diff --git a/CMake/BuildConfigurations/PhenotypingRelease.cmake b/CMake/BuildConfigurations/PhenotypingRelease.cmake new file mode 100644 index 0000000000..15c1467ec2 --- /dev/null +++ b/CMake/BuildConfigurations/PhenotypingRelease.cmake @@ -0,0 +1,15 @@ +include(${CMAKE_CURRENT_LIST_DIR}/WorkbenchRelease.cmake) + +list(APPEND MITK_CONFIG_PACKAGES + Vigra +) + +list(APPEND MITK_CONFIG_PLUGINS + org.mitk.gui.qt.basicimageprocessing + org.mitk.gui.qt.radiomics +) + +if(NOT MITK_USE_SUPERBUILD) + set(BUILD_BasicImageProcessingMiniApps ON CACHE BOOL "" FORCE) + set(BUILD_ClassificationMiniApps ON CACHE BOOL "" FORCE) +endif() diff --git a/CMake/BuildConfigurations/WorkbenchRelease.cmake b/CMake/BuildConfigurations/WorkbenchRelease.cmake index e4b4da592b..694b4b9e35 100644 --- a/CMake/BuildConfigurations/WorkbenchRelease.cmake +++ b/CMake/BuildConfigurations/WorkbenchRelease.cmake @@ -1,24 +1,28 @@ include(${CMAKE_CURRENT_LIST_DIR}/Default.cmake) set(MITK_CONFIG_PACKAGES ${MITK_CONFIG_PACKAGES} MatchPoint ) set(MITK_CONFIG_PLUGINS ${MITK_CONFIG_PLUGINS} org.mitk.gui.qt.multilabelsegmentation org.mitk.matchpoint.core.helper org.mitk.gui.qt.matchpoint.algorithm.browser org.mitk.gui.qt.matchpoint.algorithm.control org.mitk.gui.qt.matchpoint.mapper org.mitk.gui.qt.matchpoint.framereg org.mitk.gui.qt.matchpoint.visualizer org.mitk.gui.qt.matchpoint.evaluator org.mitk.gui.qt.matchpoint.manipulator ) +if(NOT MITK_USE_SUPERBUILD) + set(BUILD_CoreCmdApps ON CACHE BOOL "" FORCE) +endif() + set(MITK_VTK_DEBUG_LEAKS OFF CACHE BOOL "Enable VTK Debug Leaks" FORCE) find_package(Doxygen REQUIRED) # Ensure that the in-application help can be build set(BLUEBERRY_QT_HELP_REQUIRED ON CACHE BOOL "Required Qt help documentation in plug-ins" FORCE) diff --git a/Modules/CoreCmdApps/CMakeLists.txt b/Modules/CoreCmdApps/CMakeLists.txt index 12d751c887..5841e7e289 100644 --- a/Modules/CoreCmdApps/CMakeLists.txt +++ b/Modules/CoreCmdApps/CMakeLists.txt @@ -1,7 +1,6 @@ option(BUILD_CoreCmdApps "Build command-line apps of the MitkCore module" OFF) if(BUILD_CoreCmdApps OR MITK_BUILD_ALL_APPS) mitkFunctionCreateCommandLineApp(NAME FileConverter) mitkFunctionCreateCommandLineApp(NAME ImageTypeConverter) - mitkFunctionCreateCommandLineApp(NAME RectifyImage) endif() diff --git a/Modules/CoreCmdApps/RectifyImage.cpp b/Modules/CoreCmdApps/RectifyImage.cpp deleted file mode 100644 index 664c13adb0..0000000000 --- a/Modules/CoreCmdApps/RectifyImage.cpp +++ /dev/null @@ -1,194 +0,0 @@ -/*=================================================================== - -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 -#include -#include -#include - -template -void RectifyImage(mitk::Image::Pointer inputImage, mitk::Image::Pointer outputImage) -{ - mitk::ImagePixelReadAccessor pixelReadAccess(inputImage); - mitk::ImagePixelWriteAccessor pixelWriteAccess(outputImage); - - const auto DEPTH = static_cast(outputImage->GetDimension(2)); - const auto HEIGHT = static_cast(outputImage->GetDimension(1)); - const auto WIDTH = static_cast(outputImage->GetDimension(0)); - - auto geometry = outputImage->GetGeometry(); - itk::Index<3> index; - mitk::Point3D worldCoords; - - for (index[2] = 0; index[2] < DEPTH; ++index[2]) - { - for (index[1] = 0; index[1] < HEIGHT; ++index[1]) - { - for (index[0] = 0; index[0] < WIDTH; ++index[0]) - { - geometry->IndexToWorld(index, worldCoords); - pixelWriteAccess.SetPixelByIndex(index, pixelReadAccess.GetPixelByWorldCoordinates(worldCoords)); - } - } - } -} - -int main(int argc, char* argv[]) -{ - mitkCommandLineParser parser; - - parser.setTitle("Rectify Image"); - parser.setCategory("Basic Image Processing"); - parser.setDescription("Resample image based on standard world to index transform"); - parser.setContributor("German Cancer Research Center (DKFZ)"); - - parser.setArgumentPrefix("--", "-"); - parser.addArgument("input", "i", mitkCommandLineParser::Image, "Input Image", "Path to input image", us::Any(), false); - parser.addArgument("output", "o", mitkCommandLineParser::Image, "Output Image", "Path to output image", us::Any(), false); - - auto parsedArgs = parser.parseArguments(argc, argv); - - if (2 != parsedArgs.size() || 0 == parsedArgs.count("input") || 0 == parsedArgs.count("output")) - return EXIT_FAILURE; - - auto inputImagePath = us::any_value_to_string(parsedArgs["input"]); - mitk::Image::Pointer inputImage; - - try - { - inputImage = dynamic_cast(mitk::IOUtil::Load(inputImagePath)[0].GetPointer()); - } - catch (const mitk::Exception&) - { - return EXIT_FAILURE; - } - - if (3 != inputImage->GetDimension()) - { - MITK_ERROR << "Only 3-d images are supported."; - return EXIT_FAILURE; - } - - auto inputGeometry = inputImage->GetGeometry(); - - mitk::Point3D minInputIndex; - mitk::FillVector3D(minInputIndex, 0.0, 0.0, 0.0); - - mitk::Point3D minInputIndexInWorld; - inputGeometry->IndexToWorld(minInputIndex, minInputIndexInWorld); - - mitk::Point3D maxInputIndex; - for (int i = 0; i < 3; ++i) - maxInputIndex[i] = inputGeometry->GetExtent(i) - 1; - - mitk::Point3D maxInputIndexInWorld; - inputGeometry->IndexToWorld(maxInputIndex, maxInputIndexInWorld); - - mitk::Point3D minOutputIndexInWorld; - for (int i = 0; i < 3; ++i) - minOutputIndexInWorld[i] = std::min(minInputIndexInWorld[i], maxInputIndexInWorld[i]); - - mitk::Point3D maxOutputIndexInWorld; - for (int i = 0; i < 3; ++i) - maxOutputIndexInWorld[i] = std::max(minInputIndexInWorld[i], maxInputIndexInWorld[i]); - - mitk::Vector3D spacing = inputGeometry->GetSpacing(); - auto transform = inputGeometry->GetIndexToWorldTransform()->Clone(); - auto matrix = transform->GetMatrix(); - - for (int i = 0; i < 3; ++i) - { - for (int j = 0; j < 3; ++j) - { - matrix[i][j] = std::abs(matrix[i][j]) / spacing[j]; - } - } - - transform->SetMatrix(matrix); - spacing = transform->TransformVector(spacing); - - mitk::Vector3D outputExtent = (maxOutputIndexInWorld - minOutputIndexInWorld + spacing); - for (int i = 0; i < 3; ++i) - outputExtent[i] /= spacing[i]; - - mitk::Point3D origin = minOutputIndexInWorld; - - mitk::Vector3D right; - mitk::FillVector3D(right, outputExtent[0], 0.0, 0.0); - - mitk::Vector3D down; - mitk::FillVector3D(down, 0.0, outputExtent[1], 0.0); - - auto planeGeometry = mitk::PlaneGeometry::New(); - planeGeometry->InitializeStandardPlane(right, down, &spacing); - planeGeometry->SetOrigin(origin); - planeGeometry->SetImageGeometry(true); - - auto slicedGeometry = mitk::SlicedGeometry3D::New(); - slicedGeometry->InitializeEvenlySpaced(planeGeometry, static_cast(outputExtent[2])); - - auto outputGeometry = mitk::ProportionalTimeGeometry::New(); - outputGeometry->SetTimeStepGeometry(slicedGeometry, 0); - - auto pixelType = inputImage->GetPixelType(); - - auto outputImage = mitk::Image::New(); - outputImage->Initialize(pixelType, *outputGeometry); - - try - { - switch (pixelType.GetComponentType()) - { - case itk::ImageIOBase::CHAR: - RectifyImage(inputImage, outputImage); - break; - - case itk::ImageIOBase::UCHAR: - RectifyImage(inputImage, outputImage); - break; - - case itk::ImageIOBase::SHORT: - RectifyImage(inputImage, outputImage); - break; - - case itk::ImageIOBase::USHORT: - RectifyImage(inputImage, outputImage); - break; - - default: - MITK_ERROR << "Pixel type is not supported."; - return EXIT_FAILURE; - } - } - catch (const mitk::Exception &e) - { - MITK_ERROR << e.GetDescription(); - return EXIT_FAILURE; - } - - auto outputImagePath = us::any_value_to_string(parsedArgs["output"]); - - try - { - mitk::IOUtil::Save(outputImage, outputImagePath); - } - catch (const mitk::Exception &) - { - return EXIT_FAILURE; - } - - return EXIT_SUCCESS; -}