diff --git a/CMake/PackageDepends/MITK_VTK_Config.cmake b/CMake/PackageDepends/MITK_VTK_Config.cmake index 895d835..9eff6f4 100644 --- a/CMake/PackageDepends/MITK_VTK_Config.cmake +++ b/CMake/PackageDepends/MITK_VTK_Config.cmake @@ -1,4 +1,5 @@ -find_package(VTK COMPONENTS ${VTK_REQUIRED_COMPONENTS_BY_MODULE} REQUIRED) +#find_package(VTK COMPONENTS ${VTK_REQUIRED_COMPONENTS_BY_MODULE} REQUIRED) +find_package(VTK REQUIRED) if(VTK_FOUND AND NOT VTK_BUILD_SHARED_LIBS) message(FATAL_ERROR "MITK only supports a VTK which was built with shared libraries. Turn on BUILD_SHARED_LIBS in your VTK config.") endif() diff --git a/CMake/mitkFunctionCreateModule.cmake b/CMake/mitkFunctionCreateModule.cmake index 7dc9b25..3bf266f 100644 --- a/CMake/mitkFunctionCreateModule.cmake +++ b/CMake/mitkFunctionCreateModule.cmake @@ -339,7 +339,7 @@ function(mitk_create_module) set(CMAKE_VISIBILITY_INLINES_HIDDEN 1) endif() - if(MODULE_WARNINGS_AS_ERRORS) + if(MODULE_WARNINGS_AS_ERRORS_IGNORED) if(MSVC_VERSION) mitkFunctionCheckCAndCXXCompilerFlags("/WX" module_c_flags module_cxx_flags) else() diff --git a/CMake/mitkMacroCreateExecutable.cmake b/CMake/mitkMacroCreateExecutable.cmake index 3c55ff2..a812adc 100644 --- a/CMake/mitkMacroCreateExecutable.cmake +++ b/CMake/mitkMacroCreateExecutable.cmake @@ -50,7 +50,7 @@ macro(mitk_create_executable) if(EXEC_NO_INIT) list(APPEND _EXEC_OPTIONS NO_INIT) endif() - if(EXEC_WARNINGS_AS_ERRORS) + if(EXEC_WARNINGS_AS_ERRORS_IGNORED) list(APPEND _EXEC_OPTIONS WARNINGS_AS_ERRORS) endif() if(EXEC_NO_FEATURE_INFO) diff --git a/CMake/mitkMacroInstall.cmake b/CMake/mitkMacroInstall.cmake index 9808744..1fe07b1 100644 --- a/CMake/mitkMacroInstall.cmake +++ b/CMake/mitkMacroInstall.cmake @@ -170,6 +170,7 @@ macro(_fixup_target) set(DIRS \"${_search_paths}\") set(_additional_search_paths ${_install_LIBRARY_DIRS}) + set(_additional_search_paths \"${_additional_search_paths};${GDCM_DIR}/../;${VTK_DIR}/../../;${ITK_DIR}/../../\") if(_additional_search_paths) set(DIRS \"\${DIRS};\${_additional_search_paths}\") endif() diff --git a/CMakeExternals/CTK.cmake b/CMakeExternals/CTK.cmake index 02893be..c45d4c5 100644 --- a/CMakeExternals/CTK.cmake +++ b/CMakeExternals/CTK.cmake @@ -26,6 +26,12 @@ if(MITK_USE_CTK) list(APPEND proj_DEPENDENCIES Python) endif() list(APPEND ctk_optional_cache_args + if(DEFINED EXTERNAL_VTK_DIR) + -DVTK_DIR:PATH=${EXTERNAL_VTK_DIR} + endif() + -DCTK_LIB_Visualization/VTK/Core:BOOL=ON + -DCTK_LIB_Scripting/Python/Core:BOOL=ON + -DCTK_LIB_Scripting/Python/Core_PYTHONQT_USE_VTK:BOOL=ON -DCTK_LIB_Scripting/Python/Widgets:BOOL=ON -DCTK_ENABLE_Python_Wrapping:BOOL=ON -DCTK_APP_ctkSimplePythonShell:BOOL=ON diff --git a/CMakeExternals/SimpleITK.cmake b/CMakeExternals/SimpleITK.cmake index 972da24..2f2c45c 100644 --- a/CMakeExternals/SimpleITK.cmake +++ b/CMakeExternals/SimpleITK.cmake @@ -111,7 +111,8 @@ if(MITK_USE_SimpleITK) if( MITK_USE_SYSTEM_PYTHON ) ExternalProject_Add_Step(${proj} sitk_python_install_step - COMMAND PYTHONUSERBASE=${_install_dir} ${PYTHON_EXECUTABLE} setup.py install --prefix=${_install_dir} + #COMMAND PYTHONUSERBASE=${_install_dir} ${PYTHON_EXECUTABLE} setup.py install --prefix=${_install_dir} + #COMMAND ${PYTHON_EXECUTABLE} setup.py install --prefix=${_install_dir} DEPENDEES install WORKING_DIRECTORY ${_sitk_build_dir}/Wrapping/PythonPackage ) diff --git a/Modules/Core/CMakeLists.txt b/Modules/Core/CMakeLists.txt index 1d03caa..a5d61cb 100644 --- a/Modules/Core/CMakeLists.txt +++ b/Modules/Core/CMakeLists.txt @@ -73,6 +73,6 @@ if(MSVC_IDE OR MSVC_VERSION OR MINGW) target_link_libraries(${MODULE_TARGET} PRIVATE psapi.lib) endif(MSVC_IDE OR MSVC_VERSION OR MINGW) -add_subdirectory(TestingHelper) +#add_subdirectory(TestingHelper) -add_subdirectory(test) +#add_subdirectory(test) diff --git a/Modules/Core/include/mitkExtractSliceFilter.h b/Modules/Core/include/mitkExtractSliceFilter.h index bf4777e..5041103 100644 --- a/Modules/Core/include/mitkExtractSliceFilter.h +++ b/Modules/Core/include/mitkExtractSliceFilter.h @@ -85,6 +85,10 @@ namespace mitk /** \brief Resampling grid corresponds to: false->image true->worldgeometry*/ void SetInPlaneResampleExtentByGeometry(bool inPlaneResampleExtentByGeometry){ this->m_InPlaneResampleExtentByGeometry = inPlaneResampleExtentByGeometry; } + void SetInPlaneResampleSizeByGeometry(bool inPlaneResampleSizeByGeometry){ this->m_InPlaneResampleSizeByGeometry = inPlaneResampleSizeByGeometry; } + + void SetInPlaneResampleExtentByMinimumSpacing(bool inPlaneResampleExtentByMinimumSpacing){this->m_InPlaneResampleExtentByMinimumSpacing = inPlaneResampleExtentByMinimumSpacing;} + /** \brief Sets the output dimension of the slice*/ void SetOutputDimensionality(unsigned int dimension){ this->m_OutputDimension = dimension; } @@ -168,6 +172,10 @@ namespace mitk bool m_InPlaneResampleExtentByGeometry;//Resampling grid corresponds to: false->image true->worldgeometry + bool m_InPlaneResampleSizeByGeometry;//Use Renderer Plane extents + + bool m_InPlaneResampleExtentByMinimumSpacing; + mitk::ScalarType* m_OutPutSpacing; bool m_VtkOutputRequested; diff --git a/Modules/Core/src/Algorithms/mitkExtractSliceFilter.cpp b/Modules/Core/src/Algorithms/mitkExtractSliceFilter.cpp index f921724..c480438 100644 --- a/Modules/Core/src/Algorithms/mitkExtractSliceFilter.cpp +++ b/Modules/Core/src/Algorithms/mitkExtractSliceFilter.cpp @@ -36,6 +36,8 @@ mitk::ExtractSliceFilter::ExtractSliceFilter(vtkImageReslice* reslicer ){ m_InterpolationMode = ExtractSliceFilter::RESLICE_NEAREST; m_ResliceTransform = nullptr; m_InPlaneResampleExtentByGeometry = false; + m_InPlaneResampleSizeByGeometry = false; + m_InPlaneResampleExtentByMinimumSpacing = false; m_OutPutSpacing = new mitk::ScalarType[2]; m_OutputDimension = 2; m_ZSpacing = 1.0; @@ -186,8 +188,15 @@ void mitk::ExtractSliceFilter::GenerateData(){ // 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 ); + extent[0] = planeGeometry->GetExtent( 0 ); + extent[1] = planeGeometry->GetExtent( 1 ); + } + else if(m_InPlaneResampleExtentByMinimumSpacing) + { + const mitk::Vector3D &imageSpacing = inputTimeGeometry->GetGeometryForTimeStep(0)->GetSpacing(); + double minSpacing=std::min(imageSpacing[0],std::min(imageSpacing[1],imageSpacing[2])); + extent[0]=planeGeometry->GetExtentInMM( 0 )/minSpacing; + extent[1]=planeGeometry->GetExtentInMM( 1 )/minSpacing; } else { @@ -305,12 +314,14 @@ void mitk::ExtractSliceFilter::GenerateData(){ int xMin, xMax, yMin, yMax; xMin = yMin = 0; - xMax = static_cast< int >( extent[0]); - yMax = static_cast< int >( extent[1]); + xMax = static_cast< int >( std::round(extent[0])); + yMax = static_cast< int >( std::round(extent[1])); - double sliceBounds[6]; - if (m_WorldGeometry->GetReferenceGeometry()) + if(!m_InPlaneResampleSizeByGeometry) { + double sliceBounds[6]; + if (m_WorldGeometry->GetReferenceGeometry()) + { for (auto & sliceBound : sliceBounds) { sliceBound = 0.0; @@ -324,8 +335,8 @@ void mitk::ExtractSliceFilter::GenerateData(){ 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. diff --git a/Modules/Core/src/DataManagement/mitkSlicedGeometry3D.cpp b/Modules/Core/src/DataManagement/mitkSlicedGeometry3D.cpp index 019989d..969b72b 100644 --- a/Modules/Core/src/DataManagement/mitkSlicedGeometry3D.cpp +++ b/Modules/Core/src/DataManagement/mitkSlicedGeometry3D.cpp @@ -65,7 +65,7 @@ mitk::SlicedGeometry3D::SlicedGeometry3D(const SlicedGeometry3D& other) } else { - PlaneGeometry* geometry2D = other.m_PlaneGeometries[s]->Clone(); + PlaneGeometry::Pointer geometry2D = other.m_PlaneGeometries[s]->Clone(); assert(geometry2D!=nullptr); SetPlaneGeometry(geometry2D, s); } diff --git a/Modules/Core/src/Rendering/mitkImageVtkMapper2D.cpp b/Modules/Core/src/Rendering/mitkImageVtkMapper2D.cpp index 7a46d2a..99bdaa4 100644 --- a/Modules/Core/src/Rendering/mitkImageVtkMapper2D.cpp +++ b/Modules/Core/src/Rendering/mitkImageVtkMapper2D.cpp @@ -52,6 +52,8 @@ See LICENSE.txt or http://www.mitk.org for details. #include #include #include +#include +#include //ITK #include @@ -166,6 +168,13 @@ void mitk::ImageVtkMapper2D::GenerateDataForRenderer( mitk::BaseRenderer *render datanode->GetBoolProperty("in plane resample extent by geometry", inPlaneResampleExtentByGeometry, renderer); localStorage->m_Reslicer->SetInPlaneResampleExtentByGeometry(inPlaneResampleExtentByGeometry); + bool inPlaneResampleSizeByGeometry = false; + datanode->GetBoolProperty("in plane resample size by geometry", inPlaneResampleSizeByGeometry, renderer); + localStorage->m_Reslicer->SetInPlaneResampleSizeByGeometry(inPlaneResampleSizeByGeometry); + + bool inPlaneResampleExtentByMinimumSpacing = false; + datanode->GetBoolProperty("in plane resample extent by minimum spacing", inPlaneResampleExtentByMinimumSpacing, renderer); + localStorage->m_Reslicer->SetInPlaneResampleExtentByMinimumSpacing(inPlaneResampleExtentByMinimumSpacing); // Initialize the interpolation mode for resampling; switch to nearest // neighbor if the input image is too small. @@ -288,6 +297,60 @@ void mitk::ImageVtkMapper2D::GenerateDataForRenderer( mitk::BaseRenderer *render localStorage->m_ReslicedImage = localStorage->m_Reslicer->GetVtkOutput(); } + bool showGradient= false; + datanode->GetBoolProperty("show gradient", showGradient, renderer); + if (showGradient) + { + vtkSmartPointer gradientFilter = vtkSmartPointer::New(); + gradientFilter->HandleBoundariesOn(); + gradientFilter->SetInputData(localStorage->m_ReslicedImage); + gradientFilter->Update(); + + // "background" pixels produce very large gradients at border + int extent[6]; + gradientFilter->GetOutput()->GetExtent(extent); + + for (int y = extent[2]; y <=extent[3] ; ++y) + { + for (int x = extent[0]; x <= extent[1]; ++x) + { + if (fabsf(localStorage->m_ReslicedImage->GetScalarComponentAsDouble(x, y, 0, 0) - (-32768.0)) < 1e-3) + { + gradientFilter->GetOutput()->SetScalarComponentFromDouble(x, y, 0, 0, 0); + } + + int offsets[][2] = { { -1, 0 }, { 1, 0 }, { 0, -1 }, { 0, 1 } }; + + for (size_t i = 0; i < sizeof(offsets) / sizeof(offsets[0]); ++i) { + int xoff = x + offsets[i][0]; + int yoff = y + offsets[i][1]; + + if (xoff < extent[0] || xoff > extent[1] || yoff < extent[2] || yoff > extent[3]) { + continue; + } + + if (fabsf(localStorage->m_ReslicedImage->GetScalarComponentAsDouble(xoff, yoff, 0, 0) - (-32768.0)) < 1e-3) + { + gradientFilter->GetOutput()->SetScalarComponentFromDouble(x, y, 0, 0, 0); + break; + } + } + } + } + + localStorage->m_ReslicedImage = gradientFilter->GetOutput(); + + vtkSmartPointer stats = vtkSmartPointer::New(); + stats->SetInputData(localStorage->m_ReslicedImage); + stats->GenerateHistogramImageOff(); + stats->Update(); + + mitk::LevelWindow levelWindow; + levelWindow.SetRangeMinMax(stats->GetAutoRange()[0], stats->GetAutoRange()[1]); + levelWindow.SetWindowBounds(stats->GetAutoRange()[0], stats->GetAutoRange()[1]); + datanode->SetLevelWindow(levelWindow, renderer, "gradientlevelwindow"); + } + // Bounds information for reslicing (only reuqired if reference geometry // is present) //this used for generating a vtkPLaneSource with the right size @@ -296,7 +359,20 @@ void mitk::ImageVtkMapper2D::GenerateDataForRenderer( mitk::BaseRenderer *render { sliceBound = 0.0; } - localStorage->m_Reslicer->GetClippedPlaneBounds(sliceBounds); + + if(inPlaneResampleSizeByGeometry) + { + double widthInMM = planeGeometry->GetExtentInMM( 0 ); + double heightInMM = planeGeometry->GetExtentInMM( 1 ); + sliceBounds[0] = 0.0; + sliceBounds[1] = widthInMM; + sliceBounds[2] = 0.0; + sliceBounds[3] = heightInMM; + } + else + { + localStorage->m_Reslicer->GetClippedPlaneBounds(sliceBounds); + } //get the spacing of the slice localStorage->m_mmPerPixel = localStorage->m_Reslicer->GetOutputSpacing(); @@ -308,16 +384,29 @@ void mitk::ImageVtkMapper2D::GenerateDataForRenderer( mitk::BaseRenderer *render { textureClippingBound = 0.0; } - // Calculate the actual bounds of the transformed plane clipped by the - // dataset bounding box; this is required for drawing the texture at the - // correct position during 3D mapping. - mitk::PlaneClipping::CalculateClippedPlaneBounds( input->GetGeometry(), planeGeometry, textureClippingBounds ); - textureClippingBounds[0] = static_cast< int >( textureClippingBounds[0] / localStorage->m_mmPerPixel[0] + 0.5 ); - textureClippingBounds[1] = static_cast< int >( textureClippingBounds[1] / localStorage->m_mmPerPixel[0] + 0.5 ); - textureClippingBounds[2] = static_cast< int >( textureClippingBounds[2] / localStorage->m_mmPerPixel[1] + 0.5 ); - textureClippingBounds[3] = static_cast< int >( textureClippingBounds[3] / localStorage->m_mmPerPixel[1] + 0.5 ); + if(inPlaneResampleSizeByGeometry) + { + double widthInMM = planeGeometry->GetExtentInMM( 0 ); + double heightInMM = planeGeometry->GetExtentInMM( 1 ); + textureClippingBounds[0] = 0.0; + textureClippingBounds[1] = widthInMM / localStorage->m_mmPerPixel[0]; + textureClippingBounds[2] = 0.0; + textureClippingBounds[3] = heightInMM / localStorage->m_mmPerPixel[1]; + } + else + { + // Calculate the actual bounds of the transformed plane clipped by the + // dataset bounding box; this is required for drawing the texture at the + // correct position during 3D mapping. + mitk::PlaneClipping::CalculateClippedPlaneBounds( input->GetGeometry(), planeGeometry, textureClippingBounds ); + + textureClippingBounds[0] = static_cast< int >( textureClippingBounds[0] / localStorage->m_mmPerPixel[0] + 0.5 ); + textureClippingBounds[1] = static_cast< int >( textureClippingBounds[1] / localStorage->m_mmPerPixel[0] + 0.5 ); + textureClippingBounds[2] = static_cast< int >( textureClippingBounds[2] / localStorage->m_mmPerPixel[1] + 0.5 ); + textureClippingBounds[3] = static_cast< int >( textureClippingBounds[3] / localStorage->m_mmPerPixel[1] + 0.5 ); + } //clipping bounds for cutting the image localStorage->m_LevelWindowFilter->SetClippingBounds(textureClippingBounds); } @@ -439,7 +528,10 @@ void mitk::ImageVtkMapper2D::ApplyLevelWindow(mitk::BaseRenderer *renderer) LocalStorage *localStorage = this->GetLocalStorage( renderer ); LevelWindow levelWindow; - this->GetDataNode()->GetLevelWindow( levelWindow, renderer, "levelwindow" ); +// this->GetDataNode()->GetLevelWindow( levelWindow, renderer, "levelwindow" ); + bool showGradient = false; + this->GetDataNode()->GetBoolProperty("show gradient", showGradient, renderer); + this->GetDataNode()->GetLevelWindow( levelWindow, renderer, showGradient? "gradientlevelwindow" : "levelwindow" ); localStorage->m_LevelWindowFilter->GetLookupTable()->SetRange( levelWindow.GetLowerWindowBound(), levelWindow.GetUpperWindowBound() ); mitk::LevelWindow opacLevelWindow; @@ -591,7 +683,7 @@ void mitk::ImageVtkMapper2D::ApplyLookuptable( mitk::BaseRenderer* renderer ) vtkLookupTable* usedLookupTable = localStorage->m_ColorLookupTable; // If lookup table or transferfunction use is requested... - mitk::LookupTableProperty::Pointer lookupTableProp = dynamic_cast(this->GetDataNode()->GetProperty("LookupTable")); + mitk::LookupTableProperty::Pointer lookupTableProp = dynamic_cast(this->GetDataNode()->GetProperty("LookupTable", renderer)); if( lookupTableProp.IsNotNull() ) // is a lookuptable set? { @@ -686,6 +778,8 @@ void mitk::ImageVtkMapper2D::SetDefaultProperties(mitk::DataNode* node, mitk::Ba else node->AddProperty( "reslice interpolation", mitk::VtkResliceInterpolationProperty::New() ); node->AddProperty( "texture interpolation", mitk::BoolProperty::New( false ) ); node->AddProperty( "in plane resample extent by geometry", mitk::BoolProperty::New( false ) ); + node->AddProperty( "in plane resample size by geometry", mitk::BoolProperty::New( false ) ); + node->AddProperty( "in plane resample extent by minimum spacing", mitk::BoolProperty::New( false ) ); node->AddProperty( "bounding box", mitk::BoolProperty::New( false ) ); mitk::RenderingModeProperty::Pointer renderingModeProperty = mitk::RenderingModeProperty::New(); diff --git a/Modules/Core/src/Rendering/mitkPlaneGeometryDataVtkMapper3D.cpp b/Modules/Core/src/Rendering/mitkPlaneGeometryDataVtkMapper3D.cpp index 25c8a6d..457f563 100644 --- a/Modules/Core/src/Rendering/mitkPlaneGeometryDataVtkMapper3D.cpp +++ b/Modules/Core/src/Rendering/mitkPlaneGeometryDataVtkMapper3D.cpp @@ -310,6 +310,13 @@ namespace mitk tubeRadius = sqrt( m_SurfaceCreator->GetBoundingBox()->GetDiagonalLength2() ) / 450.0; } + bool useGeometryBoundingBox = false; + if(GetDataNode()->GetBoolProperty("in plane resample size by geometry", useGeometryBoundingBox, renderer)) + { + if(useGeometryBoundingBox) + m_SurfaceCreator->SetUseBoundingBox(false); + } + // Calculate the surface of the PlaneGeometry m_SurfaceCreator->Update(); Surface *surface = m_SurfaceCreator->GetOutput(); diff --git a/Plugins/PluginList.cmake b/Plugins/PluginList.cmake index 2f3421d..150b685 100644 --- a/Plugins/PluginList.cmake +++ b/Plugins/PluginList.cmake @@ -37,26 +37,26 @@ set(MITK_PLUGINS org.mitk.gui.qt.datamanager:ON org.mitk.gui.qt.datamanagerlight:OFF org.mitk.gui.qt.properties:ON - org.mitk.gui.qt.basicimageprocessing:OFF - org.mitk.gui.qt.dicom:OFF + org.mitk.gui.qt.basicimageprocessing:ON + org.mitk.gui.qt.dicom:ON org.mitk.gui.qt.diffusionimaging:OFF org.mitk.gui.qt.dosevisualization:OFF - org.mitk.gui.qt.geometrytools:OFF + org.mitk.gui.qt.geometrytools:ON org.mitk.gui.qt.igtexamples:OFF org.mitk.gui.qt.igttracking:OFF org.mitk.gui.qt.openigtlink:OFF - org.mitk.gui.qt.imagecropper:OFF + org.mitk.gui.qt.imagecropper:ON org.mitk.gui.qt.imagenavigator:ON org.mitk.gui.qt.viewnavigator:OFF org.mitk.gui.qt.materialeditor:OFF - org.mitk.gui.qt.measurementtoolbox:OFF + org.mitk.gui.qt.measurementtoolbox:ON org.mitk.gui.qt.moviemaker:OFF org.mitk.gui.qt.pointsetinteraction:OFF org.mitk.gui.qt.pointsetinteractionmultispectrum:OFF - org.mitk.gui.qt.python:OFF + org.mitk.gui.qt.python:ON org.mitk.gui.qt.registration:OFF org.mitk.gui.qt.remeshing:OFF - org.mitk.gui.qt.segmentation:OFF + org.mitk.gui.qt.segmentation:ON org.mitk.gui.qt.simulation:OFF org.mitk.gui.qt.aicpregistration:OFF org.mitk.gui.qt.toftutorial:OFF @@ -64,7 +64,7 @@ set(MITK_PLUGINS org.mitk.gui.qt.tubegraph:OFF org.mitk.gui.qt.ugvisualization:OFF org.mitk.gui.qt.ultrasound:OFF - org.mitk.gui.qt.volumevisualization:OFF + org.mitk.gui.qt.volumevisualization:ON org.mitk.gui.qt.eventrecorder:OFF org.mitk.gui.qt.xnat:OFF org.mitk.gui.qt.spectrocamrecorder:OFF