diff --git a/Modules/Core/TestingHelper/src/mitkTestDynamicImageGenerator.cpp b/Modules/Core/TestingHelper/src/mitkTestDynamicImageGenerator.cpp
index 73a8af779d..bca01c2eeb 100644
--- a/Modules/Core/TestingHelper/src/mitkTestDynamicImageGenerator.cpp
+++ b/Modules/Core/TestingHelper/src/mitkTestDynamicImageGenerator.cpp
@@ -1,253 +1,212 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkTestDynamicImageGenerator.h"
#include "mitkArbitraryTimeGeometry.h"
#include "mitkImageCast.h"
+#include "mitkTemporalJoinImagesFilter.h"
namespace mitk
{
typedef itk::Image<double, 3> FrameITKImageType;
typedef itk::Image<double, 4> DynamicITKImageType;
typedef itk::Image<unsigned char, 3> MaskITKImageType;
TestImageType::Pointer GenerateTestImage(int factor)
{
TestImageType::Pointer image = TestImageType::New();
TestImageType::IndexType start;
start[0] = 0; // first index on X
start[1] = 0; // first index on Y
TestImageType::SizeType size;
size[0] = 3; // size along X
size[1] = 3; // size along Y
TestImageType::RegionType region;
region.SetSize(size);
region.SetIndex(start);
image->SetRegions(region);
image->Allocate();
itk::ImageRegionIterator<TestImageType> it = itk::ImageRegionIterator<TestImageType>(image,
image->GetLargestPossibleRegion());
int count = 1;
while (!it.IsAtEnd())
{
it.Set(count * factor);
++it;
++count;
}
return image;
}
TestMaskType::Pointer GenerateTestMask()
{
TestMaskType::Pointer image = TestMaskType::New();
TestMaskType::IndexType start;
start[0] = 0; // first index on X
start[1] = 0; // first index on Y
TestMaskType::SizeType size;
size[0] = 3; // size along X
size[1] = 3; // size along Y
TestMaskType::RegionType region;
region.SetSize(size);
region.SetIndex(start);
image->SetRegions(region);
image->Allocate();
itk::ImageRegionIterator<TestMaskType> it = itk::ImageRegionIterator<TestMaskType>(image,
image->GetLargestPossibleRegion());
int count = 1;
while (!it.IsAtEnd())
{
if (count > 1 && count < 5)
{
it.Set(1);
}
else
{
it.Set(0);
}
++it;
++count;
}
return image;
}
Image::Pointer GenerateTestFrame(double timePoint)
{
FrameITKImageType::Pointer image = FrameITKImageType::New();
FrameITKImageType::IndexType start;
start[0] = 0; // first index on X
start[1] = 0; // first index on Y
start[2] = 0; // first index on Z
FrameITKImageType::SizeType size;
size[0] = 3; // size along X
size[1] = 3; // size along Y
size[2] = 3; // size along Z
FrameITKImageType::RegionType region;
region.SetSize(size);
region.SetIndex(start);
image->SetRegions(region);
image->Allocate();
itk::ImageRegionIterator<FrameITKImageType> it = itk::ImageRegionIterator<FrameITKImageType>(image,
image->GetLargestPossibleRegion());
int count = 0;
while (!it.IsAtEnd())
{
double slope = count % (size[0] * size[1]);
double offset = itk::Math::Floor<double, double>(count / (size[0] * size[1])) * 10;
it.Set(slope * timePoint + offset);
++it;
++count;
}
mitk::Image::Pointer mitkImage = mitk::Image::New();
mitkImage->InitializeByItk(image.GetPointer());
mitkImage->SetVolume(image->GetBufferPointer());
return mitkImage;
}
Image::Pointer GenerateTestMaskMITK()
{
MaskITKImageType::Pointer image = MaskITKImageType::New();
MaskITKImageType::IndexType start;
start[0] = 0; // first index on X
start[1] = 0; // first index on Y
start[2] = 0; // first index on Z
MaskITKImageType::SizeType size;
size[0] = 3; // size along X
size[1] = 3; // size along Y
size[2] = 3; // size along Z
MaskITKImageType::RegionType region;
region.SetSize(size);
region.SetIndex(start);
image->SetRegions(region);
image->Allocate();
itk::ImageRegionIterator<MaskITKImageType> it = itk::ImageRegionIterator<MaskITKImageType>(image,
image->GetLargestPossibleRegion());
int count = 0;
while (!it.IsAtEnd())
{
if (count < 14)
{
it.Set(1);
}
else
{
it.Set(0);
}
++it;
++count;
}
mitk::Image::Pointer mitkImage = mitk::Image::New();
mitkImage->InitializeByItk(image.GetPointer());
mitkImage->SetVolume(image->GetBufferPointer());
return mitkImage;
}
Image::Pointer GenerateDynamicTestImageMITK()
{
+ auto filter = mitk::TemporalJoinImagesFilter::New();
- mitk::Image::Pointer tempImage = GenerateTestFrame(1);
- mitk::Image::Pointer dynamicImage = mitk::Image::New();
-
- DynamicITKImageType::Pointer dynamicITKImage = DynamicITKImageType::New();
- DynamicITKImageType::RegionType dynamicITKRegion;
- DynamicITKImageType::PointType dynamicITKOrigin;
- DynamicITKImageType::IndexType dynamicITKIndex;
- DynamicITKImageType::SpacingType dynamicITKSpacing;
-
- dynamicITKSpacing[0] = tempImage->GetGeometry()->GetSpacing()[0];
- dynamicITKSpacing[1] = tempImage->GetGeometry()->GetSpacing()[1];
- dynamicITKSpacing[2] = tempImage->GetGeometry()->GetSpacing()[2];
- dynamicITKSpacing[3] = 5.0;
-
- dynamicITKIndex[0] = 0; // The first pixel of the REGION
- dynamicITKIndex[1] = 0;
- dynamicITKIndex[2] = 0;
- dynamicITKIndex[3] = 0;
-
- dynamicITKRegion.SetSize(0, tempImage->GetDimension(0));
- dynamicITKRegion.SetSize(1, tempImage->GetDimension(1));
- dynamicITKRegion.SetSize(2, tempImage->GetDimension(2));
- dynamicITKRegion.SetSize(3, 10);
-
- dynamicITKRegion.SetIndex(dynamicITKIndex);
-
- dynamicITKOrigin[0] = tempImage->GetGeometry()->GetOrigin()[0];
- dynamicITKOrigin[1] = tempImage->GetGeometry()->GetOrigin()[1];
- dynamicITKOrigin[2] = tempImage->GetGeometry()->GetOrigin()[2];
-
- dynamicITKImage->SetOrigin(dynamicITKOrigin);
- dynamicITKImage->SetSpacing(dynamicITKSpacing);
- dynamicITKImage->SetRegions(dynamicITKRegion);
- dynamicITKImage->Allocate();
- dynamicITKImage->FillBuffer(0); //not sure if this is necessary
-
- // Convert
- mitk::CastToMitkImage(dynamicITKImage, dynamicImage);
-
- ArbitraryTimeGeometry::Pointer timeGeometry = ArbitraryTimeGeometry::New();
- timeGeometry->ClearAllGeometries();
-
-
+ mitk::TemporalJoinImagesFilter::TimeBoundsVectorType bounds;
for (int i = 0; i < 10; ++i)
{
- mitk::Image::Pointer frameImage = GenerateTestFrame(1 + (dynamicITKSpacing[3] * i));
- mitk::ImageReadAccessor accessor(frameImage);
- dynamicImage->SetVolume(accessor.GetData(), i);
-
- timeGeometry->AppendNewTimeStepClone(frameImage->GetGeometry(), 1 + (dynamicITKSpacing[3] * i),
- 1 + (dynamicITKSpacing[3]*(i+1)));
+ filter->SetInput(i, GenerateTestFrame(1 + (5.0 * i)));
+ bounds.push_back(1 + (5.0 * (i + 1)));
}
- dynamicImage->SetTimeGeometry(timeGeometry);
+ filter->SetFirstMinTimeBound(1.);
+ filter->SetMaxTimeBounds(bounds);
+
+ filter->Update();
- return dynamicImage;
+ return filter->GetOutput();
}
}
diff --git a/Modules/Core/files.cmake b/Modules/Core/files.cmake
index e13405173c..78ae1b7ad2 100644
--- a/Modules/Core/files.cmake
+++ b/Modules/Core/files.cmake
@@ -1,323 +1,324 @@
file(GLOB_RECURSE H_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}/include/*")
set(CPP_FILES
mitkCoreActivator.cpp
mitkCoreObjectFactoryBase.cpp
mitkCoreObjectFactory.cpp
mitkCoreServices.cpp
mitkException.cpp
Algorithms/mitkBaseDataSource.cpp
Algorithms/mitkClippedSurfaceBoundsCalculator.cpp
Algorithms/mitkCompareImageDataFilter.cpp
Algorithms/mitkCompositePixelValueToString.cpp
Algorithms/mitkConvert2Dto3DImageFilter.cpp
Algorithms/mitkDataNodeSource.cpp
Algorithms/mitkExtractSliceFilter.cpp
Algorithms/mitkExtractSliceFilter2.cpp
Algorithms/mitkHistogramGenerator.cpp
Algorithms/mitkImageChannelSelector.cpp
Algorithms/mitkImageSliceSelector.cpp
Algorithms/mitkImageSource.cpp
Algorithms/mitkImageTimeSelector.cpp
Algorithms/mitkImageToImageFilter.cpp
Algorithms/mitkImageToSurfaceFilter.cpp
Algorithms/mitkMultiComponentImageDataComparisonFilter.cpp
Algorithms/mitkPlaneGeometryDataToSurfaceFilter.cpp
Algorithms/mitkPointSetSource.cpp
Algorithms/mitkPointSetToPointSetFilter.cpp
Algorithms/mitkRGBToRGBACastImageFilter.cpp
Algorithms/mitkSubImageSelector.cpp
Algorithms/mitkSurfaceSource.cpp
Algorithms/mitkSurfaceToImageFilter.cpp
Algorithms/mitkSurfaceToSurfaceFilter.cpp
Algorithms/mitkUIDGenerator.cpp
Algorithms/mitkVolumeCalculator.cpp
+ Algorithms/mitkTemporalJoinImagesFilter.cpp
Controllers/mitkBaseController.cpp
Controllers/mitkCallbackFromGUIThread.cpp
Controllers/mitkCameraController.cpp
Controllers/mitkCameraRotationController.cpp
Controllers/mitkLimitedLinearUndo.cpp
Controllers/mitkOperationEvent.cpp
Controllers/mitkPlanePositionManager.cpp
Controllers/mitkProgressBar.cpp
Controllers/mitkRenderingManager.cpp
Controllers/mitkSliceNavigationController.cpp
Controllers/mitkSlicesCoordinator.cpp
Controllers/mitkStatusBar.cpp
Controllers/mitkStepper.cpp
Controllers/mitkTestManager.cpp
Controllers/mitkUndoController.cpp
Controllers/mitkVerboseLimitedLinearUndo.cpp
Controllers/mitkVtkLayerController.cpp
DataManagement/mitkAnatomicalStructureColorPresets.cpp
DataManagement/mitkArbitraryTimeGeometry.cpp
DataManagement/mitkAbstractTransformGeometry.cpp
DataManagement/mitkAnnotationProperty.cpp
DataManagement/mitkApplicationCursor.cpp
DataManagement/mitkApplyTransformMatrixOperation.cpp
DataManagement/mitkBaseData.cpp
DataManagement/mitkBaseGeometry.cpp
DataManagement/mitkBaseProperty.cpp
DataManagement/mitkChannelDescriptor.cpp
DataManagement/mitkClippingProperty.cpp
DataManagement/mitkColorProperty.cpp
DataManagement/mitkDataNode.cpp
DataManagement/mitkDataStorage.cpp
DataManagement/mitkEnumerationProperty.cpp
DataManagement/mitkFloatPropertyExtension.cpp
DataManagement/mitkGeometry3D.cpp
DataManagement/mitkGeometryData.cpp
DataManagement/mitkGeometryTransformHolder.cpp
DataManagement/mitkGroupTagProperty.cpp
DataManagement/mitkGenericIDRelationRule.cpp
DataManagement/mitkIdentifiable.cpp
DataManagement/mitkImageAccessorBase.cpp
DataManagement/mitkImageCaster.cpp
DataManagement/mitkImageCastPart1.cpp
DataManagement/mitkImageCastPart2.cpp
DataManagement/mitkImageCastPart3.cpp
DataManagement/mitkImageCastPart4.cpp
DataManagement/mitkImage.cpp
DataManagement/mitkImageDataItem.cpp
DataManagement/mitkImageDescriptor.cpp
DataManagement/mitkImageReadAccessor.cpp
DataManagement/mitkImageStatisticsHolder.cpp
DataManagement/mitkImageVtkAccessor.cpp
DataManagement/mitkImageVtkReadAccessor.cpp
DataManagement/mitkImageVtkWriteAccessor.cpp
DataManagement/mitkImageWriteAccessor.cpp
DataManagement/mitkIntPropertyExtension.cpp
DataManagement/mitkIPersistenceService.cpp
DataManagement/mitkIPropertyAliases.cpp
DataManagement/mitkIPropertyDescriptions.cpp
DataManagement/mitkIPropertyExtensions.cpp
DataManagement/mitkIPropertyFilters.cpp
DataManagement/mitkIPropertyOwner.cpp
DataManagement/mitkIPropertyPersistence.cpp
DataManagement/mitkIPropertyProvider.cpp
DataManagement/mitkLandmarkProjectorBasedCurvedGeometry.cpp
DataManagement/mitkLandmarkProjector.cpp
DataManagement/mitkLevelWindow.cpp
DataManagement/mitkLevelWindowManager.cpp
DataManagement/mitkLevelWindowPreset.cpp
DataManagement/mitkLevelWindowProperty.cpp
DataManagement/mitkLine.cpp
DataManagement/mitkLookupTable.cpp
DataManagement/mitkLookupTableProperty.cpp
DataManagement/mitkLookupTables.cpp # specializations of GenericLookupTable
DataManagement/mitkMaterial.cpp
DataManagement/mitkMemoryUtilities.cpp
DataManagement/mitkModalityProperty.cpp
DataManagement/mitkModifiedLock.cpp
DataManagement/mitkNodePredicateAnd.cpp
DataManagement/mitkNodePredicateBase.cpp
DataManagement/mitkNodePredicateCompositeBase.cpp
DataManagement/mitkNodePredicateData.cpp
DataManagement/mitkNodePredicateDataType.cpp
DataManagement/mitkNodePredicateDataUID.cpp
DataManagement/mitkNodePredicateDimension.cpp
DataManagement/mitkNodePredicateFirstLevel.cpp
DataManagement/mitkNodePredicateFunction.cpp
DataManagement/mitkNodePredicateGeometry.cpp
DataManagement/mitkNodePredicateNot.cpp
DataManagement/mitkNodePredicateOr.cpp
DataManagement/mitkNodePredicateProperty.cpp
DataManagement/mitkNodePredicateDataProperty.cpp
DataManagement/mitkNodePredicateSource.cpp
DataManagement/mitkNumericConstants.cpp
DataManagement/mitkPlaneGeometry.cpp
DataManagement/mitkPlaneGeometryData.cpp
DataManagement/mitkPlaneOperation.cpp
DataManagement/mitkPlaneOrientationProperty.cpp
DataManagement/mitkPointOperation.cpp
DataManagement/mitkPointSet.cpp
DataManagement/mitkPointSetShapeProperty.cpp
DataManagement/mitkProperties.cpp
DataManagement/mitkPropertyAliases.cpp
DataManagement/mitkPropertyDescriptions.cpp
DataManagement/mitkPropertyExtension.cpp
DataManagement/mitkPropertyExtensions.cpp
DataManagement/mitkPropertyFilter.cpp
DataManagement/mitkPropertyFilters.cpp
DataManagement/mitkPropertyKeyPath.cpp
DataManagement/mitkPropertyList.cpp
DataManagement/mitkPropertyListReplacedObserver.cpp
DataManagement/mitkPropertyNameHelper.cpp
DataManagement/mitkPropertyObserver.cpp
DataManagement/mitkPropertyPersistence.cpp
DataManagement/mitkPropertyPersistenceInfo.cpp
DataManagement/mitkPropertyRelationRuleBase.cpp
DataManagement/mitkProportionalTimeGeometry.cpp
DataManagement/mitkRenderingModeProperty.cpp
DataManagement/mitkResliceMethodProperty.cpp
DataManagement/mitkRestorePlanePositionOperation.cpp
DataManagement/mitkRotationOperation.cpp
DataManagement/mitkScaleOperation.cpp
DataManagement/mitkSlicedData.cpp
DataManagement/mitkSlicedGeometry3D.cpp
DataManagement/mitkSmartPointerProperty.cpp
DataManagement/mitkStandaloneDataStorage.cpp
DataManagement/mitkStringProperty.cpp
DataManagement/mitkSurface.cpp
DataManagement/mitkSurfaceOperation.cpp
DataManagement/mitkSourceImageRelationRule.cpp
DataManagement/mitkThinPlateSplineCurvedGeometry.cpp
DataManagement/mitkTimeGeometry.cpp
DataManagement/mitkTransferFunction.cpp
DataManagement/mitkTransferFunctionInitializer.cpp
DataManagement/mitkTransferFunctionProperty.cpp
DataManagement/mitkTemporoSpatialStringProperty.cpp
DataManagement/mitkUIDManipulator.cpp
DataManagement/mitkVector.cpp
DataManagement/mitkVectorProperty.cpp
DataManagement/mitkVtkInterpolationProperty.cpp
DataManagement/mitkVtkRepresentationProperty.cpp
DataManagement/mitkVtkResliceInterpolationProperty.cpp
DataManagement/mitkVtkScalarModeProperty.cpp
DataManagement/mitkVtkVolumeRenderingProperty.cpp
DataManagement/mitkWeakPointerProperty.cpp
DataManagement/mitkIPropertyRelations.cpp
DataManagement/mitkPropertyRelations.cpp
Interactions/mitkAction.cpp
Interactions/mitkBindDispatcherInteractor.cpp
Interactions/mitkCrosshairPositionEvent.cpp
Interactions/mitkDataInteractor.cpp
Interactions/mitkDispatcher.cpp
Interactions/mitkDisplayActionEventBroadcast.cpp
Interactions/mitkDisplayActionEventFunctions.cpp
Interactions/mitkDisplayActionEventHandler.cpp
Interactions/mitkDisplayActionEventHandlerDesynchronized.cpp
Interactions/mitkDisplayActionEventHandlerStd.cpp
Interactions/mitkDisplayActionEventHandlerSynchronized.cpp
Interactions/mitkDisplayCoordinateOperation.cpp
Interactions/mitkDisplayInteractor.cpp
Interactions/mitkEventConfig.cpp
Interactions/mitkEventFactory.cpp
Interactions/mitkEventRecorder.cpp
Interactions/mitkEventStateMachine.cpp
Interactions/mitkInteractionEventConst.cpp
Interactions/mitkInteractionEvent.cpp
Interactions/mitkInteractionEventHandler.cpp
Interactions/mitkInteractionEventObserver.cpp
Interactions/mitkInteractionKeyEvent.cpp
Interactions/mitkInteractionPositionEvent.cpp
Interactions/mitkInteractionSchemeSwitcher.cpp
Interactions/mitkInternalEvent.cpp
Interactions/mitkMouseDoubleClickEvent.cpp
Interactions/mitkMouseModeSwitcher.cpp
Interactions/mitkMouseMoveEvent.cpp
Interactions/mitkMousePressEvent.cpp
Interactions/mitkMouseReleaseEvent.cpp
Interactions/mitkMouseWheelEvent.cpp
Interactions/mitkPointSetDataInteractor.cpp
Interactions/mitkSinglePointDataInteractor.cpp
Interactions/mitkStateMachineAction.cpp
Interactions/mitkStateMachineCondition.cpp
Interactions/mitkStateMachineContainer.cpp
Interactions/mitkStateMachineState.cpp
Interactions/mitkStateMachineTransition.cpp
Interactions/mitkVtkEventAdapter.cpp
Interactions/mitkVtkInteractorStyle.cxx
Interactions/mitkXML2EventParser.cpp
IO/mitkAbstractFileIO.cpp
IO/mitkAbstractFileReader.cpp
IO/mitkAbstractFileWriter.cpp
IO/mitkCustomMimeType.cpp
IO/mitkFileReader.cpp
IO/mitkFileReaderRegistry.cpp
IO/mitkFileReaderSelector.cpp
IO/mitkFileReaderWriterBase.cpp
IO/mitkFileWriter.cpp
IO/mitkFileWriterRegistry.cpp
IO/mitkFileWriterSelector.cpp
IO/mitkGeometry3DToXML.cpp
IO/mitkIFileIO.cpp
IO/mitkIFileReader.cpp
IO/mitkIFileWriter.cpp
IO/mitkGeometryDataReaderService.cpp
IO/mitkGeometryDataWriterService.cpp
IO/mitkImageGenerator.cpp
IO/mitkImageVtkLegacyIO.cpp
IO/mitkImageVtkXmlIO.cpp
IO/mitkIMimeTypeProvider.cpp
IO/mitkIOConstants.cpp
IO/mitkIOMimeTypes.cpp
IO/mitkIOUtil.cpp
IO/mitkItkImageIO.cpp
IO/mitkItkLoggingAdapter.cpp
IO/mitkLegacyFileReaderService.cpp
IO/mitkLegacyFileWriterService.cpp
IO/mitkLocaleSwitch.cpp
IO/mitkLog.cpp
IO/mitkMimeType.cpp
IO/mitkMimeTypeProvider.cpp
IO/mitkOperation.cpp
IO/mitkPixelType.cpp
IO/mitkPointSetReaderService.cpp
IO/mitkPointSetWriterService.cpp
IO/mitkProportionalTimeGeometryToXML.cpp
IO/mitkRawImageFileReader.cpp
IO/mitkStandardFileLocations.cpp
IO/mitkSurfaceStlIO.cpp
IO/mitkSurfaceVtkIO.cpp
IO/mitkSurfaceVtkLegacyIO.cpp
IO/mitkSurfaceVtkXmlIO.cpp
IO/mitkVtkLoggingAdapter.cpp
IO/mitkPreferenceListReaderOptionsFunctor.cpp
Rendering/mitkAbstractAnnotationRenderer.cpp
Rendering/mitkAnnotationUtils.cpp
Rendering/mitkBaseRenderer.cpp
#Rendering/mitkGLMapper.cpp Moved to deprecated LegacyGL Module
Rendering/mitkGradientBackground.cpp
Rendering/mitkImageVtkMapper2D.cpp
Rendering/mitkMapper.cpp
Rendering/mitkAnnotation.cpp
Rendering/mitkPlaneGeometryDataMapper2D.cpp
Rendering/mitkPlaneGeometryDataVtkMapper3D.cpp
Rendering/mitkPointSetVtkMapper2D.cpp
Rendering/mitkPointSetVtkMapper3D.cpp
Rendering/mitkRenderWindowBase.cpp
Rendering/mitkRenderWindow.cpp
Rendering/mitkRenderWindowFrame.cpp
#Rendering/mitkSurfaceGLMapper2D.cpp Moved to deprecated LegacyGL Module
Rendering/mitkSurfaceVtkMapper2D.cpp
Rendering/mitkSurfaceVtkMapper3D.cpp
Rendering/mitkVtkEventProvider.cpp
Rendering/mitkVtkMapper.cpp
Rendering/mitkVtkPropRenderer.cpp
Rendering/mitkVtkWidgetRendering.cpp
Rendering/vtkMitkLevelWindowFilter.cpp
Rendering/vtkMitkRectangleProp.cpp
Rendering/vtkMitkRenderProp.cpp
Rendering/vtkMitkThickSlicesFilter.cpp
Rendering/vtkNeverTranslucentTexture.cpp
)
set(RESOURCE_FILES
Interactions/globalConfig.xml
Interactions/DisplayInteraction.xml
Interactions/DisplayConfig.xml
Interactions/DisplayConfigPACS.xml
Interactions/DisplayConfigPACSPan.xml
Interactions/DisplayConfigPACSScroll.xml
Interactions/DisplayConfigPACSZoom.xml
Interactions/DisplayConfigPACSLevelWindow.xml
Interactions/DisplayConfigMITK.xml
Interactions/DisplayConfigMITKNoCrosshair.xml
Interactions/DisplayConfigMITKRotation.xml
Interactions/DisplayConfigMITKRotationUnCoupled.xml
Interactions/DisplayConfigMITKSwivel.xml
Interactions/DisplayConfigMITKLimited.xml
Interactions/PointSet.xml
Interactions/Legacy/StateMachine.xml
Interactions/Legacy/DisplayConfigMITKTools.xml
Interactions/PointSetConfig.xml
mitkLevelWindowPresets.xml
mitkAnatomicalStructureColorPresets.xml
)
diff --git a/Modules/Core/include/mitkLocaleSwitch.h b/Modules/Core/include/mitkLocaleSwitch.h
index 96af6c09b6..601ac02d63 100644
--- a/Modules/Core/include/mitkLocaleSwitch.h
+++ b/Modules/Core/include/mitkLocaleSwitch.h
@@ -1,61 +1,72 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef __mitkLocaleSwitch_h
#define __mitkLocaleSwitch_h
#include "MitkCoreExports.h"
namespace mitk
{
/**
\brief Convenience class to temporarily change the current locale.
This helper class can be used to switch to a specific locale
for a couple of operations. Once the class is destroyed, the previous
locale will be restored. This avoids calling or forgetting to call
setlocale() in multiple return locations.
Typically this is used to switch to a "C" locale when parsing or
printing numbers, in order to consistently get "." and not "," as
a decimal separator.
+ WARNING: Please be aware that using setlocale and there for is not thread
+ safe. So use this class with care (see tast T24295 for more information.
+ This switch is especially use full if you have to deal with third party code
+ where you have to controll the locale via set locale
\code
-
- std::string toString(int number)
{
mitk::LocaleSwitch localeSwitch("C");// installs C locale until the end of the function
- std::stringstream parser;
- parser << number;
+ ExternalLibraryCall(); //that might throw or what ever.
+ }
+ \endcode
+ If you just want to control you own stringstream operations use imbue instead, as it is
+ threadsafe. E.G.:
+ \code
+ std::string toString(int number)
+ {
+ std::ostringstream parser;
+ parser.imbue(std::locale("C"));
+ parser << number;
return parser.str();
}
\endcode
*/
struct MITKCORE_EXPORT LocaleSwitch
{
explicit LocaleSwitch(const char *newLocale);
~LocaleSwitch();
LocaleSwitch(LocaleSwitch &) = delete;
LocaleSwitch operator=(LocaleSwitch &) = delete;
private:
struct Impl;
Impl *m_LocaleSwitchImpl;
};
}
#endif // __mitkLocaleSwitch_h
diff --git a/Modules/Core/include/mitkTemporalJoinImagesFilter.h b/Modules/Core/include/mitkTemporalJoinImagesFilter.h
new file mode 100644
index 0000000000..b03f905221
--- /dev/null
+++ b/Modules/Core/include/mitkTemporalJoinImagesFilter.h
@@ -0,0 +1,62 @@
+/*============================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center (DKFZ)
+All rights reserved.
+
+Use of this source code is governed by a 3-clause BSD license that can be
+found in the LICENSE file.
+
+============================================================================*/
+
+#ifndef TEMPORALJOINIMAGESFILTER_H
+#define TEMPORALJOINIMAGESFILTER_H
+
+
+#include "mitkImageToImageFilter.h"
+#include "mitkCommon.h"
+
+#include "MitkCoreExports.h"
+
+namespace mitk
+{
+ /** Filter that takes n mitk images as inputs and fuse them to a new image (with n time points).
+ Preconditions of this filter are, that all input images have the same pixel type and geometry.
+ The sequence of frames in the output image is the same then the sequence of inputs.
+ It no time bounds are defined the dynamic image will start at 0 ms and each time step has a duration
+ of 1 ms.*/
+ class MITKCORE_EXPORT TemporalJoinImagesFilter : public ImageToImageFilter
+ {
+ public:
+ mitkClassMacro(TemporalJoinImagesFilter, ImageToImageFilter);
+ itkFactorylessNewMacro(TemporalJoinImagesFilter);
+
+ typedef std::vector<mitk::TimePointType> TimeBoundsVectorType;
+
+ itkGetConstMacro(FirstMinTimeBound, mitk::TimePointType);
+ /**Set custom min time bound for the first time step.*/
+ itkSetMacro(FirstMinTimeBound, mitk::TimePointType);
+
+ itkGetConstMacro(MaxTimeBounds, TimeBoundsVectorType);
+ /**Set custom max time bounds for all time steps.*/
+ void SetMaxTimeBounds(const TimeBoundsVectorType &bounds);
+
+ protected:
+ TemporalJoinImagesFilter(){};
+ ~TemporalJoinImagesFilter() override{};
+
+ void GenerateInputRequestedRegion() override;
+
+ void GenerateOutputInformation() override;
+
+ void GenerateData() override;
+
+ private:
+ TimeBoundsVectorType m_MaxTimeBounds;
+ mitk::TimePointType m_FirstMinTimeBound = 0.0;
+ };
+}
+
+
+#endif // MODELSIGNALIMAGEGENERATOR_H
diff --git a/Modules/Core/src/Algorithms/mitkTemporalJoinImagesFilter.cpp b/Modules/Core/src/Algorithms/mitkTemporalJoinImagesFilter.cpp
new file mode 100644
index 0000000000..7b22a3760f
--- /dev/null
+++ b/Modules/Core/src/Algorithms/mitkTemporalJoinImagesFilter.cpp
@@ -0,0 +1,122 @@
+/*============================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center (DKFZ)
+All rights reserved.
+
+Use of this source code is governed by a 3-clause BSD license that can be
+found in the LICENSE file.
+
+============================================================================*/
+
+#include "mitkTemporalJoinImagesFilter.h"
+
+#include <numeric>
+
+#include "mitkArbitraryTimeGeometry.h"
+#include "mitkImageReadAccessor.h"
+#include "mitkTemporoSpatialStringProperty.h"
+
+void mitk::TemporalJoinImagesFilter::SetMaxTimeBounds(const TimeBoundsVectorType& timeBounds)
+{
+ m_MaxTimeBounds = timeBounds;
+ this->Modified();
+}
+
+void mitk::TemporalJoinImagesFilter::GenerateInputRequestedRegion()
+{
+ Superclass::GenerateInputRequestedRegion();
+ const auto nrOfInputs = this->GetNumberOfInputs();
+ for (DataObjectPointerArraySizeType pos = 0; pos < nrOfInputs; ++pos)
+ {
+ this->GetInput(pos)->SetRequestedRegionToLargestPossibleRegion();
+ }
+}
+
+void mitk::TemporalJoinImagesFilter::GenerateOutputInformation()
+{
+ mitk::Image::ConstPointer input = this->GetInput();
+ mitk::Image::Pointer output = this->GetOutput();
+
+ const auto nrOfInputs = this->GetNumberOfInputs();
+ auto timeBounds = m_MaxTimeBounds;
+
+ if (timeBounds.empty())
+ {
+ timeBounds.resize(nrOfInputs);
+ std::iota(timeBounds.begin(), timeBounds.end(), 1.0);
+ }
+ else if(timeBounds.size() != nrOfInputs)
+ {
+ mitkThrow() << "User defined max time bounds do not match the number if inputs (" << nrOfInputs << "). Size of max timebounds is " << timeBounds.size() << ", but it should be " << nrOfInputs << ".";
+ }
+
+ timeBounds.insert(timeBounds.begin(), m_FirstMinTimeBound);
+
+ auto timeGeo = mitk::ArbitraryTimeGeometry::New();
+ timeGeo->ReserveSpaceForGeometries(nrOfInputs);
+
+ for (DataObjectPointerArraySizeType pos = 0; pos < nrOfInputs; ++pos)
+ {
+ timeGeo->AppendNewTimeStepClone(this->GetInput(pos)->GetGeometry(), timeBounds[pos], timeBounds[pos + 1]);
+ }
+ output->Initialize(input->GetPixelType(), *timeGeo);
+
+ auto newPropList = input->GetPropertyList()->Clone();
+ for (DataObjectPointerArraySizeType pos = 1; pos < nrOfInputs; ++pos)
+ {
+ const auto otherList = this->GetInput(pos)->GetPropertyList();
+ for (const auto& key : otherList->GetPropertyKeys())
+ {
+ auto prop = newPropList->GetProperty(key);
+ if (prop == nullptr)
+ {
+ newPropList->SetProperty(key, otherList->GetProperty(key)->Clone());
+ }
+ else
+ {
+ auto tempoSpatialProp = dynamic_cast<mitk::TemporoSpatialStringProperty*>(prop);
+ auto oTempoSpatialProp = dynamic_cast<mitk::TemporoSpatialStringProperty*>(otherList->GetProperty(key));
+ if (prop != nullptr && oTempoSpatialProp != nullptr)
+ {
+ auto availabelSlices = oTempoSpatialProp->GetAvailableSlices(0);
+
+ for (const auto& sliceID : availabelSlices)
+ {
+ tempoSpatialProp->SetValue(pos, sliceID, oTempoSpatialProp->GetValueBySlice(sliceID));
+ }
+ }
+ //other prop types can be ignored, we only use the values of the first frame.
+ }
+ }
+ }
+
+ output->SetPropertyList(newPropList);
+}
+
+
+void mitk::TemporalJoinImagesFilter::GenerateData()
+{
+ mitk::Image::Pointer output = this->GetOutput();
+ mitk::Image::ConstPointer refInput = this->GetInput();
+ const auto nrOfInputs = this->GetNumberOfInputs();
+
+ for (DataObjectPointerArraySizeType pos = 0; pos < nrOfInputs; ++pos)
+ {
+ if (!Equal(*(refInput->GetGeometry()), *(this->GetInput(pos)->GetGeometry()), mitk::eps, false))
+ {
+ mitkThrow() << "Cannot fuse images. At least image #" << pos << " has another geometry than the first image.";
+ }
+ if (refInput->GetPixelType() != this->GetInput(pos)->GetPixelType())
+ {
+ mitkThrow() << "Cannot fuse images. At least image #" << pos << " has another pixeltype than the first image.";
+ }
+ }
+
+ for (DataObjectPointerArraySizeType pos = 0; pos < nrOfInputs; ++pos)
+ {
+ mitk::ImageReadAccessor accessor(this->GetInput(pos));
+ output->SetVolume(accessor.GetData(), pos);
+ }
+}
diff --git a/Modules/Core/test/files.cmake b/Modules/Core/test/files.cmake
index f98fb8a5df..5efc282bfa 100644
--- a/Modules/Core/test/files.cmake
+++ b/Modules/Core/test/files.cmake
@@ -1,193 +1,194 @@
# tests with no extra command line parameter
set(MODULE_TESTS
# IMPORTANT: If you plan to deactivate / comment out a test please write a bug number to the commented out line of code.
#
# Example: #mitkMyTest #this test is commented out because of bug 12345
#
# It is important that the bug is open and that the test will be activated again before the bug is closed. This assures that
# no test is forgotten after it was commented out. If there is no bug for your current problem, please add a new one and
# mark it as critical.
################## DISABLED TESTS #################################################
#mitkAbstractTransformGeometryTest.cpp #seems as tested class mitkExternAbstractTransformGeometry doesnt exist any more
#mitkStateMachineContainerTest.cpp #rewrite test, indirect since no longer exported Bug 14529
#mitkRegistrationBaseTest.cpp #tested class mitkRegistrationBase doesn't exist any more
#mitkSegmentationInterpolationTest.cpp #file doesn't exist!
#mitkPipelineSmartPointerCorrectnessTest.cpp #file doesn't exist!
#mitkITKThreadingTest.cpp #test outdated because itk::Semaphore was removed from ITK
#mitkAbstractTransformPlaneGeometryTest.cpp #mitkVtkAbstractTransformPlaneGeometry doesn't exist any more
#mitkTestUtilSharedLibrary.cpp #Linker problem with this test...
#mitkTextOverlay2DSymbolsRenderingTest.cpp #Implementation of the tested feature is not finished yet. Ask Christoph or see bug 15104 for details.
################# RUNNING TESTS ###################################################
mitkAccessByItkTest.cpp
mitkCoreObjectFactoryTest.cpp
mitkDataNodeTest.cpp
mitkMaterialTest.cpp
mitkActionTest.cpp
mitkDispatcherTest.cpp
mitkEnumerationPropertyTest.cpp
mitkFileReaderRegistryTest.cpp
#mitkFileWriterRegistryTest.cpp
mitkFloatToStringTest.cpp
mitkGenericPropertyTest.cpp
mitkGeometry3DTest.cpp
mitkGeometry3DEqualTest.cpp
mitkGeometryDataIOTest.cpp
mitkGeometryDataToSurfaceFilterTest.cpp
mitkImageCastTest.cpp
mitkImageDataItemTest.cpp
mitkImageGeneratorTest.cpp
mitkIOUtilTest.cpp
mitkBaseDataTest.cpp
mitkImportItkImageTest.cpp
mitkGrabItkImageMemoryTest.cpp
mitkInstantiateAccessFunctionTest.cpp
mitkLevelWindowTest.cpp
mitkMessageTest.cpp
mitkPixelTypeTest.cpp
mitkPlaneGeometryTest.cpp
mitkPointSetTest.cpp
mitkPointSetEqualTest.cpp
mitkPointSetFileIOTest.cpp
mitkPointSetOnEmptyTest.cpp
mitkPointSetLocaleTest.cpp
mitkPointSetWriterTest.cpp
mitkPointSetPointOperationsTest.cpp
mitkProgressBarTest.cpp
mitkPropertyTest.cpp
mitkPropertyListTest.cpp
mitkPropertyPersistenceTest.cpp
mitkPropertyPersistenceInfoTest.cpp
mitkPropertyRelationRuleBaseTest.cpp
mitkPropertyRelationsTest.cpp
mitkSlicedGeometry3DTest.cpp
mitkSliceNavigationControllerTest.cpp
mitkSurfaceTest.cpp
mitkSurfaceEqualTest.cpp
mitkSurfaceToSurfaceFilterTest.cpp
mitkTimeGeometryTest.cpp
mitkProportionalTimeGeometryTest.cpp
mitkUndoControllerTest.cpp
mitkVtkWidgetRenderingTest.cpp
mitkVerboseLimitedLinearUndoTest.cpp
mitkWeakPointerTest.cpp
mitkTransferFunctionTest.cpp
mitkStepperTest.cpp
mitkRenderingManagerTest.cpp
mitkCompositePixelValueToStringTest.cpp
vtkMitkThickSlicesFilterTest.cpp
mitkNodePredicateSourceTest.cpp
mitkNodePredicateDataPropertyTest.cpp
mitkNodePredicateFunctionTest.cpp
mitkVectorTest.cpp
mitkClippedSurfaceBoundsCalculatorTest.cpp
mitkExceptionTest.cpp
mitkExtractSliceFilterTest.cpp
mitkLogTest.cpp
mitkImageDimensionConverterTest.cpp
mitkLoggingAdapterTest.cpp
mitkUIDGeneratorTest.cpp
mitkPlanePositionManagerTest.cpp
mitkAffineTransformBaseTest.cpp
mitkPropertyAliasesTest.cpp
mitkPropertyDescriptionsTest.cpp
mitkPropertyExtensionsTest.cpp
mitkPropertyFiltersTest.cpp
mitkPropertyKeyPathTest.cpp
mitkTinyXMLTest.cpp
mitkRawImageFileReaderTest.cpp
mitkInteractionEventTest.cpp
mitkLookupTableTest.cpp
mitkSTLFileReaderTest.cpp
mitkPointTypeConversionTest.cpp
mitkVectorTypeConversionTest.cpp
mitkMatrixTypeConversionTest.cpp
mitkArrayTypeConversionTest.cpp
mitkSurfaceToImageFilterTest.cpp
mitkBaseGeometryTest.cpp
mitkImageToSurfaceFilterTest.cpp
mitkEqualTest.cpp
mitkLineTest.cpp
mitkArbitraryTimeGeometryTest.cpp
mitkItkImageIOTest.cpp
mitkLevelWindowManagerCppUnitTest.cpp
mitkVectorPropertyTest.cpp
mitkTemporoSpatialStringPropertyTest.cpp
mitkPropertyNameHelperTest.cpp
mitkNodePredicateGeometryTest.cpp
mitkPreferenceListReaderOptionsFunctorTest.cpp
mitkGenericIDRelationRuleTest.cpp
mitkSourceImageRelationRuleTest.cpp
mitkPointSetDataInteractorTest.cpp #since mitkInteractionTestHelper is currently creating a vtkRenderWindow
mitkSurfaceVtkMapper2DTest.cpp #new rendering test in CppUnit style
mitkSurfaceVtkMapper2D3DTest.cpp # comparisons/consistency 2D/3D
+ mitkTemporalJoinImagesFilterTest.cpp
)
# test with image filename as an extra command line parameter
set(MODULE_IMAGE_TESTS
mitkImageTimeSelectorTest.cpp #only runs on images
mitkImageAccessorTest.cpp #only runs on images
)
set(MODULE_SURFACE_TESTS
mitkSurfaceVtkWriterTest.cpp #only runs on surfaces
)
# list of images for which the tests are run
set(MODULE_TESTIMAGE
US4DCyl.nrrd
Pic3D.nrrd
Pic2DplusT.nrrd
BallBinary30x30x30.nrrd
Png2D-bw.png
)
set(MODULE_TESTSURFACE
binary.stl
ball.stl
)
set(MODULE_CUSTOM_TESTS
mitkDataStorageTest.cpp
mitkDataNodeTest.cpp
mitkEventConfigTest.cpp
mitkPointSetLocaleTest.cpp
mitkImageTest.cpp
mitkImageVtkMapper2DTest.cpp
mitkImageVtkMapper2DLevelWindowTest.cpp
mitkImageVtkMapper2DOpacityTest.cpp
mitkImageVtkMapper2DResliceInterpolationPropertyTest.cpp
mitkImageVtkMapper2DColorTest.cpp
mitkImageVtkMapper2DSwivelTest.cpp
mitkImageVtkMapper2DTransferFunctionTest.cpp
mitkImageVtkMapper2DOpacityTransferFunctionTest.cpp
mitkImageVtkMapper2DLookupTableTest.cpp
mitkSurfaceVtkMapper3DTest.cpp
mitkVolumeCalculatorTest.cpp
mitkLevelWindowManagerTest.cpp
mitkPointSetVtkMapper2DTest.cpp
mitkPointSetVtkMapper2DImageTest.cpp
mitkPointSetVtkMapper2DGlyphTypeTest.cpp
mitkPointSetVtkMapper2DTransformedPointsTest.cpp
mitkVTKRenderWindowSizeTest.cpp
mitkMultiComponentImageDataComparisonFilterTest.cpp
mitkImageToItkTest.cpp
mitkImageSliceSelectorTest.cpp
mitkPointSetReaderTest.cpp
mitkImageEqualTest.cpp
mitkRotatedSlice4DTest.cpp
mitkPlaneGeometryDataMapper2DTest.cpp
)
# Currently not working on windows because of a rendering timing issue
# see bug 18083 for details
if(NOT WIN32)
set(MODULE_CUSTOM_TESTS ${MODULE_CUSTOM_TESTS} mitkSurfaceDepthSortingTest.cpp)
endif()
set(RESOURCE_FILES
Interactions/AddAndRemovePoints.xml
Interactions/globalConfig.xml
Interactions/StatemachineTest.xml
Interactions/StatemachineConfigTest.xml
)
diff --git a/Modules/Core/test/mitkTemporalJoinImagesFilterTest.cpp b/Modules/Core/test/mitkTemporalJoinImagesFilterTest.cpp
new file mode 100644
index 0000000000..4f2035ef7e
--- /dev/null
+++ b/Modules/Core/test/mitkTemporalJoinImagesFilterTest.cpp
@@ -0,0 +1,188 @@
+/*============================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center (DKFZ)
+All rights reserved.
+
+Use of this source code is governed by a 3-clause BSD license that can be
+found in the LICENSE file.
+
+============================================================================*/
+
+#include "mitkImagePixelReadAccessor.h"
+
+#include "mitkTemporalJoinImagesFilter.h"
+#include "mitkTestFixture.h"
+#include "mitkTestingMacros.h"
+
+#include <limits>
+#include "mitkTestDynamicImageGenerator.h"
+#include "mitkStringProperty.h"
+#include "mitkTemporoSpatialStringProperty.h"
+
+class mitkTemporalJoinImagesFilterTestSuite : public mitk::TestFixture
+{
+ CPPUNIT_TEST_SUITE(mitkTemporalJoinImagesFilterTestSuite);
+
+ MITK_TEST(InvalidUsage);
+ MITK_TEST(FuseDefault);
+ MITK_TEST(FuseUseDefinedTimeBounds);
+
+ CPPUNIT_TEST_SUITE_END();
+
+private:
+ mitk::Image::Pointer t0;
+ mitk::Image::Pointer t1;
+ mitk::Image::Pointer t2;
+
+ mitk::Image::Pointer invalidPixel;
+ mitk::Image::Pointer invalidGeometry;
+
+public:
+ void setUp() override
+ {
+ t0 = mitk::GenerateTestFrame(1);
+ t0->SetProperty("all", mitk::StringProperty::New("all_0"));
+ t0->SetProperty("ts", mitk::TemporoSpatialStringProperty::New("ts_0"));
+
+ t1 = mitk::GenerateTestFrame(20);
+ t1->SetProperty("all", mitk::StringProperty::New("all_1"));
+ t1->SetProperty("ts", mitk::TemporoSpatialStringProperty::New("ts_1"));
+ t1->SetProperty("special", mitk::StringProperty::New("special_1"));
+
+ t2 = mitk::GenerateTestFrame(300);
+ t2->SetProperty("all", mitk::StringProperty::New("all_2"));
+ t2->SetProperty("ts", mitk::TemporoSpatialStringProperty::New("ts_2"));
+
+ invalidPixel = mitk::Image::New();
+ invalidPixel->Initialize(mitk::MakePixelType<int, int, 1>(), *(t0->GetTimeGeometry()));
+
+ invalidGeometry = mitk::Image::New();
+ invalidGeometry->Initialize(t0);
+ invalidGeometry->SetGeometry(mitk::Geometry3D::New());
+ }
+
+ void tearDown() override {}
+
+ void InvalidUsage()
+ {
+ auto filter = mitk::TemporalJoinImagesFilter::New();
+
+ filter->SetInput(0, t0);
+ filter->SetInput(1, invalidPixel);
+
+ CPPUNIT_ASSERT_THROW(filter->Update(), mitk::Exception);
+
+ filter = mitk::TemporalJoinImagesFilter::New();
+
+ filter->SetInput(0, t0);
+ filter->SetInput(1, invalidGeometry);
+
+ CPPUNIT_ASSERT_THROW(filter->Update(), mitk::Exception);
+
+ filter = mitk::TemporalJoinImagesFilter::New();
+
+ filter->SetInput(0, t0);
+ filter->SetInput(1, t1);
+ filter->SetMaxTimeBounds({ 3 });
+
+ CPPUNIT_ASSERT_THROW(filter->Update(), mitk::Exception);
+ }
+
+ void FuseDefault()
+ {
+ auto filter = mitk::TemporalJoinImagesFilter::New();
+
+ filter->SetInput(0, t0);
+ filter->SetInput(1, t1);
+ filter->SetInput(2, t2);
+
+ filter->Update();
+ auto output = filter->GetOutput();
+
+ CPPUNIT_ASSERT(output->GetTimeSteps() == 3);
+ auto allProp = output->GetProperty("all");
+ CPPUNIT_ASSERT(allProp->GetValueAsString() == "all_0");
+ auto specialProp = output->GetProperty("special");
+ CPPUNIT_ASSERT(specialProp->GetValueAsString() == "special_1");
+ auto tsProp = dynamic_cast<const mitk::TemporoSpatialStringProperty*>(output->GetProperty("ts").GetPointer());
+ CPPUNIT_ASSERT(tsProp->GetValueByTimeStep(0) == "ts_0");
+ CPPUNIT_ASSERT(tsProp->GetValueByTimeStep(1) == "ts_1");
+ CPPUNIT_ASSERT(tsProp->GetValueByTimeStep(2) == "ts_2");
+
+ CPPUNIT_ASSERT(mitk::Equal(*(t0->GetGeometry()), *(output->GetGeometry()), mitk::eps, true));
+ CPPUNIT_ASSERT(output->GetTimeGeometry()->GetMinimumTimePoint(0) == 0.);
+ CPPUNIT_ASSERT(output->GetTimeGeometry()->GetMaximumTimePoint(0) == 1.);
+ CPPUNIT_ASSERT(output->GetTimeGeometry()->GetMinimumTimePoint(1) == 1.);
+ CPPUNIT_ASSERT(output->GetTimeGeometry()->GetMaximumTimePoint(1) == 2.);
+ CPPUNIT_ASSERT(output->GetTimeGeometry()->GetMinimumTimePoint(2) == 2.);
+ CPPUNIT_ASSERT(output->GetTimeGeometry()->GetMaximumTimePoint(2) == 3.);
+
+ mitk::ImagePixelReadAccessor<mitk::ScalarType, 4> accessor(output);
+ itk::Index<4> testIndex0;
+ testIndex0.Fill(2);
+ testIndex0[3] = 0;
+ itk::Index<4> testIndex1;
+ testIndex1.Fill(2);
+ testIndex1[3] = 1;
+ itk::Index<4> testIndex2;
+ testIndex2.Fill(2);
+ testIndex2[3] = 2;
+
+ CPPUNIT_ASSERT_EQUAL(28., accessor.GetPixelByIndex(testIndex0));
+ CPPUNIT_ASSERT_EQUAL(180., accessor.GetPixelByIndex(testIndex1));
+ CPPUNIT_ASSERT_EQUAL(2420., accessor.GetPixelByIndex(testIndex2));
+ }
+
+ void FuseUseDefinedTimeBounds()
+ {
+ auto filter = mitk::TemporalJoinImagesFilter::New();
+
+ filter->SetInput(0, t0);
+ filter->SetInput(1, t1);
+ filter->SetInput(2, t2);
+
+ filter->SetFirstMinTimeBound(10);
+ filter->SetMaxTimeBounds({ 20,30,40 });
+
+ filter->Update();
+ auto output = filter->GetOutput();
+
+ CPPUNIT_ASSERT(output->GetTimeSteps() == 3);
+ auto allProp = output->GetProperty("all");
+ CPPUNIT_ASSERT(allProp->GetValueAsString() == "all_0");
+ auto specialProp = output->GetProperty("special");
+ CPPUNIT_ASSERT(specialProp->GetValueAsString() == "special_1");
+ auto tsProp = dynamic_cast<const mitk::TemporoSpatialStringProperty*>(output->GetProperty("ts").GetPointer());
+ CPPUNIT_ASSERT(tsProp->GetValueByTimeStep(0) == "ts_0");
+ CPPUNIT_ASSERT(tsProp->GetValueByTimeStep(1) == "ts_1");
+ CPPUNIT_ASSERT(tsProp->GetValueByTimeStep(2) == "ts_2");
+
+ CPPUNIT_ASSERT(mitk::Equal(*(t0->GetGeometry()), *(output->GetGeometry()), mitk::eps, true));
+ CPPUNIT_ASSERT(output->GetTimeGeometry()->GetMinimumTimePoint(0) == 10.);
+ CPPUNIT_ASSERT(output->GetTimeGeometry()->GetMaximumTimePoint(0) == 20.);
+ CPPUNIT_ASSERT(output->GetTimeGeometry()->GetMinimumTimePoint(1) == 20.);
+ CPPUNIT_ASSERT(output->GetTimeGeometry()->GetMaximumTimePoint(1) == 30.);
+ CPPUNIT_ASSERT(output->GetTimeGeometry()->GetMinimumTimePoint(2) == 30.);
+ CPPUNIT_ASSERT(output->GetTimeGeometry()->GetMaximumTimePoint(2) == 40.);
+
+ mitk::ImagePixelReadAccessor<mitk::ScalarType, 4> accessor(output);
+ itk::Index<4> testIndex0;
+ testIndex0.Fill(2);
+ testIndex0[3] = 0;
+ itk::Index<4> testIndex1;
+ testIndex1.Fill(2);
+ testIndex1[3] = 1;
+ itk::Index<4> testIndex2;
+ testIndex2.Fill(2);
+ testIndex2[3] = 2;
+
+ CPPUNIT_ASSERT_EQUAL(28., accessor.GetPixelByIndex(testIndex0));
+ CPPUNIT_ASSERT_EQUAL(180., accessor.GetPixelByIndex(testIndex1));
+ CPPUNIT_ASSERT_EQUAL(2420., accessor.GetPixelByIndex(testIndex2));
+ }
+
+};
+
+MITK_TEST_SUITE_REGISTRATION(mitkTemporalJoinImagesFilter)
diff --git a/Modules/ModelFit/cmdapps/CMakeLists.txt b/Modules/ModelFit/cmdapps/CMakeLists.txt
index f78ad56dda..cda6e31973 100644
--- a/Modules/ModelFit/cmdapps/CMakeLists.txt
+++ b/Modules/ModelFit/cmdapps/CMakeLists.txt
@@ -1,34 +1,35 @@
option(BUILD_ModelFitMiniApps "Build commandline tools for the ModelFit module" OFF)
if(BUILD_ModelFitMiniApps OR MITK_BUILD_ALL_APPS)
# needed include directories
include_directories(
${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_BINARY_DIR}
)
# list of miniapps
# if an app requires additional dependencies
# they are added after a "^^" and separated by "_"
set( miniapps
GenericFittingMiniApp^^
PixelDumpMiniApp^^
+ Fuse3Dto4DImageMiniApp^^
)
foreach(miniapp ${miniapps})
# extract mini app name and dependencies
string(REPLACE "^^" "\\;" miniapp_info ${miniapp})
set(miniapp_info_list ${miniapp_info})
list(GET miniapp_info_list 0 appname)
list(GET miniapp_info_list 1 raw_dependencies)
string(REPLACE "_" "\\;" dependencies "${raw_dependencies}")
set(dependencies_list ${dependencies})
mitkFunctionCreateCommandLineApp(
NAME ${appname}
DEPENDS MitkCore MitkModelFit ${dependencies_list}
PACKAGE_DEPENDS ITK
)
endforeach()
endif(BUILD_ModelFitMiniApps OR MITK_BUILD_ALL_APPS)
diff --git a/Modules/ModelFit/cmdapps/Fuse3Dto4DImageMiniApp.cpp b/Modules/ModelFit/cmdapps/Fuse3Dto4DImageMiniApp.cpp
new file mode 100644
index 0000000000..a2cd40129f
--- /dev/null
+++ b/Modules/ModelFit/cmdapps/Fuse3Dto4DImageMiniApp.cpp
@@ -0,0 +1,167 @@
+/*============================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center (DKFZ)
+All rights reserved.
+
+Use of this source code is governed by a 3-clause BSD license that can be
+found in the LICENSE file.
+
+============================================================================*/
+
+// std includes
+#include <string>
+#include <numeric>
+
+// itk includes
+#include "itksys/SystemTools.hxx"
+
+// CTK includes
+#include "mitkCommandLineParser.h"
+
+// MITK includes
+#include <mitkIOUtil.h>
+#include <mitkPreferenceListReaderOptionsFunctor.h>
+#include <mitkTemporalJoinImagesFilter.h>
+
+mitkCommandLineParser::StringContainerType inFilenames;
+std::string outFileName;
+
+std::vector<mitk::Image::Pointer> images;
+std::vector<mitk::TimePointType> timebounds;
+
+void setupParser(mitkCommandLineParser& parser)
+{
+ // set general information about your MiniApp
+ parser.setCategory("Dynamic Data Analysis Tools");
+ parser.setTitle("Fuse 3D to 4D Image");
+ parser.setDescription("MiniApp that allows to fuse several 3D images (with same geometry) into a 3D+t (4D) image that can be processed as dynamic data.");
+ parser.setContributor("DKFZ MIC");
+ //! [create parser]
+
+ //! [add arguments]
+ // how should arguments be prefixed
+ parser.setArgumentPrefix("--", "-");
+ // add each argument, unless specified otherwise each argument is optional
+ // see mitkCommandLineParser::addArgument for more information
+ parser.beginGroup("Required I/O parameters");
+ parser.addArgument(
+ "inputs", "i", mitkCommandLineParser::StringList, "Input files", "Pathes to the input images that should be fused", us::Any(), false, false, false, mitkCommandLineParser::Input);
+ parser.addArgument("output",
+ "o",
+ mitkCommandLineParser::File,
+ "Output file path",
+ "Path to the fused 3D+t image.",
+ us::Any(),
+ false, false, false, mitkCommandLineParser::Output);
+ parser.endGroup();
+
+ parser.beginGroup("Optional parameters");
+ parser.addArgument(
+ "time", "t", mitkCommandLineParser::StringList, "Time bounds", "Defines the time geometry of the resulting dynamic image in [ms]. The first number is the start time point of the first time step. All other numbers are the max bound of a time step. So the structure is [minBound0 maxBound1 [maxBound2 [... maxBoundN]]]; e.g. \"2 3.5 10\" encodes a time geometry with two time steps and that starts at 2 ms and the second time step starts at 3.5 ms and ends at 10 ms. If not set e propertional time geometry with 1 ms duration will be generated!", us::Any(), true, false, false, mitkCommandLineParser::Input);
+ parser.addArgument("help", "h", mitkCommandLineParser::Bool, "Help:", "Show this help text");
+ parser.endGroup();
+ //! [add arguments]
+}
+
+bool configureApplicationSettings(std::map<std::string, us::Any> parsedArgs)
+{
+ if (parsedArgs.size() == 0)
+ return false;
+
+ inFilenames = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["inputs"]);
+ outFileName = us::any_cast<std::string>(parsedArgs["output"]);
+
+ if (parsedArgs.count("time"))
+ {
+ auto timeBoundsStr = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["time"]);
+ for (const auto& timeBoundStr : timeBoundsStr)
+ {
+ std::istringstream stream;
+ stream.imbue(std::locale("C"));
+ stream.str(timeBoundStr);
+ mitk::TimePointType time = 0 ;
+ stream >> time;
+ timebounds.emplace_back(time);
+ }
+ }
+
+ return true;
+}
+
+int main(int argc, char* argv[])
+{
+ mitkCommandLineParser parser;
+ setupParser(parser);
+
+ mitk::PreferenceListReaderOptionsFunctor readerFilterFunctor = mitk::PreferenceListReaderOptionsFunctor({ "MITK DICOM Reader v2 (classic config)" }, { "MITK DICOM Reader" });
+
+ const std::map<std::string, us::Any>& parsedArgs = parser.parseArguments(argc, argv);
+ if (!configureApplicationSettings(parsedArgs))
+ {
+ return EXIT_FAILURE;
+ };
+
+ // Show a help message
+ if (parsedArgs.count("help") || parsedArgs.count("h"))
+ {
+ std::cout << parser.helpText();
+ return EXIT_SUCCESS;
+ }
+
+ if (timebounds.empty())
+ {
+ timebounds.resize(inFilenames.size()+1);
+ std::iota(timebounds.begin(), timebounds.end(), 0.0);
+ }
+ else if (inFilenames.size() + 1 != timebounds.size())
+ {
+ std::cerr << "Cannot fuse images. Explicitly specified time bounds do not match. Use --help for more information on how to specify time bounds correctly.";
+ return EXIT_FAILURE;
+ };
+
+ //! [do processing]
+ try
+ {
+ std::cout << "Load images:" << std::endl;
+
+ auto filter = mitk::TemporalJoinImagesFilter::New();
+
+ unsigned int step = 0;
+ for (auto path : inFilenames)
+ {
+ std::cout << "Time step #"<<step<<" @ "<<timebounds[step]<< " ms: " << path << std::endl;
+ auto image = mitk::IOUtil::Load<mitk::Image>(path, &readerFilterFunctor);
+ images.push_back(image);
+ filter->SetInput(step, image);
+ ++step;
+ }
+
+ filter->SetFirstMinTimeBound(timebounds[0]);
+ filter->SetMaxTimeBounds({ timebounds.begin() + 1, timebounds.end() });
+
+ std::cout << "Fuse the images ..." << std::endl;
+
+ filter->Update();
+ auto output = filter->GetOutput();
+
+ std::cout << "Save output image: " << outFileName << std::endl;
+
+ mitk::IOUtil::Save(output, outFileName);
+
+ std::cout << "Processing finished." << std::endl;
+
+ return EXIT_SUCCESS;
+ }
+ catch (const std::exception& e)
+ {
+ MITK_ERROR << e.what();
+ return EXIT_FAILURE;
+ }
+ catch (...)
+ {
+ MITK_ERROR << "Unexpected error encountered.";
+ return EXIT_FAILURE;
+ }
+}