The Image-based Vascular Analysis Toolkit (IvanTk)

Macia, Ivan1*
1.Vicomtech Foundation
Abstract
The Image-based Vascular Analysis Toolkit (IvanTk)

Abstract

This document describes the Image-based Vascular Analysis Toolkit (IvanTk), a set of cross-platform C++ open source software libraries for the detection, extraction and modeling of vessels in 2D/3D medical images based on the Insight Toolkit. We provide an overview of the libraries and their purpose and describe their functional modules and future directions of the toolkit.

Keywords

vascularvesselnessmedialnessVessel extractiontubeVessel detectionBlood vessels
Manuscript
Source Code and Data

Source Code and Data

CMakeLists.txt5.6 KBDataTestingInputCircularFlatConvolvedTube_1_0.mhd347 BCircularFlatConvolvedTube_1_0.zraw259 BCircularFlatConvolvedTube_1_0_noise10.mhd357 BCircularFlatConvolvedTube_1_0_noise10.zraw12 KBCircularFlatConvolvedTube_1_0_noise25.mhd357 BCircularFlatConvolvedTube_1_0_noise25.zraw13.3 KBCircularFlatConvolvedTube_1_0_noise50.mhd357 BCircularFlatConvolvedTube_1_0_noise50.zraw13.9 KBCircularFlatConvolvedTube_1_0_noise75.mhd357 BCircularFlatConvolvedTube_1_50.mhd348 BCircularFlatConvolvedTube_1_0_noise75.zraw14.4 KBCircularFlatConvolvedTube_1_50_noise10.mhd358 BCircularFlatConvolvedTube_1_50.zraw280 BCircularFlatConvolvedTube_1_50_noise25.mhd358 BCircularFlatConvolvedTube_1_50_noise10.zraw21.9 KBCircularFlatConvolvedTube_1_50_noise25.zraw24.8 KBCircularFlatConvolvedTube_1_50_noise50.mhd358 BCircularFlatConvolvedTube_1_50_noise50.zraw25.9 KBCircularFlatConvolvedTube_1_50_noise75.mhd358 BCircularFlatConvolvedTube_1_50_noise75.zraw26.7 KBCircularFlatConvolvedTube_2_25.mhd348 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KBCircularGaussianTube_7_59.zraw14.3 KBCircularGaussianTube_7_59_Centerline.txt1.8 KBCircularGaussianTube_7_59_noise10.mhd355 BCircularGaussianTube_7_59_noise25.mhd355 BCircularGaussianTube_7_59_noise10.zraw525.6 KBCircularGaussianTube_7_59_noise50.mhd355 BCircularGaussianTube_7_59_noise25.zraw605.4 KBCircularGaussianTube_7_59_noise75.mhd355 BCircularGaussianTube_7_59_noise50.zraw644.1 KBCircularGaussianTube_7_59_noise75.zraw666.1 KBGaussianCircularHelix_sigma3_0_R50_0_H50_0.mhd367 BGaussianCircularHelix_sigma3_0_R50_0_H50_0.txt30.3 KBGaussianCircularHelix_sigma3_0_R50_0_H50_0_params.txt110 BGaussianCircularHelix_sigma3_0_R50_0_H50_0.zraw324.1 KBGaussianCircularToroid_sigma1_0_R25_0.mhd330 BGaussianCircularToroid_sigma1_0_R25_0.raw30.1 KBGaussianCircularToroid_sigma3_0_R50_0.mhd359 BGaussianCircularToroid_sigma3_0_R50_0.txt3.3 KBGaussianCircularToroid_sigma3_0_R50_0.zraw14.1 KBGaussianCircularToroid_sigma3_0_R50_0_params.txt100 BDocDoxyfile.in63.7 KBCopyright.txt269 BIVANConfig.cmake.in2.4 KBIVANIncludeDirectories.cmake1.6 KBREADME7.8 KBLICENSE16.7 KBSourcesCMakeLists.txt116 BCommonCMakeLists.txt742 BivanAngularValue.h2.2 KBivanGlobals.h3.2 KBivanGraphCountNodeVisitor.h2.7 KBivanGraphCountNodeVisitor.hxx1.9 KBivanGraphNode.cxx10.2 KBivanGraphNode.h12 KBivanGraphNodeVisitor.cxx2.2 KBivanGraphNodeVisitor.h8 KBivanImage3DPlaneFunctionToCostFunctionAdaptor.h5.6 KBivanGraphNodeVisitorDispatcher.h2.8 KBivanImageFunctionToCostFunctionAdaptor.h4.5 KBivanImage3DPlaneFunctionToCostFunctionAdaptor.hxx4.6 KBivanImageFunctionToCostFunctionAdaptor.hxx2.3 KBivanImageToVesselDataObjectFilter.h3.8 KBivanImageToVesselDataObjectFilter.hxx3.3 KBivanMacros.h1.5 KBivanVesselCommon.h1.5 KBivanVesselDataObject.h2.6 KBivanVesselDataObjectSource.h4.4 KBivanVesselDataObjectSource.hxx2.8 KBExperimentalivanImageToCircleFitCostFunction.h5.4 KBivanImageToCircleFitCostFunction.hxx7.9 KBivanMedialnessVesselRadiusFitCostFunction.h7.4 KBivanMedialnessVesselRadiusFitCostFunction.hxx10.7 KBivanMedialnessVesselSectionAndRadiusFitCostFunction.h7.2 KBivanMedialnessVesselSectionAndRadiusFitCostFunction.hxx26.4 KBivanRadiusAndSectionEstimationVesselNetworkFilter.h3.6 KBivanRadiusAndSectionEstimationVesselNetworkFilter.hxx10.2 KBivanRadiusEstimationVesselNetworkFilter.h3.5 KBivanRadiusEstimationVesselNetworkFilter.hxx9.7 KBDetectionCMakeLists.txt2.1 KBivanCircularSectionFluxImageFunction.h7.2 KBivanCircularSectionFluxImageFunction.hxx9.2 KBivanDiscreteGradientGaussianImageFunction.h10.4 KBivanDiscreteGradientGaussianImageFunction.hxx11.6 KBivanDiscreteHessianGaussianImageFunction.h11.2 KBivanDiscreteHessianGaussianImageFunction.hxx12.4 KBivanFilterByEigenValuesVesselnessImageFunction.h7.3 KBivanFilterByEigenValuesVesselnessImageFunction.hxx2.9 KBivanFluxBasedVesselnessImageFunction.h6.2 KBivanFluxBasedVesselnessImageFunction.hxx3.2 KBivanFrangiVesselnessImageFunction.h4.7 KBivanFrangiVesselnessImageFunction.h.old3.4 KBivanFrangiVesselnessImageFunction.hxx4.4 KBivanFrangiVesselnessImageFunction.txx.old2.2 KBivanGaussianDerivativeOperator.hxx12.4 KBivanGaussianDerivativeOperator.h9.2 KBivanHessianBasedVesselnessImageFunction.hxx9.2 KBivanHessianBasedVesselnessImageFunction.h9.9 KBivanHessianEigenValuesImageFunction.h4.9 KBivanHessianEigenValuesImageFunction.hxx2.4 KBivanHessianOnlyBasedVesselnessImageFunction.h5.6 KBivanHessianOnlyBasedVesselnessImageFunction.hxx3 KBivanImageFunctionBasedImageFilter.h5.4 KBivanImageFunctionBasedImageFilter.hxx4 KBivanImageFunctionInitializerBase.h2.8 KBivanMultiscaleAnalysisImageFilter.h8.9 KBivanMultiscaleAnalysisImageFilter.hxx12.6 KBivanMultiscaleImageFunction.h7.1 KBivanMultiscaleImageFunction.hxx7.6 KBivanMultiscaleMedialnessImageFilter.h7.1 KBivanMultiscaleMedialnessImageFilter.hxx26 KBivanNonLinearSteerableFluxImageFunction.h5.4 KBivanNonLinearSteerableFluxImageFunction.hxx7.5 KBivanObjectnessMeasureImageFunction.h5.3 KBivanObjectnessMeasureImageFunction.hxx5.3 KBivanOffsetMedialnessImageFunction.h11 KBivanOffsetMedialnessImageFunction.hxx15.1 KBivanOffsetMedialnessImageFunctionInitializer.h7 KBivanOptimallyOrientedFluxVesselnessImageFunction.h7.3 KBivanOptimallyOrientedFluxVesselnessImageFunction.hxx3 KBivanOptimallyOrientedFluxVesselnessImageFunctionInitializer.h3.6 KBivanOrientedFluxMatrixBasedVesselnessImageFunction.h9.1 KBivanOrientedFluxMatrixImageFunction.h6 KBivanOrientedFluxMatrixBasedVesselnessImageFunction.hxx8.4 KBivanPolarProfileVesselnessImageFunction.hxx8.3 KBivanPolarProfileVesselnessImageFunction.h6.4 KBivanSatoVesselnessImageFunction.hxx3.5 KBivanSatoVesselnessImageFunction.h5.4 KBivanScaleSpaceImageFunctionInitializer.h3 KBivanSphereGridBasedImageFunction.h6 KBivanSphereGridBasedImageFunction.hxx8.3 KBIOivanVesselCenterlineXMLReader.h2.7 KBivanVesselCenterlineXMLWriter.hxx1.9 KBExtractionCMakeLists.txt2.5 KBivanBSplineVesselCenterlineInterpolator.h3.3 KBivanBSplineVesselCenterlineInterpolator.hxx2.1 KBivanCylindricalOffsetMedialnessVesselSectionFitCostFunction.h6.4 KBivanCylindricalOffsetMedialnessVesselSectionFitCostFunction.hxx5.3 KBivanFixedScaleHessianBasedVesselSectionEstimator.h4.9 KBivanFixedScaleHessianBasedVesselSectionEstimator.hxx6.1 KBivanFixedScaleOOFBasedVesselSectionEstimator.h5.9 KBivanFixedScaleOOFBasedVesselSectionEstimator.hxx5.9 KBivanImageBasedVesselSectionEstimator.h3.2 KBivanImageBasedVesselSectionEstimator.hxx2.4 KBivanImageBasedVesselSectionFitCostFunction.h5.1 KBivanImageBasedVesselSectionFitCostFunction.hxx1.6 KBivanMaxIterationsVesselTrackerEndCondition.h3.2 KBivanMultiscaleAdaptiveHessianBasedVesselSectionEstimator.h6.8 KBivanMultiscaleAdaptiveHessianBasedVesselSectionEstimator.hxx6.7 KBivanMultiscaleAdaptiveOOFBasedVesselSectionEstimator.h7.1 KBivanMultiscaleAdaptiveOOFBasedVesselSectionEstimator.hxx6.8 KBivanMultiscaleFromImageHessianBasedVesselSectionEstimator.h5.2 KBivanMultiscaleFromImageHessianBasedVesselSectionEstimator.hxx3.3 KBivanMultiscaleFromRadiusHessianBasedVesselSectionEstimator.h5.5 KBivanMultiscaleFromRadiusHessianBasedVesselSectionEstimator.hxx3 KBivanMultiscaleHessianBasedVesselSectionEstimator.h5.5 KBivanMultiscaleHessianBasedVesselSectionEstimator.hxx2.9 KBivanMultiscaleOOFBasedVesselSectionEstimator.h5.6 KBivanMultiscaleOOFBasedVesselSectionEstimator.hxx3.2 KBivanMultiscaleTensorBasedVesselSectionEstimator.h5.7 KBivanMultiscaleTensorBasedVesselSectionEstimator.hxx8.2 KBivanMultiscaleVesselSectionEstimator.h7.3 KBivanMultiscaleVesselSectionEstimator.hxx5.9 KBivanOffsetMedialnessVesselSectionFitCostFunction.h6.3 KBivanOffsetMedialnessVesselSectionFitCostFunction.hxx5.4 KBivanOptimizedVesselSectionEstimator.h4.3 KBivanOptimizedVesselSectionEstimator.hxx6.3 KBivanOptimizedVesselnessBasedSearchVesselTrackerFilter.h7.1 KBivanOptimizedVesselnessBasedSearchVesselTrackerFilter.hxx4.6 KBivanOptimizerIterationCommand.h3.7 KBivanVesselSectionEstimator.h7.1 KBivanVesselSectionEstimator.hxx6.7 KBivanVesselSectionFitCostFunction.h3.3 KBivanVesselTrackerEndCondition.h2.6 KBivanVesselTrackerFilter.h8 KBivanVesselTrackerFilter.hxx5.4 KBivanVesselnessBasedSearchVesselTrackerFilter.h6.3 KBivanVesselnessBasedSearchVesselTrackerFilter.hxx4.1 KBivanVesselnessBasedVesselTrackerEndCondition.h4.8 KBivanVesselnessBasedVesselTrackerEndCondition.hxx2.4 KBivanVesselnessRidgeSearchVesselTrackerFilter.h6.1 KBivanVesselnessRidgeSearchVesselTrackerFilter.hxx7.8 KBITKCMakeLists.txt897 BitkAdditiveGaussianNoiseImageFilter.h4.9 KBitkAdditiveGaussianNoiseImageFilter.txx3.3 KBitkDiscreteGaussianDerivativeImageFilter.h10.3 KBitkDiscreteGaussianDerivativeImageFilter.hxx12.8 KBitkDiscreteGaussianDerivativeImageFunction.h11.3 KBitkDiscreteGaussianDerivativeImageFunction.hxx11.1 KBitkDiscreteGradientMagnitudeGaussianImageFunction.h11.3 KBitkDiscreteGradientMagnitudeGaussianImageFunction.hxx12.1 KBitkDiscreteHessianGaussianImageFunction.h11.4 KBitkDiscreteHessianGaussianImageFunction.hxx12.7 KBitkGaussianDerivativeOperator.h9.4 KBitkImageToVTKImageFilter.h3.5 KBitkGaussianDerivativeOperator.hxx12.8 KBitkThreadSafeMersenneTwisterRandomVariateGenerator.cxx2.3 KBitkImageToVTKImageFilter.hxx3.3 KBitkThreadSafeMersenneTwisterRandomVariateGenerator.h20.3 KBitkVTKImageToImageFilter.h3.1 KBitkVTKImageToImageFilter.hxx2.8 KBModelingCMakeLists.txt1.7 KBivanAneurysmModel.h2.5 KBivanAneurysmModel.cxx1.5 KBivanAorticAneurysmVesselSection.h5.1 KBivanAorticAneurysmVesselSection.hxx2.3 KBivanCircularVesselSection.h4.3 KBivanCircularVesselSection.hxx2.2 KBivanCollectNodesVisitor.h3.1 KBivanCollectNodesVisitor.hxx1.9 KBivanCompositeNode.cxx9 KBivanCompositeNode.h9 KBivanLinearPropertyInterpolator.h3.8 KBivanLinearVesselCenterlineInterpolator.h3.3 KBivanLinearVesselCenterlineInterpolator.hxx2.1 KBivanNullVesselSectionStruct.h2.5 KBivanRadialContour.h4.1 KBivanRadialContour.hxx1.9 KBivanSearchByIdNodeVisitor.cxx1.9 KBivanSearchByIdNodeVisitor.h2.6 KBivanStenosisModel.cxx1.5 KBivanStenosisModel.h2.5 KBivanUniformRadialContour.h3.9 KBivanUniformRadialContour.hxx2 KBivanVesselBifurcationNode.h3.1 KBivanVesselBifurcationNode.hxx3.1 KBivanVesselBranchNode.h3.7 KBivanVesselBranchNode.hxx2 KBivanVesselBranchNodeVisitor.h2.4 KBivanVesselCenterline.hxx2.3 KBivanVesselCenterline.h3.4 KBivanVesselCenterlineAlgorithm.h3.3 KBivanVesselCenterlineAlgorithmVisitor.h3.1 KBivanVesselCenterlineAlgorithmVisitor.hxx2.3 KBivanVesselCenterlineMetricsCalculator.hxx1.9 KBivanVesselCenterlineMetricsCalculator.h3.3 KBivanVesselCenterlineMetricsCalculatorVisitor.h2.8 KBivanVesselCenterlineMetricsCalculatorVisitor.hxx2.2 KBivanVesselCenterlineSmoother.h3.2 KBivanVesselCenterlineSmoother.hxx2 KBivanVesselElementNode.h2.9 KBivanVesselElementNode.hxx2.9 KBivanVesselFeatureModel.cxx1.5 KBivanVesselFeatureModel.h2.9 KBivanVesselFeatureNode.cxx1.6 KBivanVesselFeatureNode.h4.4 KBivanVesselGraph.h3.4 KBivanVesselNode.cxx1.5 KBivanVesselNode.h2.2 KBivanVesselNodeVisitor.h2.9 KBivanVesselNodeVisitor.hxx2.4 KBivanVesselRegion.cxx2.8 KBivanVesselRegion.h5.4 KBivanVesselSection.h4.5 KBivanVesselSectionStruct.h2.2 KBQuantificationCMakeLists.txt1.8 KBivanLocalCurveMetrics.h3.8 KBivanLocalCurveMetrics.hxx4 KBivanLocalCurveMetricsCalculator.h3.2 KBivanLocalCurveMetricsCalculator.hxx2.1 KBSyntheticivanCenterlineBasedBarTubeGenerator.h7.7 KBivanCenterlineBasedGaussianTubeGenerator.h7.6 KBivanCenterlineGenerator.h1.9 KBivanCircularBarSectionGenerator.h5.4 KBivanCircularBarHelixGenerator.h5.7 KBivanCircularBarStraightTubeGenerator.h5.8 KBivanCircularBarStraightTubeSinusoidalRadiusGenerator.h5.6 KBivanCircularBarToroidGenerator.h16 KBivanCircularBarTubeGenerator.h5.7 KBivanCircularCenterlineGenerator.h5.2 KBivanCircularGaussianHelixGenerator.h5.2 KBivanCircularGaussianSectionGenerator.h9.3 KBivanCircularGaussianSectionGenerator.h.old5.5 KBivanCircularGaussianStraightTubeGenerator.h4.6 KBivanCircularGaussianStraightTubeSinusoidalRadiusGenerator.h5.9 KBivanCircularGaussianToroidGenerator.h15.7 KBivanCircularGaussianTubeGenerator.h5.1 KBivanCircularHelixCenterlineGenerator.h4.2 KBivanCubeMeshSource.h3.4 KBivanCubeMeshSource.hxx2.1 KBivanCurvedCircularGaussianTubeGenerator.h9.3 KBivanDodecahedronMeshSource.h3.5 KBivanDodecahedronMeshSource.hxx2.5 KBivanGaussianBallGenerator.h4.8 KBivanIcosahedronMeshSource.h3.4 KBivanIcosahedronMeshSource.hxx2.5 KBivanNonUniformRadialContour.h4 KBivanNonUniformRadialContour.hxx1.9 KBivanOctahedronMeshSource.h3.4 KBivanOctahedronMeshSource.hxx2.1 KBivanPlatonicSolidMeshSource.h3.9 KBivanPlatonicSolidMeshSource.hxx3.4 KBivanRegularSphereMeshSource2.h4.6 KBivanSimpleCurvedCenterlineGenerator.h7.6 KBivanRegularSphereMeshSource2.hxx10.7 KBivanTetrahedronMeshSource.hxx2.1 KBivanTetrahedronMeshSource.h3.5 KBTestingCMakeLists.txt337 BDetectionCMakeLists.txt7.3 KBivanCircularGaussianSectionSecondDerivativeScaleInvarianceTest.cxx6.1 KBivanCircularSectionFluxImageFunctionTest.cxx3.4 KBivanDetectionTestingHelper.h6.4 KBivanDiscreteMultiscaleGaussianImageFunctionTest.cxx6.2 KBivanFilterByEigenValuesVesselnessImageFunctionTest.cxx3.3 KBivanFrangiVesselnessImageFunctionTest.cxx3.4 KBivanHessianEigenValuesImageFunctionTest.cxx6.9 KBivanMultiscaleOOFVesselnessImageFunctionTest.cxx4.8 KBivanMultiscaleOffsetMedialnessImageFunctionTest.cxx5.1 KBivanMultiscalePolarProfileVesselnessImageFunctionTest.cxx7.2 KBivanNonLinearSteerableFluxImageFunctionTest.cxx3.3 KBivanOffsetMedialnessImageFunctionTest.cxx6.2 KBivanOffsetMedialnessImageFunctionTest2.cxx4.7 KBivanOptimallyOrientedFluxVesselnessImageFunctionTest.cxx3.9 KBivanPolarProfileVesselnessImageFunctionTest.cxx7.5 KBivanSatoVesselnessImageFunctionTest.cxx3.5 KBExtractionCMakeLists.txt5.7 KBivanFixedScaleHessianBasedVesselSectionEstimatorTest.cxx11.3 KBivanFixedScaleOOFBasedVesselSectionEstimatorTest.cxx11.6 KBivanMultiscaleAdaptiveHessianBasedVesselSectionEstimatorTest.cxx9 KBivanMultiscaleAdaptiveHessianBasedVesselSectionEstimatorTest2.cxx9.4 KBivanMultiscaleAdaptiveOOFBasedVesselSectionEstimatorTest.cxx9 KBivanMultiscaleAdaptiveOOFBasedVesselSectionEstimatorTest2.cxx9.2 KBivanMultiscaleVesselnessRidgeSearchVesselTrackerFilterTest.cxx9.7 KBivanMultiscaleVesselnessRidgeSearchVesselTrackerFilterTest2.cxx10 KBivanOffsetMedialnessVesselSectionFitCostFunctionTest.cxx6.6 KBivanOptimizedVesselnessBasedSearchVesselTrackerFilterTest.cxx12.1 KBivanVesselnessRidgeSearchVesselTrackerFilterTest.cxx12.5 KBITKCMakeLists.txt718 BivanMultiscaleDiscreteGaussianDerivativeImageFilterTest.cxx4.8 KBivanMultiscaleDiscreteGaussianDerivativeOperatorTest.cxx3.7 KBModelingCMakeLists.txt1.4 KBivanCircularVesselSectionTest.cxx2.3 KBivanGraphCountNodeVisitor2.h2.9 KBivanGraphCountNodeVisitor2.txx1012 BivanVesselGraphTest.cxx3 KBivanVesselNodeVisitorSpeedTest.cxx3.8 KBivanVesselNodeVisitorTest.cxx4 KBScriptsSyntheticCircularBarHelixTube.py917 BCircularBarStraightTube.py696 BCircularBarToroidTube.py923 BCircularFlatConvolvedTubeExponentialRadius.py2.2 KBCircularFlatConvolvedTubeExponentialRadius_Gs0_7.py2.3 KBCircularFlatConvolvedTubeExponentialRadius_Gs1_0.py2.3 KBCircularFlatConvolvedTubeSinusoidalRadius.py2.2 KBCircularGaussianHelix.py2.1 KBCircularGaussianToroidTest.py1.6 KBCircularGaussianTube.py1.4 KBCircularGaussianTubeExponentialRadius.py2.3 KBCircularGaussianTubeSinusoidalRadius.py2.2 KBCircularGaussianTubeWithSpacing.py1.6 KBCurvedCircularGaussianTube2.py1.6 KBCurvedCircularGaussianTube2_parallel1.py1.6 KBCurvedCircularGaussianTube2_parallel2.py1.6 KBCurvedCircularGaussianTube2_parallel3.py1.6 KBGaussianToroid.py1.7 KBGaussianToroidRedux.py1.8 KBGaussianToroidResponseProfile.py1.8 KBNoiseAdder.py996 BTestObjects.txt291 BSyntheticCMakeLists.txt4 KBivanCircularBarConvolvedTubeTest.cxx4 KBivanCircularBarConvolvedTubeSinusoidalRadiusTest.cxx4.4 KBivanCircularBarHelixTest.cxx7.9 KBivanCircularBarSectionTest.cxx3 KBivanCircularBarStraightTubeTest.cxx7.9 KBivanCircularBarToroidTest.cxx7.9 KBivanCircularBarTubeTest.cxx3.2 KBivanCircularGaussianHelixTest.cxx4.6 KBivanCircularGaussianNStraightTubesTest.cxx6.2 KBivanCircularGaussianSectionTest.cxx3.4 KBivanCircularGaussianToroidTest.cxx4.5 KBivanCircularGaussianTubeSinusoidalRadiusTest.cxx3.6 KBivanCircularGaussianTubeTest.cxx4.6 KBivanCurvedCircularGaussianTube2Test.cxx4.4 KBivanCurvedCircularGaussianTubeTest.cxx3.1 KBivanGaussianBallTest.cxx2.9 KBUseIVAN.cmake.in1.1 KBUtilitiesCMakeLists.txt312 BGaussianNoiseAdder.cxx3.9 KBVisualizationCMakeLists.txt677 BVTKVesselTrackerPlotter.cxx13.5 KBivanCMakeMacros.cmake1.9 KBivanConfigure.h.in1.7 KBmistGenerateIVANConfig.cmake1.9 KB

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