Diffusion MITK 12f6b5044320

First draft of the GIF refactoring
12f6b5044320
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Description

First draft of the GIF refactoring

Summary:
Signed-off-by: Ralf Floca <r.floca@dkfz-heidelberg.de>

Fixed adding of additional FeatureID params

Signed-off-by: Ralf Floca <r.floca@dkfz-heidelberg.de>

Improved const correctness of PixelAccess methods

Add const overload for mitk::FastSinglePixelAccess()
Add const overload for AccessPixel() (in QmitkAdaptiveRegionGrowingToolGUI.cpp)

Signed-off-by: Ralf Floca <r.floca@dkfz-heidelberg.de>

Complete refactoring of the feature classes

compiles again
all unit tests are OK.
integration test (swigging and python scripts are missing)

Signed-off-by: Ralf Floca <r.floca@dkfz-heidelberg.de>

Test Plan: Review, unti tests and integration tests

Reviewers: O1 MITK Reviewer Group I, goetzm, kislinsk

Reviewed By: O1 MITK Reviewer Group I, goetzm, kislinsk

Subscribers: kislinsk, goetzm

Maniphest Tasks: T27341

Differential Revision: https://phabricator.mitk.org/D286

Details

Provenance

floca	Authored on Jul 16 2020, 1:46 PM
floca	Pushed on Jul 19 2020, 3:39 PM

Reviewer

O1: MITK Reviewer Group I

Differential Revision

Restricted Differential Revision

Parents

rMITK481c477b419e: bug fix in mitk::GIFNeighbourhoodGreyLevelDifference…
rMITK3679ac58bd8c: T27442 Removed unmanaged geometry

Branches

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Tags

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Tasks

T27341: Extend Classification classes and software stack to produce more structured results

Event Timeline

floca committed rMITK12f6b5044320: First draft of the GIF refactoring (authored by floca).Jul 19 2020, 3:40 PM

floca added an edge: Restricted Differential Revision.

floca added a task: T27341: Extend Classification classes and software stack to produce more structured results.

kislinsk mentioned this in T27638: 2020 Week 31.Jul 31 2020, 1:33 PM

Merged Changes

481c477b419e bug fix in mitk::GIFNeighbourhoodGreyLevelDifference…
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400c37024cb7 Fixed gcc compile error.
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6d1b20dac15b Fixed bug in GIFGreyLevelSizeZone::CalculateFeature
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4dd66bacb4b3 Activated prettyprint for the results.
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0c1a7036ce2f propose to put the resampling step (option) for the first checks
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cd5b12256d88 Ensure that always the originaly loaded data is used for the result report (to…
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716c0c4fecb4 Added reader io info to the xml result file
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d3972816d2b4 Merge branch 'master' into T27341-New_structured_classifiction_result_format
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f691dab8c6a7 Fixed gcc error
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da3af091c5a6 Fixed GCC errors
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e96f10604a06 Added XML result support to CLGlobalImageFeatureParameter
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d04c6c619aea Added CLResultXMLWriter
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1fc89e7499fd Added version to feature info
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9f2897eca263 Fixed Typo in CLResultWriter class name
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f26ae4656f29 Fixed compile errors in CLGlobalImageFeatures app.
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48bac8bde76e Complete refactoring of the feature classes
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6cefcbaca6b4 Improved const correctness of PixelAccess methods
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9d01fd4e3dab Fixed adding of additional FeatureID params
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38ac607fe8e9 First draft of the GIF refactoring
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Changes (66)

Path

Size

Packages

Modules/

Classification/

CLCore/

include/

mitkAbstractGlobalImageFeature.h

mitkIntensityQuantifier.h

src/

mitkAbstractGlobalImageFeature.cpp

mitkIntensityQuantifier.cpp

CLMiniApps/

CLGlobalImageFeatures.cpp

CLUtilities/

CMakeLists.txt

files.cmake

include/

	mitkCLResultWriter.h
	mitkCLResultWritter.h

mitkCLResultWritter.h

mitkCLResultXMLWriter.h

mitkGIFCooccurenceMatrix.h

mitkGIFCooccurenceMatrix2.h

mitkGIFCurvatureStatistic.h

mitkGIFFirstOrderHistogramStatistics.h

mitkGIFFirstOrderNumericStatistics.h

mitkGIFFirstOrderStatistics.h

mitkGIFGreyLevelDistanceZone.h

mitkGIFGreyLevelRunLength.h

mitkGIFGreyLevelSizeZone.h

mitkGIFImageDescriptionFeatures.h

mitkGIFIntensityVolumeHistogramFeatures.h

mitkGIFLocalIntensity.h

mitkGIFNeighbourhoodGreyLevelDifference.h

mitkGIFNeighbourhoodGreyToneDifferenceFeatures.h

mitkGIFNeighbouringGreyLevelDependenceFeatures.h

mitkGIFVolumetricDensityStatistics.h

mitkGIFVolumetricStatistics.h

mitkGlobalImageFeaturesParameter.h

src/

GlobalImageFeatures/

mitkGIFCooccurenceMatrix.cpp

mitkGIFCooccurenceMatrix2.cpp

mitkGIFCurvatureStatistic.cpp

mitkGIFFirstOrderHistogramStatistics.cpp

mitkGIFFirstOrderNumericStatistics.cpp

mitkGIFFirstOrderStatistics.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

	mitkCLResultWriter.cpp
	mitkCLResultWritter.cpp

mitkCLResultWritter.cpp

mitkCLResultXMLWriter.cpp

test/

mitkGIFCooc2Test.cpp

mitkGIFCurvatureStatisticTest.cpp

mitkGIFFirstOrderHistogramStatisticsTest.cpp

mitkGIFFirstOrderNumericStatisticsTest.cpp

mitkGIFFirstOrderStatisticsTest.cpp

mitkGIFGreyLevelDistanceZoneTest.cpp

mitkGIFGreyLevelSizeZoneTest.cpp

mitkGIFImageDescriptionFeaturesTest.cpp

mitkGIFIntensityVolumeHistogramTest.cpp

mitkGIFLocalIntensityTest.cpp

mitkGIFNeighbourhoodGreyToneDifferenceFeaturesTest.cpp

mitkGIFNeighbouringGreyLevelDependenceFeatureTest.cpp

mitkGIFVolumetricDensityStatisticsTest.cpp

mitkGIFVolumetricStatisticsTest.cpp

Core/

include/

mitkImagePixelReadAccessor.h

O1: MITK Reviewer Group I

Plugins/

org.mitk.gui.qt.radiomics/

src/

internal/

QmitkGIFConfigurationPanel.cpp

QmitkRadiomicsStatisticView.cpp

rMITK12f6b5044320

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Modules/Classification/CLCore/include/mitkAbstractGlobalImageFeature.h

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Modules/Classification/CLCore/include/mitkIntensityQuantifier.h

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Modules/Classification/CLCore/src/mitkAbstractGlobalImageFeature.cpp

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Modules/Classification/CLCore/src/mitkIntensityQuantifier.cpp

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Modules/Classification/CLMiniApps/CLGlobalImageFeatures.cpp

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Modules/Classification/CLUtilities/CMakeLists.txt

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Modules/Classification/CLUtilities/files.cmake

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Modules/Classification/CLUtilities/include/mitkCLResultWriter.h

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Modules/Classification/CLUtilities/include/mitkCLResultWritter.h

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Modules/Classification/CLUtilities/include/mitkCLResultXMLWriter.h

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Modules/Classification/CLUtilities/include/mitkGIFCooccurenceMatrix.h

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Modules/Classification/CLUtilities/include/mitkGIFCooccurenceMatrix2.h

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Modules/Classification/CLUtilities/include/mitkGIFCurvatureStatistic.h

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Modules/Classification/CLUtilities/include/mitkGIFFirstOrderHistogramStatistics.h

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Modules/Classification/CLUtilities/include/mitkGIFFirstOrderNumericStatistics.h

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Modules/Classification/CLUtilities/include/mitkGIFFirstOrderStatistics.h

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Modules/Classification/CLUtilities/include/mitkGIFGreyLevelDistanceZone.h

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Modules/Classification/CLUtilities/include/mitkGIFGreyLevelRunLength.h

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Modules/Classification/CLUtilities/include/mitkGIFGreyLevelSizeZone.h

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Modules/Classification/CLUtilities/include/mitkGIFImageDescriptionFeatures.h

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Modules/Classification/CLUtilities/include/mitkGIFIntensityVolumeHistogramFeatures.h

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Modules/Classification/CLUtilities/include/mitkGIFLocalIntensity.h

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Modules/Classification/CLUtilities/include/mitkGIFNeighbourhoodGreyLevelDifference.h

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Modules/Classification/CLUtilities/include/mitkGIFNeighbourhoodGreyToneDifferenceFeatures.h

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Modules/Classification/CLUtilities/include/mitkGIFNeighbouringGreyLevelDependenceFeatures.h

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Modules/Classification/CLUtilities/include/mitkGIFVolumetricDensityStatistics.h

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Modules/Classification/CLUtilities/include/mitkGIFVolumetricStatistics.h

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Modules/Classification/CLUtilities/include/mitkGlobalImageFeaturesParameter.h

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFCooccurenceMatrix.cpp

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFCooccurenceMatrix2.cpp

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFCurvatureStatistic.cpp

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFFirstOrderHistogramStatistics.cpp

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFFirstOrderNumericStatistics.cpp

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFFirstOrderStatistics.cpp

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFGreyLevelDistanceZone.cpp

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFGreyLevelRunLength.cpp

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFGreyLevelSizeZone.cpp

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFImageDescriptionFeatures.cpp

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFIntensityVolumeHistogramFeatures.cpp

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFLocalIntensity.cpp

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFNeighbourhoodGreyLevelDifference.cpp

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFNeighbourhoodGreyToneDifferenceFeatures.cpp

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFNeighbouringGreyLevelDependenceFeatures.cpp

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFVolumetricDensityStatistics.cpp

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Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFVolumetricStatistics.cpp

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

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Modules/Classification/CLUtilities/src/mitkCLResultWriter.cpp

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Modules/Classification/CLUtilities/src/mitkCLResultWritter.cpp

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Modules/Classification/CLUtilities/src/mitkCLResultXMLWriter.cpp

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Modules/Classification/CLUtilities/test/mitkGIFCooc2Test.cpp

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Modules/Classification/CLUtilities/test/mitkGIFCurvatureStatisticTest.cpp

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Modules/Classification/CLUtilities/test/mitkGIFFirstOrderHistogramStatisticsTest.cpp

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Modules/Classification/CLUtilities/test/mitkGIFFirstOrderNumericStatisticsTest.cpp

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Modules/Classification/CLUtilities/test/mitkGIFFirstOrderStatisticsTest.cpp

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Modules/Classification/CLUtilities/test/mitkGIFGreyLevelDistanceZoneTest.cpp

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Modules/Classification/CLUtilities/test/mitkGIFGreyLevelSizeZoneTest.cpp

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Modules/Classification/CLUtilities/test/mitkGIFImageDescriptionFeaturesTest.cpp

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Modules/Classification/CLUtilities/test/mitkGIFIntensityVolumeHistogramTest.cpp

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Modules/Classification/CLUtilities/test/mitkGIFLocalIntensityTest.cpp

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Modules/Classification/CLUtilities/test/mitkGIFNeighbourhoodGreyToneDifferenceFeaturesTest.cpp

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Modules/Classification/CLUtilities/test/mitkGIFNeighbouringGreyLevelDependenceFeatureTest.cpp

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Modules/Classification/CLUtilities/test/mitkGIFVolumetricDensityStatisticsTest.cpp

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Modules/Classification/CLUtilities/test/mitkGIFVolumetricStatisticsTest.cpp

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Modules/Core/include/mitkImagePixelReadAccessor.h

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Plugins/org.mitk.gui.qt.radiomics/src/internal/QmitkGIFConfigurationPanel.cpp

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Plugins/org.mitk.gui.qt.radiomics/src/internal/QmitkRadiomicsStatisticView.cpp

First draft of the GIF refactoring12f6b5044320Actions

Description

Details

Event Timeline

Merged Changes

Changes (66)

rMITK12f6b5044320

Modules/Classification/CLCore/include/mitkAbstractGlobalImageFeature.h

Modules/Classification/CLCore/include/mitkIntensityQuantifier.h

Modules/Classification/CLCore/src/mitkAbstractGlobalImageFeature.cpp

Modules/Classification/CLCore/src/mitkIntensityQuantifier.cpp

Modules/Classification/CLMiniApps/CLGlobalImageFeatures.cpp

Modules/Classification/CLUtilities/CMakeLists.txt

Modules/Classification/CLUtilities/files.cmake

Modules/Classification/CLUtilities/include/mitkCLResultWriter.h

Modules/Classification/CLUtilities/include/mitkCLResultWritter.h

Modules/Classification/CLUtilities/include/mitkCLResultXMLWriter.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/mitkGIFFirstOrderNumericStatistics.h

Modules/Classification/CLUtilities/include/mitkGIFFirstOrderStatistics.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

Modules/Classification/CLUtilities/include/mitkGIFLocalIntensity.h

Modules/Classification/CLUtilities/include/mitkGIFNeighbourhoodGreyLevelDifference.h

Modules/Classification/CLUtilities/include/mitkGIFNeighbourhoodGreyToneDifferenceFeatures.h

Modules/Classification/CLUtilities/include/mitkGIFNeighbouringGreyLevelDependenceFeatures.h

Modules/Classification/CLUtilities/include/mitkGIFVolumetricDensityStatistics.h

Modules/Classification/CLUtilities/include/mitkGIFVolumetricStatistics.h

Modules/Classification/CLUtilities/include/mitkGlobalImageFeaturesParameter.h

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFCooccurenceMatrix.cpp

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFCooccurenceMatrix2.cpp

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFCurvatureStatistic.cpp

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFFirstOrderHistogramStatistics.cpp

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFFirstOrderNumericStatistics.cpp

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFFirstOrderStatistics.cpp

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFGreyLevelDistanceZone.cpp

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFGreyLevelRunLength.cpp

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFGreyLevelSizeZone.cpp

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFImageDescriptionFeatures.cpp

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFIntensityVolumeHistogramFeatures.cpp

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFLocalIntensity.cpp

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFNeighbourhoodGreyLevelDifference.cpp

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFNeighbourhoodGreyToneDifferenceFeatures.cpp

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFNeighbouringGreyLevelDependenceFeatures.cpp

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFVolumetricDensityStatistics.cpp

Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFVolumetricStatistics.cpp

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

Modules/Classification/CLUtilities/src/mitkCLResultWriter.cpp

Modules/Classification/CLUtilities/src/mitkCLResultWritter.cpp

Modules/Classification/CLUtilities/src/mitkCLResultXMLWriter.cpp

Modules/Classification/CLUtilities/test/mitkGIFCooc2Test.cpp

Modules/Classification/CLUtilities/test/mitkGIFCurvatureStatisticTest.cpp

Modules/Classification/CLUtilities/test/mitkGIFFirstOrderHistogramStatisticsTest.cpp

Modules/Classification/CLUtilities/test/mitkGIFFirstOrderNumericStatisticsTest.cpp

Modules/Classification/CLUtilities/test/mitkGIFFirstOrderStatisticsTest.cpp

Modules/Classification/CLUtilities/test/mitkGIFGreyLevelDistanceZoneTest.cpp

Modules/Classification/CLUtilities/test/mitkGIFGreyLevelSizeZoneTest.cpp

Modules/Classification/CLUtilities/test/mitkGIFImageDescriptionFeaturesTest.cpp

Modules/Classification/CLUtilities/test/mitkGIFIntensityVolumeHistogramTest.cpp

Modules/Classification/CLUtilities/test/mitkGIFLocalIntensityTest.cpp

Modules/Classification/CLUtilities/test/mitkGIFNeighbourhoodGreyToneDifferenceFeaturesTest.cpp

Modules/Classification/CLUtilities/test/mitkGIFNeighbouringGreyLevelDependenceFeatureTest.cpp

Modules/Classification/CLUtilities/test/mitkGIFVolumetricDensityStatisticsTest.cpp

Modules/Classification/CLUtilities/test/mitkGIFVolumetricStatisticsTest.cpp

Modules/Core/include/mitkImagePixelReadAccessor.h

Plugins/org.mitk.gui.qt.radiomics/src/internal/QmitkGIFConfigurationPanel.cpp

Plugins/org.mitk.gui.qt.radiomics/src/internal/QmitkRadiomicsStatisticView.cpp

First draft of the GIF refactoring
12f6b5044320
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