Merge branch 'T19480-IntegrationOfBugfixesForRadiomics' into T19480…
5fa68f400cd9
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Merge branch 'T19480-IntegrationOfBugfixesForRadiomics' into T19480-IntegrationOfBugfixesForRadiomics2

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goetzm	Authored on Mar 12 2018, 1:13 PM
goetzm	Pushed on Mar 12 2018, 1:14 PM

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rMITK7507ec7b0dac: Adaptions for linux
rMITK5105fedbaf04: Merge branch 'T24178-CrashOnStartupWhenUSSupportIsEnabled'

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goetzm committed rMITK5fa68f400cd9: Merge branch 'T19480-IntegrationOfBugfixesForRadiomics' into T19480… (authored by goetzm).Mar 12 2018, 1:13 PM

Merged Changes

This commit merges a very large number of changes. Only the first 50 are shown.

7507ec7b0dac Adaptions for linux
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7416d12e04d7 Warning removed
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c14ae521362b Warning removed
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e133a2f3071a Changed the way the distance map is calculated to a more robust one
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cd2df0cce5e7 Adaptions for linux
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98763609f891 Code cleaning, commenting, additional features
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05b58365a5ac Linux-compatibility bug fixes (Typenames, unused variables etc..)
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f6f2fd9c18d1 Comments, Code Cleaning and smaller Bugfixes
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9f8f17fb358f Bugfixes, Added Features, Additional File Converter
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22e13d42d7ea Bugfixes and new Features.
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a419bf1b2165 Small adaptation for linux
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42d284f8c205 Changed Lung Segmentation algorithm to nearest segmentation from middle point
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3a6a5b5b7301 Smaller Adaptation
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169a9706be28 Changes for linux compatibility x
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b601e2e7df81 Linux compatibility
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3aae27f5d245 Removed Linux Errors
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36d29155e446 Added additional parameter to Xray-simulation
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c33a418d390c Removed merge problems and updated to changes
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75752bc30936 Merge branch 'T22687-AddResamplingAndMaskCleaningGUI' into T19480…
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a055953e4528 Merge branch 'T19480-IntegrationOfBugfixesForRadiomics' into T19480…
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be9de25b22d2 Added Resamplling GUI for fast prototyping
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5fef804dee53 Added simple lung segmentation miniapp
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90d532e19c0d Added missing counter
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4ce3c5a86618 Updated Dicom2Nrrd for the IOUtil-Structu
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f1f2973f6cb7 Bug Fix
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ddd2f70ff295 Error fix
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f5e13f41e644 Linux compabtibiliy
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a9913acc13d9 Added basic voxel description to First Order Statistic
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0764f35b1d5d Added Colorcoding for multiple segmentations to the Screenshot tools.
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9bc9f4782fd7 Added Script that allows screeenless run of screen-dependend tools
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e91cd60289b7 Small fix for linux compability
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0830406659fc Bugfixes and additional screenshot tool
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30f8856db120 Allow rotated geometries and select right slice
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b7303b57a5e5 Removed unused function
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5d1cec977f03 Removed unused function
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9f1b1238e8f1 Linux Bugfixes
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e59f1c041bbd Linux Bugfixes
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ec4a5f707482 Bugfixes and a new miniapp for overlay
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4a8fd9395066 Updated Run-Length and Shape Features
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unknown <goetzm@e130-pc04.inet.dkfz-heidelberg.de>
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a54bce55d7a6 Added screenshot capability
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unknown <goetzm@e130-pc04.inet.dkfz-heidelberg.de>
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7d5289316067 Added Code to save images as png's and additionl FO features
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5b21baa514ba Linux Bugfix (Missing export)
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1e718a913794 Linux bugfix
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ce7c8f74bc9b Restructing input parsing for parameter tuning
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5bbc6591ead5 Added new switch for header only on first line
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6baf58c8a3a0 Increased Version number
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78395de659be Linux warning bug fix
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c2a215c3634d Changed output format slightly
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6bd50766100a Fixed output problem
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a3d304a93027 Linux compilation bug fixes
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Changes (163)
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Packages

Modules/

Classification/

CLCore/

CMakeLists.txt

files.cmake

include/

mitkAbstractGlobalImageFeature.h

mitkConfigFileReader.h

mitkIntensityQuantifier.h

src/

mitkAbstractGlobalImageFeature.cpp

mitkIntensityQuantifier.cpp

CLImportanceWeighting/

src/

mitkGeneralizedLinearModel.cpp

CLMRUtilities/

include/

mitkMRNormLinearStatisticBasedFilter.h

src/

MRNormalization/

mitkMRNormLinearStatisticBasedFilter.cpp

CLMiniApps/

CL2Dto3DImage.cpp

CLDicom2Nrrd.cpp

CLGlobalImageFeatures.cpp

CLImageTypeConverter.cpp

CLLungSegmentation.cpp

CLMRNormalization.cpp

CLMatchPointReg.cpp

CLMultiForestPrediction.cpp

CLN4.cpp

CLNrrdToPoly.cpp

CLOverlayRoiCenterOfMass.cpp

CLPlanarFigureToNrrd.cpp

CLPointSetToSegmentation.cpp

	CLPurfVoxelClassification.cpp
	CLVoxelClassification.cpp

CLRandomSampling.cpp

CLRemoveEmptyVoxels.cpp

CLResampleImageToReference.cpp

CLScreenshot.cpp

CLSkullMask.cpp

CLVoxelClassification.cpp

CLVoxelFeatures.cpp

CLWeighting.cpp

CMakeLists.txt

XRaxSimulationFromCT.cpp

CLUtilities/

CMakeLists.txt

files.cmake

include/

	itkEnhancedHistogramToNeighbourhoodGreyLevelDifferenceFeaturesFilter.h
	itkEnhancedHistogramToRunLengthFeaturesFilter.h

itkEnhancedHistogramToNeighbourhoodGreyLevelDifferenceFeaturesFilter.hxx

itkEnhancedHistogramToRunLengthFeaturesFilter.h

itkEnhancedHistogramToRunLengthFeaturesFilter.hxx

itkEnhancedHistogramToSizeZoneFeaturesFilter.h

itkEnhancedHistogramToSizeZoneFeaturesFilter.hxx

itkEnhancedHistogramToTextureFeaturesFilter.h

itkEnhancedHistogramToTextureFeaturesFilter.hxx

	itkEnhancedScalarImageToNeighbourhoodGreyLevelDifferenceFeaturesFilter.h
	itkEnhancedScalarImageToRunLengthFeaturesFilter.h

	itkEnhancedScalarImageToNeighbourhoodGreyLevelDifferenceFeaturesFilter.hxx
	itkEnhancedScalarImageToRunLengthFeaturesFilter.hxx

itkEnhancedScalarImageToNeighbourhoodGreyLevelDifferenceMatrixFilter.h

itkEnhancedScalarImageToNeighbourhoodGreyLevelDifferenceMatrixFilter.hxx

itkEnhancedScalarImageToRunLengthFeaturesFilter.h

itkEnhancedScalarImageToRunLengthFeaturesFilter.hxx

itkEnhancedScalarImageToRunLengthMatrixFilter.hxx

	itkEnhancedScalarImageToSizeZoneFeaturesFilter.h
	itkEnhancedScalarImageToRunLengthFeaturesFilter.h

	itkEnhancedScalarImageToSizeZoneFeaturesFilter.hxx
	itkEnhancedScalarImageToRunLengthFeaturesFilter.hxx

itkEnhancedScalarImageToSizeZoneMatrixFilter.h

itkEnhancedScalarImageToSizeZoneMatrixFilter.hxx

itkLocalStatisticFilter.h

itkLocalStatisticFilter.hxx

itkMultiHistogramFilter.cpp

itkMultiHistogramFilter.h

mitkCLResultWritter.h

mitkCLUtil.h

mitkGIFCooccurenceMatrix.h

mitkGIFCooccurenceMatrix2.h

mitkGIFCurvatureStatistic.h

mitkGIFFirstOrderHistogramStatistics.h

mitkGIFFirstOrderStatistics.h

mitkGIFGrayLevelRunLength.h

mitkGIFGreyLevelDistanceZone.h

mitkGIFGreyLevelRunLength.h

mitkGIFGreyLevelSizeZone.h

mitkGIFImageDescriptionFeatures.h

mitkGIFIntensityVolumeHistogramFeatures.h

mitkGIFLocalIntensity.h

	mitkGIFNeighbourhoodGreyLevelDifference.h
	mitkGIFGrayLevelRunLength.h

mitkGIFNeighbourhoodGreyToneDifferenceFeatures.h

mitkGIFNeighbouringGreyLevelDependenceFeatures.h

mitkGIFVolumetricDensityStatistics.h

mitkGIFVolumetricStatistics.h

mitkGlobalImageFeaturesParameter.h

mitkRandomImageSampler.h

src/

Algorithms/

mitkRandomImageSampler.cpp

GlobalImageFeatures/

mitkGIFCooccurenceMatrix.cpp

mitkGIFCooccurenceMatrix2.cpp

mitkGIFCurvatureStatistic.cpp

mitkGIFFirstOrderHistogramStatistics.cpp

mitkGIFFirstOrderStatistics.cpp

mitkGIFGrayLevelRunLength.cpp

mitkGIFGreyLevelDistanceZone.cpp

mitkGIFGreyLevelRunLength.cpp

mitkGIFGreyLevelSizeZone.cpp

mitkGIFImageDescriptionFeatures.cpp

mitkGIFIntensityVolumeHistogramFeatures.cpp

mitkGIFLocalIntensity.cpp

mitkGIFNeighbourhoodGreyLevelDifference.cpp

mitkGIFNeighbourhoodGreyToneDifferenceFeatures.cpp

mitkGIFNeighbouringGreyLevelDependenceFeatures.cpp

mitkGIFVolumetricDensityStatistics.cpp

mitkGIFVolumetricStatistics.cpp

MiniAppUtils

mitkGlobalImageFeaturesParameter.cpp

mitkSplitParameterToVector.cpp

mitkCLResultWritter.cpp

mitkCLUtil.cpp

test/

mitkGlobalFeaturesTest.cpp

CLVigraRandomForest/

files.cmake

include/

mitkAdditionalRFData.h

mitkImpurityLoss.h

mitkLinearSplitting.h

	mitkPUImpurityLoss.h
	mitkImpurityLoss.h

	mitkPURFClassifier.h
	mitkVigraRandomForestClassifier.h

mitkThresholdSplit.h

mitkVigraRandomForestClassifier.h

src/

Classifier/

	mitkPURFClassifier.cpp
	mitkVigraRandomForestClassifier.cpp

mitkVigraRandomForestClassifier.cpp

Splitter/

mitkAdditionalRFData.cpp

mitkImpurityLoss.cpp

mitkLinearSplitting.cpp

mitkPUImpurityLoss.cpp

mitkThresholdSplit.cpp

DataCollection/

Utilities/

mitkCollectionStatistic.h

Scripts

xvfb-run-save.sh

DiffusionImaging/

MiniApps/

ExtractAllGradients.cpp

ImageStatistics/

mitkPlanarFigureMaskGenerator.cpp

O1: MITK Reviewer Group I

mitkPlanarFigureMaskGenerator.h

O1: MITK Reviewer Group I

ModuleList.cmake

	Modules/	Classification/	CLUtilities/	include/
	Plugins/	org.mitk.gui.qt.classificationsegmentation/	src/	internal/

	mitkSplitParameterToVector.h
	org_mitk_gui_qt_classificationsegmentation_Activator.cpp

Plugins/

PluginList.cmake

org.mitk.gui.qt.classificationsegmentation/

files.cmake

plugin.xml

src/

internal/

ClassificationRegionGrow.cpp

ClassificationRegionGrow.h

ClassificationRegionGrowControls.ui

	org_mitk_gui_qt_classificationregiongrow_Activator.cpp
	org_mitk_gui_qt_classificationsegmentation_Activator.cpp

	org_mitk_gui_qt_classificationregiongrow_Activator.h
	org_mitk_gui_qt_classificationsegmentation_Activator.h

org_mitk_gui_qt_classificationsegmentation_Activator.cpp

org_mitk_gui_qt_classificationsegmentation_Activator.h

org.mitk.gui.qt.preprocessing.resampling

CMakeLists.txt

documentation

UserManual

QmitkBasicImageProcessing.dox

QmitkBasicImageProcessing_BIP_Overview.png

QmitkBasicImageProcessing_ImageProcessing_48.png

doxygen

modules.dox

files.cmake

manifest_headers.cmake

plugin.xml

resources

ImageProcessing_64.xpm

QmitkPreprocessingResamplingView.qrc

lena.xpm

src

internal

QmitkPreprocessingResamplingView.cpp

QmitkPreprocessingResamplingView.h

QmitkPreprocessingResamplingViewControls.ui

	org.mitk.gui.qt.preprocessing.resampling/	src/	internal/
	org.mitk.gui.qt.classificationsegmentation/	src/	internal/

	mitkPreprocessingResamplingActivator.cpp
	org_mitk_gui_qt_classificationsegmentation_Activator.cpp

	mitkPreprocessingResamplingActivator.h
	org_mitk_gui_qt_classificationsegmentation_Activator.h

Wrapper

swigutils.cmake

rMITK5fa68f400cd9

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Modules/Classification/CLUtilities/src/MiniAppUtils/mitkSplitParameterToVector.cpp

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Modules/Classification/CLUtilities/src/mitkCLResultWritter.cpp

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Modules/Classification/CLUtilities/src/mitkCLUtil.cpp

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Modules/Classification/CLVigraRandomForest/src/Classifier/mitkPURFClassifier.cpp

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Modules/Classification/CLVigraRandomForest/src/Classifier/mitkVigraRandomForestClassifier.cpp

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Modules/Classification/DataCollection/Utilities/mitkCollectionStatistic.h

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Modules/Classification/Scripts/xvfb-run-save.sh

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Wrapper/swigutils.cmake

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Merge branch 'T19480-IntegrationOfBugfixesForRadiomics' into T19480…5fa68f400cd9Actions

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Changes (163)Show All Changes

Very Large Commit

rMITK5fa68f400cd9

Modules/Classification/CLCore/CMakeLists.txt

Modules/Classification/CLCore/files.cmake

Modules/Classification/CLCore/include/mitkAbstractGlobalImageFeature.h

Modules/Classification/CLCore/include/mitkConfigFileReader.h

Modules/Classification/CLCore/include/mitkIntensityQuantifier.h

Modules/Classification/CLCore/src/mitkAbstractGlobalImageFeature.cpp

Modules/Classification/CLCore/src/mitkIntensityQuantifier.cpp

Modules/Classification/CLImportanceWeighting/src/mitkGeneralizedLinearModel.cpp

Modules/Classification/CLMRUtilities/include/mitkMRNormLinearStatisticBasedFilter.h

Modules/Classification/CLMRUtilities/src/MRNormalization/mitkMRNormLinearStatisticBasedFilter.cpp

Modules/Classification/CLMiniApps/CL2Dto3DImage.cpp

Modules/Classification/CLMiniApps/CLDicom2Nrrd.cpp

Modules/Classification/CLMiniApps/CLGlobalImageFeatures.cpp

Modules/Classification/CLMiniApps/CLImageTypeConverter.cpp

Modules/Classification/CLMiniApps/CLLungSegmentation.cpp

Modules/Classification/CLMiniApps/CLMRNormalization.cpp

Modules/Classification/CLMiniApps/CLMatchPointReg.cpp

Modules/Classification/CLMiniApps/CLMultiForestPrediction.cpp

Modules/Classification/CLMiniApps/CLN4.cpp

Modules/Classification/CLMiniApps/CLNrrdToPoly.cpp

Modules/Classification/CLMiniApps/CLOverlayRoiCenterOfMass.cpp

Modules/Classification/CLMiniApps/CLPlanarFigureToNrrd.cpp

Modules/Classification/CLMiniApps/CLPointSetToSegmentation.cpp

Modules/Classification/CLMiniApps/CLPurfVoxelClassification.cpp

Modules/Classification/CLMiniApps/CLRandomSampling.cpp

Modules/Classification/CLMiniApps/CLRemoveEmptyVoxels.cpp

Modules/Classification/CLMiniApps/CLResampleImageToReference.cpp

Modules/Classification/CLMiniApps/CLScreenshot.cpp

Modules/Classification/CLMiniApps/CLSkullMask.cpp

Modules/Classification/CLMiniApps/CLVoxelClassification.cpp

Modules/Classification/CLMiniApps/CLVoxelFeatures.cpp

Modules/Classification/CLMiniApps/CLWeighting.cpp

Modules/Classification/CLMiniApps/CMakeLists.txt

Modules/Classification/CLMiniApps/XRaxSimulationFromCT.cpp

Modules/Classification/CLUtilities/CMakeLists.txt

Modules/Classification/CLUtilities/files.cmake

Modules/Classification/CLUtilities/include/itkEnhancedHistogramToNeighbourhoodGreyLevelDifferenceFeaturesFilter.h

Modules/Classification/CLUtilities/include/itkEnhancedHistogramToNeighbourhoodGreyLevelDifferenceFeaturesFilter.hxx

Modules/Classification/CLUtilities/include/itkEnhancedHistogramToRunLengthFeaturesFilter.h

Modules/Classification/CLUtilities/include/itkEnhancedHistogramToRunLengthFeaturesFilter.hxx

Modules/Classification/CLUtilities/include/itkEnhancedHistogramToSizeZoneFeaturesFilter.h

Modules/Classification/CLUtilities/include/itkEnhancedHistogramToSizeZoneFeaturesFilter.hxx

Modules/Classification/CLUtilities/include/itkEnhancedHistogramToTextureFeaturesFilter.h

Modules/Classification/CLUtilities/include/itkEnhancedHistogramToTextureFeaturesFilter.hxx

Modules/Classification/CLUtilities/include/itkEnhancedScalarImageToNeighbourhoodGreyLevelDifferenceFeaturesFilter.h

Modules/Classification/CLUtilities/include/itkEnhancedScalarImageToNeighbourhoodGreyLevelDifferenceFeaturesFilter.hxx

Modules/Classification/CLUtilities/include/itkEnhancedScalarImageToNeighbourhoodGreyLevelDifferenceMatrixFilter.h

Modules/Classification/CLUtilities/include/itkEnhancedScalarImageToNeighbourhoodGreyLevelDifferenceMatrixFilter.hxx

Modules/Classification/CLUtilities/include/itkEnhancedScalarImageToRunLengthFeaturesFilter.h

Modules/Classification/CLUtilities/include/itkEnhancedScalarImageToRunLengthFeaturesFilter.hxx

Modules/Classification/CLUtilities/include/itkEnhancedScalarImageToRunLengthMatrixFilter.hxx

Modules/Classification/CLUtilities/include/itkEnhancedScalarImageToSizeZoneFeaturesFilter.h

Modules/Classification/CLUtilities/include/itkEnhancedScalarImageToSizeZoneFeaturesFilter.hxx

Modules/Classification/CLUtilities/include/itkEnhancedScalarImageToSizeZoneMatrixFilter.h

Modules/Classification/CLUtilities/include/itkEnhancedScalarImageToSizeZoneMatrixFilter.hxx

Modules/Classification/CLUtilities/include/itkLocalStatisticFilter.h

Modules/Classification/CLUtilities/include/itkLocalStatisticFilter.hxx

Modules/Classification/CLUtilities/include/itkMultiHistogramFilter.cpp

Modules/Classification/CLUtilities/include/itkMultiHistogramFilter.h

Modules/Classification/CLUtilities/include/mitkCLResultWritter.h

Modules/Classification/CLUtilities/include/mitkCLUtil.h

Modules/Classification/CLUtilities/include/mitkGIFCooccurenceMatrix.h

Modules/Classification/CLUtilities/include/mitkGIFCooccurenceMatrix2.h

Modules/Classification/CLUtilities/include/mitkGIFCurvatureStatistic.h

Modules/Classification/CLUtilities/include/mitkGIFFirstOrderHistogramStatistics.h

Modules/Classification/CLUtilities/include/mitkGIFFirstOrderStatistics.h

Modules/Classification/CLUtilities/include/mitkGIFGrayLevelRunLength.h

Modules/Classification/CLUtilities/include/mitkGIFGreyLevelDistanceZone.h

Modules/Classification/CLUtilities/include/mitkGIFGreyLevelRunLength.h

Modules/Classification/CLUtilities/include/mitkGIFGreyLevelSizeZone.h

Modules/Classification/CLUtilities/include/mitkGIFImageDescriptionFeatures.h

Modules/Classification/CLUtilities/include/mitkGIFIntensityVolumeHistogramFeatures.h

Merge branch 'T19480-IntegrationOfBugfixesForRadiomics' into T19480…
5fa68f400cd9
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Changes (163)
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