diff --git a/Applications/PluginGenerator/ProjectTemplate/CMakeExternals/MITK.cmake b/Applications/PluginGenerator/ProjectTemplate/CMakeExternals/MITK.cmake index 4d47582bbe..960505af33 100644 --- a/Applications/PluginGenerator/ProjectTemplate/CMakeExternals/MITK.cmake +++ b/Applications/PluginGenerator/ProjectTemplate/CMakeExternals/MITK.cmake @@ -1,217 +1,217 @@ #----------------------------------------------------------------------------- # MITK #----------------------------------------------------------------------------- set(MITK_DEPENDS) set(proj_DEPENDENCIES) set(proj MITK) if(NOT MITK_DIR) #----------------------------------------------------------------------------- # Create CMake options to customize the MITK build #----------------------------------------------------------------------------- option(MITK_USE_SUPERBUILD "Use superbuild for MITK" ON) option(MITK_USE_BLUEBERRY "Build the BlueBerry platform in MITK" ON) option(MITK_BUILD_EXAMPLES "Build the MITK examples" OFF) option(MITK_BUILD_ALL_PLUGINS "Build all MITK plugins" OFF) option(MITK_BUILD_TESTING "Build the MITK unit tests" OFF) option(MITK_USE_ACVD "Use Approximated Centroidal Voronoi Diagrams" OFF) option(MITK_USE_CTK "Use CTK in MITK" ${MITK_USE_BLUEBERRY}) option(MITK_USE_DCMTK "Use DCMTK in MITK" ON) option(MITK_USE_QT "Use Nokia's Qt library in MITK" ON) option(MITK_USE_Boost "Use the Boost library in MITK" OFF) option(MITK_USE_OpenCV "Use Intel's OpenCV library" OFF) option(MITK_USE_SOFA "Use Simulation Open Framework Architecture" OFF) option(MITK_USE_Python "Enable Python wrapping in MITK" OFF) if(MITK_USE_BLUEBERRY AND NOT MITK_USE_CTK) message("Forcing MITK_USE_CTK to ON because of MITK_USE_BLUEBERRY") set(MITK_USE_CTK ON CACHE BOOL "Use CTK in MITK" FORCE) endif() if(MITK_USE_CTK AND NOT MITK_USE_QT) message("Forcing MITK_USE_QT to ON because of MITK_USE_CTK") set(MITK_USE_QT ON CACHE BOOL "Use Nokia's Qt library in MITK" FORCE) endif() set(MITK_USE_CableSwig ${MITK_USE_Python}) set(MITK_USE_GDCM 1) set(MITK_USE_ITK 1) set(MITK_USE_VTK 1) mark_as_advanced(MITK_USE_SUPERBUILD MITK_BUILD_ALL_PLUGINS MITK_BUILD_TESTING ) set(mitk_cmake_boolean_args MITK_USE_SUPERBUILD MITK_USE_BLUEBERRY MITK_BUILD_EXAMPLES MITK_BUILD_ALL_PLUGINS MITK_USE_ACVD MITK_USE_CTK MITK_USE_DCMTK MITK_USE_QT MITK_USE_Boost MITK_USE_OpenCV MITK_USE_SOFA MITK_USE_Python ) if(MITK_USE_QT) # Look for Qt at the superbuild level, to catch missing Qt libs early find_package(Qt4 4.7 REQUIRED) endif() set(additional_mitk_cmakevars ) # Configure the set of default pixel types set(MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES "int, unsigned int, short, unsigned short, char, unsigned char" CACHE STRING "List of integral pixel types used in AccessByItk and InstantiateAccessFunction macros") set(MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES "double, float" CACHE STRING "List of floating pixel types used in AccessByItk and InstantiateAccessFunction macros") set(MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES "" CACHE STRING "List of composite pixel types used in AccessByItk and InstantiateAccessFunction macros") set(MITK_ACCESSBYITK_DIMENSIONS "2,3" CACHE STRING "List of dimensions used in AccessByItk and InstantiateAccessFunction macros") foreach(_arg MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES MITK_ACCESSBYITK_DIMENSIONS) mark_as_advanced(${_arg}) list(APPEND additional_mitk_cmakevars "-D${_arg}:STRING=${${_arg}}") endforeach() #----------------------------------------------------------------------------- # Create options to inject pre-build dependencies #----------------------------------------------------------------------------- foreach(proj CTK DCMTK GDCM VTK ACVD ITK OpenCV SOFA CableSwig) if(MITK_USE_${proj}) set(MITK_${proj}_DIR "${${proj}_DIR}" CACHE PATH "Path to ${proj} build directory") mark_as_advanced(MITK_${proj}_DIR) if(MITK_${proj}_DIR) list(APPEND additional_mitk_cmakevars "-D${proj}_DIR:PATH=${MITK_${proj}_DIR}") endif() endif() endforeach() if(MITK_USE_Boost) set(MITK_BOOST_ROOT "${BOOST_ROOT}" CACHE PATH "Path to Boost directory") mark_as_advanced(MITK_BOOST_ROOT) if(MITK_BOOST_ROOT) list(APPEND additional_mitk_cmakevars "-DBOOST_ROOT:PATH=${MITK_BOOST_ROOT}") endif() endif() set(MITK_SOURCE_DIR "" CACHE PATH "MITK source code location. If empty, MITK will be cloned from MITK_GIT_REPOSITORY") set(MITK_GIT_REPOSITORY "http://git.mitk.org/MITK.git" CACHE STRING "The git repository for cloning MITK") - set(MITK_GIT_TAG "origin/master" CACHE STRING "The git tag/hash to be used when cloning from MITK_GIT_REPOSITORY") + set(MITK_GIT_TAG "releases/2014-03" CACHE STRING "The git tag/hash to be used when cloning from MITK_GIT_REPOSITORY") mark_as_advanced(MITK_SOURCE_DIR MITK_GIT_REPOSITORY MITK_GIT_TAG) #----------------------------------------------------------------------------- # Create the final variable containing superbuild boolean args #----------------------------------------------------------------------------- set(mitk_boolean_args) foreach(mitk_cmake_arg ${mitk_cmake_boolean_args}) list(APPEND mitk_boolean_args -D${mitk_cmake_arg}:BOOL=${${mitk_cmake_arg}}) endforeach() #----------------------------------------------------------------------------- # Additional MITK CMake variables #----------------------------------------------------------------------------- if(MITK_USE_QT AND QT_QMAKE_EXECUTABLE) list(APPEND additional_mitk_cmakevars "-DQT_QMAKE_EXECUTABLE:FILEPATH=${QT_QMAKE_EXECUTABLE}") endif() if(MITK_USE_CTK) list(APPEND additional_mitk_cmakevars "-DGIT_EXECUTABLE:FILEPATH=${GIT_EXECUTABLE}") endif() if(MITK_INITIAL_CACHE_FILE) list(APPEND additional_mitk_cmakevars "-DMITK_INITIAL_CACHE_FILE:INTERNAL=${MITK_INITIAL_CACHE_FILE}") endif() if(MITK_USE_SUPERBUILD) set(MITK_BINARY_DIR ${proj}-superbuild) else() set(MITK_BINARY_DIR ${proj}-build) endif() set(proj_DEPENDENCIES) set(MITK_DEPENDS ${proj}) # Configure the MITK souce code location if(NOT MITK_SOURCE_DIR) set(mitk_source_location SOURCE_DIR ${CMAKE_BINARY_DIR}/${proj} GIT_REPOSITORY ${MITK_GIT_REPOSITORY} GIT_TAG ${MITK_GIT_TAG} ) else() set(mitk_source_location SOURCE_DIR ${MITK_SOURCE_DIR} ) endif() ExternalProject_Add(${proj} ${mitk_source_location} BINARY_DIR ${MITK_BINARY_DIR} PREFIX ${proj}${ep_suffix} INSTALL_COMMAND "" CMAKE_GENERATOR ${gen} CMAKE_ARGS ${ep_common_args} ${mitk_boolean_args} ${additional_mitk_cmakevars} -DBUILD_SHARED_LIBS:BOOL=ON -DBUILD_TESTING:BOOL=${MITK_BUILD_TESTING} DEPENDS ${proj_DEPENDENCIES} ) if(MITK_USE_SUPERBUILD) set(MITK_DIR "${CMAKE_CURRENT_BINARY_DIR}/${MITK_BINARY_DIR}/MITK-build") else() set(MITK_DIR "${CMAKE_CURRENT_BINARY_DIR}/${MITK_BINARY_DIR}") endif() else() # The project is provided using MITK_DIR, nevertheless since other # projects may depend on MITK, let's add an 'empty' one MacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") # Further, do some sanity checks in the case of a pre-built MITK set(my_itk_dir ${ITK_DIR}) set(my_vtk_dir ${VTK_DIR}) set(my_qmake_executable ${QT_QMAKE_EXECUTABLE}) find_package(MITK REQUIRED) if(my_itk_dir AND NOT my_itk_dir STREQUAL ${ITK_DIR}) message(FATAL_ERROR "ITK packages do not match:\n ${MY_PROJECT_NAME}: ${my_itk_dir}\n MITK: ${ITK_DIR}") endif() if(my_vtk_dir AND NOT my_vtk_dir STREQUAL ${VTK_DIR}) message(FATAL_ERROR "VTK packages do not match:\n ${MY_PROJECT_NAME}: ${my_vtk_dir}\n MITK: ${VTK_DIR}") endif() if(my_qmake_executable AND NOT my_qmake_executable STREQUAL ${MITK_QMAKE_EXECUTABLE}) message(FATAL_ERROR "Qt qmake does not match:\n ${MY_PROJECT_NAME}: ${my_qmake_executable}\n MITK: ${MITK_QMAKE_EXECUTABLE}") endif() endif() diff --git a/Applications/PluginGenerator/ProjectTemplate/CMakeLists.txt b/Applications/PluginGenerator/ProjectTemplate/CMakeLists.txt index 75552138d7..dc7b7b78ca 100644 --- a/Applications/PluginGenerator/ProjectTemplate/CMakeLists.txt +++ b/Applications/PluginGenerator/ProjectTemplate/CMakeLists.txt @@ -1,365 +1,365 @@ cmake_minimum_required(VERSION 2.8.8) # Change project and application name to your own set(MY_PROJECT_NAME $(project-name)) set(MY_APP_NAME $(project-app-name)) #----------------------------------------------------------------------------- # Set a default build type if none was specified #----------------------------------------------------------------------------- if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES) message(STATUS "Setting build type to 'Debug' as none was specified.") set(CMAKE_BUILD_TYPE Debug CACHE STRING "Choose the type of build." FORCE) # Set the possible values of build type for cmake-gui set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo") endif() #----------------------------------------------------------------------------- # Superbuild Option - Enabled by default #----------------------------------------------------------------------------- option(${MY_PROJECT_NAME}_USE_SUPERBUILD "Build ${MY_PROJECT_NAME} and the projects it depends on via SuperBuild.cmake." ON) if(${MY_PROJECT_NAME}_USE_SUPERBUILD) project(${MY_PROJECT_NAME}-superbuild) set(${MY_PROJECT_NAME}_SOURCE_DIR ${PROJECT_SOURCE_DIR}) set(${MY_PROJECT_NAME}_BINARY_DIR ${PROJECT_BINARY_DIR}) else() project(${MY_PROJECT_NAME}) endif() #----------------------------------------------------------------------------- # See http://cmake.org/cmake/help/cmake-2-8-docs.html#section_Policies for details #----------------------------------------------------------------------------- set(project_policies CMP0001 # NEW: CMAKE_BACKWARDS_COMPATIBILITY should no longer be used. CMP0002 # NEW: Logical target names must be globally unique. CMP0003 # NEW: Libraries linked via full path no longer produce linker search paths. CMP0004 # NEW: Libraries linked may NOT have leading or trailing whitespace. CMP0005 # NEW: Preprocessor definition values are now escaped automatically. CMP0006 # NEW: Installing MACOSX_BUNDLE targets requires a BUNDLE DESTINATION. CMP0007 # NEW: List command no longer ignores empty elements. CMP0008 # NEW: Libraries linked by full-path must have a valid library file name. CMP0009 # NEW: FILE GLOB_RECURSE calls should not follow symlinks by default. CMP0010 # NEW: Bad variable reference syntax is an error. CMP0011 # NEW: Included scripts do automatic cmake_policy PUSH and POP. CMP0012 # NEW: if() recognizes numbers and boolean constants. CMP0013 # NEW: Duplicate binary directories are not allowed. CMP0014 # NEW: Input directories must have CMakeLists.txt ) foreach(policy ${project_policies}) if(POLICY ${policy}) cmake_policy(SET ${policy} NEW) endif() endforeach() #----------------------------------------------------------------------------- # Update CMake module path #------------------------------------------------------------------------------ set(CMAKE_MODULE_PATH ${${MY_PROJECT_NAME}_SOURCE_DIR}/CMake ${CMAKE_MODULE_PATH} ) #----------------------------------------------------------------------------- # CMake Function(s) and Macro(s) #----------------------------------------------------------------------------- include(MacroEmptyExternalProject) #----------------------------------------------------------------------------- # Output directories. #----------------------------------------------------------------------------- foreach(type LIBRARY RUNTIME ARCHIVE) set(output_dir ${${MY_PROJECT_NAME}_BINARY_DIR}/bin) set(CMAKE_${type}_OUTPUT_DIRECTORY ${output_dir} CACHE INTERNAL "Single output directory for building all libraries.") mark_as_advanced(CMAKE_${type}_OUTPUT_DIRECTORY) endforeach() #----------------------------------------------------------------------------- # Additional Options (also shown during superbuild) #----------------------------------------------------------------------------- option(BUILD_SHARED_LIBS "Build ${MY_PROJECT_NAME} with shared libraries" ON) option(WITH_COVERAGE "Enable/Disable coverage" OFF) option(BUILD_TESTING "Test the project" ON) option(${MY_PROJECT_NAME}_BUILD_ALL_PLUGINS "Build all ${MY_PROJECT_NAME} plugins" OFF) mark_as_advanced(${MY_PROJECT_NAME}_INSTALL_RPATH_RELATIVE ${MY_PROJECT_NAME}_BUILD_ALL_PLUGINS ) #----------------------------------------------------------------------------- # Superbuild script #----------------------------------------------------------------------------- if(${MY_PROJECT_NAME}_USE_SUPERBUILD) include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake") return() endif() #***************************************************************************** #**************************** END OF SUPERBUILD **************************** #***************************************************************************** #----------------------------------------------------------------------------- # Prerequesites #----------------------------------------------------------------------------- -find_package(MITK REQUIRED) +find_package(MITK 2014.03.00 REQUIRED) if(COMMAND mitkFunctionCheckMitkCompatibility) mitkFunctionCheckMitkCompatibility(VERSIONS MITK_VERSION_PLUGIN_SYSTEM 1 REQUIRED) else() message(SEND_ERROR "Your MITK version is too old. Please use Git hash b86bf28 or newer") endif() link_directories(${MITK_LINK_DIRECTORIES}) #----------------------------------------------------------------------------- # CMake Function(s) and Macro(s) #----------------------------------------------------------------------------- set(CMAKE_MODULE_PATH ${MITK_SOURCE_DIR}/CMake ${CMAKE_MODULE_PATH} ) include(mitkFunctionCheckCompilerFlags) include(mitkFunctionGetGccVersion) include(mitkFunctionGetVersion) #----------------------------------------------------------------------------- # Set project specific options and variables (NOT available during superbuild) #----------------------------------------------------------------------------- set(${PROJECT_NAME}_VERSION_MAJOR "0") set(${PROJECT_NAME}_VERSION_MINOR "1") set(${PROJECT_NAME}_VERSION_PATCH "1") set(${PROJECT_NAME}_VERSION_STRING "${${PROJECT_NAME}_VERSION_MAJOR}.${${PROJECT_NAME}_VERSION_MINOR}.${${PROJECT_NAME}_VERSION_PATCH}") # Ask the user if a console window should be shown with the applications option(${PROJECT_NAME}_SHOW_CONSOLE_WINDOW "Use this to enable or disable the console window when starting GUI Applications" ON) mark_as_advanced(${PROJECT_NAME}_SHOW_CONSOLE_WINDOW) if(NOT UNIX AND NOT MINGW) set(MITK_WIN32_FORCE_STATIC "STATIC") endif() set(${PROJECT_NAME}_MODULES_PACKAGE_DEPENDS_DIR "${PROJECT_SOURCE_DIR}/CMake/PackageDepends") list(APPEND MODULES_PACKAGE_DEPENDS_DIRS ${${PROJECT_NAME}_MODULES_PACKAGE_DEPENDS_DIR}) #----------------------------------------------------------------------------- # Get project version info #----------------------------------------------------------------------------- mitkFunctionGetVersion(${PROJECT_SOURCE_DIR} ${PROJECT_NAME}) #----------------------------------------------------------------------------- # Installation preparation # # These should be set before any MITK install macros are used #----------------------------------------------------------------------------- # on Mac OSX all CTK plugins get copied into every # application bundle (.app directory) specified here set(MACOSX_BUNDLE_NAMES) if(APPLE) list(APPEND MACOSX_BUNDLE_NAMES ${MY_APP_NAME}) endif(APPLE) #----------------------------------------------------------------------------- # Set symbol visibility Flags #----------------------------------------------------------------------------- # MinGW does not export all symbols automatically, so no need to set flags if(CMAKE_COMPILER_IS_GNUCXX AND NOT MINGW) # The MITK module build system does not yet support default hidden visibility set(VISIBILITY_CXX_FLAGS ) # "-fvisibility=hidden -fvisibility-inlines-hidden") endif() #----------------------------------------------------------------------------- # Set coverage Flags #----------------------------------------------------------------------------- if(WITH_COVERAGE) if(CMAKE_COMPILER_IS_GNUCXX) set(coverage_flags "-g -fprofile-arcs -ftest-coverage -O0 -DNDEBUG") set(COVERAGE_CXX_FLAGS ${coverage_flags}) set(COVERAGE_C_FLAGS ${coverage_flags}) endif() endif() #----------------------------------------------------------------------------- # Project C/CXX Flags #----------------------------------------------------------------------------- set(${PROJECT_NAME}_C_FLAGS "${MITK_C_FLAGS} ${COVERAGE_C_FLAGS}") set(${PROJECT_NAME}_C_FLAGS_DEBUG ${MITK_C_FLAGS_DEBUG}) set(${PROJECT_NAME}_C_FLAGS_RELEASE ${MITK_C_FLAGS_RELEASE}) set(${PROJECT_NAME}_CXX_FLAGS "${MITK_CXX_FLAGS} ${VISIBILITY_CXX_FLAGS} ${COVERAGE_CXX_FLAGS}") set(${PROJECT_NAME}_CXX_FLAGS_DEBUG ${MITK_CXX_FLAGS_DEBUG}) set(${PROJECT_NAME}_CXX_FLAGS_RELEASE ${MITK_CXX_FLAGS_RELEASE}) set(${PROJECT_NAME}_EXE_LINKER_FLAGS ${MITK_EXE_LINKER_FLAGS}) set(${PROJECT_NAME}_SHARED_LINKER_FLAGS ${MITK_SHARED_LINKER_FLAGS}) set(${PROJECT_NAME}_MODULE_LINKER_FLAGS ${MITK_MODULE_LINKER_FLAGS}) #----------------------------------------------------------------------------- # Set C/CXX Flags #----------------------------------------------------------------------------- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${${PROJECT_NAME}_C_FLAGS}") set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} ${${PROJECT_NAME}_C_FLAGS_DEBUG}") set(CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} ${${PROJECT_NAME}_C_FLAGS_RELEASE}") set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${${PROJECT_NAME}_CXX_FLAGS}") set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} ${${PROJECT_NAME}_CXX_FLAGS_DEBUG}") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} ${${PROJECT_NAME}_CXX_FLAGS_RELEASE}") set(CMAKE_EXE_LINKER_FLAGS ${${PROJECT_NAME}_EXE_LINKER_FLAGS}) set(CMAKE_SHARED_LINKER_FLAGS ${${PROJECT_NAME}_SHARED_LINKER_FLAGS}) set(CMAKE_MODULE_LINKER_FLAGS ${${PROJECT_NAME}_MODULE_LINKER_FLAGS}) #----------------------------------------------------------------------------- # Testing #----------------------------------------------------------------------------- if(BUILD_TESTING) enable_testing() include(CTest) mark_as_advanced(TCL_TCLSH DART_ROOT) # Setup file for setting custom ctest vars configure_file( CMake/CTestCustom.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/CTestCustom.cmake @ONLY ) # Configuration for the CMake-generated test driver set(CMAKE_TESTDRIVER_EXTRA_INCLUDES "#include ") set(CMAKE_TESTDRIVER_BEFORE_TESTMAIN " try {") set(CMAKE_TESTDRIVER_AFTER_TESTMAIN " } catch( std::exception & excp ) { fprintf(stderr,\"%s\\n\",excp.what()); return EXIT_FAILURE; } catch( ... ) { printf(\"Exception caught in the test driver\\n\"); return EXIT_FAILURE; } ") endif() #----------------------------------------------------------------------------- # ${MY_PROJECT_NAME}_SUPERBUILD_BINARY_DIR #----------------------------------------------------------------------------- # If ${MY_PROJECT_NAME}_SUPERBUILD_BINARY_DIR isn't defined, it means this project is # *NOT* build using Superbuild. In that specific case, ${MY_PROJECT_NAME}_SUPERBUILD_BINARY_DIR # should default to PROJECT_BINARY_DIR if(NOT DEFINED ${PROJECT_NAME}_SUPERBUILD_BINARY_DIR) set(${PROJECT_NAME}_SUPERBUILD_BINARY_DIR ${PROJECT_BINARY_DIR}) endif() #----------------------------------------------------------------------------- # Qt support #----------------------------------------------------------------------------- if(MITK_USE_QT) set(QT_QMAKE_EXECUTABLE ${MITK_QMAKE_EXECUTABLE}) endif() #----------------------------------------------------------------------------- # MITK modules #----------------------------------------------------------------------------- # This project's directory holding module config files #set(${PROJECT_NAME}_MODULES_CONF_DIR "${PROJECT_BINARY_DIR}/${MODULES_CONF_DIRNAME}") # Append this projects's module config directory to the global list # (This is used to get include directories for the Exports.h files right) #list(APPEND MODULES_CONF_DIRS ${${PROJECT_NAME}_MODULES_CONF_DIR}) # Clean the modulesConf directory. This ensures that modules are sorted # according to their dependencies in the Modules/CMakeLists.txt file #file(GLOB _modules_conf_files ${${PROJECT_NAME}_MODULES_CONF_DIR}/*.cmake) #if(_modules_conf_files) # file(REMOVE ${_modules_conf_files}) #endif() #add_subdirectory(Modules) #----------------------------------------------------------------------------- # CTK plugins #----------------------------------------------------------------------------- # The CMake code in this section *must* be in the top-level CMakeLists.txt file macro(GetMyTargetLibraries all_target_libraries varname) set(re_ctkplugin "^$(project-plugin-base)_[a-zA-Z0-9_]+$") set(_tmp_list) list(APPEND _tmp_list ${all_target_libraries}) ctkMacroListFilter(_tmp_list re_ctkplugin OUTPUT_VARIABLE ${varname}) endmacro() include(${CMAKE_CURRENT_SOURCE_DIR}/Plugins/Plugins.cmake) ctkMacroSetupPlugins(${PROJECT_PLUGINS} BUILD_OPTION_PREFIX ${MY_PROJECT_NAME}_ BUILD_ALL ${${MY_PROJECT_NAME}_BUILD_ALL_PLUGINS}) #----------------------------------------------------------------------------- # Add subdirectories #----------------------------------------------------------------------------- add_subdirectory(Apps/$(project-app-name)) #----------------------------------------------------------------------------- # Installation #----------------------------------------------------------------------------- # set MITK cpack variables include(mitkSetupCPack) # Customize CPack variables for this project include(CPackSetup) list(APPEND CPACK_CREATE_DESKTOP_LINKS "${MY_APP_NAME}") configure_file(${MITK_SOURCE_DIR}/MITKCPackOptions.cmake.in ${PROJECT_BINARY_DIR}/${PROJECT_NAME}CPackOptions.cmake @ONLY) set(CPACK_PROJECT_CONFIG_FILE "${PROJECT_BINARY_DIR}/${PROJECT_NAME}CPackOptions.cmake") # include CPack model once all variables are set include(CPack) # Additional installation rules include(mitkInstallRules) #----------------------------------------------------------------------------- # Last configuration steps #----------------------------------------------------------------------------- # If we are under Windows, create two batch files which correctly # set up the environment for the application and for Visual Studio if(WIN32) include(mitkFunctionCreateWindowsBatchScript) set(VS_SOLUTION_FILE "${PROJECT_BINARY_DIR}/${PROJECT_NAME}.sln") foreach(VS_BUILD_TYPE debug release) mitkFunctionCreateWindowsBatchScript("${PROJECT_SOURCE_DIR}/CMake/StartVS.bat.in" ${PROJECT_BINARY_DIR}/StartVS_${VS_BUILD_TYPE}.bat ${VS_BUILD_TYPE}) endforeach() endif(WIN32) diff --git a/CMake/mitkSetupVariables.cmake b/CMake/mitkSetupVariables.cmake index 498d88bc0d..1c3ef8910e 100644 --- a/CMake/mitkSetupVariables.cmake +++ b/CMake/mitkSetupVariables.cmake @@ -1,101 +1,101 @@ #----------------------------------- # Basic MITK CMake variables #----------------------------------- # MITK_VERSION -set(MITK_VERSION_MAJOR "2013") -set(MITK_VERSION_MINOR "12") -set(MITK_VERSION_PATCH "99") +set(MITK_VERSION_MAJOR "2014") +set(MITK_VERSION_MINOR "03") +set(MITK_VERSION_PATCH "00") set(MITK_VERSION_STRING "${MITK_VERSION_MAJOR}.${MITK_VERSION_MINOR}.${MITK_VERSION_PATCH}") if(MITK_VERSION_PATCH STREQUAL "99") set(MITK_VERSION_STRING "${MITK_VERSION_STRING}-${MITK_REVISION_SHORTID}") endif() # Needed early on for redirecting the BlueBerry documentation output dir set(MITK_DOXYGEN_OUTPUT_DIR ${PROJECT_BINARY_DIR}/Documentation/Doxygen CACHE PATH "Output directory for doxygen generated documentation." ) if(NOT UNIX AND NOT MINGW) set(MITK_WIN32_FORCE_STATIC "STATIC" CACHE INTERNAL "Use this variable to always build static libraries on non-unix platforms") endif() if(MITK_BUILD_ALL_PLUGINS) set(MITK_BUILD_ALL_PLUGINS_OPTION "FORCE_BUILD_ALL") endif() #----------------------------------- # Find external dependencies #----------------------------------- # Qt support if(MITK_USE_QT) if(DESIRED_QT_VERSION MATCHES 4) find_package(Qt4 ${MITK_QT4_MINIMUM_VERSION} REQUIRED) elseif(DESIRED_QT_VERSION MATCHES 5) find_package(Qt5Core ${MITK_QT5_MINIMUM_VERSION} REQUIRED) # at least Core required endif() endif() #----------------------------------- # Configuration of module system #----------------------------------- set(MODULES_CONF_DIRNAME modulesConf) set(MODULES_CONF_DIRS ${MITK_BINARY_DIR}/${MODULES_CONF_DIRNAME}) # Configure module naming conventions set(MITK_MODULE_NAME_REGEX_MATCH "^[A-Z].*$") set(MITK_MODULE_NAME_REGEX_NOT_MATCH "^[Mm][Ii][Tt][Kk].*$") set(MITK_MODULE_NAME_PREFIX "Mitk") set(MITK_MODULE_NAME_DEFAULTS_TO_DIRECTORY_NAME 1) #----------------------------------- # Configuration of the buid-in MITK pixel types #----------------------------------- # create a list of types for template instantiations of itk image access functions function(_create_type_seq TYPES seq_var seqdim_var) set(_seq ) set(_seq_dim ) string(REPLACE "," ";" _pixeltypes "${TYPES}") foreach(_pixeltype ${_pixeltypes}) set(_seq "${_seq}(${_pixeltype})") set(_seq_dim "${_seq_dim}((${_pixeltype},dim))") endforeach() set(${seq_var} "${_seq}" PARENT_SCOPE) set(${seqdim_var} "${_seq_dim}" PARENT_SCOPE) endfunction() set(MITK_ACCESSBYITK_PIXEL_TYPES ) set(MITK_ACCESSBYITK_PIXEL_TYPES_SEQ ) set(MITK_ACCESSBYITK_TYPES_DIMN_SEQ ) # concatenate only the simple pixel types to the MITK_ACCESSBYITK_PIXEL_TYPE_SEQ list # see Bug 12682 for detailed information foreach(_type INTEGRAL FLOATING) set(_typelist "${MITK_ACCESSBYITK_${_type}_PIXEL_TYPES}") if(_typelist) if(MITK_ACCESSBYITK_PIXEL_TYPES) set(MITK_ACCESSBYITK_PIXEL_TYPES "${MITK_ACCESSBYITK_PIXEL_TYPES},${_typelist}") else() set(MITK_ACCESSBYITK_PIXEL_TYPES "${_typelist}") endif() endif() _create_type_seq("${_typelist}" MITK_ACCESSBYITK_${_type}_PIXEL_TYPES_SEQ MITK_ACCESSBYITK_${_type}_TYPES_DIMN_SEQ) set(MITK_ACCESSBYITK_PIXEL_TYPES_SEQ "${MITK_ACCESSBYITK_PIXEL_TYPES_SEQ}${MITK_ACCESSBYITK_${_type}_PIXEL_TYPES_SEQ}") set(MITK_ACCESSBYITK_TYPES_DIMN_SEQ "${MITK_ACCESSBYITK_TYPES_DIMN_SEQ}${MITK_ACCESSBYITK_${_type}_TYPES_DIMN_SEQ}") endforeach() # separate processing of the COMPOSITE list to avoid its concatenation to to global list _create_type_seq(${MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES} MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES_SEQ MITK_ACCESSBYITK_COMPOSITE_TYPES_DIMN_SEQ) set(MITK_ACCESSBYITK_DIMENSIONS_SEQ ) string(REPLACE "," ";" _dimensions "${MITK_ACCESSBYITK_DIMENSIONS}") foreach(_dimension ${_dimensions}) set(MITK_ACCESSBYITK_DIMENSIONS_SEQ "${MITK_ACCESSBYITK_DIMENSIONS_SEQ}(${_dimension})") endforeach() diff --git a/CMakeExternals/Boost.cmake b/CMakeExternals/Boost.cmake index 347f3348b1..472d69ca3d 100644 --- a/CMakeExternals/Boost.cmake +++ b/CMakeExternals/Boost.cmake @@ -1,115 +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 ${APPLE_CMAKE_SCRIPT}) - # If compiler is clang (for newer clang versions boost does not compile with libc++) - set(APPLE_CLANG_FLAGS) - if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang") - set(APPLE_CLANG_FLAGS toolset=clang cxxflags="-stdlib=libstdc++" linkflags="-stdlib=libstdc++") - endif() - - # If is specific OSX_SYSROOT is set + # 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 ${APPLE_CLANG_FLAGS} -q 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 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/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp b/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp index 309d0170d8..4c72aa88dd 100644 --- a/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp +++ b/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp @@ -1,664 +1,666 @@ /*=================================================================== 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 "mitkLiveWireTool2D.h" - -#include "mitkToolManager.h" -#include "mitkBaseRenderer.h" -#include "mitkRenderingManager.h" - -#include "mitkLiveWireTool2D.xpm" +#include -#include -#include +#include +#include #include +#include +#include +#include +#include +#include -#include "mitkContourUtils.h" -#include "mitkContour.h" - -#include - -// us -#include -#include #include +#include #include +#include + +#include "mitkLiveWireTool2D.h" +#include "mitkLiveWireTool2D.xpm" -namespace mitk { +namespace mitk +{ MITK_TOOL_MACRO(MitkSegmentation_EXPORT, LiveWireTool2D, "LiveWire tool"); } +static void AddInteractorToGlobalInteraction(mitk::Interactor* interactor) +{ + mitk::GlobalInteraction::GetInstance()->AddInteractor(interactor); +} -mitk::LiveWireTool2D::LiveWireTool2D() -:SegTool2D("LiveWireTool") +static void RemoveInteractorFromGlobalInteraction(mitk::Interactor* interactor) { + mitk::GlobalInteraction::GetInstance()->RemoveInteractor(interactor); } +class RemoveFromDataStorage +{ +public: + RemoveFromDataStorage(mitk::DataStorage::Pointer dataStorage) + : m_DataStorage(dataStorage) + { + } + + void operator()(mitk::DataNode* dataNode) + { + m_DataStorage->Remove(dataNode); + } + + void operator()(const std::pair& dataNode) + { + m_DataStorage->Remove(dataNode.first); + } + +private: + mitk::DataStorage::Pointer m_DataStorage; +}; +mitk::LiveWireTool2D::LiveWireTool2D() + : SegTool2D("LiveWireTool") +{ +} mitk::LiveWireTool2D::~LiveWireTool2D() { - this->m_WorkingContours.clear(); - this->m_EditingContours.clear(); + this->ClearSegmentation(); } +void mitk::LiveWireTool2D::RemoveHelperObjects() +{ + DataStorage* dataStorage = m_ToolManager->GetDataStorage(); + + if (!m_EditingContours.empty()) + std::for_each(m_EditingContours.begin(), m_EditingContours.end(), RemoveFromDataStorage(dataStorage)); -void mitk::LiveWireTool2D::ConnectActionsAndFunctions() + if (!m_WorkingContours.empty()) + std::for_each(m_WorkingContours.begin(), m_WorkingContours.end(), RemoveFromDataStorage(dataStorage)); + + if (m_EditingContourNode.IsNotNull()) + dataStorage->Remove(m_EditingContourNode); + + if (m_LiveWireContourNode.IsNotNull()) + dataStorage->Remove(m_LiveWireContourNode); + + if (m_ContourModelNode.IsNotNull()) + dataStorage->Remove(m_ContourModelNode); + + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); +} + +void mitk::LiveWireTool2D::ReleaseHelperObjects() { - CONNECT_CONDITION( "CheckContourClosed", OnCheckPoint ); + this->RemoveHelperObjects(); + + if (!m_EditingContours.empty()) + m_EditingContours.clear(); + + if (!m_WorkingContours.empty()) + m_WorkingContours.clear(); + + m_EditingContourNode = NULL; + m_EditingContour = NULL; + + m_LiveWireContourNode = NULL; + m_LiveWireContour = NULL; + m_ContourModelNode = NULL; + m_Contour = NULL; +} - CONNECT_FUNCTION( "InitObject", OnInitLiveWire); - CONNECT_FUNCTION( "AddPoint", OnAddPoint); - CONNECT_FUNCTION( "MovePoint", OnMouseMoveNoDynamicCosts); - CONNECT_FUNCTION( "FinishContour", OnFinish); - CONNECT_FUNCTION( "DeletePoint", OnLastSegmentDelete); - CONNECT_FUNCTION( "MovePoint", OnMouseMoved); +void mitk::LiveWireTool2D::ReleaseInteractors() +{ + this->EnableContourLiveWireInteraction(false); + m_LiveWireInteractors.clear(); } +void mitk::LiveWireTool2D::ConnectActionsAndFunctions() +{ + CONNECT_CONDITION("CheckContourClosed", OnCheckPoint); + + CONNECT_FUNCTION("InitObject", OnInitLiveWire); + CONNECT_FUNCTION("AddPoint", OnAddPoint); + CONNECT_FUNCTION("CtrlAddPoint", OnAddPoint); + CONNECT_FUNCTION("MovePoint", OnMouseMoveNoDynamicCosts); + CONNECT_FUNCTION("FinishContour", OnFinish); + CONNECT_FUNCTION("DeletePoint", OnLastSegmentDelete); + CONNECT_FUNCTION("CtrlMovePoint", OnMouseMoved); +} const char** mitk::LiveWireTool2D::GetXPM() const { return mitkLiveWireTool2D_xpm; } us::ModuleResource mitk::LiveWireTool2D::GetIconResource() const { - us::Module* module = us::GetModuleContext()->GetModule(); - us::ModuleResource resource = module->GetResource("LiveWire_48x48.png"); - return resource; + return us::GetModuleContext()->GetModule()->GetResource("LiveWire_48x48.png"); } us::ModuleResource mitk::LiveWireTool2D::GetCursorIconResource() const { - us::Module* module = us::GetModuleContext()->GetModule(); - us::ModuleResource resource = module->GetResource("LiveWire_Cursor_32x32.png"); - return resource; + return us::GetModuleContext()->GetModule()->GetResource("LiveWire_Cursor_32x32.png"); } const char* mitk::LiveWireTool2D::GetName() const { return "Live Wire"; } void mitk::LiveWireTool2D::Activated() { Superclass::Activated(); - - //enable interaction if there are any previously created contours + this->ResetToStartState(); this->EnableContourLiveWireInteraction(true); } void mitk::LiveWireTool2D::Deactivated() { Superclass::Deactivated(); - - //disable interaction with current contours - this->EnableContourLiveWireInteraction(false); + this->ConfirmSegmentation(); } -void mitk::LiveWireTool2D::ClearContours() -{ - // for all contours in list (currently created by tool) - std::vector< std::pair >::iterator iter = this->m_WorkingContours.begin(); - while(iter != this->m_WorkingContours.end() ) - { - //remove contour node from datastorage - m_ToolManager->GetDataStorage()->Remove( iter->first ); - - ++iter; - } - - this->m_WorkingContours.clear(); - - // for all contours in list (currently created by tool) - std::vector< std::pair >::iterator itEditingContours = this->m_EditingContours.begin(); - while(itEditingContours != this->m_EditingContours.end() ) - { - //remove contour node from datastorage - m_ToolManager->GetDataStorage()->Remove( itEditingContours->first ); - ++itEditingContours; - } - - this->m_EditingContours.clear(); - - this->EnableContourLiveWireInteraction(false); - this->m_LiveWireInteractors.clear(); -} - - void mitk::LiveWireTool2D::EnableContourLiveWireInteraction(bool on) { -//for all currently created contours enable or disable interactor - std::vector< mitk::ContourModelLiveWireInteractor::Pointer >::iterator itLiveWireInteractors = this->m_LiveWireInteractors.begin(); - std::vector< mitk::ContourModelLiveWireInteractor::Pointer >::iterator end = this->m_LiveWireInteractors.end(); - while(itLiveWireInteractors != end ) - { - if(on) - { - // add interactors to globalInteraction instance - mitk::GlobalInteraction::GetInstance()->AddInteractor( *itLiveWireInteractors ); - } - else - { - // remove interactors from globalInteraction instance - mitk::GlobalInteraction::GetInstance()->RemoveInteractor( *itLiveWireInteractors ); - } - ++itLiveWireInteractors; - } + std::for_each(m_LiveWireInteractors.begin(), m_LiveWireInteractors.end(), on + ? AddInteractorToGlobalInteraction + : RemoveInteractorFromGlobalInteraction); } - void mitk::LiveWireTool2D::ConfirmSegmentation() { DataNode* workingNode( m_ToolManager->GetWorkingData(0) ); - assert ( workingNode ); + + if (!workingNode) + return; Image* workingImage = dynamic_cast(workingNode->GetData()); - assert ( workingImage ); + if (!workingImage) + return; // for all contours in list (currently created by tool) std::vector< std::pair >::iterator itWorkingContours = this->m_WorkingContours.begin(); while(itWorkingContours != this->m_WorkingContours.end() ) { // if node contains data if( itWorkingContours->first->GetData() ) { // if this is a contourModel mitk::ContourModel* contourModel = dynamic_cast(itWorkingContours->first->GetData()); if( contourModel ) { // for each timestep of this contourModel for( TimeStepType currentTimestep = 0; currentTimestep < contourModel->GetTimeGeometry()->CountTimeSteps(); ++currentTimestep) { //get the segmentation image slice at current timestep mitk::Image::Pointer workingSlice = this->GetAffectedImageSliceAs2DImage(itWorkingContours->second, workingImage, currentTimestep); mitk::ContourModel::Pointer projectedContour = mitk::ContourModelUtils::ProjectContourTo2DSlice(workingSlice, contourModel, true, false); mitk::ContourModelUtils::FillContourInSlice(projectedContour, workingSlice, 1.0); //write back to image volume this->WriteBackSegmentationResult(itWorkingContours->second, workingSlice, currentTimestep); } - - //remove contour node from datastorage - // m_ToolManager->GetDataStorage()->Remove( itWorkingContours->first ); } } ++itWorkingContours; } -/* - this->m_WorkingContours.clear(); - - // for all contours in list (currently created by tool) - std::vector< std::pair >::iterator itEditingContours = this->m_EditingContours.begin(); - while(itEditingContours != this->m_EditingContours.end() ) - { - //remove contour node from datastorage - m_ToolManager->GetDataStorage()->Remove( itEditingContours->first ); - ++itEditingContours; - } - this->m_EditingContours.clear(); - - std::vector< mitk::ContourModelLiveWireInteractor::Pointer >::iterator itLiveWireInteractors = this->m_LiveWireInteractors.begin(); - while(itLiveWireInteractors != this->m_LiveWireInteractors.end() ) - { - // remove interactors from globalInteraction instance - mitk::GlobalInteraction::GetInstance()->RemoveInteractor( *itLiveWireInteractors ); - ++itLiveWireInteractors; - } + this->ReleaseHelperObjects(); + this->ReleaseInteractors(); +} - this->m_LiveWireInteractors.clear(); -*/ - this->ClearContours(); +void mitk::LiveWireTool2D::ClearSegmentation() +{ + this->ReleaseHelperObjects(); + this->ReleaseInteractors(); + this->ResetToStartState(); } bool mitk::LiveWireTool2D::OnInitLiveWire ( StateMachineAction*, InteractionEvent* interactionEvent ) { mitk::InteractionPositionEvent* positionEvent = dynamic_cast( interactionEvent ); - //const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); + if (!positionEvent) return false; m_LastEventSender = positionEvent->GetSender(); m_LastEventSlice = m_LastEventSender->GetSlice(); int timestep = positionEvent->GetSender()->GetTimeStep(); m_Contour = mitk::ContourModel::New(); m_Contour->Expand(timestep+1); m_ContourModelNode = mitk::DataNode::New(); m_ContourModelNode->SetData( m_Contour ); m_ContourModelNode->SetName("working contour node"); + m_ContourModelNode->SetProperty( "layer", IntProperty::New(100)); + m_ContourModelNode->AddProperty( "fixedLayer", BoolProperty::New(true)); m_ContourModelNode->SetProperty( "helper object", mitk::BoolProperty::New(true)); m_ContourModelNode->AddProperty( "contour.color", ColorProperty::New(1, 1, 0), NULL, true ); m_ContourModelNode->AddProperty( "contour.points.color", ColorProperty::New(1.0, 0.0, 0.1), NULL, true ); m_ContourModelNode->AddProperty( "contour.controlpoints.show", BoolProperty::New(true), NULL, true ); m_LiveWireContour = mitk::ContourModel::New(); m_LiveWireContour->Expand(timestep+1); m_LiveWireContourNode = mitk::DataNode::New(); m_LiveWireContourNode->SetData( m_LiveWireContour ); m_LiveWireContourNode->SetName("active livewire node"); - m_LiveWireContourNode->SetProperty( "layer", IntProperty::New(100)); + m_LiveWireContourNode->SetProperty( "layer", IntProperty::New(101)); + m_LiveWireContourNode->AddProperty( "fixedLayer", BoolProperty::New(true)); m_LiveWireContourNode->SetProperty( "helper object", mitk::BoolProperty::New(true)); m_LiveWireContourNode->AddProperty( "contour.color", ColorProperty::New(0.1, 1.0, 0.1), NULL, true ); m_LiveWireContourNode->AddProperty( "contour.width", mitk::FloatProperty::New( 4.0 ), NULL, true ); m_EditingContour = mitk::ContourModel::New(); m_EditingContour->Expand(timestep+1); m_EditingContourNode = mitk::DataNode::New(); m_EditingContourNode->SetData( m_EditingContour ); m_EditingContourNode->SetName("editing node"); - m_EditingContourNode->SetProperty( "layer", IntProperty::New(100)); + m_EditingContourNode->SetProperty( "layer", IntProperty::New(102)); + m_EditingContourNode->AddProperty( "fixedLayer", BoolProperty::New(true)); m_EditingContourNode->SetProperty( "helper object", mitk::BoolProperty::New(true)); m_EditingContourNode->AddProperty( "contour.color", ColorProperty::New(0.1, 1.0, 0.1), NULL, true ); m_EditingContourNode->AddProperty( "contour.points.color", ColorProperty::New(0.0, 0.0, 1.0), NULL, true ); m_EditingContourNode->AddProperty( "contour.width", mitk::FloatProperty::New( 4.0 ), NULL, true ); - m_ToolManager->GetDataStorage()->Add( m_ContourModelNode ); - m_ToolManager->GetDataStorage()->Add( m_LiveWireContourNode ); - m_ToolManager->GetDataStorage()->Add( m_EditingContourNode ); + mitk::DataNode* workingDataNode = m_ToolManager->GetWorkingData(0); + + m_ToolManager->GetDataStorage()->Add(m_ContourModelNode, workingDataNode); + m_ToolManager->GetDataStorage()->Add(m_LiveWireContourNode, workingDataNode); + m_ToolManager->GetDataStorage()->Add(m_EditingContourNode, workingDataNode); //set current slice as input for ImageToLiveWireContourFilter m_WorkingSlice = this->GetAffectedReferenceSlice(positionEvent); //Transfer LiveWire's center based contour output to corner based via the adaption of the input //slice image. Just in case someone stumbles across the 0.5 here I know what I'm doing ;-). m_WorkingSlice->GetSlicedGeometry()->ChangeImageGeometryConsideringOriginOffset(false); mitk::Point3D newOrigin = m_WorkingSlice->GetSlicedGeometry()->GetOrigin(); m_WorkingSlice->GetSlicedGeometry()->WorldToIndex(newOrigin, newOrigin); newOrigin[2] += 0.5; m_WorkingSlice->GetSlicedGeometry()->IndexToWorld(newOrigin, newOrigin); m_WorkingSlice->GetSlicedGeometry()->SetOrigin(newOrigin); m_LiveWireFilter = mitk::ImageLiveWireContourModelFilter::New(); m_LiveWireFilter->SetInput(m_WorkingSlice); //map click to pixel coordinates mitk::Point3D click = positionEvent->GetPositionInWorld(); itk::Index<3> idx; m_WorkingSlice->GetGeometry()->WorldToIndex(click, idx); // get the pixel the gradient in region of 5x5 itk::Index<3> indexWithHighestGradient; AccessFixedDimensionByItk_2(m_WorkingSlice, FindHighestGradientMagnitudeByITK, 2, idx, indexWithHighestGradient); // itk::Index to mitk::Point3D click[0] = indexWithHighestGradient[0]; click[1] = indexWithHighestGradient[1]; click[2] = indexWithHighestGradient[2]; m_WorkingSlice->GetGeometry()->IndexToWorld(click, click); //set initial start point m_Contour->AddVertex( click, true, timestep ); m_LiveWireFilter->SetStartPoint(click); m_CreateAndUseDynamicCosts = true; //render assert( positionEvent->GetSender()->GetRenderWindow() ); mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() ); return true; } bool mitk::LiveWireTool2D::OnAddPoint ( StateMachineAction*, InteractionEvent* interactionEvent ) { //complete LiveWire interaction for last segment //add current LiveWire contour to the finished contour and reset //to start new segment and computation /* check if event can be handled */ mitk::InteractionPositionEvent* positionEvent = dynamic_cast( interactionEvent ); - //const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (!positionEvent) return false; int timestep = positionEvent->GetSender()->GetTimeStep(); //add repulsive points to avoid to get the same path again typedef mitk::ImageLiveWireContourModelFilter::InternalImageType::IndexType IndexType; mitk::ContourModel::ConstVertexIterator iter = m_LiveWireContour->IteratorBegin(timestep); for (;iter != m_LiveWireContour->IteratorEnd(timestep); iter++) { IndexType idx; this->m_WorkingSlice->GetGeometry()->WorldToIndex((*iter)->Coordinates, idx); this->m_LiveWireFilter->AddRepulsivePoint( idx ); } //remove duplicate first vertex, it's already contained in m_Contour m_LiveWireContour->RemoveVertexAt(0, timestep); // set last added point as control point m_LiveWireContour->SetControlVertexAt(m_LiveWireContour->GetNumberOfVertices(timestep)-1, timestep); //merge contours m_Contour->Concatenate(m_LiveWireContour, timestep); //clear the livewire contour and reset the corresponding datanode m_LiveWireContour->Clear(timestep); //set new start point m_LiveWireFilter->SetStartPoint(positionEvent->GetPositionInWorld()); if( m_CreateAndUseDynamicCosts ) { //use dynamic cost map for next update m_LiveWireFilter->CreateDynamicCostMap(m_Contour); m_LiveWireFilter->SetUseDynamicCostMap(true); //m_CreateAndUseDynamicCosts = false; } //render assert( positionEvent->GetSender()->GetRenderWindow() ); mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() ); return true; } bool mitk::LiveWireTool2D::OnMouseMoved( StateMachineAction*, InteractionEvent* interactionEvent ) { //compute LiveWire segment from last control point to current mouse position - mitk::InteractionPositionEvent* positionEvent = dynamic_cast( interactionEvent ); - //const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (!positionEvent) return false; // actual LiveWire computation int timestep = positionEvent->GetSender()->GetTimeStep(); m_LiveWireFilter->SetEndPoint(positionEvent->GetPositionInWorld()); m_LiveWireFilter->SetTimeStep( timestep ); m_LiveWireFilter->Update(); m_LiveWireContour = this->m_LiveWireFilter->GetOutput(); m_LiveWireContourNode->SetData( this->m_LiveWireContour ); //render assert( positionEvent->GetSender()->GetRenderWindow() ); positionEvent->GetSender()->GetRenderingManager()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() ); return true; } bool mitk::LiveWireTool2D::OnMouseMoveNoDynamicCosts( StateMachineAction*, InteractionEvent* interactionEvent ) { //do not use dynamic cost map m_LiveWireFilter->SetUseDynamicCostMap(false); OnMouseMoved( NULL, interactionEvent); m_LiveWireFilter->SetUseDynamicCostMap(true); return true; } bool mitk::LiveWireTool2D::OnCheckPoint( const InteractionEvent* interactionEvent) { //check double click on first control point to finish the LiveWire tool // //Check distance to first point. //Transition YES if click close to first control point // const mitk::InteractionPositionEvent* positionEvent = dynamic_cast( interactionEvent ); if (positionEvent) { int timestep = positionEvent->GetSender()->GetTimeStep(); mitk::Point3D click = positionEvent->GetPositionInWorld(); mitk::Point3D first = this->m_Contour->GetVertexAt(0, timestep)->Coordinates; if (first.EuclideanDistanceTo(click) < 4.5) { // allow to finish return true; } else { return false; } } return false; } bool mitk::LiveWireTool2D::OnFinish( StateMachineAction*, InteractionEvent* interactionEvent ) { // finish livewire tool interaction mitk::InteractionPositionEvent* positionEvent = dynamic_cast( interactionEvent ); - //const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (!positionEvent) return false; // actual timestep int timestep = positionEvent->GetSender()->GetTimeStep(); // remove last control point being added by double click m_Contour->RemoveVertexAt(m_Contour->GetNumberOfVertices(timestep) - 1, timestep); // save contour and corresponding plane geometry to list std::pair cp(m_ContourModelNode, dynamic_cast(positionEvent->GetSender()->GetCurrentWorldGeometry2D()->Clone().GetPointer()) ); this->m_WorkingContours.push_back(cp); std::pair ecp(m_EditingContourNode, dynamic_cast(positionEvent->GetSender()->GetCurrentWorldGeometry2D()->Clone().GetPointer()) ); this->m_EditingContours.push_back(ecp); m_LiveWireFilter->SetUseDynamicCostMap(false); this->FinishTool(); return true; } void mitk::LiveWireTool2D::FinishTool() { TimeStepType numberOfTimesteps = m_Contour->GetTimeGeometry()->CountTimeSteps(); //close contour in each timestep for( int i = 0; i <= numberOfTimesteps; i++) { m_Contour->Close(i); } m_ToolManager->GetDataStorage()->Remove( m_LiveWireContourNode ); // clear live wire contour node m_LiveWireContourNode = NULL; m_LiveWireContour = NULL; - //change color as visual feedback of completed livewire - //m_ContourModelNode->AddProperty( "contour.color", ColorProperty::New(1.0, 1.0, 0.1), NULL, true ); - //m_ContourModelNode->SetName("contour node"); - //set the livewire interactor to edit control points m_ContourInteractor = mitk::ContourModelLiveWireInteractor::New(m_ContourModelNode); m_ContourInteractor->SetWorkingImage(this->m_WorkingSlice); m_ContourInteractor->SetEditingContourModelNode(this->m_EditingContourNode); m_ContourModelNode->SetInteractor(m_ContourInteractor); this->m_LiveWireInteractors.push_back( m_ContourInteractor ); //add interactor to globalInteraction instance mitk::GlobalInteraction::GetInstance()->AddInteractor(m_ContourInteractor); } bool mitk::LiveWireTool2D::OnLastSegmentDelete( StateMachineAction*, InteractionEvent* interactionEvent ) { int timestep = interactionEvent->GetSender()->GetTimeStep(); //if last point of current contour will be removed go to start state and remove nodes if( m_Contour->GetNumberOfVertices(timestep) <= 1 ) { m_ToolManager->GetDataStorage()->Remove( m_LiveWireContourNode ); m_ToolManager->GetDataStorage()->Remove( m_ContourModelNode ); m_ToolManager->GetDataStorage()->Remove( m_EditingContourNode ); m_LiveWireContour = mitk::ContourModel::New(); m_Contour = mitk::ContourModel::New(); m_ContourModelNode->SetData( m_Contour ); m_LiveWireContourNode->SetData( m_LiveWireContour ); this->ResetToStartState(); //go to start state } else //remove last segment from contour and reset livewire contour { m_LiveWireContour = mitk::ContourModel::New(); m_LiveWireContourNode->SetData(m_LiveWireContour); mitk::ContourModel::Pointer newContour = mitk::ContourModel::New(); newContour->Expand(m_Contour->GetTimeSteps()); mitk::ContourModel::VertexIterator begin = m_Contour->IteratorBegin(); //iterate from last point to next active point mitk::ContourModel::VertexIterator newLast = m_Contour->IteratorBegin() + (m_Contour->GetNumberOfVertices() - 1); //go at least one down if(newLast != begin) { newLast--; } //search next active control point while(newLast != begin && !((*newLast)->IsControlPoint) ) { newLast--; } //set position of start point for livewire filter to coordinates of the new last point m_LiveWireFilter->SetStartPoint((*newLast)->Coordinates); mitk::ContourModel::VertexIterator it = m_Contour->IteratorBegin(); //fill new Contour while(it <= newLast) { newContour->AddVertex((*it)->Coordinates, (*it)->IsControlPoint, timestep); it++; } newContour->SetClosed(m_Contour->IsClosed()); //set new contour visible m_ContourModelNode->SetData(newContour); m_Contour = newContour; assert( interactionEvent->GetSender()->GetRenderWindow() ); mitk::RenderingManager::GetInstance()->RequestUpdate( interactionEvent->GetSender()->GetRenderWindow() ); } return true; } template void mitk::LiveWireTool2D::FindHighestGradientMagnitudeByITK(itk::Image* inputImage, itk::Index<3> &index, itk::Index<3> &returnIndex) { typedef itk::Image InputImageType; typedef typename InputImageType::IndexType IndexType; unsigned long xMAX = inputImage->GetLargestPossibleRegion().GetSize()[0]; unsigned long yMAX = inputImage->GetLargestPossibleRegion().GetSize()[1]; returnIndex[0] = index[0]; returnIndex[1] = index[1]; returnIndex[2] = 0.0; double gradientMagnitude = 0.0; double maxGradientMagnitude = 0.0; /* the size and thus the region of 7x7 is only used to calculate the gradient magnitude in that region not for searching the maximum value */ //maximum value in each direction for size typename InputImageType::SizeType size; size[0] = 7; size[1] = 7; //minimum value in each direction for startRegion IndexType startRegion; startRegion[0] = index[0] - 3; startRegion[1] = index[1] - 3; if(startRegion[0] < 0) startRegion[0] = 0; if(startRegion[1] < 0) startRegion[1] = 0; if(xMAX - index[0] < 7) startRegion[0] = xMAX - 7; if(yMAX - index[1] < 7) startRegion[1] = yMAX - 7; index[0] = startRegion[0] + 3; index[1] = startRegion[1] + 3; typename InputImageType::RegionType region; region.SetSize( size ); region.SetIndex( startRegion ); typedef typename itk::GradientMagnitudeImageFilter< InputImageType, InputImageType> GradientMagnitudeFilterType; typename GradientMagnitudeFilterType::Pointer gradientFilter = GradientMagnitudeFilterType::New(); gradientFilter->SetInput(inputImage); gradientFilter->GetOutput()->SetRequestedRegion(region); gradientFilter->Update(); typename InputImageType::Pointer gradientMagnImage; gradientMagnImage = gradientFilter->GetOutput(); IndexType currentIndex; currentIndex[0] = 0; currentIndex[1] = 0; // search max (approximate) gradient magnitude for( int x = -1; x <= 1; ++x) { currentIndex[0] = index[0] + x; for( int y = -1; y <= 1; ++y) { currentIndex[1] = index[1] + y; gradientMagnitude = gradientMagnImage->GetPixel(currentIndex); //check for new max if(maxGradientMagnitude < gradientMagnitude) { maxGradientMagnitude = gradientMagnitude; returnIndex[0] = currentIndex[0]; returnIndex[1] = currentIndex[1]; returnIndex[2] = 0.0; }//end if }//end for y currentIndex[1] = index[1]; }//end for x } diff --git a/Modules/Segmentation/Interactions/mitkLiveWireTool2D.h b/Modules/Segmentation/Interactions/mitkLiveWireTool2D.h index f93f7bdd6b..ed93da3efd 100644 --- a/Modules/Segmentation/Interactions/mitkLiveWireTool2D.h +++ b/Modules/Segmentation/Interactions/mitkLiveWireTool2D.h @@ -1,151 +1,156 @@ /*=================================================================== 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 mitkCorrectorTool2D_h_Included #define mitkCorrectorTool2D_h_Included #include "mitkCommon.h" #include #include "mitkSegTool2D.h" #include #include #include namespace us { class ModuleResource; } namespace mitk { /** \brief A 2D segmentation tool based on LiveWire approach. The contour between the last user added point and the current mouse position is computed by searching the shortest path according to specific features of the image. The contour thus snappest to the boundary of objects. \sa SegTool2D \sa ImageLiveWireContourModelFilter \ingroup Interaction \ingroup ToolManagerEtAl \warning Only to be instantiated by mitk::ToolManager. */ class MitkSegmentation_EXPORT LiveWireTool2D : public SegTool2D { public: mitkClassMacro(LiveWireTool2D, SegTool2D); itkFactorylessNewMacro(Self) itkCloneMacro(Self) virtual const char** GetXPM() const; virtual us::ModuleResource GetCursorIconResource() const; us::ModuleResource GetIconResource() const; virtual const char* GetName() const; /// \brief Convert all current contour objects to binary segmentation image. void ConfirmSegmentation(); + /// \brief Delete all current contour objects. + void ClearSegmentation(); + protected: LiveWireTool2D(); virtual ~LiveWireTool2D(); void ConnectActionsAndFunctions(); virtual void Activated(); virtual void Deactivated(); - /// \brief Memory release from all used contours - virtual void ClearContours(); - /// \brief Initialize tool virtual bool OnInitLiveWire ( StateMachineAction*, InteractionEvent* interactionEvent ); /// \brief Add a control point and finish current segment virtual bool OnAddPoint ( StateMachineAction*, InteractionEvent* interactionEvent ); /// \brief Actual LiveWire computation virtual bool OnMouseMoved( StateMachineAction*, InteractionEvent* interactionEvent ); /// \brief Check double click on first control point to finish the LiveWire tool virtual bool OnCheckPoint( const InteractionEvent* interactionEvent ); /// \brief Finish LiveWire tool virtual bool OnFinish( StateMachineAction*, InteractionEvent* interactionEvent ); /// \brief Close the contour virtual bool OnLastSegmentDelete( StateMachineAction*, InteractionEvent* interactionEvent ); /// \brief Don't use dynamic cost map for LiveWire calculation virtual bool OnMouseMoveNoDynamicCosts( StateMachineAction*, InteractionEvent* interactionEvent ); /// \brief Finish contour interaction. void FinishTool(); /** \brief Enable interaction with contours. * Contours that are created by the tool can be edited using LiveWire functionality. * Points can thus be inserted, moved or deleted. * \param on true to have interaction enabled. */ void EnableContourLiveWireInteraction(bool on); //the contour already set by the user mitk::ContourModel::Pointer m_Contour; //the corresponding datanode mitk::DataNode::Pointer m_ContourModelNode; //the current LiveWire computed contour mitk::ContourModel::Pointer m_LiveWireContour; //the corresponding datanode mitk::DataNode::Pointer m_LiveWireContourNode; // the contour for the editing portion mitk::ContourModel::Pointer m_EditingContour; //the corresponding datanode mitk::DataNode::Pointer m_EditingContourNode; // the corresponding contour interactor mitk::ContourModelLiveWireInteractor::Pointer m_ContourInteractor; //the current reference image mitk::Image::Pointer m_WorkingSlice; // the filter for live wire calculation mitk::ImageLiveWireContourModelFilter::Pointer m_LiveWireFilter; bool m_CreateAndUseDynamicCosts; std::vector< std::pair > m_WorkingContours; std::vector< std::pair > m_EditingContours; std::vector< mitk::ContourModelLiveWireInteractor::Pointer > m_LiveWireInteractors; template void FindHighestGradientMagnitudeByITK(itk::Image* inputImage, itk::Index<3> &index, itk::Index<3> &returnIndex); + + private: + void RemoveHelperObjects(); + void ReleaseHelperObjects(); + void ReleaseInteractors(); }; } // namespace #endif diff --git a/Modules/Segmentation/Resources/Interactions/LiveWireTool.xml b/Modules/Segmentation/Resources/Interactions/LiveWireTool.xml index 409c47d1eb..e64b4c810b 100644 --- a/Modules/Segmentation/Resources/Interactions/LiveWireTool.xml +++ b/Modules/Segmentation/Resources/Interactions/LiveWireTool.xml @@ -1,34 +1,34 @@ - - + + - + - \ No newline at end of file + diff --git a/Modules/SegmentationUI/Qmitk/QmitkLiveWireTool2DGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkLiveWireTool2DGUI.cpp index 2ce6038c2d..9bf0646ecf 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkLiveWireTool2DGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkLiveWireTool2DGUI.cpp @@ -1,69 +1,69 @@ /*=================================================================== 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 "QmitkLiveWireTool2DGUI.h" #include "QmitkNewSegmentationDialog.h" #include #include #include #include #include #include "mitkStepper.h" #include "mitkBaseRenderer.h" MITK_TOOL_GUI_MACRO(MitkSegmentationUI_EXPORT, QmitkLiveWireTool2DGUI, "") QmitkLiveWireTool2DGUI::QmitkLiveWireTool2DGUI() -:QmitkToolGUI() + : QmitkToolGUI() { m_Controls.setupUi(this); m_Controls.m_Information->hide(); - connect( m_Controls.m_ConfirmButton, SIGNAL(clicked()), this, SLOT(OnConfirmSegmentation()) ); - - connect( this, SIGNAL(NewToolAssociated(mitk::Tool*)), this, SLOT(OnNewToolAssociated(mitk::Tool*)) ); - - connect( m_Controls.m_InformationCheckBox, SIGNAL(toggled(bool)), this, SLOT(OnShowInformation(bool)) ); + connect(m_Controls.m_ConfirmButton, SIGNAL(clicked()), this, SLOT(OnConfirmSegmentation())); + connect(m_Controls.m_ClearButton, SIGNAL(clicked()), this, SLOT(OnClearSegmentation())); + connect(this, SIGNAL(NewToolAssociated(mitk::Tool*)), this, SLOT(OnNewToolAssociated(mitk::Tool*))); + connect(m_Controls.m_InformationCheckBox, SIGNAL(toggled(bool)), this, SLOT(OnShowInformation(bool))); } QmitkLiveWireTool2DGUI::~QmitkLiveWireTool2DGUI() { } void QmitkLiveWireTool2DGUI::OnNewToolAssociated(mitk::Tool* tool) { - m_LiveWireTool = dynamic_cast( tool ); + m_LiveWireTool = dynamic_cast(tool); } void QmitkLiveWireTool2DGUI::OnConfirmSegmentation() { if (m_LiveWireTool.IsNotNull()) - { m_LiveWireTool->ConfirmSegmentation(); - } } -void QmitkLiveWireTool2DGUI::OnShowInformation( bool on ) +void QmitkLiveWireTool2DGUI::OnClearSegmentation() +{ + if (m_LiveWireTool.IsNotNull()) + m_LiveWireTool->ClearSegmentation(); +} + +void QmitkLiveWireTool2DGUI::OnShowInformation(bool on) { - if (on) - m_Controls.m_Information->show(); - else - m_Controls.m_Information->hide(); + m_Controls.m_Information->setVisible(on); } diff --git a/Modules/SegmentationUI/Qmitk/QmitkLiveWireTool2DGUI.h b/Modules/SegmentationUI/Qmitk/QmitkLiveWireTool2DGUI.h index 6d8f2cfc95..f78235a138 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkLiveWireTool2DGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitkLiveWireTool2DGUI.h @@ -1,68 +1,70 @@ /*=================================================================== 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 QmitkLiveWireTool2DGUI_h_Included #define QmitkLiveWireTool2DGUI_h_Included #include "QmitkToolGUI.h" #include #include "mitkLiveWireTool2D.h" #include "ui_QmitkLiveWireTool2DGUIControls.h" class QSlider; class QLabel; class QFrame; class QPushButton; #include #include "QmitkStepperAdapter.h" class QmitkLiveWireTool2DGUIControls; /** \ingroup org_mitk_gui_qt_interactivesegmentation_internal \brief GUI for mitk::LiveWireTool. \sa mitk::LiveWireTool2D */ class MitkSegmentationUI_EXPORT QmitkLiveWireTool2DGUI : public QmitkToolGUI { Q_OBJECT public: mitkClassMacro(QmitkLiveWireTool2DGUI, QmitkToolGUI); itkFactorylessNewMacro(Self) itkCloneMacro(Self) protected slots: void OnNewToolAssociated(mitk::Tool*); void OnConfirmSegmentation(); + void OnClearSegmentation(); + void OnShowInformation( bool on ); protected: QmitkLiveWireTool2DGUI(); virtual ~QmitkLiveWireTool2DGUI(); Ui::QmitkLiveWireTool2DGUIControls m_Controls; mitk::LiveWireTool2D::Pointer m_LiveWireTool; }; #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkLiveWireTool2DGUIControls.ui b/Modules/SegmentationUI/Qmitk/QmitkLiveWireTool2DGUIControls.ui index ebef715799..b14b68769b 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkLiveWireTool2DGUIControls.ui +++ b/Modules/SegmentationUI/Qmitk/QmitkLiveWireTool2DGUIControls.ui @@ -1,116 +1,115 @@ QmitkLiveWireTool2DGUIControls 0 0 421 355 0 0 0 0 QmitkLiveWireTool2DGUIControls Confirm all previous contour. - - 0 - - - 0 - - - 0 - - + 0 Confirm Segmentation + + + + Clear Segmentation + + + Qt::Vertical QSizePolicy::Fixed 20 15 Show usage information 0 150 12 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } -</style></head><body style=" font-family:'Cantarell'; font-size:12pt; font-weight:400; font-style:normal;"> +</style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:12pt; font-weight:400; font-style:normal;"> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans'; font-size:10pt;">The tool is started by a double-click near the object of interest.</span></p> -<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans'; font-size:10pt;">You can fix the preview segments by setting an ancor point with single left mouse button click. Pushing delete will remove each last segment. To close the contour and finish current segmentation perform a double click on the first ancor point.</span></p> +<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'Sans'; font-size:10pt;"><br /></p> +<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans'; font-size:10pt;">You can fix preview segments by adding ancor points with a single left mouse button click. Pressing &quot;Delete&quot; will remove the last segment. To close a contour and finish current segmentation perform a double click on the first ancor point.</span></p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'Sans'; font-size:10pt;"><br /></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans'; font-size:10pt;">After finishing a segmentation the contour will be still editable. You can move, insert and delete its ancor points.</span></p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'Sans'; font-size:10pt;"><br /></p> -<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans'; font-size:10pt;">Use the button &quot;Confirm Segmentation&quot; to fill all contours in the working image that were created with LiveWire tool.</span></p></body></html> +<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans'; font-size:10pt;">Push the &quot;Confirm Segmentation&quot; button or deactivate the Live Wire Tool to fill all contours in the working image. Push the &quot;Clear Segmentation&quot; button to delete all unconfirmed contours.</span></p></body></html> diff --git a/Modules/US/USHardwareTelemed/CMakeLists.txt b/Modules/US/USHardwareTelemed/CMakeLists.txt index 40fa96df73..265c4b6237 100644 --- a/Modules/US/USHardwareTelemed/CMakeLists.txt +++ b/Modules/US/USHardwareTelemed/CMakeLists.txt @@ -1,19 +1,19 @@ IF(WIN32) OPTION(MITK_USE_US_TELEMED_SDK "Enable support for Telemed api devices" OFF) IF(MITK_USE_US_TELEMED_SDK) SET(MITK_US_TELEMED_SDK_PATH "" CACHE PATH "Path to Telemed SDK header files.") -MITK_CREATE_MODULE(MitkUSHardwareTelemed +MITK_CREATE_MODULE( SUBPROJECTS DEPENDS MitkUS INCLUDE_DIRS "${MITK_US_TELEMED_SDK_PATH}" INTERNAL_INCLUDE_DIRS ${INCLUDE_DIRS_INTERNAL} AUTOLOAD_WITH MitkUS ) ENDIF(MITK_USE_US_TELEMED_SDK) -ENDIF(WIN32) \ No newline at end of file +ENDIF(WIN32) diff --git a/Plugins/org.mitk.gui.qt.segmentation/files.cmake b/Plugins/org.mitk.gui.qt.segmentation/files.cmake index 87782b75d3..24a87be816 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/files.cmake +++ b/Plugins/org.mitk.gui.qt.segmentation/files.cmake @@ -1,75 +1,78 @@ set(SRC_CPP_FILES QmitkSegmentationPreferencePage.cpp ) set(INTERNAL_CPP_FILES mitkPluginActivator.cpp QmitkSegmentationView.cpp QmitkThresholdAction.cpp QmitkCreatePolygonModelAction.cpp #QmitkStatisticsAction.cpp QmitkAutocropAction.cpp QmitkDeformableClippingPlaneView.cpp Common/QmitkDataSelectionWidget.cpp SegmentationUtilities/QmitkSegmentationUtilitiesView.cpp SegmentationUtilities/QmitkSegmentationUtilityWidget.cpp SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidget.cpp SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.cpp SegmentationUtilities/MorphologicalOperations/QmitkMorphologicalOperationsWidget.cpp SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidget.cpp SegmentationUtilities/CTKWidgets/QmitkCTKWidgetsWidget.cpp ) set(UI_FILES src/internal/QmitkSegmentationControls.ui src/internal/QmitkDeformableClippingPlaneViewControls.ui src/internal/Common/QmitkDataSelectionWidgetControls.ui src/internal/SegmentationUtilities/QmitkSegmentationUtilitiesViewControls.ui src/internal/SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidgetControls.ui src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui src/internal/SegmentationUtilities/MorphologicalOperations/QmitkMorphologicalOperationsWidgetControls.ui src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidgetControls.ui ) set(MOC_H_FILES src/QmitkSegmentationPreferencePage.h src/internal/mitkPluginActivator.h src/internal/QmitkSegmentationView.h src/internal/QmitkThresholdAction.h src/internal/QmitkCreatePolygonModelAction.h #src/internal/QmitkStatisticsAction.h src/internal/QmitkAutocropAction.h src/internal/QmitkDeformableClippingPlaneView.h src/internal/Common/QmitkDataSelectionWidget.h src/internal/SegmentationUtilities/QmitkSegmentationUtilitiesView.h src/internal/SegmentationUtilities/QmitkSegmentationUtilityWidget.h src/internal/SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidget.h src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.h src/internal/SegmentationUtilities/MorphologicalOperations/QmitkMorphologicalOperationsWidget.h src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidget.h src/internal/SegmentationUtilities/CTKWidgets/QmitkCTKWidgetsWidget.h ) set(CACHED_RESOURCE_FILES resources/segmentation.png resources/deformablePlane.png + resources/clipping_plane_translate_48x48.png + resources/clipping_plane_rotate48x48.png + resources/clipping_plane_deform48x48.png resources/SegmentationUtilities_48x48.png plugin.xml ) set(QRC_FILES resources/segmentation.qrc resources/SegmentationUtilities.qrc resources/BooleanOperationsWidget.qrc resources/MorphologicalOperationsWidget.qrc ) set(CPP_FILES) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.segmentation/resources/clipping_plane_deform48x48.png b/Plugins/org.mitk.gui.qt.segmentation/resources/clipping_plane_deform48x48.png new file mode 100644 index 0000000000..d8ae43e57c Binary files /dev/null and b/Plugins/org.mitk.gui.qt.segmentation/resources/clipping_plane_deform48x48.png differ diff --git a/Plugins/org.mitk.gui.qt.segmentation/resources/clipping_plane_rotate48x48.png b/Plugins/org.mitk.gui.qt.segmentation/resources/clipping_plane_rotate48x48.png new file mode 100644 index 0000000000..89f016df7a Binary files /dev/null and b/Plugins/org.mitk.gui.qt.segmentation/resources/clipping_plane_rotate48x48.png differ diff --git a/Plugins/org.mitk.gui.qt.segmentation/resources/clipping_plane_translate_48x48.png b/Plugins/org.mitk.gui.qt.segmentation/resources/clipping_plane_translate_48x48.png new file mode 100644 index 0000000000..fa3fc20cdd Binary files /dev/null and b/Plugins/org.mitk.gui.qt.segmentation/resources/clipping_plane_translate_48x48.png differ diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkDeformableClippingPlaneView.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkDeformableClippingPlaneView.cpp index 5bfc026303..696e238a12 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkDeformableClippingPlaneView.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkDeformableClippingPlaneView.cpp @@ -1,591 +1,608 @@ /*=================================================================== 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 "QmitkDeformableClippingPlaneView.h" #include "mitkAffineDataInteractor3D.h" #include "mitkHeightFieldSurfaceClipImageFilter.h" #include "mitkImageToSurfaceFilter.h" #include "mitkInteractionConst.h" #include "mitkLabeledImageLookupTable.h" #include "mitkLabeledImageVolumeCalculator.h" #include "mitkLevelWindowProperty.h" #include "mitkLookupTableProperty.h" #include "mitkNodePredicateProperty.h" #include "mitkNodePredicateDataType.h" #include "mitkPlane.h" #include "mitkRenderingModeProperty.h" #include "mitkRotationOperation.h" #include "mitkSurfaceDeformationDataInteractor3D.h" #include "mitkSurfaceVtkMapper3D.h" #include "mitkVtkRepresentationProperty.h" #include "usModuleRegistry.h" #include "vtkFloatArray.h" #include "vtkPointData.h" #include "vtkProperty.h" const std::string QmitkDeformableClippingPlaneView::VIEW_ID = "org.mitk.views.deformableclippingplane"; QmitkDeformableClippingPlaneView::QmitkDeformableClippingPlaneView() : QmitkFunctionality() , m_MultiWidget(NULL) , m_ReferenceNode(NULL) , m_WorkingNode(NULL) { } QmitkDeformableClippingPlaneView::~QmitkDeformableClippingPlaneView() { } void QmitkDeformableClippingPlaneView::CreateQtPartControl(QWidget *parent) { // create GUI widgets m_Controls.setupUi(parent); this->CreateConnections(); } void QmitkDeformableClippingPlaneView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkDeformableClippingPlaneView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkDeformableClippingPlaneView::CreateConnections() { mitk::NodePredicateProperty::Pointer clipPredicate = mitk::NodePredicateProperty::New("clippingPlane",mitk::BoolProperty::New(true)); //set only clipping planes in the list of the selector m_Controls.clippingPlaneSelector->SetDataStorage(this->GetDefaultDataStorage()); m_Controls.clippingPlaneSelector->SetPredicate(clipPredicate); //No working data set, yet m_Controls.volumeGroupBox->setEnabled(false); m_Controls.interactionSelectionBox->setEnabled(false); m_Controls.noSelectedImageLabel->show(); m_Controls.planesWarningLabel->hide(); connect (m_Controls.translationPushButton, SIGNAL(toggled(bool)), this, SLOT(OnTranslationMode(bool))); connect (m_Controls.rotationPushButton, SIGNAL(toggled(bool)), this, SLOT(OnRotationMode(bool))); connect (m_Controls.deformationPushButton, SIGNAL(toggled(bool)), this, SLOT(OnDeformationMode(bool))); connect (m_Controls.createNewPlanePushButton, SIGNAL(clicked()), this, SLOT(OnCreateNewClippingPlane())); connect (m_Controls.updateVolumePushButton, SIGNAL(clicked()), this, SLOT(OnCalculateClippingVolume())); connect (m_Controls.clippingPlaneSelector, SIGNAL(OnSelectionChanged(const mitk::DataNode*)), this, SLOT(OnComboBoxSelectionChanged(const mitk::DataNode*))); } void QmitkDeformableClippingPlaneView::Activated() { QmitkFunctionality::Activated(); + //If a tube graph already exist in the data storage, set the working node correctly + m_WorkingNode = m_Controls.clippingPlaneSelector->GetSelectedNode(); + this->UpdateView(); } void QmitkDeformableClippingPlaneView::Deactivated() { + if(m_WorkingNode.IsNotNull()) + { + if(m_WorkingNode->GetDataInteractor().IsNotNull()) + m_WorkingNode->SetDataInteractor(NULL); + } QmitkFunctionality::Deactivated(); } void QmitkDeformableClippingPlaneView::OnComboBoxSelectionChanged( const mitk::DataNode* node ) { mitk::DataNode* selectedNode = const_cast(node); if( selectedNode != NULL ) { if(m_WorkingNode.IsNotNull()) selectedNode->SetDataInteractor(m_WorkingNode->GetDataInteractor()); m_WorkingNode = selectedNode; } this->UpdateView(); } void QmitkDeformableClippingPlaneView::OnSelectionChanged(mitk::DataNode* node) { std::vector nodes; nodes.push_back(node); this->OnSelectionChanged(nodes); } void QmitkDeformableClippingPlaneView::OnSelectionChanged(std::vector nodes) { bool isClippingPlane(false); for(unsigned int i = 0; i < nodes.size(); ++i) { if(nodes.at(i)->GetBoolProperty("clippingPlane", isClippingPlane)) m_Controls.clippingPlaneSelector->setCurrentIndex( m_Controls.clippingPlaneSelector->Find(nodes.at(i)) ); else { if(dynamic_cast (nodes.at(i)->GetData())&& nodes.at(i)) { if(m_ReferenceNode.IsNotNull() && nodes.at(i)->GetData() == m_ReferenceNode->GetData()) return; m_ReferenceNode =nodes.at(i); } } } this->UpdateView(); } void::QmitkDeformableClippingPlaneView::NodeChanged(const mitk::DataNode* /*node*/) { this->UpdateView(); } void QmitkDeformableClippingPlaneView::NodeRemoved(const mitk::DataNode* node) { bool isClippingPlane(false); if (node->GetBoolProperty("clippingPlane", isClippingPlane)) { if(this->GetAllClippingPlanes()->Size()<=1) { m_WorkingNode = NULL; this->UpdateView(); } else { if (GetAllClippingPlanes()->front()!= node) this->OnSelectionChanged(GetAllClippingPlanes()->front()); else this->OnSelectionChanged(GetAllClippingPlanes()->ElementAt(1)); } } else { if(m_ReferenceNode.IsNotNull()) { if(node->GetData() == m_ReferenceNode->GetData()) { m_ReferenceNode = NULL; m_Controls.volumeList->clear(); } this->UpdateView(); } } } void QmitkDeformableClippingPlaneView::UpdateView() { if (m_ReferenceNode.IsNotNull()) { m_Controls.noSelectedImageLabel->hide(); m_Controls.selectedImageLabel->setText(QString::fromUtf8(m_ReferenceNode->GetName().c_str())); if (m_WorkingNode.IsNotNull()) { bool isSegmentation(false); m_ReferenceNode->GetBoolProperty("binary", isSegmentation); m_Controls.interactionSelectionBox->setEnabled(true); m_Controls.volumeGroupBox->setEnabled(isSegmentation); //clear list --> than search for all shown clipping plans (max 7 planes) m_Controls.selectedVolumePlanesLabel->setText(""); m_Controls.planesWarningLabel->hide(); int volumePlanes=0; mitk::DataStorage::SetOfObjects::ConstPointer allClippingPlanes = this->GetAllClippingPlanes(); for (mitk::DataStorage::SetOfObjects::ConstIterator itPlanes = allClippingPlanes->Begin(); itPlanes != allClippingPlanes->End(); itPlanes++) { bool isVisible(false); itPlanes.Value()->GetBoolProperty("visible",isVisible); if (isVisible) { if (volumePlanes<7) { volumePlanes ++; m_Controls.selectedVolumePlanesLabel->setText(m_Controls.selectedVolumePlanesLabel->text().append(QString::fromStdString(itPlanes.Value()->GetName()+"\n"))); } else { m_Controls.planesWarningLabel->show(); return; } } } } else { m_Controls.volumeGroupBox->setEnabled(false); m_Controls.interactionSelectionBox->setEnabled(false); m_Controls.selectedVolumePlanesLabel->setText(""); m_Controls.volumeList->clear(); } } else { m_Controls.volumeGroupBox->setEnabled(false); m_Controls.noSelectedImageLabel->show(); m_Controls.selectedImageLabel->setText(""); m_Controls.selectedVolumePlanesLabel->setText(""); m_Controls.planesWarningLabel->hide(); if(m_WorkingNode.IsNull()) m_Controls.interactionSelectionBox->setEnabled(false); else m_Controls.interactionSelectionBox->setEnabled(true); } } void QmitkDeformableClippingPlaneView::OnCreateNewClippingPlane() { mitk::Image::Pointer referenceImage = mitk::Image::New(); //the new clipping plane mitk::Plane::Pointer plane = mitk::Plane::New(); double imageDiagonal = 200; if (m_ReferenceNode.IsNotNull()) { referenceImage = dynamic_cast (m_ReferenceNode->GetData()); if (referenceImage.IsNotNull()) { // check if user wants a surface model if(m_Controls.surfaceModelCheckBox->isChecked()) { //Check if there is a surface node from the image. If not, create one bool createSurfaceFromImage(true); mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); mitk::NodePredicateDataType::Pointer isSurface = mitk::NodePredicateDataType::New("Surface"); mitk::DataStorage::SetOfObjects::ConstPointer childNodes = GetDataStorage()->GetDerivations(m_ReferenceNode,isSurface, true); for (mitk::DataStorage::SetOfObjects::ConstIterator itChildNodes = childNodes->Begin(); itChildNodes != childNodes->End(); itChildNodes++) { if (itChildNodes.Value().IsNotNull()) createSurfaceFromImage=false; } if(createSurfaceFromImage) { //Lsg 2: Surface for the 3D-perspective mitk::ImageToSurfaceFilter::Pointer surfaceFilter = mitk::ImageToSurfaceFilter::New(); surfaceFilter->SetInput(referenceImage); surfaceFilter->SetThreshold(1); surfaceFilter->SetSmooth(true); //Downsampling surfaceFilter->SetDecimate(mitk::ImageToSurfaceFilter::DecimatePro); mitk::DataNode::Pointer surfaceNode = mitk::DataNode::New(); surfaceNode->SetData(surfaceFilter->GetOutput()); surfaceNode->SetProperty("color", m_ReferenceNode->GetProperty("color")); surfaceNode->SetOpacity(0.5); surfaceNode->SetName(m_ReferenceNode->GetName()); GetDataStorage()->Add(surfaceNode, m_ReferenceNode); } } //If an image is selected trim the plane to this. imageDiagonal = referenceImage->GetGeometry()->GetDiagonalLength(); plane->SetOrigin( referenceImage->GetGeometry()->GetCenter()); // Rotate plane mitk::Vector3D rotationAxis; mitk::FillVector3D(rotationAxis, 0.0, 1.0, 0.0); mitk::RotationOperation op(mitk::OpROTATE, referenceImage->GetGeometry()->GetCenter(), rotationAxis, 90.0); plane->GetGeometry()->ExecuteOperation(&op); } } //set some properties for the clipping plane plane->SetExtent(imageDiagonal * 0.9, imageDiagonal * 0.9); plane->SetResolution(64, 64); // Set scalars (for colorization of plane) vtkFloatArray *scalars = vtkFloatArray::New(); scalars->SetName("Distance"); scalars->SetNumberOfComponents(1); for ( unsigned int i = 0; i < plane->GetVtkPolyData(0)->GetNumberOfPoints(); ++i) { scalars->InsertNextValue(-1.0); } plane->GetVtkPolyData(0)->GetPointData()->SetScalars(scalars); plane->GetVtkPolyData(0)->GetPointData()->Update(); mitk::DataNode::Pointer planeNode = mitk::DataNode::New(); planeNode->SetData(plane); std::stringstream planeName; planeName << "ClippingPlane "; planeName << this->GetAllClippingPlanes()->Size() + 1; planeNode->SetName(planeName.str()); planeNode->AddProperty("clippingPlane",mitk::BoolProperty::New(true)); // Make plane pickable planeNode->SetBoolProperty("pickable", true); mitk::SurfaceVtkMapper3D::SetDefaultProperties(planeNode); // Don't include plane in bounding box! planeNode->SetProperty("includeInBoundingBox", mitk::BoolProperty::New(false)); // Set lookup table for plane surface visualization vtkSmartPointer lookupTable = vtkSmartPointer::New(); lookupTable->SetHueRange(0.6, 0.0); lookupTable->SetSaturationRange(1.0, 1.0); lookupTable->SetValueRange(1.0, 1.0); lookupTable->SetTableRange(-1.0, 1.0); lookupTable->Build(); mitk::LookupTable::Pointer lut = mitk::LookupTable::New(); lut->SetVtkLookupTable(lookupTable); mitk::LookupTableProperty::Pointer prop = mitk::LookupTableProperty::New(lut); planeNode->SetProperty("LookupTable", prop); planeNode->SetBoolProperty("scalar visibility", true); planeNode->SetBoolProperty("color mode", true); planeNode->SetFloatProperty("ScalarsRangeMinimum", -1.0); planeNode->SetFloatProperty("ScalarsRangeMaximum", 1.0); // Configure material so that only scalar colors are shown planeNode->SetColor(0.0f,0.0f,0.0f); planeNode->SetOpacity(1.0f); planeNode->SetFloatProperty("material.wireframeLineWidth",2.0f); //Set view of plane to wireframe planeNode->SetProperty("material.representation", mitk::VtkRepresentationProperty::New(VTK_WIREFRAME)); //Set the plane as working data for the tools and selected it this->OnSelectionChanged (planeNode); //Add the plane to data storage this->GetDataStorage()->Add(planeNode); //Change the index of the selector to the new generated node m_Controls.clippingPlaneSelector->setCurrentIndex( m_Controls.clippingPlaneSelector->Find(planeNode) ); m_Controls.interactionSelectionBox->setEnabled(true); // set crosshair invisible mitk::DataNode* dataNode; dataNode = this->m_MultiWidget->GetWidgetPlane1(); if(dataNode) dataNode->SetVisibility(false); dataNode = this->m_MultiWidget->GetWidgetPlane2(); if(dataNode) dataNode->SetVisibility(false); dataNode = this->m_MultiWidget->GetWidgetPlane3(); if(dataNode) dataNode->SetVisibility(false); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkDeformableClippingPlaneView::OnCalculateClippingVolume() { bool isSegmentation(false); m_ReferenceNode->GetBoolProperty("binary", isSegmentation); if(m_ReferenceNode.IsNull() || !isSegmentation) { MITK_ERROR << "No segmentation selected! Can't calculate volume"; return; } std::vector clippingPlanes; mitk::DataStorage::SetOfObjects::ConstPointer allClippingPlanes = this->GetAllClippingPlanes(); for (mitk::DataStorage::SetOfObjects::ConstIterator itPlanes = allClippingPlanes->Begin(); itPlanes != allClippingPlanes->End(); itPlanes++) { bool isVisible(false); itPlanes.Value()->GetBoolProperty("visible",isVisible); mitk::Surface* plane = dynamic_cast(itPlanes.Value()->GetData()); if (isVisible && plane) clippingPlanes.push_back(plane); } if (clippingPlanes.empty()) { MITK_ERROR << "No clipping plane selected! Can't calculate volume"; return; } // deactivate Tools m_Controls.translationPushButton->setChecked(false); m_Controls.rotationPushButton->setChecked(false); m_Controls.deformationPushButton->setChecked(false); //Clear the list of volumes, before calculating the new values m_Controls.volumeList->clear(); m_ReferenceNode->SetBoolProperty("visible", false); //set some properties for clipping the image-->Output: labled Image mitk::HeightFieldSurfaceClipImageFilter::Pointer surfaceClipFilter = mitk::HeightFieldSurfaceClipImageFilter::New(); surfaceClipFilter->SetInput(dynamic_cast (m_ReferenceNode->GetData())); surfaceClipFilter->SetClippingModeToMultiPlaneValue(); surfaceClipFilter->SetClippingSurfaces(clippingPlanes); surfaceClipFilter->Update(); //delete the old clipped image node mitk::DataStorage::SetOfObjects::ConstPointer oldClippedNode = this->GetDataStorage()->GetSubset(mitk::NodePredicateProperty::New("name", mitk::StringProperty::New("Clipped Image"))); if (oldClippedNode.IsNotNull()) this->GetDataStorage()->Remove(oldClippedNode); //add the new clipped image node mitk::DataNode::Pointer clippedNode = mitk::DataNode::New(); mitk::Image::Pointer clippedImage = surfaceClipFilter->GetOutput(); clippedImage->DisconnectPipeline(); clippedNode->SetData(clippedImage); //clippedNode->SetProperty("helper object", mitk::BoolProperty::New(true)); clippedNode->SetName("Clipped Image"); clippedNode->SetColor(1.0,1.0,1.0); // color property will not be used, labeled image lookuptable will be used instead clippedNode->SetProperty ("use color", mitk::BoolProperty::New(false)); clippedNode->SetOpacity(0.4); this->GetDataStorage()->Add(clippedNode); mitk::LabeledImageVolumeCalculator::Pointer volumeCalculator = mitk::LabeledImageVolumeCalculator::New(); volumeCalculator->SetImage(clippedImage); volumeCalculator->Calculate(); std::vector volumes = volumeCalculator->GetVolumes(); mitk::LabeledImageLookupTable::Pointer lut = mitk::LabeledImageLookupTable::New(); int lablesWithVolume=0; for(unsigned int i = 1; i < volumes.size(); ++i) { if(volumes.at(i)!=0) { lablesWithVolume++; mitk::Color color (GetLabelColor(lablesWithVolume)); lut->SetColorForLabel(i,color.GetRed(), color.GetGreen(), color.GetBlue(), 1.0); QColor qcolor; qcolor.setRgbF(color.GetRed(), color.GetGreen(), color.GetBlue(), 0.7); //output volume as string "x.xx ml" std::stringstream stream; stream<< std::fixed << std::setprecision(2)<setText(QString::fromStdString(stream.str())); item->setBackgroundColor(qcolor); m_Controls.volumeList->addItem(item); } } //set the rendering mode to use the lookup table and level window clippedNode->SetProperty("Image Rendering.Mode", mitk::RenderingModeProperty::New(mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR)); mitk::LookupTableProperty::Pointer lutProp = mitk::LookupTableProperty::New(lut.GetPointer()); clippedNode->SetProperty("LookupTable", lutProp); // it is absolutely important, to use the LevelWindow settings provided by // the LUT generator, otherwise, it is not guaranteed, that colors show // up correctly. clippedNode->SetProperty("levelwindow", mitk::LevelWindowProperty::New(lut->GetLevelWindow())); } mitk::DataStorage::SetOfObjects::ConstPointer QmitkDeformableClippingPlaneView::GetAllClippingPlanes() { mitk::NodePredicateProperty::Pointer clipPredicate= mitk::NodePredicateProperty::New("clippingPlane",mitk::BoolProperty::New(true)); mitk::DataStorage::SetOfObjects::ConstPointer allPlanes = GetDataStorage()->GetSubset(clipPredicate); return allPlanes; } mitk::Color QmitkDeformableClippingPlaneView::GetLabelColor(int label) { float red, green, blue; switch ( label % 6 ) { case 0: {red = 1.0; green = 0.0; blue = 0.0; break;} case 1: {red = 0.0; green = 1.0; blue = 0.0; break;} case 2: {red = 0.0; green = 0.0; blue = 1.0;break;} case 3: {red = 1.0; green = 1.0; blue = 0.0;break;} case 4: {red = 1.0; green = 0.0; blue = 1.0;break;} case 5: {red = 0.0; green = 1.0; blue = 1.0;break;} default: {red = 0.0; green = 0.0; blue = 0.0;} } float tmp[3] = { red, green, blue }; double factor; int outerCycleNr = label / 6; int cycleSize = pow(2.0,(int)(log((double)(outerCycleNr))/log( 2.0 ))); if (cycleSize==0) cycleSize = 1; int insideCycleCounter = outerCycleNr % cycleSize; if ( outerCycleNr == 0) factor = 255; else factor = ( 256 / ( 2 * cycleSize ) ) + ( insideCycleCounter * ( 256 / cycleSize ) ); tmp[0]= tmp[0]/256*factor; tmp[1]= tmp[1]/256*factor; tmp[2]= tmp[2]/256*factor; return mitk::Color(tmp); } void QmitkDeformableClippingPlaneView::OnTranslationMode(bool check) { if(check) - { + { //uncheck all other buttons + m_Controls.rotationPushButton->setChecked(false); + m_Controls.deformationPushButton->setChecked(false); + mitk::AffineDataInteractor3D::Pointer affineDataInteractor = mitk::AffineDataInteractor3D::New(); affineDataInteractor->LoadStateMachine("AffineInteraction3D.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt")); affineDataInteractor->SetEventConfig("AffineTranslationConfig.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt")); affineDataInteractor->SetDataNode(m_WorkingNode); } else m_WorkingNode->SetDataInteractor(NULL); } void QmitkDeformableClippingPlaneView::OnRotationMode(bool check) { if(check) - { + { //uncheck all other buttons + m_Controls.translationPushButton->setChecked(false); + m_Controls.deformationPushButton->setChecked(false); + mitk::AffineDataInteractor3D::Pointer affineDataInteractor = mitk::AffineDataInteractor3D::New(); affineDataInteractor->LoadStateMachine("AffineInteraction3D.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt")); affineDataInteractor->SetEventConfig("AffineRotationConfig.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt")); affineDataInteractor->SetDataNode(m_WorkingNode); } else m_WorkingNode->SetDataInteractor(NULL); } void QmitkDeformableClippingPlaneView::OnDeformationMode(bool check) { if(check) - { + { //uncheck all other buttons + m_Controls.translationPushButton->setChecked(false); + m_Controls.rotationPushButton->setChecked(false); + mitk::SurfaceDeformationDataInteractor3D::Pointer surfaceDataInteractor = mitk::SurfaceDeformationDataInteractor3D::New(); surfaceDataInteractor->LoadStateMachine("AffineInteraction3D.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt")); surfaceDataInteractor->SetEventConfig("AffineDeformationConfig.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt")); surfaceDataInteractor->SetDataNode(m_WorkingNode); } else m_WorkingNode->SetDataInteractor(NULL); } diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkDeformableClippingPlaneViewControls.ui b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkDeformableClippingPlaneViewControls.ui index 68899ad83d..8507259989 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkDeformableClippingPlaneViewControls.ui +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkDeformableClippingPlaneViewControls.ui @@ -1,564 +1,611 @@ QmitkDeformableClippingPlaneViewControls 0 0 - 601 - 837 + 422 + 642 0 0 QmitkDeformableSurface 0 0 197 0 0 191 0 0 189 0 0 197 0 0 191 0 0 189 0 0 120 120 120 120 120 120 120 120 120 Please select an image! false false 0 0 Create new clipping plane Qt::RightToLeft ...with surface model true 0 0 0 0 16777215 16777215 Plane 0 0 QComboBox::AdjustToMinimumContentsLength true 50 false 0 0 - 0 + 20 50 - + Translation + + + + + + :/org.mitk.gui.qt.segmentation/resources/clipping_plane_translate_48x48.png:/org.mitk.gui.qt.segmentation/resources/clipping_plane_translate_48x48.png + + + + 32 + 32 + + true false - true + false 0 0 - 0 + 20 50 - + Rotation + + + + + + :/org.mitk.gui.qt.segmentation/resources/clipping_plane_rotate48x48.png:/org.mitk.gui.qt.segmentation/resources/clipping_plane_rotate48x48.png + + + + 32 + 32 + + true - true + false 0 0 - 0 + 20 50 - + Deformation + + + + + + :/org.mitk.gui.qt.segmentation/resources/clipping_plane_deform48x48.png:/org.mitk.gui.qt.segmentation/resources/clipping_plane_deform48x48.png + + + + 32 + 32 + + true - true + false Qt::Vertical QSizePolicy::Preferred 20 20 0 0 197 0 0 191 0 0 189 0 0 197 0 0 191 0 0 189 0 0 120 120 120 120 120 120 120 120 120 Please select less or equal 6 clipping planes! - + 0 0 0 0 Referenced image 0 0 Clipping planes Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop true 0 0 MS Shell Dlg 2 8 50 false 8 Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop Update Volumina Qt::Vertical QSizePolicy::Preferred 20 20 true + + + 0 + 0 + + QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 - + + +