diff --git a/CMake/PackageDepends/MITK_Boost_Config.cmake b/CMake/PackageDepends/MITK_Boost_Config.cmake index 1f2eb572f2..0414b37a77 100644 --- a/CMake/PackageDepends/MITK_Boost_Config.cmake +++ b/CMake/PackageDepends/MITK_Boost_Config.cmake @@ -1,29 +1,29 @@ if(MITK_USE_Boost) if(NOT MITK_USE_SYSTEM_Boost) set(Boost_NO_SYSTEM_PATHS 1) endif() set(Boost_USE_MULTITHREADED 1) set(Boost_USE_STATIC_LIBS 0) set(Boost_USE_STATIC_RUNTIME 0) if(MITK_USE_Boost_LIBRARIES) if(NOT MITK_USE_SYSTEM_Boost) set(BOOST_INCLUDEDIR ${CMAKE_BINARY_DIR}/../Boost-install/include) set(BOOST_LIBRARYDIR ${CMAKE_BINARY_DIR}/../Boost-install/lib) - set(Boost_ADDITIONAL_VERSIONS 1.55) + set(Boost_ADDITIONAL_VERSIONS 1.56) endif() - find_package(Boost 1.55.0 REQUIRED COMPONENTS ${MITK_USE_Boost_LIBRARIES} QUIET) + find_package(Boost 1.56.0 REQUIRED COMPONENTS ${MITK_USE_Boost_LIBRARIES} QUIET) else() - find_package(Boost 1.55.0 REQUIRED QUIET) + find_package(Boost 1.56.0 REQUIRED QUIET) endif() list(APPEND ALL_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIRS}) if(Boost_LIBRARIES) list(APPEND ALL_LIBRARIES ${Boost_LIBRARIES}) link_directories(${Boost_LIBRARY_DIRS}) endif() endif(MITK_USE_Boost) diff --git a/CMakeExternals/Boost.cmake b/CMakeExternals/Boost.cmake index 472d69ca3d..6b609f1d7d 100644 --- a/CMakeExternals/Boost.cmake +++ b/CMakeExternals/Boost.cmake @@ -1,109 +1,109 @@ #----------------------------------------------------------------------------- # Boost #----------------------------------------------------------------------------- if(MITK_USE_Boost) # Sanity checks if(DEFINED BOOST_ROOT AND NOT EXISTS ${BOOST_ROOT}) message(FATAL_ERROR "BOOST_ROOT variable is defined but corresponds to non-existing directory") endif() string(REPLACE "^^" ";" MITK_USE_Boost_LIBRARIES "${MITK_USE_Boost_LIBRARIES}") set(proj Boost) set(proj_DEPENDENCIES ) set(Boost_DEPENDS ${proj}) if(NOT DEFINED BOOST_ROOT AND NOT MITK_USE_SYSTEM_Boost) set(_boost_libs ) set(INSTALL_COMMAND "") if(MITK_USE_Boost_LIBRARIES) # Set the boost root to the libraries install directory set(BOOST_ROOT "${CMAKE_CURRENT_BINARY_DIR}/${proj}-install") # We need binary boost libraries foreach(_boost_lib ${MITK_USE_Boost_LIBRARIES}) set(_boost_libs ${_boost_libs} --with-${_boost_lib}) endforeach() if(WIN32) set(_boost_variant "") set(_shell_extension .bat) if(CMAKE_SIZEOF_VOID_P EQUAL 8) set(_boost_address_model "address-model=64") else() set(_boost_address_model "address-model=32") endif() if(MSVC) if(MSVC_VERSION EQUAL 1400) set(_boost_toolset "toolset=msvc-8.0") elseif(MSVC_VERSION EQUAL 1500) set(_boost_toolset "toolset=msvc-9.0") elseif(MSVC_VERSION EQUAL 1600) set(_boost_toolset "toolset=msvc-10.0") elseif(MSVC_VERSION EQUAL 1700) set(_boost_toolset "toolset=msvc-11.0") endif() endif() else() if(CMAKE_BUILD_TYPE STREQUAL "Debug") set(_boost_variant "variant=debug") else() set(_boost_variant "variant=release") endif() set(_shell_extension .sh) endif() if(APPLE) set(APPLE_CMAKE_SCRIPT ${CMAKE_CURRENT_BINARY_DIR}/${proj}-cmake/ChangeBoostLibsInstallNameForMac.cmake) configure_file(${CMAKE_CURRENT_SOURCE_DIR}/CMakeExternals/ChangeBoostLibsInstallNameForMac.cmake.in ${APPLE_CMAKE_SCRIPT} @ONLY) set(INSTALL_COMMAND ${CMAKE_COMMAND} -P ${APPLE_CMAKE_SCRIPT}) # Set OSX_SYSROOT set (APPLE_SYSROOT_FLAG) if (NOT ${CMAKE_OSX_SYSROOT} STREQUAL "") set (APPLE_SYSROOT_FLAG --sysroot=${CMAKE_OSX_SYSROOT}) endif() # Set the boost build command for apple set(_boost_build_cmd ${CMAKE_CURRENT_BINARY_DIR}/${proj}-src/bjam ${APPLE_SYSROOT_FLAG} --builddir=${CMAKE_CURRENT_BINARY_DIR}/${proj}-build --prefix=${CMAKE_CURRENT_BINARY_DIR}/${proj}-install ${_boost_toolset} ${_boost_address_model} ${_boost_variant} ${_boost_libs} link=shared,static threading=multi runtime-link=shared -q install) else() set(_boost_build_cmd ${CMAKE_CURRENT_BINARY_DIR}/${proj}-src/bjam --build-dir=${CMAKE_CURRENT_BINARY_DIR}/${proj}-build --prefix=${CMAKE_CURRENT_BINARY_DIR}/${proj}-install ${_boost_toolset} ${_boost_address_model} ${_boost_variant} ${_boost_libs} link=shared,static threading=multi runtime-link=shared -q install) endif() set(_boost_cfg_cmd ${CMAKE_CURRENT_BINARY_DIR}/${proj}-src/bootstrap${_shell_extension}) else() # If no libraries are specified set the boost root to the boost src directory set(BOOST_ROOT "${CMAKE_CURRENT_BINARY_DIR}/${proj}-src") set(_boost_cfg_cmd ) set(_boost_build_cmd ) endif() ExternalProject_Add(${proj} SOURCE_DIR ${CMAKE_BINARY_DIR}/${proj}-src # Boost needs in-source builds BINARY_DIR ${proj}-src PREFIX ${proj}-cmake - URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/boost_1_55_0.tar.bz2 - URL_MD5 d6eef4b4cacb2183f2bf265a5a03a354 + URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/boost_1_56_0.tar.bz2 + URL_MD5 a744cf167b05d72335f27c88115f211d INSTALL_DIR ${proj}-install CONFIGURE_COMMAND "${_boost_cfg_cmd}" BUILD_COMMAND "${_boost_build_cmd}" INSTALL_COMMAND "${INSTALL_COMMAND}" DEPENDS ${proj_DEPENDENCIES} ) else() mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") endif() endif() diff --git a/CMakeExternals/SOFA.cmake b/CMakeExternals/SOFA.cmake index ea2caaa3ca..78974ecf1a 100644 --- a/CMakeExternals/SOFA.cmake +++ b/CMakeExternals/SOFA.cmake @@ -1,100 +1,100 @@ #----------------------------------------------------------------------------- # SOFA #----------------------------------------------------------------------------- if(MITK_USE_SOFA) # Sanity checks if(DEFINED SOFA_DIR AND NOT EXISTS ${SOFA_DIR}) message(FATAL_ERROR "SOFA_DIR variable is defined but corresponds to non-existing directory") endif() set(proj SOFA) set(proj_DEPENDENCIES Boost GLEW) set(SOFA_DEPENDS ${proj}) set(preconfigure_cmake_args -DGLEW_DIR:PATH=${GLEW_DIR} -DSOFA-APPLICATION_MODELER:BOOL=OFF -DSOFA-APPLICATION_RUNSOFA:BOOL=OFF -DSOFA-APPLICATION_SOFABATCH:BOOL=OFF -DSOFA-EXTERNAL_BOOST:BOOL=ON -DSOFA-EXTERNAL_BOOST_PATH:PATH=${CMAKE_BINARY_DIR}/Boost-install/lib -DSOFA-EXTERNAL_CSPARSE:BOOL=ON -DSOFA-EXTERNAL_GLEW:BOOL=ON -DSOFA-EXTERNAL_PNG:BOOL=OFF -DSOFA-EXTERNAL_ZLIB:BOOL=OFF -DSOFA-LIB_COMPONENT_SPARSE_SOLVER:BOOL=ON -DSOFA-LIB_GUI_GLUT:BOOL=OFF -DSOFA-LIB_GUI_QT:BOOL=OFF -DSOFA-LIB_GUI_QTVIEWER:BOOL=OFF -DSOFA-TUTORIAL_CHAIN_HYBRID:BOOL=OFF -DSOFA-TUTORIAL_COMPOSITE_OBJECT:BOOL=OFF -DSOFA-TUTORIAL_MIXED_PENDULUM:BOOL=OFF -DSOFA-TUTORIAL_ONE_PARTICLE:BOOL=OFF -DSOFA-TUTORIAL_ONE_TETRAHEDRON:BOOL=OFF ) if(NOT APPLE) list(APPEND proj_DEPENDENCIES GLUT) list(APPEND preconfigure_cmake_args -DSOFA-EXTERNAL_FREEGLUT:BOOL=ON -DGLUT_DIR:PATH=${GLUT_DIR} ) endif() if(NOT MITK_USE_SYSTEM_Boost) list(APPEND preconfigure_cmake_args -DBoost_NO_SYSTEM_PATHS:BOOL=ON -DBOOST_INCLUDEDIR:PATH=${CMAKE_BINARY_DIR}/Boost-install/include -DBOOST_LIBRARYDIR:PATH=${CMAKE_BINARY_DIR}/Boost-install/lib - -DBoost_ADDITIONAL_VERSIONS:STRING=1.55 + -DBoost_ADDITIONAL_VERSIONS:STRING=1.56 ) endif() if(MITK_USE_SOFA_PLUGINS_DIR) list(APPEND preconfigure_cmake_args -DSOFA_APPLICATIONS_PLUGINS_DIR:PATH=${MITK_USE_SOFA_PLUGINS_DIR} ) foreach(plugin ${MITK_USE_SOFA_PLUGINS}) string(TOUPPER ${plugin} plugin) list(APPEND preconfigure_cmake_args -DSOFA-PLUGIN_${plugin}:BOOL=ON ) endforeach() endif() set(rev "10669") set(SOFA_PATCH_COMMAND ${CMAKE_COMMAND} -DTEMPLATE_FILE:FILEPATH=${MITK_SOURCE_DIR}/CMakeExternals/EmptyFileForPatching.dummy -P ${MITK_SOURCE_DIR}/CMakeExternals/PatchSOFA-rev${rev}.cmake) set(SOFA_PRECONFIGURE_COMMAND ${CMAKE_COMMAND} -G${gen} ${ep_common_args} ${preconfigure_cmake_args} ${boost_cmake_args} ${CMAKE_BINARY_DIR}/${proj}-src) if(NOT DEFINED SOFA_DIR) ExternalProject_Add(${proj} SOURCE_DIR ${CMAKE_BINARY_DIR}/${proj}-src BINARY_DIR ${proj}-build PREFIX ${proj}-cmake URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/SOFA-rev${rev}.tar.gz URL_MD5 d01a194f54b933f4cdfdfc75b2f81a2f PATCH_COMMAND ${SOFA_PATCH_COMMAND} INSTALL_COMMAND "" CMAKE_GENERATOR ${gen} CMAKE_ARGS ${ep_common_args} DEPENDS ${proj_DEPENDENCIES} ) ExternalProject_Add_Step(${proj} preconfigure COMMAND ${SOFA_PRECONFIGURE_COMMAND} WORKING_DIRECTORY ${proj}-build DEPENDEES patch DEPENDERS configure LOG 1 ) set(SOFA_DIR ${CMAKE_CURRENT_BINARY_DIR}/${proj}-build) else() mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") endif() endif() diff --git a/Documentation/Doxygen/DeveloperManual/Starting/SettingUpMITK/BuildInstructions.dox b/Documentation/Doxygen/DeveloperManual/Starting/SettingUpMITK/BuildInstructions.dox index 67fa18d753..dab91b2be2 100644 --- a/Documentation/Doxygen/DeveloperManual/Starting/SettingUpMITK/BuildInstructions.dox +++ b/Documentation/Doxygen/DeveloperManual/Starting/SettingUpMITK/BuildInstructions.dox @@ -1,204 +1,204 @@ /** \page BuildInstructionsPage Build Instructions \tableofcontents \section BuildInstructions_Introduction Introduction The MITK build system (which is based on CMake) supports a "superbuild" process, meaning that it will download, configure, and build all required third-party libraries (except Qt) automatically. These instructions will show you how to use the MITK superbuild. \note This page explains explicitly how to build MITK itself. If you want to create your own project based on MITK, the process described below is completely automated. Please see \ref HowToNewProject. For more advanced users, the last sections explain how to inject custom build libraries into the superbuild process. \section BuildInstructions_Prerequisites Prerequisites You need: -# Git from http://git-scm.com (there are also numerous third-party graphical clients available). We recomment using Git, but see below for a way how to get the current source code without using it. -# CMake (version \minimumCMakeVersion or higher) -# Qt 4.x if you plan to develop Qt-based applications (version \minimumQt4Version or above is required, Qt 5.x is only supported experimentally for a very limited number of modules) -# If you are using Mac OS X you need an Xcode installation as this provides the neccessary compilers and SDKs \section BuildInstructions_Qt A note about Qt Nokia provides several binary packages for Qt. You must make sure that the package you download matches your toolchain. On Linux, getting Qt by installing the packages provided by your Linux package manager is the preferred way. On Windows, the Nokia provided binaries are compiled for 32bit architectures. You cannot build your own project for a 64bit machine and use the 32bit Qt libraries. You have two options for a 64bit Qt-based application: -# Download an inofficial 64bit installer, for example here. Note that we cannot offer support for problems with MITK due to the usage of this kind of installers. -# Compile Qt yourself. This is shortly described below. To compile Qt on Windows using Visual Studio, follow the steps below: -# Download the Qt sources and unpack them, e.g. to C:/qt-everywhere-opensource-src-4.7.4 -# Open a Visual Studio command prompt. Make sure to use the appropriate command prompt for either a 32 bit or 64 bit build. Note that Visual Studio Express does not come with 64bit compilers out of the box (the Professional version does). -# Configure Qt by executing the configure.exe command in your Qt source directory. The following configure options will build a Qt compatible with MITK: \verbatim configure.exe -prefix C:\Qt\4.7.4_vc9_x64 -debug-and-release -qt-sql-sqlite -no-multimedia -no-audio-backend -no-phonon -no-phonon-backend -no-declarative -mp -nomake examples -nomake demos -nomake docs \endverbatim -# Build and install the Qt libraries \verbatim nmake nmake install \endverbatim After "nmake install" completed successfully, you may delete your Qt source directory. \section BuildInstructions_Get_Source Get a source tree Since MITK is under active development we recommend to use git to check out the latest stable release from the homepage. If you decide to use the most current nightly release, make sure to get a stable tree: Check the MITK dashboard before checking out. If the build tree is not clean, you can specify an older revision for the checkout or get a stable tar ball from www.mitk.org. If you don't want to use Git, you may also download the current source code (or any other older version) as a tar.gz package by clicking on the snapshot link. You can then skip the clone step below. To clone MITK's current git repository do: \code git clone http://git.mitk.org/MITK.git \endcode \section BuildInstructions_Build_With_CMake Build MITK with CMake Create a new directory for the superbuild binary tree, change to it and call CMake: In the shell (assuming you current directory is the same as the one where you issued the git clone command): \code mkdir MITK-superbuild cd MITK-superbuild ccmake ../MITK \endcode If you use Windows, then you just start the CMake GUI and enter the location of the source and of the binary tree, choose a suitable generator and configure the project. If you use Mac OS X you will have to tweak the CMake configuration: - First of all you have to check the selected compilers, i.e.: - CMAKE_CXX_COMPILER - CMAKE_C_COMPILER - both should be either apple's clang or apple's gcc compiler - Next you have to assure hat CMAKE_OSX_SYSROOT points to the correct SDK location: - This is either /Developer/SDKs/Developer/SDKs/MacOSX10.7.sdk or if you have installed Xcode 4.3+ it is located in /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/ CMake will present you a couple of options, these are the most important ones: - MITK_USE_ACVD Build MITK code which depends on ACVD (this will download and build ACVD) - MITK_USE_BLUEBERRY Build the BlueBerry application framework - - MITK_USE_Boost Build MITK code which depends on Boost (this will download Boost 1.55) + - MITK_USE_Boost Build MITK code which depends on Boost (this will download Boost 1.56) - MITK_USE_Boost_LIBRARIES If you need binary Boost libraries, specify them here. - MITK_USE_OpenCV Build MITK code which depends on OpenCV (this will download and build OpenCV 2.4) - MITK_USE_Python Enables Python wrapping in MITK. This will also configure ITK, VTK, and OpenCV (if enabled) to build Python wrappers. - MITK_USE_QT Build MITK code which depends on Qt - MITK_USE_SOFA Build MITK code which depends on SOFA (this will download and build SOFA) - QT_QMAKE_EXECUTABLE The path to the qmake executable of your Qt installation If you are satisfied with the configuration of your MITK superbuild, generate the project files with CMake by pressing "Generate". Linux and Mac OS X users usually just enter "make" (optionally supplying the number threads to be used for a parallel build): \code make -j4 \endcode \note On Mac OS X: If you follow these steps CMake will produce Makefiles and therefore you cannot use Xcode but you have to use e.g. the QtCreator for programming. At the moment developing MITK with Xcode is not supported and using Xcode the superbuild doesn't complete without errors. Windows users using Visual Studio can open the generated MITK-superbuild.sln solution file in the MITK-superbuild directory and start the build by building the BUILD_ALL project. \section BuildInstructions_Customize Customize your MITK superbuild The MITK superbuild configured MITK with all needed external libraries. The build directories of these libraries, and of MITK itself are located inside the MITK-superbuild directory. For example, the directory layout may look like: \code MITK-superbuild |- ITK-build |- VTK-build |- MITK-build \endcode To change the configuration of the MITK build, choose the MITK-build directory as the binary directory in the CMake GUI. After generating the project files, build the MITK project by either issuing "make" in the MITK-build directory (Linux), or by opening MITK-build/MITK.sln and building the project with Visual Studio. You may also change the configuration of any project configured via the superbuild process. Make sure to also build the changed project and also the projects which depend on it. \section BuildInstructions_Running Running Applications On Linux, just execute the application you want to run. MITK executables are located in MITK-superbuild/MITK-build/bin On Windows, the PATH environment variable must contain the directories containging third-party libraries. The MITK build system generated Windows Batch files in the MITK-build directory which set up a correct environment and opens the appropriate Visual Studio solution file. Use (and maybe modify/enhance) these Batch files to be able to start and debug MITK applications from inside Visual Studio. \section BuildInstructions_Documentation Documentation If you have the Doxygen documentation tool installed, you get a new project (Visual Studio) or "make" target named "doc". You can build this to generate the HTML documentation of MITK in the Documentation/Doxygen directory of your MITK-build binary tree or in the MITK_DOXYGEN_OUTPUT_DIR CMake variable (if specified). \section BuildInstructions_Extending Extend MITK on your own (using the application framework BlueBerry) Please see \ref NewPluginPage \section BuildInstructions_As_Toolkit Use MITK in your own project (as a toolkit) To use MITK in your external project, add the CMake command find_package(MITK REQUIRED) to your CMakeLists.txt and make use of the CMake macros MITK_CHECK_MODULE(result_var ) and MITK_USE_MODULE() provided by MITK. Here is an example CMakeLists.txt (from the Examples/QtAppExample/ directory) which allows you to create a Qt based application using MITK to display an image. \include QtAppExample/CMakeLists.txt \section BuildInstructions_Advanced_Customization Superbuild Customization You can inject pre-build third-party libraries into the MITK superbuild by setting certain CMake variables before the first configure step. MITK will then use these third-party libraries instead of downloading and building them itself. Note you must take care to configure those libraries with all options MITK requires. The variables listed below are provided for injecting third-party libraries. Their occurrence in the CMake GUI or in ccmake may depend on specific MITK_USE_* options set to ON. You may also use the variable names below without the EXTERNAL_ prefix, for example when providing their values on a command line call to CMake. - EXTERNAL_BOOST_ROOT Set this variable to your custom Boost installation - EXTERNAL_CTK_DIR Set this variable to your CTK binary tree (the directory containing the CTKConfig.cmake file) - EXTERNAL_CableSwig_DIR Set this variable to your CableSwig binary tree for Python wrapping (the directory containing the CableSwigConfig.cmake file) - EXTERNAL_DCMTK_DIR Set this variable to your DCMTK binary tree (the directory containing the DCMTKConfig.cmake file) - EXTERNAL_GDCM_DIR Set this variable to your GDCM binary tree (the directory containing the GDCMConfig.cmake file) - EXTERNAL_ITK_DIR Set this variable to your ITK binary tree (the directory containing the ITKConfig.cmake file) - EXTERNAL_OpenCV_DIR Set this variable to your OpenCV binary tree (the directory containing the OpenCVConfig.cmake file) - EXTERNAL_SOFA_DIR Set this variable to your SOFA binary tree (the directory containing the SOFAConfig.cmake file) - EXTERNAL_VTK_DIR Set this variable to your VTK binary tree (the directory containing the VTKConfig.cmake file) To set CMake options before the first configure step is invoked, supply them on the command line, i.e. \code ccmake -DITK_DIR:PATH=/opt/ITK-release ../MITK \endcode See the following link for more information about how to configure third-party libraries: \subpage BuildToolkits "How to build ITK, VTK and QT" */ diff --git a/Modules/DiffusionImaging/DiffusionCore/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCore/CMakeLists.txt index bd38665a82..c6bbc6b951 100644 --- a/Modules/DiffusionImaging/DiffusionCore/CMakeLists.txt +++ b/Modules/DiffusionImaging/DiffusionCore/CMakeLists.txt @@ -1,11 +1,15 @@ +# With apple gcc 4.2.1 the following waring leads to an build error if boost is enabled +if(APPLE) + mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=empty-body" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) +endif() MITK_CREATE_MODULE( SUBPROJECTS MITK-DTI INCLUDE_DIRS Algorithms Algorithms/Reconstruction Algorithms/Registration Algorithms/Reconstruction/MultishellProcessing DicomImport IODataStructures/DiffusionWeightedImages IODataStructures/QBallImages IODataStructures/TensorImages IODataStructures Rendering ${CMAKE_CURRENT_BINARY_DIR} DEPENDS MitkMapperExt MitkPlanarFigure MitkImageExtraction MitkSceneSerializationBase MitkDICOMReader PACKAGE_DEPENDS VTK|vtkFiltersProgrammable ITK|ITKDistanceMap+ITKRegistrationCommon+ITKLabelVoting+ITKVTK Boost ITK|ITKMetricsv4+ITKRegistrationMethodsv4 WARNINGS_AS_ERRORS ) add_subdirectory(Testing) diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp index d443e5924a..1142b15b42 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp @@ -1,689 +1,689 @@ /*=================================================================== 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 #include #include template< class ScalarType > mitk::FiberfoxParameters< ScalarType >::FiberfoxParameters() : m_NoiseModel(NULL) { } template< class ScalarType > mitk::FiberfoxParameters< ScalarType >::~FiberfoxParameters() { // if (m_NoiseModel!=NULL) // delete m_NoiseModel; } void mitk::SignalGenerationParameters::GenerateGradientHalfShell() { int NPoints = 2*m_NumGradients; m_GradientDirections.clear(); m_NumBaseline = NPoints/20; if (m_NumBaseline==0) m_NumBaseline=1; GradientType g; g.Fill(0.0); for (unsigned int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*M_PI); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i mitk::SignalGenerationParameters::GetBaselineIndices() { std::vector< int > result; for( unsigned int i=0; im_GradientDirections.size(); i++) if (m_GradientDirections.at(i).GetNorm()<0.0001) result.push_back(i); return result; } unsigned int mitk::SignalGenerationParameters::GetFirstBaselineIndex() { for( unsigned int i=0; im_GradientDirections.size(); i++) if (m_GradientDirections.at(i).GetNorm()<0.0001) return i; return -1; } bool mitk::SignalGenerationParameters::IsBaselineIndex(unsigned int idx) { if (m_GradientDirections.size()>idx && m_GradientDirections.at(idx).GetNorm()<0.0001) return true; return false; } unsigned int mitk::SignalGenerationParameters::GetNumWeightedVolumes() { return m_NumGradients; } unsigned int mitk::SignalGenerationParameters::GetNumBaselineVolumes() { return m_NumBaseline; } unsigned int mitk::SignalGenerationParameters::GetNumVolumes() { return m_GradientDirections.size(); } mitk::SignalGenerationParameters::GradientListType mitk::SignalGenerationParameters::GetGradientDirections() { return m_GradientDirections; } mitk::SignalGenerationParameters::GradientType mitk::SignalGenerationParameters::GetGradientDirection(unsigned int i) { return m_GradientDirections.at(i); } void mitk::SignalGenerationParameters::SetNumWeightedVolumes(int numGradients) { m_NumGradients = numGradients; GenerateGradientHalfShell(); } void mitk::SignalGenerationParameters::SetGradienDirections(GradientListType gradientList) { m_GradientDirections = gradientList; m_NumGradients = 0; m_NumBaseline = 0; for( unsigned int i=0; im_GradientDirections.size(); i++) { if (m_GradientDirections.at(i).GetNorm()>0.0001) m_NumGradients++; else m_NumBaseline++; } } void mitk::SignalGenerationParameters::SetGradienDirections(mitk::DiffusionImage::GradientDirectionContainerType::Pointer gradientList) { m_NumGradients = 0; m_NumBaseline = 0; m_GradientDirections.clear(); for( unsigned int i=0; iSize(); i++) { GradientType g; g[0] = gradientList->at(i)[0]; g[1] = gradientList->at(i)[1]; g[2] = gradientList->at(i)[2]; m_GradientDirections.push_back(g); if (m_GradientDirections.at(i).GetNorm()>0.0001) m_NumGradients++; else m_NumBaseline++; } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::SaveParameters(string filename) { if(filename.empty()) return; if(".ffp"!=filename.substr(filename.size()-4, 4)) filename += ".ffp"; boost::property_tree::ptree parameters; // fiber generation parameters parameters.put("fiberfox.fibers.distribution", m_FiberGen.m_Distribution); parameters.put("fiberfox.fibers.variance", m_FiberGen.m_Variance); parameters.put("fiberfox.fibers.density", m_FiberGen.m_Density); parameters.put("fiberfox.fibers.spline.sampling", m_FiberGen.m_Sampling); parameters.put("fiberfox.fibers.spline.tension", m_FiberGen.m_Tension); parameters.put("fiberfox.fibers.spline.continuity", m_FiberGen.m_Continuity); parameters.put("fiberfox.fibers.spline.bias", m_FiberGen.m_Bias); parameters.put("fiberfox.fibers.rotation.x", m_FiberGen.m_Rotation[0]); parameters.put("fiberfox.fibers.rotation.y", m_FiberGen.m_Rotation[1]); parameters.put("fiberfox.fibers.rotation.z", m_FiberGen.m_Rotation[2]); parameters.put("fiberfox.fibers.translation.x", m_FiberGen.m_Translation[0]); parameters.put("fiberfox.fibers.translation.y", m_FiberGen.m_Translation[1]); parameters.put("fiberfox.fibers.translation.z", m_FiberGen.m_Translation[2]); parameters.put("fiberfox.fibers.scale.x", m_FiberGen.m_Scale[0]); parameters.put("fiberfox.fibers.scale.y", m_FiberGen.m_Scale[1]); parameters.put("fiberfox.fibers.scale.z", m_FiberGen.m_Scale[2]); // image generation parameters parameters.put("fiberfox.image.basic.size.x", m_SignalGen.m_ImageRegion.GetSize(0)); parameters.put("fiberfox.image.basic.size.y", m_SignalGen.m_ImageRegion.GetSize(1)); parameters.put("fiberfox.image.basic.size.z", m_SignalGen.m_ImageRegion.GetSize(2)); parameters.put("fiberfox.image.basic.spacing.x", m_SignalGen.m_ImageSpacing[0]); parameters.put("fiberfox.image.basic.spacing.y", m_SignalGen.m_ImageSpacing[1]); parameters.put("fiberfox.image.basic.spacing.z", m_SignalGen.m_ImageSpacing[2]); parameters.put("fiberfox.image.basic.origin.x", m_SignalGen.m_ImageOrigin[0]); parameters.put("fiberfox.image.basic.origin.y", m_SignalGen.m_ImageOrigin[1]); parameters.put("fiberfox.image.basic.origin.z", m_SignalGen.m_ImageOrigin[2]); parameters.put("fiberfox.image.basic.direction.1", m_SignalGen.m_ImageDirection[0][0]); parameters.put("fiberfox.image.basic.direction.2", m_SignalGen.m_ImageDirection[0][1]); parameters.put("fiberfox.image.basic.direction.3", m_SignalGen.m_ImageDirection[0][2]); parameters.put("fiberfox.image.basic.direction.4", m_SignalGen.m_ImageDirection[1][0]); parameters.put("fiberfox.image.basic.direction.5", m_SignalGen.m_ImageDirection[1][1]); parameters.put("fiberfox.image.basic.direction.6", m_SignalGen.m_ImageDirection[1][2]); parameters.put("fiberfox.image.basic.direction.7", m_SignalGen.m_ImageDirection[2][0]); parameters.put("fiberfox.image.basic.direction.8", m_SignalGen.m_ImageDirection[2][1]); parameters.put("fiberfox.image.basic.direction.9", m_SignalGen.m_ImageDirection[2][2]); parameters.put("fiberfox.image.basic.numgradients", m_SignalGen.GetNumWeightedVolumes()); for( unsigned int i=0; im_SignalGen.GetNumVolumes(); i++) { parameters.put("fiberfox.image.gradients."+boost::lexical_cast(i)+".x", m_SignalGen.GetGradientDirection(i)[0]); parameters.put("fiberfox.image.gradients."+boost::lexical_cast(i)+".y", m_SignalGen.GetGradientDirection(i)[1]); parameters.put("fiberfox.image.gradients."+boost::lexical_cast(i)+".z", m_SignalGen.GetGradientDirection(i)[2]); } parameters.put("fiberfox.image.signalScale", m_SignalGen.m_SignalScale); parameters.put("fiberfox.image.tEcho", m_SignalGen.m_tEcho); parameters.put("fiberfox.image.tLine", m_SignalGen.m_tLine); parameters.put("fiberfox.image.tInhom", m_SignalGen.m_tInhom); parameters.put("fiberfox.image.bvalue", m_SignalGen.m_Bvalue); parameters.put("fiberfox.image.simulatekspace", m_SignalGen.m_SimulateKspaceAcquisition); parameters.put("fiberfox.image.axonRadius", m_SignalGen.m_AxonRadius); parameters.put("fiberfox.image.diffusiondirectionmode", m_SignalGen.m_DiffusionDirectionMode); parameters.put("fiberfox.image.fiberseparationthreshold", m_SignalGen.m_FiberSeparationThreshold); parameters.put("fiberfox.image.doSimulateRelaxation", m_SignalGen.m_DoSimulateRelaxation); parameters.put("fiberfox.image.doDisablePartialVolume", m_SignalGen.m_DoDisablePartialVolume); parameters.put("fiberfox.image.artifacts.spikesnum", m_SignalGen.m_Spikes); parameters.put("fiberfox.image.artifacts.spikesscale", m_SignalGen.m_SpikeAmplitude); parameters.put("fiberfox.image.artifacts.kspaceLineOffset", m_SignalGen.m_KspaceLineOffset); parameters.put("fiberfox.image.artifacts.eddyStrength", m_SignalGen.m_EddyStrength); parameters.put("fiberfox.image.artifacts.eddyTau", m_SignalGen.m_Tau); parameters.put("fiberfox.image.artifacts.aliasingfactor", m_SignalGen.m_CroppingFactor); parameters.put("fiberfox.image.artifacts.addringing", m_SignalGen.m_DoAddGibbsRinging); parameters.put("fiberfox.image.artifacts.doAddMotion", m_SignalGen.m_DoAddMotion); parameters.put("fiberfox.image.artifacts.randomMotion", m_SignalGen.m_DoRandomizeMotion); parameters.put("fiberfox.image.artifacts.translation0", m_SignalGen.m_Translation[0]); parameters.put("fiberfox.image.artifacts.translation1", m_SignalGen.m_Translation[1]); parameters.put("fiberfox.image.artifacts.translation2", m_SignalGen.m_Translation[2]); parameters.put("fiberfox.image.artifacts.rotation0", m_SignalGen.m_Rotation[0]); parameters.put("fiberfox.image.artifacts.rotation1", m_SignalGen.m_Rotation[1]); parameters.put("fiberfox.image.artifacts.rotation2", m_SignalGen.m_Rotation[2]); parameters.put("fiberfox.image.artifacts.addnoise", m_Misc.m_CheckAddNoiseBox); parameters.put("fiberfox.image.artifacts.addghosts", m_Misc.m_CheckAddGhostsBox); parameters.put("fiberfox.image.artifacts.addaliasing", m_Misc.m_CheckAddAliasingBox); parameters.put("fiberfox.image.artifacts.addspikes", m_Misc.m_CheckAddSpikesBox); parameters.put("fiberfox.image.artifacts.addeddycurrents", m_Misc.m_CheckAddEddyCurrentsBox); parameters.put("fiberfox.image.artifacts.doAddDistortions", m_Misc.m_CheckAddDistortionsBox); parameters.put("fiberfox.image.outputvolumefractions", m_Misc.m_CheckOutputVolumeFractionsBox); parameters.put("fiberfox.image.showadvanced", m_Misc.m_CheckAdvancedSignalOptionsBox); parameters.put("fiberfox.image.signalmodelstring", m_Misc.m_SignalModelString); parameters.put("fiberfox.image.artifactmodelstring", m_Misc.m_ArtifactModelString); parameters.put("fiberfox.image.outpath", m_Misc.m_OutputPath); parameters.put("fiberfox.fibers.realtime", m_Misc.m_CheckRealTimeFibersBox); parameters.put("fiberfox.fibers.showadvanced", m_Misc.m_CheckAdvancedFiberOptionsBox); parameters.put("fiberfox.fibers.constantradius", m_Misc.m_CheckConstantRadiusBox); parameters.put("fiberfox.fibers.includeFiducials", m_Misc.m_CheckIncludeFiducialsBox); if (m_NoiseModel!=NULL) { parameters.put("fiberfox.image.artifacts.noisevariance", m_NoiseModel->GetNoiseVariance()); if (dynamic_cast*>(m_NoiseModel)) parameters.put("fiberfox.image.artifacts.noisetype", "rice"); else if (dynamic_cast*>(m_NoiseModel)) parameters.put("fiberfox.image.artifacts.noisetype", "chisquare"); } for (int i=0; i* signalModel = NULL; if (i(i)+".type", "fiber"); } else { signalModel = m_NonFiberModelList.at(i-m_FiberModelList.size()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".type", "non-fiber"); } if (dynamic_cast*>(signalModel)) { mitk::StickModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "stick"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d", model->GetDiffusivity()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t2", model->GetT2()); } else if (dynamic_cast*>(signalModel)) { mitk::TensorModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "tensor"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d1", model->GetDiffusivity1()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d2", model->GetDiffusivity2()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d3", model->GetDiffusivity3()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t2", model->GetT2()); } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "prototype"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".minFA", model->GetFaRange().first); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".maxFA", model->GetFaRange().second); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".minADC", model->GetAdcRange().first); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".maxADC", model->GetAdcRange().second); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".maxNumSamples", model->GetMaxNumKernels()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".numSamples", model->GetNumberOfKernels()); int shOrder = model->GetShOrder(); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".numCoeffs", (shOrder*shOrder + shOrder + 2)/2 + shOrder); for (unsigned int j=0; jGetNumberOfKernels(); j++) { vnl_vector< double > coeffs = model->GetCoefficients(j); for (unsigned int k=0; k(i)+".kernels."+boost::lexical_cast(j)+".coeffs."+boost::lexical_cast(k), coeffs[k]); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".kernels."+boost::lexical_cast(j)+".B0", model->GetBaselineSignal(j)); } } else if (dynamic_cast*>(signalModel)) { mitk::BallModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "ball"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d", model->GetDiffusivity()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t2", model->GetT2()); } else if (dynamic_cast*>(signalModel)) { mitk::AstroStickModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "astrosticks"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d", model->GetDiffusivity()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t2", model->GetT2()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".randomize", model->GetRandomizeSticks()); } else if (dynamic_cast*>(signalModel)) { mitk::DotModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "dot"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t2", model->GetT2()); } if (signalModel!=NULL) { parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".ID", signalModel->m_CompartmentId); if (signalModel->GetVolumeFractionImage().IsNotNull()) { try{ itk::ImageFileWriter::Pointer writer = itk::ImageFileWriter::New(); writer->SetFileName(filename+"_VOLUME"+boost::lexical_cast(signalModel->m_CompartmentId)+".nrrd"); writer->SetInput(signalModel->GetVolumeFractionImage()); writer->Update(); MITK_INFO << "Volume fraction image for compartment "+boost::lexical_cast(signalModel->m_CompartmentId)+" saved."; } catch(...) { } } } } - boost::property_tree::xml_writer_settings writerSettings(' ', 2); + boost::property_tree::xml_writer_settings writerSettings(' ', 2); boost::property_tree::xml_parser::write_xml(filename, parameters, std::locale(), writerSettings); try{ itk::ImageFileWriter::Pointer writer = itk::ImageFileWriter::New(); writer->SetFileName(filename+"_FMAP.nrrd"); writer->SetInput(m_SignalGen.m_FrequencyMap); writer->Update(); } catch(...) { MITK_INFO << "No frequency map saved."; } try{ itk::ImageFileWriter::Pointer writer = itk::ImageFileWriter::New(); writer->SetFileName(filename+"_MASK.nrrd"); writer->SetInput(m_SignalGen.m_MaskImage); writer->Update(); } catch(...) { MITK_INFO << "No mask image saved."; } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::LoadParameters(string filename) { if(filename.empty()) return; boost::property_tree::ptree parameterTree; boost::property_tree::xml_parser::read_xml(filename, parameterTree); m_FiberModelList.clear(); m_NonFiberModelList.clear(); if (m_NoiseModel!=NULL) delete m_NoiseModel; BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameterTree.get_child("fiberfox") ) { if( v1.first == "fibers" ) { m_Misc.m_CheckRealTimeFibersBox = v1.second.get("realtime", m_Misc.m_CheckRealTimeFibersBox); m_Misc.m_CheckAdvancedFiberOptionsBox = v1.second.get("showadvanced", m_Misc.m_CheckAdvancedFiberOptionsBox); m_Misc.m_CheckConstantRadiusBox = v1.second.get("constantradius", m_Misc.m_CheckConstantRadiusBox); m_Misc.m_CheckIncludeFiducialsBox = v1.second.get("includeFiducials", m_Misc.m_CheckIncludeFiducialsBox); switch (v1.second.get("distribution", 0)) { case 0: m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; break; case 1: m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_GAUSSIAN; break; default: m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; } m_FiberGen.m_Variance = v1.second.get("variance", m_FiberGen.m_Variance); m_FiberGen.m_Density = v1.second.get("density", m_FiberGen.m_Density); m_FiberGen.m_Sampling = v1.second.get("spline.sampling", m_FiberGen.m_Sampling); m_FiberGen.m_Tension = v1.second.get("spline.tension", m_FiberGen.m_Tension); m_FiberGen.m_Continuity = v1.second.get("spline.continuity", m_FiberGen.m_Continuity); m_FiberGen.m_Bias = v1.second.get("spline.bias", m_FiberGen.m_Bias); m_FiberGen.m_Rotation[0] = v1.second.get("rotation.x", m_FiberGen.m_Rotation[0]); m_FiberGen.m_Rotation[1] = v1.second.get("rotation.y", m_FiberGen.m_Rotation[1]); m_FiberGen.m_Rotation[2] = v1.second.get("rotation.z", m_FiberGen.m_Rotation[2]); m_FiberGen.m_Translation[0] = v1.second.get("translation.x", m_FiberGen.m_Translation[0]); m_FiberGen.m_Translation[1] = v1.second.get("translation.y", m_FiberGen.m_Translation[1]); m_FiberGen.m_Translation[2] = v1.second.get("translation.z", m_FiberGen.m_Translation[2]); m_FiberGen.m_Scale[0] = v1.second.get("scale.x", m_FiberGen.m_Scale[0]); m_FiberGen.m_Scale[1] = v1.second.get("scale.y", m_FiberGen.m_Scale[1]); m_FiberGen.m_Scale[2] = v1.second.get("scale.z", m_FiberGen.m_Scale[2]); } else if ( v1.first == "image" ) { m_Misc.m_SignalModelString = v1.second.get("signalmodelstring", m_Misc.m_SignalModelString); m_Misc.m_ArtifactModelString = v1.second.get("artifactmodelstring", m_Misc.m_ArtifactModelString); m_Misc.m_OutputPath = v1.second.get("outpath", m_Misc.m_OutputPath); m_Misc.m_CheckOutputVolumeFractionsBox = v1.second.get("outputvolumefractions", m_Misc.m_CheckOutputVolumeFractionsBox); m_Misc.m_CheckAdvancedSignalOptionsBox = v1.second.get("showadvanced", m_Misc.m_CheckAdvancedSignalOptionsBox); m_Misc.m_CheckAddDistortionsBox = v1.second.get("artifacts.doAddDistortions", m_Misc.m_CheckAddDistortionsBox); m_Misc.m_CheckAddNoiseBox = v1.second.get("artifacts.addnoise", m_Misc.m_CheckAddNoiseBox); m_Misc.m_CheckAddGhostsBox = v1.second.get("artifacts.addghosts", m_Misc.m_CheckAddGhostsBox); m_Misc.m_CheckAddAliasingBox = v1.second.get("artifacts.addaliasing", m_Misc.m_CheckAddAliasingBox); m_Misc.m_CheckAddSpikesBox = v1.second.get("artifacts.addspikes", m_Misc.m_CheckAddSpikesBox); m_Misc.m_CheckAddEddyCurrentsBox = v1.second.get("artifacts.addeddycurrents", m_Misc.m_CheckAddEddyCurrentsBox); m_SignalGen.m_ImageRegion.SetSize(0, v1.second.get("basic.size.x",m_SignalGen.m_ImageRegion.GetSize(0))); m_SignalGen.m_ImageRegion.SetSize(1, v1.second.get("basic.size.y",m_SignalGen.m_ImageRegion.GetSize(1))); m_SignalGen.m_ImageRegion.SetSize(2, v1.second.get("basic.size.z",m_SignalGen.m_ImageRegion.GetSize(2))); m_SignalGen.m_ImageSpacing[0] = v1.second.get("basic.spacing.x",m_SignalGen.m_ImageSpacing[0]); m_SignalGen.m_ImageSpacing[1] = v1.second.get("basic.spacing.y",m_SignalGen.m_ImageSpacing[1]); m_SignalGen.m_ImageSpacing[2] = v1.second.get("basic.spacing.z",m_SignalGen.m_ImageSpacing[2]); m_SignalGen.m_ImageOrigin[0] = v1.second.get("basic.origin.x",m_SignalGen.m_ImageOrigin[0]); m_SignalGen.m_ImageOrigin[1] = v1.second.get("basic.origin.y",m_SignalGen.m_ImageOrigin[1]); m_SignalGen.m_ImageOrigin[2] = v1.second.get("basic.origin.z",m_SignalGen.m_ImageOrigin[2]); m_SignalGen.m_ImageDirection[0][0] = v1.second.get("basic.direction.1",m_SignalGen.m_ImageDirection[0][0]); m_SignalGen.m_ImageDirection[0][1] = v1.second.get("basic.direction.2",m_SignalGen.m_ImageDirection[0][1]); m_SignalGen.m_ImageDirection[0][2] = v1.second.get("basic.direction.3",m_SignalGen.m_ImageDirection[0][2]); m_SignalGen.m_ImageDirection[1][0] = v1.second.get("basic.direction.4",m_SignalGen.m_ImageDirection[1][0]); m_SignalGen.m_ImageDirection[1][1] = v1.second.get("basic.direction.5",m_SignalGen.m_ImageDirection[1][1]); m_SignalGen.m_ImageDirection[1][2] = v1.second.get("basic.direction.6",m_SignalGen.m_ImageDirection[1][2]); m_SignalGen.m_ImageDirection[2][0] = v1.second.get("basic.direction.7",m_SignalGen.m_ImageDirection[2][0]); m_SignalGen.m_ImageDirection[2][1] = v1.second.get("basic.direction.8",m_SignalGen.m_ImageDirection[2][1]); m_SignalGen.m_ImageDirection[2][2] = v1.second.get("basic.direction.9",m_SignalGen.m_ImageDirection[2][2]); m_SignalGen.m_SignalScale = v1.second.get("signalScale", m_SignalGen.m_SignalScale); m_SignalGen.m_tEcho = v1.second.get("tEcho", m_SignalGen.m_tEcho); m_SignalGen.m_tLine = v1.second.get("tLine", m_SignalGen.m_tLine); m_SignalGen.m_tInhom = v1.second.get("tInhom", m_SignalGen.m_tInhom); m_SignalGen.m_Bvalue = v1.second.get("bvalue", m_SignalGen.m_Bvalue); m_SignalGen.m_SimulateKspaceAcquisition = v1.second.get("simulatekspace", m_SignalGen.m_SimulateKspaceAcquisition); m_SignalGen.m_AxonRadius = v1.second.get("axonRadius", m_SignalGen.m_AxonRadius); switch (v1.second.get("diffusiondirectionmode", 0)) { case 0: m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS; break; case 1: m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::MAIN_FIBER_DIRECTIONS; break; case 2: m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::RANDOM_DIRECTIONS; break; default: m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS; } m_SignalGen.m_FiberSeparationThreshold = v1.second.get("fiberseparationthreshold", m_SignalGen.m_FiberSeparationThreshold); m_SignalGen.m_Spikes = v1.second.get("artifacts.spikesnum", m_SignalGen.m_Spikes); m_SignalGen.m_SpikeAmplitude = v1.second.get("artifacts.spikesscale", m_SignalGen.m_SpikeAmplitude); m_SignalGen.m_KspaceLineOffset = v1.second.get("artifacts.kspaceLineOffset", m_SignalGen.m_KspaceLineOffset); m_SignalGen.m_EddyStrength = v1.second.get("artifacts.eddyStrength", m_SignalGen.m_EddyStrength); m_SignalGen.m_Tau = v1.second.get("artifacts.eddyTau", m_SignalGen.m_Tau); m_SignalGen.m_CroppingFactor = v1.second.get("artifacts.aliasingfactor", m_SignalGen.m_CroppingFactor); m_SignalGen.m_DoAddGibbsRinging = v1.second.get("artifacts.addringing", m_SignalGen.m_DoAddGibbsRinging); m_SignalGen.m_DoSimulateRelaxation = v1.second.get("doSimulateRelaxation", m_SignalGen.m_DoSimulateRelaxation); m_SignalGen.m_DoDisablePartialVolume = v1.second.get("doDisablePartialVolume", m_SignalGen.m_DoDisablePartialVolume); m_SignalGen.m_DoAddMotion = v1.second.get("artifacts.doAddMotion", m_SignalGen.m_DoAddMotion); m_SignalGen.m_DoRandomizeMotion = v1.second.get("artifacts.randomMotion", m_SignalGen.m_DoRandomizeMotion); m_SignalGen.m_Translation[0] = v1.second.get("artifacts.translation0", m_SignalGen.m_Translation[0]); m_SignalGen.m_Translation[1] = v1.second.get("artifacts.translation1", m_SignalGen.m_Translation[1]); m_SignalGen.m_Translation[2] = v1.second.get("artifacts.translation2", m_SignalGen.m_Translation[2]); m_SignalGen.m_Rotation[0] = v1.second.get("artifacts.rotation0", m_SignalGen.m_Rotation[0]); m_SignalGen.m_Rotation[1] = v1.second.get("artifacts.rotation1", m_SignalGen.m_Rotation[1]); m_SignalGen.m_Rotation[2] = v1.second.get("artifacts.rotation2", m_SignalGen.m_Rotation[2]); // m_SignalGen.SetNumWeightedVolumes(v1.second.get("numgradients", m_SignalGen.GetNumWeightedVolumes())); SignalGenerationParameters::GradientListType gradients; BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second.get_child("gradients") ) { SignalGenerationParameters::GradientType g; g[0] = v2.second.get("x"); g[1] = v2.second.get("y"); g[2] = v2.second.get("z"); gradients.push_back(g); } m_SignalGen.SetGradienDirections(gradients); try { if (v1.second.get("artifacts.noisetype")=="rice") { m_NoiseModel = new mitk::RicianNoiseModel(); m_NoiseModel->SetNoiseVariance(v1.second.get("artifacts.noisevariance")); } } catch(...) {} try { if (v1.second.get("artifacts.noisetype")=="chisquare") { m_NoiseModel = new mitk::ChiSquareNoiseModel(); m_NoiseModel->SetNoiseVariance(v1.second.get("artifacts.noisevariance")); } } catch(...){ } BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second.get_child("compartments") ) { mitk::DiffusionSignalModel* signalModel = NULL; std::string model = v2.second.get("model"); if (model=="stick") { mitk::StickModel* model = new mitk::StickModel(); model->SetDiffusivity(v2.second.get("d")); model->SetT2(v2.second.get("t2")); model->m_CompartmentId = v2.second.get("ID"); if (v2.second.get("type")=="fiber") m_FiberModelList.push_back(model); else if (v2.second.get("type")=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="tensor") { mitk::TensorModel* model = new mitk::TensorModel(); model->SetDiffusivity1(v2.second.get("d1")); model->SetDiffusivity2(v2.second.get("d2")); model->SetDiffusivity3(v2.second.get("d3")); model->SetT2(v2.second.get("t2")); model->m_CompartmentId = v2.second.get("ID"); if (v2.second.get("type")=="fiber") m_FiberModelList.push_back(model); else if (v2.second.get("type")=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="ball") { mitk::BallModel* model = new mitk::BallModel(); model->SetDiffusivity(v2.second.get("d")); model->SetT2(v2.second.get("t2")); model->m_CompartmentId = v2.second.get("ID"); if (v2.second.get("type")=="fiber") m_FiberModelList.push_back(model); else if (v2.second.get("type")=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="astrosticks") { mitk::AstroStickModel* model = new AstroStickModel(); model->SetDiffusivity(v2.second.get("d")); model->SetT2(v2.second.get("t2")); model->SetRandomizeSticks(v2.second.get("randomize")); model->m_CompartmentId = v2.second.get("ID"); if (v2.second.get("type")=="fiber") m_FiberModelList.push_back(model); else if (v2.second.get("type")=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="dot") { mitk::DotModel* model = new mitk::DotModel(); model->SetT2(v2.second.get("t2")); model->m_CompartmentId = v2.second.get("ID"); if (v2.second.get("type")=="fiber") m_FiberModelList.push_back(model); else if (v2.second.get("type")=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="prototype") { mitk::RawShModel* model = new mitk::RawShModel(); model->SetMaxNumKernels(v2.second.get("maxNumSamples")); model->SetFaRange(v2.second.get("minFA"), v2.second.get("maxFA")); model->SetAdcRange(v2.second.get("minADC"), v2.second.get("maxADC")); model->m_CompartmentId = v2.second.get("ID"); unsigned int numCoeffs = v2.second.get("numCoeffs"); unsigned int numSamples = v2.second.get("numSamples"); for (unsigned int j=0; j coeffs(numCoeffs); for (unsigned int k=0; k("kernels."+boost::lexical_cast(j)+".coeffs."+boost::lexical_cast(k)); } model->SetShCoefficients( coeffs, v2.second.get("kernels."+boost::lexical_cast(j)+".B0") ); } if (v2.second.get("type")=="fiber") m_FiberModelList.push_back(model); else if (v2.second.get("type")=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } if (signalModel!=NULL) { signalModel->SetGradientList(gradients); try{ itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); reader->SetFileName(filename+"_VOLUME"+v2.second.get("ID")+".nrrd"); reader->Update(); signalModel->SetVolumeFractionImage(reader->GetOutput()); } catch(...) { } } } } } try{ itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); reader->SetFileName(filename+"_FMAP.nrrd"); reader->Update(); m_SignalGen.m_FrequencyMap = reader->GetOutput(); } catch(...) { MITK_INFO << "No frequency map saved."; } try{ itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); reader->SetFileName(filename+"_MASK.nrrd"); reader->Update(); m_SignalGen.m_MaskImage = reader->GetOutput(); } catch(...) { MITK_INFO << "No mask image saved."; } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::PrintSelf() { MITK_INFO << "Not implemented :("; } diff --git a/Modules/DiffusionImaging/Quantification/CMakeLists.txt b/Modules/DiffusionImaging/Quantification/CMakeLists.txt index 434d7cdf06..4c677be959 100644 --- a/Modules/DiffusionImaging/Quantification/CMakeLists.txt +++ b/Modules/DiffusionImaging/Quantification/CMakeLists.txt @@ -1,9 +1,14 @@ +# With apple gcc 4.2.1 the following waring leads to an build error if boost is enabled +if(APPLE) + mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=empty-body" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) +endif() + #DiffusionImaging/Quantification MITK_CREATE_MODULE( SUBPROJECTS MITK-DTI INCLUDE_DIRS Algorithms IODataStructures IODataStructures/TbssImages Rendering ${CMAKE_CURRENT_BINARY_DIR} DEPENDS MitkDiffusionCore MitkFiberTracking MitkGraphAlgorithms WARNINGS_AS_ERRORS ) add_subdirectory(Testing)