######################################################") 11 | message("# DMRITOOL should not be configured & built in the DMRITOOL source directory") 12 | message("# You must run cmake in a build directory.") 13 | message("######################################################") 14 | message(FATAL_ERROR "Quitting configuration") 15 | endif() 16 | endfunction() 17 | 18 | AssureOutOfSourceBuilds() 19 | -------------------------------------------------------------------------------- /CMake/UseDMRITOOL.cmake.in: -------------------------------------------------------------------------------- 1 | # 2 | # This file sets up include directories, link directories, and 3 | # compiler settings for a project to use DMRITOOL. It should not be 4 | # included directly, but rather through the DMRITOOL_USE_FILE setting 5 | # obtained from DMRITOOLConfig.cmake. 6 | # 7 | if(DMRITOOL_USE_FILE_INCLUDED) 8 | return() 9 | endif() 10 | set(DMRITOOL_USE_FILE_INCLUDED 1) 11 | 12 | # Update CMAKE_MODULE_PATH so includes work. 13 | list(APPEND CMAKE_MODULE_PATH ${DMRITOOL_CMAKE_DIR}) 14 | 15 | 16 | # Add include directories needed to use DMRITOOL. 17 | include_directories(BEFORE ${DMRITOOL_INCLUDE_DIRS}) 18 | 19 | # Add link directories needed to use DMRITOOL. 20 | link_directories(${DMRITOOL_LIBRARY_DIRS}) 21 | 22 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec003.txt: -------------------------------------------------------------------------------- 1 | -0.100796 0.994902 0.003109 2 | -0.9949 -0.100783 -0.004049 3 | -0.003715 -0.003501 0.999987 4 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec004.txt: -------------------------------------------------------------------------------- 1 | -0.02156 -0.304929 0.952131 2 | -0.94922 -0.06461 0.307906 3 | 0.491865 0.65679 0.571572 4 | 0.435796 -0.897108 0.072653 5 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec005.txt: -------------------------------------------------------------------------------- 1 | -0.810867 -0.496465 0.309866 2 | 0.307318 -0.931254 0.195761 3 | -0.171601 -0.145829 0.974314 4 | -0.894745 0.169209 -0.41328 5 | 0.13961 0.736549 0.661819 6 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec006.txt: -------------------------------------------------------------------------------- 1 | -0.006226 -0.064447 0.997902 2 | 0.636679 -0.653135 0.409945 3 | -0.399917 -0.82842 0.392157 4 | 0.789559 0.384929 0.47794 5 | -0.887689 0.101313 0.449159 6 | 0.152552 -0.851204 -0.502175 7 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec007.txt: -------------------------------------------------------------------------------- 1 | 0.055396 -0.824375 0.563326 2 | 0.811301 -0.575497 0.102927 3 | -0.229063 0.783589 0.577511 4 | -0.881413 -0.159849 0.444477 5 | 0.564952 0.817041 0.115211 6 | 0.707747 0.119062 0.696361 7 | -0.150399 -0.035322 0.987994 8 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec008.txt: -------------------------------------------------------------------------------- 1 | -0.590425 -0.804665 -0.062549 2 | 0.027408 -0.732319 -0.68041 3 | 0.756064 -0.645224 0.109787 4 | 0.952343 0.144115 0.268837 5 | 0.391908 -0.03299 0.919413 6 | 0.101437 -0.919831 0.378974 7 | -0.389232 -0.418658 0.820502 8 | -0.751151 0.241893 0.614215 9 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec009.txt: -------------------------------------------------------------------------------- 1 | 0.393918 -0.259108 0.881868 2 | 0.625857 0.591521 0.508337 3 | 0.517317 -0.817156 0.254244 4 | -0.758341 0.441699 0.479396 5 | -0.234181 0.114957 0.965373 6 | 0.958459 -0.08074 0.273564 7 | -0.041437 0.894887 0.444364 8 | -0.237557 -0.849808 0.470524 9 | 0.818447 0.402205 -0.410335 10 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec010.txt: -------------------------------------------------------------------------------- 1 | 0.557836 0.789965 0.254507 2 | 0.569859 -0.258762 -0.779937 3 | -0.195499 -0.880727 0.431393 4 | 0.932196 -0.349524 -0.094038 5 | 0.549517 -0.660507 0.511627 6 | -0.015038 -0.296982 0.954765 7 | 0.81859 0.0957 0.56635 8 | -0.833628 -0.392682 0.388415 9 | 0.175157 0.478983 0.860172 10 | -0.299722 0.912303 0.279053 11 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec011.txt: -------------------------------------------------------------------------------- 1 | 0.511351 0.804163 0.303054 2 | -0.794769 -0.503466 0.338916 3 | 0.174571 0.221229 0.95947 4 | -0.234636 -0.431883 0.870875 5 | 0.815945 0.188147 0.546657 6 | -0.981514 0.181966 0.059311 7 | -0.59954 0.800343 0.001858 8 | -0.081149 -0.946839 0.311306 9 | -0.636726 0.218439 0.739503 10 | 0.517936 -0.498952 0.69483 11 | -0.1612 0.795247 0.584462 12 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec012.txt: -------------------------------------------------------------------------------- 1 | 0.42518 0.315653 0.848284 2 | 0.185196 -0.382898 0.905037 3 | -0.480267 -0.117082 0.869273 4 | -0.477164 -0.715637 0.510077 5 | -0.702985 0.558424 -0.440426 6 | -0.707505 -0.69026 -0.151584 7 | 0.944077 0.041899 -0.327051 8 | -0.264785 0.510148 0.818314 9 | 0.918467 0.068806 0.389467 10 | 0.085525 0.922253 0.377009 11 | -0.144817 0.947629 -0.284652 12 | -0.704094 0.656651 0.270298 13 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec013.txt: -------------------------------------------------------------------------------- 1 | 0.608489 0.354732 0.709863 2 | 0.840005 0.542193 0.020474 3 | -0.380743 -0.814648 0.437474 4 | 0.207531 -0.233095 0.950051 5 | -0.789643 0.613015 -0.025996 6 | -0.93746 -0.021576 0.347425 7 | 0.304986 -0.753712 0.582152 8 | 0.873326 -0.161334 0.459645 9 | 0.321048 0.871575 0.370521 10 | -0.486692 -0.248656 0.837437 11 | -0.041337 0.427363 0.903135 12 | -0.582926 0.527413 0.618088 13 | -0.220542 0.971625 0.085473 14 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec014.txt: -------------------------------------------------------------------------------- 1 | -0.52923 -0.838809 0.127733 2 | -0.502637 0.855008 -0.127741 3 | -0.313344 0.635274 0.705863 4 | -7e-06 3e-06 1 5 | 0.601859 0.028092 -0.798108 6 | -0.33312 -0.625125 -0.705868 7 | 0.923984 0.258254 -0.282062 8 | 0.301096 -0.657339 0.69083 9 | 0.821113 -0.458657 -0.339715 10 | 0.835101 0.432657 0.339727 11 | -0.015439 -0.98355 -0.179977 12 | 0.915418 -0.28713 0.282075 13 | 0.321591 0.647564 -0.690826 14 | 0.600669 -0.04697 0.798117 15 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec015.txt: -------------------------------------------------------------------------------- 1 | 0.957387 -0.187071 0.220034 2 | 0.190618 0.585245 0.788133 3 | 0.325492 -0.844583 -0.425129 4 | 0.022796 -0.678409 0.734331 5 | -0.596977 -0.258722 0.759395 6 | -0.41625 0.343103 0.842031 7 | 0.734448 0.292307 0.612489 8 | 0.581881 -0.362502 0.728016 9 | 0.928822 0.354407 -0.108098 10 | -0.861661 0.322776 0.391608 11 | 0.52577 0.761172 -0.379714 12 | -0.034273 0.991162 -0.128153 13 | 0.084508 -0.056169 0.994838 14 | 0.630413 -0.756662 0.173326 15 | 0.491239 0.826626 0.274542 16 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec016.txt: -------------------------------------------------------------------------------- 1 | 0.554077 0.486008 0.675866 2 | -0.495011 0.455826 0.739721 3 | 0.944451 0.224351 0.240166 4 | -0.818498 -0.461979 0.341521 5 | 0.629291 -0.144331 0.76365 6 | -0.302298 -0.787745 0.536725 7 | 0.011914 0.814134 0.580555 8 | 0.030663 -0.999031 0.031565 9 | 0.589202 -0.783569 -0.197131 10 | 0.562891 0.816715 0.127007 11 | 0.052951 0.220175 0.974022 12 | 0.067168 -0.416946 0.906446 13 | 0.878961 -0.413143 0.238202 14 | -0.522802 -0.177477 0.833775 15 | 0.409735 -0.76726 0.493386 16 | -0.919674 0.17072 0.35363 17 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec017.txt: -------------------------------------------------------------------------------- 1 | -0.084677 -0.798978 0.595368 2 | -0.285378 0.382557 0.878755 3 | 0.239575 -0.008537 0.97084 4 | -0.826274 0.479411 -0.295697 5 | -0.933601 0.272403 0.23278 6 | -0.585702 0.695361 0.416445 7 | 0.348167 0.536125 0.768993 8 | 0.687326 0.597291 -0.413312 9 | -0.788627 -0.069187 -0.610967 10 | 0.672858 0.682522 0.285353 11 | -0.729422 -0.025495 0.683588 12 | -0.028902 0.887279 0.460327 13 | 0.432026 -0.525413 0.733004 14 | -0.386679 0.91066 -0.145523 15 | -0.269733 -0.320655 0.907978 16 | -0.266447 -0.962145 0.05729 17 | -0.969994 -0.241445 -0.028553 18 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec018.txt: -------------------------------------------------------------------------------- 1 | -0.358616 0.232844 0.903979 2 | 0.990653 -0.112342 0.077367 3 | -0.28293 0.716688 0.637423 4 | -0.891249 -0.417614 0.176844 5 | -0.733882 -0.178601 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-------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec022.txt: -------------------------------------------------------------------------------- 1 | -0.882341 0.332209 -0.333333 2 | -0.352361 -0.935864 0 3 | 0.986663 0.162779 0 4 | 0.341948 0.773385 0.533805 5 | -0.498797 0.682828 -0.533805 6 | 0.728872 0.598025 -0.333333 7 | -0 -0 1 8 | 0.634302 -0.773086 0 9 | 0.15869 -0.961879 0.222724 10 | 0.087078 -0.527812 0.844886 11 | 0.41356 0.339318 0.844886 12 | -0.840745 -0.090557 0.533805 13 | 0.446341 0.366214 -0.816497 14 | -0.540321 0.203436 -0.816497 15 | -0.825279 -0.184302 -0.533805 16 | 0.912357 -0.34351 -0.222724 17 | -0.753667 -0.618369 -0.222724 18 | 0.253029 0.806863 -0.533805 19 | -0.57225 0.622562 0.533805 20 | -0.153469 0.930235 0.333333 21 | -0.09398 0.56965 0.816497 22 | 0.500637 -0.188494 -0.844886 23 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec023.txt: -------------------------------------------------------------------------------- 1 | 0.461401 -0.470194 0.752347 2 | -0.001035 -0.702076 0.712101 3 | 0.335322 0.027683 0.941697 4 | -0.165846 0.814522 0.555922 5 | 0.663968 0.730147 -0.161344 6 | 0.801328 -0.534568 0.268534 7 | 0.604447 -0.778192 -0.170471 8 | 0.411647 0.852388 0.322461 9 | -0.640902 -0.026697 0.767158 10 | 0.788165 -0.084222 0.609674 11 | -0.080094 0.992163 0.095902 12 | 0.223489 0.927836 -0.298619 13 | 0.991384 -0.050116 0.121023 14 | 0.903221 0.247278 -0.350777 15 | -0.871316 -0.449293 -0.197343 16 | 0.896749 -0.315784 -0.310034 17 | -0.525387 -0.54106 0.656675 18 | -0.188149 0.259579 0.947216 19 | 0.20072 0.574644 0.793408 20 | -0.128638 -0.262416 0.956342 21 | 0.378311 -0.859291 0.344239 22 | 0.644524 0.418362 0.639971 23 | -0.564167 0.497659 0.658826 24 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec024.txt: -------------------------------------------------------------------------------- 1 | 0.132723 0.739879 -0.659517 2 | -0.918278 -0.379929 0.11144 3 | -0.965426 0.153303 0.210835 4 | 0.608607 -0.784469 0.119187 5 | 0.63915 0.437609 0.632444 6 | 0.789542 0.209334 -0.576891 7 | 0.135008 -0.36254 0.922138 8 | 0.344276 0.093474 0.934204 9 | 0.682349 0.70647 0.187884 10 | 0.141671 0.550473 0.822745 11 | 0.699577 -0.167742 0.69459 12 | -0.591356 -0.690452 0.416621 13 | 0.935168 0.136207 0.326968 14 | 0.644819 -0.248547 -0.722795 15 | -0.727042 0.600675 0.332565 16 | -0.156172 0.940576 -0.30154 17 | -0.19618 0.149388 0.969122 18 | 0.293367 0.952754 -0.078708 19 | 0.467415 -0.628758 0.621439 20 | 0.242627 0.862959 0.443209 21 | -0.321942 0.668161 0.670756 22 | 0.229728 -0.943726 -0.237921 23 | -0.391999 -0.321717 0.861879 24 | 0.887686 -0.387799 0.248245 25 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec025.txt: 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/Data/ElectricRepulsion/Elec026.txt: -------------------------------------------------------------------------------- 1 | -0.170472 -0.438955 0.882189 2 | 0.554683 -0.770371 0.314414 3 | 0.345112 -0.727674 -0.59278 4 | -0.416733 0.254294 0.872736 5 | -0.763875 0.349438 0.542576 6 | 0.747465 -0.374683 0.548551 7 | 0.284346 -0.587046 0.757974 8 | 0.636315 -0.740927 -0.214778 9 | -0 0 1 10 | 0.432938 0.379714 0.817546 11 | 0.006321 0.520762 0.853679 12 | 0.451156 -0.136178 0.881994 13 | -0.150889 -0.863141 -0.481893 14 | 0.599057 0.67613 0.428928 15 | 0.226535 0.973861 -0.016605 16 | -0.946988 -0.026404 0.320181 17 | -0.625272 -0.775587 0.0866 18 | -0.765174 -0.460884 0.449549 19 | -0.363201 -0.745474 0.558887 20 | 0.895953 -0.443971 0.012599 21 | -0.592938 -0.176069 0.785763 22 | 0.079483 -0.89904 0.430592 23 | -0.903853 -0.419147 -0.08582 24 | 0.978816 -0.037941 0.201195 25 | 0.791067 0.176959 0.585575 26 | -0.233199 0.968071 0.091965 27 | 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| 0.928918 -0.196774 0.313674 21 | 0.958288 0.284151 -0.030686 22 | 0.674417 -0.210137 0.707817 23 | -0.349431 -0.911036 -0.218888 24 | 0.274834 -0.561372 0.780594 25 | -0.469528 0.803671 0.365589 26 | -0.861943 -0.128115 0.490552 27 | 0.642962 -0.608202 0.465499 28 | -0.569978 0.095177 0.816129 29 | -0.754108 0.41902 0.505711 30 | -------------------------------------------------------------------------------- /Data/ElectricRepulsion/Elec030.txt: -------------------------------------------------------------------------------- 1 | -0.546405 0.619202 0.563943 2 | -0.398931 -0.600006 0.693432 3 | 0.587973 0.521686 0.618168 4 | 0.055894 -0.991971 -0.113444 5 | -0.666933 -0.677984 0.309094 6 | 0.163684 0.533013 0.830123 7 | 0.542826 0.133898 0.829102 8 | -0.074751 -0.350412 0.933608 9 | 0.845751 -0.478624 -0.235847 10 | 0.767148 -0.610673 0.196372 11 | -0.28381 0.381633 0.879664 12 | 0.537228 -0.616249 0.575868 13 | -0.711387 0.197778 0.674398 14 | 0.886511 0.219025 0.407586 15 | 0.296061 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0.8700878468 33 | -0.8572501135 0.5142319729 -0.02622443334 34 | -0.760240549 0.5411420055 0.3594435109 35 | 0.745929629 0.199676203 0.6353883872 36 | -0.3751988688 -0.4749556524 0.7960169201 37 | 0.2678230721 -0.9619108614 0.05475670517 38 | 0.1101757382 0.7877187788 0.6061026581 39 | 0.5494454978 0.5464580393 0.6320547889 40 | -0.4301093025 -0.8230198123 -0.3710045506 41 | 0.5992850211 0.1454368055 -0.7872138205 42 | -------------------------------------------------------------------------------- /Data/PreComputedTables/sh3integral.hdr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DiffusionMRITool/dmritool/860d86b449457312459e40046b41b5ea8b09e930/Data/PreComputedTables/sh3integral.hdr -------------------------------------------------------------------------------- /Data/PreComputedTables/sh3integral.img: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DiffusionMRITool/dmritool/860d86b449457312459e40046b41b5ea8b09e930/Data/PreComputedTables/sh3integral.img -------------------------------------------------------------------------------- /Data/Tessellation/directions_t1.txt: -------------------------------------------------------------------------------- 1 | -0.850651 -0.525731 0 2 | 0.850651 -0.525731 0 3 | 0.525731 0 0.850651 4 | -0.525731 0 0.850651 5 | 0 0.850651 0.525731 6 | 0 -0.850651 0.525731 7 | -------------------------------------------------------------------------------- /Data/Tessellation/directions_t2.txt: -------------------------------------------------------------------------------- 1 | -0.850651 -0.525731 0 2 | 0.850651 -0.525731 0 3 | 0.525731 0 0.850651 4 | -0.525731 0 0.850651 5 | 0 0.850651 0.525731 6 | 0 -0.850651 0.525731 7 | 0.309017 0.5 0.809017 8 | -0.309017 0.5 0.809017 9 | 0 0 1 10 | -0.309017 -0.5 0.809017 11 | 0.309017 -0.5 0.809017 12 | 0.809017 0.309017 0.5 13 | 0.809017 -0.309017 0.5 14 | 1 0 0 15 | -0.809017 -0.309017 0.5 16 | -0.809017 0.309017 0.5 17 | 0.5 0.809017 0.309017 18 | -0.5 0.809017 0.309017 19 | 0 -1 0 20 | 0.5 -0.809017 0.309017 21 | -0.5 -0.809017 0.309017 22 | -------------------------------------------------------------------------------- /Documentation/Doxygen/Modules.dox: -------------------------------------------------------------------------------- 1 | 2 | /** \defgroup utl 3 | * \brief helper functions and classes. 4 | **/ 5 | 6 | /** \defgroup utlMath 7 | * \brief math related helper functions. 8 | * \ingroup utl Math 9 | **/ 10 | 11 | /** \defgroup utlHelperFunctions 12 | * \brief helper functions. 13 | * \ingroup utl 14 | **/ 15 | 16 | /** 17 | * \defgroup utlNDArray 18 | * \brief utl::NDArray with supports for expression template, blas, mkl. 19 | * \ingroup utl 20 | **/ 21 | 22 | /** \defgroup Math 23 | * \brief math related functions and classes. 24 | **/ 25 | 26 | /** 27 | * \defgroup OptimizationSolver 28 | * \brief Solvers for optimization problems. 29 | * \ingroup Math 30 | **/ 31 | 32 | /** 33 | * \defgroup SamplingScheme 34 | * \brief Sampling scheme in q-space. 35 | **/ 36 | 37 | /** \defgroup DWIProcessing 38 | * \brief simulation and processing of DWI. 39 | **/ 40 | 41 | /** 42 | * \defgroup DiffusionModels 43 | * \brief Diffusion models used in diffusion data reconstruction. 44 | **/ 45 | 46 | /** 47 | * \defgroup Visualization 48 | * \brief Visualization of diffusion data. 49 | **/ 50 | -------------------------------------------------------------------------------- /Documentation/Sphinx/HelperFunctions.rst: -------------------------------------------------------------------------------- 1 | ../../Modules/HelperFunctions/README.rst -------------------------------------------------------------------------------- /Documentation/Sphinx/_static/GitHub.png: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | ============ 2 | Code Modules 3 | ============ 4 | 5 | .. meta:: 6 | :description: code modules of dmritool 7 | .. include:: meta_keywords.txt 8 | .. include:: links.inc 9 | 10 | .. toctree:: 11 | :maxdepth: 2 12 | 13 | HelperFunctions 14 | 15 | -------------------------------------------------------------------------------- /Documentation/Sphinx/developers.rst: -------------------------------------------------------------------------------- 1 | ========== 2 | Developers 3 | ========== 4 | 5 | .. meta:: 6 | :description: developers of dmritool 7 | .. include:: meta_keywords.txt 8 | .. include:: links.inc 9 | 10 | DMRITool core development team includes: 11 | 12 | * **Jian Cheng**, `Section on Quantitative Imaging and Tissue Sciences (SQITS)`_, `National Institutes of Health`_ 13 | 14 | 15 | Some wonderful contributors: 16 | 17 | * **Pew-Thian Yap**, `MIND Lab`_, `IDEA Group`_, `University of North Carolina at Chapel Hill`_ 18 | 19 | 20 | People who are interested in diffusion MRI methodologies are welcome to join the development team. 21 | We can collaborate via `github `__. 22 | 23 | Online web statistics on the DMRITool_ development activity are available below: 24 | 25 | .. raw:: html 26 | 27 | 28 | 29 | 32 | 35 | 36 |
30 | 31 | 33 | 34 |
37 | -------------------------------------------------------------------------------- /Documentation/Sphinx/license.rst: -------------------------------------------------------------------------------- 1 | 2 | ======= 3 | License 4 | ======= 5 | 6 | .. meta:: 7 | :description: license of dmritool 8 | .. include:: meta_keywords.txt 9 | .. include:: links.inc 10 | 11 | License for DMRITool 12 | ==================== 13 | 14 | DMRITool_ is a free open source software. It is currently under the GPL_, 15 | because it uses GSL_ for mathematical special functions and spams_ for some optimization problems. 16 | 17 | The software under the license is distributed on an "as is" basis, without warranties. 18 | It is user's responsibility to validate the behavior of the routines and their accuracy using the released source code. 19 | 20 | 21 | Licenses for third parties 22 | ========================== 23 | 24 | spams 25 | ----- 26 | 27 | See folder ``ThirdParty/Spams``. 28 | It was modified from Spams_ which uses GPL_ license. 29 | 30 | 31 | vtkviewer 32 | --------- 33 | 34 | See folder ``QTApplications/vtkviewer``. 35 | It was modified from vtkviewer_ which uses Apache License. 36 | 37 | 38 | Electrostatic point sets 39 | ------------------------ 40 | 41 | See folder ``Data/ElectricRepulsion``. 42 | The electrostatic point sets were copied from CAMINO_ which is under Artistic License. 43 | 44 | Spherical packing point sets 45 | ---------------------------- 46 | 47 | See folder ``Data/Packing``. 48 | The spherical packing point sets were copied from `Neil J. A. Sloane' collection `__. 49 | 50 | -------------------------------------------------------------------------------- /Documentation/Sphinx/meta_keywords.txt: -------------------------------------------------------------------------------- 1 | .. meta:: 2 | :keywords: Diffusion MRI, software, tool, dmritool, diffusionmritool, 3 | dmri, Spherical Polar Fourier Imaging, Spherical Polar Fourier, 4 | Sampling scheme, Uniform sampling, sphere, 5 | HARDI, Orientation Distribution Function, ODF, Ensemble Average Propagator, EAP, Diffusion Propagator, 6 | q-space, q space, 7 | visualization, spherical function, spherical harmonics 8 | 9 | 10 | 11 | .. |br| raw:: html 12 | 13 |
14 | -------------------------------------------------------------------------------- /Documentation/Sphinx/newCommands.tex: -------------------------------------------------------------------------------- 1 | 2 | \newcommand{\q}{\ensuremath{\mathbf{q}}} 3 | \newcommand{\uu}{\ensuremath{\mathbf{u}}} 4 | \newcommand{\rr}{\ensuremath{\mathbf{r}}} 5 | \newcommand{\RR}{\ensuremath{\mathbf{R}}} 6 | 7 | \newcommand{\VV}[1]{\ensuremath{\textbf{\textit{#1}}}} 8 | \newcommand{\Vt}{\mathbi{t}} 9 | \newcommand{\Vx}{\mathbi{x}} 10 | \newcommand{\Vy}{\mathbi{y}} 11 | \newcommand{\Vz}{\mathbi{z}} 12 | \newcommand{\Vu}{\mathbi{u}} 13 | \newcommand{\Vv}{\mathbi{v}} 14 | \newcommand{\Vc}{\mathbi{c}} 15 | \newcommand{\Vb}{\mathbi{b}} 16 | \newcommand{\Va}{\mathbi{a}} 17 | \newcommand{\Ve}{\mathbi{e}} 18 | \newcommand{\Vw}{\mathbi{w}} 19 | \newcommand{\Vm}{\mathbi{m}} 20 | 21 | -------------------------------------------------------------------------------- /Documentation/Sphinx/support.rst: -------------------------------------------------------------------------------- 1 | 2 | ======= 3 | Support 4 | ======= 5 | 6 | .. meta:: 7 | :description: support of dmritool 8 | .. include:: meta_keywords.txt 9 | .. include:: links.inc 10 | 11 | Thank you for your interests on DMRITool_. 12 | We are glad to hear your feedback and support you. 13 | 14 | Mailing List 15 | ============ 16 | 17 | If you have questions about DMRITool_, please contact us via dmritool-discussion@www.nitrc.org. 18 | We are glad to answer your questions when you post them to the mailing list. 19 | For support and discussion, please subscribe to the dmritool-discussion_ mailing list by `nitrc `__. 20 | 21 | Issue Tracker 22 | ============= 23 | 24 | If you want to require a new feature or report a bug, please use `the issue tracker in github `__. 25 | 26 | .. include:: links.inc 27 | -------------------------------------------------------------------------------- /Documentation/Sphinx/tools/make_tutorial_outputs.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | """ 3 | Generate outputs for tutorils. 4 | It may take a long time 5 | """ 6 | 7 | import os, subprocess, argparse 8 | 9 | parser = argparse.ArgumentParser(description=__doc__) 10 | parser.add_argument('sphinxDir', nargs=1, help='dmritool sphinx dir') 11 | args = parser.parse_args() 12 | 13 | sphinxDir = os.path.abspath(args.sphinxDir[0]) 14 | origWD = os.getcwd() 15 | 16 | f = open(os.path.join(sphinxDir, 'tutoriallist.txt'),"r") 17 | tutorial_list = f.readlines() 18 | f.close() 19 | tutorial_list = [t.strip() for t in tutorial_list if t.strip() ] 20 | 21 | for tutorial in tutorial_list: 22 | 23 | print '\n#Tutorial: ', tutorial 24 | rstfile = os.path.join(sphinxDir, tutorial + '.rst') 25 | if not os.path.isfile(rstfile): 26 | raise Exception('no file: ' + rstfile) 27 | 28 | runpath = os.path.join(sphinxDir, '.' + tutorial) 29 | if os.path.exists(runpath): 30 | subprocess.call(['rm', '-rf', runpath]) 31 | os.makedirs(runpath) 32 | os.chdir(runpath) 33 | 34 | shfile = os.path.join(runpath, tutorial + '.sh') 35 | subprocess.call(('python', os.path.join(sphinxDir, 'tools/extract_bash_from_rst.py'), rstfile, shfile, '--with-comments' )) 36 | subprocess.call(['sh', shfile]) 37 | 38 | os.chdir(origWD) 39 | 40 | -------------------------------------------------------------------------------- /Documentation/Sphinx/tools/publish_matlabdemos.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash - 2 | 3 | matlab -nosplash -nodesktop -r " \ 4 | publish('demo_separate_sets.m');\ 5 | publish('demo_separate_t4_1shell.m');\ 6 | publish('demo_separate_t4_28x3.m');\ 7 | publish('demo_separate_HCPQ390x3_30x3.m');\ 8 | publish('demo_separate_HCPQ390x3_45x3.m');\ 9 | publish('demo_mutishell_IMOC_1Opt_CNLO.m');\ 10 | publish('demo_singleshell_IMOC_1Opt_CNLO.m');\ 11 | exit;" 12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /Documentation/Sphinx/tools/upload_doxygen.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash - 2 | 3 | repo="git@github.com:DiffusionMRITool/dmritool-doxygen.git" 4 | 5 | USAGE="$0 DMRITOOL_BUILD_DIR" 6 | BUILD_DIR=$1 7 | if [ -z "$BUILD_DIR" ]; then 8 | echo $USAGE 9 | exit 1 10 | fi 11 | 12 | HTML_DIR=${BUILD_DIR}/Documentation/Doxygen/html 13 | 14 | if [ ! -e "$HTML_DIR/index.html" ]; then 15 | echo "$HTML_DIR does not contain an index.html" 16 | exit 1 17 | fi 18 | 19 | cd $HTML_DIR 20 | rm -rf .git 21 | git init 22 | git checkout -b gh-pages 23 | git add * -f 24 | touch .nojekyll 25 | git add .nojekyll 26 | git commit -a -m "Doxygen document. No history." 27 | git remote add origin $repo 28 | git push origin gh-pages --force 29 | rm -rf .git 30 | -------------------------------------------------------------------------------- /Documentation/Sphinx/tools/upload_ghpages.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash - 2 | 3 | repo="git@github.com:DiffusionMRITool/DiffusionMRITool.github.io.git" 4 | 5 | DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd ) 6 | HTML_DIR=${DIR}/../_build/html 7 | 8 | if [ ! -e "$HTML_DIR/index.html" ]; then 9 | echo "$HTML_DIR does not contain an index.html" 10 | exit 1 11 | fi 12 | 13 | cd $HTML_DIR 14 | rm -rf .git 15 | git init 16 | git add * -f 17 | touch .nojekyll 18 | git add .nojekyll 19 | git commit -a -m "dmritool homepage by sphinx. No history." 20 | git remote add origin $repo 21 | git push origin master --force 22 | rm -rf .git 23 | -------------------------------------------------------------------------------- /Documentation/Sphinx/tutoriallist.txt: -------------------------------------------------------------------------------- 1 | tutorial_dwisimulation 2 | tutorial_qspacesampling 3 | tutorial_spfi 4 | -------------------------------------------------------------------------------- /Documentation/Sphinx/tutorials.rst: -------------------------------------------------------------------------------- 1 | ========= 2 | Tutorials 3 | ========= 4 | 5 | .. meta:: 6 | :description: tutorials of dmritool 7 | .. include:: meta_keywords.txt 8 | .. include:: links.inc 9 | 10 | .. toctree:: 11 | :maxdepth: 2 12 | 13 | tutorial_dwisimulation 14 | tutorial_spfi 15 | tutorial_qspacesampling 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | -------------------------------------------------------------------------------- /Examples/Elec060.txt: -------------------------------------------------------------------------------- 1 | ../Data/ElectricRepulsion/Elec060.txt -------------------------------------------------------------------------------- /Examples/directions_t3.txt: -------------------------------------------------------------------------------- 1 | ../Data/Tessellation/directions_t3.txt -------------------------------------------------------------------------------- /Examples/directions_t4.txt: -------------------------------------------------------------------------------- 1 | ../Data/Tessellation/directions_t4.txt -------------------------------------------------------------------------------- /Examples/dwi_crossingCylinder_3x3.txt: -------------------------------------------------------------------------------- 1 | NDims = 3 2 | DimSize = 3 3 1 3 | ElementSpacing = 1 1 1 4 | Scale = 1 5 | RicianNoiseSigma = 0 6 | BackgroundScale = 1 7 | ModelType = CYLINDER_SPHERICAL_MODEL 8 | 9 | DiffusionParameters = 0 1 0 90 0 1 10 | DiffusionParameters = 2 1 0 90 0 1 11 | DiffusionParameters = 1 0 0 90 90 1 12 | DiffusionParameters = 1 2 0 90 90 1 13 | DiffusionParameters = 1 1 0 90 90 0.5 90 0 0.5 14 | 15 | 16 | -------------------------------------------------------------------------------- /Examples/dwi_diagonal_spherical.txt: -------------------------------------------------------------------------------- 1 | NDims = 3 2 | DimSize = 4 4 1 3 | ElementSpacing = 2 2 2 4 | Scale = 1 5 | RicianNoiseSigma = 0 6 | BackgroundScale = 1 7 | 8 | ModelType = SYMMETRICAL_TENSOR_IN_SPHERICAL_COORDS 9 | 10 | DiffusionParameters = 1 1 0 90 45 0.0015 0.0003 0.5 90 -15 0.0015 0.0003 0.5 11 | DiffusionParameters = 0 1 0 90 45 0.0015 0.0003 1 12 | DiffusionParameters = 1 0 0 90 -15 0.0015 0.0003 1 13 | DiffusionParameters = 2 2 0 90 45 0.0015 0.0003 1 14 | 15 | BackgroundDiffusionParameters = 0 0 0.0007 0.0007 1 16 | 17 | 18 | -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- 1 | /* 2 | * 3 | * Copyright 2013-present by the DMRITOOL development team 4 | * 5 | * Licensed under the GNU General Public License; 6 | * you may not use this file except in compliance with the License. 7 | * You may obtain a copy of the License at 8 | * 9 | * http://www.gnu.org/copyleft/gpl.html 10 | * 11 | * Unless required by applicable law or agreed to in writing, software 12 | * distributed under the License is distributed on an "AS IS" BASIS, 13 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 | * See the License for the specific language governing permissions and 15 | * limitations under the License. 16 | * 17 | * 18 | */ 19 | -------------------------------------------------------------------------------- /Matlab/Demos/demo_separate_t4_1shell.m: -------------------------------------------------------------------------------- 1 | %% Uniformly select a single subset from a given set 2 | % 3 | % This is a demo to uniformly separate a subset from a given set by 4 | % using Mixed Integer Linear Programming (MILP) 5 | % 6 | % 7 | % Reference: 8 | % 9 | % 1. "Single- and Multiple-Shell Uniform Sampling Schemes for Diffusion MRI Using Spherical Codes", 10 | % Jian Cheng, Dinggang Shen, Pew-Thian Yap, Peter J. Basser, IEEE Transactions on Medical Imaging, 2017. 11 | % 12 | % 2. "Designing Single- and Multiple-Shell Sampling Schemes for Diffusion MRI Using Spherical Code", 13 | % Jian Cheng, Dinggang Shen, Pew-Thian Yap, MICCAI 2014. 14 | % 15 | % Copyright (c) 2013, Jian Cheng (jian.cheng.1983@gmail.com) 16 | % 17 | 18 | %% read sphere tessellation with 321 samples in the hemisphere 19 | grad_t4 = ReadDirections([getenv('HOME'), '/.dmritool/Data/Tessellation/directions_t4.txt']); 20 | 21 | VisualizeMultiShellScheme(grad_t4); 22 | title(['Sphere tessellation with 321 samples in the hemisphere']); 23 | 24 | %% extract 30 samples from grad_t4 using MILP 25 | clear params grbParams 26 | params.numSamples = 30; 27 | % set a lower bound, it can be 0 or covering radius from an existing scheme 28 | params.lbCost = 0.24; 29 | 30 | % grb parameters 31 | % MIPFocus 1 seems better 32 | grbParams.MIPFocus=1; 33 | % set time limit as 10 minutes or more 34 | grbParams.TimeLimit=600; 35 | % print verbose output from gurobi 36 | grbParams.OutputFlag=true; 37 | % grbParams.OutputFlag=false; 38 | % params.ModelFile='model.mps'; 39 | 40 | % run 41 | [grad,grb] = OptimalSamplingSingleSubset(grad_t4, params, grbParams); 42 | 43 | %% visualize the result 44 | VisualizeMultiShellScheme(grad); 45 | title({'Estimated Scheme.', ['Covering radius = ', num2str(CoveringRadius(grad)*180/pi), ' degree']}); 46 | -------------------------------------------------------------------------------- /Matlab/README.md: -------------------------------------------------------------------------------- 1 | 2 | Matlab Codes 3 | ============ 4 | 5 | This folder contains some prototype matlab codes. 6 | These codes are mainly used for demos. 7 | Some codes will be re-implemented using c++ in dmritool for better efficiency. 8 | -------------------------------------------------------------------------------- /Matlab/SamplingScheme/CartesianToSpherical.m: -------------------------------------------------------------------------------- 1 | function [theta, phi, r] = CartesianToSpherical(x,y,z) 2 | % Convert x,y,z to theta, phi, r. 3 | % 4 | % x = r.*sin(theta).*cos(phi) 5 | % y = r.*sin(theta).*sin(phi) 6 | % z = r.*cos(theta) 7 | % 8 | % USAGE: 9 | % [theta, phi, r] = CartesianToSpherical(x,y,z) 10 | % 11 | % INPUT 12 | % x : Nx1 vector with x coordinates. 13 | % y : Nx1 vector with y coordinates. 14 | % z : Nx1 vector with z coordinates. 15 | % 16 | % OUTPUT 17 | % theta, phi, r : Nx1 vectors 18 | % 19 | % Copyright (c) 2014, Jian Cheng 20 | % 21 | 22 | r = sqrt(x.^2+y.^2+z.^2); 23 | if (r==0) 24 | theta = 0; 25 | phi = 0; 26 | else 27 | theta = acos(z./r); 28 | phi = atan2(y,x); 29 | end 30 | -------------------------------------------------------------------------------- /Matlab/SamplingScheme/CoveringRadius.m: -------------------------------------------------------------------------------- 1 | function radius = CoveringRadius(grad, ind) 2 | % Calculate the covering radius of the given samples. 3 | % 4 | % USAGE: 5 | % radius = CoveringRadius(grad) 6 | % radius = CoveringRadius(grad, ind) 7 | % 8 | % INPUT 9 | % grad : Nx3 matrix, each row is a point in sphere. 10 | % ind : If it is given, calculate the minimal distance between 11 | % the ind-th sample and the other samples in grad. 12 | % 13 | % 14 | % OUTPUT 15 | % radius : covering radius, i.e., the minimal spherical distance between any two samples. 16 | % 17 | % 18 | % References: 19 | % 1. http://mathworld.wolfram.com/SphericalCode.html 20 | % 2. "Single- and Multiple-Shell Uniform Sampling Schemes for Diffusion MRI Using Spherical Codes", 21 | % Jian Cheng, Dinggang Shen, Pew-Thian Yap, Peter J. Basser, IEEE Transactions on Medical Imaging, 2017. 22 | % 3. "Designing Single- and Multiple-Shell Sampling Schemes for Diffusion MRI Using Spherical Code", 23 | % Jian Cheng, Dinggang Shen, Pew-Thian Yap, MICCAI 2014. 24 | % 4. "Novel single and multiple shell uniform sampling schemes for diffusion MRI using spherical codes", 25 | % Jian Cheng, Dinggang Shen, Pew-Thian Yap, Peter J. Basser, MICCAI 2015. 26 | % 27 | % Copyright (c) 2014, Jian Cheng 28 | % 29 | 30 | %% 31 | if nargin == 1 32 | innerProductAll = abs(grad*grad'); 33 | radius = acos(max(innerProductAll(triu(innerProductAll,1)>0))); 34 | else 35 | if ind>size(grad,1) || ind<=0 36 | error('wrong index'); 37 | end 38 | innerProduct = abs(grad(ind,:)*grad'); 39 | radius = acos(max([innerProduct(1:ind-1), innerProduct(ind+1:end)])); 40 | end 41 | 42 | -------------------------------------------------------------------------------- /Matlab/SamplingScheme/CoveringRadiusUpperBound.m: -------------------------------------------------------------------------------- 1 | function ub = CoveringRadiusUpperBound(N) 2 | % calculate the upper bound () of the minimal distance for a given number of points. 3 | % Note: for N antipodal symmetric samples, use CoveringRadiusUpperBound(2*N). 4 | % 5 | % USAGE: 6 | % ub = CoveringRadiusUpperBound(N) 7 | % 8 | % INPUT 9 | % N : an integer number. 10 | % 11 | % 12 | % OUTPUT 13 | % up : an upper bound (spherical distance in radian) 14 | % 15 | % References: 16 | % 1. http://mathworld.wolfram.com/SphericalCode.html 17 | % 2. "Single- and Multiple-Shell Uniform Sampling Schemes for Diffusion MRI Using Spherical Codes", 18 | % Jian Cheng, Dinggang Shen, Pew-Thian Yap, Peter J. Basser, IEEE Transactions on Medical Imaging, 2017. 19 | % 3. "Designing Single- and Multiple-Shell Sampling Schemes for Diffusion MRI Using Spherical Code", 20 | % Jian Cheng, Dinggang Shen, Pew-Thian Yap, MICCAI 2014. 21 | % 22 | % 23 | % Copyright (c) 2014, Jian Cheng 24 | % 25 | 26 | %% 27 | upperBoundEuc = sqrt( 4-csc( pi*N./(6*(N-2)) ).^2 ); 28 | ub = acos((2.0-upperBoundEuc.*upperBoundEuc)./2.0); 29 | 30 | end 31 | -------------------------------------------------------------------------------- /Matlab/SamplingScheme/GetGradAllShells.m: -------------------------------------------------------------------------------- 1 | function gradAll = GetGradAllShells(gradCell) 2 | % Get Nx3 gradient table from gradients in all shells. 3 | % 4 | % USAGE: 5 | % gradAll = GetGradAllShells(gradCell) 6 | % 7 | % INPUT 8 | % gradCell : a cell array with M gradient matrix from M shells. 9 | % 10 | % 11 | % OUTPUT 12 | % gradAll : Nx3 gradient matrix from all M shells. 13 | % 14 | % Copyright (c) 2014, Jian Cheng 15 | % 16 | 17 | numShells = numel(gradCell); 18 | numSamples = zeros(numShells,1); 19 | for i = 1 : numShells 20 | [numSamples(i),~] = size(gradCell{i}); 21 | end 22 | 23 | gradAll = zeros(sum(numSamples),3); 24 | index=1; 25 | for k = 1 : numShells 26 | gradAll(index:index+numSamples(k)-1,:) = gradCell{k}; 27 | index = index+numSamples(k); 28 | end 29 | 30 | end 31 | -------------------------------------------------------------------------------- /Matlab/SamplingScheme/ReadDirections.m: -------------------------------------------------------------------------------- 1 | function grad = ReadDirections(filename) 2 | % read direction file into a matrix 3 | % 4 | % USAGE: 5 | % grad = ReadDirections(filename) 6 | % 7 | % INPUT 8 | % filename : direction file name (.txt) 9 | % 10 | % 11 | % OUTPUT 12 | % grad : Nx3 matrix, each row is a point in sphere. 13 | % 14 | % Copyright (c) 2014, Jian Cheng 15 | % 16 | 17 | 18 | %% 19 | fid = fopen(filename); 20 | gradC = textscan(fid, '%f %f %f'); 21 | fclose(fid); 22 | 23 | % for some directions which the first line shows the number of directions 24 | grad = [gradC{1} gradC{2} gradC{3}]; 25 | if int16(grad(1,1)) == grad(1,1) && grad(1,2)~=grad(1,2) 26 | grad = grad(2:end, :); 27 | end 28 | 29 | normFactor = sqrt(sum(grad.^2,2)); 30 | for i = 1 : size(grad,1) 31 | if (normFactor(i)>0) 32 | grad(i,:) = grad(i,:) / normFactor(i); 33 | end 34 | end 35 | 36 | -------------------------------------------------------------------------------- /Matlab/SamplingScheme/VisualizeMultiShellScheme.m: -------------------------------------------------------------------------------- 1 | function VisualizeMultiShellScheme(varargin) 2 | % visualize single or multiple shell schemes 3 | % 4 | % USAGE: 5 | % VisualizeMultiShellScheme(grad1) 6 | % VisualizeMultiShellScheme(grad1, grad2, grad3) 7 | % 8 | % INPUT 9 | % varargin : One or more matrix for schemes in different shells. 10 | % Each matrix has size N_ix3, N_i is the number of samples in the i-th shell. 11 | % 12 | % Copyright (c) 2014, Jian Cheng 13 | % 14 | 15 | 16 | colors{1} = 'ro'; 17 | colors{2} = 'go'; 18 | colors{3} = 'bo'; 19 | colors{4} = 'co'; 20 | colors{5} = 'ko'; 21 | ss=100; 22 | 23 | figure; 24 | axis equal; 25 | allDirection = []; 26 | for i = 1 : nargin 27 | direction = varargin{i}; 28 | scatter3([direction(:,1);-direction(:,1)], [direction(:,2); -direction(:,2)], [direction(:,3); -direction(:,3)],ss, colors{i}, 'filled'); hold on; 29 | allDirection=[allDirection; direction; -direction; ]; 30 | end 31 | 32 | DT=DelaunayTri(allDirection); 33 | tetramesh(DT, 'FaceColor', [0.8 0.8 0.8]); axis equal; 34 | rotate3d 35 | 36 | -------------------------------------------------------------------------------- /Matlab/SamplingScheme/WriteDirections.m: -------------------------------------------------------------------------------- 1 | function WriteDirections(grad, gradStr) 2 | % Write gradient table to a file 3 | % 4 | % USAGE: 5 | % WriteDirections(grad, gradStr) 6 | % 7 | % INPUT: 8 | % grad : Nx3 matrix 9 | % gradStr : output file name 10 | % 11 | % Copyright (c) 2014, Jian Cheng 12 | % 13 | 14 | 15 | dlmwrite(gradStr, grad, 'delimiter',' ','precision',8); 16 | 17 | -------------------------------------------------------------------------------- /Matlab/Utils/CopyDefaultStructParams.m: -------------------------------------------------------------------------------- 1 | function paramReal = CopyDefaultStructParams(paramDefault, param) 2 | % Copy default parameter struct into a given user parameter struct 3 | % 4 | % USAGE: 5 | % paramReal = CopyDefaultStructParams(paramDefault, param) 6 | % 7 | % INPUT 8 | % paraDefault : Parameter struct with all default values. 9 | % param : The input parameter 10 | % 11 | % INPUT 12 | % paramReal : Real parameter struct used in the following codes with a combination of paramDefault and param. 13 | % The default values in paramDefault are overriden by param 14 | % 15 | % Copyright (c) 2014, Jian Cheng (jian.cheng.1983@gmail.com) 16 | % 17 | 18 | %% 19 | fields = fieldnames(paramDefault); 20 | paramReal = param; 21 | 22 | for i = 1 : numel(fields) 23 | if ~isfield(param, fields{i}) 24 | paramReal = setfield(paramReal, fields{i}, getfield(paramDefault, fields{i})); 25 | end 26 | end 27 | 28 | -------------------------------------------------------------------------------- /Modules/Common/test/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_test_application(itkVectorImageRegionIteratorWithIndexTest itkVectorImageRegionIteratorWithIndexTest ${ITK_LIBRARIES}) 3 | 4 | add_clp_test_application(itkUnaryFunctorVectorImageFilterTest itkUnaryFunctorVectorImageFilterTest ${ITK_LIBRARIES} ${BLAS_LIBRARIES}) 5 | -------------------------------------------------------------------------------- /Modules/DWIProcessing/test/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_clp_test_application(itkDWIReaderTest itkDWIReaderTest ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES}) 2 | 3 | -------------------------------------------------------------------------------- /Modules/DiffusionModels/test/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_clp_test_application(itkSHBasisGeneratorTest itkSHBasisGeneratorTest ${ITK_LIBRARIES} ${GSL_LIBRARIES}) 2 | add_test_application(itkDiffusionTensorTest itkDiffusionTensorTest ${ITK_LIBRARIES}) 3 | 4 | -------------------------------------------------------------------------------- /Modules/DiffusionModels/test/itkSHBasisGeneratorTest.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file test_SHBasis.cxx 3 | * @brief 4 | * 5 | * 6 | * @author Dr. Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * @internal 9 | * Created "09-20-2012 10 | * Revision 1.0 11 | * Compiler gcc/g++ 12 | * Company IDEA@UNC-CH 13 | * Copyright Copyright (c) 2012, Jian Cheng 14 | * 15 | * ===================================================================================== 16 | */ 17 | 18 | 19 | #include "itkSHBasisGeneratorTestCLP.h" 20 | #include "utl.h" 21 | 22 | 23 | 24 | /** 25 | * \brief test Spherical Harmonic basis 26 | */ 27 | int 28 | main (int argc, char const* argv[]) 29 | { 30 | 31 | // GenerateCLP 32 | PARSE_ARGS; 33 | 34 | typedef float TScalarType; 35 | 36 | typedef utl::NDArray MatrixType; 37 | utl_shared_ptr mat = utl::ReadGrad(_dataOrientationsFile, DIRECTION_NODUPLICATE, CARTESIAN_TO_CARTESIAN); 38 | std::cout << "mat = \n" << *mat << std::endl << std::flush; 39 | 40 | utl_shared_ptr matT3 = utl::ReadGrad(3, DIRECTION_NODUPLICATE, CARTESIAN_TO_CARTESIAN); 41 | std::cout << "mat t3 = \n" << *matT3 << std::endl << std::flush; 42 | 43 | 44 | utl_shared_ptr basisMatrix = utl::ComputeSHMatrix(4, *matT3, CARTESIAN_TO_SPHERICAL); 45 | 46 | if (_verbose) 47 | std::cout << "basisMatrix: \n" << *basisMatrix; 48 | 49 | return 0; 50 | } 51 | -------------------------------------------------------------------------------- /Modules/DiffusionModels/test/itkSHBasisGeneratorTest.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Test 4 | Test the Spherical Harmonic Basis 5 | Test the Spherical Harmonic Basis. 6 | 7 | Jian Cheng (jian.cheng.1983@gmail.com) 8 | 9 | 10 | 11 | _dataOrientationsFile 12 | 13 | Text file that contains the gradient orientations of the data 14 | 0 15 | input 16 | 17 | 18 | 19 | _maxOrder 20 | 4 21 | 22 | Maximum order (rank) 23 | r 24 | --maxorder 25 | 26 | 27 | 28 | _verbose 29 | 30 | v 31 | verbose 32 | --verbose 33 | false 34 | 35 | 36 | 37 | 38 | 39 | -------------------------------------------------------------------------------- /Modules/HelperFunctions/include/utlConstants.h: -------------------------------------------------------------------------------- 1 | /** 2 | * @file utlConstants.h 3 | * @brief 4 | * Created "09-22-2016 5 | * 6 | * @author Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * ===================================================================================== 9 | */ 10 | 11 | #ifndef __utlConstants_h 12 | #define __utlConstants_h 13 | 14 | #include "utlSTDHeaders.h" 15 | 16 | namespace utl 17 | { 18 | 19 | /** @addtogroup utlMath 20 | @{ */ 21 | 22 | /** Pi */ 23 | __UTL_constexpr static double PI = 3.14159265358979323846264338328; 24 | /** E */ 25 | __UTL_constexpr static double E = 2.71828182845904523536028747135; 26 | /** log_2 (e) */ 27 | __UTL_constexpr static double LOG2E = 1.44269504088896340735992468100; 28 | /** log_10 (e) */ 29 | __UTL_constexpr static double LOG10E = 0.43429448190325182765112891892; 30 | /** sqrt(2) */ 31 | __UTL_constexpr static double SQRT2 = 1.41421356237309504880168872421; 32 | /** sqrt(1/2) */ 33 | __UTL_constexpr static double SQRT1_2 = 0.70710678118654752440084436210; 34 | /** sqrt(3) */ 35 | __UTL_constexpr static double SQRT3 = 1.73205080756887729352744634151; 36 | /** Pi/2 */ 37 | __UTL_constexpr static double PI_2 = 1.57079632679489661923132169164; 38 | /** Pi/4 */ 39 | __UTL_constexpr static double PI_4 = 0.78539816339744830961566084582; 40 | /** sqrt(Pi) */ 41 | __UTL_constexpr static double SQRTPI = 1.77245385090551602729816748334; 42 | 43 | 44 | /** @} */ 45 | 46 | } 47 | 48 | 49 | #endif 50 | -------------------------------------------------------------------------------- /Modules/HelperFunctions/include/utlITKConceptChecking.h: -------------------------------------------------------------------------------- 1 | /** 2 | * @file utlITKConceptChecking.h 3 | * @brief 4 | * Created "06-10-2016 5 | * 6 | * @author Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * ===================================================================================== 9 | */ 10 | 11 | #ifndef __utlITKConceptChecking_h 12 | #define __utlITKConceptChecking_h 13 | 14 | #include 15 | 16 | namespace itk 17 | { 18 | 19 | namespace Detail 20 | { 21 | } 22 | 23 | namespace Concept 24 | { 25 | 26 | template< int D1, int D2 > 27 | struct SameInteger 28 | { 29 | struct Constraints 30 | { 31 | typedef Detail::UniqueType_int< D1 > DT1; 32 | typedef Detail::UniqueType_int< D2 > DT2; 33 | void constraints() 34 | { 35 | DT1 a = DT2(); 36 | 37 | Detail::IgnoreUnusedVariable(a); 38 | } 39 | }; 40 | itkConceptConstraintsMacro(); 41 | }; 42 | 43 | 44 | } 45 | 46 | } 47 | 48 | 49 | #endif 50 | -------------------------------------------------------------------------------- /Modules/HelperFunctions/include/utlOpenMP.h: -------------------------------------------------------------------------------- 1 | /** 2 | * @file utlOpenMP.h 3 | * @brief 4 | * 5 | * 6 | * @author Dr. Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * @internal 9 | * Created "06-15-2014 10 | * Revision 1.0 11 | * Compiler gcc/g++ 12 | * Company IDEA@UNC-CH 13 | * Copyright Copyright (c) 2014, Jian Cheng 14 | * 15 | * ===================================================================================== 16 | */ 17 | 18 | #ifndef __utlOpenMP_h 19 | #define __utlOpenMP_h 20 | 21 | 22 | #include 23 | 24 | namespace utl 25 | { 26 | 27 | } 28 | 29 | 30 | #endif 31 | -------------------------------------------------------------------------------- /Modules/HelperFunctions/include/utlVTKMacro.h: -------------------------------------------------------------------------------- 1 | /** 2 | * @file utlVTKMacro.h 3 | * @brief 4 | * Created "02-18-2015 5 | * 6 | * @author Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * ===================================================================================== 9 | */ 10 | 11 | #ifndef __utlVTKMacro_h 12 | #define __utlVTKMacro_h 13 | 14 | /** @addtogroup utlHelperFunctions 15 | @{ */ 16 | 17 | #if VTK_MAJOR_VERSION <= 5 18 | #define vtkSetInputData(x,y) do { (x)->SetInput(y); } while (0) 19 | #define vtkAddInputData(x,y) do { (x)->AddInput(y); } while (0) 20 | #else 21 | #define vtkSetInputData(x,y) do { (x)->SetInputData(y); } while(0) 22 | #define vtkAddInputData(x,y) do { (x)->AddInputData(y); } while(0) 23 | #endif 24 | 25 | /** @} */ 26 | 27 | #endif 28 | -------------------------------------------------------------------------------- /Modules/HelperFunctions/test/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_test_application(utlVNLBlasTest utlVNLBlasTest ${BLAS_LIBRARIES} ${ITK_LIBRARIES} ) 3 | add_test_application(utlGradientTest utlGradientTest ${BLAS_LIBRARIES} ${ITK_LIBRARIES} ) 4 | 5 | add_gtest_application(utlDMRIGTest utlDMRIGTest ${BLAS_LIBRARIES} ${ITK_LIBRARIES}) 6 | add_gtest_application(utlCoreGTest utlCoreGTest) 7 | add_gtest_application(utlCoreMKLGTest utlCoreMKLGTest ${MKL_LIBRARIES} ${ITK_LIBRARIES}) 8 | add_gtest_application(utlGTest utlGTest ${ITK_LIBRARIES} ${GSL_LIBRARIES}) 9 | add_gtest_application(utlMathGTest utlMathGTest) 10 | add_gtest_application(utlVNLBlasGTest utlVNLBlasGTest ${BLAS_LIBRARIES} ${ITK_LIBRARIES} ) 11 | add_gtest_application(utlVNLLapackGTest utlVNLLapackGTest ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES} ) 12 | 13 | add_gtest_application(utlNDArrayGTest utlNDArrayGTest ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES}) 14 | add_gtest_application(utlVectorGTest utlVectorGTest ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES}) 15 | add_gtest_application(utlMatrixGTest utlMatrixGTest ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES}) 16 | add_gtest_application(utl4thOrderTensorGTest utl4thOrderTensorGTest ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES}) 17 | 18 | # add_gtest_application(utlANNGTest utlANNGTest ANN ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES}) 19 | -------------------------------------------------------------------------------- /Modules/HelperFunctions/test/utlDMRIGTest.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file utlDMRIGTest.cxx 3 | * @brief 4 | * Created "03-01-2015 5 | * 6 | * @author Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * ===================================================================================== 9 | */ 10 | 11 | 12 | #include "gtest/gtest.h" 13 | #include "utlDMRI.h" 14 | #include "itkSphericalHarmonicsGenerator.h" 15 | #include "utlDMRIStoredTables.h" 16 | 17 | TEST(utlDMRI, GetIndexSHlm) 18 | { 19 | std::vector lmVec(2); 20 | int j=0; 21 | for ( int l = 0; l <= 20; l += 2 ) 22 | { 23 | for ( int m = -l; m <= l; m += 1 ) 24 | { 25 | lmVec = utl::GetIndexSHlm(j); 26 | EXPECT_EQ(lmVec[0], l); 27 | EXPECT_EQ(lmVec[1], m); 28 | int jj = utl::GetIndexSHj(l,m); 29 | EXPECT_EQ(jj, j); 30 | j++; 31 | } 32 | } 33 | } 34 | 35 | TEST(utlDMRIStoredTables, ReadGrad) 36 | { 37 | utl::ReadGrad(3); 38 | } 39 | 40 | TEST(utlDMRIStoredTables_DeathTest, ReadGrad) 41 | { 42 | EXPECT_DEATH(utl::ReadGrad(8), ""); 43 | } 44 | -------------------------------------------------------------------------------- /Modules/HelperFunctions/test/utlGradientTest.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file utlGradientTest.cxx 3 | * @brief 4 | * Created "10-03-2016 5 | * 6 | * @author Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * ===================================================================================== 9 | */ 10 | 11 | #include "utlCore.h" 12 | #include "itkSphericalHarmonicsGenerator.h" 13 | #include "utlDMRIStoredTables.h" 14 | #include "utlCommandLineParser.h" 15 | 16 | /** 17 | * \brief test gradient table read 18 | */ 19 | int 20 | main (int argc, char const* argv[]) 21 | { 22 | utl_usage("test gradient table read"); 23 | int tess = utl_option("-t", 3, "tess order"); 24 | bool duple = utl_option("-d", false, "DUPLICATE for directions"); 25 | bool flipx = utl_option("-flipx", false, "flipx"); 26 | bool flipy = utl_option("-flipy", false, "flipy"); 27 | bool flipz = utl_option("-flipz", false, "flipz"); 28 | int mode = utl_option("-mode", 0, "0: CARTESIAN_TO_CARTESIAN; 1: CARTESIAN_TO_SPHERICAL; 2: SPHERICAL_TO_CARTESIAN; 3: SPHERICAL_TO_SPHERICAL"); 29 | 30 | if (utl_option("-h",(const char *)NULL,0)) return 0; 31 | 32 | { 33 | utl::GradientTable::Initialize(tess); 34 | utl_shared_ptr< utl::Matrix > grad = utl::GradientTable::GetGrad(tess, duple, mode, flipx, flipy, flipz); 35 | utl::PrintUtlMatrix(*grad, "grad"); 36 | } 37 | 38 | { 39 | utl_shared_ptr< utl::Matrix > grad1 = utl::ReadGrad(tess, duple, mode, flipx, flipy, flipz); 40 | utl::PrintUtlMatrix(*grad1, "grad"); 41 | } 42 | 43 | return 0; 44 | } 45 | 46 | -------------------------------------------------------------------------------- /Modules/Math/test/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_test_application(itkUnaryFunctorLookUpTableTest itkUnaryFunctorLookUpTableTest ${BLAS_LIBRARIES} ${ITK_LIBRARIES}) 3 | add_test_application(itkFunctorHashTableTest itkFunctorHashTableTest ${BLAS_LIBRARIES} ${ITK_LIBRARIES} ${GSL_LIBRARIES} ) 4 | 5 | add_test_application(itkSphericalPolarFourierGeneratorTest itkSphericalPolarFourierGeneratorTest ${ITK_LIBRARIES} ${GSL_LIBRARIES}) 6 | add_test_application(itkSphericalHarmonicsGeneratorTest itkSphericalHarmonicsGeneratorTest ${ITK_LIBRARIES} ${GSL_LIBRARIES}) 7 | 8 | add_gtest_application(itkSpecialFunctionGeneratorGTest itkSpecialFunctionGeneratorGTest ${ITK_LIBRARIES} ${GSL_LIBRARIES}) 9 | add_gtest_application(itkSphericalHarmonicsGeneratorGTest itkSphericalHarmonicsGeneratorGTest ${ITK_LIBRARIES} ${GSL_LIBRARIES}) 10 | add_gtest_application(itkSHCoefficientsRotationGTest itkSHCoefficientsRotationGTest ${BLAS_LIBRARIES} ${ITK_LIBRARIES} ${GSL_LIBRARIES}) 11 | add_gtest_application(itkUnaryFunctorLookUpTableGTest itkUnaryFunctorLookUpTableGTest ${ITK_LIBRARIES}) 12 | -------------------------------------------------------------------------------- /Modules/Math/test/itkSphericalHarmonicsGeneratorTest.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file itkSphericalHarmonicsGeneratorTest.cxx 3 | * @brief 4 | * 5 | * 6 | * @author Dr. Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * @internal 9 | * Created "03-25-2014 10 | * Revision 1.0 11 | * Compiler gcc/g++ 12 | * Company IDEA@UNC-CH 13 | * Copyright Copyright (c) 2014, Jian Cheng 14 | * 15 | * ===================================================================================== 16 | */ 17 | 18 | #include "itkSphericalHarmonicsGenerator.h" 19 | 20 | /** 21 | * \brief test itkSphericalHarmonicsGenerator 22 | */ 23 | int 24 | main (int argc, char const* argv[]) 25 | { 26 | std::cout << "RealTripleIntegration(6,-2,4,0,2,-2,false) = " << itk::SphericalHarmonicsGenerator::RealTripleIntegration(6,-2,4,0,2,-2, false) << std::endl << std::flush; 27 | std::cout << "RealTripleIntegration(6,-2,4,0,2,-2,true) = " << itk::SphericalHarmonicsGenerator::RealTripleIntegration(6,-2,4,0,2,-2, true) << std::endl << std::flush; 28 | return 0; 29 | } 30 | -------------------------------------------------------------------------------- /Modules/Math/test/itkSphericalPolarFourierGeneratorTest.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file itkSphericalPolarFourierGeneratorTest.cxx 3 | * @brief 4 | * 5 | * 6 | * @author Dr. Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * @internal 9 | * Created "05-05-2013 10 | * Revision 1.0 11 | * Compiler gcc/g++ 12 | * Company IDEA@UNC-CH 13 | * Copyright Copyright (c) 2013, Jian Cheng 14 | * 15 | * ===================================================================================== 16 | */ 17 | 18 | #include "itkSphericalPolarFourierGenerator.h" 19 | #include "utl.h" 20 | 21 | 22 | /** 23 | * \brief test itkSphericalPolarFourierGenerator 24 | */ 25 | int 26 | main (int argc, char const* argv[]) 27 | { 28 | double md0 = 0.7e-3; 29 | double tau = ONE_OVER_4_PI_2; 30 | double scale = 1.0 / (8*M_PI*M_PI*tau*md0); 31 | int N=1, L=4; 32 | double radius = 0.015; 33 | 34 | typedef itk::SphericalPolarFourierRadialGenerator SPFGenerator; 35 | SPFGenerator::Pointer spf = SPFGenerator::New(); 36 | spf->SetScale(scale); 37 | spf->SetSPFType(SPFGenerator::SPF); 38 | spf->SetN(N); 39 | spf->SetL(L); 40 | double spfValue = spf->Evaluate(radius,false); 41 | 42 | utlPrintVar4(true, N, L, radius, spfValue ); 43 | 44 | return 0; 45 | } 46 | -------------------------------------------------------------------------------- /Modules/Solvers/test/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_test_application(itkL1RegularizedLeastSquaresFISTASolverTest itkL1RegularizedLeastSquaresFISTASolverTest ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES} ${BLAS_LIBRARIES} ) 2 | 3 | add_test_application(itkSpamsWeightedLassoSolverTest itkSpamsWeightedLassoSolverTest ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES} ${BLAS_LIBRARIES} ) 4 | -------------------------------------------------------------------------------- /Modules/Tractography/test/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_test_application(test_fibertTacksReaderWriter test_fibertTacksReaderWriter ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES} ) 3 | -------------------------------------------------------------------------------- /Modules/Tractography/test/test_fibertTacksReaderWriter.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file test_fibertTacksReaderWriter.cxx 3 | * @brief 4 | * Created "08-23-2017 5 | * 6 | * @author Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * ===================================================================================== 9 | */ 10 | 11 | #include "itkFiberTractsReader.h" 12 | #include "itkFiberTractsWriter.h" 13 | 14 | #include "utlCommandLineParser.h" 15 | 16 | 17 | int 18 | main (int argc, char const* argv[]) 19 | { 20 | std::string _fileIn = utl_option("-i", "", "input file of tracks"); 21 | std::string _fileOut = utl_option("-o", "", "output file of tracks"); 22 | 23 | utl_showdoc("-h"); 24 | utl_showdoc("--help"); 25 | 26 | itk::FiberTractsReader::Pointer reader = itk::FiberTractsReader::New(); 27 | reader->SetFileName(_fileIn); 28 | 29 | reader->Update(); 30 | 31 | itk::FiberTracts<>::Pointer fibers = reader->GetOutput(); 32 | 33 | fibers->Print(std::cout<<"fibers=\n"); 34 | 35 | if (_fileOut!="") 36 | { 37 | itk::FiberTractsWriter::Pointer writer = itk::FiberTractsWriter::New(); 38 | writer->SetFileName(_fileOut); 39 | writer->SetFiberTracts(fibers); 40 | writer->Update(); 41 | } 42 | 43 | return 0; 44 | } 45 | -------------------------------------------------------------------------------- /QTApplications/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | ADD_SUBDIRECTORY(vtkviewer) 3 | -------------------------------------------------------------------------------- /QTApplications/vtkviewer/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # VTK Viewer 2 | # Written 2012 Hal Canary 3 | # Copyright 2012 University of North Carolina at Chapel Hill. 4 | # 5 | # Licensed under the Apache License, Version 2.0 (the "License"); you 6 | # may not use this file except in compliance with the License. You 7 | # may obtain a copy of the License at 8 | # 9 | # LICENSE.md in this repository or 10 | # http://www.apache.org/licenses/LICENSE-2.0 11 | # 12 | # Unless required by applicable law or agreed to in writing, software 13 | # distributed under the License is distributed on an "AS IS" BASIS, 14 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or 15 | # implied. See the License for the specific language governing 16 | # permissions and limitations under the License. 17 | cmake_minimum_required(VERSION 2.6) 18 | project(vtkviewer) 19 | # set(CMAKE_BUILD_TYPE debug) 20 | if (NOT VTK_FOUND) 21 | set(VTK_DIR "VTK_DIR-NOTFOUND" CACHE PATH "location of VTK libraries" ) 22 | find_package(VTK REQUIRED) 23 | include(${VTK_USE_FILE}) 24 | endif() 25 | set(QT_USE_OPENGL TRUE) 26 | find_package(Qt4 COMPONENTS QtCore QtGui REQUIRED) 27 | include(${QT_USE_FILE}) 28 | add_definitions(${QT_DEFINITIONS}) 29 | qt4_wrap_cpp(MOC_GENERATED VTKViewer.h) 30 | add_executable(vtkviewer main.cxx VTKViewer.cxx ${MOC_GENERATED}) 31 | target_link_libraries(vtkviewer ${VTK_LIBRARIES} ${QT_QTOPENGL_LIBRARY}) 32 | -------------------------------------------------------------------------------- /QTApplications/vtkviewer/VTKViewer.h: -------------------------------------------------------------------------------- 1 | // VTK Viewer 2 | // Written 2012 Hal Canary 3 | // Copyright 2012 University of North Carolina at Chapel Hill. 4 | // 5 | // Licensed under the Apache License, Version 2.0 (the "License"); you 6 | // may not use this file except in compliance with the License. You 7 | // may obtain a copy of the License at 8 | // 9 | // LICENSE.md in this repository or 10 | // http://www.apache.org/licenses/LICENSE-2.0 11 | // 12 | // Unless required by applicable law or agreed to in writing, software 13 | // distributed under the License is distributed on an "AS IS" BASIS, 14 | // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or 15 | // implied. See the License for the specific language governing 16 | // permissions and limitations under the License. 17 | #ifndef VTKVIEWER_H 18 | #define VTKVIEWER_H 19 | #include 20 | #include 21 | #include 22 | #include 23 | #include 24 | class vtkPolyData; 25 | 26 | class VTKViewer : public QVTKWidget { 27 | Q_OBJECT; 28 | public: 29 | VTKViewer(); 30 | void add(vtkPolyData * polyData); 31 | void add(const char * file_name); 32 | public slots: 33 | void rotate(); 34 | void toggleRotate(); 35 | void toggleStereo(); 36 | void setStereoType(int vtkStereoType); 37 | void nextStereoType(); 38 | void screenshot(); 39 | void setsize(double s1, double s2); 40 | private: 41 | QTimer m_timer; 42 | vtkSmartPointer < vtkRenderer > m_renderer; 43 | 44 | double m_size[2]; 45 | }; 46 | 47 | #endif /* VTKVIEWER_H */ 48 | -------------------------------------------------------------------------------- /Testing/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DiffusionMRITool/dmritool/860d86b449457312459e40046b41b5ea8b09e930/Testing/CMakeLists.txt -------------------------------------------------------------------------------- /ThirdParty/Spams/README: -------------------------------------------------------------------------------- 1 | SPAMS (SPArse Modeling Software) is an optimization toolbox for solving various sparse estimation problems. 2 | http://spams-devel.gforge.inria.fr/ 3 | 4 | It was integrated in dmritool project by Jian Cheng (JC), jian.cheng.1983@gmail.com 5 | 6 | 01/01/2013 7 | -------------------------------------------------------------------------------- /ThirdParty/Spams/test/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | ADD_EXECUTABLE(test_spamsCppLasso cppLasso.cpp) 3 | TARGET_LINK_LIBRARIES(test_spamsCppLasso ${ITK_LIBRARIES} ${BLAS_LIBRARIES}) 4 | 5 | add_test_application(test_spamsLasso spamsLassoTest ${ITK_LIBRARIES} ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES}) 6 | add_test_application(test_spamsMatrix spamsMatrixTest ${ITK_LIBRARIES} ${BLAS_LIBRARIES}) 7 | -------------------------------------------------------------------------------- /ThirdParty/Spams/test/cppLasso.cpp: -------------------------------------------------------------------------------- 1 | #include "linalg.h" 2 | #include "decomp.h" 3 | 4 | int main(int argc, char** argv) { 5 | int m = 10; 6 | int p = 20; 7 | /// external allocation for the matrix 8 | double* prD = new double[m*p]; 9 | spams::Matrix D(prD,m,p); 10 | D.setAleat(); 11 | D.normalize(); 12 | 13 | /// Allocate a matrix of size m x p 14 | spams::Matrix D2(m,p); 15 | D2.setAleat(); 16 | D2.normalize(); 17 | 18 | int n = 100; 19 | spams::Matrix X(m,n); 20 | X.setAleat(); 21 | 22 | /// create empty sparse matrix 23 | spams::SpMatrix spa; 24 | 25 | spams::lasso2(X,D,spa,10,0.15); // first simple example 26 | D.print("D"); 27 | X.print("X"); 28 | spa.print("spa"); 29 | 30 | /// extern allocation for the matrix D requires 31 | /// manually unallocating prD 32 | delete[](prD); 33 | } 34 | -------------------------------------------------------------------------------- /ThirdParty/Spams/test/spamsLassoTest.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file spamsLassoTest.cxx 3 | * @brief 4 | * 5 | * 6 | * @author Dr. Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * @internal 9 | * Created 01-02-2013 10 | * Revision 1.0 11 | * Compiler gcc/g++ 12 | * Company IDEA@UNC-CH 13 | * Copyright Copyright (c) 2012, Jian Cheng 14 | * 15 | * ===================================================================================== 16 | */ 17 | 18 | #include "linalg.h" 19 | #include "decomp.h" 20 | 21 | 22 | int main(int argc, char** argv) 23 | { 24 | 25 | 26 | spams::Matrix D(3,2); 27 | D(0,0) = 1; D(0,1) = 1; 28 | D(1,0) = -1; D(1,1) = 2; 29 | D(2,0) = 2; D(2,1) = 1; 30 | D.print("D"); 31 | 32 | double lambda = 1.0; 33 | 34 | spams::Matrix X(3,1); 35 | X(0,0)=2, X(1,0)=2, X(2,0)=-3; 36 | spams::SpMatrix alpha; 37 | 38 | // lasso 39 | spams::lasso2(X,D,alpha,2,lambda); 40 | alpha.print("alpha"); 41 | 42 | // lasso (Cholesky-based) 43 | spams::lasso(X,D,alpha,2,lambda); 44 | alpha.print("alpha"); 45 | 46 | // lasso (non-negativity) 47 | spams::constraint_type mode = spams::PENALTY; 48 | spams::lasso(X,D,alpha,2,lambda,0.0, mode, true); 49 | alpha.print("alpha"); 50 | 51 | } 52 | -------------------------------------------------------------------------------- /ThirdParty/Spams/test/spamsMatrixTest.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file spamsMatrixTest.cxx 3 | * @brief 4 | * 5 | * 6 | * @author Dr. Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * @internal 9 | * Created "01-02-2013 10 | * Revision 1.0 11 | * Compiler gcc/g++ 12 | * Company IDEA@UNC-CH 13 | * Copyright Copyright (c) 2013, Jian Cheng 14 | * 15 | * ===================================================================================== 16 | */ 17 | 18 | #include "utlVNL.h" 19 | #include "linalg.h" 20 | #include "utlITKSpams.h" 21 | 22 | 23 | 24 | /** 25 | * \brief test Vector Matrix in spams 26 | */ 27 | int 28 | main (int argc, char const* argv[]) 29 | { 30 | 31 | // test matrix 32 | double mmatrix [] = 33 | { 34 | 2.2700 , -1.5400 , 1.1500 , -1.9400, 35 | 0.2800 , -1.6700 , 0.9400 , -0.7800, 36 | -0.4800 , -3.0900 , 0.9900 , -0.2100, 37 | 1.0700 , 1.2200 , 0.7900 , 0.6300, 38 | -2.3500 , 2.9300 , -1.4500 , 2.3000, 39 | 0.6200 , -7.3900 , 1.0300 , -2.5700 40 | }; 41 | 42 | 43 | vnl_matrix M (mmatrix, 6, 4); 44 | M.print(std::cout<<"M:\n"); 45 | 46 | spams::Matrix DM(mmatrix, 4,6); 47 | DM.print("DM"); 48 | 49 | DM.setData(mmatrix, 4,6); 50 | DM.print("DM2"); 51 | 52 | spams::VnlMatrixToMatrix(M, DM); 53 | DM.print("DM3"); 54 | 55 | spams::MatrixToVnlMatrix(DM, M); 56 | M.print(std::cout<<"M:\n"); 57 | 58 | spams::Vector v; 59 | DM.copyCol(2, v); 60 | v.print("v"); 61 | 62 | vnl_vector v2; 63 | spams::VectorToVnlVector(v, v2); 64 | utl::PrintVnlVector(v2, "v2"); 65 | 66 | return 0; 67 | } 68 | 69 | -------------------------------------------------------------------------------- /ThirdParty/SpatiallyDenseSparseVectorImage/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | project(ITKSpatiallyDenseSparseVectorImage) 2 | itk_module_impl() 3 | -------------------------------------------------------------------------------- /ThirdParty/SpatiallyDenseSparseVectorImage/README.md: -------------------------------------------------------------------------------- 1 | General 2 | ------- 3 | 4 | 5 | Spatially Dense Sparse Vector Image 6 | ----------------------------------- 7 | 8 | An n-dimensional vector image with a sparse memory model. 9 | 10 | The elements for this image are stored in a hash table, catering to very 11 | large images with a small number of relevant pixels. The image is spatially 12 | dense, allowing fast random access and thread-safe operations. 13 | 14 | 15 | Getting Started 16 | --------------- 17 | 18 | This is a module for ITK: The Insight Toolkit for Segmentation and 19 | Registration. It is designed to work with the ITKv4 modular system and 20 | to be placed in ITK/Modules/External. Build ITK with the module selected. 21 | 22 | 23 | Author 24 | ------ 25 | 26 | Pew-Thian Yap 27 | 28 | -------------------------------------------------------------------------------- /ThirdParty/SpatiallyDenseSparseVectorImage/itk-module.cmake: -------------------------------------------------------------------------------- 1 | # the top-level README is used for describing this module, just 2 | # re-used it for documentation here 3 | get_filename_component( MY_CURENT_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) 4 | file( READ "${MY_CURENT_DIR}/README.md" DOCUMENTATION ) 5 | 6 | 7 | itk_module(ITKSpatiallyDenseSparseVectorImage 8 | DEPENDS 9 | ITKIOImageBase 10 | TEST_DEPENDS 11 | ITKTestKernel 12 | DESCRIPTION 13 | "${DOCUMENTATION}" 14 | ) 15 | -------------------------------------------------------------------------------- /ThirdParty/SpatiallyDenseSparseVectorImage/src/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DiffusionMRITool/dmritool/860d86b449457312459e40046b41b5ea8b09e930/ThirdParty/SpatiallyDenseSparseVectorImage/src/CMakeLists.txt -------------------------------------------------------------------------------- /ThirdParty/SpatiallyDenseSparseVectorImage/test/Baseline/itkSpatiallyDenseSparseVectorImageTestBaseline_Dense.nii.gz.md5: -------------------------------------------------------------------------------- 1 | 8aa5e9cfc494db5bca20b704fbeba407 -------------------------------------------------------------------------------- /ThirdParty/SpatiallyDenseSparseVectorImage/test/Baseline/itkSpatiallyDenseSparseVectorImageTestBaseline_Sparse.spr.md5: -------------------------------------------------------------------------------- 1 | f79a0d24bfcb637d8bd4363cdfea1ebe -------------------------------------------------------------------------------- /ThirdParty/SpatiallyDenseSparseVectorImage/test/Baseline/itkSpatiallyDenseSparseVectorImageTestBaseline_Sparse_key.nrrd.md5: -------------------------------------------------------------------------------- 1 | c2d8ed2068bddb9d8b761d84d6670d65 -------------------------------------------------------------------------------- /ThirdParty/SpatiallyDenseSparseVectorImage/test/Baseline/itkSpatiallyDenseSparseVectorImageTestBaseline_Sparse_value.nrrd.md5: -------------------------------------------------------------------------------- 1 | eb124ae62a2ea3305c21a01aac27eb1a -------------------------------------------------------------------------------- /ThirdParty/SpatiallyDenseSparseVectorImage/test/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | itk_module_test() 2 | set(ITKSpatiallyDenseSparseVectorImageTests 3 | itkVectorToSparseVectorImageTest.cxx 4 | itkSparseVectorToVectorImageTest.cxx 5 | ) 6 | 7 | CreateTestDriver(ITKSpatiallyDenseSparseVectorImage "${ITKSparseVectorImage-Test_LIBRARIES}" "${ITKSparseVectorImageTests}") 8 | 9 | # Test I/O convertor 10 | itk_add_test( NAME itkVectorToSparseVectorImageTest 11 | COMMAND ITKSpatiallyDenseSparseVectorImageTestDriver 12 | --compare DATA{Baseline/itkSpatiallyDenseSparseVectorImageTestBaseline_Sparse_key.nrrd} ${ITK_TEST_OUTPUT_DIR}/itkSpatiallyDenseSparseVectorImageTestOutput_Sparse_key.nrrd 13 | --compare DATA{Baseline/itkSpatiallyDenseSparseVectorImageTestBaseline_Sparse_value.nrrd} ${ITK_TEST_OUTPUT_DIR}/itkSpatiallyDenseSparseVectorImageTestOutput_Sparse_value.nrrd 14 | itkVectorToVectorImageTest DATA{Baseline/itkSpatiallyDenseSparseVectorImageTestBaseline_Dense.nii.gz} ${ITK_TEST_OUTPUT_DIR}/itkSpatiallyDenseSparseVectorImageTestOutput_Sparse.spr 15 | ) 16 | 17 | itk_add_test( NAME itkSparseVectorToVectorImageTest 18 | COMMAND ITKSpatiallyDenseSparseVectorImageTestDriver 19 | --compare DATA{Baseline/itkSpatiallyDenseSparseVectorImageTestBaseline_Dense.nii.gz} ${ITK_TEST_OUTPUT_DIR}/itkSpatiallyDenseSparseVectorImageTestOutput_Dense.nii.gz 20 | itkSparseVectorToVectorImageTest DATA{Baseline/itkSpatiallyDenseSparseVectorImageTestBaseline_Sparse.spr} ${ITK_TEST_OUTPUT_DIR}/itkSpatiallyDenseSparseVectorImageTestOutput_Dense.nii.gz 21 | ) 22 | 23 | -------------------------------------------------------------------------------- /ThirdParty/VariableLengthVectorImage/src/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DiffusionMRITool/dmritool/860d86b449457312459e40046b41b5ea8b09e930/ThirdParty/VariableLengthVectorImage/src/CMakeLists.txt -------------------------------------------------------------------------------- /ThirdParty/VariableLengthVectorImage/test/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_test_application(test_VariableLengthVectorImage test_VariableLengthVectorImage ${ITK_LIBRARIES}) 3 | -------------------------------------------------------------------------------- /ThirdParty/exprtk/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8.8) 2 | project(exprtk_builder C CXX) 3 | include(ExternalProject) 4 | 5 | ExternalProject_Add(exprtk 6 | GIT_REPOSITORY https://github.com/ArashPartow/exprtk.git 7 | CMAKE_ARGS "" 8 | CONFIGURE_COMMAND "" 9 | PREFIX "${CMAKE_CURRENT_BINARY_DIR}" 10 | # Disable install step 11 | BUILD_COMMAND "" 12 | INSTALL_COMMAND "" 13 | UPDATE_COMMAND "" 14 | ) 15 | 16 | # Specify include dir 17 | ExternalProject_Get_Property(exprtk source_dir) 18 | message("source_dir=${source_dir}") 19 | set(EXPRTK_INCLUDE_DIRS ${source_dir} PARENT_SCOPE) 20 | set(EXPRTK_INCLUDE_DIRS ${source_dir}) 21 | 22 | 23 | message("EXPRTK_INCLUDE_DIRS=${EXPRTK_INCLUDE_DIRS}") 24 | include_directories(${EXPRTK_INCLUDE_DIRS}) 25 | 26 | # add_subdirectory(test) 27 | 28 | -------------------------------------------------------------------------------- /ThirdParty/exprtk/README.md: -------------------------------------------------------------------------------- 1 | 2 | C++ Mathematical Expression Library 3 | 4 | http://partow.net/programming/exprtk/index.html 5 | 6 | Free use of the C++ Mathematical Expression Library is permitted under the guidelines and in accordance with the MIT License. 7 | -------------------------------------------------------------------------------- /ThirdParty/exprtk/include/exprtk_lib.h: -------------------------------------------------------------------------------- 1 | /** 2 | * @file exprtk_lib.h 3 | * @brief 4 | * Created "04-04-2017 5 | * 6 | * @author Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * ===================================================================================== 9 | */ 10 | 11 | #ifndef __exprtk_lib_h 12 | #define __exprtk_lib_h 13 | 14 | /** http://partow.net/programming/exprtk/index.html */ 15 | #include "exprtk.hpp" 16 | 17 | 18 | // use extern to build libs, so that it is fast in building 19 | // Use extern template instantiations (since C++11) 20 | // http://stackoverflow.com/questions/373142/what-techniques-can-be-used-to-speed-up-c-compilation-times 21 | 22 | extern template class exprtk::expression; 23 | //extern template class exprtk::symbol_table; 24 | extern template class exprtk::parser; 25 | 26 | #endif 27 | 28 | 29 | -------------------------------------------------------------------------------- /ThirdParty/exprtk/src/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_library(exprtk_lib exprtk_lib.cxx) 3 | -------------------------------------------------------------------------------- /ThirdParty/exprtk/src/exprtk_lib.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file exprtk_lib.cpp 3 | * @brief 4 | * Created "04-04-2017 5 | * 6 | * @author Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * ===================================================================================== 9 | */ 10 | 11 | #include "exprtk_lib.h" 12 | 13 | template class exprtk::expression; 14 | // template class exprtk::symbol_table; 15 | template class exprtk::parser; 16 | 17 | 18 | -------------------------------------------------------------------------------- /ThirdParty/exprtk/test/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_executable(test_exprtk test_exprtk.cxx) 3 | target_link_libraries(test_exprtk ${EXPRTK_LIBRARY}) 4 | 5 | -------------------------------------------------------------------------------- /ThirdParty/gtest/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8.8) 2 | project(gtest_builder C CXX) 3 | include(ExternalProject) 4 | 5 | ExternalProject_Add(googletest 6 | GIT_REPOSITORY https://github.com/google/googletest.git 7 | CMAKE_ARGS -DCMAKE_ARCHIVE_OUTPUT_DIRECTORY_DEBUG:PATH=DebugLibs 8 | -DCMAKE_ARCHIVE_OUTPUT_DIRECTORY_RELEASE:PATH=ReleaseLibs 9 | -DCMAKE_CXX_FLAGS=${MSVC_COMPILER_DEFS} 10 | -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} 11 | -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} 12 | -Dgtest_force_shared_crt=ON 13 | PREFIX "${CMAKE_CURRENT_BINARY_DIR}" 14 | # Disable install step 15 | INSTALL_COMMAND "" 16 | UPDATE_COMMAND "" 17 | ) 18 | 19 | # Specify include dir 20 | ExternalProject_Get_Property(googletest source_dir) 21 | set(GTEST_INCLUDE_DIRS ${source_dir}/googletest/include PARENT_SCOPE) 22 | set(GTEST_INCLUDE_DIRS ${source_dir}/googletest/include) 23 | 24 | # Specify MainTest's link libraries 25 | ExternalProject_Get_Property(googletest binary_dir) 26 | set(GTEST_LIBS_DIR ${binary_dir}/googlemock/gtest PARENT_SCOPE) 27 | set(GTEST_LIBS_DIR ${binary_dir}/googlemock/gtest) 28 | 29 | 30 | include_directories(${GTEST_INCLUDE_DIRS}) 31 | 32 | # add_subdirectory(test) 33 | -------------------------------------------------------------------------------- /ThirdParty/gtest/test/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_gtest_application(gtest_test gtest_test) 3 | -------------------------------------------------------------------------------- /ThirdParty/gtest/test/gtest_test.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file gtest_test.cxx 3 | * @brief 4 | * 5 | * 6 | * @author Dr. Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * @internal 9 | * Created "07-19-2014 10 | * Revision 1.0 11 | * Compiler gcc/g++ 12 | * Company IDEA@UNC-CH 13 | * Copyright Copyright (c) 2014, Jian Cheng 14 | * 15 | * ===================================================================================== 16 | */ 17 | 18 | #include 19 | #include "gtest/gtest.h" 20 | #include 21 | 22 | TEST(gtest_test, build) 23 | { 24 | double a=0.1+0.2, b=0.3; 25 | std::cout << "(0.1+0.2)-0.3 = " << a-b << std::endl << std::flush; 26 | std::cout << "(0.1+0.2) == 0.3 = " << (a==b) << std::endl << std::flush; 27 | EXPECT_LE(std::fabs(0.1+0.2-0.3), 1e-10); 28 | EXPECT_EQ(5*5, 25+1e-15); 29 | } 30 | 31 | TEST(gtest_test, build2) 32 | { 33 | EXPECT_EQ(5+5, 10); 34 | } 35 | 36 | -------------------------------------------------------------------------------- /ThirdPartyApplications/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | ADD_SUBDIRECTORY(SpatiallyDenseSparseImage) 3 | -------------------------------------------------------------------------------- /ThirdPartyApplications/SpatiallyDenseSparseImage/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(SparseImage) 2 | 3 | add_clp_application(SparseToVectorImageConverter SparseToVectorImageConverter ${ITK_LIBRARIES}) 4 | add_clp_application(VectorToSparseImageConverter VectorToSparseImageConverter ${ITK_LIBRARIES}) 5 | 6 | 7 | -------------------------------------------------------------------------------- /ThirdPartyApplications/SpatiallyDenseSparseImage/SparseToVectorImageConverter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Converter 4 | Sparse Image to Vector Image Converter 5 | Convert a sparse image to a vector image. 6 | 7 | http://www.unc.edu/~ptyap 8 | 9 | Pew-Thian Yap (ptyap@med.unc.edu) 10 | 11 | 12 | http://www.unc.edu/~ptyap 13 | 14 | 15 | 16 | 17 | _InputFile 18 | 19 | Input file. 20 | 0 21 | input 22 | 23 | 24 | 25 | _OutputFile 26 | 27 | Output file. 28 | 1 29 | output 30 | 31 | 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /ThirdPartyApplications/SpatiallyDenseSparseImage/VectorToSparseImageConverter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Converter 4 | Vector Image to sparse Image Converter 5 | Convert a vector image to a sparse image. 6 | 7 | http://www.unc.edu/~ptyap 8 | 9 | Pew-Thian Yap (ptyap@med.unc.edu) 10 | 11 | 12 | http://www.unc.edu/~ptyap 13 | 14 | 15 | 16 | 17 | _InputFile 18 | 19 | Input file. 20 | 0 21 | input 22 | 23 | 24 | 25 | _OutputFile 26 | 27 | Output file. 28 | 1 29 | output 30 | 31 | 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /Utilities/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | 3 | -------------------------------------------------------------------------------- /Utilities/GUnzip.py: -------------------------------------------------------------------------------- 1 | # Simple gunzip 2 | import gzip 3 | import sys 4 | 5 | input = gzip.open(sys.argv[1], 'rb') 6 | content = input.read() 7 | input.close() 8 | output = open(sys.argv[1][:-3], 'wb') 9 | output.write(content) 10 | output.close() 11 | -------------------------------------------------------------------------------- /Wrapping/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | SET(DMRITOOL_DIR ${DMRITOOL_BINARY_DIR}) 3 | 4 | OPTION(DMRITOOL_WRAP_MATLAB "Build matlab interface" OFF) 5 | IF (DMRITOOL_WRAP_MATLAB) 6 | ADD_SUBDIRECTORY(Matlab) 7 | ENDIF() 8 | -------------------------------------------------------------------------------- /Wrapping/Matlab/CMake/FindGSL.cmake: -------------------------------------------------------------------------------- 1 | ../../../CMake/FindGSL.cmake -------------------------------------------------------------------------------- /Wrapping/Matlab/CMake/FindLAPACK.cmake: -------------------------------------------------------------------------------- 1 | ../../../CMake/FindLAPACK.cmake -------------------------------------------------------------------------------- /Wrapping/Matlab/CMake/FindMKL.cmake: -------------------------------------------------------------------------------- 1 | ../../../CMake/FindMKL.cmake -------------------------------------------------------------------------------- /Wrapping/Matlab/CMake/FindOpenBLAS.cmake: -------------------------------------------------------------------------------- 1 | ../../../CMake/FindOpenBLAS.cmake -------------------------------------------------------------------------------- /Wrapping/Matlab/CMake/ProjectCMakeFunctions.cmake: -------------------------------------------------------------------------------- 1 | 2 | FUNCTION(add_matlab_cpp_executable appName mainFile) 3 | 4 | # setup doc for matlab functions 5 | set(MATLAB_FUNCTION_NAME ${appName}) 6 | configure_file(${appName}.m ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${appName}.m) 7 | 8 | add_library(${appName} ${mainFile} ) 9 | target_link_libraries(${appName} ${MATLAB_LIBRARIES} ${ARGN}) 10 | 11 | if(MSYS) 12 | target_link_libraries(${appName} stdc++) 13 | endif() 14 | 15 | add_custom_command(TARGET ${appName} 16 | POST_BUILD 17 | COMMAND ${CMAKE_COMMAND} -E make_directory ${PROJECT_BINARY_DIR}/bin 18 | COMMAND ${PROJECT_SOURCE_DIR}/utilsMEX/mex_link.sh ${appName} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY} ${PROJECT_SOURCE_DIR}/utilsMEX/mex_stub.cpp 19 | ) 20 | 21 | ENDFUNCTION(add_matlab_cpp_executable) 22 | 23 | 24 | FUNCTION(add_matlab_c_executable appName mainFile) 25 | 26 | # setup doc for matlab functions 27 | set(MATLAB_FUNCTION_NAME ${appName}) 28 | configure_file(${appName}.m ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${appName}.m) 29 | 30 | add_library(${appName} ${mainFile} ) 31 | target_link_libraries(${appName} ${MATLAB_LIBRARIES} ${ARGN}) 32 | 33 | if(MSYS) 34 | target_link_libraries(${appName} stdc++) 35 | endif() 36 | 37 | add_custom_command(TARGET ${appName} 38 | POST_BUILD 39 | COMMAND ${CMAKE_COMMAND} -E make_directory ${PROJECT_BINARY_DIR}/bin 40 | COMMAND ${PROJECT_SOURCE_DIR}/utilsMEX/mex_link.sh ${appName} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY} ${PROJECT_SOURCE_DIR}/utilsMEX/mex_stub.c 41 | ) 42 | 43 | ENDFUNCTION(add_matlab_c_executable) 44 | 45 | -------------------------------------------------------------------------------- /Wrapping/Matlab/Common/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_mex_file(mexITKImageRead mexITKImageRead.cxx ${ITK_LIBRARIES}) 3 | add_mex_file(mexITKImageWrite mexITKImageWrite.cxx ${ITK_LIBRARIES}) 4 | -------------------------------------------------------------------------------- /Wrapping/Matlab/Common/mexITKImageRead.m: -------------------------------------------------------------------------------- 1 | % @MATLAB_FUNCTION_NAME@: read images stored as any format recognized by ITK 2 | % 3 | % Usage: 4 | % [image, origin, spacing] = @MATLAB_FUNCTION_NAME@('filename') 5 | % or 6 | % image = @MATLAB_FUNCTION_NAME@('filename') 7 | % 8 | % 'filename' is the path to an image readable by ITK 9 | % 10 | % Copyright (c) 2013, Jian Cheng 11 | % 12 | -------------------------------------------------------------------------------- /Wrapping/Matlab/Common/mexITKImageWrite.m: -------------------------------------------------------------------------------- 1 | % @MATLAB_FUNCTION_NAME@: write Matlab image matrix to any image format supported by ITK using itk::Image and itk::VectorImage. 2 | % 3 | % Usage: 4 | % @MATLAB_FUNCTION_NAME@('filename', image, [params]) 5 | % 6 | % INPUT 7 | % filename : file name to save. 8 | % image : 4D matlab matrix 9 | % 10 | % params.origin : origin in image 11 | % params.spacing : spacing in image 12 | % params.vectorImage : If it is true, save 3D itk::VectorImage, otherwise save 4D itk::Image (default). 13 | % 14 | % Copyright (c) 2013, Jian Cheng 15 | % 16 | -------------------------------------------------------------------------------- /Wrapping/Matlab/DWIProcessing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_mex_file(mexReadDWIList mexReadDWIList.cxx ${BLAS_LIBRARIES} ${ITK_LIBRARIES}) 3 | -------------------------------------------------------------------------------- /Wrapping/Matlab/DiffusionModels/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_mex_file(mexGetSHBasisMatrix mexGetSHBasisMatrix.cxx ${ITK_LIBRARIES} ${GSL_LIBRARIES}) 3 | add_mex_file(mexGetSPFBasisMatrix mexGetSPFBasisMatrix.cxx ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES} ${GSL_LIBRARIES}) 4 | 5 | add_mex_file(mexSphericalPolarFourierImaging mexSphericalPolarFourierImaging.cxx ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES} ${GSL_LIBRARIES} ) 6 | add_mex_file(mexGetSamplesFromSPFCoefficients mexGetSamplesFromSPFCoefficients.cxx ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ITK_LIBRARIES} ${GSL_LIBRARIES}) 7 | -------------------------------------------------------------------------------- /Wrapping/Matlab/DiffusionModels/mexGetSHBasisMatrix.m: -------------------------------------------------------------------------------- 1 | % @MATLAB_FUNCTION_NAME@: get sh matrix based on given order and orientationMatrix 2 | % 3 | % Usage: 4 | % shMatrix = @MATLAB_FUNCTION_NAME@(order, orientationMatrix, mode) 5 | % 6 | % Inputs: 7 | % order: SH order 8 | % orientationMatrix : orientation matrix where each row is an orientation (x,y,z) 9 | % mode: 'spherical' or 'cartesian' (default), for the coordinates in orientationMatrix. 10 | % 11 | % Outputs: 12 | % shMatrix: each column is a real SH basis 13 | % 14 | % Copyright (c) 2013, Jian Cheng 15 | % 16 | 17 | 18 | -------------------------------------------------------------------------------- /Wrapping/Matlab/DiffusionModels/mexGetSPFBasisMatrix.m: -------------------------------------------------------------------------------- 1 | % @MATLAB_FUNCTION_NAME@: get SPF basis matrix with given spherical and radial orders, orientationMatrix, bVector 2 | % 3 | % Usage: 4 | % spfMatrix = @MATLAB_FUNCTION_NAME@(shOrder, radialOrder, orientationMatrix, bVector) 5 | % spfMatrix = @MATLAB_FUNCTION_NAME@(shOrder, radialOrder, orientationMatrix, bVector, params) 6 | % 7 | % Inputs: 8 | % shOrder: SH order 9 | % radialOrder: order in radial part 10 | % orientationMatrix : orientation matrix where each row is an orientation (x,y,z), caresian format 11 | % bVector: b values in a vector, each row is a b value 12 | % params.scale : (optional) scale value for the SPF basis in radial part 13 | % params.tau: (optional) tau value to calculate qVector from bVector, b=4\pi^2 \tau q^2 14 | % params.original: (optional) true: (default) original SPF basis matrix 15 | % false: independent SPF basis matrix, considering E(0)=1 16 | % 17 | % Outputs: 18 | % spfMatrix: each column is a SPF basis 19 | % 20 | % 21 | % Reference: 22 | % 1. "Model-Free, Regularized, Fast, and Robust Analytical Orientation Distribution Function Estimation", 23 | % Jian Cheng, Aurobrata Ghosh, Rachid Deriche, Tianzi Jiang, Medical Image Computing and Computer-Assisted Intervention (MICCAI'10), vol. 6361, pp. 648–656, sep, 2010. 24 | % 2. "Model-free and Analytical EAP Reconstruction via Spherical Polar Fourier Diffusion MRI", 25 | % Jian Cheng, Aurobrata Ghosh, Tianzi Jiang, Rachid Deriche, Medical Image Computing and Computer-Assisted Intervention (MICCAI'10), vol. 6361, pp. 590–597, sep, 2010. 26 | % 27 | % Copyright (c) 2013, Jian Cheng 28 | % 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /Wrapping/Matlab/MEXHelperFunctions/mexSTD.h: -------------------------------------------------------------------------------- 1 | /** 2 | * @file mexSTD.h 3 | * @brief 4 | * 5 | * 6 | * @author Dr. Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * @internal 9 | * Created "09-27-2013 10 | * Revision 1.0 11 | * Compiler gcc/g++ 12 | * Company IDEA@UNC-CH 13 | * Copyright Copyright (c) 2013, Jian Cheng 14 | * 15 | * ===================================================================================== 16 | */ 17 | 18 | #ifndef __mexSTD_h 19 | #define __mexSTD_h 20 | 21 | #include 22 | #include "mexutils.h" 23 | #include "utlCoreMacro.h" 24 | 25 | namespace utl 26 | { 27 | 28 | template 29 | inline void 30 | GetSTDVectorFromMXArray ( const mxArray* pr, std::vector* vec ) 31 | { 32 | const mwSize* dims = mxGetDimensions(pr); 33 | int row = static_cast(dims[0]); 34 | int column = static_cast(dims[1]); 35 | 36 | double * data = mxGetPr(pr); 37 | 38 | if (row==1) 39 | { 40 | vec->resize(column); 41 | for ( int i = 0; i < column; i += 1 ) 42 | (*vec)[i] = data[i]; 43 | } 44 | else if (column==1) 45 | { 46 | vec->resize(row); 47 | for ( int i = 0; i < row; i += 1 ) 48 | (*vec)[i] = data[i]; 49 | } 50 | else 51 | utlException(true, "the matrix should be a vector"); 52 | } 53 | 54 | /** convert a std::vector to a colume vector */ 55 | template 56 | inline void 57 | GetMXArrayFromSTDVector ( const std::vector* vec, mxArray*& pr ) 58 | { 59 | utlException (!vec || (vec && vec->size()==0), "the vector is null"); 60 | 61 | int row = vec->size(); 62 | int column = 1; 63 | 64 | pr = CreateMatrix(row, 1); 65 | double * data = mxGetPr(pr); 66 | for ( int i = 0; i < row; i += 1 ) 67 | data[i] = (*vec)[i]; 68 | } 69 | 70 | } 71 | 72 | #endif 73 | 74 | -------------------------------------------------------------------------------- /Wrapping/Matlab/README.md: -------------------------------------------------------------------------------- 1 | DMRITOOL matlab interface 2 | 3 | Author: Jian Cheng (jian.cheng.1983@gmail.com) 4 | -------------------------------------------------------------------------------- /Wrapping/Matlab/SamplingScheme/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_mex_file(mexReadGrad mexReadGrad.cxx ${ITK_LIBRARIES}) 3 | -------------------------------------------------------------------------------- /Wrapping/Matlab/SamplingScheme/mexReadGrad.m: -------------------------------------------------------------------------------- 1 | % @MATLAB_FUNCTION_NAME@: read gradient files into a matrix 2 | % 3 | % Usage: 4 | % gradMatrix = @MATLAB_FUNCTION_NAME@(type, number) 5 | % gradMatrix = @MATLAB_FUNCTION_NAME@('grad.txt') 6 | % 7 | % INPUT 8 | % type : gradient type or gradient file name (.txt) 9 | % 'elec': gradients from camino based on electrostatic energy. 10 | % 'tess': gradients based on tessellation. 11 | % 12 | % number : if type=='elec', then number means the number of samples. 13 | % if type=='tess', then number means tessellation order. 14 | % 15 | % OUTPUT 16 | % grad : Nx3 matrix, each row is a point in sphere. 17 | % 18 | % Copyright (c) 2013, Jian Cheng 19 | % 20 | -------------------------------------------------------------------------------- /Wrapping/Matlab/Tests/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_executable(test_purecpp test_purecpp.cxx) 3 | target_link_libraries(test_purecpp ${ITK_LIBRARIES} ${GSL_LIBRARIES}) 4 | 5 | add_mex_file(test_puremex test_puremex ) 6 | add_mex_file(test_puremexitk test_puremexitk ${ITK_LIBRARIES}) 7 | add_mex_file(test_Spams test_Spams ${ITK_LIBRARIES} ${BLAS_LIBRARIES}) 8 | add_mex_file(test_Spams2 test_Spams2 ${ITK_LIBRARIES} ${BLAS_LIBRARIES}) 9 | 10 | 11 | if (DMRITOOL_USE_OPENMP) 12 | add_mex_file(test_puremexOpenmp test_puremexOpenmp ) 13 | endif() 14 | -------------------------------------------------------------------------------- /Wrapping/Matlab/Tests/test_GetSPFBaissMatrix.m: -------------------------------------------------------------------------------- 1 | % function test_GetSPFBaissMatrix 2 | 3 | grad_t3 = readGrad('tess',3); 4 | bVec = 1500*ones(size(grad_t3,1),1); 5 | 6 | D0 = 0.7e-3; 7 | tau = 0.02533; 8 | param.scale = 1.0 / (8*pi^2*tau*D0); 9 | param.original=false; 10 | % param.original=true; 11 | 12 | qVec = sqrt(bVec./(4*pi*pi*tau)); 13 | 14 | spfMatrix = GetSPFBasisMatrix(4,1,grad_t3,bVec,param); 15 | -------------------------------------------------------------------------------- /Wrapping/Matlab/Tests/test_purecpp.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file test_purecpp.cxx 3 | * @brief 4 | * 5 | * 6 | * @author Dr. Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * @internal 9 | * Created "11-07-2013 10 | * Revision 1.0 11 | * Compiler gcc/g++ 12 | * Company IDEA@UNC-CH 13 | * Copyright Copyright (c) 2013, Jian Cheng 14 | * 15 | * ===================================================================================== 16 | */ 17 | 18 | #include "utl.h" 19 | 20 | /** 21 | * \brief test pure cpp code 22 | */ 23 | int 24 | main (int argc, char const* argv[]) 25 | { 26 | std::vector > strMatrix; 27 | utl::ReadLines("aa.txt", strMatrix); 28 | utlGlobalException(true, "adad"); 29 | return 0; 30 | } 31 | -------------------------------------------------------------------------------- /Wrapping/Matlab/Tests/test_puremex.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file test_puremex.cxx 3 | * @brief 4 | * 5 | * 6 | * @author Dr. Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * @internal 9 | * Created "11-09-2013 10 | * Revision 1.0 11 | * Compiler gcc/g++ 12 | * Company IDEA@UNC-CH 13 | * Copyright Copyright (c) 2013, Jian Cheng 14 | * 15 | * ===================================================================================== 16 | */ 17 | 18 | #include 19 | #include "mex.h" 20 | // #include "mexutils.h" 21 | 22 | void mexFunction(int nlhs, mxArray *plhs[], 23 | int nrhs, const mxArray *prhs[]) 24 | { 25 | // utlGlobalException(nrhs!=1, "Bad number of inputs arguments"); 26 | // double num = mxGetScalar(prhs[0]); 27 | std::cout << "num = " << 15 << std::endl << std::flush; 28 | } 29 | -------------------------------------------------------------------------------- /Wrapping/Matlab/Tests/test_puremexOpenmp.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file test_puremexOpenmp.cxx 3 | * @brief 4 | * 5 | * 6 | * @author Dr. Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * @internal 9 | * Created "11-09-2013 10 | * Revision 1.0 11 | * Compiler gcc/g++ 12 | * Company IDEA@UNC-CH 13 | * Copyright Copyright (c) 2013, Jian Cheng 14 | * 15 | * ===================================================================================== 16 | */ 17 | 18 | #include "mex.h" 19 | #include 20 | 21 | void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) 22 | { 23 | // omp_set_dynamic(1); 24 | // omp_set_num_threads(3); 25 | #pragma omp parallel 26 | { 27 | mexPrintf("Max num threads %d.\n", omp_get_max_threads()); 28 | #pragma omp for 29 | for (int i = 0; i < 10; i++) 30 | { 31 | mexPrintf("Num threads %d, thread ID %d.\n", omp_get_num_threads(), omp_get_thread_num()); 32 | } 33 | } 34 | } 35 | 36 | -------------------------------------------------------------------------------- /Wrapping/Matlab/Tests/test_puremexitk.cxx: -------------------------------------------------------------------------------- 1 | /** 2 | * @file test_puremex.cxx 3 | * @brief 4 | * 5 | * 6 | * @author Dr. Jian Cheng (JC), jian.cheng.1983@gmail.com 7 | * 8 | * @internal 9 | * Created "11-09-2013 10 | * Revision 1.0 11 | * Compiler gcc/g++ 12 | * Company IDEA@UNC-CH 13 | * Copyright Copyright (c) 2013, Jian Cheng 14 | * 15 | * ===================================================================================== 16 | */ 17 | 18 | #include 19 | #include "mex.h" 20 | #include "tr1/memory" 21 | #include 22 | #include "itkImage.h" 23 | 24 | void mexFunction(int nlhs, mxArray *plhs[], 25 | int nrhs, const mxArray *prhs[]) 26 | { 27 | // utlGlobalException(nrhs!=1, "Bad number of inputs arguments"); 28 | // double num = mxGetScalar(prhs[0]); 29 | std::tr1::shared_ptr > pp(new std::vector()); 30 | std::cout << "num = " << 15 << std::endl << std::flush; 31 | 32 | typedef itk::Image ImageType; 33 | ImageType::Pointer image = ImageType::New(); 34 | 35 | } 36 | --------------------------------------------------------------------------------