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 <mitkCommandLineParser.h>
-#include <mitkImagePixelReadAccessor.h>
-#include <mitkImagePixelWriteAccessor.h>
-#include <mitkIOUtil.h>
-
-template <typename TPixelType>
-void RectifyImage(mitk::Image::Pointer inputImage, mitk::Image::Pointer outputImage)
-{
- mitk::ImagePixelReadAccessor<TPixelType, 3> pixelReadAccess(inputImage);
- mitk::ImagePixelWriteAccessor<TPixelType, 3> pixelWriteAccess(outputImage);
-
- const auto DEPTH = static_cast<itk::IndexValueType>(outputImage->GetDimension(2));
- const auto HEIGHT = static_cast<itk::IndexValueType>(outputImage->GetDimension(1));
- const auto WIDTH = static_cast<itk::IndexValueType>(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::Image*>(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<unsigned int>(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<char>(inputImage, outputImage);
- break;
-
- case itk::ImageIOBase::UCHAR:
- RectifyImage<unsigned char>(inputImage, outputImage);
- break;
-
- case itk::ImageIOBase::SHORT:
- RectifyImage<short>(inputImage, outputImage);
- break;
-
- case itk::ImageIOBase::USHORT:
- RectifyImage<unsigned short>(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;
-}