diff --git a/CMakeExternals/MITKData.cmake b/CMakeExternals/MITKData.cmake index 631899689f..3d35510fbd 100644 --- a/CMakeExternals/MITKData.cmake +++ b/CMakeExternals/MITKData.cmake @@ -1,35 +1,35 @@ #----------------------------------------------------------------------------- # MITK Data #----------------------------------------------------------------------------- # Sanity checks if(DEFINED MITK_DATA_DIR AND NOT EXISTS ${MITK_DATA_DIR}) message(FATAL_ERROR "MITK_DATA_DIR variable is defined but corresponds to non-existing directory") endif() set(proj MITK-Data) set(proj_DEPENDENCIES) set(MITK-Data_DEPENDS ${proj}) if(BUILD_TESTING) - set(revision_tag 2f58ecf9) + set(revision_tag dc06cc67) ExternalProject_Add(${proj} URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/MITK-Data_${revision_tag}.tar.gz UPDATE_COMMAND "" CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" DEPENDS ${proj_DEPENDENCIES} ) set(MITK_DATA_DIR ${ep_source_dir}/${proj}) else() mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") endif(BUILD_TESTING) diff --git a/Core/Code/Algorithms/mitkExtractSliceFilter.cpp b/Core/Code/Algorithms/mitkExtractSliceFilter.cpp index 2facb86401..19ce4201ea 100644 --- a/Core/Code/Algorithms/mitkExtractSliceFilter.cpp +++ b/Core/Code/Algorithms/mitkExtractSliceFilter.cpp @@ -1,485 +1,486 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkExtractSliceFilter.h" #include #include #include #include #include #include #include mitk::ExtractSliceFilter::ExtractSliceFilter(vtkImageReslice* reslicer ){ if(reslicer == NULL){ m_Reslicer = vtkSmartPointer::New(); } else { m_Reslicer = reslicer; } m_TimeStep = 0; m_Reslicer->ReleaseDataFlagOn(); m_InterpolationMode = ExtractSliceFilter::RESLICE_NEAREST; m_ResliceTransform = NULL; m_InPlaneResampleExtentByGeometry = false; m_OutPutSpacing = new mitk::ScalarType[2]; m_OutputDimension = 2; m_ZSpacing = 1.0; m_ZMin = 0; m_ZMax = 0; m_VtkOutputRequested = false; } mitk::ExtractSliceFilter::~ExtractSliceFilter(){ m_ResliceTransform = NULL; m_WorldGeometry = NULL; delete [] m_OutPutSpacing; } void mitk::ExtractSliceFilter::GenerateOutputInformation(){ Superclass::GenerateOutputInformation(); //TODO try figure out how to set the specs of the slice before it is actually extracted /*Image::Pointer output = this->GetOutput(); Image::ConstPointer input = this->GetInput(); if (input.IsNull()) return; unsigned int dimensions[2]; dimensions[0] = m_WorldGeometry->GetExtent(0); dimensions[1] = m_WorldGeometry->GetExtent(1); output->Initialize(input->GetPixelType(), 2, dimensions, 1);*/ } void mitk::ExtractSliceFilter::GenerateInputRequestedRegion(){ //As we want all pixel information fo the image in our plane, the requested region //is set to the largest possible region in the image. //This is needed because an oblique plane has a larger extent then the image //and the in pipeline it is checked via PropagateResquestedRegion(). But the //extent of the slice is actually fitting because it is oblique within the image. ImageToImageFilter::InputImagePointer input = const_cast< ImageToImageFilter::InputImageType* > ( this->GetInput() ); input->SetRequestedRegionToLargestPossibleRegion(); } mitk::ScalarType* mitk::ExtractSliceFilter::GetOutputSpacing(){ return m_OutPutSpacing; } void mitk::ExtractSliceFilter::GenerateData(){ mitk::Image *input = const_cast< mitk::Image * >( this->GetInput() ); if (!input) { MITK_ERROR << "mitk::ExtractSliceFilter: No input image available. Please set the input!" << std::endl; itkExceptionMacro("mitk::ExtractSliceFilter: No input image available. Please set the input!"); return; } if(!m_WorldGeometry) { MITK_ERROR << "mitk::ExtractSliceFilter: No Geometry for reslicing available." << std::endl; itkExceptionMacro("mitk::ExtractSliceFilter: No Geometry for reslicing available."); return; } const TimeSlicedGeometry *inputTimeGeometry = this->GetInput()->GetTimeSlicedGeometry(); if ( ( inputTimeGeometry == NULL ) || ( inputTimeGeometry->GetTimeSteps() == 0 ) ) { itkWarningMacro(<<"Error reading input image TimeSlicedGeometry."); return; } // is it a valid timeStep? if ( inputTimeGeometry->IsValidTime( m_TimeStep ) == false ) { itkWarningMacro(<<"This is not a valid timestep: "<< m_TimeStep ); return; } // check if there is something to display. if ( ! input->IsVolumeSet( m_TimeStep ) ) { itkWarningMacro(<<"No volume data existent at given timestep "<< m_TimeStep ); return; } /*================#BEGIN setup vtkImageRslice properties================*/ Point3D origin; Vector3D right, bottom, normal; double widthInMM, heightInMM; Vector2D extent; const PlaneGeometry* planeGeometry = dynamic_cast(m_WorldGeometry); if ( planeGeometry != NULL ) { //if the worldGeomatry is a PlaneGeometry everthing is straight forward origin = planeGeometry->GetOrigin(); right = planeGeometry->GetAxisVector( 0 ); bottom = planeGeometry->GetAxisVector( 1 ); normal = planeGeometry->GetNormal(); if ( m_InPlaneResampleExtentByGeometry ) { // Resampling grid corresponds to the current world geometry. This // means that the spacing of the output 2D image depends on the // currently selected world geometry, and *not* on the image itself. extent[0] = m_WorldGeometry->GetExtent( 0 ); extent[1] = m_WorldGeometry->GetExtent( 1 ); } else { // Resampling grid corresponds to the input geometry. This means that // the spacing of the output 2D image is directly derived from the // associated input image, regardless of the currently selected world // geometry. Vector3D rightInIndex, bottomInIndex; inputTimeGeometry->GetGeometry3D( m_TimeStep )->WorldToIndex( right, rightInIndex ); inputTimeGeometry->GetGeometry3D( m_TimeStep )->WorldToIndex( bottom, bottomInIndex ); extent[0] = rightInIndex.GetNorm(); extent[1] = bottomInIndex.GetNorm(); } // Get the extent of the current world geometry and calculate resampling // spacing therefrom. widthInMM = m_WorldGeometry->GetExtentInMM( 0 ); heightInMM = m_WorldGeometry->GetExtentInMM( 1 ); m_OutPutSpacing[0] = widthInMM / extent[0]; m_OutPutSpacing[1] = heightInMM / extent[1]; right.Normalize(); bottom.Normalize(); normal.Normalize(); /* * Transform the origin to center based coordinates. * Note: * This is needed besause vtk's origin is center based too (!!!) ( see 'The VTK book' page 88 ) * and the worldGeometry surrouding the image is no imageGeometry. So the worldGeometry * has its origin at the corner of the voxel and needs to be transformed. */ origin += right * ( m_OutPutSpacing[0] * 0.5 ); origin += bottom * ( m_OutPutSpacing[1] * 0.5 ); //set the tranform for reslicing. // Use inverse transform of the input geometry for reslicing the 3D image. // This is needed if the image volume already transformed if(m_ResliceTransform.IsNotNull()) m_Reslicer->SetResliceTransform(m_ResliceTransform->GetVtkTransform()->GetLinearInverse()); // Set background level to TRANSLUCENT (see Geometry2DDataVtkMapper3D), // else the background of the image turns out gray m_Reslicer->SetBackgroundLevel( -32768 ); } else{ //Code for curved planes, mostly taken 1:1 from imageVtkMapper2D and not tested yet. // Do we have an AbstractTransformGeometry? // This is the case for AbstractTransformGeometry's (e.g. a ThinPlateSplineCurvedGeometry ) const mitk::AbstractTransformGeometry* abstractGeometry = dynamic_cast< const AbstractTransformGeometry * >(m_WorldGeometry); if(abstractGeometry != NULL) { m_ResliceTransform = abstractGeometry; extent[0] = abstractGeometry->GetParametricExtent(0); extent[1] = abstractGeometry->GetParametricExtent(1); widthInMM = abstractGeometry->GetParametricExtentInMM(0); heightInMM = abstractGeometry->GetParametricExtentInMM(1); m_OutPutSpacing[0] = widthInMM / extent[0]; m_OutPutSpacing[1] = heightInMM / extent[1]; origin = abstractGeometry->GetPlane()->GetOrigin(); right = abstractGeometry->GetPlane()->GetAxisVector(0); right.Normalize(); bottom = abstractGeometry->GetPlane()->GetAxisVector(1); bottom.Normalize(); normal = abstractGeometry->GetPlane()->GetNormal(); normal.Normalize(); // Use a combination of the InputGeometry *and* the possible non-rigid // AbstractTransformGeometry for reslicing the 3D Image vtkSmartPointer composedResliceTransform = vtkSmartPointer::New(); composedResliceTransform->Identity(); composedResliceTransform->Concatenate( inputTimeGeometry->GetGeometry3D( m_TimeStep )->GetVtkTransform()->GetLinearInverse() ); composedResliceTransform->Concatenate( abstractGeometry->GetVtkAbstractTransform() ); m_Reslicer->SetResliceTransform( composedResliceTransform ); // Set background level to BLACK instead of translucent, to avoid // boundary artifacts (see Geometry2DDataVtkMapper3D) m_Reslicer->SetBackgroundLevel( -1023 ); } else { itkExceptionMacro("mitk::ExtractSliceFilter: No fitting geometry for reslice axis!"); return; } } if(m_ResliceTransform.IsNotNull()){ //if the resliceTransform is set the reslice axis are recalculated. //Thus the geometry information is not fitting. Therefor a unitSpacingFilter //is used to set up a global spacing of 1 and compensate the transform. vtkSmartPointer unitSpacingImageFilter = vtkSmartPointer::New() ; unitSpacingImageFilter->ReleaseDataFlagOn(); unitSpacingImageFilter->SetOutputSpacing( 1.0, 1.0, 1.0 ); unitSpacingImageFilter->SetInput( input->GetVtkImageData(m_TimeStep) ); m_Reslicer->SetInput(unitSpacingImageFilter->GetOutput() ); } else { //if no tranform is set the image can be used directly m_Reslicer->SetInput(input->GetVtkImageData(m_TimeStep)); } /*setup the plane where vktImageReslice extracts the slice*/ //ResliceAxesOrigin is the ancor point of the plane double originInVtk[3]; itk2vtk(origin, originInVtk); m_Reslicer->SetResliceAxesOrigin(originInVtk); //the cosines define the plane: x and y are the direction vectors, n is the planes normal //this specifies a matrix 3x3 // x1 y1 n1 // x2 y2 n2 // x3 y3 n3 double cosines[9]; vnl2vtk(right.GetVnlVector(), cosines);//x vnl2vtk(bottom.GetVnlVector(), cosines + 3);//y vnl2vtk(normal.GetVnlVector(), cosines + 6);//n m_Reslicer->SetResliceAxesDirectionCosines(cosines); //we only have one slice, not a volume m_Reslicer->SetOutputDimensionality(m_OutputDimension); //set the interpolation mode for slicing switch(this->m_InterpolationMode){ case RESLICE_NEAREST: m_Reslicer->SetInterpolationModeToNearestNeighbor(); break; case RESLICE_LINEAR: m_Reslicer->SetInterpolationModeToLinear(); break; case RESLICE_CUBIC: m_Reslicer->SetInterpolationModeToCubic(); + break; default: //the default interpolation used by mitk m_Reslicer->SetInterpolationModeToNearestNeighbor(); } /*========== BEGIN setup extent of the slice ==========*/ int xMin, xMax, yMin, yMax; xMin = yMin = 0; xMax = static_cast< int >( extent[0]); yMax = static_cast< int >( extent[1]); vtkFloatingPointType sliceBounds[6]; if (m_WorldGeometry->GetReferenceGeometry()) { for ( int i = 0; i < 6; ++i ) { sliceBounds[i] = 0.0; } if (this->GetClippedPlaneBounds( m_WorldGeometry->GetReferenceGeometry(), planeGeometry, sliceBounds )) { // Calculate output extent (integer values) xMin = static_cast< int >( sliceBounds[0] / m_OutPutSpacing[0] + 0.5 ); xMax = static_cast< int >( sliceBounds[1] / m_OutPutSpacing[0] + 0.5 ); yMin = static_cast< int >( sliceBounds[2] / m_OutPutSpacing[1] + 0.5 ); yMax = static_cast< int >( sliceBounds[3] / m_OutPutSpacing[1] + 0.5 ); } // ELSE we use the default values } // Set the output extents! First included pixel index and last included pixel index // xMax and yMax are one after the last pixel. so they have to be decremented by 1. // In case we have a 2D image, xMax or yMax might be 0. in this case, do not decrement, but take 0. m_Reslicer->SetOutputExtent(xMin, std::max(0, xMax-1), yMin, std::max(0, yMax-1), m_ZMin, m_ZMax ); /*========== END setup extent of the slice ==========*/ m_Reslicer->SetOutputOrigin( 0.0, 0.0, 0.0 ); m_Reslicer->SetOutputSpacing( m_OutPutSpacing[0], m_OutPutSpacing[1], m_ZSpacing ); //TODO check the following lines, they are responsible wether vtk error outputs appear or not m_Reslicer->UpdateWholeExtent(); //this produces a bad allocation error for 2D images //m_Reslicer->GetOutput()->UpdateInformation(); //m_Reslicer->GetOutput()->SetUpdateExtentToWholeExtent(); //start the pipeline m_Reslicer->Update(); /*================ #END setup vtkImageRslice properties================*/ if(m_VtkOutputRequested){ return; //no converting to mitk //no mitk geometry will be set, as the output is vtkImageData only!!! } else { /*================ #BEGIN Get the slice from vtkImageReslice and convert it to mit::Image================*/ vtkImageData* reslicedImage; reslicedImage = m_Reslicer->GetOutput(); if(!reslicedImage) { itkWarningMacro(<<"Reslicer returned empty image"); return; } mitk::Image::Pointer resultImage = this->GetOutput(); //initialize resultimage with the specs of the vtkImageData object returned from vtkImageReslice if (reslicedImage->GetDataDimension() == 1) { // If original image was 2D, the slice might have an y extent of 0. // Still i want to ensure here that Image is 2D resultImage->Initialize(reslicedImage,1,-1,-1,1); } else { resultImage->Initialize(reslicedImage); } //transfer the voxel data resultImage->SetVolume(reslicedImage->GetScalarPointer()); //set the geometry from current worldgeometry for the reusultimage //this is needed that the image has the correct mitk geometry //the originalGeometry is the Geometry of the result slice // mitk::AffineGeometryFrame3D::Pointer originalGeometryAGF = m_WorldGeometry->Clone(); // Geometry2D::Pointer originalGeometry = dynamic_cast( originalGeometryAGF.GetPointer() ); Geometry2D::Pointer originalGeometry = m_WorldGeometry->Clone(); originalGeometry->GetIndexToWorldTransform()->SetMatrix(m_WorldGeometry->GetIndexToWorldTransform()->GetMatrix()); //the origin of the worldGeometry is transformed to center based coordinates to be an imageGeometry Point3D sliceOrigin = originalGeometry->GetOrigin(); sliceOrigin += right * ( m_OutPutSpacing[0] * 0.5 ); sliceOrigin += bottom * ( m_OutPutSpacing[1] * 0.5 ); //a worldGeometry is no imageGeometry, thus it is manually set to true originalGeometry->ImageGeometryOn(); /*At this point we have to adjust the geometry because the origin isn't correct. The wrong origin is related to the rotation of the current world geometry plane. This causes errors on transfering world to index coordinates. We just shift the origin in each direction about the amount of the expanding (needed while rotating the plane). */ Vector3D axis0 = originalGeometry->GetAxisVector(0); Vector3D axis1 = originalGeometry->GetAxisVector(1); axis0.Normalize(); axis1.Normalize(); //adapt the origin. Note that for orthogonal planes the minima are '0' and thus the origin stays the same. sliceOrigin += (axis0 * (xMin * m_OutPutSpacing[0])) + (axis1 * (yMin * m_OutPutSpacing[1])); originalGeometry->SetOrigin(sliceOrigin); originalGeometry->Modified(); resultImage->SetGeometry( originalGeometry ); /*the bounds as well as the extent of the worldGeometry are not adapted correctly during crosshair rotation. This is only a quick fix and has to be evaluated. The new bounds are set via the max values of the calcuted slice extent. It will look like [ 0, x, 0, y, 0, 1]. */ mitk::BoundingBox::BoundsArrayType boundsCopy; boundsCopy[0] = boundsCopy[2] = boundsCopy[4] = 0; boundsCopy[5] = 1; boundsCopy[1] = xMax - xMin; boundsCopy[3] = yMax - yMin; resultImage->GetGeometry()->SetBounds(boundsCopy); /*================ #END Get the slice from vtkImageReslice and convert it to mitk Image================*/ } } bool mitk::ExtractSliceFilter::GetClippedPlaneBounds(vtkFloatingPointType bounds[6]){ if(!m_WorldGeometry || !this->GetInput()) return false; return this->GetClippedPlaneBounds(m_WorldGeometry->GetReferenceGeometry(), dynamic_cast< const PlaneGeometry * >( m_WorldGeometry ), bounds); } bool mitk::ExtractSliceFilter::GetClippedPlaneBounds( const Geometry3D *boundingGeometry, const PlaneGeometry *planeGeometry, vtkFloatingPointType *bounds ) { bool b = mitk::PlaneClipping::CalculateClippedPlaneBounds(boundingGeometry, planeGeometry, bounds); return b; } diff --git a/Core/Code/Algorithms/mitkExtractSliceFilter.h b/Core/Code/Algorithms/mitkExtractSliceFilter.h index 8dd9ac2a14..57b6d1813e 100644 --- a/Core/Code/Algorithms/mitkExtractSliceFilter.h +++ b/Core/Code/Algorithms/mitkExtractSliceFilter.h @@ -1,174 +1,174 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef mitkExtractSliceFilter_h_Included #define mitkExtractSliceFilter_h_Included #include "MitkExports.h" #include "mitkImageToImageFilter.h" #include #include #include #include #include #include #include namespace mitk { /** \brief ExtractSliceFilter extracts a 2D abitrary oriented slice from a 3D volume. The filter can reslice in all orthogonal planes such as sagittal, coronal and axial, and is also able to reslice a abitrary oriented oblique plane. Curved planes are specified via an AbstractTransformGeometry as the input worldgeometry. The convinient workflow is: 1. Set an image as input. 2. Set the worldGeometry2D. This defines a grid where the slice is being extracted 3. And then start the pipeline. There are a few more properties that can be set to modify the behavior of the slicing. The properties are: - interpolation mode either Nearestneighbor, Linear or Cubic. - a transform this is a convinient way to adapt the reslice axis for the case that the image is transformed e.g. rotated. - time step the time step in a timesliced volume. - resample by geometry wether the resampling grid corresponds to the specs of the worldgeometry or is directly derived from the input image By default the properties are set to: - interpolation mode Nearestneighbor. - a transform NULL (No transform is set). - time step 0. - resample by geometry false (Corresponds to input image). */ class MITK_CORE_EXPORT ExtractSliceFilter : public ImageToImageFilter { public: mitkClassMacro(ExtractSliceFilter, ImageToImageFilter); itkNewMacro(ExtractSliceFilter); mitkNewMacro1Param(Self, vtkImageReslice*); /** \brief Set the axis where to reslice at.*/ void SetWorldGeometry(const Geometry2D* geometry ){ this->m_WorldGeometry = geometry; this->Modified(); } /** \brief Set the time step in the 4D volume */ void SetTimeStep( unsigned int timestep){ this->m_TimeStep = timestep; } unsigned int GetTimeStep(){ return this->m_TimeStep; } /** \brief Set a transform for the reslice axes. * This transform is needed if the image volume itself is transformed. (Effects the reslice axis) */ void SetResliceTransformByGeometry(const Geometry3D* transform){ this->m_ResliceTransform = transform; } /** \brief Resampling grid corresponds to: false->image true->worldgeometry*/ void SetInPlaneResampleExtentByGeometry(bool inPlaneResampleExtentByGeometry){ this->m_InPlaneResampleExtentByGeometry = inPlaneResampleExtentByGeometry; } /** \brief Sets the output dimension of the slice*/ void SetOutputDimensionality(unsigned int dimension){ this->m_OutputDimension = dimension; } /** \brief Set the spacing in z direction manually. * Required if the outputDimension is > 2. */ void SetOutputSpacingZDirection(double zSpacing){ this->m_ZSpacing = zSpacing; } /** \brief Set the extent in pixel for direction z manualy. Required if the output dimension is > 2. */ void SetOutputExtentZDirection(int zMin, int zMax) { this->m_ZMin = zMin; this->m_ZMax = zMax; } /** \brief Get the bounding box of the slice [xMin, xMax, yMin, yMax, zMin, zMax] * The method uses the input of the filter to calculate the bounds. * It is recommended to use * GetClippedPlaneBounds(const Geometry3D*, const PlaneGeometry*, vtkFloatingPointType*) * if you are not sure about the input. */ bool GetClippedPlaneBounds(double bounds[6]); /** \brief Get the bounding box of the slice [xMin, xMax, yMin, yMax, zMin, zMax]*/ bool GetClippedPlaneBounds( const Geometry3D *boundingGeometry, const PlaneGeometry *planeGeometry, vtkFloatingPointType *bounds ); /** \brief Get the spacing of the slice. returns mitk::ScalarType[2] */ mitk::ScalarType* GetOutputSpacing(); /** \brief Get Output as vtkImageData. * Note: * SetVtkOutputRequest(true) has to be called at least once before * GetVtkOutput(). Otherwise the output is empty for the first update step. */ vtkImageData* GetVtkOutput(){ m_VtkOutputRequested = true; return m_Reslicer->GetOutput(); } /** Set VtkOutPutRequest to suppress the convertion of the image. * It is suggested to use this with GetVtkOutput(). * Note: * SetVtkOutputRequest(true) has to be called at least once before * GetVtkOutput(). Otherwise the output is empty for the first update step. */ void SetVtkOutputRequest(bool isRequested){ m_VtkOutputRequested = isRequested; } /** \brief Get the reslices axis matrix. * Note: the axis are recalculated when calling SetResliceTransformByGeometry. */ vtkMatrix4x4* GetResliceAxes(){ return this->m_Reslicer->GetResliceAxes(); } - enum ResliceInterpolation { RESLICE_NEAREST, RESLICE_LINEAR, RESLICE_CUBIC }; + enum ResliceInterpolation { RESLICE_NEAREST=0, RESLICE_LINEAR=1, RESLICE_CUBIC=3 }; void SetInterpolationMode( ExtractSliceFilter::ResliceInterpolation interpolation){ this->m_InterpolationMode = interpolation; } protected: ExtractSliceFilter(vtkImageReslice* reslicer = NULL); virtual ~ExtractSliceFilter(); virtual void GenerateData(); virtual void GenerateOutputInformation(); virtual void GenerateInputRequestedRegion(); const Geometry2D* m_WorldGeometry; vtkSmartPointer m_Reslicer; unsigned int m_TimeStep; unsigned int m_OutputDimension; double m_ZSpacing; int m_ZMin; int m_ZMax; ResliceInterpolation m_InterpolationMode; Geometry3D::ConstPointer m_ResliceTransform; bool m_InPlaneResampleExtentByGeometry;//Resampling grid corresponds to: false->image true->worldgeometry mitk::ScalarType* m_OutPutSpacing; bool m_VtkOutputRequested; }; } #endif // mitkExtractSliceFilter_h_Included diff --git a/Core/Code/Testing/CMakeLists.txt b/Core/Code/Testing/CMakeLists.txt index a62859587f..0ee2d8510d 100644 --- a/Core/Code/Testing/CMakeLists.txt +++ b/Core/Code/Testing/CMakeLists.txt @@ -1,125 +1,141 @@ # The core tests need relaxed compiler flags... # TODO fix core tests to compile without these additional no-error flags if(MSVC_VERSION) # disable deprecated warnings (they would lead to errors) mitkFunctionCheckCAndCXXCompilerFlags("/wd4996" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) else() mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=deprecated" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=deprecated-declarations" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) endif() MITK_CREATE_MODULE_TESTS(LABELS MITK-Core) # MITK_INSTALL_TARGETS(EXECUTABLES MitkTestDriver) mitkAddCustomModuleTest(mitkDICOMLocaleTest_spacingOk_CT mitkDICOMLocaleTest ${MITK_DATA_DIR}/spacing-ok-ct.dcm) mitkAddCustomModuleTest(mitkDICOMLocaleTest_spacingOk_MR mitkDICOMLocaleTest ${MITK_DATA_DIR}/spacing-ok-mr.dcm) mitkAddCustomModuleTest(mitkDICOMLocaleTest_spacingOk_SC mitkDICOMLocaleTest ${MITK_DATA_DIR}/spacing-ok-sc.dcm) mitkAddCustomModuleTest(mitkVolumeCalculatorTest_Png2D-bw mitkVolumeCalculatorTest ${MITK_DATA_DIR}/Png2D-bw.png ${MITK_DATA_DIR}/Pic2DplusT.nrrd) mitkAddCustomModuleTest(mitkEventMapperTest_Test1And2 mitkEventMapperTest ${MITK_DATA_DIR}/TestStateMachine1.xml ${MITK_DATA_DIR}/TestStateMachine2.xml) mitkAddCustomModuleTest(mitkEventConfigTest_CreateObjectInDifferentWays mitkEventConfigTest ${MITK_SOURCE_DIR}/Core/Code/Testing/Resources/Interactions/StatemachineConfigTest.xml) #mitkAddCustomModuleTest(mitkNodeDependentPointSetInteractorTest mitkNodeDependentPointSetInteractorTest ${MITK_DATA_DIR}/Pic3D.pic.gz ${MITK_DATA_DIR}/BallBinary30x30x30.pic.gz) mitkAddCustomModuleTest(mitkNodeDependentPointSetInteractorTest mitkNodeDependentPointSetInteractorTest ${MITK_DATA_DIR}/Pic3D.nrrd ${MITK_DATA_DIR}/BallBinary30x30x30.nrrd) mitkAddCustomModuleTest(mitkDataStorageTest_US4DCyl mitkDataStorageTest ${MITK_DATA_DIR}/US4DCyl.nrrd) mitkAddCustomModuleTest(mitkStateMachineFactoryTest_TestStateMachine1_2 mitkStateMachineFactoryTest ${MITK_DATA_DIR}/TestStateMachine1.xml ${MITK_DATA_DIR}/TestStateMachine2.xml) mitkAddCustomModuleTest(mitkDicomSeriesReaderTest_CTImage mitkDicomSeriesReaderTest ${MITK_DATA_DIR}/TinyCTAbdomen) mitkAddCustomModuleTest(mitkPointSetReaderTest mitkPointSetReaderTest ${MITK_DATA_DIR}/PointSetReaderTestData.mps) mitkAddCustomModuleTest(mitkImageTest_4DImageData mitkImageTest ${MITK_DATA_DIR}/US4DCyl.nrrd) mitkAddCustomModuleTest(mitkImageTest_2D+tImageData mitkImageTest ${MITK_DATA_DIR}/Pic2DplusT.nrrd) mitkAddCustomModuleTest(mitkImageTest_3DImageData mitkImageTest ${MITK_DATA_DIR}/Pic3D.nrrd) mitkAddCustomModuleTest(mitkImageTest_brainImage mitkImageTest ${MITK_DATA_DIR}/brain.mhd) #mitkAddCustomModuleTest(mitkImageTest_color2DImage mitkImageTest ${MITK_DATA_DIR}/NrrdWritingTestImage.jpg) mitkAddCustomModuleTest(mitkIOUtilTest mitkIOUtilTest #test for a randomly chosen Pic3D swivelled slice ${MITK_DATA_DIR}/Pic3D.nrrd ${MITK_DATA_DIR}/pointSet.mps ${MITK_DATA_DIR}/binary.stl ) mitkAddCustomModuleTest(mitkLevelWindowManagerTest mitkLevelWindowManagerTest ${MITK_DATA_DIR}/Pic3D.nrrd ) if(WIN32 OR APPLE OR MITK_ENABLE_GUI_TESTING) ### since the rendering test's do not run in ubuntu, yet, we build them only for other systems or if the user explicitly sets the variable MITK_ENABLE_GUI_TESTING mitkAddCustomModuleTest(mitkImageVtkMapper2D_rgbaImage640x480 mitkImageVtkMapper2DTest ${MITK_DATA_DIR}/RenderingTestData/rgbaImage.png #input image to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/rgbaImage640x480REF.png #corresponding reference screenshot ) mitkAddCustomModuleTest(mitkImageVtkMapper2D_pic3d640x480 mitkImageVtkMapper2DTest #test for standard Pic3D axial slice ${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3d640x480REF.png #corresponding reference screenshot ) mitkAddCustomModuleTest(mitkImageVtkMapper2D_pic3dColorBlue640x480 mitkImageVtkMapper2DColorTest #test for color property (=blue) Pic3D sagittal slice ${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dColorBlue640x480REF.png #corresponding reference screenshot ) mitkAddCustomModuleTest(mitkImageVtkMapper2D_pic3dLevelWindow640x480 mitkImageVtkMapper2DLevelWindowTest #test for levelwindow property (=blood) #Pic3D sagittal slice ${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dLevelWindowBlood640x480REF.png #corresponding reference #screenshot ) mitkAddCustomModuleTest(mitkImageVtkMapper2D_pic3dOpacity640x480 mitkImageVtkMapper2DOpacityTest #test for opacity (=0.5) Pic3D coronal slice ${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dOpacity640x480REF.png corresponding reference screenshot ) mitkAddCustomModuleTest(mitkImageVtkMapper2D_pic3dSwivel640x480 mitkImageVtkMapper2DSwivelTest #test for a randomly chosen Pic3D swivelled slice ${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dSwivel640x480REF.png #corresponding reference screenshot ) +#Test reslice interpolation +#note: nearest mode is already tested by swivel test +mitkAddCustomModuleTest(ResliceInterpolationIsLinear mitkImageVtkMapper2DResliceInterpolationPropertyTest + 1 #linear + ${MITK_DATA_DIR}/Pic3D.nrrd + -V + ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dRefLinear.png #corresponding reference screenshot LINEAR +) + +mitkAddCustomModuleTest(ResliceInterpolationIsCubic mitkImageVtkMapper2DResliceInterpolationPropertyTest + 3 #cubic + ${MITK_DATA_DIR}/Pic3D.nrrd + -V + ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dRefCubic.png #corresponding reference screenshot CUBIC +) +#End test reslice interpolation # Testing of the rendering of binary images mitkAddCustomModuleTest(mitkImageVtkMapper2D_binaryTestImage640x480 mitkImageVtkMapper2DTest #test for standard Pic3D axial slice ${MITK_DATA_DIR}/RenderingTestData/binaryImage.nrrd #input image to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/binaryImage640x480REF.png #corresponding reference screenshot ) mitkAddCustomModuleTest(mitkImageVtkMapper2D_binaryTestImageWithRef640x480 mitkImageVtkMapper2DTest #test for standard Pic3D axial slice ${MITK_DATA_DIR}/Pic3D.nrrd ${MITK_DATA_DIR}/RenderingTestData/binaryImage.nrrd #input image to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/binaryImageWithRef640x480REF.png #corresponding reference screenshot ) # End of binary image tests mitkAddCustomModuleTest(mitkSurfaceVtkMapper3DTest_TextureProperty mitkSurfaceVtkMapper3DTest ${MITK_DATA_DIR}/ToF-Data/Kinect_LiverPhantom.vtp ${MITK_DATA_DIR}/ToF-Data/Kinect_LiverPhantom_RGBImage.nrrd -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/texturedLiver640x480REF.png #corresponding reference screenshot ) mitkAddCustomModuleTest(mitkImageVtkMapper2DTransferFunctionTest_Png2D-bw mitkImageVtkMapper2DTransferFunctionTest ${MITK_DATA_DIR}/Png2D-bw.png -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/Png2D-bw-TransferFunctionRGBImage640x480REF.png #corresponding reference screenshot ) #mitkAddCustomModuleTest(mitkSurfaceVtkMapper3DTexturedSphereTest_Football mitkSurfaceVtkMapper3DTexturedSphereTest # ${MITK_DATA_DIR}/RenderingTestData/texture.jpg #input texture # -V # ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/texturedSphere640x480REF.png corresponding reference screenshot #) SET_PROPERTY(TEST mitkImageVtkMapper2D_rgbaImage640x480 mitkImageVtkMapper2D_pic3d640x480 mitkImageVtkMapper2D_pic3dColorBlue640x480 mitkImageVtkMapper2D_pic3dLevelWindow640x480 mitkImageVtkMapper2D_pic3dSwivel640x480 mitkImageVtkMapper2DTransferFunctionTest_Png2D-bw mitkImageVtkMapper2D_pic3dOpacity640x480 #mitkSurfaceVtkMapper3DTest_TextureProperty #mitkSurfaceVtkMapper3DTexturedSphereTest_Football PROPERTY RUN_SERIAL TRUE) endif() add_test(mitkPointSetLocaleTest ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TESTDRIVER} mitkPointSetLocaleTest ${MITK_DATA_DIR}/pointSet.mps) set_property(TEST mitkPointSetLocaleTest PROPERTY LABELS MITK-Core) add_test(mitkImageWriterTest_nrrdImage ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TESTDRIVER} mitkImageWriterTest ${MITK_DATA_DIR}/NrrdWritingTestImage.jpg) add_test(mitkImageWriterTest_2DPNGImage ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TESTDRIVER} mitkImageWriterTest ${MITK_DATA_DIR}/Png2D-bw.png) add_test(mitkImageWriterTest_rgbPNGImage ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TESTDRIVER} mitkImageWriterTest ${MITK_DATA_DIR}/RenderingTestData/rgbImage.png) add_test(mitkImageWriterTest_rgbaPNGImage ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TESTDRIVER} mitkImageWriterTest ${MITK_DATA_DIR}/RenderingTestData/rgbaImage.png) set_property(TEST mitkImageWriterTest_nrrdImage PROPERTY LABELS MITK-Core) set_property(TEST mitkImageWriterTest_2DPNGImage PROPERTY LABELS MITK-Core) set_property(TEST mitkImageWriterTest_rgbPNGImage PROPERTY LABELS MITK-Core) set_property(TEST mitkImageWriterTest_rgbaPNGImage PROPERTY LABELS MITK-Core) add_subdirectory(DICOMTesting) diff --git a/Core/Code/Testing/files.cmake b/Core/Code/Testing/files.cmake index a048395961..6b914a3728 100644 --- a/Core/Code/Testing/files.cmake +++ b/Core/Code/Testing/files.cmake @@ -1,144 +1,145 @@ # tests with no extra command line parameter set(MODULE_TESTS mitkAccessByItkTest.cpp mitkCoreObjectFactoryTest.cpp mitkMaterialTest.cpp mitkActionTest.cpp mitkDispatcherTest.cpp mitkEnumerationPropertyTest.cpp mitkEventTest.cpp mitkFocusManagerTest.cpp mitkGenericPropertyTest.cpp mitkGeometry3DTest.cpp mitkGeometryDataToSurfaceFilterTest.cpp mitkGlobalInteractionTest.cpp mitkImageDataItemTest.cpp #mitkImageMapper2DTest.cpp mitkImageGeneratorTest.cpp mitkBaseDataTest.cpp #mitkImageToItkTest.cpp mitkInstantiateAccessFunctionTest.cpp mitkInteractorTest.cpp #mitkITKThreadingTest.cpp mitkLevelWindowTest.cpp mitkMessageTest.cpp #mitkPipelineSmartPointerCorrectnessTest.cpp mitkPixelTypeTest.cpp mitkPlaneGeometryTest.cpp mitkPointSetFileIOTest.cpp mitkPointSetTest.cpp mitkPointSetWriterTest.cpp mitkPointSetReaderTest.cpp mitkPointSetInteractorTest.cpp mitkPropertyTest.cpp mitkPropertyListTest.cpp #mitkRegistrationBaseTest.cpp #mitkSegmentationInterpolationTest.cpp mitkSlicedGeometry3DTest.cpp mitkSliceNavigationControllerTest.cpp mitkStateMachineTest.cpp ##mitkStateMachineContainerTest.cpp ## rewrite test, indirect since no longer exported Bug 14529 mitkStateTest.cpp mitkSurfaceTest.cpp mitkSurfaceToSurfaceFilterTest.cpp mitkTimeSlicedGeometryTest.cpp mitkTransitionTest.cpp mitkUndoControllerTest.cpp mitkVtkWidgetRenderingTest.cpp mitkVerboseLimitedLinearUndoTest.cpp mitkWeakPointerTest.cpp mitkTransferFunctionTest.cpp #mitkAbstractTransformGeometryTest.cpp mitkStepperTest.cpp itkTotalVariationDenoisingImageFilterTest.cpp mitkRenderingManagerTest.cpp vtkMitkThickSlicesFilterTest.cpp mitkNodePredicateSourceTest.cpp mitkVectorTest.cpp mitkClippedSurfaceBoundsCalculatorTest.cpp #QmitkRenderingTestHelper.cpp mitkExceptionTest.cpp mitkExtractSliceFilterTest.cpp mitkLogTest.cpp mitkImageDimensionConverterTest.cpp mitkLoggingAdapterTest.cpp mitkUIDGeneratorTest.cpp mitkShaderRepositoryTest.cpp ) # test with image filename as an extra command line parameter set(MODULE_IMAGE_TESTS mitkPlanePositionManagerTest.cpp mitkSurfaceVtkWriterTest.cpp #mitkImageSliceSelectorTest.cpp mitkImageTimeSelectorTest.cpp # mitkVtkPropRendererTest.cpp mitkDataNodeFactoryTest.cpp #mitkSTLFileReaderTest.cpp mitkImageAccessorTest.cpp ) # list of images for which the tests are run set(MODULE_TESTIMAGES # Pic-Factory no more available in Core, test images now in .nrrd format US4DCyl.nrrd Pic3D.nrrd Pic2DplusT.nrrd BallBinary30x30x30.nrrd binary.stl ball.stl ) set(MODULE_CUSTOM_TESTS #mitkLabeledImageToSurfaceFilterTest.cpp #mitkExternalToolsTest.cpp mitkDataStorageTest.cpp mitkDataNodeTest.cpp mitkDicomSeriesReaderTest.cpp mitkDICOMLocaleTest.cpp mitkEventMapperTest.cpp mitkEventConfigTest.cpp mitkNodeDependentPointSetInteractorTest.cpp mitkStateMachineFactoryTest.cpp mitkPointSetLocaleTest.cpp mitkImageTest.cpp mitkImageWriterTest.cpp mitkImageVtkMapper2DTest.cpp mitkImageVtkMapper2DLevelWindowTest.cpp mitkImageVtkMapper2DOpacityTest.cpp + mitkImageVtkMapper2DResliceInterpolationPropertyTest.cpp mitkImageVtkMapper2DColorTest.cpp mitkImageVtkMapper2DSwivelTest.cpp mitkImageVtkMapper2DTransferFunctionTest.cpp mitkIOUtilTest.cpp mitkSurfaceVtkMapper3DTest mitkSurfaceVtkMapper3DTexturedSphereTest.cpp mitkVolumeCalculatorTest.cpp mitkLevelWindowManagerTest.cpp ) set(MODULE_RESOURCE_FILES Interactions/AddAndRemovePoints.xml Interactions/globalConfig.xml Interactions/StatemachineTest.xml Interactions/StatemachineConfigTest.xml ) # Create an artificial module initializing class for # the usServiceListenerTest.cpp usFunctionGenerateModuleInit(testdriver_init_file NAME ${MODULE_NAME}TestDriver DEPENDS "Mitk" VERSION "0.1.0" EXECUTABLE ) # Embed the resources set(testdriver_resources ) usFunctionEmbedResources(testdriver_resources EXECUTABLE_NAME ${MODULE_NAME}TestDriver ROOT_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Resources FILES ${MODULE_RESOURCE_FILES} ) set(TEST_CPP_FILES ${testdriver_init_file} ${testdriver_resources}) diff --git a/Core/Code/Testing/mitkImageVtkMapper2DResliceInterpolationPropertyTest.cpp b/Core/Code/Testing/mitkImageVtkMapper2DResliceInterpolationPropertyTest.cpp new file mode 100644 index 0000000000..a83bfaf590 --- /dev/null +++ b/Core/Code/Testing/mitkImageVtkMapper2DResliceInterpolationPropertyTest.cpp @@ -0,0 +1,85 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +//MITK +#include "mitkTestingMacros.h" +#include "mitkRenderingTestHelper.h" +#include +#include "mitkIOUtil.h" +#include "mitkDataNode.h" + +//VTK +#include +#include + + +int mitkImageVtkMapper2DResliceInterpolationPropertyTest(int argc, char* argv[]) +{ + //load all arguments into a datastorage, take last argument as reference + //setup a renderwindow of fixed size X*Y + //render the datastorage + //compare rendering to reference image + //note: this test is supposed to test the reslice interpolation modes not the swiveling itself + MITK_TEST_BEGIN("mitkImageVtkMapper2DResliceInterpolationPropertyTest") + + mitkRenderingTestHelper renderingHelper(640, 480, argc, argv); + + //get resliceInterpolation from comandline arg + int resliceInterpolation = atoi(argv[argc-4]); + + //Set interpolation mode for rendering + renderingHelper.SetImageProperty("reslice interpolation", mitk::VtkResliceInterpolationProperty::New( resliceInterpolation )); + + /*+++rotate plane+++*/ + //center point for rotation + mitk::Point3D centerPoint; + centerPoint.Fill(0.0f); + //vector for rotating the slice + mitk::Vector3D rotationVector; + rotationVector.SetElement(0, 0.2); + rotationVector.SetElement(1, 0.3); + rotationVector.SetElement(2, 0.5); + //sets a swivel direction for the image + + //new version of setting the center point: + mitk::Image::Pointer image = static_cast(renderingHelper.GetDataStorage()->GetNode(mitk::NodePredicateDataType::New("Image"))->GetData()); + + //get the center point of the image + centerPoint = image->GetGeometry()->GetCenter(); + + //rotate the image arround its own center + renderingHelper.ReorientSlices(centerPoint, rotationVector); + + + //use this to generate a reference screenshot or save the file: + bool generateReferenceScreenshot = false; + if(generateReferenceScreenshot) + { + renderingHelper.Render(); + renderingHelper.SaveReferenceScreenShot("C:\\Users\\schroedt\\Pictures\\RenderingTestData\\Pic3dRefLinear.png"); + } + + //threshold for CompareRenderWindowAgainstReference + double threshold = 0.15;//difference between interpolation modes is very small + + //### Usage of CompareRenderWindowAgainstReference: See docu of mitkRrenderingTestHelper + MITK_TEST_CONDITION( renderingHelper.CompareRenderWindowAgainstReference(argc, argv, threshold) == true, "CompareRenderWindowAgainstReference test result positive?" ); + + + + + MITK_TEST_END(); +}