diff --git a/Applications/CMakeLists.txt b/Applications/CMakeLists.txt
index 67222278ec..558a531c3e 100644
--- a/Applications/CMakeLists.txt
+++ b/Applications/CMakeLists.txt
@@ -1,35 +1,36 @@
set(MITK_CPACK_PACKAGE_EXECUTABLES "" CACHE INTERNAL "Collecting windows shortcuts to executables" FORCE)
set(MITK_DIR ${PROJECT_BINARY_DIR})
set(MITK_EXPORTS_FILE_INCLUDED 1)
if(MITK_USE_Qt5)
+ #[[ See T27701
if(MITK_USE_CTK)
add_subdirectory(PluginGenerator)
- endif()
+ endif()]]
if(MITK_USE_BLUEBERRY)
foreach(MITK_EXTENSION_DIR ${MITK_DIR_PLUS_EXTENSION_DIRS})
set(MITK_APPLICATIONS_EXTENSION_DIR ${MITK_EXTENSION_DIR}/Applications)
get_filename_component(MITK_APPLICATIONS_EXTENSION_DIR ${MITK_APPLICATIONS_EXTENSION_DIR} ABSOLUTE)
if(EXISTS ${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake)
set(MITK_APPS "")
include(${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake)
foreach(mitk_app ${MITK_APPS})
# extract target_dir and option_name
string(REPLACE "^^" "\\;" target_info ${mitk_app})
set(target_info_list ${target_info})
list(GET target_info_list 0 target_dir)
list(GET target_info_list 1 option_name)
# check if the application is enabled
if(${option_name} OR MITK_BUILD_ALL_APPS)
add_subdirectory(${MITK_APPLICATIONS_EXTENSION_DIR}/${target_dir} ${target_dir})
endif()
endforeach()
endif()
endforeach()
endif()
endif()
diff --git a/Applications/PluginGenerator/CMakeLists.txt b/Applications/PluginGenerator/CMakeLists.txt
index 81765479ad..aebbe5def5 100644
--- a/Applications/PluginGenerator/CMakeLists.txt
+++ b/Applications/PluginGenerator/CMakeLists.txt
@@ -1,78 +1,73 @@
if (${CMAKE_SOURCE_DIR} EQUAL ${PROJECT_SOURCE_DIR})
cmake_minimum_required(VERSION 3.14.5 FATAL_ERROR)
endif()
project(MitkPluginGenerator)
set(VERSION_MAJOR 1)
set(VERSION_MINOR 5)
set(VERSION_PATCH 0)
set(VERSION_STRING "${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH}")
if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
set(standalone_build 1)
else()
set(standalone_build 0)
endif()
#-----------------------------------------------------------------------------
# Prerequisites
#-----------------------------------------------------------------------------
find_package(Qt5Core REQUIRED)
configure_file("${CMAKE_CURRENT_SOURCE_DIR}/PluginGeneratorConfig.h.in"
"${CMAKE_CURRENT_BINARY_DIR}/PluginGeneratorConfig.h" @ONLY)
include_directories("${CMAKE_CURRENT_BINARY_DIR}")
#-----------------------------------------------------------------------------
# Executable
#-----------------------------------------------------------------------------
set(src_files
PluginGenerator.cpp
ctkCommandLineParser.cpp
)
qt5_wrap_cpp(src_files ctkCommandLineParser.h OPTIONS -DBOOST_NO_TEMPLATE_PARTIAL_SPECIALIZATION)
qt5_add_resources(src_files plugin_template.qrc project_template.qrc)
set(exec_target ${PROJECT_NAME})
add_executable(${exec_target} ${src_files})
-set_property(TARGET ${exec_target} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Plugins/PluginGenerator")
+set_property(TARGET ${exec_target} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Applications/PluginGenerator")
target_link_libraries(${exec_target} Qt5::Core)
-if(NOT standalone_build)
- # subproject support
- add_dependencies(MITK-CoreUI ${exec_target})
-endif()
-
#-----------------------------------------------------------------------------
# Win32 Convenience
#-----------------------------------------------------------------------------
if(WIN32 AND NOT standalone_build)
file(TO_NATIVE_PATH "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}" native_runtime_dir)
add_custom_target(NewPlugin start "MITK PluginGenerator" /D "${native_runtime_dir}" cmd /K ${exec_target}.exe -h
DEPENDS ${exec_target})
- set_property(TARGET NewPlugin PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Plugins/PluginGenerator")
+ set_property(TARGET NewPlugin PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Applications/PluginGenerator")
endif()
#-----------------------------------------------------------------------------
# Testing
#-----------------------------------------------------------------------------
if(NOT standalone_build)
# Test the plugin generator
include(mitkTestPluginGenerator)
endif()
#-----------------------------------------------------------------------------
# Packaging support
#-----------------------------------------------------------------------------
if(standalone_build)
include(SetupPackaging.cmake)
endif()
diff --git a/Applications/PluginGenerator/ProjectTemplate/CMake/CTestCustom.cmake.in b/Applications/PluginGenerator/ProjectTemplate/CMake/CTestCustom.cmake.in
deleted file mode 100644
index fb9b4d60f6..0000000000
--- a/Applications/PluginGenerator/ProjectTemplate/CMake/CTestCustom.cmake.in
+++ /dev/null
@@ -1,80 +0,0 @@
-set(CTEST_CUSTOM_COVERAGE_EXCLUDE
- ${CTEST_CUSTOM_COVERAGE_EXCLUDE}
-
- # Exclude try_compile sources from coverage results:
- "/CMakeFiles/CMakeTmp/"
-
- # Exclude files generated by the moc pre-compiler
- ".*/moc_.*"
-
- # Exclude files generated by the uic pre-compiler
- ".*/ui_.*"
-
- # Exclude files from the Testing directories
- ".*/Testing/.*"
-
- ".*/CMakeExternals/.*"
-
- )
-
-# The following tests should not be run under valgrind
-set(CTEST_CUSTOM_MEMCHECK_IGNORE
-
- )
-
-set(CTEST_CUSTOM_ERROR_MATCH
- ${CTEST_CUSTOM_ERROR_MATCH}
- "CMake Error[ :]"
- )
-
-set(CTEST_CUSTOM_WARNING_MATCH
- ${CTEST_CUSTOM_WARNING_MATCH}
- "CMake Warning[ :]"
- )
-
-set(CTEST_CUSTOM_WARNING_EXCEPTION
- ${CTEST_CUSTOM_WARNING_EXCEPTION}
-
- # kwstyle suppressions
- "[Kk][Ww][Ss]tyle.*kws.*cxx"
- "[Kk][Ww][Ss]tyle.*kws.*h"
- "[Kk][Ww][Ss]tyle.*metaCommand.*cxx"
-
- # vtk suppressions
- "vtkfreetype"
- "Utilities.vtktiff"
- "VTK.*IO.vtkMySQLQuery.cxx"
- "VTK.*Utilities.vtkexodus2"
- "VTK.*Utilities.vtklibproj"
- "VTK.*Utilities.vtksqlite"
- "VTK.*Utilities.vtkmetaio"
- "VTK.*warn_unused_result"
- "VTK.*Filtering.*cxx"
- "VTK.*IO.*cxx"
- "VTK.*Infovis.*cxx"
-
- # qt suppressions from vtk...
- # Some VTK dashboards include building bits of Qt which produce lots of
- # the following warnings when built with the MS compilers. Qt guys should
- # fix their code. Until they do, keep the Qt chatter off the VTK dashboard
- # results:
- "include.[Qq]t([Cc]ore|[Gg]ui).*warning C4127: conditional expression is constant"
- "[Qq]t.*h.*warning.*declaration of .* shadows a member of .this"
- "[Qq]t.*h.*warning.*(copy constructor|assignment operator) could not be generated"
-
- # Suppress warning caused when QT 'foreach' loops are combined
- ".*warning: declaration of '_container_' shadows a previous local"
-
- # PythonQt suppressions
- "PythonQt.*src.*PythonQt.*(cpp|h)"
- "include.PythonQt.PythonQt.*h"
-
- # Suppressing warnings about duplicate libraries in Darwin
- # At some point this may be addressed by CMake feature request:
- # http://public.kitware.com/Bug/view.php?id=10179
- "ld: warning: duplicate dylib.*"
-
- # Visual studio spurious warnings...
- "The following environment variables were not found"
-
- )
diff --git a/Applications/PluginGenerator/ProjectTemplate/CMakeLists.txt b/Applications/PluginGenerator/ProjectTemplate/CMakeLists.txt
index 887f5c0d30..1618e04c80 100644
--- a/Applications/PluginGenerator/ProjectTemplate/CMakeLists.txt
+++ b/Applications/PluginGenerator/ProjectTemplate/CMakeLists.txt
@@ -1,339 +1,329 @@
cmake_minimum_required(VERSION 3.14.5 FATAL_ERROR)
# Change project and application name to your own
set(MY_PROJECT_NAME $(project-name))
set(MY_APP_NAME $(project-app-name))
#-----------------------------------------------------------------------------
# Set the language standard (MITK requires C++14)
#-----------------------------------------------------------------------------
set(CMAKE_CXX_STANDARD 14)
set(CMAKE_CXX_STANDARD_REQUIRED 1)
set(CMAKE_CXX_EXTENSIONS 0)
#-----------------------------------------------------------------------------
# Set a default build type if none was specified
#-----------------------------------------------------------------------------
if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
message(STATUS "Setting build type to 'Debug' as none was specified.")
set(CMAKE_BUILD_TYPE Debug CACHE STRING "Choose the type of build." FORCE)
# Set the possible values of build type for cmake-gui
set_property(CACHE CMAKE_BUILD_TYPE PROPERTY
STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
endif()
#-----------------------------------------------------------------------------
# Superbuild Option - Enabled by default
#-----------------------------------------------------------------------------
option(${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
CMP0020 # NEW: Automatically link Qt executables to qtmain target on Windows.
CMP0028 # NEW: Double colon in target name means ALIAS or IMPORTED target.
)
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(CTest)
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("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake")
return()
endif()
#*****************************************************************************
#**************************** END OF SUPERBUILD ****************************
#*****************************************************************************
#-----------------------------------------------------------------------------
# Prerequesites
#-----------------------------------------------------------------------------
set(${PROJECT_NAME}_MODULES_PACKAGE_DEPENDS_DIR "${PROJECT_SOURCE_DIR}/CMake/PackageDepends")
set(MODULES_PACKAGE_DEPENDS_DIRS ${${PROJECT_NAME}_MODULES_PACKAGE_DEPENDS_DIR})
find_package(MITK 2018.04.99 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(${PROJECT_NAME}_SHOW_CONSOLE_WINDOW)
if(NOT UNIX)
set(MITK_WIN32_FORCE_STATIC "STATIC")
endif()
#-----------------------------------------------------------------------------
# Get project version info
#-----------------------------------------------------------------------------
mitkFunctionGetVersion(${PROJECT_SOURCE_DIR} ${PROJECT_NAME})
#-----------------------------------------------------------------------------
# Installation preparation
#
# These should be set before any MITK install macros are used
#-----------------------------------------------------------------------------
# on macOS 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
#-----------------------------------------------------------------------------
if(CMAKE_COMPILER_IS_GNUCXX)
# 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 <stdexcept>")
set(CMAKE_TESTDRIVER_BEFORE_TESTMAIN "
try
{")
- set(CMAKE_TESTDRIVER_AFTER_TESTMAIN " }
- catch ( const std::exception & excp )
- {
- fprintf(stderr,\"%s\\n\",excp.what());
+ set(CMAKE_TESTDRIVER_AFTER_TESTMAIN "
+ }
+ catch (const std::exception& e)
+ {
+ fprintf(stderr, \"%s\\n\", e.what());
return EXIT_FAILURE;
- }
- catch( ... )
- {
+ }
+ 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 ${PROJECT_BINARY_DIR})
endif()
#-----------------------------------------------------------------------------
# MITK modules
#-----------------------------------------------------------------------------
#add_subdirectory(Modules)
#-----------------------------------------------------------------------------
# CTK plugins
#-----------------------------------------------------------------------------
# The CMake code in this section *must* be in the top-level CMakeLists.txt file
macro(GetMyTargetLibraries all_target_libraries varname)
set(re_ctkplugin "^$(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
#-----------------------------------------------------------------------------
diff --git a/Applications/PluginGenerator/project_template.qrc b/Applications/PluginGenerator/project_template.qrc
index 85b8e2c88a..0a59ca2311 100644
--- a/Applications/PluginGenerator/project_template.qrc
+++ b/Applications/PluginGenerator/project_template.qrc
@@ -1,17 +1,16 @@
<RCC>
<qresource prefix="/">
<file>ProjectTemplate/CMakeLists.txt</file>
<file>ProjectTemplate/LICENSE</file>
<file>ProjectTemplate/SuperBuild.cmake</file>
<file>ProjectTemplate/Apps/TemplateApp/CMakeLists.txt</file>
<file>ProjectTemplate/Apps/TemplateApp/startTemplateApp.bat.in</file>
<file>ProjectTemplate/Apps/TemplateApp/TemplateApp.cpp</file>
<file>ProjectTemplate/Apps/TemplateApp/TemplateApp.ini</file>
<file>ProjectTemplate/CMake/CPackSetup.cmake</file>
- <file>ProjectTemplate/CMake/CTestCustom.cmake.in</file>
<file>ProjectTemplate/CMake/MacroEmptyExternalProject.cmake</file>
<file>ProjectTemplate/CMakeExternals/MITK.cmake</file>
<file>ProjectTemplate/Plugins/Plugins.cmake</file>
<file>LICENSE</file>
</qresource>
</RCC>
diff --git a/CMake/BuildConfigurations/ClassificationCmdApps.cmake b/CMake/BuildConfigurations/ClassificationCmdApps.cmake
new file mode 100644
index 0000000000..5b6b3f5cee
--- /dev/null
+++ b/CMake/BuildConfigurations/ClassificationCmdApps.cmake
@@ -0,0 +1,26 @@
+#Configuration for a minimal setup to build all cmd apps provided by the core and classification module
+include(${CMAKE_CURRENT_LIST_DIR}/CoreCmdApps.cmake)
+
+set(MITK_WHITELIST "ClassificationCmdApps" CACHE STRING "" FORCE)
+set(MITK_USE_Vigra ON CACHE BOOL "" FORCE)
+
+#Following packages are needed due to the current dependency
+#of some classification cmd apps to QtWidgetExt (see also
+#disucssion in T27702)
+set(MITK_USE_Qt5 ON CACHE BOOL "" FORCE)
+set(MITK_USE_CTK ON CACHE BOOL "" FORCE)
+set(MITK_USE_Qwt ON CACHE BOOL "" FORCE)
+
+#Following packages are needed due to the current dependency
+#of some classification cmd apps to QtWidgetExt (see also
+#disucssion in T27702)
+set(MITK_CONFIG_PACKAGES
+ Qt5
+ CTK
+ Qwt
+ Vigra
+)
+
+if(NOT MITK_USE_SUPERBUILD)
+ set(BUILD_ClassificationMiniApps ON CACHE BOOL "" FORCE)
+endif()
diff --git a/CMake/CTestCustom.cmake.in b/CMake/CTestCustom.cmake.in
deleted file mode 100644
index 09fb1b8137..0000000000
--- a/CMake/CTestCustom.cmake.in
+++ /dev/null
@@ -1,83 +0,0 @@
-set(CTEST_CUSTOM_COVERAGE_EXCLUDE
- ${CTEST_CUSTOM_COVERAGE_EXCLUDE}
-
- # Exclude try_compile sources from coverage results:
- "/CMakeFiles/CMakeTmp/"
-
- # Exclude files generated by the moc pre-compiler
- ".*/moc_.*"
-
- # Exclude files generated by the uic pre-compiler
- ".*/ui_.*"
-
- # Exclude files from the Testing directories
- ".*/Testing/.*"
-
- ".*/CMakeExternals/.*"
-
- )
-
-# The following tests should not be run under valgrind
-set(CTEST_CUSTOM_MEMCHECK_IGNORE
-
- )
-
-set(CTEST_CUSTOM_ERROR_MATCH
- ${CTEST_CUSTOM_ERROR_MATCH}
- "CMake Error[ :]"
- )
-
-set(CTEST_CUSTOM_WARNING_MATCH
- ${CTEST_CUSTOM_WARNING_MATCH}
- "CMake Warning[ :]"
- )
-
-set(CTEST_CUSTOM_WARNING_EXCEPTION
- ${CTEST_CUSTOM_WARNING_EXCEPTION}
-
- # MITK Utilities
- "Utilities/Poco/"
-
- # kwstyle suppressions
- "[Kk][Ww][Ss]tyle.*kws.*cxx"
- "[Kk][Ww][Ss]tyle.*kws.*h"
- "[Kk][Ww][Ss]tyle.*metaCommand.*cxx"
-
- # vtk suppressions
- "vtkfreetype"
- "Utilities.vtktiff"
- "VTK.*IO.vtkMySQLQuery.cxx"
- "VTK.*Utilities.vtkexodus2"
- "VTK.*Utilities.vtklibproj"
- "VTK.*Utilities.vtksqlite"
- "VTK.*Utilities.vtkmetaio"
- "VTK.*warn_unused_result"
- "VTK.*Filtering.*cxx"
- "VTK.*IO.*cxx"
- "VTK.*Infovis.*cxx"
-
- # qt suppressions from vtk...
- # Some VTK dashboards include building bits of Qt which produce lots of
- # the following warnings when built with the MS compilers. Qt guys should
- # fix their code. Until they do, keep the Qt chatter off the VTK dashboard
- # results:
- "include.[Qq]t([Cc]ore|[Gg]ui).*warning C4127: conditional expression is constant"
- "[Qq]t.*h.*warning.*declaration of .* shadows a member of .this"
- "[Qq]t.*h.*warning.*(copy constructor|assignment operator) could not be generated"
-
- # Suppress warning caused when QT 'foreach' loops are combined
- ".*warning: declaration of '_container_' shadows a previous local"
-
- # PythonQt suppressions
- "PythonQt.*src.*PythonQt.*(cpp|h)"
- "include.PythonQt.PythonQt.*h"
-
- # Suppressing warnings about duplicate libraries in Darwin
- # At some point this may be addressed by CMake feature request:
- # http://public.kitware.com/Bug/view.php?id=10179
- "ld: warning: duplicate dylib.*"
-
- # Visual studio spurious warnings...
- "The following environment variables were not found"
-
- )
diff --git a/CMake/MITKDashboardDriverScript.cmake b/CMake/MITKDashboardDriverScript.cmake
deleted file mode 100644
index 08f10cd767..0000000000
--- a/CMake/MITKDashboardDriverScript.cmake
+++ /dev/null
@@ -1,529 +0,0 @@
-
-#
-# Included from a dashboard script, this cmake file will drive the configure and build
-# steps of MITK
-#
-
-#-----------------------------------------------------------------------------
-# The following variable are expected to be define in the top-level script:
-set(expected_variables
- CTEST_NOTES_FILES
- CTEST_SITE
- CTEST_DASHBOARD_ROOT
- CTEST_CMAKE_COMMAND
- CTEST_CMAKE_GENERATOR
- WITH_MEMCHECK
- WITH_COVERAGE
- WITH_DOCUMENTATION
- CTEST_BUILD_CONFIGURATION
- CTEST_TEST_TIMEOUT
- CTEST_BUILD_FLAGS
- TEST_TO_EXCLUDE_REGEX
- CTEST_SOURCE_DIRECTORY
- CTEST_BINARY_DIRECTORY
- CTEST_BUILD_NAME
- SCRIPT_MODE
- CTEST_COVERAGE_COMMAND
- CTEST_MEMORYCHECK_COMMAND
- CTEST_GIT_COMMAND
- PROJECT_BUILD_DIR
- )
-
-foreach(var ${expected_variables})
- if(NOT DEFINED ${var})
- message(FATAL_ERROR "Variable ${var} should be defined in top-level script !")
- endif()
-endforeach()
-
-string(REPLACE " " "%20" _build_name_escaped "${CTEST_BUILD_NAME}")
-
-# Check if "mbits" is reachable
-file(DOWNLOAD "http://mbits" "${CTEST_SCRIPT_DIRECTORY}/mbits.html" TIMEOUT 2 STATUS _status)
-list(GET _status 0 _status_code)
-if(_status_code EQUAL 0) # successful completion
- set(MBITS_AVAILABLE 1)
-else()
- set(MBITS_AVAILABLE 0)
-endif()
-
-#
-# Site specific options
-#
-if(NOT CDASH_ADMIN_URL_PREFIX AND MBITS_AVAILABLE)
- set(CDASH_ADMIN_URL_PREFIX "http://mbits")
-endif()
-
-if(NOT DEFINED GIT_BRANCH OR GIT_BRANCH STREQUAL "")
- set(GIT_BRANCH "")
-else()
- set(GIT_BRANCH "-b ${GIT_BRANCH}")
-endif()
-
-# Should binary directory be cleaned?
-set(empty_binary_directory FALSE)
-
-# Attempt to build and test also if 'ctest_update' returned an error
-set(initial_force_build FALSE)
-
-# Set model options
-set(model "")
-if(SCRIPT_MODE STREQUAL "experimental")
- set(empty_binary_directory FALSE)
- set(initial_force_build TRUE)
- set(model Experimental)
-elseif(SCRIPT_MODE STREQUAL "continuous")
- set(empty_binary_directory FALSE)
- set(initial_force_build FALSE)
- set(model Continuous)
-elseif(SCRIPT_MODE STREQUAL "nightly")
- set(empty_binary_directory TRUE)
- set(initial_force_build TRUE)
- set(model Nightly)
-else()
- message(FATAL_ERROR "Unknown script mode: '${SCRIPT_MODE}'. Script mode should be either 'experimental', 'continuous' or 'nightly'")
-endif()
-
-#message("script_mode:${SCRIPT_MODE}")
-#message("model:${model}")
-#message("empty_binary_directory:${empty_binary_directory}")
-#message("force_build:${initial_force_build}")
-
-set(CTEST_CONFIGURATION_TYPE ${CTEST_BUILD_CONFIGURATION})
-
-if(empty_binary_directory)
- message("Clean \"${CTEST_BINARY_DIRECTORY}\"")
- ctest_empty_binary_directory(${CTEST_BINARY_DIRECTORY})
-endif()
-
-if(NOT DEFINED CTEST_CHECKOUT_DIR)
- set(CTEST_CHECKOUT_DIR ${CTEST_SOURCE_DIRECTORY})
-endif()
-
-if(NOT EXISTS "${CTEST_CHECKOUT_DIR}")
- set(CTEST_CHECKOUT_COMMAND "\"${CTEST_GIT_COMMAND}\" clone ${GIT_BRANCH} ${GIT_REPOSITORY} \"${CTEST_CHECKOUT_DIR}\"")
-endif()
-
-set(CTEST_UPDATE_TYPE "git")
-set(CTEST_UPDATE_COMMAND "${CTEST_GIT_COMMAND}")
-
-#----------------------------------------------------------------------
-# Utility macros
-#----------------------------------------------------------------------
-
-function(func_build_target target build_dir)
- set(CTEST_BUILD_TARGET ${target})
- ctest_build(BUILD "${build_dir}" APPEND
- RETURN_VALUE res
- NUMBER_ERRORS num_errors
- NUMBER_WARNINGS num_warnings)
- ctest_submit(PARTS Build RETRY_DELAY 3 RETRY_COUNT 3)
-
- if(num_errors)
- math(EXPR build_errors "${build_errors} + ${num_errors}")
- set(build_errors ${build_errors} PARENT_SCOPE)
- endif()
- if(num_warnings)
- math(EXPR build_warnings "${build_warnings} + ${num_warnings}")
- set(build_warnings ${build_warnings} PARENT_SCOPE)
- endif()
-endfunction()
-
-function(func_test label build_dir)
- if(NOT TESTING_PARALLEL_LEVEL)
- set(TESTING_PARALLEL_LEVEL 8)
- endif()
-
- if(label MATCHES "Unlabeled")
- set(_include_label EXCLUDE_LABEL .*)
- else()
- set(_include_label INCLUDE_LABEL ${label})
- endif()
-
- ctest_test(BUILD "${build_dir}"
- ${_include_label}
- PARALLEL_LEVEL ${TESTING_PARALLEL_LEVEL}
- EXCLUDE ${TEST_TO_EXCLUDE_REGEX}
- RETURN_VALUE res
- )
- ctest_submit(PARTS Test RETRY_DELAY 3 RETRY_COUNT 3)
-
- if(res)
- math(EXPR test_errors "${test_errors} + 1")
- set(test_errors ${test_errors} PARENT_SCOPE)
- endif()
-
- if(ARG3)
- set(WITH_COVERAGE ${ARG3})
- endif()
- if(ARG4)
- set(WITH_MEMCHECK ${ARG4})
- endif()
-
- if(WITH_COVERAGE AND CTEST_COVERAGE_COMMAND)
- message("----------- [ Coverage ${label} ] -----------")
- ctest_coverage(BUILD "${build_dir}" LABELS ${label})
- ctest_submit(PARTS Coverage RETRY_DELAY 3 RETRY_COUNT 3)
- endif()
-
- if(WITH_MEMCHECK AND CTEST_MEMORYCHECK_COMMAND)
- if(NOT CTEST_MEMORYCHECK_SUPPRESSIONS_FILE)
- if(EXISTS "${CTEST_SOURCE_DIRECTORY}/CMake/valgrind.supp")
- set(CTEST_MEMORYCHECK_SUPPRESSIONS_FILE "${CTEST_SOURCE_DIRECTORY}/CMake/valgrind.supp")
- endif()
- endif()
- if(NOT CTEST_MEMORYCHECK_COMMAND_OPTIONS)
- set(CTEST_MEMORYCHECK_COMMAND_OPTIONS "-q --tool=memcheck --leak-check=yes --show-reachable=no --show-possibly-lost=no --workaround-gcc296-bugs=yes --num-callers=50")
- endif()
- ctest_memcheck(BUILD "${build_dir}" INCLUDE_LABEL ${label})
- ctest_submit(PARTS MemCheck RETRY_DELAY 3 RETRY_COUNT 3)
- endif()
-
-endfunction()
-
-macro(finalize_submission)
-
- # Note should be at the end
- ctest_submit(PARTS Notes Done RETRY_DELAY 3 RETRY_COUNT 3)
-
- # Send status to the "CDash Web Admin"
- if(CDASH_ADMIN_URL_PREFIX)
- set(cdash_admin_url "${CDASH_ADMIN_URL_PREFIX}/cdashadmin-web/index.php?pw=4da12ca9c06d46d3171d7f73974c900f")
- string(REGEX REPLACE ".*\\?project=(.*)&?" "\\1" _ctest_project "${CTEST_DROP_LOCATION}")
- file(DOWNLOAD
- "${cdash_admin_url}&action=submit&name=${_build_name_escaped}&hasTestErrors=${test_errors}&hasBuildErrors=${build_errors}&hasBuildWarnings=${build_warnings}&ctestDropSite=${CTEST_DROP_SITE}&ctestProject=${_ctest_project}"
- "${CTEST_BINARY_DIRECTORY}/cdashadmin.txt"
- STATUS status
- )
- list(GET status 0 error_code)
- list(GET status 1 error_msg)
- if(error_code)
- message(FATAL_ERROR "error: Failed to communicate with cdashadmin-web - ${error_msg}")
- endif()
- endif()
-
-endmacro()
-
-macro(check_for_errors)
-
- set(_curr_target ${ARGV0})
- if(build_errors AND _curr_target)
- # try to remove the stamp file for external projects
- set(_stamp_file "${CTEST_BINARY_DIRECTORY}/ep/src/${_curr_target}-stamp/${_curr_target}-configure")
- if(EXISTS "${_stamp_file}")
- file(REMOVE "${_stamp_file}")
- endif()
- endif()
-
- if(build_errors OR test_errors)
- finalize_submission()
- # this should return from run_ctest()
- return()
- endif()
-
-endmacro()
-
-#---------------------------------------------------------------------
-# run_ctest macro
-#---------------------------------------------------------------------
-function(run_ctest)
-
- set(build_warnings 0)
- set(build_errors 0)
- set(test_errors 0)
-
- set(force_build ${initial_force_build})
-
- ctest_start(${model})
-
- if(MITK_EXTENSIONS)
- foreach(extension ${MITK_EXTENSIONS})
- if(extension MATCHES "([^|]+)\\|([^|]+)\\|(.+)")
- set(extension_repo ${CMAKE_MATCH_1})
- set(extension_tag ${CMAKE_MATCH_2})
- set(extension_source_dir ${CMAKE_MATCH_3})
- if(NOT EXISTS "${CTEST_DASHBOARD_ROOT}/${extension_source_dir}")
- message("Clone ${extension_repo} (${extension_tag})")
- execute_process(
- COMMAND ${CTEST_GIT_COMMAND} clone -b ${extension_tag} ${extension_repo} ${extension_source_dir}
- WORKING_DIRECTORY ${CTEST_DASHBOARD_ROOT})
- else()
- set(working_dir "${CTEST_DASHBOARD_ROOT}/${extension_source_dir}")
- message("Update ${extension_repo} (${extension_tag})")
- execute_process(
- COMMAND ${CTEST_GIT_COMMAND} fetch origin ${extension_tag}
- WORKING_DIRECTORY "${working_dir}"
- RESULT_VARIABLE exit_code)
-
- if(exit_code EQUAL 0)
- execute_process(
- COMMAND ${CTEST_GIT_COMMAND} diff --quiet HEAD FETCH_HEAD
- WORKING_DIRECTORY "${working_dir}"
- RESULT_VARIABLE exit_code)
-
- if(NOT exit_code EQUAL 0)
- execute_process(
- COMMAND ${CTEST_GIT_COMMAND} reset --hard FETCH_HEAD
- WORKING_DIRECTORY "${working_dir}")
- set(force_build TRUE)
- endif()
- else()
- message(FATAL_ERROR "Could not update ${extension_repo} (${extension_tag})")
- endif()
- endif()
- endif()
- endforeach()
- endif()
-
- message("Update MITK")
- ctest_update(SOURCE "${CTEST_CHECKOUT_DIR}" RETURN_VALUE res)
-
- if(res LESS 0)
- # update error
- math(EXPR build_errors "${build_errors} + 1")
- endif()
-
- # force a build if this is the first run and the build dir is empty
- if(NOT EXISTS "${CTEST_BINARY_DIRECTORY}/CMakeCache.txt")
- message("First time build - Initialize CMakeCache.txt")
- set(res 1)
-
- # Write initial cache.
- if(NOT DEFINED BUILD_TESTING)
- set(BUILD_TESTING ON)
- endif()
-
- # Write initial cache.
- file(WRITE "${CTEST_BINARY_DIRECTORY}/CMakeCache.txt" "
-CTEST_USE_LAUNCHERS:BOOL=${CTEST_USE_LAUNCHERS}
-CTEST_PROJECT_ADDITIONAL_TARGETS:INTERNAL=${CTEST_PROJECT_ADDITIONAL_TARGETS}
-BUILD_TESTING:BOOL=${BUILD_TESTING}
-MITK_CTEST_SCRIPT_MODE:STRING=${SCRIPT_MODE}
-CMAKE_BUILD_TYPE:STRING=${CTEST_BUILD_CONFIGURATION}
-WITH_COVERAGE:BOOL=${WITH_COVERAGE}
-MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL:STRING=${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}
-${INITIAL_CMAKECACHE_OPTIONS}
-")
- endif()
-
- if(res GREATER 0 OR force_build)
-
- # Clear the forced rerun request
- if(CDASH_ADMIN_URL_PREFIX AND cdash_remove_rerun_url)
- file(DOWNLOAD "${cdash_remove_rerun_url}" "${CTEST_BINARY_DIRECTORY}/tmp.txt")
- file(REMOVE "${CTEST_BINARY_DIRECTORY}/tmp.txt")
- endif()
-
- if(CTEST_PROJECT_NAME_SUPERBUILD)
- set(ctest_project_name_orig ${CTEST_PROJECT_NAME})
- set(CTEST_PROJECT_NAME ${CTEST_PROJECT_NAME_SUPERBUILD})
- endif()
-
- message("----------- [ Configure SuperBuild ] -----------")
-
- set_property(GLOBAL PROPERTY SubProject SuperBuild)
- set_property(GLOBAL PROPERTY Label SuperBuild)
-
- if(MITK_EXTENSIONS)
- set(SUPERBUILD_CONFIG_OPTIONS -D MITK_EXTENSION_DIRS:STRING=${MITK_EXTENSION_DIRS})
- endif()
-
- ctest_configure(BUILD "${CTEST_BINARY_DIRECTORY}" RETURN_VALUE res OPTIONS "${SUPERBUILD_CONFIG_OPTIONS}")
-
- if(res)
- math(EXPR build_errors "${build_errors} + 1")
- endif()
-
- # Project.xml is generated during the superbuild configure step
- ctest_submit(FILES "${CTEST_BINARY_DIRECTORY}/Project.xml" RETRY_DELAY 3 RETRY_COUNT 3)
-
- ctest_read_custom_files("${CTEST_BINARY_DIRECTORY}")
-
- ctest_submit(PARTS Configure RETRY_DELAY 3 RETRY_COUNT 3)
-
- # submit the update results *after* the submitting the Configure info,
- # otherwise CDash is somehow confused and cannot add the update info
- # to the superbuild project
- ctest_submit(PARTS Update RETRY_DELAY 3 RETRY_COUNT 3)
-
- check_for_errors()
-
- # To get CTEST_PROJECT_SUBPROJECTS and CTEST_PROJECT_EXTERNALS definition
- include("${CTEST_BINARY_DIRECTORY}/CTestConfigSubProject.cmake")
-
- # Read in a list of super-build targets (SUPERBUILD_TARGETS). If an error
- # occurs in one of the listed projects, the ctest superbuild make step stops
- # and the error is reported in the dashboard. If this variable would be empty
- # the errors are still reported but make would keep building external
- # projects which leads to potentially more errors because of dependencies.
- set(MITK_SUPERBUILD_TARGETS_FILE "${CTEST_BINARY_DIRECTORY}/SuperBuildTargets.cmake")
- if(EXISTS "${MITK_SUPERBUILD_TARGETS_FILE}")
- include("${MITK_SUPERBUILD_TARGETS_FILE}")
- endif()
-
- # Build top level (either all or the supplied targets at
- # superbuild level
- if(SUPERBUILD_TARGETS)
- foreach(superbuild_target ${SUPERBUILD_TARGETS})
-
- message("----------- [ Build ${superbuild_target} - SuperBuild ] -----------")
- func_build_target(${superbuild_target} "${CTEST_BINARY_DIRECTORY}")
- check_for_errors(${superbuild_target})
-
- # runs only tests that have a LABELS property matching "SuperBuild"
- func_test("SuperBuild" "${CTEST_BINARY_DIRECTORY}")
- check_for_errors()
- endforeach()
-
- # HACK Unfortunately ctest_coverage ignores the build argument, back-up the original dirs
- file(READ "${CTEST_BINARY_DIRECTORY}/CMakeFiles/TargetDirectories.txt" old_coverage_dirs)
-
- # explicitly build requested external projects as subprojects
- foreach(external_project_with_build_dir ${CTEST_PROJECT_EXTERNALS})
-
- string(REPLACE "^^" ";" external_project_with_build_dir_list "${external_project_with_build_dir}")
- list(GET external_project_with_build_dir_list 0 external_project_name)
- list(GET external_project_with_build_dir_list 1 external_project_builddir)
-
- set_property(GLOBAL PROPERTY SubProject ${external_project_name})
- set_property(GLOBAL PROPERTY Label ${external_project_name})
-
- message("----------- [ Build ${external_project_name} ] -----------")
-
- func_build_target("${external_project_name}" "${CTEST_BINARY_DIRECTORY}")
- check_for_errors()
-
- # HACK Unfortunately ctest_coverage ignores the build argument, try to force it...
- file(READ "${CTEST_BINARY_DIRECTORY}/${external_project_builddir}/CMakeFiles/TargetDirectories.txt" mitk_build_coverage_dirs)
- file(APPEND "${CTEST_BINARY_DIRECTORY}/CMakeFiles/TargetDirectories.txt" "${mitk_build_coverage_dirs}")
-
- message("----------- [ Test ${external_project_name} ] -----------")
-
- # runs only tests that have a LABELS property matching "${external_project_name}"
- func_test(${external_project_name} "${CTEST_BINARY_DIRECTORY}/${external_project_builddir}")
-
- # restore old coverage dirs
- file(WRITE "${CTEST_BINARY_DIRECTORY}/CMakeFiles/TargetDirectories.txt" "${old_coverage_dirs}")
-
- endforeach()
-
- # switch back to SuperBuild label
- set_property(GLOBAL PROPERTY SubProject SuperBuild)
- set_property(GLOBAL PROPERTY Label SuperBuild)
-
- message("----------- [ Finish SuperBuild ] -----------")
- else()
- message("----------- [ Build SuperBuild ] -----------")
- endif()
-
- # build everything at superbuild level which has not yet been built
- func_build_target("" "${CTEST_BINARY_DIRECTORY}")
- check_for_errors()
-
- # runs only tests that have a LABELS property matching "SuperBuild"
- #func_test("SuperBuild" "${CTEST_BINARY_DIRECTORY}")
-
- set(build_dir "${CTEST_BINARY_DIRECTORY}/${PROJECT_BUILD_DIR}")
- if(CTEST_PROJECT_NAME_SUPERBUILD)
- set(CTEST_PROJECT_NAME ${ctest_project_name_orig})
- endif()
-
- message("----------- [ Configure ${build_dir} ] -----------")
- # Configure target
- ctest_configure(BUILD "${build_dir}"
- OPTIONS "-DCTEST_USE_LAUNCHERS=${CTEST_USE_LAUNCHERS}"
- RETURN_VALUE res
- )
- ctest_read_custom_files("${CTEST_BINARY_DIRECTORY}")
- ctest_submit(PARTS Configure RETRY_DELAY 3 RETRY_COUNT 3)
-
- if(res)
- math(EXPR build_errors "${build_errors} + 1")
- endif()
- check_for_errors()
-
- foreach(subproject ${CTEST_PROJECT_SUBPROJECTS})
- set_property(GLOBAL PROPERTY SubProject ${subproject})
- set_property(GLOBAL PROPERTY Label ${subproject})
-
- if(subproject MATCHES "Unlabeled")
- message("----------- [ Build All (Unlabeled) ] -----------")
- # Build target
- func_build_target("" "${build_dir}")
- else()
- message("----------- [ Build ${subproject} ] -----------")
- # Build target
- func_build_target(${subproject} "${build_dir}")
- endif()
- check_for_errors()
- endforeach()
-
- # HACK Unfortunately ctest_coverage ignores the build argument, try to force it...
- file(READ ${build_dir}/CMakeFiles/TargetDirectories.txt mitk_build_coverage_dirs)
- file(APPEND "${CTEST_BINARY_DIRECTORY}/CMakeFiles/TargetDirectories.txt" "${mitk_build_coverage_dirs}")
-
- foreach(subproject ${CTEST_PROJECT_SUBPROJECTS})
- set_property(GLOBAL PROPERTY SubProject ${subproject})
- set_property(GLOBAL PROPERTY Label ${subproject})
- message("----------- [ Test ${subproject} ] -----------")
-
- # runs only tests that have a LABELS property matching "${subproject}"
- func_test(${subproject} "${build_dir}")
- endforeach()
-
- # Build any additional target which is not build by "all"
- # i.e. the "package" target
- if(CTEST_PROJECT_ADDITIONAL_TARGETS)
- foreach(additional_target ${CTEST_PROJECT_ADDITIONAL_TARGETS})
- set_property(GLOBAL PROPERTY SubProject ${additional_target})
- set_property(GLOBAL PROPERTY Label ${additional_target})
-
- message("----------- [ Build ${additional_target} ] -----------")
- func_build_target(${additional_target} "${build_dir}")
- check_for_errors()
-
- message("----------- [ Test ${additional_target} ] -----------")
- # runs only tests that have a LABELS property matching "${subproject}"
- func_test(${additional_target} "${build_dir}")
- endforeach()
- endif()
-
- if(WITH_DOCUMENTATION)
- message("----------- [ Build Documentation ] -----------")
- set(ctest_use_launchers_orig ${CTEST_USE_LAUNCHERS})
- set(CTEST_USE_LAUNCHERS 0)
- # Build Documentation target
- set_property(GLOBAL PROPERTY SubProject Documentation)
- set_property(GLOBAL PROPERTY Label Documentation)
- func_build_target("doc" "${build_dir}")
- set(CTEST_USE_LAUNCHERS ${ctest_use_launchers_orig})
- endif()
-
- set_property(GLOBAL PROPERTY SubProject SuperBuild)
- set_property(GLOBAL PROPERTY Label SuperBuild)
-
- # Global coverage ...
- if(WITH_COVERAGE AND CTEST_COVERAGE_COMMAND)
- message("----------- [ Global coverage ] -----------")
- ctest_coverage(BUILD "${build_dir}" APPEND)
- ctest_submit(PARTS Coverage RETRY_DELAY 3 RETRY_COUNT 3)
- endif()
-
- # Global dynamic analysis ...
- if(WITH_MEMCHECK AND CTEST_MEMORYCHECK_COMMAND)
- message("----------- [ Global memcheck ] -----------")
- ctest_memcheck(BUILD "${build_dir}")
- ctest_submit(PARTS MemCheck RETRY_DELAY 3 RETRY_COUNT 3)
- endif()
-
- check_for_errors()
- finalize_submission()
-
- endif()
-
- # Clear the CTEST_CHECKOUT_COMMAND variable to prevent continuous clients
- # to try to checkout again
- set(CTEST_CHECKOUT_COMMAND "")
-
-endfunction()
-
-run_ctest()
diff --git a/CMake/MITKDashboardScript.TEMPLATE.cmake b/CMake/MITKDashboardScript.TEMPLATE.cmake
deleted file mode 100644
index 0d459014e1..0000000000
--- a/CMake/MITKDashboardScript.TEMPLATE.cmake
+++ /dev/null
@@ -1,143 +0,0 @@
-#
-# OS: Ubuntu 9.04 2.6.28-18-generic
-# Hardware: x86_64 GNU/Linux
-# GPU: NA
-#
-
-# Note: The specific version and processor type of this machine should be reported in the
-# header above. Indeed, this file will be send to the dashboard as a NOTE file.
-
-cmake_minimum_required(VERSION 3.14.5 FATAL_ERROR)
-
-#
-# Dashboard properties
-#
-
-set(MY_COMPILER "gcc-4.9.x")
-# For Windows, e.g.
-#set(MY_COMPILER "VC12.0")
-
-set(CTEST_CMAKE_COMMAND "/usr/bin/cmake")
-set(CTEST_CMAKE_GENERATOR "Unix Makefiles")
-set(CTEST_DASHBOARD_ROOT "/opt/dartclients")
-# For Windows, e.g.
-#set(CTEST_CMAKE_COMMAND "cmake")
-#set(CTEST_CMAKE_GENERATOR "Visual Studio 16 2019")
-#set(CTEST_CMAKE_GENERATOR_PLATFORM "x64")
-#set(CTEST_DASHBOARD_ROOT "D:/dc")
-
-set(MITK_EXTENSIONS # "<repo>|<branch/tag/commit>|<src dir>"
-# "https://phabricator.mitk.org/source/mitk-projecttemplate.git|master|MITK-ProjectTemplate"
-# "https://phabricator.mitk.org/source/mitk-diffusion.git|master|MITK-Diffusion"
-)
-
-#
-# Dashboard options
-#
-set(WITH_KWSTYLE FALSE)
-set(WITH_MEMCHECK FALSE)
-set(WITH_COVERAGE FALSE)
-set(WITH_DOCUMENTATION FALSE)
-#set(DOCUMENTATION_ARCHIVES_OUTPUT_DIRECTORY ) # for example: $ENV{HOME}/Projects/Doxygen
-set(CTEST_BUILD_CONFIGURATION "Release")
-set(CTEST_TEST_TIMEOUT 500)
-if(UNIX)
- set(CTEST_BUILD_FLAGS "-j4") # Use multiple CPU cores to build
-else()
- set(CTEST_BUILD_FLAGS "")
-endif()
-
-# experimental:
-# - run_ctest() macro will be called *ONE* time
-# - binary directory will *NOT* be cleaned
-# continuous:
-# - run_ctest() macro will be called EVERY 5 minutes ...
-# - binary directory will *NOT* be cleaned
-# - configure/build will be executed *ONLY* if the repository has been updated
-# nightly:
-# - run_ctest() macro will be called *ONE* time
-# - binary directory *WILL BE* cleaned
-set(SCRIPT_MODE "experimental") # "experimental", "continuous", "nightly"
-
-#
-# Project specific properties
-#
-# In order to shorten the global path length, the build directory for each DartClient
-# uses the following abrevation sceme:
-# For build configuration:
-# Debug -> d
-# Release -> r
-# For scripte mode:
-# continuous -> c
-# nightly -> n
-# experimental -> e
-# Example directory: /MITK-sb-d-n/ for a nightly MITK superbuild in debug mode.
-set(short_of_ctest_build_configuration "")
-set(short_of_script_mode "")
-string(SUBSTRING ${CTEST_BUILD_CONFIGURATION} 0 1 short_of_ctest_build_configuration)
-string(SUBSTRING ${SCRIPT_MODE} 0 1 short_of_script_mode)
-set(CTEST_SOURCE_DIRECTORY "${CTEST_DASHBOARD_ROOT}/MITK")
-set(CTEST_BINARY_DIRECTORY "${CTEST_DASHBOARD_ROOT}/MITK-sb-${short_of_ctest_build_configuration}-${short_of_script_mode}")
-
-# Create an initial cache file for MITK. This file is used to configure the MITK-Build. Use ADDITIONAL_CMAKECACHE_OPTION
-# to configure the MITK-Superbuild. The
-set(MITK_INITIAL_CACHE "
-# Example how to set a boolean variable in the MITK-Build via this script:
-#set(MITK_ENABLE_TOF_HARDWARE \"TRUE\" CACHE INTERNAL \"Enable ToF Hardware\")
-# Example how to set a path variable in the MITK-Build via this script:
-#set(MITK_PMD_LIB \"/home/kilgus/thomas/PMDSDK2/Linux_x86_64/bin/libpmdaccess2.so\" CACHE INTERNAL \"PMD lib\")
-")
-
-set(ADDITIONAL_CMAKECACHE_OPTION "
-# Superbuild variables are not passed through to the MITK-Build (or any other build like ITK, VTK, ...)
-# Use the MITK_INITIAL_CACHE the pass variables to the MITK-Build.
-# add entries like this
-#MITK_USE_OpenCV:BOOL=OFF
-CMAKE_PREFIX_PATH:PATH=${CMAKE_PREFIX_PATH}
-")
-
-# List of test that should be explicitly disabled on this machine
-set(TEST_TO_EXCLUDE_REGEX "")
-
-# set any extra environment variables here
-set(ENV{PATH} "$ENV{PATH}")
-
-find_program(CTEST_COVERAGE_COMMAND NAMES gcov)
-find_program(CTEST_MEMORYCHECK_COMMAND NAMES valgrind)
-find_program(CTEST_GIT_COMMAND NAMES git)
-
-#
-# Git repository - Overwrite the default value provided by the driver script
-#
-# The git repository containing MITK code
-#set(GIT_REPOSITORY "/home/username/MITK")
-# The branch of the MITK git repository to check out
-#set(GIT_BRANCH "develop")
-
-##########################################
-# WARNING: DO NOT EDIT BEYOND THIS POINT #
-##########################################
-
-#
-# Convenient macro allowing to download a file
-#
-macro(downloadFile url dest)
- file(DOWNLOAD "${url}" "${dest}" STATUS status)
- list(GET status 0 error_code)
- list(GET status 1 error_msg)
- if(error_code)
- message(FATAL_ERROR "error: Failed to download ${url} - ${error_msg}")
- endif()
-endmacro()
-
-if(NOT GIT_BRANCH)
- set(GIT_BRANCH "master")
-endif()
-
-#
-# Download and include setup script
-#
-set(url "https://raw.githubusercontent.com/MITK/MITK/${GIT_BRANCH}/CMake/MITKDashboardSetup.cmake")
-set(dest ${CTEST_SCRIPT_DIRECTORY}/${CTEST_SCRIPT_NAME}.setup)
-downloadFile("${url}" "${dest}")
-include(${dest})
diff --git a/CMake/MITKDashboardScript.cmake b/CMake/MITKDashboardScript.cmake
new file mode 100644
index 0000000000..cad483cf01
--- /dev/null
+++ b/CMake/MITKDashboardScript.cmake
@@ -0,0 +1,178 @@
+#[============================================================================[
+
+ Configuration
+
+ ]============================================================================]
+
+set(CTEST_CMAKE_GENERATOR
+# "Unix Makefiles"
+ "Visual Studio 16 2019"
+)
+
+set(CTEST_CMAKE_GENERATOR_PLATFORM
+# "Win32"
+ "x64"
+)
+
+set(CTEST_BUILD_CONFIGURATION
+# "Debug"
+ "Release"
+# "MinSizeRel"
+# "RelWithDebInfo"
+)
+
+set(CTEST_DASHBOARD_MODEL
+# "Continuous"
+ "Experimental"
+# "Nightly"
+)
+
+# If empty: Default site name is the name of this computer
+set(CTEST_SITE
+ ""
+)
+
+# If empty: Default build name is based on OS, compiler,
+# CTEST_BUILD_CONFIGURATION, and MITK_BUILD_CONFIGURATION
+set(CTEST_BUILD_NAME
+ ""
+)
+
+set(CTEST_BUILD_FLAGS
+# "-j8"
+)
+
+# If empty: Default URL is CTEST_SUBMIT_URL (CTestConfig.cmake)
+set(MITK_SUBMIT_URL
+ "https://cdash.mitk.org/submit.php?project=MITK"
+)
+
+set(MITK_BUILD_CONFIGURATION
+# "All"
+ "WorkbenchRelease"
+# "Minimal"
+)
+
+set(MITK_BUILD_DOCUMENTATION
+ OFF
+)
+
+set(MITK_SUPERBUILD_OPTIONS
+# "MITK_WHITELIST:STRING=Minimal"
+ "Qt5_DIR:PATH=C:/Qt/5.12.9/msvc2017_64/lib/cmake/Qt5"
+ "MITK_AUTOCLEAN_EXTERNAL_PROJECTS:BOOL=ON"
+ "MITK_FAST_TESTING:BOOL=ON"
+ "MITK_XVFB_TESTING:BOOL=OFF"
+)
+
+set(MITK_BUILD_OPTIONS
+ ""
+)
+
+set(MITK_REPOSITORY
+ "https://phabricator.mitk.org/source/mitk.git"
+)
+
+# Branch name, tag, or commit hash
+set(MITK_BRANCH
+ "develop"
+# "master"
+)
+
+# Three list items per MITK extension: <name> <URL> <branch>
+set(MITK_EXTENSIONS
+# "MITK-ProjectTemplate"
+# "https://phabricator.mitk.org/source/mitk-projecttemplate.git"
+# "master"
+# "MITK Diffusion"
+# "https://phabricator.mitk.org/source/mitk-diffusion.git"
+# "master"
+)
+
+#[============================================================================[
+
+ Helper functions
+
+ ]============================================================================]
+
+function(get_temp_directory)
+ set(temp_directory "${CMAKE_CURRENT_SOURCE_DIR}/temp")
+
+ if(NOT EXISTS "${temp_directory}")
+ file(MAKE_DIRECTORY "${temp_directory}")
+ elseif(NOT IS_DIRECTORY "${temp_directory}")
+ message(FATAL_ERROR "Temporary directory location blocked by file \"${temp_directory}\"")
+ endif()
+
+ set(${ARGV0} "${temp_directory}" PARENT_SCOPE)
+endfunction()
+
+function(download_file)
+ cmake_parse_arguments(PARSE_ARGV 0 ARG "QUIET" "URL;OUTPUT_FILE;ERROR_CODE" "")
+
+ get_filename_component(output_dir "${ARG_OUTPUT_FILE}" DIRECTORY)
+ get_filename_component(output_filename "${ARG_OUTPUT_FILE}" NAME)
+
+ if(NOT output_dir)
+ set(output_dir "${CMAKE_CURRENT_SOURCE_DIR}")
+ endif()
+
+ set(output_file "${output_dir}/${output_filename}")
+
+ if(NOT ARG_QUIET)
+ message("Download file\n from: ${ARG_URL}\n to: ${output_file}")
+ endif()
+
+ get_temp_directory(temp_dir)
+ string(RANDOM random_filename)
+
+ while(EXISTS "${temp_dir}/${random_filename}")
+ string(RANDOM random_filename)
+ endwhile()
+
+ set(temp_output_file "${temp_dir}/${random_filename}")
+
+ file(DOWNLOAD "${ARG_URL}" "${temp_output_file}" STATUS status)
+
+ list(GET status 0 error_code)
+ list(GET status 1 error_message)
+ set(error_message "${error_message} (${error_code})")
+
+ if(NOT 0 EQUAL error_code)
+ if(EXISTS "${temp_output_file}")
+ file(REMOVE "${temp_output_file}")
+ endif()
+
+ if(NOT ARG_ERROR_CODE)
+ message(FATAL_ERROR "${error_message}")
+ elseif(NOT ARG_QUIET)
+ message(" error: ${error_message}")
+ endif()
+ else()
+ file(RENAME "${temp_output_file}" "${output_file}")
+ endif()
+
+ if(ARG_ERROR_CODE)
+ set(${ARG_ERROR_CODE} ${error_code} PARENT_SCOPE)
+ endif()
+endfunction()
+
+#[============================================================================[
+
+ Download and include actual script
+
+ ]============================================================================]
+
+include("MITKDashboardScript.local.cmake" OPTIONAL RESULT_VARIABLE found)
+
+if(NOT found)
+ get_temp_directory(temp_dir)
+ set(script "${temp_dir}/MITKDashboardScript.cmake")
+
+ download_file(
+ URL "https://raw.githubusercontent.com/MITK/MITK/${MITK_BRANCH}/CMake/MITKDashboardScript.download.cmake"
+ OUTPUT_FILE "${script}"
+ )
+
+ include("${script}")
+endif()
diff --git a/CMake/MITKDashboardScript.download.cmake b/CMake/MITKDashboardScript.download.cmake
new file mode 100644
index 0000000000..717a2269a5
--- /dev/null
+++ b/CMake/MITKDashboardScript.download.cmake
@@ -0,0 +1,649 @@
+#[============================================================================[
+
+ Helper functions
+
+ ]============================================================================]
+
+function(get_macos_codename)
+ set(macos_codename "")
+
+ set(software_license_file "\
+/System/Library/CoreServices/Setup Assistant.app\
+/Contents/Resources/en.lproj/OSXSoftwareLicense.rtf")
+
+ if(EXISTS "${software_license_file}")
+ file(READ "${software_license_file}" software_license)
+
+ if(software_license MATCHES "SOFTWARE LICENSE AGREEMENT FOR macOS ([^\n]+)")
+ set(macos_codename "${CMAKE_MATCH_1}")
+ endif()
+ endif()
+
+ set(${ARGV0} ${macos_codename} PARENT_SCOPE)
+endfunction()
+
+function(get_macos_name)
+ set(macos_name "macOS")
+
+ get_macos_codename(macos_codename)
+
+ if(macos_codename)
+ set(macos_name "${macos_name} ${macos_codename}")
+ endif()
+
+ execute_process(
+ RESULT_VARIABLE error_code
+ OUTPUT_VARIABLE version
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+ COMMAND "sw_vers" "-productVersion")
+
+ if(0 EQUAL error_code AND version)
+ set(macos_name "${macos_name} ${version}")
+ endif()
+
+ set(${ARGV0} ${macos_name} PARENT_SCOPE)
+endfunction()
+
+function(get_linux_name)
+ set(linux_name "Linux")
+ set(os_release_file "/etc/os-release")
+
+ if(EXISTS "${os_release_file}")
+ file(STRINGS "${os_release_file}" os_release)
+
+ set(name "")
+ set(version_id "")
+
+ foreach(line ${os_release})
+ if(NOT name AND line MATCHES "^NAME=[\"]?([^\"]+)")
+ set(name "${CMAKE_MATCH_1}")
+ continue()
+ endif()
+
+ if(NOT version_id AND line MATCHES "^VERSION_ID=\"?([^\"]+)")
+ set(version_id "${CMAKE_MATCH_1}")
+ continue()
+ endif()
+
+ if(name AND version_id)
+ break()
+ endif()
+ endforeach()
+
+ if(name)
+ set(linux_name "${name}")
+ endif()
+
+ if(version_id)
+ set(linux_name "${linux_name} ${version_id}")
+ endif()
+ endif()
+
+ set(${ARGV0} ${linux_name} PARENT_SCOPE)
+endfunction()
+
+function(get_windows_name)
+ set(windows_name "Windows")
+
+ execute_process(
+ RESULT_VARIABLE error_code
+ OUTPUT_VARIABLE version
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+ COMMAND "wmic" "os" "get" "Version" "-value")
+
+ if(0 EQUAL error_code AND version)
+ if(version MATCHES "Version=([0-9]+)\\.([0-9]+)")
+ set(windows_name "${windows_name} ${CMAKE_MATCH_1}")
+ if(NOT 0 EQUAL CMAKE_MATCH_2)
+ set(windows_name "${windows_name}.${CMAKE_MATCH_2}")
+ endif()
+ endif()
+ endif()
+
+ set(${ARGV0} ${windows_name} PARENT_SCOPE)
+endfunction()
+
+function(get_os_name)
+ set(os_name "")
+
+ if(APPLE)
+ get_macos_name(os_name)
+ elseif(UNIX)
+ get_linux_name(os_name)
+ elseif(WIN32)
+ get_windows_name(os_name)
+ endif()
+
+ set(${ARGV0} ${os_name} PARENT_SCOPE)
+endfunction()
+
+function(download_string)
+ cmake_parse_arguments(PARSE_ARGV 0 ARG "" "URL;OUTPUT_VARIABLE" "")
+
+ get_temp_directory(temp_dir)
+ string(RANDOM random_filename)
+
+ while(EXISTS "${temp_dir}/${random_filename}")
+ string(RANDOM random_filename)
+ endwhile()
+
+ set(temp_output_file "${temp_dir}/${random_filename}")
+
+ download_file(
+ URL ${ARG_URL}
+ OUTPUT_FILE ${temp_output_file}
+ ERROR_CODE error_code)
+
+ set(output "")
+
+ if(EXISTS "${temp_output_file}")
+ file(READ "${temp_output_file}" output)
+ file(REMOVE "${temp_output_file}")
+ endif()
+
+ set(${ARG_OUTPUT_VARIABLE} ${output} PARENT_SCOPE)
+endfunction()
+
+function(find_vswhere)
+ get_temp_directory(temp_dir)
+ set(latest_vswhere "${temp_dir}/vswhere.exe")
+ set(vswhere "vswhere.exe-NOTFOUND")
+
+ if(EXISTS "${latest_vswhere}")
+ set(vswhere "${latest_vswhere}")
+ else()
+ set(program_files_x86 "PROGRAMFILES(X86)")
+ set(program_files_x86 "$ENV{${program_files_x86}}")
+ set(system_vswhere "${program_files_x86}/Microsoft Visual Studio/Installer/vswhere.exe")
+
+ if(EXISTS "${system_vswhere}")
+ set(vswhere "${system_vswhere}")
+ else()
+ download_string(
+ URL "https://api.github.com/repos/microsoft/vswhere/releases/latest"
+ OUTPUT_VARIABLE latest_vswhere_json)
+
+ if(latest_vswhere_json MATCHES "\"browser_download_url\": *\"([^\"]*)\"")
+ download_file(
+ URL "${CMAKE_MATCH_1}"
+ OUTPUT_FILE "${latest_vswhere}"
+ ERROR_CODE error_code)
+
+ if (0 EQUAL error_code)
+ set(vswhere "${latest_vswhere}")
+ endif()
+ endif()
+ endif()
+ endif()
+
+ set(${ARGV0} "${vswhere}" PARENT_SCOPE)
+endfunction()
+
+function(vswhere)
+ cmake_parse_arguments(PARSE_ARGV 0 ARG "" "PROPERTY;OUTPUT_VARIABLE" "")
+
+ set(property_value "")
+
+ if(CTEST_CMAKE_GENERATOR MATCHES "^Visual Studio ([0-9]+)")
+ set(major_version "${CMAKE_MATCH_1}")
+ math(EXPR next_major_version "${major_version} + 1")
+
+ find_vswhere(vswhere)
+
+ if (vswhere)
+ execute_process(
+ OUTPUT_VARIABLE property_value
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+ COMMAND ${vswhere}
+ "-requires" "Microsoft.VisualStudio.Workload.NativeDesktop"
+ "-version" "[${major_version},${next_major_version})"
+ "-property" "${ARG_PROPERTY}"
+ "-format" "value")
+ endif()
+ endif()
+
+ set(${ARG_OUTPUT_VARIABLE} ${property_value} PARENT_SCOPE)
+endfunction()
+
+function(get_visual_studio_name)
+ set(visual_studio_name "Visual Studio")
+
+ if(CTEST_CMAKE_GENERATOR MATCHES "^Visual Studio [0-9]+ ([0-9]+)")
+ set(product_line_version "${CMAKE_MATCH_1}")
+ set(visual_studio_name "${visual_studio_name} ${product_line_version}")
+
+ vswhere(PROPERTY "catalog_productDisplayVersion" OUTPUT_VARIABLE product_display_version)
+
+ if(product_display_version)
+ set(visual_studio_name "${visual_studio_name} ${product_display_version}")
+ endif()
+ endif()
+
+ set(${ARGV0} ${visual_studio_name} PARENT_SCOPE)
+endfunction()
+
+function(get_compiler_name)
+ set(compiler_name "")
+
+ if(CTEST_CMAKE_GENERATOR MATCHES "^Visual Studio")
+ get_visual_studio_name(compiler_name)
+ else()
+ get_temp_directory(temp_dir)
+
+ file(WRITE "${temp_dir}/src/CMakeLists.txt" "\
+project(probe C)
+message(STATUS \"CMAKE_C_COMPILER_ID=\\\"\${CMAKE_C_COMPILER_ID}\\\"\")
+message(STATUS \"CMAKE_C_COMPILER_VERSION=\\\"\${CMAKE_C_COMPILER_VERSION}\\\"\")")
+
+ file(REMOVE_RECURSE "${temp_dir}/build")
+
+ unset(options)
+
+ foreach(option ${MITK_SUPERBUILD_OPTIONS})
+ list(APPEND options "-D" "${option}")
+ endforeach()
+
+ execute_process(
+ RESULT_VARIABLE error_code
+ OUTPUT_VARIABLE compiler
+ ERROR_QUIET
+ COMMAND ${CMAKE_COMMAND}
+ "-S" "${temp_dir}/src"
+ "-B" "${temp_dir}/build"
+ "-G" "${CTEST_CMAKE_GENERATOR}"
+ ${options})
+
+ if(0 EQUAL error_code)
+ if(compiler MATCHES "CMAKE_C_COMPILER_ID=\"([^\"]*)\"")
+ set(compiler_name "${CMAKE_MATCH_1}")
+
+ if(compiler MATCHES "CMAKE_C_COMPILER_VERSION=\"([^\"]*)\"")
+ set(version "${CMAKE_MATCH_1}")
+
+ if(version MATCHES "^([0-9]+\\.[0-9]+\\.[0-9]+)")
+ set(version "${CMAKE_MATCH_1}")
+ endif()
+
+ string(REGEX REPLACE "\\.0$" "" version "${version}")
+
+ set(compiler_name "${compiler_name} ${version}")
+ endif()
+ endif()
+ endif()
+ endif()
+
+ set(${ARGV0} ${compiler_name} PARENT_SCOPE)
+endfunction()
+
+function(get_default_build_name)
+ get_os_name(default_build_name)
+ get_compiler_name(compiler_name)
+
+ if(compiler_name)
+ set(default_build_name "${default_build_name} ${compiler_name}")
+ endif()
+
+ set(default_build_name "${default_build_name} ${CTEST_BUILD_CONFIGURATION}")
+
+ if(MITK_BUILD_CONFIGURATION)
+ set(default_build_name "${default_build_name} ${MITK_BUILD_CONFIGURATION}")
+ endif()
+
+ set(${ARGV0} ${default_build_name} PARENT_SCOPE)
+endfunction()
+
+function(git)
+ cmake_parse_arguments(PARSE_ARGV 0 ARG "" "WORKING_DIRECTORY;OUTPUT_VARIABLE;RESULT_VARIABLE" "")
+
+ if(NOT ARG_WORKING_DIRECTORY)
+ set(ARG_WORKING_DIRECTORY "${CTEST_SOURCE_DIRECTORY}")
+ endif()
+
+ execute_process(
+ WORKING_DIRECTORY "${ARG_WORKING_DIRECTORY}"
+ RESULT_VARIABLE error_code
+ OUTPUT_VARIABLE output
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+ COMMAND "${CTEST_GIT_COMMAND}" ${ARG_UNPARSED_ARGUMENTS})
+
+ if(ARG_OUTPUT_VARIABLE)
+ set(${ARG_OUTPUT_VARIABLE} ${output} PARENT_SCOPE)
+ endif()
+
+ if(ARG_RESULT_VARIABLE)
+ set(${ARG_RESULT_VARIABLE} ${error_code} PARENT_SCOPE)
+ endif()
+endfunction()
+
+function(git_log)
+ cmake_parse_arguments(PARSE_ARGV 0 ARG "" "WORKING_DIRECTORY;COMMIT_HASH;COMMITTER;SUBJECT" "")
+
+ if(NOT ARG_WORKING_DIRECTORY)
+ set(ARG_WORKING_DIRECTORY "${CTEST_SOURCE_DIRECTORY}")
+ endif()
+
+ set(args WORKING_DIRECTORY "${ARG_WORKING_DIRECTORY}" "log" "-1")
+
+ if(ARG_COMMIT_HASH)
+ unset(commit_hash)
+ git(OUTPUT_VARIABLE commit_hash ${args} "--pretty=%h" )
+ if(commit_hash)
+ set(${ARG_COMMIT_HASH} ${commit_hash} PARENT_SCOPE)
+ endif()
+ endif()
+
+ if(ARG_COMMITTER)
+ unset(committer)
+ git(OUTPUT_VARIABLE committer ${args} "--pretty=%cn" )
+ if(committer)
+ set(${ARG_COMMITTER} ${committer} PARENT_SCOPE)
+ endif()
+ endif()
+
+ if(ARG_SUBJECT)
+ unset(subject)
+ git(OUTPUT_VARIABLE subject ${args} "--pretty=%s" )
+ if(subject)
+ set(${ARG_SUBJECT} ${subject} PARENT_SCOPE)
+ endif()
+ endif()
+endfunction()
+
+function(submit)
+ cmake_parse_arguments(PARSE_ARGV 0 ARG "" "" "PARTS")
+
+ if(MITK_SUBMIT_URL)
+ set(submit_url "SUBMIT_URL" "${MITK_SUBMIT_URL}")
+ else()
+ unset(submit_url)
+ endif()
+
+ ctest_submit(${submit_url} RETRY_COUNT 3 RETRY_DELAY 5 PARTS ${ARG_PARTS})
+endfunction()
+
+#[============================================================================[
+
+ Actual script
+
+ ]============================================================================]
+
+cmake_minimum_required(VERSION 3.15 FATAL_ERROR)
+
+find_program(CTEST_GIT_COMMAND git)
+
+if(NOT CTEST_GIT_COMMAND)
+ message(FATAL_ERROR "Git not found")
+endif()
+
+if(NOT CTEST_CMAKE_GENERATOR MATCHES "^Visual Studio")
+ unset(CTEST_CMAKE_GENERATOR_PLATFORM)
+endif()
+
+if(CTEST_CMAKE_GENERATOR MATCHES "^(Unix Makefiles|Ninja)$")
+ set(CTEST_USE_LAUNCHERS ON)
+endif()
+
+if(NOT CTEST_SITE)
+ unset(CTEST_SITE)
+ site_name(CTEST_SITE)
+endif()
+
+if(NOT CTEST_BUILD_NAME)
+ get_default_build_name(CTEST_BUILD_NAME)
+endif()
+
+set(CTEST_SOURCE_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/src/MITK")
+set(CTEST_BINARY_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/build")
+
+set(indent " ")
+
+message("CTest settings")
+
+if(MITK_SUBMIT_URL)
+ message("${indent}Submit URL: ${MITK_SUBMIT_URL}")
+endif()
+
+message("\
+${indent}Dashboard model: ${CTEST_DASHBOARD_MODEL}
+${indent}Build name: ${CTEST_BUILD_NAME}
+${indent}Site: ${CTEST_SITE}")
+
+message("MITK repository")
+
+if(NOT EXISTS "${CTEST_SOURCE_DIRECTORY}")
+ message("\
+${indent}Clone repository: ${MITK_REPOSITORY}
+${indent}Branch: ${MITK_BRANCH}")
+
+ set(CTEST_CHECKOUT_COMMAND "\"${CTEST_GIT_COMMAND}\" clone --branch=${MITK_BRANCH} -- ${MITK_REPOSITORY} MITK")
+
+ ctest_start(${CTEST_DASHBOARD_MODEL})
+else()
+ git_log(COMMIT_HASH old_revision COMMITTER committer SUBJECT subject)
+
+ message("\
+${indent}Update repository: ${CTEST_SOURCE_DIRECTORY}
+${indent}Branch: ${MITK_BRANCH}
+${indent}Old revision: ${old_revision} (committed by ${committer})
+${indent}${indent}${subject}")
+
+ ctest_start(${CTEST_DASHBOARD_MODEL})
+
+ set(CTEST_UPDATE_OPTIONS "origin ${MITK_BRANCH}")
+
+ ctest_update(RETURN_VALUE return_value)
+
+ if(-1 EQUAL return_value)
+ return()
+ endif()
+
+ git_log(COMMIT_HASH new_revision)
+
+ if(new_revision STREQUAL old_revision)
+ message("${indent}New revision: up-to-date")
+ else()
+ git_log(COMMITTER committer SUBJECT subject)
+
+ message("\
+${indent}New revision: ${new_revision} (committed by ${committer})
+${indent}${indent}${subject}")
+ endif()
+endif()
+
+unset(extension_dirs)
+
+if(MITK_EXTENSIONS)
+ list(LENGTH MITK_EXTENSIONS mitk_extensions_size)
+ math(EXPR max_index "${mitk_extensions_size} - 1")
+
+ foreach(name_index RANGE 0 ${max_index} 3)
+ list(GET MITK_EXTENSIONS ${name_index} name)
+
+ math(EXPR url_index "${name_index} + 1")
+ list(GET MITK_EXTENSIONS ${url_index} url)
+
+ math(EXPR branch_index "${name_index} + 2")
+ list(GET MITK_EXTENSIONS ${branch_index} branch)
+
+ message("${name} repository")
+
+ set(extension_dir "${CMAKE_CURRENT_SOURCE_DIR}/src/${name}")
+ list(APPEND extension_dirs "${extension_dir}")
+
+ if(NOT EXISTS "${extension_dir}")
+ message("\
+${indent}Clone repository: ${url}
+${indent}Branch: ${branch}")
+
+ git("clone" "--quiet" "--branch=${branch}" "${url}" "${name}"
+ WORKING_DIRECTORY "${extension_dir}/..")
+ else()
+ git_log(COMMIT_HASH old_revision COMMITTER committer SUBJECT subject
+ WORKING_DIRECTORY "${extension_dir}")
+
+ message("\
+${indent}Update repository: ${extension_dir}
+${indent}Branch: ${branch}
+${indent}Old revision: ${old_revision} (committed by ${committer})
+${indent}${indent}${subject}")
+
+ git("fetch" "--quiet" "origin" "${branch}"
+ WORKING_DIRECTORY "${extension_dir}")
+
+ git("diff" "--quiet" "HEAD" "FETCH_HEAD"
+ WORKING_DIRECTORY "${extension_dir}"
+ RESULT_VARIABLE error_code)
+
+ if(NOT error_code EQUAL 0)
+ git("reset" "--quiet" "--hard" "FETCH_HEAD"
+ WORKING_DIRECTORY "${extension_dir}")
+ endif()
+
+ git_log(COMMIT_HASH new_revision
+ WORKING_DIRECTORY "${extension_dir}")
+
+ if(new_revision STREQUAL old_revision)
+ message("${indent}New revision: up-to-date")
+ else()
+ git_log(COMMITTER committer SUBJECT subject
+ WORKING_DIRECTORY "${extension_dir}")
+
+ message("\
+${indent}New revision: ${new_revision} (committed by ${committer})
+${indent}${indent}${subject}")
+ endif()
+ endif()
+ endforeach()
+endif()
+
+submit(PARTS Update)
+
+set(options
+ "-D" "MITK_CTEST_SCRIPT_MODE:STRING=${CTEST_DASHBOARD_MODEL}"
+# "-D" "SUPERBUILD_EXCLUDE_MITKBUILD_TARGET:BOOL=TRUE"
+)
+
+if(extension_dirs)
+ string (REPLACE ";" "\\\;" extension_dirs "${extension_dirs}")
+ list(APPEND options "-D" "MITK_EXTENSION_DIRS:STRING=${extension_dirs}")
+endif()
+
+if(MITK_BUILD_CONFIGURATION)
+ list(APPEND options "-D" "MITK_BUILD_CONFIGURATION:STRING=${MITK_BUILD_CONFIGURATION}")
+endif()
+
+foreach(option ${MITK_SUPERBUILD_OPTIONS})
+ list(APPEND options "-D" "${option}")
+endforeach()
+
+ctest_configure(OPTIONS "${options}" RETURN_VALUE return_value)
+submit(PARTS Configure)
+
+if(NOT 0 EQUAL return_value)
+ submit(PARTS Done)
+ return()
+endif()
+
+include("${CTEST_BINARY_DIRECTORY}/SuperBuildTargets.cmake")
+
+if(NOT SUPERBUILD_TARGETS)
+ submit(PARTS Done)
+ message(FATAL_ERROR "SUPERBUILD_TARGETS variable not set in SuperBuildTargets.cmake")
+else()
+ set(mitk_targets
+ MITK-Data
+ MITK-Utilities
+ MITK-Configure
+ MITK-build
+ )
+
+ list(LENGTH SUPERBUILD_TARGETS n)
+ list(LENGTH mitk_targets num_mitk_targets)
+ math(EXPR n "${n} + ${num_mitk_targets}")
+ set(i 1)
+
+ unset(append)
+
+ foreach(target ${SUPERBUILD_TARGETS} ${mitk_targets})
+ message("MITK superbuild - [${i}/${n}] Build ${target}")
+
+ if(NOT target IN_LIST mitk_targets)
+ list(APPEND CTEST_CUSTOM_WARNING_EXCEPTION ".*")
+ set(pop_warning_exception TRUE)
+ else()
+ set(pop_warning_exception FALSE)
+ endif()
+
+ ctest_build(TARGET ${target}
+ NUMBER_ERRORS num_build_errors
+ NUMBER_WARNINGS num_build_warnings
+ RETURN_VALUE return_value
+ ${append})
+
+ if(pop_warning_exception)
+ list(POP_BACK CTEST_CUSTOM_WARNING_EXCEPTION)
+ endif()
+
+ submit(PARTS Build)
+
+ if(0 LESS num_build_warnings)
+ message("${indent}${num_build_warnings} warning(s)")
+ endif()
+
+ if(NOT (0 EQUAL return_value AND 0 EQUAL num_build_errors))
+ submit(PARTS Done)
+ message("${indent}${num_build_errors} error(s)")
+ return()
+ else()
+ message("${indent}${target} was built successfully")
+ endif()
+
+ if(NOT append)
+ set(append APPEND)
+ endif()
+
+ math(EXPR i "${i} + 1")
+ endforeach()
+endif()
+
+if(MITK_BUILD_DOCUMENTATION)
+ message("MITK build - Build documentation")
+
+ list(APPEND CTEST_CUSTOM_WARNING_EXCEPTION ".*")
+
+ ctest_build(TARGET doc
+ BUILD "${CTEST_BINARY_DIRECTORY}/MITK-build"
+ NUMBER_ERRORS num_doc_errors
+ NUMBER_WARNINGS num_doc_warnings
+ RETURN_VALUE return_value
+ APPEND
+ )
+
+ list(POP_BACK CTEST_CUSTOM_WARNING_EXCEPTION)
+
+ submit(PARTS Build)
+
+ if(0 LESS num_doc_warnings)
+ message("${indent}${num_doc_warnings} warning(s)")
+ endif()
+
+ if(NOT (0 EQUAL return_value AND 0 EQUAL num_doc_errors))
+ submit(PARTS Done)
+ message("${indent}${num_doc_errors} error(s)")
+ return()
+ else()
+ message("${indent}Documentation was built successfully")
+ endif()
+endif()
+
+message("Run unit tests...")
+
+set(CTEST_CONFIGURATION_TYPE "${CTEST_BUILD_CONFIGURATION}")
+
+ctest_test(
+ BUILD "${CTEST_BINARY_DIRECTORY}/MITK-build"
+ PARALLEL_LEVEL 4)
+
+submit(PARTS Test Done)
+
+message("Done")
diff --git a/CMake/MITKDashboardSetup.cmake b/CMake/MITKDashboardSetup.cmake
deleted file mode 100644
index a1befe0885..0000000000
--- a/CMake/MITKDashboardSetup.cmake
+++ /dev/null
@@ -1,134 +0,0 @@
-# This file is intended to be included at the end of a custom MITKDashboardScript.TEMPLATE.cmake file
-
-list(APPEND CTEST_NOTES_FILES "${CTEST_SCRIPT_DIRECTORY}/${CTEST_SCRIPT_NAME}")
-
-#
-# Automatically determined properties
-#
-set(MY_OPERATING_SYSTEM )
-
-if(UNIX)
- set(url "https://raw.githubusercontent.com/MITK/MITK/${GIT_BRANCH}/CMake/mitkDetectOS.sh")
- set(dest "${CTEST_SCRIPT_DIRECTORY}/mitkDetectOS.sh")
- downloadFile("${url}" "${dest}")
- execute_process(COMMAND sh "${dest}"
- RESULT_VARIABLE _result OUTPUT_VARIABLE _out
- OUTPUT_STRIP_TRAILING_WHITESPACE)
-
- if(NOT _result)
- set(MY_OPERATING_SYSTEM "${_out}")
- endif()
-endif()
-
-if(NOT MY_OPERATING_SYSTEM)
- set(MY_OPERATING_SYSTEM "${CMAKE_HOST_SYSTEM}") # Windows 7, Linux-2.6.32, Darwin...
-endif()
-
-site_name(CTEST_SITE)
-
-if(NOT DEFINED MITK_USE_Qt5)
- set(MITK_USE_Qt5 1)
-endif()
-
-#
-# Project specific properties
-#
-if(NOT CTEST_BUILD_NAME)
- if(MITK_USE_Qt5)
- set(CTEST_BUILD_NAME "${MY_OPERATING_SYSTEM} ${MY_COMPILER} ${CTEST_BUILD_CONFIGURATION}")
- else()
- set(CTEST_BUILD_NAME "${MY_OPERATING_SYSTEM} ${MY_COMPILER} ${CTEST_BUILD_CONFIGURATION}")
- endif()
- set(CTEST_BUILD_NAME "${CTEST_BUILD_NAME}${CTEST_BUILD_NAME_SUFFIX}")
-endif()
-set(PROJECT_BUILD_DIR "MITK-build")
-
-set(CTEST_PATH "$ENV{PATH}")
-if(WIN32)
- if("${CTEST_CMAKE_GENERATOR_PLATFORM}" STREQUAL "x64")
- set(CMAKE_LIBRARY_ARCHITECTURE x64)
- else()
- set(CMAKE_LIBRARY_ARCHITECTURE x86)
- endif()
- string(SUBSTRING "${MY_COMPILER}" 2 2 vc_version)
-
- set(OPENCV_BIN_DIR "${CTEST_BINARY_DIRECTORY}/ep/${CMAKE_LIBRARY_ARCHITECTURE}/vc${vc_version}/bin")
-
- set(BLUEBERRY_RUNTIME_DIR "${CTEST_BINARY_DIRECTORY}/MITK-build/bin/plugins/${CTEST_BUILD_CONFIGURATION}")
-
- set(PYTHON_BINARY_DIRS "${CTEST_BINARY_DIRECTORY}/ep/src/CTK-build/CMakeExternals/Install/bin")
- get_filename_component(_python_dir "${Python3_EXECUTABLE}" DIRECTORY)
- list(APPEND PYTHON_BINARY_DIRS "${_python_dir}")
-
- set(CTEST_PATH "${CTEST_PATH};${CTEST_BINARY_DIRECTORY}/ep/bin;${BLUEBERRY_RUNTIME_DIR};${OPENCV_BIN_DIR};${PYTHON_BINARY_DIRS}")
-endif()
-set(ENV{PATH} "${CTEST_PATH}")
-
-# If the dashscript doesn't define a GIT_REPOSITORY variable, let's define it here.
-if(NOT DEFINED GIT_REPOSITORY OR GIT_REPOSITORY STREQUAL "")
- set(GIT_REPOSITORY "https://phabricator.mitk.org/source/mitk.git")
-endif()
-
-#
-# Display build info
-#
-message("Site name: ${CTEST_SITE}")
-message("Build name: ${CTEST_BUILD_NAME}")
-message("Script Mode: ${SCRIPT_MODE}")
-message("Coverage: ${WITH_COVERAGE}, MemCheck: ${WITH_MEMCHECK}")
-
-#
-# Set initial cache options
-#
-if(CTEST_CMAKE_GENERATOR MATCHES ".*Makefiles.*")
- set(CTEST_USE_LAUNCHERS 1)
-else()
- set(CTEST_USE_LAUNCHERS 0)
-endif()
-set(ENV{CTEST_USE_LAUNCHERS_DEFAULT} ${CTEST_USE_LAUNCHERS})
-
-if(NOT DEFINED MITK_BUILD_CONFIGURATION)
- set(MITK_BUILD_CONFIGURATION "All")
-endif()
-
-if(NOT DEFINED MITK_VTK_DEBUG_LEAKS)
- set(MITK_VTK_DEBUG_LEAKS 1)
-endif()
-
-set(INITIAL_CMAKECACHE_OPTIONS "
-SUPERBUILD_EXCLUDE_MITKBUILD_TARGET:BOOL=TRUE
-MITK_BUILD_CONFIGURATION:STRING=${MITK_BUILD_CONFIGURATION}
-MITK_VTK_DEBUG_LEAKS:BOOL=${MITK_VTK_DEBUG_LEAKS}
-${ADDITIONAL_CMAKECACHE_OPTION}
-")
-
-# Write a cache file for populating the MITK initial cache (not the superbuild cache).
-# This can be used to provide variables which are not passed through the
-# superbuild process to the MITK configure step)
-if(MITK_INITIAL_CACHE)
- set(mitk_cache_file "${CTEST_SCRIPT_DIRECTORY}/mitk_initial_cache.txt")
- file(WRITE "${mitk_cache_file}" "${MITK_INITIAL_CACHE}")
- set(INITIAL_CMAKECACHE_OPTIONS "${INITIAL_CMAKECACHE_OPTIONS}
-MITK_INITIAL_CACHE_FILE:INTERNAL=${mitk_cache_file}
-")
-endif()
-
-if(MITK_EXTENSIONS)
- set(MITK_EXTENSION_DIRS "")
- foreach(extension ${MITK_EXTENSIONS})
- if(extension MATCHES "[^|]+\\|[^|]+\\|(.+)")
- if(MITK_EXTENSION_DIRS)
- set(MITK_EXTENSION_DIRS "${MITK_EXTENSION_DIRS};")
- endif()
- set(MITK_EXTENSION_DIRS "${MITK_EXTENSION_DIRS}${CTEST_DASHBOARD_ROOT}/${CMAKE_MATCH_1}")
- endif()
- endforeach()
-endif()
-
-#
-# Download and include dashboard driver script
-#
-set(url "https://raw.githubusercontent.com/MITK/MITK/${GIT_BRANCH}/CMake/MITKDashboardDriverScript.cmake")
-set(dest ${CTEST_SCRIPT_DIRECTORY}/${CTEST_SCRIPT_NAME}.driver)
-downloadFile("${url}" "${dest}")
-include(${dest})
diff --git a/CMake/NSIS.template.in b/CMake/NSIS.template.in
index 774d02ffc4..f111eadbc1 100644
--- a/CMake/NSIS.template.in
+++ b/CMake/NSIS.template.in
@@ -1,1094 +1,1086 @@
; CPack install script designed for a nmake build
;--------------------------------
; You must define these values
!define VERSION "@CPACK_PACKAGE_VERSION@"
!define PATCH "@CPACK_PACKAGE_VERSION_PATCH@"
!define INST_DIR "@CPACK_TEMPORARY_DIRECTORY@"
;--------------------------------
;Variables
Var MUI_TEMP
Var STARTMENU_FOLDER
Var SV_ALLUSERS
Var START_MENU
Var DO_NOT_ADD_TO_PATH
Var ADD_TO_PATH_ALL_USERS
Var ADD_TO_PATH_CURRENT_USER
Var INSTALL_DESKTOP
Var IS_DEFAULT_INSTALLDIR
;--------------------------------
;Include Modern UI
!include "MUI.nsh"
;Default installation folder
InstallDir "@CPACK_NSIS_INSTALL_ROOT@\@CPACK_PACKAGE_INSTALL_DIRECTORY@"
;Allow for very long title on the welcome page
!define MUI_WELCOMEPAGE_TITLE_3LINES
;--------------------------------
;General
;Name and file
Name "@CPACK_NSIS_PACKAGE_NAME@"
OutFile "@CPACK_TOPLEVEL_DIRECTORY@/@CPACK_OUTPUT_FILE_NAME@"
;Set compression
SetCompressor @CPACK_NSIS_COMPRESSOR@
RequestExecutionLevel user
@CPACK_NSIS_DEFINES@
!include Sections.nsh
;--- Component support macros: ---
; The code for the add/remove functionality is from:
; http://nsis.sourceforge.net/Add/Remove_Functionality
; It has been modified slightly and extended to provide
; inter-component dependencies.
Var AR_SecFlags
Var AR_RegFlags
@CPACK_NSIS_SECTION_SELECTED_VARS@
; Loads the "selected" flag for the section named SecName into the
; variable VarName.
!macro LoadSectionSelectedIntoVar SecName VarName
SectionGetFlags ${${SecName}} $${VarName}
IntOp $${VarName} $${VarName} & ${SF_SELECTED} ;Turn off all other bits
!macroend
; Loads the value of a variable... can we get around this?
!macro LoadVar VarName
IntOp $R0 0 + $${VarName}
!macroend
; Sets the value of a variable
!macro StoreVar VarName IntValue
IntOp $${VarName} 0 + ${IntValue}
!macroend
!macro InitSection SecName
; This macro reads component installed flag from the registry and
;changes checked state of the section on the components page.
;Input: section index constant name specified in Section command.
ClearErrors
;Reading component status from registry
ReadRegDWORD $AR_RegFlags HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@\Components\${SecName}" "Installed"
IfErrors "default_${SecName}"
;Status will stay default if registry value not found
;(component was never installed)
IntOp $AR_RegFlags $AR_RegFlags & ${SF_SELECTED} ;Turn off all other bits
SectionGetFlags ${${SecName}} $AR_SecFlags ;Reading default section flags
IntOp $AR_SecFlags $AR_SecFlags & 0xFFFE ;Turn lowest (enabled) bit off
IntOp $AR_SecFlags $AR_RegFlags | $AR_SecFlags ;Change lowest bit
; Note whether this component was installed before
!insertmacro StoreVar ${SecName}_was_installed $AR_RegFlags
IntOp $R0 $AR_RegFlags & $AR_RegFlags
;Writing modified flags
SectionSetFlags ${${SecName}} $AR_SecFlags
"default_${SecName}:"
!insertmacro LoadSectionSelectedIntoVar ${SecName} ${SecName}_selected
!macroend
!macro FinishSection SecName
; This macro reads section flag set by user and removes the section
;if it is not selected.
;Then it writes component installed flag to registry
;Input: section index constant name specified in Section command.
SectionGetFlags ${${SecName}} $AR_SecFlags ;Reading section flags
;Checking lowest bit:
IntOp $AR_SecFlags $AR_SecFlags & ${SF_SELECTED}
IntCmp $AR_SecFlags 1 "leave_${SecName}"
;Section is not selected:
;Calling Section uninstall macro and writing zero installed flag
!insertmacro "Remove_${${SecName}}"
WriteRegDWORD HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@\Components\${SecName}" \
"Installed" 0
Goto "exit_${SecName}"
"leave_${SecName}:"
;Section is selected:
WriteRegDWORD HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@\Components\${SecName}" \
"Installed" 1
"exit_${SecName}:"
!macroend
-!macro RemoveSection SecName
- ; This macro is used to call section's Remove_... macro
- ;from the uninstaller.
- ;Input: section index constant name specified in Section command.
-
- !insertmacro "Remove_${${SecName}}"
-!macroend
-
; NSIS example code to only include some code if a file exists at compile time (whereas IfFileExists works at runtime)
; See http://nsis.sourceforge.net/Check_if_a_file_exists_at_compile_time for documentation
!macro !defineifexist _VAR_NAME _FILE_NAME
!tempfile _TEMPFILE
!system 'if exist "${_FILE_NAME}" echo !define ${_VAR_NAME} > "${_TEMPFILE}"'
!include '${_TEMPFILE}'
!delfile '${_TEMPFILE}'
!undef _TEMPFILE
!macroend
!define !defineifexist "!insertmacro !defineifexist"
; Determine whether the selection of SecName changed
!macro MaybeSelectionChanged SecName
!insertmacro LoadVar ${SecName}_selected
SectionGetFlags ${${SecName}} $R1
IntOp $R1 $R1 & ${SF_SELECTED} ;Turn off all other bits
; See if the status has changed:
IntCmp $R0 $R1 "${SecName}_unchanged"
!insertmacro LoadSectionSelectedIntoVar ${SecName} ${SecName}_selected
IntCmp $R1 ${SF_SELECTED} "${SecName}_was_selected"
!insertmacro "Deselect_required_by_${SecName}"
goto "${SecName}_unchanged"
"${SecName}_was_selected:"
!insertmacro "Select_${SecName}_depends"
"${SecName}_unchanged:"
!macroend
;--- End of Add/Remove macros ---
;--------------------------------
;Interface Settings
!define MUI_HEADERIMAGE
!define MUI_ABORTWARNING
;--------------------------------
; path functions
!verbose 3
!include "WinMessages.NSH"
!verbose 4
;----------------------------------------
; based upon a script of "Written by KiCHiK 2003-01-18 05:57:02"
;----------------------------------------
!verbose 3
!include "WinMessages.NSH"
!verbose 4
;====================================================
; get_NT_environment
; Returns: the selected environment
; Output : head of the stack
;====================================================
!macro select_NT_profile UN
Function ${UN}select_NT_profile
StrCmp $ADD_TO_PATH_ALL_USERS "1" 0 environment_single
DetailPrint "Selected environment for all users"
Push "all"
Return
environment_single:
DetailPrint "Selected environment for current user only."
Push "current"
Return
FunctionEnd
!macroend
!insertmacro select_NT_profile ""
!insertmacro select_NT_profile "un."
;----------------------------------------------------
!define NT_current_env 'HKCU "Environment"'
!define NT_all_env 'HKLM "SYSTEM\CurrentControlSet\Control\Session Manager\Environment"'
!ifndef WriteEnvStr_RegKey
!ifdef ALL_USERS
!define WriteEnvStr_RegKey \
'HKLM "SYSTEM\CurrentControlSet\Control\Session Manager\Environment"'
!else
!define WriteEnvStr_RegKey 'HKCU "Environment"'
!endif
!endif
; AddToPath - Adds the given dir to the search path.
; Input - head of the stack
; Note - Win9x systems requires reboot
Function AddToPath
Exch $0
Push $1
Push $2
Push $3
# don't add if the path doesn't exist
IfFileExists "$0\*.*" "" AddToPath_done
ReadEnvStr $1 PATH
; if the path is too long for a NSIS variable NSIS will return a 0
; length string. If we find that, then warn and skip any path
; modification as it will trash the existing path.
StrLen $2 $1
IntCmp $2 0 CheckPathLength_ShowPathWarning CheckPathLength_Done CheckPathLength_Done
CheckPathLength_ShowPathWarning:
DetailPrint "Warning: Could not modify PATH variable - current PATH is too long.\n\
This does not impact the functionality of MITK itself, but you will not be able to start\
it from anywhere via command line."
; The message box is probably too much of an escalation, most users won't care or notice
;Messagebox MB_OK|MB_ICONEXCLAMATION "Warning! PATH too long installer unable to modify PATH!"
Goto AddToPath_done
CheckPathLength_Done:
Push "$1;"
Push "$0;"
Call StrStr
Pop $2
StrCmp $2 "" "" AddToPath_done
Push "$1;"
Push "$0\;"
Call StrStr
Pop $2
StrCmp $2 "" "" AddToPath_done
GetFullPathName /SHORT $3 $0
Push "$1;"
Push "$3;"
Call StrStr
Pop $2
StrCmp $2 "" "" AddToPath_done
Push "$1;"
Push "$3\;"
Call StrStr
Pop $2
StrCmp $2 "" "" AddToPath_done
Call IsNT
Pop $1
StrCmp $1 1 AddToPath_NT
; Not on NT
StrCpy $1 $WINDIR 2
FileOpen $1 "$1\autoexec.bat" a
FileSeek $1 -1 END
FileReadByte $1 $2
IntCmp $2 26 0 +2 +2 # DOS EOF
FileSeek $1 -1 END # write over EOF
FileWrite $1 "$\r$\nSET PATH=%PATH%;$3$\r$\n"
FileClose $1
SetRebootFlag true
Goto AddToPath_done
AddToPath_NT:
StrCmp $ADD_TO_PATH_ALL_USERS "1" ReadAllKey
ReadRegStr $1 ${NT_current_env} "PATH"
Goto DoTrim
ReadAllKey:
ReadRegStr $1 ${NT_all_env} "PATH"
DoTrim:
StrCmp $1 "" AddToPath_NTdoIt
Push $1
Call Trim
Pop $1
StrCpy $0 "$1;$0"
AddToPath_NTdoIt:
StrCmp $ADD_TO_PATH_ALL_USERS "1" WriteAllKey
WriteRegExpandStr ${NT_current_env} "PATH" $0
Goto DoSend
WriteAllKey:
WriteRegExpandStr ${NT_all_env} "PATH" $0
DoSend:
SendMessage ${HWND_BROADCAST} ${WM_WININICHANGE} 0 "STR:Environment" /TIMEOUT=5000
AddToPath_done:
Pop $3
Pop $2
Pop $1
Pop $0
FunctionEnd
; RemoveFromPath - Remove a given dir from the path
; Input: head of the stack
Function un.RemoveFromPath
Exch $0
Push $1
Push $2
Push $3
Push $4
Push $5
Push $6
IntFmt $6 "%c" 26 # DOS EOF
Call un.IsNT
Pop $1
StrCmp $1 1 unRemoveFromPath_NT
; Not on NT
StrCpy $1 $WINDIR 2
FileOpen $1 "$1\autoexec.bat" r
GetTempFileName $4
FileOpen $2 $4 w
GetFullPathName /SHORT $0 $0
StrCpy $0 "SET PATH=%PATH%;$0"
Goto unRemoveFromPath_dosLoop
unRemoveFromPath_dosLoop:
FileRead $1 $3
StrCpy $5 $3 1 -1 # read last char
StrCmp $5 $6 0 +2 # if DOS EOF
StrCpy $3 $3 -1 # remove DOS EOF so we can compare
StrCmp $3 "$0$\r$\n" unRemoveFromPath_dosLoopRemoveLine
StrCmp $3 "$0$\n" unRemoveFromPath_dosLoopRemoveLine
StrCmp $3 "$0" unRemoveFromPath_dosLoopRemoveLine
StrCmp $3 "" unRemoveFromPath_dosLoopEnd
FileWrite $2 $3
Goto unRemoveFromPath_dosLoop
unRemoveFromPath_dosLoopRemoveLine:
SetRebootFlag true
Goto unRemoveFromPath_dosLoop
unRemoveFromPath_dosLoopEnd:
FileClose $2
FileClose $1
StrCpy $1 $WINDIR 2
Delete "$1\autoexec.bat"
CopyFiles /SILENT $4 "$1\autoexec.bat"
Delete $4
Goto unRemoveFromPath_done
unRemoveFromPath_NT:
StrCmp $ADD_TO_PATH_ALL_USERS "1" unReadAllKey
ReadRegStr $1 ${NT_current_env} "PATH"
Goto unDoTrim
unReadAllKey:
ReadRegStr $1 ${NT_all_env} "PATH"
unDoTrim:
StrCpy $5 $1 1 -1 # copy last char
StrCmp $5 ";" +2 # if last char != ;
StrCpy $1 "$1;" # append ;
Push $1
Push "$0;"
Call un.StrStr ; Find `$0;` in $1
Pop $2 ; pos of our dir
StrCmp $2 "" unRemoveFromPath_done
; else, it is in path
# $0 - path to add
# $1 - path var
StrLen $3 "$0;"
StrLen $4 $2
StrCpy $5 $1 -$4 # $5 is now the part before the path to remove
StrCpy $6 $2 "" $3 # $6 is now the part after the path to remove
StrCpy $3 $5$6
StrCpy $5 $3 1 -1 # copy last char
StrCmp $5 ";" 0 +2 # if last char == ;
StrCpy $3 $3 -1 # remove last char
StrCmp $ADD_TO_PATH_ALL_USERS "1" unWriteAllKey
WriteRegExpandStr ${NT_current_env} "PATH" $3
Goto unDoSend
unWriteAllKey:
WriteRegExpandStr ${NT_all_env} "PATH" $3
unDoSend:
SendMessage ${HWND_BROADCAST} ${WM_WININICHANGE} 0 "STR:Environment" /TIMEOUT=5000
unRemoveFromPath_done:
Pop $6
Pop $5
Pop $4
Pop $3
Pop $2
Pop $1
Pop $0
FunctionEnd
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; Uninstall stuff
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
###########################################
# Utility Functions #
###########################################
;====================================================
; IsNT - Returns 1 if the current system is NT, 0
; otherwise.
; Output: head of the stack
;====================================================
; IsNT
; no input
; output, top of the stack = 1 if NT or 0 if not
;
; Usage:
; Call IsNT
; Pop $R0
; ($R0 at this point is 1 or 0)
!macro IsNT un
Function ${un}IsNT
Push $0
ReadRegStr $0 HKLM "SOFTWARE\Microsoft\Windows NT\CurrentVersion" CurrentVersion
StrCmp $0 "" 0 IsNT_yes
; we are not NT.
Pop $0
Push 0
Return
IsNT_yes:
; NT!!!
Pop $0
Push 1
FunctionEnd
!macroend
!insertmacro IsNT ""
!insertmacro IsNT "un."
; StrStr
; input, top of stack = string to search for
; top of stack-1 = string to search in
; output, top of stack (replaces with the portion of the string remaining)
; modifies no other variables.
;
; Usage:
; Push "this is a long ass string"
; Push "ass"
; Call StrStr
; Pop $R0
; ($R0 at this point is "ass string")
!macro StrStr un
Function ${un}StrStr
Exch $R1 ; st=haystack,old$R1, $R1=needle
Exch ; st=old$R1,haystack
Exch $R2 ; st=old$R1,old$R2, $R2=haystack
Push $R3
Push $R4
Push $R5
StrLen $R3 $R1
StrCpy $R4 0
; $R1=needle
; $R2=haystack
; $R3=len(needle)
; $R4=cnt
; $R5=tmp
loop:
StrCpy $R5 $R2 $R3 $R4
StrCmp $R5 $R1 done
StrCmp $R5 "" done
IntOp $R4 $R4 + 1
Goto loop
done:
StrCpy $R1 $R2 "" $R4
Pop $R5
Pop $R4
Pop $R3
Pop $R2
Exch $R1
FunctionEnd
!macroend
!insertmacro StrStr ""
!insertmacro StrStr "un."
Function Trim ; Added by Pelaca
Exch $R1
Push $R2
Loop:
StrCpy $R2 "$R1" 1 -1
StrCmp "$R2" " " RTrim
StrCmp "$R2" "$\n" RTrim
StrCmp "$R2" "$\r" RTrim
StrCmp "$R2" ";" RTrim
GoTo Done
RTrim:
StrCpy $R1 "$R1" -1
Goto Loop
Done:
Pop $R2
Exch $R1
FunctionEnd
Function ConditionalAddToRegisty
Pop $0
Pop $1
StrCmp "$0" "" ConditionalAddToRegisty_EmptyString
WriteRegStr SHCTX "Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@" \
"$1" "$0"
;MessageBox MB_OK "Set Registry: '$1' to '$0'"
DetailPrint "Set install registry entry: '$1' to '$0'"
ConditionalAddToRegisty_EmptyString:
FunctionEnd
;--------------------------------
!ifdef CPACK_USES_DOWNLOAD
Function DownloadFile
IfFileExists $INSTDIR\* +2
CreateDirectory $INSTDIR
Pop $0
; Skip if already downloaded
IfFileExists $INSTDIR\$0 0 +2
Return
StrCpy $1 "@CPACK_DOWNLOAD_SITE@"
try_again:
NSISdl::download "$1/$0" "$INSTDIR\$0"
Pop $1
StrCmp $1 "success" success
StrCmp $1 "Cancelled" cancel
MessageBox MB_OK "Download failed: $1"
cancel:
Return
success:
FunctionEnd
!endif
;--------------------------------
; Installation types
@CPACK_NSIS_INSTALLATION_TYPES@
;--------------------------------
; Component sections
@CPACK_NSIS_COMPONENT_SECTIONS@
;--------------------------------
; Define some macro setting for the gui
@CPACK_NSIS_INSTALLER_MUI_ICON_CODE@
@CPACK_NSIS_INSTALLER_ICON_CODE@
@CPACK_NSIS_INSTALLER_MUI_COMPONENTS_DESC@
@CPACK_NSIS_INSTALLER_MUI_FINISHPAGE_RUN_CODE@
;--------------------------------
;Pages
!insertmacro MUI_PAGE_WELCOME
!insertmacro MUI_PAGE_LICENSE "@CPACK_RESOURCE_FILE_LICENSE@"
Page custom InstallOptionsPage
!insertmacro MUI_PAGE_DIRECTORY
;Start Menu Folder Page Configuration
!define MUI_STARTMENUPAGE_REGISTRY_ROOT "SHCTX"
!define MUI_STARTMENUPAGE_REGISTRY_KEY "Software\@CPACK_PACKAGE_VENDOR@\@CPACK_PACKAGE_INSTALL_REGISTRY_KEY@"
!define MUI_STARTMENUPAGE_REGISTRY_VALUENAME "Start Menu Folder"
!insertmacro MUI_PAGE_STARTMENU Application $STARTMENU_FOLDER
@CPACK_NSIS_PAGE_COMPONENTS@
!insertmacro MUI_PAGE_INSTFILES
!insertmacro MUI_PAGE_FINISH
!insertmacro MUI_UNPAGE_CONFIRM
!insertmacro MUI_UNPAGE_INSTFILES
;--------------------------------
;Languages
!insertmacro MUI_LANGUAGE "English" ;first language is the default language
!insertmacro MUI_LANGUAGE "Albanian"
!insertmacro MUI_LANGUAGE "Arabic"
!insertmacro MUI_LANGUAGE "Basque"
!insertmacro MUI_LANGUAGE "Belarusian"
!insertmacro MUI_LANGUAGE "Bosnian"
!insertmacro MUI_LANGUAGE "Breton"
!insertmacro MUI_LANGUAGE "Bulgarian"
!insertmacro MUI_LANGUAGE "Croatian"
!insertmacro MUI_LANGUAGE "Czech"
!insertmacro MUI_LANGUAGE "Danish"
!insertmacro MUI_LANGUAGE "Dutch"
!insertmacro MUI_LANGUAGE "Estonian"
!insertmacro MUI_LANGUAGE "Farsi"
!insertmacro MUI_LANGUAGE "Finnish"
!insertmacro MUI_LANGUAGE "French"
!insertmacro MUI_LANGUAGE "German"
!insertmacro MUI_LANGUAGE "Greek"
!insertmacro MUI_LANGUAGE "Hebrew"
!insertmacro MUI_LANGUAGE "Hungarian"
!insertmacro MUI_LANGUAGE "Icelandic"
!insertmacro MUI_LANGUAGE "Indonesian"
!insertmacro MUI_LANGUAGE "Irish"
!insertmacro MUI_LANGUAGE "Italian"
!insertmacro MUI_LANGUAGE "Japanese"
!insertmacro MUI_LANGUAGE "Korean"
!insertmacro MUI_LANGUAGE "Kurdish"
!insertmacro MUI_LANGUAGE "Latvian"
!insertmacro MUI_LANGUAGE "Lithuanian"
!insertmacro MUI_LANGUAGE "Luxembourgish"
!insertmacro MUI_LANGUAGE "Macedonian"
!insertmacro MUI_LANGUAGE "Malay"
!insertmacro MUI_LANGUAGE "Mongolian"
!insertmacro MUI_LANGUAGE "Norwegian"
!insertmacro MUI_LANGUAGE "Polish"
!insertmacro MUI_LANGUAGE "Portuguese"
!insertmacro MUI_LANGUAGE "PortugueseBR"
!insertmacro MUI_LANGUAGE "Romanian"
!insertmacro MUI_LANGUAGE "Russian"
!insertmacro MUI_LANGUAGE "Serbian"
!insertmacro MUI_LANGUAGE "SerbianLatin"
!insertmacro MUI_LANGUAGE "SimpChinese"
!insertmacro MUI_LANGUAGE "Slovak"
!insertmacro MUI_LANGUAGE "Slovenian"
!insertmacro MUI_LANGUAGE "Spanish"
!insertmacro MUI_LANGUAGE "Swedish"
!insertmacro MUI_LANGUAGE "Thai"
!insertmacro MUI_LANGUAGE "TradChinese"
!insertmacro MUI_LANGUAGE "Turkish"
!insertmacro MUI_LANGUAGE "Ukrainian"
!insertmacro MUI_LANGUAGE "Welsh"
;--------------------------------
;Reserve Files
;These files should be inserted before other files in the data block
;Keep these lines before any File command
;Only for solid compression (by default, solid compression is enabled for BZIP2 and LZMA)
ReserveFile "NSIS.InstallOptions.ini"
!insertmacro MUI_RESERVEFILE_INSTALLOPTIONS
;--------------------------------
;Installer Sections
Section "-Core installation"
;Use the entire tree produced by the INSTALL target. Keep the
;list of directories here in sync with the RMDir commands below.
SetOutPath "$INSTDIR"
@CPACK_NSIS_FULL_INSTALL@
; Check whether redistributables need to be installed
Call RedistributablePage
;Store installation folder
WriteRegStr SHCTX "Software\@CPACK_PACKAGE_VENDOR@\@CPACK_PACKAGE_INSTALL_REGISTRY_KEY@" "" $INSTDIR
;Create uninstaller
WriteUninstaller "$INSTDIR\Uninstall.exe"
Push "DisplayName"
Push "@CPACK_NSIS_DISPLAY_NAME@"
Call ConditionalAddToRegisty
Push "DisplayVersion"
Push "@CPACK_PACKAGE_VERSION@"
Call ConditionalAddToRegisty
Push "Publisher"
Push "@CPACK_PACKAGE_VENDOR@"
Call ConditionalAddToRegisty
Push "UninstallString"
Push "$INSTDIR\Uninstall.exe"
Call ConditionalAddToRegisty
Push "NoRepair"
Push "1"
Call ConditionalAddToRegisty
!ifdef CPACK_NSIS_ADD_REMOVE
;Create add/remove functionality
Push "ModifyPath"
Push "$INSTDIR\AddRemove.exe"
Call ConditionalAddToRegisty
!else
Push "NoModify"
Push "1"
Call ConditionalAddToRegisty
!endif
; Optional registration
Push "DisplayIcon"
Push "$INSTDIR\@CPACK_NSIS_INSTALLED_ICON_NAME@"
Call ConditionalAddToRegisty
Push "HelpLink"
Push "@CPACK_NSIS_HELP_LINK@"
Call ConditionalAddToRegisty
Push "URLInfoAbout"
Push "@CPACK_NSIS_URL_INFO_ABOUT@"
Call ConditionalAddToRegisty
Push "Contact"
Push "@CPACK_NSIS_CONTACT@"
Call ConditionalAddToRegisty
!insertmacro MUI_INSTALLOPTIONS_READ $INSTALL_DESKTOP "NSIS.InstallOptions.ini" "Field 5" "State"
!insertmacro MUI_STARTMENU_WRITE_BEGIN Application
;Create shortcuts
CreateDirectory "$SMPROGRAMS\$STARTMENU_FOLDER"
@CPACK_NSIS_CREATE_ICONS@
@CPACK_NSIS_CREATE_ICONS_EXTRA@
CreateShortCut "$SMPROGRAMS\$STARTMENU_FOLDER\Uninstall.lnk" "$INSTDIR\Uninstall.exe"
;Read a value from an InstallOptions INI file
!insertmacro MUI_INSTALLOPTIONS_READ $DO_NOT_ADD_TO_PATH "NSIS.InstallOptions.ini" "Field 2" "State"
!insertmacro MUI_INSTALLOPTIONS_READ $ADD_TO_PATH_ALL_USERS "NSIS.InstallOptions.ini" "Field 3" "State"
!insertmacro MUI_INSTALLOPTIONS_READ $ADD_TO_PATH_CURRENT_USER "NSIS.InstallOptions.ini" "Field 4" "State"
; Write special uninstall registry entries
Push "StartMenu"
Push "$STARTMENU_FOLDER"
Call ConditionalAddToRegisty
Push "DoNotAddToPath"
Push "$DO_NOT_ADD_TO_PATH"
Call ConditionalAddToRegisty
Push "AddToPathAllUsers"
Push "$ADD_TO_PATH_ALL_USERS"
Call ConditionalAddToRegisty
Push "AddToPathCurrentUser"
Push "$ADD_TO_PATH_CURRENT_USER"
Call ConditionalAddToRegisty
Push "InstallToDesktop"
Push "$INSTALL_DESKTOP"
Call ConditionalAddToRegisty
!insertmacro MUI_STARTMENU_WRITE_END
@CPACK_NSIS_EXTRA_INSTALL_COMMANDS@
SectionEnd
Section "-Add to path"
Push $INSTDIR\bin
StrCmp "@CPACK_NSIS_MODIFY_PATH@" "ON" 0 doNotAddToPath
StrCmp $DO_NOT_ADD_TO_PATH "1" doNotAddToPath 0
Call AddToPath
doNotAddToPath:
SectionEnd
;--------------------------------
; Create custom pages
Function InstallOptionsPage
!insertmacro MUI_HEADER_TEXT "Install Options" "Choose options for installing @CPACK_NSIS_PACKAGE_NAME@"
!insertmacro MUI_INSTALLOPTIONS_DISPLAY "NSIS.InstallOptions.ini"
FunctionEnd
; Author: Lilla (lilla@earthlink.net) 2003-06-13
; function IsUserAdmin uses plugin \NSIS\PlusgIns\UserInfo.dll
; This function is based upon code in \NSIS\Contrib\UserInfo\UserInfo.nsi
; This function was tested under NSIS 2 beta 4 (latest CVS as of this writing).
;
; Usage:
; Call IsUserAdmin
; Pop $R0 ; at this point $R0 is "true" or "false"
;
Function IsUserAdmin
Push $R0
Push $R1
Push $R2
ClearErrors
UserInfo::GetName
IfErrors Win9x
Pop $R1
UserInfo::GetAccountType
Pop $R2
StrCmp $R2 "Admin" 0 Continue
; Observation: I get here when running Win98SE. (Lilla)
; The functions UserInfo.dll looks for are there on Win98 too,
; but just don't work. So UserInfo.dll, knowing that admin isn't required
; on Win98, returns admin anyway. (per kichik)
; MessageBox MB_OK 'User "$R1" is in the Administrators group'
StrCpy $R0 "true"
Goto Done
Continue:
; You should still check for an empty string because the functions
; UserInfo.dll looks for may not be present on Windows 95. (per kichik)
StrCmp $R2 "" Win9x
StrCpy $R0 "false"
;MessageBox MB_OK 'User "$R1" is in the "$R2" group'
Goto Done
Win9x:
; comment/message below is by UserInfo.nsi author:
; This one means you don't need to care about admin or
; not admin because Windows 9x doesn't either
;MessageBox MB_OK "Error! This DLL can't run under Windows 9x!"
StrCpy $R0 "true"
Done:
;MessageBox MB_OK 'User= "$R1" AccountType= "$R2" IsUserAdmin= "$R0"'
Pop $R2
Pop $R1
Exch $R0
FunctionEnd
Function RedistributablePage
; Check whether the appropriate redistributable for this installer has been installed
StrCmp '@CPACK_LIBRARY_ARCHITECTURE@' 'x64' 0 +3
SetRegView 64
Goto done
StrCmp '@CPACK_LIBRARY_ARCHITECTURE@' 'x86' 0 +3
SetRegView 32
Goto done
; The following line should not be reached, use for debugging
; MessageBox MB_OK "Could not determine x86/x64 architecture during CPack installer configuration."
done:
ReadRegDword $1 HKLM "SOFTWARE\Microsoft\DevDiv\vc\Servicing\@CPACK_VISUAL_STUDIO_VERSION_MAJOR@.0\RuntimeMinimum" "Install"
; If installed show installed, else offer installation
StrCmp $1 1 RedistInstalled
; Offer Installation
; MessageBox MB_YESNO "MITK requires the @CPACK_VISUAL_STUDIO_PRODUCT_NAME@ Redistributable to function. Do you wish to install it?" /SD IDYES IDNO endInstallationMissingRedist
; Verify that user has admin privileges
; Otherwise they are not able to install the redistributable
Call IsUserAdmin
Exch $R0
StrCmp $R0 "false" NoAdminRights
Pop $R0
SetOutPath $INSTDIR\thirdpartyinstallers
; We need compile time information on whether the redistributable installer exists.
; If it does not exist using the "File" command will lead to errors.
${!defineifexist} REDIST_INSTALLER_PRESENT @CPACK_PACKAGE_FILE_NAME@\thirdpartyinstallers\@CPACK_REDISTRIBUTABLE_FILE_NAME@
!ifdef REDIST_INSTALLER_PRESENT
; Check at runtime whether the redistributable installer is available
IfFileExists $INSTDIR\thirdpartyinstallers\@CPACK_REDISTRIBUTABLE_FILE_NAME@ InstallRedist NoRedistInstaller
InstallRedist:
ClearErrors
File "@CPACK_PACKAGE_FILE_NAME@\thirdpartyinstallers\@CPACK_REDISTRIBUTABLE_FILE_NAME@"
ExecWait '"$INSTDIR\thirdpartyinstallers\@CPACK_REDISTRIBUTABLE_FILE_NAME@" /passive /norestart'
IfErrors endInstallationMissingRedist
Goto RedistInstalled
endInstallationMissingRedist:
Abort "Installation aborted. Missing required @CPACK_VISUAL_STUDIO_PRODUCT_NAME@ @CPACK_LIBRARY_ARCHITECTURE@ Redistributable"
!endif
; We are missing the redistributable installer, inform the user
NoRedistInstaller:
MessageBox MB_OK "Missing required @CPACK_VISUAL_STUDIO_PRODUCT_NAME@ @CPACK_LIBRARY_ARCHITECTURE@ Redistributable. You need to install it to use MITK."
Goto End
; The user does not have the required rights to install redistributables
NoAdminRights:
MessageBox MB_OK|MB_ICONSTOP "This MITK version requires the @CPACK_VISUAL_STUDIO_PRODUCT_NAME@ @CPACK_LIBRARY_ARCHITECTURE@ Redistributable.$\r$\n\
Your user account does not have administrator privileges.$\r$\n\
Please ask your system administrator to install the @CPACK_VISUAL_STUDIO_PRODUCT_NAME@ @CPACK_LIBRARY_ARCHITECTURE@ Redistributable."
Pop $R0
Goto End
; No need to do anything
RedistInstalled:
Goto End
End:
FunctionEnd
;--------------------------------
; determine admin versus local install
Function un.onInit
ClearErrors
UserInfo::GetName
IfErrors noLM
Pop $0
UserInfo::GetAccountType
Pop $1
StrCmp $1 "Admin" 0 +3
SetShellVarContext all
;MessageBox MB_OK 'User "$0" is in the Admin group'
Goto done
StrCmp $1 "Power" 0 +3
SetShellVarContext all
;MessageBox MB_OK 'User "$0" is in the Power Users group'
Goto done
noLM:
;Get installation folder from registry if available
done:
FunctionEnd
;--- Add/Remove callback functions: ---
!macro SectionList MacroName
;This macro used to perform operation on multiple sections.
;List all of your components in following manner here.
@CPACK_NSIS_COMPONENT_SECTION_LIST@
!macroend
Section -FinishComponents
;Removes unselected components and writes component status to registry
!insertmacro SectionList "FinishSection"
!ifdef CPACK_NSIS_ADD_REMOVE
; Get the name of the installer executable
System::Call 'kernel32::GetModuleFileNameA(i 0, t .R0, i 1024) i r1'
StrCpy $R3 $R0
; Strip off the last 13 characters, to see if we have AddRemove.exe
StrLen $R1 $R0
IntOp $R1 $R0 - 13
StrCpy $R2 $R0 13 $R1
StrCmp $R2 "AddRemove.exe" addremove_installed
; We're not running AddRemove.exe, so install it
CopyFiles $R3 $INSTDIR\AddRemove.exe
addremove_installed:
!endif
SectionEnd
;--- End of Add/Remove callback functions ---
;--------------------------------
; Component dependencies
Function .onSelChange
!insertmacro SectionList MaybeSelectionChanged
FunctionEnd
;--------------------------------
;Uninstaller Section
Section "Uninstall"
ReadRegStr $START_MENU SHCTX \
"Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@" "StartMenu"
;MessageBox MB_OK "Start menu is in: $START_MENU"
ReadRegStr $DO_NOT_ADD_TO_PATH SHCTX \
"Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@" "DoNotAddToPath"
ReadRegStr $ADD_TO_PATH_ALL_USERS SHCTX \
"Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@" "AddToPathAllUsers"
ReadRegStr $ADD_TO_PATH_CURRENT_USER SHCTX \
"Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@" "AddToPathCurrentUser"
;MessageBox MB_OK "Add to path: $DO_NOT_ADD_TO_PATH all users: $ADD_TO_PATH_ALL_USERS"
ReadRegStr $INSTALL_DESKTOP SHCTX \
"Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@" "InstallToDesktop"
;MessageBox MB_OK "Install to desktop: $INSTALL_DESKTOP "
@CPACK_NSIS_EXTRA_UNINSTALL_COMMANDS@
;Remove files we installed.
;Keep the list of directories here in sync with the File commands above.
@CPACK_NSIS_DELETE_FILES@
@CPACK_NSIS_DELETE_DIRECTORIES@
!ifdef CPACK_NSIS_ADD_REMOVE
;Remove the add/remove program
Delete "$INSTDIR\AddRemove.exe"
!endif
;Remove the uninstaller itself.
Delete "$INSTDIR\Uninstall.exe"
DeleteRegKey SHCTX "Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@"
;Remove the installation directory if it is empty.
RMDir "$INSTDIR"
; Remove the registry entries.
DeleteRegKey SHCTX "Software\@CPACK_PACKAGE_VENDOR@\@CPACK_PACKAGE_INSTALL_REGISTRY_KEY@"
; Removes all optional components
!insertmacro SectionList "RemoveSection"
!insertmacro MUI_STARTMENU_GETFOLDER Application $MUI_TEMP
Delete "$SMPROGRAMS\$MUI_TEMP\Uninstall.lnk"
@CPACK_NSIS_DELETE_ICONS@
@CPACK_NSIS_DELETE_ICONS_EXTRA@
;Delete empty start menu parent diretories
StrCpy $MUI_TEMP "$SMPROGRAMS\$MUI_TEMP"
startMenuDeleteLoop:
ClearErrors
RMDir $MUI_TEMP
GetFullPathName $MUI_TEMP "$MUI_TEMP\.."
IfErrors startMenuDeleteLoopDone
StrCmp "$MUI_TEMP" "$SMPROGRAMS" startMenuDeleteLoopDone startMenuDeleteLoop
startMenuDeleteLoopDone:
; If the user changed the shortcut, then untinstall may not work. This should
; try to fix it.
StrCpy $MUI_TEMP "$START_MENU"
Delete "$SMPROGRAMS\$MUI_TEMP\Uninstall.lnk"
@CPACK_NSIS_DELETE_ICONS_EXTRA@
;Delete empty start menu parent diretories
StrCpy $MUI_TEMP "$SMPROGRAMS\$MUI_TEMP"
secondStartMenuDeleteLoop:
ClearErrors
RMDir $MUI_TEMP
GetFullPathName $MUI_TEMP "$MUI_TEMP\.."
IfErrors secondStartMenuDeleteLoopDone
StrCmp "$MUI_TEMP" "$SMPROGRAMS" secondStartMenuDeleteLoopDone secondStartMenuDeleteLoop
secondStartMenuDeleteLoopDone:
DeleteRegKey /ifempty SHCTX "Software\@CPACK_PACKAGE_VENDOR@\@CPACK_PACKAGE_INSTALL_REGISTRY_KEY@"
Push $INSTDIR\bin
StrCmp $DO_NOT_ADD_TO_PATH_ "1" doNotRemoveFromPath 0
Call un.RemoveFromPath
doNotRemoveFromPath:
SectionEnd
;--------------------------------
; determine admin versus local install
; Is install for "AllUsers" or "JustMe"?
; Default to "JustMe" - set to "AllUsers" if admin or on Win9x
; This function is used for the very first "custom page" of the installer.
; This custom page does not show up visibly, but it executes prior to the
; first visible page and sets up $INSTDIR properly...
; Choose different default installation folder based on SV_ALLUSERS...
; "Program Files" for AllUsers, "My Documents" for JustMe...
Function .onInit
; Reads components status for registry
!insertmacro SectionList "InitSection"
; check to see if /D has been used to change
; the install directory by comparing it to the
; install directory that is expected to be the
; default
StrCpy $IS_DEFAULT_INSTALLDIR 0
StrCmp "$INSTDIR" "@CPACK_NSIS_INSTALL_ROOT@\@CPACK_PACKAGE_INSTALL_DIRECTORY@" 0 +2
StrCpy $IS_DEFAULT_INSTALLDIR 1
StrCpy $SV_ALLUSERS "JustMe"
; if default install dir then change the default
; if it is installed for JustMe
StrCmp "$IS_DEFAULT_INSTALLDIR" "1" 0 +2
StrCpy $INSTDIR "$DOCUMENTS\@CPACK_PACKAGE_INSTALL_DIRECTORY@"
ClearErrors
UserInfo::GetName
IfErrors noLM
Pop $0
UserInfo::GetAccountType
Pop $1
StrCmp $1 "Admin" 0 +3
SetShellVarContext all
;MessageBox MB_OK 'User "$0" is in the Admin group'
StrCpy $SV_ALLUSERS "AllUsers"
Goto done
StrCmp $1 "Power" 0 +3
SetShellVarContext all
;MessageBox MB_OK 'User "$0" is in the Power Users group'
StrCpy $SV_ALLUSERS "AllUsers"
Goto done
noLM:
StrCpy $SV_ALLUSERS "AllUsers"
;Get installation folder from registry if available
done:
StrCmp $SV_ALLUSERS "AllUsers" 0 +3
StrCmp "$IS_DEFAULT_INSTALLDIR" "1" 0 +2
StrCpy $INSTDIR "@CPACK_NSIS_INSTALL_ROOT@\@CPACK_PACKAGE_INSTALL_DIRECTORY@"
StrCmp "@CPACK_NSIS_MODIFY_PATH@" "ON" 0 noOptionsPage
!insertmacro MUI_INSTALLOPTIONS_EXTRACT "NSIS.InstallOptions.ini"
noOptionsPage:
FunctionEnd
diff --git a/CMake/SuperbuildCTestCustom.cmake.in b/CMake/SuperbuildCTestCustom.cmake.in
deleted file mode 100644
index 55266955f0..0000000000
--- a/CMake/SuperbuildCTestCustom.cmake.in
+++ /dev/null
@@ -1,5 +0,0 @@
-set(CTEST_CUSTOM_ERROR_EXCEPTION
- ${CTEST_CUSTOM_ERROR_EXCEPTION}
- "link.jam: No such file or directory"
- )
-
diff --git a/CMake/Whitelists/ClassificationCmdApps.cmake b/CMake/Whitelists/ClassificationCmdApps.cmake
new file mode 100644
index 0000000000..a8b1d36b67
--- /dev/null
+++ b/CMake/Whitelists/ClassificationCmdApps.cmake
@@ -0,0 +1,22 @@
+include(${CMAKE_CURRENT_LIST_DIR}/CoreCmdApps.cmake)
+
+list(APPEND enabled_modules
+ Classification
+ CLCore
+ CLVigraRandomForest
+ CLUtilities
+ CLMRUtilities
+ CLImportanceWeighting
+ Segmentation
+ DataCollection
+ IpSegmentation
+ IpFunc
+ SurfaceInterpolation
+ GraphAlgorithms
+ ImageStatistics
+ ImageExtraction
+ PlanarFigure
+ QtWidgets
+ QtWidgetsExt
+)
+
diff --git a/CMake/mitkDetectOS.sh b/CMake/mitkDetectOS.sh
deleted file mode 100755
index be296a336c..0000000000
--- a/CMake/mitkDetectOS.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/sh
-# Detects which OS and if it is Linux then it will detect which Linux Distribution.
-
-OS=`uname -s`
-MACH=`uname -m`
-
-if [ "${OS}" = "SunOS" ] ; then
- OS=Solaris
- ARCH=`uname -p`
- OSSTR="${OS} ${REV} (${ARCH} `uname -v`)"
-elif [ "${OS}" = "AIX" ] ; then
- OSSTR="${OS} `oslevel` (`oslevel -r`)"
-elif [ "${OS}" = "Linux" ] ; then
- if [ -f /etc/os-release ] ; then
- DIST=`cat /etc/os-release | tr "\n" ' ' | sed s/.*PRETTY_NAME=\"// | sed s/\".*//`
- elif [ -f /etc/redhat-release ] ; then
- DIST=`cat /etc/redhat-release | sed s/\ release.*//`
- VERSION=`cat /etc/redhat-release | sed s/.*release\ //`
- elif [ -f /etc/SUSE-release ] ; then
- DIST=`cat /etc/SUSE-release | tr "\n" ' '| sed s/VERSION.*//`
- VERSION=`cat /etc/SUSE-release | tr "\n" ' ' | sed s/.*=\ //`
- elif [ -f /etc/mandrake-release ] ; then
- DIST='Mandrake'
- VERSION=`cat /etc/mandrake-release | sed s/.*release\ //`
- elif [ -f /etc/debian_version ] ; then
- DIST="Debian"
- VERSION=`cat /etc/debian_version`
- fi
-
- OSSTR="${DIST} ${VERSION} ${MACH}"
-fi
-
-echo ${OSSTR}
diff --git a/CMake/mitkFunctionAddCustomModuleTest.cmake b/CMake/mitkFunctionAddCustomModuleTest.cmake
index 3c57b8cfd3..4893b55495 100644
--- a/CMake/mitkFunctionAddCustomModuleTest.cmake
+++ b/CMake/mitkFunctionAddCustomModuleTest.cmake
@@ -1,28 +1,27 @@
#!
#! \brief Add a custom test for MITK module
#!
#! \param test_name Unique identifier for the test
#! \param test_function Name of the test function (the one with the argc,argv signature)
#!
#! Additional parameters will be passed as command line parameters to the test.
#!
function(mitkAddCustomModuleTest test_name test_function)
if (BUILD_TESTING AND MODULE_IS_ENABLED)
if(MITK_XVFB_TESTING)
set(xvfb_run ${MITK_XVFB_TESTING_COMMAND})
else()
set(xvfb_run )
endif()
add_test(NAME ${test_name} COMMAND ${xvfb_run} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TESTDRIVER} ${test_function} ${ARGN})
- set_property(TEST ${test_name} PROPERTY LABELS ${MODULE_SUBPROJECTS} MITK)
mitkFunctionGetLibrarySearchPaths(MITK_RUNTIME_PATH_RELEASE release RELEASE)
mitkFunctionGetLibrarySearchPaths(MITK_RUNTIME_PATH_DEBUG debug DEBUG)
set(test_env_path ${MITK_RUNTIME_PATH_RELEASE} ${MITK_RUNTIME_PATH_DEBUG} $ENV{PATH})
list(REMOVE_DUPLICATES test_env_path)
string (REGEX REPLACE "\;" "\\\;" test_env_path "${test_env_path}")
set_property(TEST ${test_name} PROPERTY ENVIRONMENT "PATH=${test_env_path}" APPEND)
set_property(TEST ${test_name} PROPERTY SKIP_RETURN_CODE 77)
endif()
endfunction()
diff --git a/CMake/mitkFunctionAddTestLabel.cmake b/CMake/mitkFunctionAddTestLabel.cmake
deleted file mode 100644
index 57d44da7bc..0000000000
--- a/CMake/mitkFunctionAddTestLabel.cmake
+++ /dev/null
@@ -1,15 +0,0 @@
-#
-# Use to attach a CTest/CDash label to a test (already added via ADD_TEST)
-#
-# Call with or without an explicit second parameter. If no second parameter is given,
-# ${MITK_DEFAULT_SUBPROJECTS} will be used as standard label
-#
-function(mitkFunctionAddTestLabel test_name)
- set(label ${MITK_DEFAULT_SUBPROJECTS})
- if(ARGN)
- set(label ${ARGN})
- endif()
- set_property(TEST ${test_name} APPEND PROPERTY LABELS ${label})
-endfunction(mitkFunctionAddTestLabel)
-
-
diff --git a/CMake/mitkFunctionCompileSnippets.cmake b/CMake/mitkFunctionCompileSnippets.cmake
index ea5ca47ef5..e6632fe0fb 100644
--- a/CMake/mitkFunctionCompileSnippets.cmake
+++ b/CMake/mitkFunctionCompileSnippets.cmake
@@ -1,50 +1,49 @@
function(mitkFunctionCompileSnippets snippet_path)
# get all files called "main.cpp"
file(GLOB_RECURSE main_cpp_list "${snippet_path}/main.cpp")
foreach(main_cpp_file ${main_cpp_list})
# get the directory containing the main.cpp file
get_filename_component(main_cpp_dir "${main_cpp_file}" PATH)
set(snippet_src_files )
# If there exists a "files.cmake" file in the snippet directory,
# include it and assume it sets the variable "snippet_src_files"
# to a list of source files for the snippet.
if(EXISTS "${main_cpp_dir}/files.cmake")
include("${main_cpp_dir}/files.cmake")
set(_tmp_src_files ${snippet_src_files})
set(snippet_src_files )
foreach(_src_file ${_tmp_src_files})
if(IS_ABSOLUTE ${_src_file})
list(APPEND snippet_src_files ${_src_file})
else()
list(APPEND snippet_src_files ${main_cpp_dir}/${_src_file})
endif()
endforeach()
else()
# glob all files in the directory and add them to the snippet src list
file(GLOB_RECURSE snippet_src_files "${main_cpp_dir}/*")
endif()
# Uset the top-level directory name as the executable name
string(REPLACE "/" ";" main_cpp_dir_tokens "${main_cpp_dir}")
list(GET main_cpp_dir_tokens -1 snippet_exec_name)
set(snippet_target_name "Snippet-${snippet_exec_name}")
add_executable(${snippet_target_name} ${snippet_src_files})
if(ARGN)
target_link_libraries(${snippet_target_name} ${ARGN})
endif()
set_target_properties(${snippet_target_name} PROPERTIES
- LABELS Documentation
RUNTIME_OUTPUT_DIRECTORY "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/snippets"
ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_ARCHIVE_OUTPUT_DIRECTORY}/snippets"
LIBRARY_OUTPUT_DIRECTORY "${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/snippets"
OUTPUT_NAME ${snippet_exec_name}
FOLDER "${MITK_ROOT_FOLDER}/Documentation/Snippets"
)
endforeach()
endfunction()
diff --git a/CMake/mitkFunctionCreateModule.cmake b/CMake/mitkFunctionCreateModule.cmake
index 6e17f8a5ed..e89c11457f 100644
--- a/CMake/mitkFunctionCreateModule.cmake
+++ b/CMake/mitkFunctionCreateModule.cmake
@@ -1,677 +1,646 @@
##################################################################
#
# mitk_create_module
#
#! Creates a module for the automatic module dependency system within MITK.
#!
#! Example:
#!
#! \code
#! mitk_create_module(
#! DEPENDS PUBLIC MitkCore
#! PACKAGE_DEPENDS
#! PRIVATE Qt5|Xml+Networking
#! PUBLIC ITK|Watershed
#! \endcode
#!
#! The <moduleName> parameter specifies the name of the module which is used
#! to create a logical target name. The parameter is optional in case the
#! MITK_MODULE_NAME_DEFAULTS_TO_DIRECTORY_NAME variable evaluates to TRUE. The
#! module name will then be derived from the directory name in which this
#! function is called.
#!
#! If set, the following variables will be used to validate the module name:
#!
#! MITK_MODULE_NAME_REGEX_MATCH The module name must match this regular expression.
#! MITK_MODULE_NAME_REGEX_NOT_MATCH The module name must not match this regular expression.
#!
#! If the MITK_MODULE_NAME_PREFIX variable is set, the module name will be prefixed
#! with its contents.
#!
#! A modules source files are specified in a separate CMake file usually
#! called files.cmake, located in the module root directory. The
#! mitk_create_module() macro evaluates the following CMake variables
#! from the files.cmake file:
#!
#! - CPP_FILES A list of .cpp files
#! - H_FILES A list of .h files without a corresponding .cpp file
#! - TXX_FILES A list of .txx files
#! - RESOURCE_FILES A list of files (resources) which are embedded into the module
#! - MOC_H_FILES A list of Qt header files which should be processed by the MOC
#! - UI_FILES A list of .ui Qt UI files
#! - QRC_FILES A list of .qrc Qt resource files
#! - DOX_FILES A list of .dox Doxygen files
#!
#! List of variables available after the function is called:
#! - MODULE_NAME
#! - MODULE_TARGET
#! - MODULE_IS_ENABLED
-#! - MODULE_SUBPROJECTS
#!
#! \sa mitk_create_executable
#!
#! Parameters (all optional):
#!
#! \param <moduleName> The module name (also used as target name)
#! \param FILES_CMAKE File name of a CMake file setting source list variables
#! (defaults to files.cmake)
#! \param VERSION Module version number, e.g. "1.2.0"
#! \param AUTOLOAD_WITH A module target name identifying the module which will
#! trigger the automatic loading of this module
#! \param DEPRECATED_SINCE Marks this modules as deprecated since <arg>
#! \param DESCRIPTION A description for this module
#!
#! Multi-value Parameters (all optional):
#!
-#! \param SUBPROJECTS List of CDash labels
#! \param INCLUDE_DIRS Include directories for this module:
#! \verbatim
#! [[PUBLIC|PRIVATE|INTERFACE] <dir1>...]...
#! \endverbatim
#! The default scope for include directories is PUBLIC.
#! \param DEPENDS List of module dependencies:
#! \verbatim
#! [[PUBLIC|PRIVATE|INTERFACE] <module1>...]...
#! \endverbatim
#! The default scope for module dependencies is PUBLIC.
#! \param PACKAGE_DEPENDS List of public packages dependencies (e.g. Qt, VTK, etc.).
#! Package dependencies have the following syntax:
#! \verbatim
#! [PUBLIC|PRIVATE|INTERFACE] PACKAGE[|COMPONENT1[+COMPONENT2]...]
#! \endverbatim
#! The default scope for package dependencies is PRIVATE.
#! \param ADDITIONAL_LIBS List of additional private libraries linked to this module.
#! The folder containing the library will be added to the global list of library search paths.
#! \param CPP_FILES List of source files for this module. If the list is non-empty,
#! the module does not need to provide a files.cmake file or FILES_CMAKE argument.
#! \param H_FILES List of public header files for this module. It is recommended to use
#! a files.cmake file instead.
#!
#! Options (optional)
#!
#! \param FORCE_STATIC Force building this module as a static library
#! \param GCC_DEFAULT_VISIBILITY Do not use gcc visibility flags - all
#! symbols will be exported
#! \param NO_INIT Do not create CppMicroServices initialization code
#! \param NO_FEATURE_INFO Do not create a feature info by calling add_feature_info()
#! \param WARNINGS_NO_ERRORS Do not treat compiler warnings as errors
#
##################################################################
function(mitk_create_module)
set(_macro_params
VERSION # module version number, e.g. "1.2.0"
EXPORT_DEFINE # export macro name for public symbols of this module (DEPRECATED)
AUTOLOAD_WITH # a module target name identifying the module which will trigger the
# automatic loading of this module
FILES_CMAKE # file name of a CMake file setting source list variables
# (defaults to files.cmake)
DEPRECATED_SINCE # marks this modules as deprecated
DESCRIPTION # a description for this module
)
set(_macro_multiparams
- SUBPROJECTS # list of CDash labels
+ SUBPROJECTS # list of CDash labels (deprecated)
INCLUDE_DIRS # include directories: [PUBLIC|PRIVATE|INTERFACE] <list>
INTERNAL_INCLUDE_DIRS # include dirs internal to this module (DEPRECATED)
DEPENDS # list of modules this module depends on: [PUBLIC|PRIVATE|INTERFACE] <list>
DEPENDS_INTERNAL # list of modules this module internally depends on (DEPRECATED)
PACKAGE_DEPENDS # list of "packages this module depends on (e.g. Qt, VTK, etc.): [PUBLIC|PRIVATE|INTERFACE] <package-list>
TARGET_DEPENDS # list of CMake targets this module should depend on
ADDITIONAL_LIBS # list of addidtional private libraries linked to this module.
CPP_FILES # list of cpp files
H_FILES # list of header files: [PUBLIC|PRIVATE] <list>
)
set(_macro_options
FORCE_STATIC # force building this module as a static library
HEADERS_ONLY # this module is a headers-only library
GCC_DEFAULT_VISIBILITY # do not use gcc visibility flags - all symbols will be exported
NO_DEFAULT_INCLUDE_DIRS # do not add default include directories like "include" or "."
NO_INIT # do not create CppMicroServices initialization code
NO_FEATURE_INFO # do not create a feature info by calling add_feature_info()
WARNINGS_NO_ERRORS # do not treat compiler warnings as errors
EXECUTABLE # create an executable; do not use directly, use mitk_create_executable() instead
C_MODULE # compile all source files as C sources
CXX_MODULE # compile all source files as C++ sources
)
cmake_parse_arguments(MODULE "${_macro_options}" "${_macro_params}" "${_macro_multiparams}" ${ARGN})
set(MODULE_NAME ${MODULE_UNPARSED_ARGUMENTS})
# -----------------------------------------------------------------
# Sanity checks
if(NOT MODULE_NAME)
if(MITK_MODULE_NAME_DEFAULTS_TO_DIRECTORY_NAME)
get_filename_component(MODULE_NAME ${CMAKE_CURRENT_SOURCE_DIR} NAME)
else()
message(SEND_ERROR "The module name must not be empty")
endif()
endif()
set(_deprecated_args INTERNAL_INCLUDE_DIRS DEPENDS_INTERNAL EXPORT_DEFINE TARGET_DEPENDS HEADERS_ONLY)
foreach(_deprecated_arg ${_deprecated_args})
if(MODULE_${_deprecated_arg})
message(WARNING "The ${_deprecated_arg} argument is deprecated")
endif()
endforeach()
set(_module_type module)
set(_Module_type Module)
if(MODULE_EXECUTABLE)
set(_module_type executable)
set(_Module_type Executable)
endif()
if(MITK_MODULE_NAME_REGEX_MATCH)
if(NOT ${MODULE_NAME} MATCHES ${MITK_MODULE_NAME_REGEX_MATCH})
message(SEND_ERROR "The ${_module_type} name \"${MODULE_NAME}\" does not match the regular expression \"${MITK_MODULE_NAME_REGEX_MATCH}\".")
endif()
endif()
if(MITK_MODULE_NAME_REGEX_NOT_MATCH)
if(${MODULE_NAME} MATCHES ${MITK_MODULE_NAME_REGEX_NOT_MATCH})
message(SEND_ERROR "The ${_module_type} name \"${MODULE_NAME}\" must not match the regular expression \"${MITK_MODULE_NAME_REGEX_NOT_MATCH}\".")
endif()
endif()
if(MITK_MODULE_NAME_PREFIX AND NOT MODULE_NAME MATCHES "^${MITK_MODULE_NAME_PREFIX}.*$")
set(MODULE_NAME "${MITK_MODULE_NAME_PREFIX}${MODULE_NAME}")
endif()
if(NOT MODULE_FILES_CMAKE)
set(MODULE_FILES_CMAKE files.cmake)
endif()
if(NOT IS_ABSOLUTE ${MODULE_FILES_CMAKE})
set(MODULE_FILES_CMAKE ${CMAKE_CURRENT_SOURCE_DIR}/${MODULE_FILES_CMAKE})
endif()
- if(NOT MODULE_SUBPROJECTS)
- if(MITK_DEFAULT_SUBPROJECTS)
- set(MODULE_SUBPROJECTS ${MITK_DEFAULT_SUBPROJECTS})
- elseif(TARGET MITK-Modules)
- set(MODULE_SUBPROJECTS MITK-Modules)
- endif()
- endif()
-
- # check if the subprojects exist as targets
- if(MODULE_SUBPROJECTS)
- foreach(subproject ${MODULE_SUBPROJECTS})
- if(NOT TARGET ${subproject})
- message(SEND_ERROR "The subproject ${subproject} does not have a corresponding target")
- endif()
- endforeach()
- endif()
-
# -----------------------------------------------------------------
# Check if module should be build
set(MODULE_TARGET ${MODULE_NAME})
# assume worst case
set(MODULE_IS_ENABLED 0)
# first we check if we have an explicit module build list
if(MITK_MODULES_TO_BUILD)
list(FIND MITK_MODULES_TO_BUILD ${MODULE_NAME} _MOD_INDEX)
if(_MOD_INDEX EQUAL -1)
set(MODULE_IS_EXCLUDED 1)
endif()
endif()
if(NOT MODULE_IS_EXCLUDED)
# first of all we check for the dependencies
_mitk_parse_package_args(${MODULE_PACKAGE_DEPENDS})
mitk_check_module_dependencies(MODULES ${MODULE_DEPENDS}
PACKAGES ${PACKAGE_NAMES}
MISSING_DEPENDENCIES_VAR _MISSING_DEP
PACKAGE_DEPENDENCIES_VAR PACKAGE_NAMES)
if(_MISSING_DEP)
if(MODULE_NO_FEATURE_INFO)
message("${_Module_type} ${MODULE_NAME} won't be built, missing dependency: ${_MISSING_DEP}")
endif()
set(MODULE_IS_ENABLED 0)
else()
foreach(dep ${MODULE_DEPENDS})
if(TARGET ${dep})
get_target_property(AUTLOAD_DEP ${dep} MITK_AUTOLOAD_DIRECTORY)
if (AUTLOAD_DEP)
message(SEND_ERROR "Module \"${MODULE_NAME}\" has an invalid dependency on autoload module \"${dep}\". Check MITK_CREATE_MODULE usage for \"${MODULE_NAME}\".")
endif()
endif()
endforeach(dep)
set(MODULE_IS_ENABLED 1)
# now check for every package if it is enabled. This overlaps a bit with
# MITK_CHECK_MODULE ...
foreach(_package ${PACKAGE_NAMES})
if((DEFINED MITK_USE_${_package}) AND NOT (MITK_USE_${_package}))
message("${_Module_type} ${MODULE_NAME} won't be built. Turn on MITK_USE_${_package} if you want to use it.")
set(MODULE_IS_ENABLED 0)
break()
endif()
endforeach()
endif()
endif()
# -----------------------------------------------------------------
# Start creating the module
if(MODULE_IS_ENABLED)
# clear variables defined in files.cmake
set(RESOURCE_FILES )
set(CPP_FILES )
set(H_FILES )
set(TXX_FILES )
set(DOX_FILES )
set(UI_FILES )
set(MOC_H_FILES )
set(QRC_FILES )
# clear other variables
set(Q${KITNAME}_GENERATED_CPP )
set(Q${KITNAME}_GENERATED_MOC_CPP )
set(Q${KITNAME}_GENERATED_QRC_CPP )
set(Q${KITNAME}_GENERATED_UI_CPP )
# check and set-up auto-loading
if(MODULE_AUTOLOAD_WITH)
if(NOT TARGET "${MODULE_AUTOLOAD_WITH}")
message(SEND_ERROR "The module target \"${MODULE_AUTOLOAD_WITH}\" specified as the auto-loading module for \"${MODULE_NAME}\" does not exist")
endif()
endif()
set(_module_autoload_meta_target "${CMAKE_PROJECT_NAME}-autoload")
# create a meta-target if it does not already exist
if(NOT TARGET ${_module_autoload_meta_target})
add_custom_target(${_module_autoload_meta_target})
set_property(TARGET ${_module_autoload_meta_target} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Modules/Autoload")
endif()
if(NOT MODULE_EXPORT_DEFINE)
set(MODULE_EXPORT_DEFINE ${MODULE_NAME}_EXPORT)
endif()
if(MITK_GENERATE_MODULE_DOT)
message("MODULEDOTNAME ${MODULE_NAME}")
foreach(dep ${MODULE_DEPENDS})
message("MODULEDOT \"${MODULE_NAME}\" -> \"${dep}\" ; ")
endforeach(dep)
endif(MITK_GENERATE_MODULE_DOT)
if (EXISTS ${MODULE_FILES_CMAKE})
include(${MODULE_FILES_CMAKE})
endif()
if(MODULE_CPP_FILES)
list(APPEND CPP_FILES ${MODULE_CPP_FILES})
endif()
if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/src")
# Preprend the "src" directory to the cpp file list
set(_cpp_files ${CPP_FILES})
set(CPP_FILES )
foreach(_cpp_file ${_cpp_files})
list(APPEND CPP_FILES "src/${_cpp_file}")
endforeach()
endif()
if(CPP_FILES OR RESOURCE_FILES OR UI_FILES OR MOC_H_FILES OR QRC_FILES)
set(MODULE_HEADERS_ONLY 0)
if(MODULE_C_MODULE)
set_source_files_properties(${CPP_FILES} PROPERTIES LANGUAGE C)
elseif(MODULE_CXX_MODULE)
set_source_files_properties(${CPP_FILES} PROPERTIES LANGUAGE CXX)
endif()
else()
set(MODULE_HEADERS_ONLY 1)
if(MODULE_AUTOLOAD_WITH)
message(SEND_ERROR "A headers only module cannot be auto-loaded")
endif()
endif()
set(module_c_flags )
set(module_c_flags_debug )
set(module_c_flags_release )
set(module_cxx_flags )
set(module_cxx_flags_debug )
set(module_cxx_flags_release )
if(MODULE_GCC_DEFAULT_VISIBILITY OR NOT CMAKE_COMPILER_IS_GNUCXX)
# We only support hidden visibility for gcc for now. Clang still has troubles with
# correctly marking template declarations and explicit template instantiations as exported.
# See http://comments.gmane.org/gmane.comp.compilers.clang.scm/50028
# and http://llvm.org/bugs/show_bug.cgi?id=10113
set(CMAKE_CXX_VISIBILITY_PRESET default)
set(CMAKE_VISIBILITY_INLINES_HIDDEN 0)
else()
set(CMAKE_CXX_VISIBILITY_PRESET hidden)
set(CMAKE_VISIBILITY_INLINES_HIDDEN 1)
endif()
if(NOT MODULE_WARNINGS_NO_ERRORS)
if(MSVC_VERSION)
mitkFunctionCheckCAndCXXCompilerFlags("/WX" module_c_flags module_cxx_flags)
# this would turn on unused parameter warnings, but unfortunately MSVC cannot
# distinguish yet between internal and external headers so this would be triggered
# a lot by external code. There is support for it on the way so this line could be
# reactivated after https://gitlab.kitware.com/cmake/cmake/issues/17904 has been fixed.
# mitkFunctionCheckCAndCXXCompilerFlags("/w34100" module_c_flags module_cxx_flags)
else()
mitkFunctionCheckCAndCXXCompilerFlags(-Werror module_c_flags module_cxx_flags)
# The flag "c++0x-static-nonintegral-init" has been renamed in newer Clang
# versions to "static-member-init", see
# http://clang-developers.42468.n3.nabble.com/Wc-0x-static-nonintegral-init-gone-td3999651.html
#
# Also, older Clang and seemingly all gcc versions do not warn if unknown
# "-no-*" flags are used, so CMake will happily append any -Wno-* flag to the
# command line. This may get confusing if unrelated compiler errors happen and
# the error output then additionally contains errors about unknown flags (which
# is not the case if there were no compile errors).
#
# So instead of using -Wno-* we use -Wno-error=*, which will be properly rejected by
# the compiler and if applicable, prints the specific warning as a real warning and
# not as an error (although -Werror was given).
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=c++0x-static-nonintegral-init" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=static-member-init" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=unknown-warning" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=gnu" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=class-memaccess" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=inconsistent-missing-override" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=deprecated-copy" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=cast-function-type" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=deprecated-declarations" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=type-limits" module_c_flags module_cxx_flags)
endif()
endif()
if(MODULE_FORCE_STATIC)
set(_STATIC STATIC)
else()
set(_STATIC )
endif(MODULE_FORCE_STATIC)
if(NOT MODULE_HEADERS_ONLY)
if(NOT MODULE_NO_INIT OR RESOURCE_FILES)
find_package(CppMicroServices QUIET NO_MODULE REQUIRED)
endif()
if(NOT MODULE_NO_INIT)
usFunctionGenerateModuleInit(CPP_FILES)
endif()
set(binary_res_files )
set(source_res_files )
if(RESOURCE_FILES)
if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/resource")
set(res_dir resource)
elseif(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/Resources")
set(res_dir Resources)
else()
message(SEND_ERROR "Resources specified but ${CMAKE_CURRENT_SOURCE_DIR}/resource directory not found.")
endif()
foreach(res_file ${RESOURCE_FILES})
if(EXISTS ${CMAKE_CURRENT_BINARY_DIR}/${res_dir}/${res_file})
list(APPEND binary_res_files "${res_file}")
else()
list(APPEND source_res_files "${res_file}")
endif()
endforeach()
# Add a source level dependencies on resource files
usFunctionGetResourceSource(TARGET ${MODULE_TARGET} OUT CPP_FILES)
endif()
endif()
if(MITK_USE_Qt5)
if(UI_FILES)
qt5_wrap_ui(Q${KITNAME}_GENERATED_UI_CPP ${UI_FILES})
endif()
if(MOC_H_FILES)
qt5_wrap_cpp(Q${KITNAME}_GENERATED_MOC_CPP ${MOC_H_FILES} OPTIONS -DBOOST_NO_TEMPLATE_PARTIAL_SPECIALIZATION)
endif()
if(QRC_FILES)
qt5_add_resources(Q${KITNAME}_GENERATED_QRC_CPP ${QRC_FILES})
endif()
endif()
set(Q${KITNAME}_GENERATED_CPP ${Q${KITNAME}_GENERATED_CPP} ${Q${KITNAME}_GENERATED_UI_CPP} ${Q${KITNAME}_GENERATED_MOC_CPP} ${Q${KITNAME}_GENERATED_QRC_CPP})
mitkFunctionOrganizeSources(
SOURCE ${CPP_FILES}
HEADER ${H_FILES}
TXX ${TXX_FILES}
DOC ${DOX_FILES}
UI ${UI_FILES}
QRC ${QRC_FILES}
MOC ${Q${KITNAME}_GENERATED_MOC_CPP}
GEN_QRC ${Q${KITNAME}_GENERATED_QRC_CPP}
GEN_UI ${Q${KITNAME}_GENERATED_UI_CPP}
)
set(coverage_sources
${CPP_FILES} ${H_FILES} ${GLOBBED__H_FILES} ${CORRESPONDING__H_FILES} ${TXX_FILES}
${TOOL_CPPS} ${TOOL_GUI_CPPS})
- if(MODULE_SUBPROJECTS)
- set_property(SOURCE ${coverage_sources} APPEND PROPERTY LABELS ${MODULE_SUBPROJECTS} MITK)
- endif()
-
# ---------------------------------------------------------------
# Create the actual module target
if(MODULE_HEADERS_ONLY)
add_library(${MODULE_TARGET} INTERFACE)
# INTERFACE_LIBRARY targets may only have whitelisted properties. The property "FOLDER" is not allowed.
# set_property(TARGET ${MODULE_TARGET} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Modules")
else()
if(MODULE_EXECUTABLE)
add_executable(${MODULE_TARGET}
${MODULE_CPP_FILES} ${coverage_sources} ${CPP_FILES_GENERATED} ${Q${KITNAME}_GENERATED_CPP}
${DOX_FILES} ${UI_FILES} ${QRC_FILES})
set_property(TARGET ${MODULE_TARGET} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Modules/Executables")
set(_us_module_name main)
else()
add_library(${MODULE_TARGET} ${_STATIC}
${coverage_sources} ${CPP_FILES_GENERATED} ${Q${KITNAME}_GENERATED_CPP}
${DOX_FILES} ${UI_FILES} ${QRC_FILES})
set_property(TARGET ${MODULE_TARGET} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Modules")
set(_us_module_name ${MODULE_TARGET})
endif()
# Apply properties to the module target.
target_compile_definitions(${MODULE_TARGET} PRIVATE US_MODULE_NAME=${_us_module_name})
if(MODULE_C_MODULE)
if(module_c_flags)
string(REPLACE " " ";" module_c_flags "${module_c_flags}")
target_compile_options(${MODULE_TARGET} PRIVATE ${module_c_flags})
endif()
if(module_c_flags_debug)
string(REPLACE " " ";" module_c_flags_debug "${module_c_flags_debug}")
target_compile_options(${MODULE_TARGET} PRIVATE $<$<CONFIG:Debug>:${module_c_flags_debug}>)
endif()
if(module_c_flags_release)
string(REPLACE " " ";" module_c_flags_release "${module_c_flags_release}")
target_compile_options(${MODULE_TARGET} PRIVATE $<$<CONFIG:Release>:${module_c_flags_release}>)
endif()
else()
if(module_cxx_flags)
string(REPLACE " " ";" module_cxx_flags "${module_cxx_flags}")
target_compile_options(${MODULE_TARGET} PRIVATE ${module_cxx_flags})
endif()
if(module_cxx_flags_debug)
string(REPLACE " " ";" module_cxx_flags_debug "${module_cxx_flags_debug}")
target_compile_options(${MODULE_TARGET} PRIVATE $<$<CONFIG:Debug>:${module_cxx_flags_debug}>)
endif()
if(module_cxx_flags_release)
string(REPLACE " " ";" module_cxx_flags_release "${module_cxx_flags_release}")
target_compile_options(${MODULE_TARGET} PRIVATE $<$<CONFIG:Release>:${module_cxx_flags_release}>)
endif()
endif()
set_property(TARGET ${MODULE_TARGET} PROPERTY US_MODULE_NAME ${_us_module_name})
# Add additional library search directories to a global property which
# can be evaluated by other CMake macros, e.g. our install scripts.
if(MODULE_ADDITIONAL_LIBS)
target_link_libraries(${MODULE_TARGET} PRIVATE ${MODULE_ADDITIONAL_LIBS})
get_property(_mitk_additional_library_search_paths GLOBAL PROPERTY MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS)
foreach(_lib_filepath ${MODULE_ADDITIONAL_LIBS})
get_filename_component(_search_path "${_lib_filepath}" PATH)
if(_search_path)
list(APPEND _mitk_additional_library_search_paths "${_search_path}")
endif()
endforeach()
if(_mitk_additional_library_search_paths)
list(REMOVE_DUPLICATES _mitk_additional_library_search_paths)
set_property(GLOBAL PROPERTY MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS ${_mitk_additional_library_search_paths})
endif()
endif()
# add the target name to a global property which is used in the top-level
# CMakeLists.txt file to export the target
set_property(GLOBAL APPEND PROPERTY MITK_MODULE_TARGETS ${MODULE_TARGET})
if(MODULE_AUTOLOAD_WITH)
# for auto-loaded modules, adapt the output directory
add_dependencies(${_module_autoload_meta_target} ${MODULE_TARGET})
if(WIN32)
set(_module_output_prop RUNTIME_OUTPUT_DIRECTORY)
else()
set(_module_output_prop LIBRARY_OUTPUT_DIRECTORY)
endif()
set(_module_output_dir ${CMAKE_${_module_output_prop}}/${MODULE_AUTOLOAD_WITH})
get_target_property(_module_is_imported ${MODULE_AUTOLOAD_WITH} IMPORTED)
if(NOT _module_is_imported)
# if the auto-loading module is not imported, get its location
# and put the auto-load module relative to it.
get_target_property(_module_output_dir ${MODULE_AUTOLOAD_WITH} ${_module_output_prop})
set_target_properties(${MODULE_TARGET} PROPERTIES
${_module_output_prop} ${_module_output_dir}/${MODULE_AUTOLOAD_WITH})
else()
set_target_properties(${MODULE_TARGET} PROPERTIES
${_module_output_prop} ${CMAKE_${_module_output_prop}}/${MODULE_AUTOLOAD_WITH})
endif()
set_target_properties(${MODULE_TARGET} PROPERTIES
MITK_AUTOLOAD_DIRECTORY ${MODULE_AUTOLOAD_WITH})
# add the auto-load module name as a property
set_property(TARGET ${MODULE_AUTOLOAD_WITH} APPEND PROPERTY MITK_AUTOLOAD_TARGETS ${MODULE_TARGET})
endif()
if(binary_res_files)
usFunctionAddResources(TARGET ${MODULE_TARGET}
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${res_dir}
FILES ${binary_res_files})
endif()
if(source_res_files)
usFunctionAddResources(TARGET ${MODULE_TARGET}
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/${res_dir}
FILES ${source_res_files})
endif()
if(binary_res_files OR source_res_files)
usFunctionEmbedResources(TARGET ${MODULE_TARGET})
endif()
if(MODULE_DEPRECATED_SINCE)
set_property(TARGET ${MODULE_TARGET} PROPERTY MITK_MODULE_DEPRECATED_SINCE ${MODULE_DEPRECATED_SINCE})
endif()
# create export macros
if (NOT MODULE_EXECUTABLE)
set(_export_macro_name )
if(MITK_LEGACY_EXPORT_MACRO_NAME)
set(_export_macro_names
EXPORT_MACRO_NAME ${MODULE_EXPORT_DEFINE}
NO_EXPORT_MACRO_NAME ${MODULE_NAME}_NO_EXPORT
DEPRECATED_MACRO_NAME ${MODULE_NAME}_DEPRECATED
NO_DEPRECATED_MACRO_NAME ${MODULE_NAME}_NO_DEPRECATED
)
endif()
generate_export_header(${MODULE_NAME}
${_export_macro_names}
EXPORT_FILE_NAME ${MODULE_NAME}Exports.h
)
endif()
target_include_directories(${MODULE_TARGET} PUBLIC ${CMAKE_CURRENT_BINARY_DIR})
endif()
# ---------------------------------------------------------------
# Properties for both header-only and compiled modules
if(MODULE_HEADERS_ONLY)
set(_module_property_type INTERFACE)
else()
set(_module_property_type PUBLIC)
endif()
if(MODULE_TARGET_DEPENDS)
add_dependencies(${MODULE_TARGET} ${MODULE_TARGET_DEPENDS})
endif()
- if(MODULE_SUBPROJECTS AND NOT MODULE_HEADERS_ONLY)
- set_property(TARGET ${MODULE_TARGET} PROPERTY LABELS ${MODULE_SUBPROJECTS} MITK)
- foreach(subproject ${MODULE_SUBPROJECTS})
- add_dependencies(${subproject} ${MODULE_TARGET})
- endforeach()
- endif()
-
set(DEPENDS "${MODULE_DEPENDS}")
if(NOT MODULE_NO_INIT AND NOT MODULE_HEADERS_ONLY)
# Add a CppMicroServices dependency implicitly, since it is
# needed for the generated "module initialization" code.
set(DEPENDS "CppMicroServices;${DEPENDS}")
endif()
if(DEPENDS OR MODULE_PACKAGE_DEPENDS)
mitk_use_modules(TARGET ${MODULE_TARGET}
MODULES ${DEPENDS}
PACKAGES ${MODULE_PACKAGE_DEPENDS}
)
endif()
if(NOT MODULE_C_MODULE)
target_compile_features(${MODULE_TARGET} ${_module_property_type} ${MITK_CXX_FEATURES})
endif()
# add include directories
if(MODULE_INTERNAL_INCLUDE_DIRS)
target_include_directories(${MODULE_TARGET} PRIVATE ${MODULE_INTERNAL_INCLUDE_DIRS})
endif()
if(NOT MODULE_NO_DEFAULT_INCLUDE_DIRS)
if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(${MODULE_TARGET} ${_module_property_type} include)
else()
target_include_directories(${MODULE_TARGET} ${_module_property_type} .)
endif()
if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/src)
target_include_directories(${MODULE_TARGET} PRIVATE src)
endif()
endif()
target_include_directories(${MODULE_TARGET} ${_module_property_type} ${MODULE_INCLUDE_DIRS})
endif()
# -----------------------------------------------------------------
# Record missing dependency information
if(_MISSING_DEP)
if(MODULE_DESCRIPTION)
set(MODULE_DESCRIPTION "${MODULE_DESCRIPTION} (missing dependencies: ${_MISSING_DEP})")
else()
set(MODULE_DESCRIPTION "(missing dependencies: ${_MISSING_DEP})")
endif()
endif()
if(NOT MODULE_NO_FEATURE_INFO)
add_feature_info(${MODULE_NAME} MODULE_IS_ENABLED "${MODULE_DESCRIPTION}")
endif()
set(MODULE_NAME ${MODULE_NAME} PARENT_SCOPE)
set(MODULE_TARGET ${MODULE_TARGET} PARENT_SCOPE)
set(MODULE_IS_ENABLED ${MODULE_IS_ENABLED} PARENT_SCOPE)
- set(MODULE_SUBPROJECTS ${MODULE_SUBPROJECTS} PARENT_SCOPE)
endfunction()
diff --git a/CMake/mitkFunctionCreatePlugin.cmake b/CMake/mitkFunctionCreatePlugin.cmake
index 72fa8012d9..680bc2c38d 100644
--- a/CMake/mitkFunctionCreatePlugin.cmake
+++ b/CMake/mitkFunctionCreatePlugin.cmake
@@ -1,365 +1,350 @@
#! \brief Creates a MITK CTK plugin.
#!
#! This function should be called from the plugins CMakeLists.txt file.
#! The target name is available after the macro call as ${PLUGIN_TARGET}
#! to add additional libraries in your CMakeLists.txt. Include paths and link
#! libraries are set depending on the value of the Required-Plugins header
#! in your manifest_headers.cmake file.
#!
#! This function internally calls ctkMacroBuildPlugin() and adds support
#! for Qt Help files and installers.
#!
#! Options:
#! \param TEST_PLUGIN Mark this plug-in as a testing plug-in.
#! \param NO_INSTALL Don't install this plug-in.
#!
#! Parameters:
#!
#! \param EXPORT_DIRECTIVE (required) The export directive to use in the generated
#! <plugin_target>_Exports.h file.
#!
#! Multi-value parameters (all optional):
#!
#! \param EXPORTED_INCLUDE_SUFFIXES A list of sub-directories which should
#! be added to the current source directory. The resulting directories
#! will be available in the set of include directories of depending plug-ins.
#! \param MODULE_DEPENDS (optional) A list of Modules this plug-in depends on.
#! \param PACKAGE_DEPENDS (optional) A list of external packages this plug-in depends on.
#! \param DOXYGEN_TAGFILES (optional) Which external tag files should be available for the plugin documentation
#! \param MOC_OPTIONS (optional) Additional options to pass to the Qt MOC compiler
#! \param WARNINGS_NO_ERRORS (optional) Do not handle compiler warnings as errors
function(mitk_create_plugin)
# options
set(arg_options
TEST_PLUGIN # Mark this plug-in as a testing plug-in
NO_INSTALL # Don't install this plug-in
NO_QHP_TRANSFORM
WARNINGS_NO_ERRORS
)
# single value arguments
set(arg_single
EXPORT_DIRECTIVE # (required) TODO: could be generated via CMake as it is done for MITK modules already
)
# multiple value arguments
set(arg_multiple
EXPORTED_INCLUDE_SUFFIXES # (optional) additional public include directories
MODULE_DEPENDS # (optional)
PACKAGE_DEPENDS
DOXYGEN_TAGFILES
MOC_OPTIONS
- SUBPROJECTS
+ SUBPROJECTS # deprecated
)
cmake_parse_arguments(_PLUGIN "${arg_options}" "${arg_single}" "${arg_multiple}" ${ARGN})
if(_PLUGIN_TEST_PLUGIN)
set(_PLUGIN_NO_INSTALL 1)
set(is_test_plugin "TEST_PLUGIN")
else()
set(is_test_plugin)
endif()
set(_PLUGIN_MOC_OPTIONS "-DBOOST_NO_TEMPLATE_PARTIAL_SPECIALIZATION -DBOOST_TT_HAS_OPERATOR_HPP_INCLUDED ${_PLUGIN_MOC_OPTIONS}")
set(PLUGIN_TARGET ${PROJECT_NAME})
mitk_check_module_dependencies(MODULES ${_PLUGIN_MODULE_DEPENDS}
PACKAGES ${_PLUGIN_PACKAGE_DEPENDS}
MISSING_DEPENDENCIES_VAR _missing_deps
MODULE_DEPENDENCIES_VAR _module_deps
PACKAGE_DEPENDENCIES_VAR _package_deps)
if(_missing_deps)
if(NOT MITK_BUILD_ALL_PLUGINS)
message(SEND_ERROR "${PROJECT_NAME} is missing requirements and won't be built. Missing: ${_missing_deps}")
else()
message(STATUS "${PROJECT_NAME} is missing requirements and won't be built. Missing: ${_missing_deps}")
endif()
return()
endif()
foreach(_module_dep ${_PLUGIN_MODULE_DEPENDS})
if(TARGET ${_module_dep})
get_target_property(AUTLOAD_DEP ${_module_dep} MITK_AUTOLOAD_DIRECTORY)
if (AUTLOAD_DEP)
message(SEND_ERROR "Plugin \"${PROJECT_NAME}\" has an invalid dependency on autoload module \"${_module_dep}\". Check MITK_CREATE_PLUGIN usage for \"${PROJECT_NAME}\".")
endif()
endif()
endforeach()
# -------------- All dependencies are resolved ------------------
message(STATUS "Creating CTK plugin ${PROJECT_NAME}")
include(files.cmake)
set(_PLUGIN_CPP_FILES ${CPP_FILES})
set(_PLUGIN_MOC_H_FILES ${MOC_H_FILES})
set(_PLUGIN_UI_FILES ${UI_FILES})
set(_PLUGIN_CACHED_RESOURCE_FILES ${CACHED_RESOURCE_FILES})
set(_PLUGIN_TRANSLATION_FILES ${TRANSLATION_FILES})
set(_PLUGIN_QRC_FILES ${QRC_FILES})
set(_PLUGIN_H_FILES ${H_FILES})
set(_PLUGIN_TXX_FILES ${TXX_FILES})
set(_PLUGIN_DOX_FILES ${DOX_FILES})
set(_PLUGIN_CMAKE_FILES ${CMAKE_FILES} files.cmake)
set(_PLUGIN_FILE_DEPENDENCIES ${FILE_DEPENDENCIES})
if(CTK_PLUGINS_OUTPUT_DIR)
set(_output_dir "${CTK_PLUGINS_OUTPUT_DIR}")
else()
set(_output_dir "")
endif()
# Compute the plugin dependencies
ctkFunctionGetTargetLibraries(_PLUGIN_target_libraries "")
#------------------------------------------------------------#
#------------------ Qt Help support -------------------------#
set(PLUGIN_GENERATED_QCH_FILES )
if(BLUEBERRY_USE_QT_HELP AND
EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/documentation/UserManual")
set(PLUGIN_DOXYGEN_INPUT_DIR "${CMAKE_CURRENT_SOURCE_DIR}/documentation/UserManual")
set(PLUGIN_DOXYGEN_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}/documentation/UserManual")
# Create a list of Doxygen tag files from the plug-in dependencies
set(PLUGIN_DOXYGEN_TAGFILES)
foreach(_dep_target ${_PLUGIN_target_libraries})
string(REPLACE _ . _dep ${_dep_target})
get_target_property(_is_imported ${_dep_target} IMPORTED)
if(_is_imported)
get_target_property(_import_loc_debug ${_dep_target} IMPORTED_LOCATION_DEBUG)
get_target_property(_import_loc_release ${_dep_target} IMPORTED_LOCATION_RELEASE)
# There is not necessarily a debug and release build
if(_import_loc_release)
set(_import_loc ${_import_loc_release})
else()
set(_import_loc ${_import_loc_debug})
endif()
get_filename_component(_target_filename "${_import_loc}" NAME)
# on windows there might be a Debug or Release subdirectory
string(REGEX REPLACE "/bin/plugins/(Debug/|Release/)?${_target_filename}" "/Plugins/${_dep}/documentation/UserManual" plugin_tag_dir "${_import_loc}" )
else()
set(plugin_tag_dir "${CMAKE_BINARY_DIR}/Plugins/${_dep}/documentation/UserManual")
endif()
set(_tag_file "${plugin_tag_dir}/${_dep_target}.tag")
if(EXISTS ${_tag_file})
set(PLUGIN_DOXYGEN_TAGFILES "${PLUGIN_DOXYGEN_TAGFILES} \"${_tag_file}=qthelp://${_dep}/bundle/\"")
endif()
endforeach()
if(_PLUGIN_DOXYGEN_TAGFILES)
set(PLUGIN_DOXYGEN_TAGFILES "${PLUGIN_DOXYGEN_TAGFILES} ${_PLUGIN_DOXYGEN_TAGFILES}")
endif()
#message("PLUGIN_DOXYGEN_TAGFILES: ${PLUGIN_DOXYGEN_TAGFILES}")
if(_PLUGIN_NO_QHP_TRANSFORM)
set(_use_qhp_xsl 0)
else()
set(_use_qhp_xsl 1)
endif()
_FUNCTION_CREATE_CTK_QT_COMPRESSED_HELP(PLUGIN_GENERATED_QCH_FILES ${_use_qhp_xsl})
list(APPEND _PLUGIN_CACHED_RESOURCE_FILES ${PLUGIN_GENERATED_QCH_FILES})
endif()
#------------------------------------------------------------#
#------------------ Create Plug-in --------------------------#
mitkFunctionOrganizeSources(
SOURCE ${_PLUGIN_CPP_FILES}
HEADER ${_PLUGIN_H_FILES}
TXX ${_PLUGIN_TXX_FILES}
DOC ${_PLUGIN_DOX_FILES}
UI ${_PLUGIN_UI_FILES}
QRC ${_PLUGIN_QRC_FILES} ${_PLUGIN_CACHED_RESOURCE_FILES}
META ${_PLUGIN_META_FILES}
MOC ${MY_MOC_CPP}
GEN_UI ${MY_UI_CPP}
GEN_QRC ${MY_QRC_SRCS}
)
ctkMacroBuildPlugin(
NAME ${PLUGIN_TARGET}
EXPORT_DIRECTIVE ${_PLUGIN_EXPORT_DIRECTIVE}
SRCS ${_PLUGIN_CPP_FILES} ${_PLUGIN_H_FILES} ${CORRESPONDING__H_FILES} ${GLOBBED__H_FILES}
MOC_SRCS ${_PLUGIN_MOC_H_FILES}
MOC_OPTIONS ${_PLUGIN_MOC_OPTIONS}
UI_FORMS ${_PLUGIN_UI_FILES}
EXPORTED_INCLUDE_SUFFIXES ${_PLUGIN_EXPORTED_INCLUDE_SUFFIXES}
RESOURCES ${_PLUGIN_QRC_FILES}
TARGET_LIBRARIES ${_PLUGIN_target_libraries}
CACHED_RESOURCEFILES ${_PLUGIN_CACHED_RESOURCE_FILES}
TRANSLATIONS ${_PLUGIN_TRANSLATION_FILES}
OUTPUT_DIR ${_output_dir}
NO_INSTALL # we install the plug-in ourselves
${is_test_plugin}
)
mitk_use_modules(TARGET ${PLUGIN_TARGET}
MODULES ${_PLUGIN_MODULE_DEPENDS}
PACKAGES ${_PLUGIN_PACKAGE_DEPENDS}
)
set_property(TARGET ${PLUGIN_TARGET} APPEND PROPERTY COMPILE_DEFINITIONS US_MODULE_NAME=${PLUGIN_TARGET})
set_property(TARGET ${PLUGIN_TARGET} PROPERTY US_MODULE_NAME ${PLUGIN_TARGET})
if(NOT CMAKE_CURRENT_SOURCE_DIR MATCHES "^${CMAKE_SOURCE_DIR}.*")
foreach(MITK_EXTENSION_DIR ${MITK_EXTENSION_DIRS})
if(CMAKE_CURRENT_SOURCE_DIR MATCHES "^${MITK_EXTENSION_DIR}.*")
get_filename_component(MITK_EXTENSION_ROOT_FOLDER ${MITK_EXTENSION_DIR} NAME)
set_property(TARGET ${PLUGIN_TARGET} PROPERTY FOLDER "${MITK_EXTENSION_ROOT_FOLDER}/Plugins")
break()
endif()
endforeach()
else()
set_property(TARGET ${PLUGIN_TARGET} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Plugins")
endif()
set(plugin_c_flags)
set(plugin_cxx_flags)
if(NOT _PLUGIN_WARNINGS_NO_ERRORS)
if(MSVC_VERSION)
mitkFunctionCheckCAndCXXCompilerFlags("/WX" plugin_c_flags plugin_cxx_flags)
else()
mitkFunctionCheckCAndCXXCompilerFlags(-Werror plugin_c_flags plugin_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=c++0x-static-nonintegral-init" plugin_c_flags plugin_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=static-member-init" plugin_c_flags plugin_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=unknown-warning" plugin_c_flags plugin_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=gnu" plugin_c_flags plugin_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=cast-function-type" plugin_c_flags plugin_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=inconsistent-missing-override" plugin_c_flags plugin_cxx_flags)
endif()
endif()
if(plugin_c_flags)
string(REPLACE " " ";" plugin_c_flags "${plugin_c_flags}")
target_compile_options(${PLUGIN_TARGET} PRIVATE ${plugin_c_flags})
endif()
if(plugin_cxx_flags)
string(REPLACE " " ";" plugin_cxx_flags "${plugin_cxx_flags}")
target_compile_options(${PLUGIN_TARGET} PRIVATE ${plugin_cxx_flags})
endif()
- if(NOT MY_SUBPROJECTS)
- if(MITK_DEFAULT_SUBPROJECTS)
- set(MY_SUBPROJECTS ${MITK_DEFAULT_SUBPROJECTS})
- elseif(TARGET MITK-Plugins)
- set(MY_SUBPROJECTS MITK-Plugins)
- endif()
- endif()
-
- if(MY_SUBPROJECTS)
- set_property(TARGET ${PLUGIN_TARGET} PROPERTY LABELS ${MY_SUBPROJECTS})
- foreach(subproject ${MY_SUBPROJECTS})
- add_dependencies(${subproject} ${PLUGIN_TARGET})
- endforeach()
- endif()
-
if(_PLUGIN_TEST_PLUGIN)
find_package(CppUnit REQUIRED)
target_include_directories(${PLUGIN_TARGET} PRIVATE ${CppUnit_INCLUDE_DIRS})
target_link_libraries(${PLUGIN_TARGET} PRIVATE ${CppUnit_LIBRARIES})
endif()
if(mbilog_FOUND)
target_link_libraries(${PLUGIN_TARGET} PRIVATE mbilog)
endif()
set(_PLUGIN_META_FILES "${CMAKE_CURRENT_SOURCE_DIR}/manifest_headers.cmake")
if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/plugin.xml")
list(APPEND _PLUGIN_META_FILES "${CMAKE_CURRENT_SOURCE_DIR}/plugin.xml")
endif()
set(PLUGIN_TARGET ${PLUGIN_TARGET} PARENT_SCOPE)
#------------------------------------------------------------#
#------------------ Installer support -----------------------#
if(NOT _PLUGIN_NO_INSTALL)
set(install_directories "")
if(NOT MACOSX_BUNDLE_NAMES)
set(install_directories bin/plugins)
else(NOT MACOSX_BUNDLE_NAMES)
foreach(bundle_name ${MACOSX_BUNDLE_NAMES})
list(APPEND install_directories ${bundle_name}.app/Contents/MacOS/plugins)
endforeach(bundle_name)
endif(NOT MACOSX_BUNDLE_NAMES)
foreach(install_subdir ${install_directories})
mitkFunctionInstallCTKPlugin(TARGETS ${PLUGIN_TARGET}
DESTINATION ${install_subdir})
endforeach()
set(_autoload_targets )
foreach(_dependency ${_module_deps})
get_target_property(_dep_autoloads ${_dependency} MITK_AUTOLOAD_TARGETS)
if (_dep_autoloads)
list(APPEND _autoload_targets ${_dep_autoloads})
endif()
endforeach()
# The MITK_AUTOLOAD_TARGETS property is used in the mitkFunctionInstallAutoLoadModules
# macro which expects a list of plug-in targets.
if (_autoload_targets)
list(REMOVE_DUPLICATES _autoload_targets)
set_target_properties(${PLUGIN_TARGET} PROPERTIES MITK_AUTOLOAD_TARGETS "${_autoload_targets}")
endif()
endif()
endfunction()
function(_FUNCTION_CREATE_CTK_QT_COMPRESSED_HELP qch_file use_xsl)
set(_manifest_path "${CMAKE_CURRENT_SOURCE_DIR}/manifest_headers.cmake")
if(NOT EXISTS ${_manifest_path})
message(FATAL_ERROR "${_manifest_path} not found")
endif()
include(${_manifest_path})
string(REPLACE "_" "." Plugin-SymbolicName "${PLUGIN_TARGET}")
configure_file(${MITK_SOURCE_DIR}/Documentation/doxygen_plugin_manual.conf.in
${PLUGIN_DOXYGEN_OUTPUT_DIR}/doxygen.conf
)
set(_qhp_xsl_file "${MITK_SOURCE_DIR}/Documentation/qhp_toc.xsl")
set(_generated_qhp_file "${PLUGIN_DOXYGEN_OUTPUT_DIR}/html/index.qhp")
set(_transformed_qhp_file "${PLUGIN_DOXYGEN_OUTPUT_DIR}/html/${PLUGIN_TARGET}.qhp")
set(${qch_file} "${CMAKE_CURRENT_BINARY_DIR}/resources/${PLUGIN_TARGET}.qch")
set(_xsl_command )
if(use_xsl)
set(_xsl_command COMMAND ${QT_XMLPATTERNS_EXECUTABLE} ${_qhp_xsl_file} ${_generated_qhp_file} -output ${_transformed_qhp_file})
endif()
file(GLOB _file_dependencies "${PLUGIN_DOXYGEN_INPUT_DIR}/*")
add_custom_command(OUTPUT ${${qch_file}}
# Generate a Qt help project (index.qhp) with doxygen
COMMAND ${DOXYGEN_EXECUTABLE} ${PLUGIN_DOXYGEN_OUTPUT_DIR}/doxygen.conf
# Use a XSL transformation to get rid of the top-level entry
${_xsl_command}
# Generate the final Qt compressed help file (.qch)
COMMAND ${QT_HELPGENERATOR_EXECUTABLE} ${_transformed_qhp_file} -o ${${qch_file}}
DEPENDS ${PLUGIN_DOXYGEN_OUTPUT_DIR}/doxygen.conf ${_file_dependencies}
)
#set_source_files_properties(${qch_file} PROPERTIES GENERATED 1)
set(${qch_file} ${${qch_file}} PARENT_SCOPE)
endfunction()
function(MACRO_CREATE_MITK_CTK_PLUGIN)
message(SEND_ERROR "The function MACRO_CREATE_MITK_CTK_PLUGIN was renamed to mitk_create_plugin in MITK 2015.05.")
endfunction()
diff --git a/CMake/mitkFunctionGenerateProjectXml.cmake b/CMake/mitkFunctionGenerateProjectXml.cmake
deleted file mode 100644
index 2d3f4c91a5..0000000000
--- a/CMake/mitkFunctionGenerateProjectXml.cmake
+++ /dev/null
@@ -1,45 +0,0 @@
-
-
-function(mitkFunctionGenerateProjectXml dir name targets is_superbuild)
- if(NOT EXISTS ${dir})
- message(FATAL_ERROR "Directory ${dir} doesn't exist!")
- endif()
-
- set(xml_subprojects )
-
- if(${is_superbuild})
- set(xml_subprojects ${xml_subprojects} " <SubProject name=\"SuperBuild\"/>\n")
- endif()
-
- foreach(target ${targets})
-
- # Remarks: Project.xml should contains all sub-project. That way
- # all dashboards should submit a similar file.
-
- set(xml_subprojects ${xml_subprojects} " <SubProject name=\"${target}\">\n")
-
- if(${is_superbuild})
- set(xml_subprojects ${xml_subprojects} " <Dependency name=\"SuperBuild\"/>\n")
- endif()
-
- # Generate XML related to the dependencies
- #foreach(dependency_name ${dependencies})
- # set(xml_subprojects ${xml_subprojects} " <Dependency name=\"${dependency_name}\"/>\n")
- #endforeach()
-
- set(xml_subprojects ${xml_subprojects} " </SubProject>\n")
- endforeach()
-
- set(xml_subprojects ${xml_subprojects} " <SubProject name=\"Documentation\">\n")
- foreach(subproject ${targets})
- set(xml_subprojects ${xml_subprojects} " <Dependency name=\"${subproject}\"/>\n")
- endforeach()
- set(xml_subprojects ${xml_subprojects} " </SubProject>\n")
-
- set(xml_content "<Project name=\"${name}\">\n${xml_subprojects}</Project>")
- set(filename "${dir}/Project.xml")
-
- file(WRITE ${filename} ${xml_content})
- message(STATUS "Generated: ${filename}")
-endfunction()
-
diff --git a/CMake/mitkMacroCreateDefaultTests.cmake b/CMake/mitkMacroCreateDefaultTests.cmake
index 5a5f87dd04..0f14e4145c 100644
--- a/CMake/mitkMacroCreateDefaultTests.cmake
+++ b/CMake/mitkMacroCreateDefaultTests.cmake
@@ -1,70 +1,66 @@
# Create TestDriver and default tests for MITK
#
# CMake variables used:
#
# ${${KITNAME}_GUI_TESTS} : filenames of all tests that run without a parameter
# ${${KITNAME}_IMAGE_GUI_TESTS : filenames of all tests that run with an image filename as parameter
# ${${KITNAME}_TESTS} : filenames of all tests that run without a parameter
# ${${KITNAME}_IMAGE_TESTS : filenames of all tests that run with an image filename as parameter
# ${${KITNAME}_TESTIMAGES} : list of images passed as parameter for the IMAGE_TESTS
# ${${KITNAME}_CUSTOM_TESTS} : filenames of custom tests which are just added to the TestDriver. Execution
# of these has to be specified manually with the ADD_TEST CMake command.
#
macro(MITK_CREATE_DEFAULT_TESTS)
# add tests which need a GUI if it is not disabled
if(NOT MITK_GUI_TESTS_DISABLED)
set( ${KITNAME}_TESTS ${${KITNAME}_TESTS} ${${KITNAME}_GUI_TESTS} )
set( ${KITNAME}_IMAGE_TESTS ${${KITNAME}_IMAGE_TESTS} ${${KITNAME}_IMAGE_GUI_TESTS} )
endif()
#
# Create the TestDriver binary which contains all the tests.
#
create_test_sourcelist(MITKTEST_SOURCE ${KITNAME}TestDriver.cpp
${${KITNAME}_TESTS} ${${KITNAME}_IMAGE_TESTS} ${${KITNAME}_CUSTOM_TESTS}
)
add_executable(${KITNAME}TestDriver ${MITKTEST_SOURCE})
- set_property(TARGET ${KITNAME}TestDriver PROPERTY LABELS ${PROJECT_NAME})
target_link_libraries(${KITNAME}TestDriver ${${KITNAME}_CORE_LIBRARIES} ${${KITNAME}_LIBRARIES} ${LIBRARIES_FOR_${KITNAME}_CORE})
#
# Now tell CMake which tests should be run. This is done automatically
# for all tests in ${KITNAME}_TESTS and ${KITNAME}_IMAGE_TESTS. The IMAGE_TESTS
# are run for each image in the TESTIMAGES list.
#
foreach( test ${${KITNAME}_TESTS} )
get_filename_component(TName ${test} NAME_WE)
add_test(${TName} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${KITNAME}TestDriver ${TName})
- set_property(TEST ${TName} PROPERTY LABELS ${PROJECT_NAME})
-
mitkFunctionGetLibrarySearchPaths(MITK_RUNTIME_PATH_RELEASE release RELEASE)
mitkFunctionGetLibrarySearchPaths(MITK_RUNTIME_PATH_DEBUG debug DEBUG)
string (REGEX REPLACE "\;" "\\\;" MITK_RUNTIME_PATH_RELEASE "${MITK_RUNTIME_PATH_RELEASE}")
string (REGEX REPLACE "\;" "\\\;" MITK_RUNTIME_PATH_DEBUG "${MITK_RUNTIME_PATH_DEBUG}")
set_property(TEST ${TName} PROPERTY ENVIRONMENT "PATH=${MITK_RUNTIME_PATH_RELEASE}\;${MITK_RUNTIME_PATH_DEBUG}" APPEND)
set_property(TEST ${TName} PROPERTY SKIP_RETURN_CODE 77)
endforeach()
foreach(image ${${KITNAME}_TESTIMAGES} ${ADDITIONAL_TEST_IMAGES} )
if(EXISTS "${image}")
set(IMAGE_FULL_PATH ${image})
else()
# todo: maybe search other paths as well
# yes, please in mitk/Testing/Data, too
set(IMAGE_FULL_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Data/${image})
endif()
if(EXISTS "${IMAGE_FULL_PATH}")
foreach( test ${${KITNAME}_IMAGE_TESTS} )
get_filename_component(TName ${test} NAME_WE)
get_filename_component(ImageName ${IMAGE_FULL_PATH} NAME)
add_test(${TName}_${ImageName} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${KITNAME}TestDriver ${TName} ${IMAGE_FULL_PATH})
- set_property(TEST ${TName}_${ImageName} PROPERTY LABELS ${PROJECT_NAME})
set_property(TEST ${TName}_${ImageName} PROPERTY ENVIRONMENT "PATH=${MITK_RUNTIME_PATH_RELEASE}\;${MITK_RUNTIME_PATH_DEBUG}" APPEND)
set_property(TEST ${TName}_${ImageName} PROPERTY SKIP_RETURN_CODE 77)
endforeach()
else()
message("!!!!! No such file: ${IMAGE_FULL_PATH} !!!!!")
endif()
endforeach()
endmacro()
diff --git a/CMake/mitkMacroCreateExecutable.cmake b/CMake/mitkMacroCreateExecutable.cmake
index c9c9d130ed..7ff9f7f7e9 100644
--- a/CMake/mitkMacroCreateExecutable.cmake
+++ b/CMake/mitkMacroCreateExecutable.cmake
@@ -1,117 +1,116 @@
##################################################################
#
# MITK_CREATE_EXECUTABLE
#
#! Creates an executable with MITK dependencies and batch files
#! for proper application start-up.
#!
#! USAGE:
#!
#! \code
#! MITK_CREATE_EXECUTABLE( [<exectuableName>]
#! [DEPENDS <modules we need>]
#! [PACKAGE_DEPENDS <packages we need, like ITK, VTK, QT>]
#! [INCLUDE_DIRS <list of additional include directories>]
#! [TARGET_DEPENDS <list of additional dependencies>
#! [WARNINGS_NO_ERRORS]
#! [NO_INSTALL]
#! \endcode
#!
#! \param EXECUTABLE_NAME The name for the new executable target
##################################################################
macro(mitk_create_executable)
set(_macro_params
VERSION # version number, e.g. "1.2.0"
FILES_CMAKE # file name of a CMake file setting source list variables
# (defaults to files.cmake)
DESCRIPTION # a description for the executable
)
set(_macro_multiparams
- SUBPROJECTS # list of CDash labels
+ SUBPROJECTS # list of CDash labels (deprecated)
INCLUDE_DIRS # additional include dirs
DEPENDS # list of modules this module depends on
PACKAGE_DEPENDS # list of "packages" this module depends on (e.g. Qt, VTK, etc.)
TARGET_DEPENDS # list of CMake targets this executable should depend on
ADDITIONAL_LIBS # list of additional libraries linked to this executable
CPP_FILES # (optional) list of cpp files
)
set(_macro_options
NO_INIT # do not create CppMicroServices initialization code
NO_FEATURE_INFO # do not create a feature info by calling add_feature_info()
NO_BATCH_FILE # do not create batch files on Windows
WARNINGS_NO_ERRORS # do not treat compiler warnings as errors
NO_INSTALL
)
cmake_parse_arguments(EXEC "${_macro_options}" "${_macro_params}" "${_macro_multiparams}" ${ARGN})
set(_EXEC_OPTIONS EXECUTABLE)
if(EXEC_NO_INIT)
list(APPEND _EXEC_OPTIONS NO_INIT)
endif()
if(EXEC_WARNINGS_NO_ERRORS)
list(APPEND _EXEC_OPTIONS WARNINGS_NO_ERRORS)
endif()
if(EXEC_NO_FEATURE_INFO)
list(APPEND _EXEC_OPTIONS NO_FEATURE_INFO)
endif()
mitk_create_module(${EXEC_UNPARSED_ARGUMENTS}
- SUBPROJECTS ${EXEC_SUBPROJECTS}
VERSION ${EXEC_VERSION}
INCLUDE_DIRS ${EXEC_INCLUDE_DIRS}
DEPENDS ${EXEC_DEPENDS}
PACKAGE_DEPENDS ${EXEC_PACKAGE_DEPENDS}
TARGET_DEPENDS ${EXEC_TARGET_DEPENDS}
ADDITIONAL_LIBS ${EXEC_ADDITIONAL_LIBS}
FILES_CMAKE ${EXEC_FILES_CMAKE}
CPP_FILES ${EXEC_CPP_FILES}
DESCRIPTION "${DESCRIPTION}"
${_EXEC_OPTIONS}
)
set(EXECUTABLE_IS_ENABLED ${MODULE_IS_ENABLED})
set(EXECUTABLE_TARGET ${MODULE_TARGET})
if(EXECUTABLE_IS_ENABLED)
set_property(GLOBAL APPEND PROPERTY MITK_EXECUTABLE_TARGETS ${EXECUTABLE_TARGET})
if(EXEC_NO_INSTALL)
set_target_properties(${EXECUTABLE_TARGET} PROPERTIES NO_INSTALL TRUE)
endif()
# Add meta dependencies (e.g. on auto-load modules from depending modules)
if(TARGET ${CMAKE_PROJECT_NAME}-autoload)
add_dependencies(${MODULE_TARGET} ${CMAKE_PROJECT_NAME}-autoload)
endif()
# Create batch and VS user files for Windows platforms
include(mitkFunctionCreateWindowsBatchScript)
if(WIN32)
set(_batch_file_in "${CMAKE_CURRENT_SOURCE_DIR}/${MODULE_TARGET}.bat.in")
if(NOT EXISTS "${_batch_file_in}")
set(_batch_file_in "${MITK_CMAKE_DIR}/StartApp.bat.in")
endif()
if(CMAKE_RUNTIME_OUTPUT_DIRECTORY)
set(_batch_file_out_dir "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}")
else()
set(_batch_file_out_dir "${CMAKE_CURRENT_BINARY_DIR}")
endif()
if(NOT EXEC_NO_BATCH_FILE)
if(NOT EXEC_NAME)
set(EXEC_NAME ${MODULE_TARGET})
endif()
foreach(BUILD_TYPE debug release)
mitkFunctionCreateWindowsBatchScript(
${_batch_file_in} ${_batch_file_out_dir}/${MODULE_TARGET}_${BUILD_TYPE}.bat
${BUILD_TYPE}
)
endforeach()
endif()
mitkFunctionConfigureVisualStudioUserProjectFile(
NAME ${MODULE_TARGET}
)
endif()
endif()
endmacro()
diff --git a/CMake/mitkMacroCreateModuleTests.cmake b/CMake/mitkMacroCreateModuleTests.cmake
index a60564cac2..1ce68e4558 100644
--- a/CMake/mitkMacroCreateModuleTests.cmake
+++ b/CMake/mitkMacroCreateModuleTests.cmake
@@ -1,109 +1,100 @@
#
# Create tests and testdriver for this module
#
# Usage: MITK_CREATE_MODULE_TESTS( [EXTRA_DRIVER_INIT init_code] )
#
# EXTRA_DRIVER_INIT is inserted as c++ code in the testdriver and will be executed before each test
#
macro(MITK_CREATE_MODULE_TESTS)
cmake_parse_arguments(MODULE_TEST
"US_MODULE;NO_INIT" "EXTRA_DRIVER_INIT;EXTRA_DRIVER_INCLUDE" "EXTRA_DEPENDS;DEPENDS;PACKAGE_DEPENDS" ${ARGN})
if(BUILD_TESTING AND MODULE_IS_ENABLED)
include(files.cmake)
include_directories(.)
set(TESTDRIVER ${MODULE_NAME}TestDriver)
set(MODULE_TEST_EXTRA_DRIVER_INIT "${MODULE_TEST_EXTRA_DRIVER_INIT}")
if(MITK_XVFB_TESTING)
set(xvfb_run ${MITK_XVFB_TESTING_COMMAND})
else()
set(xvfb_run )
endif()
if(MODULE_TEST_US_MODULE)
message(WARNING "The US_MODULE argument is deprecated and should be removed")
endif()
if(MODULE_TEST_US_MODULE AND MODULE_TEST_NO_INIT)
message(WARNING "Conflicting arguments US_MODULE and NO_INIT: NO_INIT wins.")
endif()
set(_no_init)
if(MODULE_TEST_NO_INIT)
set(_no_init NO_INIT)
endif()
set(MITK_MODULE_NAME_REGEX_MATCH )
set(MITK_MODULE_NAME_REGEX_NOT_MATCH )
set(_testdriver_file_list ${CMAKE_CURRENT_BINARY_DIR}/testdriver_files.cmake)
configure_file(${MITK_CMAKE_DIR}/mitkTestDriverFiles.cmake.in ${_testdriver_file_list} @ONLY)
mitk_create_executable(${TESTDRIVER}
DEPENDS ${MODULE_NAME} ${MODULE_TEST_DEPENDS} ${MODULE_TEST_EXTRA_DEPENDS} MitkTestingHelper
PACKAGE_DEPENDS ${MODULE_TEST_PACKAGE_DEPENDS}
- SUBPROJECTS ${MODULE_SUBPROJECTS}
FILES_CMAKE ${_testdriver_file_list}
NO_FEATURE_INFO
NO_BATCH_FILE
NO_INSTALL
${_no_init})
set_property(TARGET ${EXECUTABLE_TARGET} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Modules/Tests")
#
# Now tell CMake which tests should be run. This is done automatically
# for all tests in ${KITNAME}_TESTS and ${KITNAME}_IMAGE_TESTS. The IMAGE_TESTS
# are run for each image in the TESTIMAGES list.
#
include(files.cmake)
foreach( test ${MODULE_TESTS} )
get_filename_component(TName ${test} NAME_WE)
add_test(NAME ${TName} COMMAND ${xvfb_run} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TESTDRIVER} ${TName})
- # Add labels for CDash subproject support
- if(MODULE_SUBPROJECTS)
- set_property(TEST ${TName} PROPERTY LABELS ${MODULE_SUBPROJECTS} MITK)
- endif()
mitkFunctionGetLibrarySearchPaths(MITK_RUNTIME_PATH_RELEASE release RELEASE)
mitkFunctionGetLibrarySearchPaths(MITK_RUNTIME_PATH_DEBUG debug DEBUG)
set(test_env_path ${MITK_RUNTIME_PATH_RELEASE} ${MITK_RUNTIME_PATH_DEBUG} $ENV{PATH})
list(REMOVE_DUPLICATES test_env_path)
string (REGEX REPLACE "\;" "\\\;" test_env_path "${test_env_path}")
set_property(TEST ${TName} PROPERTY ENVIRONMENT "PATH=${test_env_path}" APPEND)
set_property(TEST ${TName} PROPERTY SKIP_RETURN_CODE 77)
endforeach()
set(TEST_TYPES IMAGE SURFACE POINTSET) # add other file types here
foreach(test_type ${TEST_TYPES})
foreach(test_data ${MODULE_TEST${test_type}} ${ADDITIONAL_TEST_${test_type}})
if(EXISTS ${test_data})
set(TEST_DATA_FULL_PATH ${test_data})
else()
# todo: maybe search other paths as well
# yes, please in mitk/Testing/Data, too
set(TEST_DATA_FULL_PATH ${MITK_DATA_DIR}/${test_data})
endif()
if(EXISTS ${TEST_DATA_FULL_PATH})
foreach( test ${MODULE_${test_type}_TESTS})
get_filename_component(TName ${test} NAME_WE)
get_filename_component(DName ${TEST_DATA_FULL_PATH} NAME)
add_test(NAME ${TName}_${DName} COMMAND ${xvfb_run} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TESTDRIVER} ${TName} ${TEST_DATA_FULL_PATH})
- # Add labels for CDash subproject support
- if(MODULE_SUBPROJECTS)
- set_property(TEST ${TName}_${DName} PROPERTY LABELS ${MODULE_SUBPROJECTS} MITK)
- endif()
set_property(TEST ${TName}_${DName} PROPERTY ENVIRONMENT "PATH=${test_env_path}" APPEND)
set_property(TEST ${TName}_${DName} PROPERTY SKIP_RETURN_CODE 77)
endforeach()
else()
message("!!!!! No such file: ${TEST_DATA_FULL_PATH} !!!!!")
endif()
endforeach()
endforeach()
endif()
endmacro()
diff --git a/CMake/mitkPackageTest.cmake b/CMake/mitkPackageTest.cmake
index 615870dc1f..c263ed8cb8 100644
--- a/CMake/mitkPackageTest.cmake
+++ b/CMake/mitkPackageTest.cmake
@@ -1,26 +1,21 @@
if(BUILD_TESTING)
#package testing
if(NOT MITK_FAST_TESTING)
# package testing in windows only for release
if(WIN32)
add_test(NAME mitkPackageTest CONFIGURATIONS Release
COMMAND ${CMAKE_COMMAND} --build ${MITK_BINARY_DIR} --config Release --target package)
- set_tests_properties( mitkPackageTest PROPERTIES
- TIMEOUT 14400
- LABELS "MITK;MITK-Plugins;PACKAGE_TESTS")
+ set_tests_properties(mitkPackageTest PROPERTIES TIMEOUT 14400)
elseif(CMAKE_BUILD_TYPE)
add_test( NAME mitkPackageTest
COMMAND ${CMAKE_COMMAND} --build ${MITK_BINARY_DIR} --config ${CMAKE_BUILD_TYPE} --target package)
- set_tests_properties( mitkPackageTest PROPERTIES
- TIMEOUT 14400
- LABELS "MITK;MITK-Plugins;PACKAGE_TESTS"
- RUN_SERIAL TRUE)
+ set_tests_properties(mitkPackageTest PROPERTIES TIMEOUT 14400 RUN_SERIAL TRUE)
endif()
endif() # NOT MITK_FAST_TESTING
endif(BUILD_TESTING)
diff --git a/CMake/mitkTestPluginGenerator.cmake b/CMake/mitkTestPluginGenerator.cmake
index cf63eeefe3..318a20f120 100644
--- a/CMake/mitkTestPluginGenerator.cmake
+++ b/CMake/mitkTestPluginGenerator.cmake
@@ -1,113 +1,109 @@
if(BUILD_TESTING)
set(proj GP) # Means GenerateProject (use a short name due to Windows limitations)
set(test_project_out_dir "${MITK_BINARY_DIR}")
set(test_project_source_dir "${MITK_BINARY_DIR}/${proj}")
set(test_project_binary_dir "${MITK_BINARY_DIR}/${proj}-bin")
add_test(NAME mitkPluginGeneratorCleanTest
COMMAND ${CMAKE_COMMAND} -E remove_directory "${test_project_source_dir}"
)
- set_tests_properties(mitkPluginGeneratorCleanTest PROPERTIES
- LABELS "MITK;BlueBerry")
add_test(NAME mitkPluginGeneratorCleanTest2
COMMAND ${CMAKE_COMMAND} -E remove_directory "${test_project_binary_dir}"
)
- set_tests_properties(mitkPluginGeneratorCleanTest2 PROPERTIES
- LABELS "MITK;BlueBerry")
add_test(NAME mitkPluginGeneratorCleanTest3
COMMAND ${CMAKE_COMMAND} -E make_directory "${test_project_binary_dir}"
)
set_tests_properties(mitkPluginGeneratorCleanTest3 PROPERTIES
- DEPENDS mitkPluginGeneratorCleanTest2
- LABELS "MITK;BlueBerry")
+ DEPENDS mitkPluginGeneratorCleanTest2)
add_test(NAME mitkPluginGeneratorCreateTest
COMMAND ${exec_target} --project-name "${proj}" --project-app-name "TestApp"
-ps org.test.plugin -pn "Test Plugin" -vn "Test View"
-o ${test_project_out_dir} -y
)
set_tests_properties(mitkPluginGeneratorCreateTest PROPERTIES
- DEPENDS "${exec_target};mitkPluginGeneratorCleanTest;mitkPluginGeneratorCleanTest3"
- LABELS "MITK;BlueBerry")
+ DEPENDS "${exec_target};mitkPluginGeneratorCleanTest;mitkPluginGeneratorCleanTest3")
+
+ mitkFunctionGetLibrarySearchPaths(MITK_RUNTIME_PATH_RELEASE release RELEASE)
+ mitkFunctionGetLibrarySearchPaths(MITK_RUNTIME_PATH_DEBUG debug DEBUG)
+ set(test_env_path ${MITK_RUNTIME_PATH_RELEASE} ${MITK_RUNTIME_PATH_DEBUG} $ENV{PATH})
+ list(REMOVE_DUPLICATES test_env_path)
+ string (REGEX REPLACE "\;" "\\\;" test_env_path "${test_env_path}")
+ set_property(TEST mitkPluginGeneratorCreateTest APPEND PROPERTY ENVIRONMENT "PATH=${test_env_path}")
+ set_property(TEST mitkPluginGeneratorCreateTest PROPERTY SKIP_RETURN_CODE 77)
set(configure_options
-DMITK_DIR:PATH=${MITK_BINARY_DIR}
-DCMAKE_C_COMPILER:STRING=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER:STRING=${CMAKE_CXX_COMPILER}
-DCMAKE_OSX_SYSROOT:PATH=${CMAKE_OSX_SYSROOT}
-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=${CMAKE_OSX_DEPLOYMENT_TARGET}
-DCMAKE_OSX_ARCHITECTURES:STRING=${CMAKE_OSX_ARCHITECTURES}
-G${CMAKE_GENERATOR}
-C "${MITK_BINARY_DIR}/mitkTestInitialCache.txt"
)
if(CMAKE_PREFIX_PATH)
string (REPLACE ";" "$<SEMICOLON>" CMAKE_PREFIX_PATH "${CMAKE_PREFIX_PATH}")
list(APPEND configure_options -DCMAKE_PREFIX_PATH:PATH=${CMAKE_PREFIX_PATH})
endif()
if(CMAKE_CONFIGURATION_TYPES)
foreach(config ${CMAKE_CONFIGURATION_TYPES})
add_test(NAME mitkPluginGeneratorConfigureTest-${config} CONFIGURATIONS ${config}
WORKING_DIRECTORY "${test_project_binary_dir}"
COMMAND ${CMAKE_COMMAND} ${configure_options}
"${test_project_source_dir}")
set_tests_properties(mitkPluginGeneratorConfigureTest-${config} PROPERTIES
- DEPENDS mitkPluginGeneratorCreateTest
- LABELS "MITK;BlueBerry")
+ DEPENDS mitkPluginGeneratorCreateTest)
add_test(NAME mitkPluginGeneratorBuildTest-${config} CONFIGURATIONS ${config}
COMMAND ${CMAKE_COMMAND} --build ${test_project_binary_dir} --config ${config})
set_tests_properties(mitkPluginGeneratorBuildTest-${config} PROPERTIES
- DEPENDS mitkPluginGeneratorConfigureTest-${config}
- LABELS "MITK;BlueBerry")
+ DEPENDS mitkPluginGeneratorConfigureTest-${config})
endforeach()
else()
add_test(NAME mitkPluginGeneratorConfigureTest-${CMAKE_BUILD_TYPE}
WORKING_DIRECTORY "${test_project_binary_dir}"
COMMAND ${CMAKE_COMMAND} ${configure_options}
-DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
"${test_project_source_dir}")
set_tests_properties(mitkPluginGeneratorConfigureTest-${CMAKE_BUILD_TYPE} PROPERTIES
- DEPENDS mitkPluginGeneratorCreateTest
- LABELS "MITK;BlueBerry")
+ DEPENDS mitkPluginGeneratorCreateTest)
add_test(NAME mitkPluginGeneratorBuildTest-${CMAKE_BUILD_TYPE}
COMMAND ${CMAKE_COMMAND} --build ${test_project_binary_dir} --config ${CMAKE_BUILD_TYPE})
set_tests_properties(mitkPluginGeneratorBuildTest-${CMAKE_BUILD_TYPE} PROPERTIES
- DEPENDS mitkPluginGeneratorConfigureTest-${CMAKE_BUILD_TYPE}
- LABELS "MITK;BlueBerry")
+ DEPENDS mitkPluginGeneratorConfigureTest-${CMAKE_BUILD_TYPE})
endif()
set(package_test_configurations)
if(WIN32)
# Only test packaging if build type is "Release" on Windows
set(package_test_configurations CONFIGURATIONS Release)
endif()
if(NOT MITK_FAST_TESTING)
if(WIN32)
# Only test packaging if build type is "Release" on Windows
add_test(NAME mitkPluginGeneratorPackageTest CONFIGURATIONS Release
COMMAND ${CMAKE_COMMAND} --build ${test_project_binary_dir}/${proj}-build --config Release --target package)
set_tests_properties(mitkPluginGeneratorPackageTest PROPERTIES
DEPENDS mitkPluginGeneratorBuildTest-Release
- TIMEOUT 6000
- LABELS "MITK;BlueBerry;PACKAGE_TESTS")
+ TIMEOUT 6000)
elseif(CMAKE_BUILD_TYPE)
add_test(mitkPluginGeneratorPackageTest
${CMAKE_COMMAND} --build ${test_project_binary_dir}/${proj}-build --config ${CMAKE_BUILD_TYPE} --target package)
set_tests_properties(mitkPluginGeneratorPackageTest PROPERTIES
DEPENDS mitkPluginGeneratorBuildTest-${CMAKE_BUILD_TYPE}
- TIMEOUT 6000
- LABELS "MITK;BlueBerry;PACKAGE_TESTS")
+ TIMEOUT 6000)
endif()
endif()
endif()
diff --git a/CMakeLists.txt b/CMakeLists.txt
index e5f75b83e0..504c27f89e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,1477 +1,1413 @@
set(MITK_CMAKE_MINIMUM_REQUIRED_VERSION 3.14.5)
cmake_minimum_required(VERSION ${MITK_CMAKE_MINIMUM_REQUIRED_VERSION})
#-----------------------------------------------------------------------------
# See https://cmake.org/cmake/help/v3.14/manual/cmake-policies.7.html for details
#-----------------------------------------------------------------------------
set(project_policies )
foreach(policy ${project_policies})
if(POLICY ${policy})
cmake_policy(SET ${policy} NEW)
endif()
endforeach()
#-----------------------------------------------------------------------------
# Superbuild Option - Enabled by default
#-----------------------------------------------------------------------------
option(MITK_USE_SUPERBUILD "Build MITK and the projects it depends on via SuperBuild.cmake." ON)
if(MITK_USE_SUPERBUILD)
project(MITK-superbuild)
set(MITK_SOURCE_DIR ${PROJECT_SOURCE_DIR})
set(MITK_BINARY_DIR ${PROJECT_BINARY_DIR})
else()
project(MITK VERSION 2018.04.99)
include_directories(SYSTEM ${MITK_SUPERBUILD_BINARY_DIR})
endif()
#-----------------------------------------------------------------------------
# MITK Extension Feature
#-----------------------------------------------------------------------------
set(MITK_EXTENSION_DIRS "" CACHE STRING "")
set(MITK_DIR_PLUS_EXTENSION_DIRS ${MITK_SOURCE_DIR} ${MITK_EXTENSION_DIRS})
#-----------------------------------------------------------------------------
# Update CMake module path
#-----------------------------------------------------------------------------
set(MITK_CMAKE_DIR ${MITK_SOURCE_DIR}/CMake)
set(CMAKE_MODULE_PATH ${MITK_CMAKE_DIR})
foreach(MITK_EXTENSION_DIR ${MITK_EXTENSION_DIRS})
set(MITK_CMAKE_EXTENSION_DIR ${MITK_EXTENSION_DIR}/CMake)
get_filename_component(MITK_CMAKE_EXTENSION_DIR ${MITK_CMAKE_EXTENSION_DIR} ABSOLUTE)
if(EXISTS ${MITK_CMAKE_EXTENSION_DIR})
list(APPEND CMAKE_MODULE_PATH ${MITK_CMAKE_EXTENSION_DIR})
endif()
endforeach()
#-----------------------------------------------------------------------------
# CMake function(s) and macro(s)
#-----------------------------------------------------------------------------
# Standard CMake macros
include(FeatureSummary)
include(CTest)
include(CMakeParseArguments)
include(FindPackageHandleStandardArgs)
# MITK macros
include(mitkFunctionGetGccVersion)
include(mitkFunctionCheckCompilerFlags)
include(mitkFunctionSuppressWarnings) # includes several functions
include(mitkMacroEmptyExternalProject)
-include(mitkFunctionGenerateProjectXml)
include(mitkFunctionEnableBuildConfiguration)
include(mitkFunctionWhitelists)
include(mitkFunctionAddExternalProject)
include(mitkFunctionAddLibrarySearchPaths)
SUPPRESS_VC_DEPRECATED_WARNINGS()
#-----------------------------------------------------------------------------
# Set a default build type if none was specified
#-----------------------------------------------------------------------------
if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
message(STATUS "Setting build type to 'Debug' as none was specified.")
set(CMAKE_BUILD_TYPE Debug CACHE STRING "Choose the type of build." FORCE)
# Set the possible values of build type for cmake-gui
set_property(CACHE CMAKE_BUILD_TYPE PROPERTY
STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
endif()
#-----------------------------------------------------------------------------
# Check miminum macOS version
#-----------------------------------------------------------------------------
# The minimum supported macOS version is 10.13. If you use a version less than 10.13, there is no guarantee that the build still works.
if(APPLE)
exec_program(sw_vers ARGS -productVersion OUTPUT_VARIABLE macos_version)
if (macos_version VERSION_LESS "10.13")
message(WARNING "Detected macOS version \"${macos_version}\" is not supported anymore. Minimum required macOS version is at least 10.13.")
endif()
if (CMAKE_OSX_DEPLOYMENT_TARGET AND CMAKE_OSX_DEPLOYMENT_TARGET VERSION_LESS 10.13)
message(WARNING "Detected macOS deployment target \"${CMAKE_OSX_DEPLOYMENT_TARGET}\" is not supported anymore. Minimum required macOS version is at least 10.13.")
endif()
endif()
#-----------------------------------------------------------------------------
# Check miminum compiler versions
#-----------------------------------------------------------------------------
if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
# require at least gcc 4.9 as provided by ppa:ubuntu-toolchain-r/test for Ubuntu 14.04
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.9)
message(FATAL_ERROR "GCC version must be at least 4.9
If you are using Ubuntu 14.04, you can easily install gcc and g++ 4.9 (or any later version available) in addition to your version ${CMAKE_CXX_COMPILER_VERSION}:
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install gcc-4.9 g++-4.9
Make sure to explicitly specify these compilers when configuring MITK:
CMAKE_C_COMPILER:FILEPATH=/usr/bin/gcc-4.9
CMAKE_CXX_COMPILER:FILEPATH=/usr/bin/g++-4.9
For more information on the proposed PPA see the Toolchain Updates section of https://wiki.ubuntu.com/ToolChain.")
endif()
elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
# require at least clang 3.4
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3.4)
message(FATAL_ERROR "Clang version must be at least 3.4")
endif()
elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "AppleClang")
# require at least clang 5.0
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0)
message(FATAL_ERROR "Apple Clang version must be at least 5.0")
endif()
elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC")
# require at least Visual Studio 2017
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 19.10)
message(FATAL_ERROR "Microsoft Visual Studio 2017 or newer required")
endif()
else()
message(WARNING "You are using an unsupported compiler! Compilation has only been tested with Clang (Linux or Apple), GCC and MSVC.")
endif()
if(CMAKE_COMPILER_IS_GNUCXX)
mitkFunctionGetGccVersion(${CMAKE_CXX_COMPILER} GCC_VERSION)
else()
set(GCC_VERSION 0)
endif()
set(MITK_CXX_STANDARD 14)
set(CMAKE_CXX_EXTENSIONS 0)
set(CMAKE_CXX_STANDARD ${MITK_CXX_STANDARD})
set(CMAKE_CXX_STANDARD_REQUIRED 1)
# This is necessary to avoid problems with compile feature checks.
# CMAKE_CXX_STANDARD seems to only set the -std=c++14 flag for targets.
# However, compile flag checks also need to be done with -std=c++14.
# The MITK_CXX14_FLAG variable is also used for external projects
# build during the MITK super-build.
mitkFunctionCheckCompilerFlags("-std=c++14" MITK_CXX14_FLAG)
#-----------------------------------------------------------------------------
# Warn if source or build path is too long
#-----------------------------------------------------------------------------
if(WIN32)
set(_src_dir_length_max 50)
set(_bin_dir_length_max 50)
if(MITK_USE_SUPERBUILD)
set(_src_dir_length_max 34) # _src_dir_length_max - strlen(ep/src/ITK-build)
set(_bin_dir_length_max 40) # _bin_dir_length_max - strlen(MITK-build)
endif()
string(LENGTH "${MITK_SOURCE_DIR}" _src_n)
string(LENGTH "${MITK_BINARY_DIR}" _bin_n)
# The warnings should be converted to errors
if(_src_n GREATER _src_dir_length_max)
message(WARNING "MITK source code directory path length is too long (${_src_n} > ${_src_dir_length_max})."
"Please move the MITK source code directory to a directory with a shorter path." )
endif()
if(_bin_n GREATER _bin_dir_length_max)
message(WARNING "MITK build directory path length is too long (${_bin_n} > ${_bin_dir_length_max})."
"Please move the MITK build directory to a directory with a shorter path." )
endif()
endif()
#-----------------------------------------------------------------------------
# Additional MITK Options (also shown during superbuild)
#-----------------------------------------------------------------------------
# -----------------------------------------
# General build options
option(BUILD_SHARED_LIBS "Build MITK with shared libraries" ON)
option(WITH_COVERAGE "Enable/Disable coverage" OFF)
option(BUILD_TESTING "Test the project" ON)
option(MITK_FAST_TESTING "Disable long-running tests like packaging" OFF)
option(MITK_XVFB_TESTING "Execute test drivers through xvfb-run" OFF)
option(MITK_BUILD_ALL_APPS "Build all MITK applications" OFF)
option(MITK_BUILD_EXAMPLES "Build the MITK Examples" OFF)
option(MITK_ENABLE_PIC_READER "Enable support for reading the DKFZ pic file format." ON)
mark_as_advanced(
MITK_XVFB_TESTING
MITK_FAST_TESTING
MITK_BUILD_ALL_APPS
MITK_ENABLE_PIC_READER
)
#-----------------------------------------------------------------------------
# Set UI testing flags
#-----------------------------------------------------------------------------
if(MITK_XVFB_TESTING)
set(MITK_XVFB_TESTING_COMMAND "xvfb-run" "--auto-servernum" CACHE STRING "Command and options to test through Xvfb")
mark_as_advanced(MITK_XVFB_TESTING_COMMAND)
endif(MITK_XVFB_TESTING)
# -----------------------------------------
# Other options
set(MITK_CUSTOM_REVISION_DESC "" CACHE STRING "Override MITK revision description")
mark_as_advanced(MITK_CUSTOM_REVISION_DESC)
set_property(GLOBAL PROPERTY MITK_EXTERNAL_PROJECTS "")
include(CMakeExternals/ExternalProjectList.cmake)
foreach(MITK_EXTENSION_DIR ${MITK_EXTENSION_DIRS})
set(MITK_CMAKE_EXTERNALS_EXTENSION_DIR ${MITK_EXTENSION_DIR}/CMakeExternals)
get_filename_component(MITK_CMAKE_EXTERNALS_EXTENSION_DIR ${MITK_CMAKE_EXTERNALS_EXTENSION_DIR} ABSOLUTE)
if(EXISTS ${MITK_CMAKE_EXTERNALS_EXTENSION_DIR}/ExternalProjectList.cmake)
include(${MITK_CMAKE_EXTERNALS_EXTENSION_DIR}/ExternalProjectList.cmake)
endif()
endforeach()
# -----------------------------------------
# Other MITK_USE_* options not related to
# external projects build via the
# MITK superbuild
option(MITK_USE_BLUEBERRY "Build the BlueBerry platform" ON)
option(MITK_USE_OpenCL "Use OpenCL GPU-Computing library" OFF)
option(MITK_USE_OpenMP "Use OpenMP" OFF)
option(MITK_USE_Python3 "Use Python 3" OFF)
#-----------------------------------------------------------------------------
# Build configurations
#-----------------------------------------------------------------------------
set(_buildConfigs "Custom")
file(GLOB _buildConfigFiles CMake/BuildConfigurations/*.cmake)
foreach(_buildConfigFile ${_buildConfigFiles})
get_filename_component(_buildConfigFile ${_buildConfigFile} NAME_WE)
list(APPEND _buildConfigs ${_buildConfigFile})
endforeach()
foreach(MITK_EXTENSION_DIR ${MITK_EXTENSION_DIRS})
file(GLOB _extBuildConfigFiles ${MITK_EXTENSION_DIR}/CMake/BuildConfigurations/*.cmake)
foreach(_extBuildConfigFile ${_extBuildConfigFiles})
get_filename_component(_extBuildConfigFile ${_extBuildConfigFile} NAME_WE)
list(APPEND _buildConfigs ${_extBuildConfigFile})
endforeach()
list(REMOVE_DUPLICATES _buildConfigs)
endforeach()
set(MITK_BUILD_CONFIGURATION "Custom" CACHE STRING "Use pre-defined MITK configurations")
set_property(CACHE MITK_BUILD_CONFIGURATION PROPERTY STRINGS ${_buildConfigs})
mitkFunctionEnableBuildConfiguration()
mitkFunctionCreateWhitelistPaths(MITK)
mitkFunctionFindWhitelists(MITK)
# -----------------------------------------
# Qt version related variables
option(MITK_USE_Qt5 "Use Qt 5 library" ON)
if(MITK_USE_Qt5)
set(MITK_QT5_MINIMUM_VERSION 5.12)
set(MITK_QT5_COMPONENTS Concurrent OpenGL PrintSupport Script Sql Svg Widgets Xml XmlPatterns WebEngineWidgets UiTools Help LinguistTools)
if(APPLE)
list(APPEND MITK_QT5_COMPONENTS DBus)
elseif(UNIX)
list(APPEND MITK_QT5_COMPONENTS X11Extras)
endif()
# Hint at default install locations of Qt
if(NOT Qt5_DIR)
if(MSVC)
set(_dir_candidates "C:/Qt")
if(CMAKE_GENERATOR MATCHES "^Visual Studio [0-9]+ ([0-9]+)")
set(_compilers "msvc${CMAKE_MATCH_1}")
elseif(CMAKE_GENERATOR MATCHES "Ninja")
include(mitkFunctionGetMSVCVersion)
mitkFunctionGetMSVCVersion()
if(VISUAL_STUDIO_PRODUCT_NAME MATCHES "^Visual Studio ([0-9]+)")
set(_compilers "msvc${CMAKE_MATCH_1}")
endif()
endif()
if(_compilers MATCHES "[0-9]+")
if (CMAKE_MATCH_0 EQUAL 2019)
list(APPEND _compilers "msvc2017") # Binary compatible to 2019
endif()
endif()
else()
set(_dir_candidates ~/Qt)
if(APPLE)
set(_compilers clang)
else()
list(APPEND _dir_candidates /opt/Qt)
set(_compilers gcc)
endif()
endif()
if(CMAKE_SIZEOF_VOID_P EQUAL 8)
foreach(_compiler ${_compilers})
list(APPEND _compilers64 "${_compiler}_64")
endforeach()
set(_compilers ${_compilers64})
endif()
foreach(_dir_candidate ${_dir_candidates})
get_filename_component(_dir_candidate ${_dir_candidate} REALPATH)
foreach(_compiler ${_compilers})
set(_glob_expression "${_dir_candidate}/5.*/${_compiler}")
file(GLOB _hints ${_glob_expression})
list(SORT _hints)
list(APPEND MITK_QT5_HINTS ${_hints})
endforeach()
endforeach()
endif()
find_package(Qt5 ${MITK_QT5_MINIMUM_VERSION} COMPONENTS ${MITK_QT5_COMPONENTS} REQUIRED HINTS ${MITK_QT5_HINTS})
if(${Qt5_VERSION} VERSION_GREATER_EQUAL 5.13)
message(WARNING "Qt version ${Qt5_VERSION_MAJOR}.${Qt5_VERSION_MINOR} is not yet supported. We recommend using version 5.12.x.")
endif()
endif()
# -----------------------------------------
# Custom dependency logic
option(MITK_USE_SYSTEM_Boost "Use the system Boost" OFF)
set(MITK_USE_Boost_LIBRARIES "" CACHE STRING "A semi-colon separated list of required Boost libraries")
if(MITK_USE_cpprestsdk)
find_package(OpenSSL QUIET)
if(NOT OpenSSL_FOUND)
set(openssl_message "Could not find OpenSSL (dependency of C++ REST SDK).\n")
if(UNIX)
if(APPLE)
set(openssl_message "${openssl_message}Please install it using your favorite package management "
"system (i.e. Homebrew or MacPorts).\n")
else()
set(openssl_message "${openssl_message}Please install the dev package of OpenSSL (i.e. libssl-dev).\n")
endif()
else()
set(openssl_message "${openssl_message}Please install Win32 OpenSSL:\n"
" https://slproweb.com/products/Win32OpenSSL.html\n")
endif()
set(openssl_message "${openssl_message}If it still cannot be found, you can hint CMake to find OpenSSL by "
"adding/setting the OPENSSL_ROOT_DIR variable to the root directory of an "
"OpenSSL installation. Make sure to clear variables of partly found "
"versions of OpenSSL before, or they will be mixed up.")
message(FATAL_ERROR ${openssl_message})
endif()
list(APPEND MITK_USE_Boost_LIBRARIES date_time regex system)
if(UNIX)
list(APPEND MITK_USE_Boost_LIBRARIES atomic chrono filesystem random thread)
endif()
list(REMOVE_DUPLICATES MITK_USE_Boost_LIBRARIES)
set(MITK_USE_Boost_LIBRARIES ${MITK_USE_Boost_LIBRARIES} CACHE STRING "A semi-colon separated list of required Boost libraries" FORCE)
endif()
if(MITK_USE_Python3)
set(MITK_USE_ZLIB ON CACHE BOOL "" FORCE)
if(APPLE AND CMAKE_FRAMEWORK_PATH AND CMAKE_FRAMEWORK_PATH MATCHES "python3\\.?([0-9]+)")
find_package(Python3 3.${CMAKE_MATCH_1} EXACT REQUIRED COMPONENTS Interpreter Development NumPy)
else()
find_package(Python3 REQUIRED COMPONENTS Interpreter Development NumPy)
endif()
if(WIN32)
string(REPLACE "\\" "/" Python3_STDARCH "${Python3_STDARCH}")
string(REPLACE "\\" "/" Python3_STDLIB "${Python3_STDLIB}")
string(REPLACE "\\" "/" Python3_SITELIB "${Python3_SITELIB}")
endif()
endif()
if(BUILD_TESTING AND NOT MITK_USE_CppUnit)
message("> Forcing MITK_USE_CppUnit to ON because BUILD_TESTING=ON")
set(MITK_USE_CppUnit ON CACHE BOOL "Use CppUnit for unit tests" FORCE)
endif()
if(MITK_USE_BLUEBERRY)
option(MITK_BUILD_ALL_PLUGINS "Build all MITK plugins" OFF)
mark_as_advanced(MITK_BUILD_ALL_PLUGINS)
if(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()
endif()
#-----------------------------------------------------------------------------
# Pixel type multiplexing
#-----------------------------------------------------------------------------
# Customize the default pixel types for multiplex macros
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
"itk::RGBPixel<unsigned char>, itk::RGBAPixel<unsigned char>"
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")
mark_as_advanced(MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES
MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES
MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES
MITK_ACCESSBYITK_DIMENSIONS
)
# consistency checks
if(NOT MITK_ACCESSBYITK_INTEGRAL_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" FORCE)
endif()
if(NOT MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES)
set(MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES
"double, float"
CACHE STRING "List of floating pixel types used in AccessByItk and InstantiateAccessFunction macros" FORCE)
endif()
if(NOT MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES)
set(MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES
"itk::RGBPixel<unsigned char>, itk::RGBAPixel<unsigned char>"
CACHE STRING "List of composite pixel types used in AccessByItk and InstantiateAccessFunction macros" FORCE)
endif()
if(NOT MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES)
string(REPLACE "," ";" _integral_types ${MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES})
string(REPLACE "," ";" _floating_types ${MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES})
foreach(_scalar_type ${_integral_types} ${_floating_types})
set(MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES
"${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES}itk::VariableLengthVector<${_scalar_type}>,")
endforeach()
string(LENGTH "${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES}" _length)
math(EXPR _length "${_length} - 1")
string(SUBSTRING "${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES}" 0 ${_length} MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES)
set(MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES ${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES}
CACHE STRING "List of vector pixel types used in AccessByItk and InstantiateAccessFunction macros for itk::VectorImage types" FORCE)
endif()
if(NOT MITK_ACCESSBYITK_DIMENSIONS)
set(MITK_ACCESSBYITK_DIMENSIONS
"2,3"
CACHE STRING "List of dimensions used in AccessByItk and InstantiateAccessFunction macros")
endif()
-#-----------------------------------------------------------------------------
-# Project.xml
-#-----------------------------------------------------------------------------
-
-# A list of topologically ordered targets
-set(CTEST_PROJECT_SUBPROJECTS)
-
-list(APPEND CTEST_PROJECT_SUBPROJECTS
- MITK-Core
- MITK-CoreUI
- MITK-IGT
- MITK-ToF
- MITK-Modules # all modules not contained in a specific subproject
- MITK-Plugins # all plugins not contained in a specific subproject
- MITK-Examples
- Unlabeled # special "subproject" catching all unlabeled targets and tests
- )
-
-foreach(MITK_EXTENSION_DIR ${MITK_EXTENSION_DIRS})
- set(MITK_CMAKE_EXTENSION_DIR ${MITK_EXTENSION_DIR}/CMake)
- get_filename_component(MITK_CMAKE_EXTENSION_DIR ${MITK_CMAKE_EXTENSION_DIR} ABSOLUTE)
- if(EXISTS ${MITK_CMAKE_EXTENSION_DIR}/CTestSubprojectList.cmake)
- set(MITK_CTEST_SUBPROJECTS "")
- include(${MITK_CMAKE_EXTENSION_DIR}/CTestSubprojectList.cmake)
- if(MITK_CTEST_SUBPROJECTS)
- list(APPEND CTEST_PROJECT_SUBPROJECTS ${MITK_CTEST_SUBPROJECTS})
- endif()
- endif()
-endforeach()
-
-# Configure CTestConfigSubProject.cmake that could be used by CTest scripts
-configure_file(${MITK_SOURCE_DIR}/CTestConfigSubProject.cmake.in
- ${MITK_BINARY_DIR}/CTestConfigSubProject.cmake)
-
-if(CTEST_PROJECT_ADDITIONAL_TARGETS)
- # those targets will be executed at the end of the ctest driver script
- # and they also get their own subproject label
- set(subproject_list "${CTEST_PROJECT_SUBPROJECTS};${CTEST_PROJECT_ADDITIONAL_TARGETS}")
-else()
- set(subproject_list "${CTEST_PROJECT_SUBPROJECTS}")
-endif()
-
-# Generate Project.xml file expected by the CTest driver script
-mitkFunctionGenerateProjectXml(${MITK_BINARY_DIR} MITK "${subproject_list}" ${MITK_USE_SUPERBUILD})
-
#-----------------------------------------------------------------------------
# Superbuild script
#-----------------------------------------------------------------------------
if(MITK_USE_SUPERBUILD)
include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake")
# Print configuration summary
message("\n\n")
feature_summary(
DESCRIPTION "------- FEATURE SUMMARY FOR ${PROJECT_NAME} -------"
WHAT ALL)
return()
endif()
#*****************************************************************************
#**************************** END OF SUPERBUILD ****************************
#*****************************************************************************
#-----------------------------------------------------------------------------
# Organize MITK targets in folders
#-----------------------------------------------------------------------------
set_property(GLOBAL PROPERTY USE_FOLDERS ON)
set(MITK_ROOT_FOLDER "MITK" CACHE STRING "")
mark_as_advanced(MITK_ROOT_FOLDER)
#-----------------------------------------------------------------------------
# CMake function(s) and macro(s)
#-----------------------------------------------------------------------------
include(WriteBasicConfigVersionFile)
include(CheckCXXSourceCompiles)
include(GenerateExportHeader)
include(mitkFunctionAddCustomModuleTest)
include(mitkFunctionCheckModuleDependencies)
include(mitkFunctionCompileSnippets)
include(mitkFunctionConfigureVisualStudioUserProjectFile)
include(mitkFunctionConvertXPSchema)
include(mitkFunctionCreateBlueBerryApplication)
include(mitkFunctionCreateCommandLineApp)
include(mitkFunctionCreateModule)
include(mitkFunctionCreatePlugin)
include(mitkFunctionCreateProvisioningFile)
include(mitkFunctionGetLibrarySearchPaths)
include(mitkFunctionGetVersion)
include(mitkFunctionGetVersionDescription)
include(mitkFunctionInstallAutoLoadModules)
include(mitkFunctionInstallCTKPlugin)
include(mitkFunctionInstallProvisioningFiles)
include(mitkFunctionInstallThirdPartyCTKPlugins)
include(mitkFunctionOrganizeSources)
include(mitkFunctionUseModules)
if( ${MITK_USE_MatchPoint} )
include(mitkFunctionCreateMatchPointDeployedAlgorithm)
endif()
include(mitkMacroConfigureItkPixelTypes)
include(mitkMacroCreateExecutable)
include(mitkMacroCreateModuleTests)
include(mitkMacroGenerateToolsLibrary)
include(mitkMacroGetLinuxDistribution)
include(mitkMacroGetPMDPlatformString)
include(mitkMacroInstall)
include(mitkMacroInstallHelperApp)
include(mitkMacroInstallTargets)
include(mitkMacroMultiplexPicType)
# Deprecated
include(mitkMacroCreateCTKPlugin)
#-----------------------------------------------------------------------------
# Global CMake variables
#-----------------------------------------------------------------------------
# Required and enabled C++14 features for all MITK code.
# These are added as PUBLIC compile features to all MITK modules.
set(MITK_CXX_FEATURES
cxx_auto_type
cxx_decltype
cxx_enum_forward_declarations
cxx_extended_friend_declarations
cxx_extern_templates
cxx_final
cxx_lambdas
cxx_local_type_template_args
cxx_long_long_type
cxx_nullptr
cxx_override
cxx_range_for
cxx_right_angle_brackets
cxx_rvalue_references
cxx_static_assert
cxx_strong_enums
cxx_template_template_parameters
cxx_trailing_return_types
cxx_variadic_macros
)
if(NOT DEFINED CMAKE_DEBUG_POSTFIX)
# We can't do this yet because the CTK Plugin Framework
# cannot cope with a postfix yet.
#set(CMAKE_DEBUG_POSTFIX d)
endif()
#-----------------------------------------------------------------------------
# Output directories.
#-----------------------------------------------------------------------------
set(_default_LIBRARY_output_dir lib)
set(_default_RUNTIME_output_dir bin)
set(_default_ARCHIVE_output_dir lib)
foreach(type LIBRARY RUNTIME ARCHIVE)
# Make sure the directory exists
if(MITK_CMAKE_${type}_OUTPUT_DIRECTORY
AND NOT EXISTS ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY})
message("Creating directory MITK_CMAKE_${type}_OUTPUT_DIRECTORY: ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}")
file(MAKE_DIRECTORY "${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}")
endif()
if(MITK_CMAKE_${type}_OUTPUT_DIRECTORY)
set(CMAKE_${type}_OUTPUT_DIRECTORY ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY})
else()
set(CMAKE_${type}_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/${_default_${type}_output_dir})
set(MITK_CMAKE_${type}_OUTPUT_DIRECTORY ${CMAKE_${type}_OUTPUT_DIRECTORY})
endif()
set(CMAKE_${type}_OUTPUT_DIRECTORY ${CMAKE_${type}_OUTPUT_DIRECTORY} CACHE INTERNAL "Output directory for ${type} files.")
mark_as_advanced(CMAKE_${type}_OUTPUT_DIRECTORY)
endforeach()
#-----------------------------------------------------------------------------
# Set MITK specific options and variables (NOT available during superbuild)
#-----------------------------------------------------------------------------
# Look for optional Doxygen package
find_package(Doxygen)
option(BLUEBERRY_DEBUG_SMARTPOINTER "Enable code for debugging smart pointers" OFF)
mark_as_advanced(BLUEBERRY_DEBUG_SMARTPOINTER)
# Ask the user to show the console window for applications
option(MITK_SHOW_CONSOLE_WINDOW "Use this to enable or disable the console window when starting MITK GUI Applications" ON)
mark_as_advanced(MITK_SHOW_CONSOLE_WINDOW)
# TODO: check if necessary
option(USE_ITKZLIB "Use the ITK zlib for pic compression." ON)
mark_as_advanced(USE_ITKZLIB)
if(NOT MITK_FAST_TESTING)
- if(DEFINED MITK_CTEST_SCRIPT_MODE
- AND (MITK_CTEST_SCRIPT_MODE STREQUAL "continuous" OR MITK_CTEST_SCRIPT_MODE STREQUAL "experimental") )
+ if(MITK_CTEST_SCRIPT_MODE STREQUAL "Continuous" OR MITK_CTEST_SCRIPT_MODE STREQUAL "Experimental")
set(MITK_FAST_TESTING ON)
endif()
endif()
if(NOT UNIX)
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()
# Configure pixel types used for ITK image access multiplexing
mitkMacroConfigureItkPixelTypes()
# 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_DEFAULT_MODULE_NAME_PREFIX "Mitk")
set(MITK_MODULE_NAME_PREFIX ${MITK_DEFAULT_MODULE_NAME_PREFIX})
set(MITK_MODULE_NAME_DEFAULTS_TO_DIRECTORY_NAME 1)
#-----------------------------------------------------------------------------
# Get MITK version info
#-----------------------------------------------------------------------------
mitkFunctionGetVersion(${MITK_SOURCE_DIR} MITK)
mitkFunctionGetVersionDescription(${MITK_SOURCE_DIR} MITK)
# MITK_VERSION
set(MITK_VERSION_STRING "${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()
#-----------------------------------------------------------------------------
# Installation preparation
#
# These should be set before any MITK install macros are used
#-----------------------------------------------------------------------------
# on macOS all BlueBerry plugins get copied into every
# application bundle (.app directory) specified here
if(MITK_USE_BLUEBERRY AND APPLE)
foreach(MITK_EXTENSION_DIR ${MITK_DIR_PLUS_EXTENSION_DIRS})
set(MITK_APPLICATIONS_EXTENSION_DIR ${MITK_EXTENSION_DIR}/Applications)
get_filename_component(MITK_APPLICATIONS_EXTENSION_DIR ${MITK_APPLICATIONS_EXTENSION_DIR} ABSOLUTE)
if(EXISTS ${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake)
set(MITK_APPS "")
include(${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake)
foreach(mitk_app ${MITK_APPS})
# extract option_name
string(REPLACE "^^" "\\;" target_info ${mitk_app})
set(target_info_list ${target_info})
list(GET target_info_list 1 option_name)
list(GET target_info_list 0 app_name)
# check if the application is enabled
if(${option_name} OR MITK_BUILD_ALL_APPS)
set(MACOSX_BUNDLE_NAMES ${MACOSX_BUNDLE_NAMES} Mitk${app_name})
endif()
endforeach()
endif()
endforeach()
endif()
#-----------------------------------------------------------------------------
# Set coverage Flags
#-----------------------------------------------------------------------------
if(WITH_COVERAGE)
if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
set(coverage_flags "-g -fprofile-arcs -ftest-coverage -O0 -DNDEBUG")
set(COVERAGE_CXX_FLAGS ${coverage_flags})
set(COVERAGE_C_FLAGS ${coverage_flags})
endif()
endif()
#-----------------------------------------------------------------------------
# MITK C/CXX Flags
#-----------------------------------------------------------------------------
set(MITK_C_FLAGS "${COVERAGE_C_FLAGS}")
set(MITK_C_FLAGS_DEBUG )
set(MITK_C_FLAGS_RELEASE )
set(MITK_CXX_FLAGS "${COVERAGE_CXX_FLAGS} ${MITK_CXX14_FLAG}")
set(MITK_CXX_FLAGS_DEBUG )
set(MITK_CXX_FLAGS_RELEASE )
set(MITK_EXE_LINKER_FLAGS )
set(MITK_SHARED_LINKER_FLAGS )
if(WIN32)
set(MITK_CXX_FLAGS "${MITK_CXX_FLAGS} -DPOCO_NO_UNWINDOWS -DWIN32_LEAN_AND_MEAN -DNOMINMAX")
mitkFunctionCheckCompilerFlags("/wd4005" MITK_CXX_FLAGS) # warning C4005: macro redefinition
mitkFunctionCheckCompilerFlags("/wd4231" MITK_CXX_FLAGS) # warning C4231: nonstandard extension used : 'extern' before template explicit instantiation
# the following line should be removed after fixing bug 17637
mitkFunctionCheckCompilerFlags("/wd4316" MITK_CXX_FLAGS) # warning C4316: object alignment on heap
mitkFunctionCheckCompilerFlags("/wd4180" MITK_CXX_FLAGS) # warning C4180: qualifier applied to function type has no meaning
mitkFunctionCheckCompilerFlags("/wd4251" MITK_CXX_FLAGS) # warning C4251: 'identifier' : class 'type' needs to have dll-interface to be used by clients of class 'type2'
endif()
if(APPLE)
set(MITK_CXX_FLAGS "${MITK_CXX_FLAGS} -DGL_SILENCE_DEPRECATION") # Apple deprecated OpenGL in macOS 10.14
endif()
if(NOT MSVC_VERSION)
foreach(_flag
-Wall
-Wextra
-Wpointer-arith
-Winvalid-pch
-Wcast-align
-Wwrite-strings
-Wno-error=gnu
-Wno-error=unknown-pragmas
# The strict-overflow warning is generated by ITK template code
-Wno-error=strict-overflow
-Woverloaded-virtual
-Wstrict-null-sentinel
#-Wold-style-cast
#-Wsign-promo
-Wno-error=deprecated-copy
-Wno-array-bounds
-fdiagnostics-show-option
)
mitkFunctionCheckCAndCXXCompilerFlags(${_flag} MITK_C_FLAGS MITK_CXX_FLAGS)
endforeach()
endif()
if(CMAKE_COMPILER_IS_GNUCXX AND NOT APPLE)
mitkFunctionCheckCompilerFlags("-Wl,--no-undefined" MITK_SHARED_LINKER_FLAGS)
mitkFunctionCheckCompilerFlags("-Wl,--as-needed" MITK_SHARED_LINKER_FLAGS)
endif()
if(CMAKE_COMPILER_IS_GNUCXX)
mitkFunctionCheckCAndCXXCompilerFlags("-fstack-protector-all" MITK_C_FLAGS MITK_CXX_FLAGS)
set(MITK_CXX_FLAGS_RELEASE "-U_FORTIFY_SOURCES -D_FORTIFY_SOURCE=2 ${MITK_CXX_FLAGS_RELEASE}")
endif()
set(MITK_MODULE_LINKER_FLAGS ${MITK_SHARED_LINKER_FLAGS})
set(MITK_EXE_LINKER_FLAGS ${MITK_SHARED_LINKER_FLAGS})
#-----------------------------------------------------------------------------
# MITK Packages
#-----------------------------------------------------------------------------
set(MITK_MODULES_PACKAGE_DEPENDS_DIR ${MITK_SOURCE_DIR}/CMake/PackageDepends)
set(MODULES_PACKAGE_DEPENDS_DIRS ${MITK_MODULES_PACKAGE_DEPENDS_DIR})
foreach(MITK_EXTENSION_DIR ${MITK_EXTENSION_DIRS})
set(MITK_PACKAGE_DEPENDS_EXTENSION_DIR ${MITK_EXTENSION_DIR}/CMake/PackageDepends)
get_filename_component(MITK_PACKAGE_DEPENDS_EXTENSION_DIR ${MITK_PACKAGE_DEPENDS_EXTENSION_DIR} ABSOLUTE)
if(EXISTS ${MITK_PACKAGE_DEPENDS_EXTENSION_DIR})
list(APPEND MODULES_PACKAGE_DEPENDS_DIRS ${MITK_PACKAGE_DEPENDS_EXTENSION_DIR})
endif()
endforeach()
if(NOT MITK_USE_SYSTEM_Boost)
set(Boost_NO_SYSTEM_PATHS 1)
endif()
set(Boost_USE_MULTITHREADED 1)
set(Boost_USE_STATIC_LIBS 0)
set(Boost_USE_STATIC_RUNTIME 0)
set(Boost_ADDITIONAL_VERSIONS 1.68 1.68.0)
# We need this later for a DCMTK workaround
set(_dcmtk_dir_orig ${DCMTK_DIR})
# This property is populated at the top half of this file
get_property(MITK_EXTERNAL_PROJECTS GLOBAL PROPERTY MITK_EXTERNAL_PROJECTS)
foreach(ep ${MITK_EXTERNAL_PROJECTS})
get_property(_package GLOBAL PROPERTY MITK_${ep}_PACKAGE)
get_property(_components GLOBAL PROPERTY MITK_${ep}_COMPONENTS)
if(MITK_USE_${ep} AND _package)
if(_components)
find_package(${_package} COMPONENTS ${_components} REQUIRED CONFIG)
else()
# Prefer config mode first because it finds external
# <proj>Config.cmake files pointed at by <proj>_DIR variables.
# Otherwise, existing Find<proj>.cmake files could fail.
if(DEFINED ${_package}_DIR)
#we store the information because it will be overwritten by find_package
#and would get lost for all EPs that use on Find<proj>.cmake instead of config
#files.
set(_temp_EP_${_package}_dir ${${_package}_DIR})
endif(DEFINED ${_package}_DIR)
find_package(${_package} QUIET CONFIG)
string(TOUPPER "${_package}" _package_uc)
if(NOT (${_package}_FOUND OR ${_package_uc}_FOUND))
if(DEFINED _temp_EP_${_package}_dir)
set(${_package}_DIR ${_temp_EP_${_package}_dir} CACHE PATH "externaly set dir of the package ${_package}" FORCE)
endif(DEFINED _temp_EP_${_package}_dir)
find_package(${_package} REQUIRED)
endif()
endif()
endif()
endforeach()
# Ensure that the MITK CMake module path comes first
set(CMAKE_MODULE_PATH
${MITK_CMAKE_DIR}
${CMAKE_MODULE_PATH}
)
if(MITK_USE_DCMTK)
# Due to the preferred CONFIG mode in find_package calls above,
# the DCMTKConfig.cmake file is read, which does not provide useful
# package information. We explictly need MODULE mode to find DCMTK.
if(${_dcmtk_dir_orig} MATCHES "${MITK_EXTERNAL_PROJECT_PREFIX}.*")
# Help our FindDCMTK.cmake script find our super-build DCMTK
set(DCMTK_DIR ${MITK_EXTERNAL_PROJECT_PREFIX})
else()
# Use the original value
set(DCMTK_DIR ${_dcmtk_dir_orig})
endif()
find_package(DCMTK REQUIRED MODULE)
endif()
if(MITK_USE_DCMQI)
# Due to the preferred CONFIG mode in find_package calls above,
# the DCMQIConfig.cmake file is read, which does not provide useful
# package information. We explictly need MODULE mode to find DCMQI.
# Help our FindDCMQI.cmake script find our super-build DCMQI
set(DCMQI_DIR ${MITK_EXTERNAL_PROJECT_PREFIX})
find_package(DCMQI REQUIRED)
endif()
link_directories(${Boost_LIBRARY_DIRS})
if(MITK_USE_OpenIGTLink)
link_directories(${OpenIGTLink_LIBRARY_DIRS})
endif()
if(MITK_USE_OpenCL)
find_package(OpenCL REQUIRED)
endif()
if(MITK_USE_OpenMP)
find_package(OpenMP REQUIRED COMPONENTS CXX)
else()
find_package(OpenMP QUIET COMPONENTS CXX)
if(OpenMP_FOUND)
set(MITK_USE_OpenMP ON CACHE BOOL "" FORCE)
elseif(APPLE AND OpenMP_libomp_LIBRARY AND NOT OpenMP_CXX_LIB_NAMES)
set(OpenMP_CXX_LIB_NAMES libomp CACHE STRING "" FORCE)
get_filename_component(openmp_lib_dir "${OpenMP_libomp_LIBRARY}" DIRECTORY)
set(openmp_include_dir "${openmp_lib_dir}/../include")
if(EXISTS "${openmp_include_dir}")
get_filename_component(openmp_include_dir "${openmp_include_dir}" REALPATH)
set(OpenMP_CXX_FLAGS "-Xpreprocessor -fopenmp -I${openmp_include_dir}" CACHE STRING "" FORCE)
find_package(OpenMP QUIET COMPONENTS CXX)
if(OpenMP_FOUND)
set(MITK_USE_OpenMP ON CACHE BOOL "" FORCE)
endif()
endif()
endif()
endif()
# Qt support
if(MITK_USE_Qt5)
find_package(Qt5Core ${MITK_QT5_MINIMUM_VERSION} REQUIRED) # at least Core required
get_target_property(_qmake_exec Qt5::qmake LOCATION)
execute_process(COMMAND ${_qmake_exec} -query QT_INSTALL_BINS
RESULT_VARIABLE _result
OUTPUT_VARIABLE QT_BINARY_DIR
ERROR_VARIABLE _error
)
string(STRIP "${QT_BINARY_DIR}" QT_BINARY_DIR)
if(_result OR NOT EXISTS "${QT_BINARY_DIR}")
message(FATAL_ERROR "Could not determine Qt binary directory: ${_result} ${QT_BINARY_DIR} ${_error}")
endif()
find_program(QT_HELPGENERATOR_EXECUTABLE
NAMES qhelpgenerator qhelpgenerator-qt5 qhelpgenerator5
PATHS ${QT_BINARY_DIR}
NO_DEFAULT_PATH
)
find_program(QT_COLLECTIONGENERATOR_EXECUTABLE
NAMES qcollectiongenerator qcollectiongenerator-qt5 qcollectiongenerator5
PATHS ${QT_BINARY_DIR}
NO_DEFAULT_PATH
)
find_program(QT_ASSISTANT_EXECUTABLE
NAMES assistant assistant-qt5 assistant5
PATHS ${QT_BINARY_DIR}
NO_DEFAULT_PATH
)
find_program(QT_XMLPATTERNS_EXECUTABLE
NAMES xmlpatterns
PATHS ${QT_BINARY_DIR}
NO_DEFAULT_PATH
)
mark_as_advanced(QT_HELPGENERATOR_EXECUTABLE
QT_COLLECTIONGENERATOR_EXECUTABLE
QT_ASSISTANT_EXECUTABLE
QT_XMLPATTERNS_EXECUTABLE
)
if(MITK_USE_BLUEBERRY)
option(BLUEBERRY_USE_QT_HELP "Enable support for integrating plugin documentation into Qt Help" ${DOXYGEN_FOUND})
mark_as_advanced(BLUEBERRY_USE_QT_HELP)
# Sanity checks for in-application BlueBerry plug-in help generation
if(BLUEBERRY_USE_QT_HELP)
set(_force_blueberry_use_qt_help_to_off 0)
if(NOT DOXYGEN_FOUND)
message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because Doxygen was not found.")
set(_force_blueberry_use_qt_help_to_off 1)
endif()
if(DOXYGEN_FOUND AND DOXYGEN_VERSION VERSION_LESS 1.8.7)
message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because Doxygen version 1.8.7 or newer not found.")
set(_force_blueberry_use_qt_help_to_off 1)
endif()
if(NOT QT_HELPGENERATOR_EXECUTABLE)
message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because QT_HELPGENERATOR_EXECUTABLE is empty.")
set(_force_blueberry_use_qt_help_to_off 1)
endif()
if(NOT MITK_USE_Qt5)
message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because MITK_USE_Qt5 is OFF.")
set(_force_blueberry_use_qt_help_to_off 1)
endif()
if(NOT QT_XMLPATTERNS_EXECUTABLE)
message("You have enabled Qt Help support, but QT_XMLPATTERNS_EXECUTABLE is empty")
set(_force_blueberry_use_qt_help_to_off 1)
endif()
if(_force_blueberry_use_qt_help_to_off)
set(BLUEBERRY_USE_QT_HELP OFF CACHE BOOL "Enable support for integrating plugin documentation into Qt Help" FORCE)
endif()
endif()
if(BLUEBERRY_QT_HELP_REQUIRED AND NOT BLUEBERRY_USE_QT_HELP)
message(FATAL_ERROR "BLUEBERRY_USE_QT_HELP is required to be set to ON")
endif()
endif()
endif()
#-----------------------------------------------------------------------------
# Testing
#-----------------------------------------------------------------------------
if(BUILD_TESTING)
- # Setup file for setting custom ctest vars
- configure_file(
- CMake/CTestCustom.cmake.in
- ${MITK_BINARY_DIR}/CTestCustom.cmake
- @ONLY
- )
-
+ #[[ See T27701
# Initial cache for ProjectTemplate and PluginGenerator tests
configure_file(
CMake/mitkTestInitialCache.txt.in
${MITK_BINARY_DIR}/mitkTestInitialCache.txt
@ONLY
- )
+ )]]
# Configuration for the CMake-generated test driver
set(CMAKE_TESTDRIVER_EXTRA_INCLUDES "#include <stdexcept>")
set(CMAKE_TESTDRIVER_BEFORE_TESTMAIN "
try
{")
set(CMAKE_TESTDRIVER_AFTER_TESTMAIN "
}
catch (const std::exception& e)
{
fprintf(stderr, \"%s\\n\", e.what());
return EXIT_FAILURE;
}
catch (...)
{
printf(\"Exception caught in the test driver\\n\");
return EXIT_FAILURE;
}")
set(MITK_TEST_OUTPUT_DIR "${MITK_BINARY_DIR}/test_output")
if(NOT EXISTS ${MITK_TEST_OUTPUT_DIR})
file(MAKE_DIRECTORY ${MITK_TEST_OUTPUT_DIR})
endif()
# Test the package target
include(mitkPackageTest)
endif()
configure_file(mitkTestingConfig.h.in ${MITK_BINARY_DIR}/mitkTestingConfig.h)
#-----------------------------------------------------------------------------
# MITK_SUPERBUILD_BINARY_DIR
#-----------------------------------------------------------------------------
# If MITK_SUPERBUILD_BINARY_DIR isn't defined, it means MITK is *NOT* build using Superbuild.
# In that specific case, MITK_SUPERBUILD_BINARY_DIR should default to MITK_BINARY_DIR
if(NOT DEFINED MITK_SUPERBUILD_BINARY_DIR)
set(MITK_SUPERBUILD_BINARY_DIR ${MITK_BINARY_DIR})
endif()
#-----------------------------------------------------------------------------
# Set C/CXX and linker flags for MITK code
#-----------------------------------------------------------------------------
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MITK_CXX_FLAGS}")
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} ${MITK_CXX_FLAGS_DEBUG}")
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} ${MITK_CXX_FLAGS_RELEASE}")
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${MITK_C_FLAGS}")
set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} ${MITK_C_FLAGS_DEBUG}")
set(CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} ${MITK_C_FLAGS_RELEASE}")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${MITK_EXE_LINKER_FLAGS}")
set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} ${MITK_SHARED_LINKER_FLAGS}")
set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} ${MITK_MODULE_LINKER_FLAGS}")
-#-----------------------------------------------------------------------------
-# Add custom targets representing CDash subprojects
-#-----------------------------------------------------------------------------
-
-foreach(subproject ${CTEST_PROJECT_SUBPROJECTS})
- if(NOT TARGET ${subproject} AND NOT subproject MATCHES "Unlabeled")
- add_custom_target(${subproject})
- set_property(TARGET ${subproject} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/CTestSubprojects")
- endif()
-endforeach()
-
#-----------------------------------------------------------------------------
# Add subdirectories
#-----------------------------------------------------------------------------
add_subdirectory(Utilities)
add_subdirectory(Modules)
include("${CMAKE_CURRENT_SOURCE_DIR}/Modules/ModuleList.cmake")
mitkFunctionWhitelistModules(MITK MITK_MODULES)
set(MITK_ROOT_FOLDER_BACKUP "${MITK_ROOT_FOLDER}")
foreach(MITK_EXTENSION_DIR ${MITK_EXTENSION_DIRS})
get_filename_component(MITK_ROOT_FOLDER ${MITK_EXTENSION_DIR} NAME)
set(MITK_MODULES_EXTENSION_DIR ${MITK_EXTENSION_DIR}/Modules)
get_filename_component(MITK_MODULES_EXTENSION_DIR ${MITK_MODULES_EXTENSION_DIR} ABSOLUTE)
if(EXISTS ${MITK_MODULES_EXTENSION_DIR}/ModuleList.cmake)
set(MITK_MODULES "")
include(${MITK_MODULES_EXTENSION_DIR}/ModuleList.cmake)
foreach(mitk_module ${MITK_MODULES})
add_subdirectory(${MITK_MODULES_EXTENSION_DIR}/${mitk_module} Modules/${mitk_module})
endforeach()
endif()
set(MITK_MODULE_NAME_PREFIX ${MITK_DEFAULT_MODULE_NAME_PREFIX})
endforeach()
set(MITK_ROOT_FOLDER "${MITK_ROOT_FOLDER_BACKUP}")
add_subdirectory(Wrapping)
set(MITK_DOXYGEN_OUTPUT_DIR "${PROJECT_BINARY_DIR}/Documentation/Doxygen" CACHE PATH
"Output directory for doxygen generated documentation.")
if(MITK_USE_BLUEBERRY)
set(BLUEBERRY_XPDOC_OUTPUT_DIR "${MITK_DOXYGEN_OUTPUT_DIR}/html/extension-points/html/")
execute_process(COMMAND ${CMAKE_COMMAND} -E make_directory ${BLUEBERRY_XPDOC_OUTPUT_DIR})
include("${CMAKE_CURRENT_SOURCE_DIR}/Plugins/PluginList.cmake")
mitkFunctionWhitelistPlugins(MITK MITK_PLUGINS)
set(mitk_plugins_fullpath "")
foreach(mitk_plugin ${MITK_PLUGINS})
list(APPEND mitk_plugins_fullpath Plugins/${mitk_plugin})
endforeach()
set(MITK_PLUGIN_REGEX_LIST "")
foreach(MITK_EXTENSION_DIR ${MITK_EXTENSION_DIRS})
set(MITK_PLUGINS_EXTENSION_DIR ${MITK_EXTENSION_DIR}/Plugins)
get_filename_component(MITK_PLUGINS_EXTENSION_DIR ${MITK_PLUGINS_EXTENSION_DIR} ABSOLUTE)
if(EXISTS ${MITK_PLUGINS_EXTENSION_DIR}/PluginList.cmake)
set(MITK_PLUGINS "")
include(${MITK_PLUGINS_EXTENSION_DIR}/PluginList.cmake)
foreach(mitk_plugin ${MITK_PLUGINS})
list(APPEND mitk_plugins_fullpath ${MITK_PLUGINS_EXTENSION_DIR}/${mitk_plugin})
endforeach()
endif()
endforeach()
if(EXISTS ${MITK_PRIVATE_MODULES}/PluginList.cmake)
include(${MITK_PRIVATE_MODULES}/PluginList.cmake)
foreach(mitk_plugin ${MITK_PRIVATE_PLUGINS})
list(APPEND mitk_plugins_fullpath ${MITK_PRIVATE_MODULES}/${mitk_plugin})
endforeach()
endif()
if(MITK_BUILD_EXAMPLES)
include("${CMAKE_CURRENT_SOURCE_DIR}/Examples/Plugins/PluginList.cmake")
set(mitk_example_plugins_fullpath )
foreach(mitk_example_plugin ${MITK_EXAMPLE_PLUGINS})
list(APPEND mitk_example_plugins_fullpath Examples/Plugins/${mitk_example_plugin})
list(APPEND mitk_plugins_fullpath Examples/Plugins/${mitk_example_plugin})
endforeach()
endif()
# Specify which plug-ins belong to this project
macro(GetMyTargetLibraries all_target_libraries varname)
set(re_ctkplugin_mitk "^org_mitk_[a-zA-Z0-9_]+$")
set(re_ctkplugin_bb "^org_blueberry_[a-zA-Z0-9_]+$")
set(_tmp_list)
list(APPEND _tmp_list ${all_target_libraries})
ctkMacroListFilter(_tmp_list re_ctkplugin_mitk re_ctkplugin_bb MITK_PLUGIN_REGEX_LIST OUTPUT_VARIABLE ${varname})
endmacro()
# Get infos about application directories and build options
set(mitk_apps_fullpath "")
foreach(MITK_EXTENSION_DIR ${MITK_DIR_PLUS_EXTENSION_DIRS})
set(MITK_APPLICATIONS_EXTENSION_DIR ${MITK_EXTENSION_DIR}/Applications)
get_filename_component(MITK_APPLICATIONS_EXTENSION_DIR ${MITK_APPLICATIONS_EXTENSION_DIR} ABSOLUTE)
if(EXISTS ${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake)
set(MITK_APPS "")
include(${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake)
foreach(mitk_app ${MITK_APPS})
# extract option_name
string(REPLACE "^^" "\\;" target_info ${mitk_app})
set(target_info_list ${target_info})
list(GET target_info_list 0 directory_name)
list(GET target_info_list 1 option_name)
if(${option_name})
list(APPEND mitk_apps_fullpath "${MITK_APPLICATIONS_EXTENSION_DIR}/${directory_name}^^${option_name}")
endif()
endforeach()
endif()
endforeach()
if (mitk_plugins_fullpath)
ctkMacroSetupPlugins(${mitk_plugins_fullpath}
BUILD_OPTION_PREFIX MITK_BUILD_
APPS ${mitk_apps_fullpath}
BUILD_ALL ${MITK_BUILD_ALL_PLUGINS}
COMPACT_OPTIONS)
endif()
set(MITK_PLUGIN_USE_FILE "${MITK_BINARY_DIR}/MitkPluginUseFile.cmake")
if(${PROJECT_NAME}_PLUGIN_LIBRARIES)
ctkFunctionGeneratePluginUseFile(${MITK_PLUGIN_USE_FILE})
else()
file(REMOVE ${MITK_PLUGIN_USE_FILE})
set(MITK_PLUGIN_USE_FILE )
endif()
endif()
#-----------------------------------------------------------------------------
# Documentation
#-----------------------------------------------------------------------------
if(DOXYGEN_FOUND)
add_subdirectory(Documentation)
endif()
#-----------------------------------------------------------------------------
# Installation
#-----------------------------------------------------------------------------
# set MITK cpack variables
# These are the default variables, which can be overwritten ( see below )
include(mitkSetupCPack)
set(use_default_config ON)
set(ALL_MITK_APPS "")
set(activated_apps_no 0)
foreach(MITK_EXTENSION_DIR ${MITK_DIR_PLUS_EXTENSION_DIRS})
set(MITK_APPLICATIONS_EXTENSION_DIR ${MITK_EXTENSION_DIR}/Applications)
get_filename_component(MITK_APPLICATIONS_EXTENSION_DIR ${MITK_APPLICATIONS_EXTENSION_DIR} ABSOLUTE)
if(EXISTS ${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake)
set(MITK_APPS "")
include(${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake)
foreach(mitk_app ${MITK_APPS})
string(REPLACE "^^" "\\;" target_info ${mitk_app})
set(target_info_list ${target_info})
list(GET target_info_list 0 directory_name)
list(GET target_info_list 1 option_name)
list(GET target_info_list 2 executable_name)
list(APPEND ALL_MITK_APPS "${MITK_EXTENSION_DIR}/Applications/${directory_name}^^${option_name}^^${executable_name}")
if(${option_name} OR MITK_BUILD_ALL_APPS)
MATH(EXPR activated_apps_no "${activated_apps_no} + 1")
endif()
endforeach()
endif()
endforeach()
list(LENGTH ALL_MITK_APPS app_count)
if(app_count EQUAL 1 AND (activated_apps_no EQUAL 1 OR MITK_BUILD_ALL_APPS))
# Corner case if there is only one app in total
set(use_project_cpack ON)
elseif(activated_apps_no EQUAL 1 AND NOT MITK_BUILD_ALL_APPS)
# Only one app is enabled (no "build all" flag set)
set(use_project_cpack ON)
else()
# Less or more then one app is enabled
set(use_project_cpack OFF)
endif()
foreach(mitk_app ${ALL_MITK_APPS})
# extract target_dir and option_name
string(REPLACE "^^" "\\;" target_info ${mitk_app})
set(target_info_list ${target_info})
list(GET target_info_list 0 target_dir)
list(GET target_info_list 1 option_name)
list(GET target_info_list 2 executable_name)
# check if the application is enabled
if(${option_name} OR MITK_BUILD_ALL_APPS)
# check whether application specific configuration files will be used
if(use_project_cpack)
# use files if they exist
if(EXISTS "${target_dir}/CPackOptions.cmake")
include("${target_dir}/CPackOptions.cmake")
endif()
if(EXISTS "${target_dir}/CPackConfig.cmake.in")
set(CPACK_PROJECT_CONFIG_FILE "${target_dir}/CPackConfig.cmake")
configure_file(${target_dir}/CPackConfig.cmake.in
${CPACK_PROJECT_CONFIG_FILE} @ONLY)
set(use_default_config OFF)
endif()
endif()
# add link to the list
list(APPEND CPACK_CREATE_DESKTOP_LINKS "${executable_name}")
endif()
endforeach()
# if no application specific configuration file was used, use default
if(use_default_config)
configure_file(${MITK_SOURCE_DIR}/MITKCPackOptions.cmake.in
${MITK_BINARY_DIR}/MITKCPackOptions.cmake @ONLY)
set(CPACK_PROJECT_CONFIG_FILE "${MITK_BINARY_DIR}/MITKCPackOptions.cmake")
endif()
# include CPack model once all variables are set
include(CPack)
# Additional installation rules
include(mitkInstallRules)
#-----------------------------------------------------------------------------
# Last configuration steps
#-----------------------------------------------------------------------------
# ---------------- Export targets -----------------
set(MITK_EXPORTS_FILE "${MITK_BINARY_DIR}/MitkExports.cmake")
file(REMOVE ${MITK_EXPORTS_FILE})
set(targets_to_export)
get_property(module_targets GLOBAL PROPERTY MITK_MODULE_TARGETS)
if(module_targets)
list(APPEND targets_to_export ${module_targets})
endif()
if(MITK_USE_BLUEBERRY)
if(MITK_PLUGIN_LIBRARIES)
list(APPEND targets_to_export ${MITK_PLUGIN_LIBRARIES})
endif()
endif()
export(TARGETS ${targets_to_export} APPEND
FILE ${MITK_EXPORTS_FILE})
set(MITK_EXPORTED_TARGET_PROPERTIES )
foreach(target_to_export ${targets_to_export})
get_target_property(autoload_targets ${target_to_export} MITK_AUTOLOAD_TARGETS)
if(autoload_targets)
set(MITK_EXPORTED_TARGET_PROPERTIES "${MITK_EXPORTED_TARGET_PROPERTIES}
set_target_properties(${target_to_export} PROPERTIES MITK_AUTOLOAD_TARGETS \"${autoload_targets}\")")
endif()
get_target_property(autoload_dir ${target_to_export} MITK_AUTOLOAD_DIRECTORY)
if(autoload_dir)
set(MITK_EXPORTED_TARGET_PROPERTIES "${MITK_EXPORTED_TARGET_PROPERTIES}
set_target_properties(${target_to_export} PROPERTIES MITK_AUTOLOAD_DIRECTORY \"${autoload_dir}\")")
endif()
get_target_property(deprecated_module ${target_to_export} MITK_MODULE_DEPRECATED_SINCE)
if(deprecated_module)
set(MITK_EXPORTED_TARGET_PROPERTIES "${MITK_EXPORTED_TARGET_PROPERTIES}
set_target_properties(${target_to_export} PROPERTIES MITK_MODULE_DEPRECATED_SINCE \"${deprecated_module}\")")
endif()
endforeach()
# ---------------- External projects -----------------
get_property(MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS_CONFIG GLOBAL PROPERTY MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS)
set(MITK_CONFIG_EXTERNAL_PROJECTS )
#string(REPLACE "^^" ";" _mitk_external_projects ${MITK_EXTERNAL_PROJECTS})
foreach(ep ${MITK_EXTERNAL_PROJECTS})
get_property(_components GLOBAL PROPERTY MITK_${ep}_COMPONENTS)
set(MITK_CONFIG_EXTERNAL_PROJECTS "${MITK_CONFIG_EXTERNAL_PROJECTS}
set(MITK_USE_${ep} ${MITK_USE_${ep}})
set(MITK_${ep}_DIR \"${${ep}_DIR}\")
set(MITK_${ep}_COMPONENTS ${_components})
")
endforeach()
foreach(ep ${MITK_EXTERNAL_PROJECTS})
get_property(_package GLOBAL PROPERTY MITK_${ep}_PACKAGE)
get_property(_components GLOBAL PROPERTY MITK_${ep}_COMPONENTS)
if(_components)
set(_components_arg COMPONENTS \${_components})
else()
set(_components_arg)
endif()
if(_package)
set(MITK_CONFIG_EXTERNAL_PROJECTS "${MITK_CONFIG_EXTERNAL_PROJECTS}
if(MITK_USE_${ep})
set(${ep}_DIR \${MITK_${ep}_DIR})
if(MITK_${ep}_COMPONENTS)
mitkMacroFindDependency(${_package} COMPONENTS \${MITK_${ep}_COMPONENTS})
else()
mitkMacroFindDependency(${_package})
endif()
endif()")
endif()
endforeach()
# ---------------- Tools -----------------
configure_file(${MITK_SOURCE_DIR}/CMake/ToolExtensionITKFactory.cpp.in
${MITK_BINARY_DIR}/ToolExtensionITKFactory.cpp.in COPYONLY)
configure_file(${MITK_SOURCE_DIR}/CMake/ToolExtensionITKFactoryLoader.cpp.in
${MITK_BINARY_DIR}/ToolExtensionITKFactoryLoader.cpp.in COPYONLY)
configure_file(${MITK_SOURCE_DIR}/CMake/ToolGUIExtensionITKFactory.cpp.in
${MITK_BINARY_DIR}/ToolGUIExtensionITKFactory.cpp.in COPYONLY)
# ---------------- Configure files -----------------
configure_file(mitkVersion.h.in ${MITK_BINARY_DIR}/mitkVersion.h)
configure_file(mitkConfig.h.in ${MITK_BINARY_DIR}/mitkConfig.h)
set(IPFUNC_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities/ipFunc)
set(UTILITIES_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities)
configure_file(mitkConfig.h.in ${MITK_BINARY_DIR}/mitkConfig.h)
configure_file(MITKConfig.cmake.in ${MITK_BINARY_DIR}/MITKConfig.cmake @ONLY)
write_basic_config_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake
VERSION ${MITK_VERSION_STRING} COMPATIBILITY AnyNewerVersion)
#-----------------------------------------------------------------------------
# MITK Applications
#-----------------------------------------------------------------------------
# This must come after MITKConfig.h was generated, since applications
# might do a find_package(MITK REQUIRED).
add_subdirectory(Applications)
if(MSVC AND TARGET MitkWorkbench)
set_directory_properties(PROPERTIES VS_STARTUP_PROJECT MitkWorkbench)
endif()
foreach(MITK_EXTENSION_DIR ${MITK_EXTENSION_DIRS})
set(MITK_APPLICATIONS_EXTENSION_DIR ${MITK_EXTENSION_DIR}/Applications)
get_filename_component(MITK_APPLICATIONS_EXTENSION_DIR ${MITK_APPLICATIONS_EXTENSION_DIR} ABSOLUTE)
if(EXISTS ${MITK_APPLICATIONS_EXTENSION_DIR}/CMakeLists.txt)
add_subdirectory(${MITK_APPLICATIONS_EXTENSION_DIR} Applications)
endif()
endforeach()
#-----------------------------------------------------------------------------
# MITK Examples
#-----------------------------------------------------------------------------
if(MITK_BUILD_EXAMPLES)
# This must come after MITKConfig.h was generated, since applications
# might do a find_package(MITK REQUIRED).
add_subdirectory(Examples)
endif()
#-----------------------------------------------------------------------------
# Print configuration summary
#-----------------------------------------------------------------------------
message("\n\n")
feature_summary(
DESCRIPTION "------- FEATURE SUMMARY FOR ${PROJECT_NAME} -------"
WHAT ALL
)
diff --git a/CTestConfig.cmake b/CTestConfig.cmake
index 81b115e712..3dabcd5f5a 100644
--- a/CTestConfig.cmake
+++ b/CTestConfig.cmake
@@ -1,5 +1,3 @@
-set(CTEST_PROJECT_NAME_SUPERBUILD "MITK-superbuild")
set(CTEST_PROJECT_NAME "MITK")
-set(CTEST_NIGHTLY_START_TIME "00:00:00 UTC")
-
+set(CTEST_NIGHTLY_START_TIME "23:00:00 UTC")
set(CTEST_SUBMIT_URL "https://cdash.mitk.org/submit.php?project=MITK")
diff --git a/CTestConfigSubProject.cmake.in b/CTestConfigSubProject.cmake.in
deleted file mode 100644
index 5bff13cd9b..0000000000
--- a/CTestConfigSubProject.cmake.in
+++ /dev/null
@@ -1,2 +0,0 @@
-set(CTEST_PROJECT_SUBPROJECTS @CTEST_PROJECT_SUBPROJECTS@)
-
diff --git a/Documentation/CMakeLists.txt b/Documentation/CMakeLists.txt
index 7ab4c59c20..d68002a508 100644
--- a/Documentation/CMakeLists.txt
+++ b/Documentation/CMakeLists.txt
@@ -1,216 +1,202 @@
-# Compile source code snippets
-add_subdirectory(Snippets)
-
# Different doxygen versions produce significantly different behaviour in the MITK documentation
# especially in regards to the MITK Qt assistant help files and markdown files.
# The HTML documentation is supposed to be build with Doxygen 1.8.7 or newer, the
# Qt assistant QCH files are supposed to be generated with Doxygen 1.8.7 or newer.
# So we check for 1.8.7 here and QCH generation support is checked in
# BlueBerry/CMakeLists.txt
set(supported_doxygen_version "1.8.7")
if(DOXYGEN_VERSION VERSION_LESS ${supported_doxygen_version})
MESSAGE(WARNING "Unsupported doxygen version ${DOXYGEN_VERSION}. The MITK HTML documentation has been tested to work with doxygen ${supported_doxygen_version} or newer.")
endif()
option(USE_DOT "Use dot program for generating graphical class diagrams with doxygen, if available" ON)
option(MITK_DOXYGEN_BUILD_ALWAYS "Always build the MITK documentation when building the default target" OFF)
option(MITK_DOXYGEN_GENERATE_QCH_FILES "Use doxygen to generate Qt compressed help files for MITK docs" OFF)
mark_as_advanced(USE_DOT MITK_DOXYGEN_BUILD_ALWAYS MITK_DOXYGEN_GENERATE_QCH_FILES)
if (MITK_DOXYGEN_GENERATE_QCH_FILES AND DOXYGEN_VERSION VERSION_LESS "1.8.7")
message(WARNING "> Forcing MITK_DOXYGEN_GENERATE_QCH_FILES to OFF because Doxygen version 1.8.7 or newer not found.")
set(MITK_DOXYGEN_GENERATE_QCH_FILES OFF CACHE BOOL "Use doxygen to generate Qt compressed help files for MITK docs" FORCE)
endif()
set(HAVE_DOT "NO")
if(DOXYGEN_DOT_EXECUTABLE AND USE_DOT)
set(HAVE_DOT "YES")
endif()
set(MITK_DOXYGEN_TAGFILE_NAME ${MITK_DOXYGEN_OUTPUT_DIR}/MITK.tag CACHE INTERNAL "MITK Doxygen tag file")
# This is relative to the working directory of the doxygen command
set(MITK_DOXYGEN_STYLESHEET mitk_doxygen_extra.css)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${MITK_DOXYGEN_STYLESHEET}
${CMAKE_CURRENT_BINARY_DIR}/${MITK_DOXYGEN_STYLESHEET} COPYONLY)
# Create QCH files for MITK and external projects
set(MITK_DOXYGEN_GENERATE_QHP "NO")
if(MITK_DOXYGEN_GENERATE_QCH_FILES)
find_program(QT_HELPGENERATOR_EXECUTABLE
NAMES qhelpgenerator qhelpgenerator-qt5 qhelpgenerator5
PATHS ${QT_BINARY_DIR}
DOC "The location of the the Qt help generator executable"
NO_DEFAULT_PATH
)
mark_as_advanced(QT_HELPGENERATOR_EXECUTABLE)
if(NOT QT_HELPGENERATOR_EXECUTABLE)
message(SEND_ERROR "The Qt help generator could not be found. Disabling qch generation")
else()
set(MITK_DOXYGEN_GENERATE_QHP "YES")
endif()
# The name of the generated MITK qch file, relative to the
# Doxygen HTML output folder
set(MITK_DOXYGEN_QCH_FILE "${MITK_BINARY_DIR}/MITK-${MITK_REVISION_ID}.qch")
# Generating ITK and VTK docs it not done yet
#option(MITK_DOXYGEN_GENERATE_VTK_QCH_FILE "Use doxygen to generate a Qt compressed help file for VTK docs" OFF)
#option(MITK_DOXYGEN_GENERATE_ITK_QCH_FILE "Use doxygen to generate a Qt compressed help file for ITK docs" OFF)
#mark_as_advanced(MITK_DOXYGEN_GENERATE_VTK_QCH_FILE MITK_DOXYGEN_GENERATE_ITK_QCH_FILE)
endif()
-
-if(MITK_USE_BLUEBERRY)
- file(RELATIVE_PATH _blueberry_doxygen_path ${MITK_DOXYGEN_OUTPUT_DIR}/html ${BLUEBERRY_DOXYGEN_OUTPUT_DIR}/html)
- set(BLUEBERRY_DOXYGEN_TAGFILE "${BLUEBERRY_DOXYGEN_TAGFILE_NAME}=${_blueberry_doxygen_path}")
- set(BLUEBERRY_DOXYGEN_LINK "<a class=\"el\" href=\"${_blueberry_doxygen_path}/index.html\">BlueBerry Documentation</a>")
- set(MITK_XP_LINK "\\ref mitkExtPointsIndex")
- configure_file(schema.css ${MITK_DOXYGEN_OUTPUT_DIR}/html/schema.css)
-
- set(MITK_DOXYGEN_ENABLED_SECTIONS "${MITK_DOXYGEN_ENABLED_SECTIONS} BLUEBERRY")
-endif(MITK_USE_BLUEBERRY)
-
# Compile a doxygen input filter for processing CMake scripts
include(mitkFunctionCMakeDoxygenFilterCompile)
mitkFunctionCMakeDoxygenFilterCompile(NAMESPACE "CMake")
# Configure some doxygen options
if(NOT MITK_DOXYGEN_INTERNAL_DOCS)
set(MITK_DOXYGEN_INTERNAL_DOCS "NO")
set(MITK_DOXYGEN_HIDE_FRIEND_COMPOUNDS "YES")
set(MITK_DOXYGEN_EXCLUDE_PATTERNS "*_p.* *Private.h */internal/*")
else()
set(MITK_DOXYGEN_HIDE_FRIEND_COMPOUNDS "NO")
set(MITK_DOXYGEN_EXCLUDE_PATTERNS "")
endif()
if(NOT MITK_DOXYGEN_GENERATE_TODOLIST)
set(MITK_DOXYGEN_GENERATE_TODOLIST "NO")
endif()
if(NOT MITK_DOXYGEN_GENERATE_BUGLIST)
set(MITK_DOXYGEN_GENERATE_BUGLIST "NO")
endif()
if(NOT MITK_DOXYGEN_HTML_DYNAMIC_SECTIONS)
set(MITK_DOXYGEN_HTML_DYNAMIC_SECTIONS "NO")
endif()
if(NOT MITK_DOXYGEN_UML_LOOK)
set(MITK_DOXYGEN_UML_LOOK "NO")
endif()
if(NOT MITK_DOXYGEN_GENERATE_DEPRECATEDLIST)
set(MITK_DOXYGEN_GENERATE_DEPRECATEDLIST "YES")
endif()
if(NOT DEFINED MITK_DOXYGEN_DOT_NUM_THREADS)
set(MITK_DOXYGEN_DOT_NUM_THREADS 0)
endif()
if(NOT DEFINED US_PLATFORM)
if(UNIX)
if(APPLE)
set(US_PLATFORM "US_PLATFORM_APPLE=1")
else()
set(US_PLATFORM "US_PLATFORM_LINUX=1")
endif()
set(US_PLATFORM "${US_PLATFORM} \\\nUS_PLATFORM_POSIX=1")
else()
set(US_PLATFORM "US_PLATFORM_WINDOWS=1")
endif()
endif()
# parse which plug-in documentation to activate
set(USERS_GUIDE_INPUT "${MITK_SOURCE_DIR}/Documentation/Doxygen/UserManual/")
if(MITK_USE_BLUEBERRY)
if(MITK_BUILD_ALL_PLUGINS)
set(USERS_GUIDE_INPUT "${USERS_GUIDE_INPUT} \\
${MITK_SOURCE_DIR}/Plugins/")
else()
foreach(mitk_plugin ${${CMAKE_PROJECT_NAME}_PLUGIN_LIBRARIES})
# we want each line to end in " \" and each directory be on a separate line
set(USERS_GUIDE_INPUT "${USERS_GUIDE_INPUT} \\
${${mitk_plugin}_SOURCE_DIR}/")
endforeach()
endif()
if(MITK_BUILD_EXAMPLES)
set(USERS_GUIDE_INPUT "${USERS_GUIDE_INPUT} \\
${MITK_SOURCE_DIR}/Examples/Plugins/")
endif()
endif()
# create output directories for the guides
file(MAKE_DIRECTORY ${MITK_DOXYGEN_OUTPUT_DIR}/Guides/Users_Guide/)
file(MAKE_DIRECTORY ${MITK_DOXYGEN_OUTPUT_DIR}/Guides/Developers_Guide/)
configure_file(doxygen.conf.in
${CMAKE_CURRENT_BINARY_DIR}/doxygen.conf)
configure_file(doxygen_users_guide.conf.in
${CMAKE_CURRENT_BINARY_DIR}/doxygen_users_guide.conf)
configure_file(doxygen_developers_guide.conf.in
${CMAKE_CURRENT_BINARY_DIR}/doxygen_developers_guide.conf)
if(MITK_DOXYGEN_BUILD_ALWAYS)
set(_doc_in_all "ALL")
else()
set(_doc_in_all "")
endif()
add_custom_target(doc ${_doc_in_all}
${DOXYGEN} ${CMAKE_CURRENT_BINARY_DIR}/doxygen.conf
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
)
add_custom_target(doc_usersguide
${DOXYGEN} ${CMAKE_CURRENT_BINARY_DIR}/doxygen_users_guide.conf
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
)
add_custom_target(doc_developersguide
${DOXYGEN} ${CMAKE_CURRENT_BINARY_DIR}/doxygen_developers_guide.conf
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
)
set_property(TARGET doc doc_usersguide doc_developersguide PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Documentation")
if(MITK_USE_BLUEBERRY)
# convert the extension points schema files into html
find_package(Ant)
set(BLUEBERRY_DOC_TOOLS_DIR "" CACHE PATH "Directory containing additional tools needed for generating the documentation")
if(ANT_FOUND AND BLUEBERRY_DOC_TOOLS_DIR)
list(APPEND MITK_XP_GLOB_EXPRESSIONS
${MITK_SOURCE_DIR}/Plugins/plugin.xml)
file(GLOB_RECURSE _plugin_xmls ${MITK_XP_GLOB_EXPRESSIONS})
mitkFunctionConvertXPSchema(INPUT ${_plugin_xmls}
OUTPUT_DIR "${MITK_DOXYGEN_OUTPUT_DIR}/html/extension-points/html"
TARGET_NAME mitkXPDoc
)
add_dependencies(doc mitkXPDoc)
else()
message(STATUS "Extension-point schema documentation generation disabled due to missing Ant and / or missing BlueBerry doc tools.")
endif()
endif(MITK_USE_BLUEBERRY)
#if(MITK_DOXYGEN_GENERATE_ITK_QCH_FILE)
# # add the command to generate the ITK documentation
# add_custom_target(doc-itk
# COMMAND ${DOXYGEN} ${CMAKE_CURRENT_BINARY_DIR}/doxygen.itk.conf)
# add_dependencies(doc doc-itk)
#endif()
#if(MITK_DOXYGEN_GENERATE_VTK_QCH_FILE)
# # add the command to generate the VTK documentation
# add_custom_target(doc-vtk
# COMMAND ${DOXYGEN} ${CMAKE_CURRENT_BINARY_DIR}/doxygen.vtk.conf)
# add_dependencies(doc doc-vtk)
#endif()
diff --git a/Documentation/Doxygen/1-Overview/Overview.dox b/Documentation/Doxygen/1-Overview/Overview.dox
index 35d1c6913b..5f25f2edf4 100644
--- a/Documentation/Doxygen/1-Overview/Overview.dox
+++ b/Documentation/Doxygen/1-Overview/Overview.dox
@@ -1,84 +1,88 @@
/**
\mainpage
![MITK Logo][logo]
-The [Medical Imaging Interaction Toolkit][mitk] (MITK) is a free and versatile open-source software project for development of medical image processing applications. It can be used as a C++ toolkit or application framework for software development.
-Below you find documentation targeting different
+The [Medical Imaging Interaction Toolkit][mitk] (MITK) is a free and versatile open-source software project for the development of medical image processing applications. It can be used as a C++ toolkit or application framework for software development.
+Below you can find documentation targeting different
usage scenarios:
<ul>
- <li> <b> I want to use MITK as an application </b>
+ <li> <b> You may want to use MITK as an application </b>
- You will use the MITK Workbench as an end user and will find user manuals in \ref UserManualPortal and \ref PluginListPage.
+ You may want to use the MITK Workbench as an end user and will find user manuals in \ref UserManualPortal and \ref PluginListPage.
-<li> <b> I want to develop my own software framework, and use some of MITK's data structures and algorithms</b>
+<li> <b> You may want to develop your own software framework, and use some of MITK's data structures and algorithms</b>
-You will use MITK as a toolkit and probably benefit most from the \ref BuildInstructionsPage and <a
+You may want to use MITK as a toolkit and probably benefit most from the \ref BuildInstructionsPage and <a
href="modules.html">MITK API Documentation</a>.
-<li> <b>I want to use the MITK and BlueBerry software framework to develop my own software </b>
+<li> <b>You may want to use the MITK and BlueBerry software framework to develop your own software </b>
-Here you have again two options.
+</ul>
+
+Here you have again two options:
-<li> <b>I want use the MITK Workbench and extend its capabilities</b>
-You are using MITK as software framework and writing your own modules and plugins for MITK. You want to read the \ref BuildInstructionsPage and further on \ref Development. Also you might want to take a look at our \ref CMAKE_FAQ.
+<ul>
+<li> <b>You may want to use the MITK Workbench and extend its capabilities</b>
+
+You may want to use MITK as a software framework and writing your own modules and plugins for MITK. You may want to read the \ref BuildInstructionsPage and \ref StartingDevelopment. Also, you might want to take a look at our \ref CMAKE_FAQ.
-<li> <b>I want to create my own application based on MITK</b>
+<li> <b>You may want to create your own application based on MITK</b>
-This is probably the most common way to use MITK. You are using MITK as software framework and building your own project and application using MITK. You want to read \ref HowToNewProject and the general information in \ref Development. Also you might want to take a look at our \ref CMAKE_FAQ.
+This is probably the most common way to use MITK. You may want to use MITK as a software framework and build your own project and application using MITK. You may want to read \ref HowToNewProject and the general information in \ref StartingDevelopment. Also, you might want to take a look at our \ref CMAKE_FAQ.
</ul>
<h2>About MITK</h2>
-MITK is an open-source framework that was originally developed as a common framework for Ph.D. students in the Division of Medical and Biological Informatics (MBI) at the German Cancer Research Center. MITK aims at supporting the development of leading-edge medical imaging software with a high degree of interaction.
+MITK is an open-source framework that was originally developed as a common framework for Ph.D. students in the Division of Medical and Biological Informatics (MBI) of the German Cancer Research Center. MITK aims to support the development of leading-edge medical imaging software with a high degree of interaction.
-MITK re-uses virtually anything from VTK and ITK. Thus, it is not at all a competitor to VTK or ITK, but an extension, which tries to ease the combination of both and to add features not supported by VTK or ITK.
+MITK re-uses virtually anything from VTK and ITK. Thus, it is not a competitor to VTK or ITK at all, but an extension, which tries to ease the combination of both, and to add features not supported by VTK or ITK.
Research institutes, medical professionals and companies alike can use MITK as a basic framework for their research and even commercial (thorough code research needed) software due to the BSD-like software license.
-Research institutes will profit from the high level of integration of ITK and VTK enhanced with data management, advanced visualization and interaction functionality in a single framework that is supported by a wide variety of researchers and developers. You will not have to reinvent the wheel over and over and can concentrate on your work.
+Research institutes will profit from the high level of integration of ITK and VTK, enhanced with data management, advanced visualization and interaction functionality in a single framework that is supported by a wide variety of researchers and developers. You don't need to reinvent the wheel over and over and can concentrate on your work.
-Medical Professionals will profit from MITK and the MITK applications by using its basic functionalities for research projects. But nonetheless they will be better off, unless they are programmers themselves, to cooperate with a research institute developing with MITK to get the functionalitiy they need. MITK and the MITK applications are not certified medical products and may be used in a research setting only. They must not be used in patient care.
+Medical Professionals will profit from MITK and MITK applications by using its basic functionalities for research projects. Nonetheless, they will be better off, unless they are programmers themselves, to cooperate with a research institute developing with MITK to get the functionality they need. MITK and MITK applications are not certified medical products and may be used in a research setting only. They must not be used in patient care.
<h2>License</h2>
Copyright (c) [German Cancer Research Center][dkfz].
MITK is available as free open-source software under a [BSD-style license][license].
<h2>Useful Links</h2>
- [Homepage][mitk]
- [Download][download]
- [Mailing List][mailinglist]
- [Bug Tracker][bugs]
[logo]: https://github.com/MITK/MITK/raw/master/mitk.png
[mitk]: http://mitk.org
[itk]: https://itk.org
[vtk]: http://vtk.org
[mitk-overview]: http://docs.mitk.org/nightly/Overview.html
[mitk-usermanual]: http://docs.mitk.org/nightly/UserManualPortal.html
[mitk-devmanual]: http://docs.mitk.org/nightly/DeveloperManualPortal.html
[mitk-apiref]: http://docs.mitk.org/nightly/usergroup0.html
[platforms]: http://docs.mitk.org/nightly/SupportedPlatformsPage.html
[dkfz]: https://www.dkfz.de
-[license]: https://github.com/MITK/MITK/blob/master/LICENSE.txt
+[license]: https://github.com/MITK/MITK/blob/master/LICENSE
[release-cycle]: http://mitk.org/MitkReleaseCycle
[download]: http://mitk.org/Download
[diffusion]: https://phabricator.mitk.org/source/mitk/
[contribute]: http://mitk.org/How_to_contribute
[cmake]: https://www.cmake.org
[build]: http://docs.mitk.org/nightly/BuildInstructionsPage.html
[mailinglist]: http://mitk.org/Mailinglist
[bugs]: https://phabricator.mitk.org/maniphest/
*/
diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox
index a34c39f999..0ec050c887 100644
--- a/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox
+++ b/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox
@@ -1,32 +1,32 @@
/**
\page PluginListGeneralPage List of General Purpose Plugins
\li \subpage org_mitk_views_basicimageprocessing
\li \subpage org_mitk_views_datamanager
\li \subpage org_mitk_views_properties
\li \subpage org_mitk_editors_dicombrowser
\li \subpage org_mitk_gui_qt_dicominspector
\li \subpage org_mitk_views_imagecropper
\li \subpage org_mitk_views_imagenavigator
- \li \subpage org_blueberry_ui_qt_log
+ \li \subpage org_blueberry_views_logview
\li \subpage org_mitk_gui_qt_matchpoint_algorithm_batch
- \li \subpage org_mitk_views_qt_matchpoint_algorithm_browser
- \li \subpage org_mitk_views_qt_matchpoint_algorithm_control
- \li \subpage org_mitk_views_qt_matchpoint_evaluator
- \li \subpage org_mitk_views_qt_matchpoint_framereg
- \li \subpage org_mitk_views_qt_matchpoint_manipulator
+ \li \subpage org_mitk_views_matchpoint_algorithm_browser
+ \li \subpage org_mitk_views_matchpoint_algorithm_control
+ \li \subpage org_mitk_views_matchpoint_evaluator
+ \li \subpage org_mitk_views_matchpoint_framereg
+ \li \subpage org_mitk_views_matchpoint_manipulator
\li \subpage org_mitk_views_matchpoint_mapper
- \li \subpage org_mitk_views_qt_matchpoint_visualizer
+ \li \subpage org_mitk_views_matchpoint_visualizer
\li \subpage org_mitk_gui_qt_measurementtoolbox
\li \subpage org_mitk_views_moviemaker
\li \subpage org_mitk_views_multilabelsegmentation
\li \subpage org_mitk_views_pointsetinteraction
\li \subpage org_mitk_gui_qt_python
\li \subpage org_mitk_gui_qt_remeshing
\li \subpage org_mitk_views_screenshotmaker
\li \subpage org_mitk_views_segmentation
\li \subpage org_mitk_gui_qt_flow_segmentation
\li \subpage org_mitk_gui_qt_viewnavigator
\li \subpage org_mitk_views_volumevisualization
*/
diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox
index 2bf2a11b12..c4d4470da7 100644
--- a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox
+++ b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox
@@ -1,84 +1,84 @@
/**
\page PluginListPage MITK Plugin Manuals
The plugins and bundles provide much of the extended functionality of MITK. Each encapsulates a solution to a problem and associated features. This way one can easily assemble the necessary capabilites for a workflow without adding a lot of bloat, by combining plugins as needed.
\subpage PluginListGeneralPage
<ul>
<li> \ref org_mitk_views_basicimageprocessing </li>
<li> \ref org_mitk_views_datamanager </li>
<li> \ref org_mitk_editors_dicombrowser </li>
<li> \ref org_mitk_gui_qt_dicominspector </li>
<li> \ref org_mitk_gui_qt_flowapplication </li>
<li> \ref org_mitk_views_imagecropper </li>
<li> \ref org_mitk_views_imagenavigator </li>
- <li> \ref org_blueberry_ui_qt_log </li>
+ <li> \ref org_blueberry_views_logview </li>
<li> \ref org_mitk_views_matchpoint_algorithm_browser</li>
<li> \ref org_mitk_views_matchpoint_algorithm_control</li>
<li> \ref org_mitk_views_matchpoint_evaluator</li>
<li> \ref org_mitk_views_matchpoint_framereg</li>
<li> \ref org_mitk_views_matchpoint_manipulator</li>
<li> \ref org_mitk_views_matchpoint_mapper</li>
<li> \ref org_mitk_views_matchpoint_visualizer</li>
<li> \ref org_mitk_gui_qt_measurementtoolbox </li>
<li> \ref org_mitk_views_moviemaker </li>
<li> \ref org_mitk_views_multilabelsegmentation </li>
<li> \ref org_mitk_views_pointsetinteraction </li>
<li> \ref org_mitk_gui_qt_python </li>
<li> \ref org_mitk_gui_qt_remeshing </li>
<li> \ref org_mitk_views_screenshotmaker </li>
<li> \ref org_mitk_views_segmentation </li>
<li> \ref org_mitk_gui_qt_flow_segmentation </li>
<li> \ref org_mitk_gui_qt_viewnavigator </li>
<li> \ref org_mitk_views_volumevisualization</li>
+ <li> \ref org_mitk_views_properties </li>
</ul>
\subpage PluginListSpecificPage
<ul>
- <li> \ref org_mitk_views_properties </li>
<li> \ref org_mitk_gui_qt_aicpregistration </li>
<li> \ref org_mitk_gui_qt_cest </li>
<li> \ref org_mitk_gui_qt_classificationsegmentation </li>
<li> \ref org_mitk_views_cmdlinemodules </li>
- <li> \ref org_mitk_gui_qt_pharmacokinetics_concentration_mri</li>
+ <li> \ref org_mitk_views_pharmacokinetics_concentration_mri</li>
<li> \ref org_mitk_views_pharmacokinetics_mri</li>
<li> \ref org_mitk_gui_qt_pharmacokinetics_pet</li>
<li> \ref org_mitk_gui_qt_eventrecorder </li>
<li> \ref org_mitk_gui_qt_examples </li>
<li> \ref org_mitk_gui_qt_geometrytools </li>
<li> \ref org_mitk_gui_qt_igtexample </li>
<li> \ref org_mitk_gui_qt_igtlplugin</li>
<li> \ref org_mitk_gui_qt_igttracking</li>
<li> \ref org_mitk_gui_qt_igttrackingsemiautomaticmeasurement</li>
<li> \ref org_mitk_views_imagestatistics</li>
<li> \ref org_mitk_gui_qt_lasercontrol</li>
- <li> \ref org_mitk_gui_qt_fit_demo </li>
+ <li> \ref org_mitk_views_fit_demo </li>
<li> \ref org_mitk_gui_qt_fit_genericfitting </li>
- <li> \ref org_mitk_gui_qt_fit_inspector </li>
+ <li> \ref org_mitk_views_fit_inspector </li>
<li> \ref org_mitkexamplesopencv</li>
<li> \ref org_mitk_gui_qt_overlaymanager</li>
<li> \ref org_mitk_gui_qt_mitkphenotyping</li>
<li> \ref org_mitk_gui_qt_photoacoustics_pausmotioncompensation</li>
<li> \ref org_mitk_example_gui_pcaexample</li>
<li> \ref org_mitk_gui_qt_preprocessing_resampling</li>
- <li> \ref org_mitk_gui_qt_pharmacokinetics_curvedescriptor</li>
+ <li> \ref org_mitk_views_pharmacokinetics_curvedescriptor</li>
<li> \ref org_mitk_gui_qt_photoacoustics_imageprocessing</li>
<li> \ref org_mitk_gui_qt_pharmacokinetics_simulation</li>
<li> \ref org_mitk_gui_qt_pointsetinteractionmultispectrum</li>
<li> \ref org_mitk_gui_qt_renderwindowmanager</li>
<li> \ref org_mitk_gui_qt_photoacoustics_spectralunmixing</li>
<li> \ref org_mitk_gui_qt_spectrocamrecorder</li>
<li> \ref org_surfacematerialeditor</li>
<li> \ref org_toftutorial</li>
<li> \ref org_blueberry_ui_qt_objectinspector</li>
<li> \ref org_mitk_gui_qt_ultrasound</li>
<li> \ref org_mitk_gui_qt_igt_app_echotrack </li>
<li> \ref org_mitk_gui_qt_xnat</li>
</ul>
*/
diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox
index 8be8a5f620..c470916167 100644
--- a/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox
+++ b/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox
@@ -1,45 +1,45 @@
/**
\page PluginListSpecificPage List of Application-specific Plugins
\li \subpage org_mitk_gui_qt_aicpregistration
\li \subpage org_mitk_gui_qt_cest
\li \subpage org_mitk_gui_qt_classificationsegmentation
\li \subpage org_mitk_gui_qt_flowapplication
\li \subpage org_mitk_views_cmdlinemodules
- \li \subpage org_mitk_gui_qt_pharmacokinetics_concentration_mri
+ \li \subpage org_mitk_views_pharmacokinetics_concentration_mri
\li \subpage org_mitk_views_pharmacokinetics_mri
\li \subpage org_mitk_gui_qt_pharmacokinetics_pet
\li \subpage org_mitk_gui_qt_eventrecorder
\li \subpage org_mitk_gui_qt_examples
\li \subpage org_mitk_gui_qt_geometrytools
\li \subpage org_mitk_gui_qt_igtexample
\li \subpage org_mitk_gui_qt_igtlplugin
\li \subpage org_mitk_gui_qt_igttracking
\li \subpage org_mitk_gui_qt_igttrackingsemiautomaticmeasurement
\li \subpage org_mitk_views_imagestatistics
\li \subpage org_mitk_gui_qt_lasercontrol
- \li \subpage org_mitk_gui_qt_fit_demo
+ \li \subpage org_mitk_views_fit_demo
\li \subpage org_mitk_gui_qt_fit_genericfitting
- \li \subpage org_mitk_gui_qt_fit_inspector
+ \li \subpage org_mitk_views_fit_inspector
\li \subpage org_mitkexamplesopencv
\li \subpage org_mitk_gui_qt_overlaymanager
\li \subpage org_mitk_gui_qt_mitkphenotyping
\li \subpage org_mitk_gui_qt_photoacoustics_pausmotioncompensation
\li \subpage org_mitk_example_gui_pcaexample
\li \subpage org_mitk_gui_qt_preprocessing_resampling
- \li \subpage org_mitk_gui_qt_pharmacokinetics_curvedescriptor
+ \li \subpage org_mitk_views_pharmacokinetics_curvedescriptor
\li \subpage org_mitk_gui_qt_photoacoustics_imageprocessing
\li \subpage org_mitk_gui_qt_pharmacokinetics_simulation
\li \subpage org_mitk_gui_qt_pointsetinteractionmultispectrum
\li \subpage org_mitk_gui_qt_renderwindowmanager
\li \subpage org_mitk_gui_qt_photoacoustics_spectralunmixing
\li \subpage org_mitk_gui_qt_spectrocamrecorder
\li \subpage org_surfacematerialeditor
\li \subpage org_blueberry_ui_qt_objectinspector
\li \subpage org_toftutorial
\li \subpage org_mitk_gui_qt_ultrasound
\li \subpage org_mitk_gui_qt_igt_app_echotrack
\li \subpage org_mitk_gui_qt_xnat
*/
\ No newline at end of file
diff --git a/Documentation/Doxygen/3-DeveloperManual/Concepts/DataInteractionTechnical.dox b/Documentation/Doxygen/3-DeveloperManual/Concepts/DataInteractionTechnical.dox
index aaf338b57f..81a9c4f992 100644
--- a/Documentation/Doxygen/3-DeveloperManual/Concepts/DataInteractionTechnical.dox
+++ b/Documentation/Doxygen/3-DeveloperManual/Concepts/DataInteractionTechnical.dox
@@ -1,115 +1,119 @@
/**
\page DataInteractionTechnicalPage Interaction Concept Implementation
\tableofcontents
This page describes some technicalities of the implementation and the workflow, for a detailed list of tutorials see \ref FurtherReadingInteraction .
\section DataInteractionTechnicalPage_Introduction Description of Interaction Concept Implementation in MITK
\section DataInteractionTechnicalPage_DispatcherSection Dispatcher
After an event is received by the mitk::Dispatcher it is given to a mitk::DataInteractor that has to decide if it can process this event.
On a high level this is done by the mitk::EventStateMachine.
First the state machine asks if the received event is known in the
configuration. If it is, the matching variant name is returned. Then the state machine checks if there exists a transition
in its current state that is triggered by this event variant. If this is the case all actions that are associated with this transition
are queried and executed. The actions themselves are implemented on mitk::DataInteractor level. The following diagram illustrates the process:
\imageMacro{sm_and_config.png,"",16}
Each mitk::BaseRenderer creates a mitk::BindDispatcherInteractor object which encapsulates the connection between the mitk::DataStorage and
the mitk::Dispatcher, and thereby allowing a mitk::DataInteractor to register with a mitk::Dispatcher when only knowing the mitk::DataNode.
mitk::BindDispatcherInteractor creates a new mitk::Dispatcher object and registers for mitk::DataNode events at the mitk::DataStorage, as a callback function the
dispatchers AddDataInteractor() and RemoveDataInteractor() functions are set.
\dot
digraph {
node [shape=record, fontname=Helvetica, fontsize=10];
a [ label="{BaseRenderer|m_BindDispatcherInteractor}"];
b [ label="{BindDispatcherInteractor|m_Dispatcher\n m_DataStorage}" ];
c [ label="Dispatcher" ];
d [ label="DataStorage" ];
a -> b;
b -> c;
b -> d;
}
\enddot
This way the mitk::Dispatcher is notified about all changes regarding
DataNodes that are shown in the mitk::BaseRenderer. When a node is added, remove or modified the mitk::Dispatcher can check if a mitk::DataInterator is set,
and accordingly add or remove this mitk::DataInteractor from its internal list.
\dot
digraph {
- node [shape=record, fontname=Helvetica, fontsize=10];
- d [ label="DataInteractor" ];
- a [ label="DataNode" ];
- b [ label="DataStorage" ];
- c [ label="Dispatcher" ];
+ node [shape=box fontname=Helvetica fontsize=10]
+
+ { rank=same b c a }
+ { rank=same e }
+
+ d [ label="DataInteractor" ]
+ a [ label="DataNode" ]
+ b [ label="DataStorage" ]
+ c [ label="Dispatcher" ]
e [ label="BaseRenderer"]
- edge [fontname=Helvetica, fontsize=10]
- d -> a [label="SetDataInteractor(this)"];
- a -> b [label="Modified()"];
- b -> c [label="NodeModified(dataNode)"];
- e -> c [label="HandleEvent(interactionEvent)"];
- { rank=same; b c a }
- { rank=same; e }
+
+ edge [fontname=Helvetica fontsize=10]
+
+ d -> a [label="SetDataInteractor(this)"]
+ a -> b [label="Modified()"]
+ b -> c [label="NodeModified(dataNode)"]
+ e -> c [label="HandleEvent(interactionEvent)"]
}
\enddot
Events that are generated within the scope of the mitk::BaseRenderer are sent to the associated mitk::Dispatcher to be handled.
\subsection DataInteractionTechnicalPage_DispatcherEventDistSection Event Distribution
A mitk::Dispatcher can operate in different processing modes, which determine how the interactor that receives an event is chosen.
These modes are managed and set by the mitk::Dispatcher itself.
<ul>
<li> \b Regular: \n
DataInteractors are sorted by their layer, and distribution is stared with the top-most.
<li> <b>Connected Mouse Action</b>: \n
A connected mouse action is described by the sequence of Mouse-Press, (optionally) Mouse-Move , Mouse-Release Events.\n
Within this sequence all events are sent to the same mitk::DataInteractor, the one which received the event from the Mouse-Press action.\n
\b m_ConnectedMouseAction - is set to true, when a Mouse-Down Event occurs and a DataInterator takes the event and
\b m_SelectedInteractor is then set to this DataInteractor.\n
\b m_ConnectedMouseAction is reset to false, after the Mouse-Release Event occurs,\n
while it is true, the m_SelectedInteractor is the only one that receives Mouse-Events.
<li> <b>Grab Input</b>:\n
Whenever a mitk::DataInteractor performs a state change into a state that is marked by the grab input-tag, the mitk::Dispatcher switches into this mode.
As long as it is in this mode ONLY the selected mitk::DataInteractor will receive the event. This mode is ended when the mitk::DataInteractor
switches back to a state without a tag/ or the REGULAR-tag.\n
\note In this mode mitk::InteractionEventObserver instances will NOT receive the events.
<li> \b Prefer \b Input: \n
Basically works as Grab Input, with the difference that if the mitk::DataInteractor is in the prefer input state but cannot process the event offered,
it will be offered to the other interactors in the regular way.\n
In this mode mitk::InteractionEventObserver instances ARE informed.
</ul>
\section DataInteractionTechnicalPage_StateMachineSection State Machine & Configuration
A mitk::EventStateMachine points to a \b state, which in turn references \b transitions
(which describe a change from one state to another) and \b actions (indicating which functions are executed when a transition is taken).
\dot
digraph {
node [shape=record, fontname=Helvetica, fontsize=10];
d [ label="{StateMachine|m_CurrentState}" ];
a [ label="{StateMachineState|m_Transitions}" ];
b [ label="{StateMachineTransitions|m_Actions}"];
c [ label="{StateMachineAction}"];
edge [fontname=Helvetica, fontsize=10]
d -> a [label="1 : 1"];
a -> b [label="1 : n"];
b -> c [label="1 : n"];
}
\enddot
*/
diff --git a/Documentation/Doxygen/3-DeveloperManual/Starting/FirstSteps/NewModule.dox b/Documentation/Doxygen/3-DeveloperManual/Starting/FirstSteps/NewModule.dox
index 609cdd831d..9170bdd620 100644
--- a/Documentation/Doxygen/3-DeveloperManual/Starting/FirstSteps/NewModule.dox
+++ b/Documentation/Doxygen/3-DeveloperManual/Starting/FirstSteps/NewModule.dox
@@ -1,122 +1,122 @@
/**
\page NewModulePage How to create a new MITK Module
\section NewModulePageCreateFolder Create a Folder for your Module
First, create a folder for your module within /Modules e.g. 'NewModule'.
-You need to add the new Folder to the CMakeLists.txt in the Module directory as well as well.
-Open /Modules/CMakeLists.txt, insert it into the set(module_dirs) section.
+You need to add the new folder to the ModuleList.cmake file in the Module directory as well.
+Open /Modules/ModuleList.cmake, append the folder to the MITK_MODULES list.
\code
-set(module_dirs
+set(MITK_MODULES
...
NewModule
)
\endcode
A simple example module is provided in the MITK/Examples/FirstSteps/NewModule directory, it includes a new data type
(more information at \ref NewDataTypePage) and adds a MiniApp for that data type (more information at \ref MiniAppCommandLineToolHowToPage).
Within the module we recommend using a Unix like directory structure. This helps others finding their way around your code.
Depending on your use case you might not need every directory.
\code
NewModule/
autoload/
cmdapps/
doc/
include/
resource/
src/
test/
\endcode
Subsequently a quick description of what each directory contains.
\subsection NewModulePageCreateFolderAutoload autoload
This directory should not directly contain files. Instead it contains further directories each of which is its own module.
These modules provide functionality which should be available at application start, but will not be included by other modules.
Examples would be a module registering readers/writers or providing an interface for specific hardware.
For an example of an autoload module take a look at NewModule/autoload/IO.
\subsection NewModulePageCreateFolderCmdApps cmdapps
This directory contains all cmdapps (command line tools) related to your module. For more information see \ref MiniAppCommandLineToolHowToPage.
\subsection NewModulePageCreateFolderDoc doc
This directory contains the documentation for your module.
\subsection NewModulePageCreateFolderInclude include
This directory contains all header files which might be included by other modules.
\subsection NewModulePageCreateFolderResource resource
This directory contains resources needed by your module, such as xmls, images or similar.
\subsection NewModulePageCreateFolderSrc src
This directory contains source and header files which should not be included by other modules. Further subdivision can help keeping it organized.
(e.g. src/DataManagement src/Algorithms)
\subsection NewModulePageCreateFolderTest test
This directory contains all tests for your module.
\section NewModulePageCreateCMakeLists Create CMakeLists.txt
Within your module create a CMakeLists.txt using the MITK_CREATE_MODULE macro:
An example:
\include Examples/FirstSteps/NewModule/CMakeLists.txt
If you do not choose a module name, one will be generated based on the folder name (In this case the resulting name will be MitkNewModule).
This name has to be unique across the entire project in order to avoid collisions. It should only contain Letters (both upper- and lowercase),
no numbers, no underscores etc.
An example of an autoload module that sets its own name is:
\include Examples/FirstSteps/NewModule/autoload/IO/CMakeLists.txt
the resulting name is MitkNewModuleIO.
\note For more information about the parameters of the new module macro see mitkFunctionCreateModule.cmake
\section NewModulePageCreatefilesdotcmake Create files.cmake
Next, create a new file and name it files.cmake, containing the files of your module.
An example:
\include Examples/FirstSteps/NewModule/autoload/IO/files.cmake
If you do not add a source file here it will not be compiled, unless it is included elsewhere.
\section NewModulePageCreateTestingEnvironment Set up the Test environment
Providing tests for your code is a very good way to save yourself a lot of debugging time and ensure
consistency. An example of a small test environment is provided in the NewModule example.
Again you need a CMakeLists.txt, e.g.:
\include Examples/FirstSteps/NewModule/test/CMakeLists.txt
a files.cmake, e.g.:
\include Examples/FirstSteps/NewModule/test/files.cmake
and an actual test, e.g.:
\include Examples/FirstSteps/NewModule/test/mitkExampleDataStructureTest.cpp
For more information regarding tests please refer to \ref AboutTestingPage.
That's it! Enjoy your new module!
-*/
\ No newline at end of file
+*/
diff --git a/Documentation/Doxygen/3-DeveloperManual/Starting/GettingToKnow/StyleGuideAndNotes.dox b/Documentation/Doxygen/3-DeveloperManual/Starting/GettingToKnow/StyleGuideAndNotes.dox
index 2ea36ad6b4..f06de7fe39 100644
--- a/Documentation/Doxygen/3-DeveloperManual/Starting/GettingToKnow/StyleGuideAndNotes.dox
+++ b/Documentation/Doxygen/3-DeveloperManual/Starting/GettingToKnow/StyleGuideAndNotes.dox
@@ -1,469 +1,469 @@
/**
\page StyleGuideAndNotesPage The MITK Style Guide and Technical Notes
\tableofcontents
The following document is a description of the accepted coding style for the Medical Imaging Interaction Toolkit (MITK). Developers who wish to contribute code to MITK should read and adhere to the standards described here.
\section StyleGuideAndNotesPage_NameConventions Naming Conventions
\li Using case change to indicate separate words
@code
ImageFilter
PixelType
DataStorage
NodePredicateProperty
@endcode
\li Underscores are not used e.g. Image_Filer, _Node
\li Variable names should convey the meaning behind the code
@code
BoundingBox::Pointer boundingBox = BoundingBox::New();
@endcode
\li Names are generally spelled out
@code
mitk::DataNode* node;
@endcode
\li Abbreviation are allowable when in common use e.g. ROI for Region of
Interest
\subsection StyleGuideAndNotesPage_NamingClasses Naming Classes
\li Classes are named beginning with a capital letter
\li Classes are named according to the following general rule:
@code
class name = <algorithm><input><concept>
@endcode
\li Examples of concepts \n
<b>Accessor</b>: Access and convert between types e.g. NullScalarAccessor \n
<b>Container</b>: A container of objects such as points or images e.g. VectorContainer \n
<b>Filter</b>: A class that participates in the data processing pipeline e.g. AddImageFilter \n
<b>Mapper</b>: Transform data from one form into another e.g. ContourMapper2D \n
<b>Reader/Writer</b>: A class that reads/writes a single data object e.g. VtkSurfaceReader \n
\subsection StyleGuideAndNotesPage_NamingFiles Naming Files
\li MITK classes like @a ExampleClass should be in namespace @a mitk and their corresponding files should be named @a mitkExampleClass.h/.cpp.
@code
mitk::DataStorage
@endcode
\li Qt specific MITK classes like @a QmitkListView should have the prefix Qmitk in their class names and their corresponding files should be named @a QmitkListView.h/.cpp.
@code
QmitkDataStorageComboBox
@endcode
\li Header Files ends with an .h and
\li Implementation Files with an .cpp or .txx for a template class
\subsection StyleGuideAndNotesPage_NamingMethodsandFunctions Naming Methods and Functions
\li Functions and methods are named beginning with a capital letter
\li Referring to class methods in code, an explicit this-> pointer should be
used
@code
mitk::DataStorage::SetOfObjects::ConstPointer all = this->GetAll();
@endcode
\subsection StyleGuideAndNotesPage_NamingSignalSlots Naming Signal/Slots Methods and Functions
\li Slots are named according to the following general rule
@code
On[variable name who send the signal][signal]();
@endcode
\li Example
@code
connect( loadImagePushButton, SIGNAL( clicked(bool ) ),
SLOT( OnLoadImagePushButtonClicked( bool ) ) );
void mitk::Image::OnLoadImagePushButtonClicked( bool )
{
... Do something ...
}
@endcode
\li Signals are named according to the following general rule
@code
Signal[MethodName]();
@endcode
\li Example
@code
emit SignalFinishedSegmentation();
@endcode
\subsection StyleGuideAndNotesPage_NamingClassDataMembers Naming Class Data Members
\li Class data members are prefixed with m_
@code
m_Volumes
m_OffsetTable
m_ImageMask
@endcode
\li An exception to this rule, Qt class Data members are not prefixed and begin with a lower-case letter
@code
loadImageButton
closeImageAction
@endcode
\subsection StyleGuideAndNotesPage_NamingLocalVariables Naming Local Variables
\li Local variables first letter is lower-case
@code
offset
data
slicesIt
@endcode
\subsection StyleGuideAndNotesPage_NamingQtVariables Naming Qt Variables
\li GUI variables ends with name of used QT tool.
@code
QPushButton* loadImagePushButton;
QAction* closeImageAction;
QCheckBox* hideImageCheckBox;
QRadioButton* binaryImageRadioButton;
@endcode
\subsection StyleGuideAndNotesPage_NamingTypedefs Naming Typedefs
\li Typedefs must end in the word Type
@code
typedef TPixel PixelType;
typedef itk::Image< TPixel, VImageDimension > ImageType;
typedef std::list<mitk::Image::Pointer> ImageListType;
@endcode
\section StyleGuideAndNotesPage_Pointer Pointer
\subsection StyleGuideAndNotesPage_DeclarationofPointers Declaration of Pointers
\li Position of * pointers are connected with the variable
@code
int *counter;
@endcode
\li Analog to references
@code
int &counter;
@endcode
\subsection StyleGuideAndNotesPage_SmartPointer SmartPointer
\li SmartPointers must be used for classes that have itk::Object as a base
class.
\li Assignment of a just created instance to a normal pointer results in a
crash, since the reference count is decreased immediately to zero and the
object is destroyed.
@code
itk::Object::Pointer object = itk::Object::New();
@endcode
\li Static declarations are also forbidden and result into an exception when
the scope of the variable is left, because the destructor is called while the
reference count is still greater than zero.
\li Note that using smart pointers requires using real (normal) pointers when
setting input. If you want to return a newly created smart pointer that
is not also kept within the class (e.g., if you write a Clone method), you
have to return a smart pointer on output (compare itkMacro.h). If the
smart pointer is kept within the class, returning a real (normal) pointer
is sufficient.
\li Testing a SmartPointer against NULL is done with the IsNull() and Is-
NotNull() methods. A simple ==NULL issues a warning.
\section StyleGuideAndNotesPage_Namespace Namespace
\li MITK classes should be in namespace @a mitk
@code
mitk::Image::Pointer mitk::ImageGenerator::MakeImage()
{
// already in namespace mitk here!
Image::Pointer image = mitk::Image::New();
ImageDecorator::Pointer decorator = mitk::ImageDecorator::New();
d->Decorate( image );
return image;
}
@endcode
\li Constants in MITK for mitk::Operation and mitk::Action are set in
namespace, so don't forget to add prefix mitk::
@code
switch (actionId)
{
case mitk::AcMOVESELECTED:
....Do something ...
break;
default:
break;
}
@endcode
\section StyleGuideAndNotesPage_CodeLayoutandIndentation Code Layout and Indentation
\subsection StyleGuideAndNotesPage_GeneralLayout General Layout
\li Each line of code should take no more than 120 characters.
\li Use lots of whitespace to separate logical blocks of code, intermixed with
comments
-\li <b>DO NOT USE TABS.</b> The standard indention is <b>2 spaces</b> (see <a href="http://www.insightsoftwareconsortium.org/documents/policies/Style.pdf">ITK Style Guide</a>). Configure your
+\li <b>DO NOT USE TABS.</b> The standard indention is <b>2 spaces</b> (see <a href="https://itk.org/Wiki/images/c/c6/ITKStyle.pdf">ITK Style Guide</a>). Configure your
editor accordingly.
\li DO NOT USE trailing whitespaces
\li Declaration of variables should be one declaration per line
@code
int sliceNumber;
char* stringName;
ImageType::Pointer image;
@endcode
\subsection StyleGuideAndNotesPage_ClassLayout Class Layout
\li Copyright
@code
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
@endcode
\li Includes [A .. Z]
@code
#include "... .h"
@endcode
\li Namespace
@code
namespace mitk
{
@endcode
DO NOT litter your header with "using namespace;"!
\li Class (Template)
@code
template <class TType>
class ClassName : public ImageBase<VImageDimension>
{
@endcode
\li Typedefs
@code
public:
....typedefs....
@endcode
\li Methods
@code
public:
....methods....
protected:
....methods....
private:
....methods....
@endcode
\li QT Signals
@code
signals:
Signal...();
@endcode
\li QT Slots
@code
public slots:
On...();
protected slots:
On...();
@endcode
\li Data Member
@code
private/protected:
....class data members....
};
}
#endif
@endcode
\section StyleGuideAndNotesPage_UseofBraces Use of Braces
\li Used to delimit the scope of an if, for, while, switch.
\li Braces are placed on a line by themselves:
@code
for ( unsigned int i = 0; i < 3; ++i )
{
... do something ...
}
@endcode
or
@code
if ( condition )
{
... do something ...
}
else if ( other condition )
{
... do something ...
}
else
{
... do something ...
}
@endcode
\li You can choose to use braces on a line with a code block when the block
consists of a single line:
@code
if ( condition ) { foo = 1; }
else if ( condition2 ) { foo = 3; }
else { return; }
@endcode
or
@code
for ( unsigned int i = 0; i < 3; ++i) { x[i] = 0.0; }
@endcode
\section StyleGuideAndNotesPage_IncludeGuards Include Guards
\li #inlcude guard is a particular construct used to avoid the problem of
double inclusion when dealing with the #include directive.
\li Naming convention for #inlcude guards is: ClassName_h
\li Following example demonstrates a problem that can arise if #include guards
are missing: Here, the file child.cpp has indirectly included two copies of the text in the
header file grandfather.h. This causes a compilation error, since the structure
type foo is apparently defined twice.
@code
grandfather.h struct foo
{
int m Member;
};
father.h #include "grandfather.h"
child.h #include "grandfather.h"
#include "father.h"
@endcode
\subsection StyleGuideAndNotesPage_Useofincludeguards Use of #include guards
\li Here, the first inclusion of grandfather.h causes the macro grandfather h to
be defined. Then, when child.cpp includes grandfather.h the second time,
the #ifndef test fails, and the preprocessor skips down to the #endif, thus
avoiding the second definition of struct foo. The program compiles correctly.
@code
grandfather.h #ifndef grandfather h
#define grandfather h
struct foo
{
int m Member;
};
father.h #include "grandfather.h"
child.h #include "grandfather.h"
#include "father.h"
@endcode
\section StyleGuideAndNotesPage_TechnicalNotes Some Technical Notes
\li Use forward declarations in header files wherever possible. Only include those header files in a header file
that are really necessary. Include the rest in the implementation file.
\li For classes inheriting directly or indirectly from @a itk::LightObject (most of the MITK-classes do so), the
class definition should include the mitkClassMacro. Additionally, if the class can be instantiated (normally the case,
if the class is not abstract) and has @em only a constructor without parameters, the constructor should be declared
protected and the @a itkFactorylessNewMacro should be used to create a @a New() method for instantiation. Here is an example:
@code
class ExampleClass : public SuperClassOfTheExampleClass
{
public:
mitkClassMacro(ExampleClass, SuperClassOfTheExampleClass)
itkFactorylessNewMacro(Self)
[...]
protected:
ExampleClass();
virtual ~ExampleClass();
}
@endcode
\li Set- and Get-methods can be created with the macros @a itkSetObjectMacro(name,type) and
@a itkGetObjectMacro(name,type), respectively, if the @a type is derived from @a itk::LightObject or
@a itk::Object. There are also macros for other types, e.g., strings, see
<a href="http://www.itk.org/Doxygen12/html/itkMacro_8h.html">itkMacro.h</a>.
\li When using inner classes of a parent class which is templated, you have
to use the keyword @a typename for gcc 3.x and standard compliance. For example,
@a TreeChangeListener is an inner class of @a Tree, therefore use:
@code
class LinkedTree : public Tree<T>
{
public:
typedef typename LinkedTree<T>::TreeChangeListener TreeChangeListener;
[...]
}
@endcode
Another example:
@code
typename std::vector<TreeChangeListener*>::iterator pos = treeChangeListenerList.begin();
@endcode
@a iterator is an inner class of @a vector.
\li Constants in MITK for mitk::Operation and mitk::Action are set in namespace, so don't forget to add prefix @a mitk::
@code
switch (actionId)
{
case mitk::AcMOVESELECTED:
@endcode
Prefixes for the constants are to be used like corresponding others. See file @a Interactions\\mitkBaseInteraction\\mitkInteractionConst.h for further details.
\section StyleGuideAndNotesPage_AutomaticCodeFormatting Automatic Code Formatting
We offer a .clang-format file, which can be used to automatically format code acceptably.
\include .clang-format
For an explanation of the different options check out http://clang.llvm.org/docs/ClangFormatStyleOptions.html
*/
diff --git a/Documentation/Snippets/CMakeLists.txt b/Documentation/Snippets/CMakeLists.txt
deleted file mode 100644
index 01142e1503..0000000000
--- a/Documentation/Snippets/CMakeLists.txt
+++ /dev/null
@@ -1,8 +0,0 @@
-if(BUILD_TESTING)
- include(mitkFunctionCompileSnippets)
-
- include_directories(${CTKPluginFramework_INCLUDE_DIRS})
-
- set(_link_libs CTKPluginFramework)
- mitkFunctionCompileSnippets("${CMAKE_CURRENT_SOURCE_DIR}" ${_link_libs})
-endif()
diff --git a/Documentation/Snippets/org.blueberry.ui.qt.help-config/main.cpp b/Documentation/Snippets/org.blueberry.ui.qt.help-config/main.cpp
deleted file mode 100644
index 473ba9d872..0000000000
--- a/Documentation/Snippets/org.blueberry.ui.qt.help-config/main.cpp
+++ /dev/null
@@ -1,123 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <QObject>
-
-#include <ctkPluginActivator.h>
-#include <ctkPluginException.h>
-#include <service/cm/ctkConfiguration.h>
-#include <service/cm/ctkConfigurationAdmin.h>
-#include <service/event/ctkEventAdmin.h>
-
-class MyApplicationPlugin : public QObject, public ctkPluginActivator
-{
- Q_OBJECT
- Q_INTERFACES(ctkPluginActivator)
-
-public:
- MyApplicationPlugin();
- ~MyApplicationPlugin() override;
-
- //! [0]
- void start(ctkPluginContext *context) override
- {
- // Get a service reference for the Config Admin service
- ctkServiceReference cmRef = context->getServiceReference<ctkConfigurationAdmin>();
- ctkConfigurationAdmin *configAdmin = nullptr;
- if (cmRef)
- {
- configAdmin = context->getService<ctkConfigurationAdmin>(cmRef);
- }
-
- // Use the CTK Configuration Admin service to configure the BlueBerry help system.
- // This assumes that the plug-in providing the Config Admin implementation is
- // already active.
- if (configAdmin)
- {
- // Get a ctkConfiguration object for the PID "org.blueberry.services.help"
- // (or create an unbound instance if it does not exist yet).
- ctkConfigurationPtr conf = configAdmin->getConfiguration("org.blueberry.services.help", QString());
-
- // Configure the help system using a custom home page
- ctkDictionary helpProps;
- helpProps.insert("homePage", "qthelp://org.company.plugin/bundle/index.html");
- conf->update(helpProps);
-
- // Unget the service
- context->ungetService(cmRef);
- }
- else
- {
- // Warn that the Config Admin service is unavailable
- }
- }
- //! [0]
-
- void stop(ctkPluginContext *context) override;
-
- //! [1]
- void requestHelp(ctkPluginContext *context)
- {
- if (context == nullptr)
- {
- // Warn that the plugin context is zero
- return;
- }
-
- // Check if the org.blueberry.ui.qt.help plug-in is installed and started
- QList<QSharedPointer<ctkPlugin>> plugins = context->getPlugins();
- foreach (QSharedPointer<ctkPlugin> p, plugins)
- {
- if (p->getSymbolicName() == "org.blueberry.ui.qt.help" && p->getState() != ctkPlugin::ACTIVE)
- {
- // The plug-in is in RESOLVED state but is not started yet.
- // Try to activate the plug-in explicitly, so that it can react
- // to events send via the CTK Event Admin.
- try
- {
- p->start(ctkPlugin::START_TRANSIENT);
- }
- catch (const ctkPluginException &)
- {
- // Warn that activating the org.blueberry.ui.qt.help plug-in failed
- return;
- }
- }
- }
-
- ctkServiceReference eventAdminRef = context->getServiceReference<ctkEventAdmin>();
- ctkEventAdmin *eventAdmin = nullptr;
- if (eventAdminRef)
- {
- eventAdmin = context->getService<ctkEventAdmin>(eventAdminRef);
- }
-
- if (eventAdmin == nullptr)
- {
- // Warn that the ctkEventAdmin service was not found
- }
- else
- {
- // Create the event and send it asynchronuously
- ctkEvent ev("org/blueberry/ui/help/CONTEXTHELP_REQUESTED");
- eventAdmin->postEvent(ev);
- }
- }
- //! [1]
-
-private:
-};
-
-int main(int /*argc*/, char * /*argv*/ [])
-{
- return 0;
-}
diff --git a/Documentation/doxygen.conf.in b/Documentation/doxygen.conf.in
index b9e99d4d17..add0ba4986 100644
--- a/Documentation/doxygen.conf.in
+++ b/Documentation/doxygen.conf.in
@@ -1,2442 +1,2433 @@
# Doxyfile 1.8.8
# This file describes the settings to be used by the documentation system
# doxygen (www.doxygen.org) for a project.
#
# All text after a double hash (##) is considered a comment and is placed in
# front of the TAG it is preceding.
#
# All text after a single hash (#) is considered a comment and will be ignored.
# The format is:
# TAG = value [value, ...]
# For lists, items can also be appended using:
# TAG += value [value, ...]
# Values that contain spaces should be placed between quotes (\" \").
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
# This tag specifies the encoding used for all characters in the config file
# that follow. The default is UTF-8 which is also the encoding used for all text
# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv
# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv
# for the list of possible encodings.
# The default value is: UTF-8.
DOXYFILE_ENCODING = UTF-8
# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
# double-quotes, unless you are using Doxywizard) that should identify the
# project for which the documentation is generated. This name is used in the
# title of most generated pages and in a few other places.
# The default value is: My Project.
PROJECT_NAME = "Medical Imaging Interaction Toolkit"
# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
# could be handy for archiving the generated documentation or if some version
# control system is used.
PROJECT_NUMBER = @MITK_VERSION_STRING@
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
# quick idea about the purpose of the project. Keep the description short.
PROJECT_BRIEF = "Medical Imaging Interaction Toolkit"
# With the PROJECT_LOGO tag one can specify an logo or icon that is included in
# the documentation. The maximum height of the logo should not exceed 55 pixels
# and the maximum width should not exceed 200 pixels. Doxygen will copy the logo
# to the output directory.
PROJECT_LOGO =
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
# into which the generated documentation will be written. If a relative path is
# entered, it will be relative to the location where doxygen was started. If
# left blank the current directory will be used.
OUTPUT_DIRECTORY = "@MITK_DOXYGEN_OUTPUT_DIR@"
# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 4096 sub-
# directories (in 2 levels) under the output directory of each output format and
# will distribute the generated files over these directories. Enabling this
# option can be useful when feeding doxygen a huge amount of source files, where
# putting all generated files in the same directory would otherwise causes
# performance problems for the file system.
# The default value is: NO.
CREATE_SUBDIRS = NO
# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
# characters to appear in the names of generated files. If set to NO, non-ASCII
# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
# U+3044.
# The default value is: NO.
ALLOW_UNICODE_NAMES = NO
# The OUTPUT_LANGUAGE tag is used to specify the language in which all
# documentation generated by doxygen is written. Doxygen will use this
# information to generate all constant output in the proper language.
# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
# Ukrainian and Vietnamese.
# The default value is: English.
OUTPUT_LANGUAGE = English
# If the BRIEF_MEMBER_DESC tag is set to YES doxygen will include brief member
# descriptions after the members that are listed in the file and class
# documentation (similar to Javadoc). Set to NO to disable this.
# The default value is: YES.
BRIEF_MEMBER_DESC = YES
# If the REPEAT_BRIEF tag is set to YES doxygen will prepend the brief
# description of a member or function before the detailed description
#
# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
# brief descriptions will be completely suppressed.
# The default value is: YES.
REPEAT_BRIEF = YES
# This tag implements a quasi-intelligent brief description abbreviator that is
# used to form the text in various listings. Each string in this list, if found
# as the leading text of the brief description, will be stripped from the text
# and the result, after processing the whole list, is used as the annotated
# text. Otherwise, the brief description is used as-is. If left blank, the
# following values are used ($name is automatically replaced with the name of
# the entity):The $name class, The $name widget, The $name file, is, provides,
# specifies, contains, represents, a, an and the.
ABBREVIATE_BRIEF =
# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
# doxygen will generate a detailed section even if there is only a brief
# description.
# The default value is: NO.
ALWAYS_DETAILED_SEC = NO
# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
# inherited members of a class in the documentation of that class as if those
# members were ordinary class members. Constructors, destructors and assignment
# operators of the base classes will not be shown.
# The default value is: NO.
INLINE_INHERITED_MEMB = NO
# If the FULL_PATH_NAMES tag is set to YES doxygen will prepend the full path
# before files name in the file list and in the header files. If set to NO the
# shortest path that makes the file name unique will be used
# The default value is: YES.
FULL_PATH_NAMES = NO
# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
# Stripping is only done if one of the specified strings matches the left-hand
# part of the path. The tag can be used to show relative paths in the file list.
# If left blank the directory from which doxygen is run is used as the path to
# strip.
#
# Note that you can specify absolute paths here, but also relative paths, which
# will be relative from the directory where doxygen is started.
# This tag requires that the tag FULL_PATH_NAMES is set to YES.
STRIP_FROM_PATH =
# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
# path mentioned in the documentation of a class, which tells the reader which
# header file to include in order to use a class. If left blank only the name of
# the header file containing the class definition is used. Otherwise one should
# specify the list of include paths that are normally passed to the compiler
# using the -I flag.
STRIP_FROM_INC_PATH =
# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
# less readable) file names. This can be useful is your file systems doesn't
# support long names like on DOS, Mac, or CD-ROM.
# The default value is: NO.
SHORT_NAMES = NO
# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
# first line (until the first dot) of a Javadoc-style comment as the brief
# description. If set to NO, the Javadoc-style will behave just like regular Qt-
# style comments (thus requiring an explicit @brief command for a brief
# description.)
# The default value is: NO.
JAVADOC_AUTOBRIEF = NO
# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
# line (until the first dot) of a Qt-style comment as the brief description. If
# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
# requiring an explicit \brief command for a brief description.)
# The default value is: NO.
QT_AUTOBRIEF = NO
# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
# a brief description. This used to be the default behavior. The new default is
# to treat a multi-line C++ comment block as a detailed description. Set this
# tag to YES if you prefer the old behavior instead.
#
# Note that setting this tag to YES also means that rational rose comments are
# not recognized any more.
# The default value is: NO.
MULTILINE_CPP_IS_BRIEF = NO
# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
# documentation from any documented member that it re-implements.
# The default value is: YES.
INHERIT_DOCS = YES
# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce a
# new page for each member. If set to NO, the documentation of a member will be
# part of the file/class/namespace that contains it.
# The default value is: NO.
SEPARATE_MEMBER_PAGES = NO
# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
# uses this value to replace tabs by spaces in code fragments.
# Minimum value: 1, maximum value: 16, default value: 4.
TAB_SIZE = 8
# This tag can be used to specify a number of aliases that act as commands in
# the documentation. An alias has the form:
# name=value
# For example adding
# "sideeffect=@par Side Effects:\n"
# will allow you to put the command \sideeffect (or @sideeffect) in the
# documentation, which will result in a user-defined paragraph with heading
# "Side Effects:". You can put \n's in the value part of an alias to insert
# newlines.
ALIASES = "FIXME=\par Fix Me's:\n" \
"BlueBerry=\if BLUEBERRY" \
"endBlueBerry=\endif" \
"bundlemainpage{1}=\page \1" \
"embmainpage{1}=\page \1" \
"github{2}=<a href=\"https://github.com/MITK/MITK/blob/master/\1\">\2</a>" \
"deprecatedSince{1}=\xrefitem deprecatedSince\1 \"\" \"Functions deprecated as of \1\" \deprecated (as of \1) " \
"minimumCMakeVersion=@MITK_CMAKE_MINIMUM_REQUIRED_VERSION@" \
"minimumQt5Version=@MITK_QT5_MINIMUM_VERSION@" \
"imageMacro{3}=\image html \1 \2 \n \image latex \1 \2 width=\3cm" \
"developersguidemainpage{1}=\page \1 " \
"usersguidemainpage{1}=\page \1 " \
"nondependentPluginLink{3}= \ref \1 \"\3\" "
-# This tag can be used to specify a number of word-keyword mappings (TCL only).
-# A mapping has the form "name=value". For example adding "class=itcl::class"
-# will allow you to use the command class in the itcl::class meaning.
-
-TCL_SUBST =
-
# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
# only. Doxygen will then generate output that is more tailored for C. For
# instance, some of the names that are used will be different. The list of all
# members will be omitted, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_FOR_C = NO
# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
# Python sources only. Doxygen will then generate output that is more tailored
# for that language. For instance, namespaces will be presented as packages,
# qualified scopes will look different, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_JAVA = NO
# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
# sources. Doxygen will then generate output that is tailored for Fortran.
# The default value is: NO.
OPTIMIZE_FOR_FORTRAN = NO
# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
# sources. Doxygen will then generate output that is tailored for VHDL.
# The default value is: NO.
OPTIMIZE_OUTPUT_VHDL = NO
# Doxygen selects the parser to use depending on the extension of the files it
# parses. With this tag you can assign which parser to use for a given
# extension. Doxygen has a built-in mapping, but you can override or extend it
# using this tag. The format is ext=language, where ext is a file extension, and
# language is one of the parsers supported by doxygen: IDL, Java, Javascript,
# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran:
# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran:
# Fortran. In the later case the parser tries to guess whether the code is fixed
# or free formatted code, this is the default for Fortran type files), VHDL. For
# instance to make doxygen treat .inc files as Fortran files (default is PHP),
# and .f files as C (default is Fortran), use: inc=Fortran f=C.
#
# Note For files without extension you can use no_extension as a placeholder.
#
# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
# the files are not read by doxygen.
EXTENSION_MAPPING = cmake=c++
# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
# according to the Markdown format, which allows for more readable
# documentation. See http://daringfireball.net/projects/markdown/ for details.
# The output of markdown processing is further processed by doxygen, so you can
# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
# case of backward compatibilities issues.
# The default value is: YES.
MARKDOWN_SUPPORT = YES
# When enabled doxygen tries to link words that correspond to documented
# classes, or namespaces to their corresponding documentation. Such a link can
# be prevented in individual cases by by putting a % sign in front of the word
# or globally by setting AUTOLINK_SUPPORT to NO.
# The default value is: YES.
AUTOLINK_SUPPORT = YES
# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
# to include (a tag file for) the STL sources as input, then you should set this
# tag to YES in order to let doxygen match functions declarations and
# definitions whose arguments contain STL classes (e.g. func(std::string);
# versus func(std::string) {}). This also make the inheritance and collaboration
# diagrams that involve STL classes more complete and accurate.
# The default value is: NO.
BUILTIN_STL_SUPPORT = YES
# If you use Microsoft's C++/CLI language, you should set this option to YES to
# enable parsing support.
# The default value is: NO.
CPP_CLI_SUPPORT = NO
# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen
# will parse them like normal C++ but will assume all classes use public instead
# of private inheritance when no explicit protection keyword is present.
# The default value is: NO.
SIP_SUPPORT = NO
# For Microsoft's IDL there are propget and propput attributes to indicate
# getter and setter methods for a property. Setting this option to YES will make
# doxygen to replace the get and set methods by a property in the documentation.
# This will only work if the methods are indeed getting or setting a simple
# type. If this is not the case, or you want to show the methods anyway, you
# should set this option to NO.
# The default value is: YES.
IDL_PROPERTY_SUPPORT = YES
# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
# tag is set to YES, then doxygen will reuse the documentation of the first
# member in the group (if any) for the other members of the group. By default
# all members of a group must be documented explicitly.
# The default value is: NO.
DISTRIBUTE_GROUP_DOC = YES
# Set the SUBGROUPING tag to YES to allow class member groups of the same type
# (for instance a group of public functions) to be put as a subgroup of that
# type (e.g. under the Public Functions section). Set it to NO to prevent
# subgrouping. Alternatively, this can be done per class using the
# \nosubgrouping command.
# The default value is: YES.
SUBGROUPING = YES
# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
# are shown inside the group in which they are included (e.g. using \ingroup)
# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
# and RTF).
#
# Note that this feature does not work in combination with
# SEPARATE_MEMBER_PAGES.
# The default value is: NO.
INLINE_GROUPED_CLASSES = NO
# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
# with only public data fields or simple typedef fields will be shown inline in
# the documentation of the scope in which they are defined (i.e. file,
# namespace, or group documentation), provided this scope is documented. If set
# to NO, structs, classes, and unions are shown on a separate page (for HTML and
# Man pages) or section (for LaTeX and RTF).
# The default value is: NO.
INLINE_SIMPLE_STRUCTS = NO
# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
# enum is documented as struct, union, or enum with the name of the typedef. So
# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
# with name TypeT. When disabled the typedef will appear as a member of a file,
# namespace, or class. And the struct will be named TypeS. This can typically be
# useful for C code in case the coding convention dictates that all compound
# types are typedef'ed and only the typedef is referenced, never the tag name.
# The default value is: NO.
TYPEDEF_HIDES_STRUCT = NO
# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
# cache is used to resolve symbols given their name and scope. Since this can be
# an expensive process and often the same symbol appears multiple times in the
# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
# doxygen will become slower. If the cache is too large, memory is wasted. The
# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
# symbols. At the end of a run doxygen will report the cache usage and suggest
# the optimal cache size from a speed point of view.
# Minimum value: 0, maximum value: 9, default value: 0.
LOOKUP_CACHE_SIZE = 0
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
# documentation are documented, even if no documentation was available. Private
# class members and static file members will be hidden unless the
# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
# Note: This will also disable the warnings about undocumented members that are
# normally produced when WARNINGS is set to YES.
# The default value is: NO.
EXTRACT_ALL = YES
# If the EXTRACT_PRIVATE tag is set to YES all private members of a class will
# be included in the documentation.
# The default value is: NO.
EXTRACT_PRIVATE = NO
# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal
# scope will be included in the documentation.
# The default value is: NO.
EXTRACT_PACKAGE = NO
# If the EXTRACT_STATIC tag is set to YES all static members of a file will be
# included in the documentation.
# The default value is: NO.
EXTRACT_STATIC = YES
# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) defined
# locally in source files will be included in the documentation. If set to NO
# only classes defined in header files are included. Does not have any effect
# for Java sources.
# The default value is: YES.
EXTRACT_LOCAL_CLASSES = @MITK_DOXYGEN_INTERNAL_DOCS@
# This flag is only useful for Objective-C code. When set to YES local methods,
# which are defined in the implementation section but not in the interface are
# included in the documentation. If set to NO only methods in the interface are
# included.
# The default value is: NO.
EXTRACT_LOCAL_METHODS = NO
# If this flag is set to YES, the members of anonymous namespaces will be
# extracted and appear in the documentation as a namespace called
# 'anonymous_namespace{file}', where file will be replaced with the base name of
# the file that contains the anonymous namespace. By default anonymous namespace
# are hidden.
# The default value is: NO.
EXTRACT_ANON_NSPACES = NO
# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
# undocumented members inside documented classes or files. If set to NO these
# members will be included in the various overviews, but no documentation
# section is generated. This option has no effect if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_MEMBERS = NO
# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
# undocumented classes that are normally visible in the class hierarchy. If set
# to NO these classes will be included in the various overviews. This option has
# no effect if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_CLASSES = NO
# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
# (class|struct|union) declarations. If set to NO these declarations will be
# included in the documentation.
# The default value is: NO.
HIDE_FRIEND_COMPOUNDS = @MITK_DOXYGEN_HIDE_FRIEND_COMPOUNDS@
# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
# documentation blocks found inside the body of a function. If set to NO these
# blocks will be appended to the function's detailed documentation block.
# The default value is: NO.
HIDE_IN_BODY_DOCS = NO
# The INTERNAL_DOCS tag determines if documentation that is typed after a
# \internal command is included. If the tag is set to NO then the documentation
# will be excluded. Set it to YES to include the internal documentation.
# The default value is: NO.
INTERNAL_DOCS = @MITK_DOXYGEN_INTERNAL_DOCS@
# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
# names in lower-case letters. If set to YES upper-case letters are also
# allowed. This is useful if you have classes or files whose names only differ
# in case and if your file system supports case sensitive file names. Windows
# and Mac users are advised to set this option to NO.
# The default value is: system dependent.
CASE_SENSE_NAMES = YES
# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
# their full class and namespace scopes in the documentation. If set to YES the
# scope will be hidden.
# The default value is: NO.
HIDE_SCOPE_NAMES = NO
# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
# the files that are included by a file in the documentation of that file.
# The default value is: YES.
SHOW_INCLUDE_FILES = YES
# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
# grouped member an include statement to the documentation, telling the reader
# which file to include in order to use the member.
# The default value is: NO.
SHOW_GROUPED_MEMB_INC = NO
# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
# files with double quotes in the documentation rather than with sharp brackets.
# The default value is: NO.
FORCE_LOCAL_INCLUDES = NO
# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
# documentation for inline members.
# The default value is: YES.
INLINE_INFO = YES
# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
# (detailed) documentation of file and class members alphabetically by member
# name. If set to NO the members will appear in declaration order.
# The default value is: YES.
SORT_MEMBER_DOCS = YES
# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
# descriptions of file, namespace and class members alphabetically by member
# name. If set to NO the members will appear in declaration order. Note that
# this will also influence the order of the classes in the class list.
# The default value is: NO.
SORT_BRIEF_DOCS = NO
# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
# (brief and detailed) documentation of class members so that constructors and
# destructors are listed first. If set to NO the constructors will appear in the
# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
# member documentation.
# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
# detailed member documentation.
# The default value is: NO.
SORT_MEMBERS_CTORS_1ST = NO
# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
# of group names into alphabetical order. If set to NO the group names will
# appear in their defined order.
# The default value is: NO.
SORT_GROUP_NAMES = NO
# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
# fully-qualified names, including namespaces. If set to NO, the class list will
# be sorted only by class name, not including the namespace part.
# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
# Note: This option applies only to the class list, not to the alphabetical
# list.
# The default value is: NO.
SORT_BY_SCOPE_NAME = YES
# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
# type resolution of all parameters of a function it will reject a match between
# the prototype and the implementation of a member function even if there is
# only one candidate or it is obvious which candidate to choose by doing a
# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
# accept a match between prototype and implementation in such cases.
# The default value is: NO.
STRICT_PROTO_MATCHING = NO
# The GENERATE_TODOLIST tag can be used to enable ( YES) or disable ( NO) the
# todo list. This list is created by putting \todo commands in the
# documentation.
# The default value is: YES.
GENERATE_TODOLIST = @MITK_DOXYGEN_GENERATE_TODOLIST@
# The GENERATE_TESTLIST tag can be used to enable ( YES) or disable ( NO) the
# test list. This list is created by putting \test commands in the
# documentation.
# The default value is: YES.
GENERATE_TESTLIST = YES
# The GENERATE_BUGLIST tag can be used to enable ( YES) or disable ( NO) the bug
# list. This list is created by putting \bug commands in the documentation.
# The default value is: YES.
GENERATE_BUGLIST = @MITK_DOXYGEN_GENERATE_BUGLIST@
# The GENERATE_DEPRECATEDLIST tag can be used to enable ( YES) or disable ( NO)
# the deprecated list. This list is created by putting \deprecated commands in
# the documentation.
# The default value is: YES.
GENERATE_DEPRECATEDLIST= @MITK_DOXYGEN_GENERATE_DEPRECATEDLIST@
# The ENABLED_SECTIONS tag can be used to enable conditional documentation
# sections, marked by \if <section_label> ... \endif and \cond <section_label>
# ... \endcond blocks.
ENABLED_SECTIONS = @MITK_DOXYGEN_ENABLED_SECTIONS@
# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
# initial value of a variable or macro / define can have for it to appear in the
# documentation. If the initializer consists of more lines than specified here
# it will be hidden. Use a value of 0 to hide initializers completely. The
# appearance of the value of individual variables and macros / defines can be
# controlled using \showinitializer or \hideinitializer command in the
# documentation regardless of this setting.
# Minimum value: 0, maximum value: 10000, default value: 30.
MAX_INITIALIZER_LINES = 0
# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
# the bottom of the documentation of classes and structs. If set to YES the list
# will mention the files that were used to generate the documentation.
# The default value is: YES.
SHOW_USED_FILES = YES
# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
# will remove the Files entry from the Quick Index and from the Folder Tree View
# (if specified).
# The default value is: YES.
SHOW_FILES = YES
# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
# page. This will remove the Namespaces entry from the Quick Index and from the
# Folder Tree View (if specified).
# The default value is: YES.
SHOW_NAMESPACES = YES
# The FILE_VERSION_FILTER tag can be used to specify a program or script that
# doxygen should invoke to get the current version for each file (typically from
# the version control system). Doxygen will invoke the program by executing (via
# popen()) the command command input-file, where command is the value of the
# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
# by doxygen. Whatever the program writes to standard output is used as the file
# version. For an example see the documentation.
FILE_VERSION_FILTER =
# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
# by doxygen. The layout file controls the global structure of the generated
# output files in an output format independent way. To create the layout file
# that represents doxygen's defaults, run doxygen with the -l option. You can
# optionally specify a file name after the option, if omitted DoxygenLayout.xml
# will be used as the name of the layout file.
#
# Note that if you run doxygen from a directory containing a file called
# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
# tag is left empty.
LAYOUT_FILE = "@MITK_SOURCE_DIR@/Documentation/MITKDoxygenLayout.xml"
# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
# the reference definitions. This must be a list of .bib files. The .bib
# extension is automatically appended if omitted. This requires the bibtex tool
# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
# For LaTeX the style of the bibliography can be controlled using
# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
# search path. See also \cite for info how to create references.
CITE_BIB_FILES =
#---------------------------------------------------------------------------
# Configuration options related to warning and progress messages
#---------------------------------------------------------------------------
# The QUIET tag can be used to turn on/off the messages that are generated to
# standard output by doxygen. If QUIET is set to YES this implies that the
# messages are off.
# The default value is: NO.
-QUIET = NO
+QUIET = YES
# The WARNINGS tag can be used to turn on/off the warning messages that are
# generated to standard error ( stderr) by doxygen. If WARNINGS is set to YES
# this implies that the warnings are on.
#
# Tip: Turn warnings on while writing the documentation.
# The default value is: YES.
WARNINGS = YES
# If the WARN_IF_UNDOCUMENTED tag is set to YES, then doxygen will generate
# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
# will automatically be disabled.
# The default value is: YES.
WARN_IF_UNDOCUMENTED = YES
# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
# potential errors in the documentation, such as not documenting some parameters
# in a documented function, or documenting parameters that don't exist or using
# markup commands wrongly.
# The default value is: YES.
WARN_IF_DOC_ERROR = YES
# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
# are documented, but have no documentation for their parameters or return
# value. If set to NO doxygen will only warn about wrong or incomplete parameter
# documentation, but not about the absence of documentation.
# The default value is: NO.
WARN_NO_PARAMDOC = NO
# The WARN_FORMAT tag determines the format of the warning messages that doxygen
# can produce. The string should contain the $file, $line, and $text tags, which
# will be replaced by the file and line number from which the warning originated
# and the warning text. Optionally the format may contain $version, which will
# be replaced by the version of the file (if it could be obtained via
# FILE_VERSION_FILTER)
# The default value is: $file:$line: $text.
WARN_FORMAT = "$file:$line: $text"
# The WARN_LOGFILE tag can be used to specify a file to which warning and error
# messages should be written. If left blank the output is written to standard
# error (stderr).
WARN_LOGFILE =
#---------------------------------------------------------------------------
# Configuration options related to the input files
#---------------------------------------------------------------------------
# The INPUT tag is used to specify the files and/or directories that contain
# documented source files. You may enter file names like myfile.cpp or
# directories like /usr/src/myproject. Separate the files or directories with
# spaces.
# Note: If this tag is empty the current directory is searched.
INPUT = @MITK_SOURCE_DIR@ \
@MITK_SOURCE_DIR@/README.md \
@MITK_BINARY_DIR@ \
@MITK_DOXYGEN_ADDITIONAL_INPUT_DIRS@
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
# documentation (see: http://www.gnu.org/software/libiconv) for the list of
# possible encodings.
# The default value is: UTF-8.
INPUT_ENCODING = UTF-8
# If the value of the INPUT tag contains directories, you can use the
# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
# *.h) to filter out the source-files in the directories. If left blank the
# following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii,
# *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp,
# *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown,
# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
# *.qsf, *.as and *.js.
FILE_PATTERNS = *.h \
- *.cpp \
*.dox \
- *.md \
- *.txx \
- *.tpp \
- *.cxx \
- *.cmake
+ *.md
# The RECURSIVE tag can be used to specify whether or not subdirectories should
# be searched for input files as well.
# The default value is: NO.
RECURSIVE = YES
# The EXCLUDE tag can be used to specify files and/or directories that should be
# excluded from the INPUT source files. This way you can easily exclude a
# subdirectory from a directory tree whose root is specified with the INPUT tag.
#
# Note that relative paths are relative to the directory from which doxygen is
# run.
EXCLUDE = "@MITK_SOURCE_DIR@/Utilities/IpFunc/" \
"@MITK_SOURCE_DIR@/Utilities/IpSegmentation/" \
"@MITK_SOURCE_DIR@/Utilities/qtsingleapplication/" \
"@MITK_SOURCE_DIR@/Applications/PluginGenerator/" \
"@MITK_SOURCE_DIR@/Modules/CppMicroServices/core/doc/snippets/" \
"@MITK_SOURCE_DIR@/Modules/CppMicroServices/core/doc/doxygen/standalone/" \
"@MITK_SOURCE_DIR@/Modules/CppMicroServices/core/test/" \
"@MITK_SOURCE_DIR@/Modules/CppMicroServices/core/examples/" \
"@MITK_SOURCE_DIR@/Modules/CppMicroServices/core/src/util/jsoncpp.cpp" \
"@MITK_SOURCE_DIR@/CMake/PackageDepends" \
"@MITK_SOURCE_DIR@/CMakeExternals" \
"@MITK_SOURCE_DIR@/Licenses" \
"@MITK_BINARY_DIR@/Documentation/Doxygen" \
"@MITK_BINARY_DIR@/bin/" \
"@MITK_BINARY_DIR@/PT/" \
"@MITK_BINARY_DIR@/GP/" \
"@MITK_BINARY_DIR@/_CPack_Packages/" \
@MITK_DOXYGEN_ADDITIONAL_EXCLUDE_DIRS@
# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
# directories that are symbolic links (a Unix file system feature) are excluded
# from the input.
# The default value is: NO.
EXCLUDE_SYMLINKS = NO
# If the value of the INPUT tag contains directories, you can use the
# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
# certain files from those directories.
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories for example use the pattern */test/*
EXCLUDE_PATTERNS = README* \
moc_* \
ui_* \
qrc_* \
wrap_* \
Register* \
*/files.cmake \
*/.git/* \
*_p.h \
*Private.* \
*/Internal/* \
*/internal/* \
*/Snippets/* \
*/snippets/* \
*/testing/* \
*/Testing/* \
+ */test/* \
+ */resource/* \
"@MITK_BINARY_DIR@/*.cmake" \
@MITK_DOXYGEN_EXCLUDE_PATTERNS@
# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
# (namespaces, classes, functions, etc.) that should be excluded from the
# output. The symbol name can be a fully qualified name, a word, or if the
# wildcard * is used, a substring. Examples: ANamespace, AClass,
# AClass::ANamespace, ANamespace::*Test
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories use the pattern */test/*
EXCLUDE_SYMBOLS =
# The EXAMPLE_PATH tag can be used to specify one or more files or directories
# that contain example code fragments that are included (see the \include
# command).
EXAMPLE_PATH = "@MITK_SOURCE_DIR@/Documentation/Snippets/" \
"@MITK_SOURCE_DIR@/Examples/" \
"@MITK_SOURCE_DIR@/Examples/Tutorial/" \
"@MITK_SOURCE_DIR@/Examples/Plugins/" \
"@MITK_SOURCE_DIR@/Examples/QtFreeRender/" \
"@MITK_SOURCE_DIR@/Modules/Core/" \
"@MITK_SOURCE_DIR@/Modules/CppMicroServices/core/doc/snippets/" \
"@MITK_SOURCE_DIR@/Modules/CppMicroServices/core/examples/" \
"@MITK_DOXYGEN_OUTPUT_DIR@/html/extension-points/html/" \
"@MITK_SOURCE_DIR@/Modules/OpenCL/Documentation/doxygen/snippets/" \
"@MITK_SOURCE_DIR@/Modules/IGT/Tutorial/" \
"@MITK_SOURCE_DIR@/Plugins/org.mitk.gui.qt.igtexamples/" \
"@MITK_SOURCE_DIR@/Plugins/org.mitk.gui.qt.igttracking/"
# If the value of the EXAMPLE_PATH tag contains directories, you can use the
# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
# *.h) to filter out the source-files in the directories. If left blank all
# files are included.
EXAMPLE_PATTERNS =
# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
# searched for input files to be used with the \include or \dontinclude commands
# irrespective of the value of the RECURSIVE tag.
# The default value is: NO.
EXAMPLE_RECURSIVE = YES
# The IMAGE_PATH tag can be used to specify one or more files or directories
# that contain images that are to be included in the documentation (see the
# \image command).
IMAGE_PATH = "@MITK_SOURCE_DIR@/Documentation/Doxygen/" \
"@MITK_SOURCE_DIR@"
# The INPUT_FILTER tag can be used to specify a program that doxygen should
# invoke to filter for each input file. Doxygen will invoke the filter program
# by executing (via popen()) the command:
#
# <filter> <input-file>
#
# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
# name of an input file. Doxygen will then use the output that the filter
# program writes to standard output. If FILTER_PATTERNS is specified, this tag
# will be ignored.
#
# Note that the filter must not add or remove lines; it is applied before the
# code is scanned, but not when the output code is generated. If lines are added
# or removed, the anchors will not be placed correctly.
INPUT_FILTER =
# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
# basis. Doxygen will compare the file name with each pattern and apply the
# filter if there is a match. The filters are a list of the form: pattern=filter
# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
# patterns match the file name, INPUT_FILTER is applied.
FILTER_PATTERNS = *.cmake=@CMakeDoxygenFilter_EXECUTABLE@
# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
# INPUT_FILTER ) will also be used to filter the input files that are used for
# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
# The default value is: NO.
FILTER_SOURCE_FILES = NO
# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
# it is also possible to disable source filtering for a specific pattern using
# *.ext= (so without naming a filter).
# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
FILTER_SOURCE_PATTERNS =
# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
# is part of the input, its contents will be placed on the main page
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.
USE_MDFILE_AS_MAINPAGE = README.md
#---------------------------------------------------------------------------
# Configuration options related to source browsing
#---------------------------------------------------------------------------
# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
# generated. Documented entities will be cross-referenced with these sources.
#
# Note: To get rid of all source code in the generated output, make sure that
# also VERBATIM_HEADERS is set to NO.
# The default value is: NO.
SOURCE_BROWSER = YES
# Setting the INLINE_SOURCES tag to YES will include the body of functions,
# classes and enums directly into the documentation.
# The default value is: NO.
INLINE_SOURCES = NO
# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
# special comment blocks from generated source code fragments. Normal C, C++ and
# Fortran comments will always remain visible.
# The default value is: YES.
STRIP_CODE_COMMENTS = YES
# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
# function all documented functions referencing it will be listed.
# The default value is: NO.
REFERENCED_BY_RELATION = YES
# If the REFERENCES_RELATION tag is set to YES then for each documented function
# all documented entities called/used by that function will be listed.
# The default value is: NO.
REFERENCES_RELATION = YES
# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
# to YES, then the hyperlinks from functions in REFERENCES_RELATION and
# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
# link to the documentation.
# The default value is: YES.
REFERENCES_LINK_SOURCE = YES
# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
# source code will show a tooltip with additional information such as prototype,
# brief description and links to the definition and documentation. Since this
# will make the HTML file larger and loading of large files a bit slower, you
# can opt to disable this feature.
# The default value is: YES.
# This tag requires that the tag SOURCE_BROWSER is set to YES.
SOURCE_TOOLTIPS = YES
# If the USE_HTAGS tag is set to YES then the references to source code will
# point to the HTML generated by the htags(1) tool instead of doxygen built-in
# source browser. The htags tool is part of GNU's global source tagging system
# (see http://www.gnu.org/software/global/global.html). You will need version
# 4.8.6 or higher.
#
# To use it do the following:
# - Install the latest version of global
# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
# - Make sure the INPUT points to the root of the source tree
# - Run doxygen as normal
#
# Doxygen will invoke htags (and that will in turn invoke gtags), so these
# tools must be available from the command line (i.e. in the search path).
#
# The result: instead of the source browser generated by doxygen, the links to
# source code will now point to the output of htags.
# The default value is: NO.
# This tag requires that the tag SOURCE_BROWSER is set to YES.
USE_HTAGS = NO
# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
# verbatim copy of the header file for each class for which an include is
# specified. Set to NO to disable this.
# See also: Section \class.
# The default value is: YES.
VERBATIM_HEADERS = YES
#---------------------------------------------------------------------------
# Configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
# compounds will be generated. Enable this if the project contains a lot of
# classes, structs, unions or interfaces.
# The default value is: YES.
ALPHABETICAL_INDEX = YES
# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
# which the alphabetical index list will be split.
# Minimum value: 1, maximum value: 20, default value: 5.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
COLS_IN_ALPHA_INDEX = 3
# In case all classes in a project start with a common prefix, all classes will
# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
# can be used to specify a prefix (or a list of prefixes) that should be ignored
# while generating the index headers.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
IGNORE_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the HTML output
#---------------------------------------------------------------------------
# If the GENERATE_HTML tag is set to YES doxygen will generate HTML output
# The default value is: YES.
GENERATE_HTML = YES
# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: html.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_OUTPUT = html
# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
# generated HTML page (for example: .htm, .php, .asp).
# The default value is: .html.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FILE_EXTENSION = .html
# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
# each generated HTML page. If the tag is left blank doxygen will generate a
# standard header.
#
# To get valid HTML the header file that includes any scripts and style sheets
# that doxygen needs, which is dependent on the configuration options used (e.g.
# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
# default header using
# doxygen -w html new_header.html new_footer.html new_stylesheet.css
# YourConfigFile
# and then modify the file new_header.html. See also section "Doxygen usage"
# for information on how to generate the default header that doxygen normally
# uses.
# Note: The header is subject to change so you typically have to regenerate the
# default header when upgrading to a newer version of doxygen. For a description
# of the possible markers and block names see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_HEADER =
# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
# generated HTML page. If the tag is left blank doxygen will generate a standard
# footer. See HTML_HEADER for more information on how to generate a default
# footer and what special commands can be used inside the footer. See also
# section "Doxygen usage" for information on how to generate the default footer
# that doxygen normally uses.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FOOTER =
# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
# sheet that is used by each HTML page. It can be used to fine-tune the look of
# the HTML output. If left blank doxygen will generate a default style sheet.
# See also section "Doxygen usage" for information on how to generate the style
# sheet that doxygen normally uses.
# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
# it is more robust and this tag (HTML_STYLESHEET) will in the future become
# obsolete.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_STYLESHEET =
# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
# cascading style sheets that are included after the standard style sheets
# created by doxygen. Using this option one can overrule certain style aspects.
# This is preferred over using HTML_STYLESHEET since it does not replace the
# standard style sheet and is therefor more robust against future updates.
# Doxygen will copy the style sheet files to the output directory.
# Note: The order of the extra stylesheet files is of importance (e.g. the last
# stylesheet in the list overrules the setting of the previous ones in the
# list). For an example see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_STYLESHEET = @MITK_DOXYGEN_STYLESHEET@
# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the HTML output directory. Note
# that these files will be copied to the base HTML output directory. Use the
# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
# files will be copied as-is; there are no commands or markers available.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_FILES = "@MITK_SOURCE_DIR@/Documentation/Doxygen/mitkLogo.jpg"
# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
# will adjust the colors in the stylesheet and background images according to
# this color. Hue is specified as an angle on a colorwheel, see
# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
# purple, and 360 is red again.
# Minimum value: 0, maximum value: 359, default value: 220.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_HUE = 220
# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
# in the HTML output. For a value of 0 the output will use grayscales only. A
# value of 255 will produce the most vivid colors.
# Minimum value: 0, maximum value: 255, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_SAT = 100
# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
# luminance component of the colors in the HTML output. Values below 100
# gradually make the output lighter, whereas values above 100 make the output
# darker. The value divided by 100 is the actual gamma applied, so 80 represents
# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
# change the gamma.
# Minimum value: 40, maximum value: 240, default value: 80.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_GAMMA = 80
# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
# page will contain the date and time when the page was generated. Setting this
# to NO can help when comparing the output of multiple runs.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_TIMESTAMP = YES
# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
# documentation will contain sections that can be hidden and shown after the
# page has loaded.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_DYNAMIC_SECTIONS = @MITK_DOXYGEN_HTML_DYNAMIC_SECTIONS@
# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
# shown in the various tree structured indices initially; the user can expand
# and collapse entries dynamically later on. Doxygen will expand the tree to
# such a level that at most the specified number of entries are visible (unless
# a fully collapsed tree already exceeds this amount). So setting the number of
# entries 1 will produce a full collapsed tree by default. 0 is a special value
# representing an infinite number of entries and will result in a full expanded
# tree by default.
# Minimum value: 0, maximum value: 9999, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_INDEX_NUM_ENTRIES = 100
# If the GENERATE_DOCSET tag is set to YES, additional index files will be
# generated that can be used as input for Apple's Xcode 3 integrated development
# environment (see: http://developer.apple.com/tools/xcode/), introduced with
# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
# Makefile in the HTML output directory. Running make will produce the docset in
# that directory and running make install will install the docset in
# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
# for more information.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_DOCSET = NO
# This tag determines the name of the docset feed. A documentation feed provides
# an umbrella under which multiple documentation sets from a single provider
# (such as a company or product suite) can be grouped.
# The default value is: Doxygen generated docs.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_FEEDNAME = "Doxygen generated docs"
# This tag specifies a string that should uniquely identify the documentation
# set bundle. This should be a reverse domain-name style string, e.g.
# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_BUNDLE_ID = org.doxygen.Project
# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
# the documentation publisher. This should be a reverse domain-name style
# string, e.g. com.mycompany.MyDocSet.documentation.
# The default value is: org.doxygen.Publisher.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_ID = org.doxygen.Publisher
# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
# The default value is: Publisher.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_NAME = Publisher
# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
# Windows.
#
# The HTML Help Workshop contains a compiler that can convert all HTML output
# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
# files are now used as the Windows 98 help format, and will replace the old
# Windows help format (.hlp) on all Windows platforms in the future. Compressed
# HTML files also contain an index, a table of contents, and you can search for
# words in the documentation. The HTML workshop also contains a viewer for
# compressed HTML files.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_HTMLHELP = NO
# The CHM_FILE tag can be used to specify the file name of the resulting .chm
# file. You can add a path in front of the file if the result should not be
# written to the html output directory.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_FILE =
# The HHC_LOCATION tag can be used to specify the location (absolute path
# including file name) of the HTML help compiler ( hhc.exe). If non-empty
# doxygen will try to run the HTML help compiler on the generated index.hhp.
# The file has to be specified with full path.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
HHC_LOCATION =
# The GENERATE_CHI flag controls if a separate .chi index file is generated (
# YES) or that it should be included in the master .chm file ( NO).
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
GENERATE_CHI = NO
# The CHM_INDEX_ENCODING is used to encode HtmlHelp index ( hhk), content ( hhc)
# and project file content.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_INDEX_ENCODING =
# The BINARY_TOC flag controls whether a binary table of contents is generated (
# YES) or a normal table of contents ( NO) in the .chm file. Furthermore it
# enables the Previous and Next buttons.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
BINARY_TOC = NO
# The TOC_EXPAND flag can be set to YES to add extra items for group members to
# the table of contents of the HTML help documentation and to the tree view.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
TOC_EXPAND = NO
# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
# (.qch) of the generated HTML documentation.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_QHP = @MITK_DOXYGEN_GENERATE_QHP@
# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
# the file name of the resulting .qch file. The path specified is relative to
# the HTML output folder.
# This tag requires that the tag GENERATE_QHP is set to YES.
QCH_FILE = @MITK_DOXYGEN_QCH_FILE@
# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
# Project output. For more information please see Qt Help Project / Namespace
# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_NAMESPACE = "org.mitk"
# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
# Help Project output. For more information please see Qt Help Project / Virtual
# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
# folders).
# The default value is: doc.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_VIRTUAL_FOLDER = MITK
# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
# filter to add. For more information please see Qt Help Project / Custom
# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
# filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_NAME =
# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
# custom filter to add. For more information please see Qt Help Project / Custom
# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
# filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_ATTRS =
# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
# project's filter section matches. Qt Help Project / Filter Attributes (see:
# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_SECT_FILTER_ATTRS =
# The QHG_LOCATION tag can be used to specify the location of Qt's
# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
# generated .qhp file.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHG_LOCATION = @QT_HELPGENERATOR_EXECUTABLE@
# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
# generated, together with the HTML files, they form an Eclipse help plugin. To
# install this plugin and make it available under the help contents menu in
# Eclipse, the contents of the directory containing the HTML and XML files needs
# to be copied into the plugins directory of eclipse. The name of the directory
# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
# After copying Eclipse needs to be restarted before the help appears.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_ECLIPSEHELP = NO
# A unique identifier for the Eclipse help plugin. When installing the plugin
# the directory name containing the HTML and XML files should also have this
# name. Each documentation set should have its own identifier.
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
ECLIPSE_DOC_ID = org.doxygen.Project
# If you want full control over the layout of the generated HTML pages it might
# be necessary to disable the index and replace it with your own. The
# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
# of each HTML page. A value of NO enables the index and the value YES disables
# it. Since the tabs in the index contain the same information as the navigation
# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
DISABLE_INDEX = NO
# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
# structure should be generated to display hierarchical information. If the tag
# value is set to YES, a side panel will be generated containing a tree-like
# index structure (just like the one that is generated for HTML Help). For this
# to work a browser that supports JavaScript, DHTML, CSS and frames is required
# (i.e. any modern browser). Windows users are probably better off using the
# HTML help feature. Via custom stylesheets (see HTML_EXTRA_STYLESHEET) one can
# further fine-tune the look of the index. As an example, the default style
# sheet generated by doxygen has an example that shows how to put an image at
# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
# the same information as the tab index, you could consider setting
# DISABLE_INDEX to YES when enabling this option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_TREEVIEW = YES
# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
# doxygen will group on one line in the generated HTML documentation.
#
# Note that a value of 0 will completely suppress the enum values from appearing
# in the overview section.
# Minimum value: 0, maximum value: 20, default value: 4.
# This tag requires that the tag GENERATE_HTML is set to YES.
ENUM_VALUES_PER_LINE = 4
# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
# to set the initial width (in pixels) of the frame in which the tree is shown.
# Minimum value: 0, maximum value: 1500, default value: 250.
# This tag requires that the tag GENERATE_HTML is set to YES.
TREEVIEW_WIDTH = 300
# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open links to
# external symbols imported via tag files in a separate window.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
EXT_LINKS_IN_WINDOW = NO
# Use this tag to change the font size of LaTeX formulas included as images in
# the HTML documentation. When you change the font size after a successful
# doxygen run you need to manually remove any form_*.png images from the HTML
# output directory to force them to be regenerated.
# Minimum value: 8, maximum value: 50, default value: 10.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_FONTSIZE = 10
# Use the FORMULA_TRANPARENT tag to determine whether or not the images
# generated for formulas are transparent PNGs. Transparent PNGs are not
# supported properly for IE 6.0, but are supported on all modern browsers.
#
# Note that when changing this option you need to delete any form_*.png files in
# the HTML output directory before the changes have effect.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_TRANSPARENT = YES
# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
# http://www.mathjax.org) which uses client side Javascript for the rendering
# instead of using prerendered bitmaps. Use this if you do not have LaTeX
# installed or if you want to formulas look prettier in the HTML output. When
# enabled you may also need to install MathJax separately and configure the path
# to it using the MATHJAX_RELPATH option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
USE_MATHJAX = YES
# When MathJax is enabled you can set the default output format to be used for
# the MathJax output. See the MathJax site (see:
# http://docs.mathjax.org/en/latest/output.html) for more details.
# Possible values are: HTML-CSS (which is slower, but has the best
# compatibility), NativeMML (i.e. MathML) and SVG.
# The default value is: HTML-CSS.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_FORMAT = HTML-CSS
# When MathJax is enabled you need to specify the location relative to the HTML
# output directory using the MATHJAX_RELPATH option. The destination directory
# should contain the MathJax.js script. For instance, if the mathjax directory
# is located at the same level as the HTML output directory, then
# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
# Content Delivery Network so you can quickly see the result without installing
# MathJax. However, it is strongly recommended to install a local copy of
# MathJax from http://www.mathjax.org before deployment.
# The default value is: http://cdn.mathjax.org/mathjax/latest.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_RELPATH = http://www.mathjax.org/mathjax
# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
# extension names that should be enabled during MathJax rendering. For example
# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_EXTENSIONS =
# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
# of code that will be used on startup of the MathJax code. See the MathJax site
# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
# example see the documentation.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_CODEFILE =
# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
# the HTML output. The underlying search engine uses javascript and DHTML and
# should work on any modern browser. Note that when using HTML help
# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
# there is already a search function so this one should typically be disabled.
# For large projects the javascript based search engine can be slow, then
# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
# search using the keyboard; to jump to the search box use <access key> + S
# (what the <access key> is depends on the OS and browser, but it is typically
# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
# key> to jump into the search results window, the results can be navigated
# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
# the search. The filter options can be selected when the cursor is inside the
# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
# to select a filter and <Enter> or <escape> to activate or cancel the filter
# option.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
SEARCHENGINE = YES
# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
# implemented using a web server instead of a web client using Javascript. There
# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
# setting. When disabled, doxygen will generate a PHP script for searching and
# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
# and searching needs to be provided by external tools. See the section
# "External Indexing and Searching" for details.
# The default value is: NO.
# This tag requires that the tag SEARCHENGINE is set to YES.
SERVER_BASED_SEARCH = NO
# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
# script for searching. Instead the search results are written to an XML file
# which needs to be processed by an external indexer. Doxygen will invoke an
# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
# search results.
#
# Doxygen ships with an example indexer ( doxyindexer) and search engine
# (doxysearch.cgi) which are based on the open source search engine library
# Xapian (see: http://xapian.org/).
#
# See the section "External Indexing and Searching" for details.
# The default value is: NO.
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTERNAL_SEARCH = NO
# The SEARCHENGINE_URL should point to a search engine hosted by a web server
# which will return the search results when EXTERNAL_SEARCH is enabled.
#
# Doxygen ships with an example indexer ( doxyindexer) and search engine
# (doxysearch.cgi) which are based on the open source search engine library
# Xapian (see: http://xapian.org/). See the section "External Indexing and
# Searching" for details.
# This tag requires that the tag SEARCHENGINE is set to YES.
SEARCHENGINE_URL =
# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
# search data is written to a file for indexing by an external tool. With the
# SEARCHDATA_FILE tag the name of this file can be specified.
# The default file is: searchdata.xml.
# This tag requires that the tag SEARCHENGINE is set to YES.
SEARCHDATA_FILE = searchdata.xml
# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
# projects and redirect the results back to the right project.
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTERNAL_SEARCH_ID =
# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
# projects other than the one defined by this configuration file, but that are
# all added to the same external search index. Each project needs to have a
# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
# to a relative location where the documentation can be found. The format is:
# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTRA_SEARCH_MAPPINGS =
#---------------------------------------------------------------------------
# Configuration options related to the LaTeX output
#---------------------------------------------------------------------------
# If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output.
# The default value is: YES.
GENERATE_LATEX = NO
# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: latex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_OUTPUT = latex
# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
# invoked.
#
# Note that when enabling USE_PDFLATEX this option is only used for generating
# bitmaps for formulas in the HTML output, but not in the Makefile that is
# written to the output directory.
# The default file is: latex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_CMD_NAME = latex
# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
# index for LaTeX.
# The default file is: makeindex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
MAKEINDEX_CMD_NAME = makeindex
# If the COMPACT_LATEX tag is set to YES doxygen generates more compact LaTeX
# documents. This may be useful for small projects and may help to save some
# trees in general.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
COMPACT_LATEX = NO
# The PAPER_TYPE tag can be used to set the paper type that is used by the
# printer.
# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
# 14 inches) and executive (7.25 x 10.5 inches).
# The default value is: a4.
# This tag requires that the tag GENERATE_LATEX is set to YES.
-PAPER_TYPE = a4wide
+PAPER_TYPE = a4
# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
# that should be included in the LaTeX output. To get the times font for
# instance you can specify
# EXTRA_PACKAGES=times
# If left blank no extra packages will be included.
# This tag requires that the tag GENERATE_LATEX is set to YES.
EXTRA_PACKAGES = amssymb
# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
# generated LaTeX document. The header should contain everything until the first
# chapter. If it is left blank doxygen will generate a standard header. See
# section "Doxygen usage" for information on how to let doxygen write the
# default header to a separate file.
#
# Note: Only use a user-defined header if you know what you are doing! The
# following commands have a special meaning inside the header: $title,
# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
# $projectbrief, $projectlogo. Doxygen will replace $title with the empy string,
# for the replacement values of the other commands the user is refered to
# HTML_HEADER.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HEADER =
# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
# generated LaTeX document. The footer should contain everything after the last
# chapter. If it is left blank doxygen will generate a standard footer. See
# LATEX_HEADER for more information on how to generate a default footer and what
# special commands can be used inside the footer.
#
# Note: Only use a user-defined footer if you know what you are doing!
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_FOOTER =
# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the LATEX_OUTPUT output
# directory. Note that the files will be copied as-is; there are no commands or
# markers available.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_EXTRA_FILES =
# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
# contain links (just like the HTML output) instead of page references. This
# makes the output suitable for online browsing using a PDF viewer.
# The default value is: YES.
# This tag requires that the tag GENERATE_LATEX is set to YES.
PDF_HYPERLINKS = NO
# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
# the PDF file directly from the LaTeX files. Set this option to YES to get a
# higher quality PDF documentation.
# The default value is: YES.
# This tag requires that the tag GENERATE_LATEX is set to YES.
USE_PDFLATEX = NO
# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
# command to the generated LaTeX files. This will instruct LaTeX to keep running
# if errors occur, instead of asking the user for help. This option is also used
# when generating formulas in HTML.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_BATCHMODE = NO
# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
# index chapters (such as File Index, Compound Index, etc.) in the output.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HIDE_INDICES = NO
# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
# code with syntax highlighting in the LaTeX output.
#
# Note that which sources are shown also depends on other settings such as
# SOURCE_BROWSER.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_SOURCE_CODE = NO
# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
# bibliography, e.g. plainnat, or ieeetr. See
# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
# The default value is: plain.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_BIB_STYLE = plain
#---------------------------------------------------------------------------
# Configuration options related to the RTF output
#---------------------------------------------------------------------------
# If the GENERATE_RTF tag is set to YES doxygen will generate RTF output. The
# RTF output is optimized for Word 97 and may not look too pretty with other RTF
# readers/editors.
# The default value is: NO.
GENERATE_RTF = NO
# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: rtf.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_OUTPUT = rtf
# If the COMPACT_RTF tag is set to YES doxygen generates more compact RTF
# documents. This may be useful for small projects and may help to save some
# trees in general.
# The default value is: NO.
# This tag requires that the tag GENERATE_RTF is set to YES.
COMPACT_RTF = NO
# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
# contain hyperlink fields. The RTF file will contain links (just like the HTML
# output) instead of page references. This makes the output suitable for online
# browsing using Word or some other Word compatible readers that support those
# fields.
#
# Note: WordPad (write) and others do not support links.
# The default value is: NO.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_HYPERLINKS = NO
# Load stylesheet definitions from file. Syntax is similar to doxygen's config
# file, i.e. a series of assignments. You only have to provide replacements,
# missing definitions are set to their default value.
#
# See also section "Doxygen usage" for information on how to generate the
# default style sheet that doxygen normally uses.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_STYLESHEET_FILE =
# Set optional variables used in the generation of an RTF document. Syntax is
# similar to doxygen's config file. A template extensions file can be generated
# using doxygen -e rtf extensionFile.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_EXTENSIONS_FILE =
#---------------------------------------------------------------------------
# Configuration options related to the man page output
#---------------------------------------------------------------------------
# If the GENERATE_MAN tag is set to YES doxygen will generate man pages for
# classes and files.
# The default value is: NO.
GENERATE_MAN = NO
# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it. A directory man3 will be created inside the directory specified by
# MAN_OUTPUT.
# The default directory is: man.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_OUTPUT = man
# The MAN_EXTENSION tag determines the extension that is added to the generated
# man pages. In case the manual section does not start with a number, the number
# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
# optional.
# The default value is: .3.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_EXTENSION = .3
# The MAN_SUBDIR tag determines the name of the directory created within
# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
# MAN_EXTENSION with the initial . removed.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_SUBDIR =
# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
# will generate one additional man file for each entity documented in the real
# man page(s). These additional files only source the real man page, but without
# them the man command would be unable to find the correct page.
# The default value is: NO.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_LINKS = NO
#---------------------------------------------------------------------------
# Configuration options related to the XML output
#---------------------------------------------------------------------------
# If the GENERATE_XML tag is set to YES doxygen will generate an XML file that
# captures the structure of the code including all documentation.
# The default value is: NO.
GENERATE_XML = NO
# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: xml.
# This tag requires that the tag GENERATE_XML is set to YES.
XML_OUTPUT = xml
# If the XML_PROGRAMLISTING tag is set to YES doxygen will dump the program
# listings (including syntax highlighting and cross-referencing information) to
# the XML output. Note that enabling this will significantly increase the size
# of the XML output.
# The default value is: YES.
# This tag requires that the tag GENERATE_XML is set to YES.
XML_PROGRAMLISTING = YES
#---------------------------------------------------------------------------
# Configuration options related to the DOCBOOK output
#---------------------------------------------------------------------------
# If the GENERATE_DOCBOOK tag is set to YES doxygen will generate Docbook files
# that can be used to generate PDF.
# The default value is: NO.
GENERATE_DOCBOOK = NO
# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
# front of it.
# The default directory is: docbook.
# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
DOCBOOK_OUTPUT = docbook
# If the DOCBOOK_PROGRAMLISTING tag is set to YES doxygen will include the
# program listings (including syntax highlighting and cross-referencing
# information) to the DOCBOOK output. Note that enabling this will significantly
# increase the size of the DOCBOOK output.
# The default value is: NO.
# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
DOCBOOK_PROGRAMLISTING = NO
#---------------------------------------------------------------------------
# Configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
# If the GENERATE_AUTOGEN_DEF tag is set to YES doxygen will generate an AutoGen
# Definitions (see http://autogen.sf.net) file that captures the structure of
# the code including all documentation. Note that this feature is still
# experimental and incomplete at the moment.
# The default value is: NO.
GENERATE_AUTOGEN_DEF = NO
#---------------------------------------------------------------------------
# Configuration options related to the Perl module output
#---------------------------------------------------------------------------
# If the GENERATE_PERLMOD tag is set to YES doxygen will generate a Perl module
# file that captures the structure of the code including all documentation.
#
# Note that this feature is still experimental and incomplete at the moment.
# The default value is: NO.
GENERATE_PERLMOD = NO
# If the PERLMOD_LATEX tag is set to YES doxygen will generate the necessary
# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
# output from the Perl module output.
# The default value is: NO.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_LATEX = NO
# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be nicely
# formatted so it can be parsed by a human reader. This is useful if you want to
# understand what is going on. On the other hand, if this tag is set to NO the
# size of the Perl module output will be much smaller and Perl will parse it
# just the same.
# The default value is: YES.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_PRETTY = YES
# The names of the make variables in the generated doxyrules.make file are
# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
# so different doxyrules.make files included by the same Makefile don't
# overwrite each other's variables.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_MAKEVAR_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
# If the ENABLE_PREPROCESSING tag is set to YES doxygen will evaluate all
# C-preprocessor directives found in the sources and include files.
# The default value is: YES.
ENABLE_PREPROCESSING = YES
# If the MACRO_EXPANSION tag is set to YES doxygen will expand all macro names
# in the source code. If set to NO only conditional compilation will be
# performed. Macro expansion can be done in a controlled way by setting
# EXPAND_ONLY_PREDEF to YES.
# The default value is: NO.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
MACRO_EXPANSION = YES
# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
# the macro expansion is limited to the macros specified with the PREDEFINED and
# EXPAND_AS_DEFINED tags.
# The default value is: NO.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
EXPAND_ONLY_PREDEF = NO
# If the SEARCH_INCLUDES tag is set to YES the includes files in the
# INCLUDE_PATH will be searched if a #include is found.
# The default value is: YES.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
SEARCH_INCLUDES = YES
# The INCLUDE_PATH tag can be used to specify one or more directories that
# contain include files that are not input files but should be processed by the
# preprocessor.
# This tag requires that the tag SEARCH_INCLUDES is set to YES.
INCLUDE_PATH =
# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
# patterns (like *.h and *.hpp) to filter out the header-files in the
# directories. If left blank, the patterns specified with FILE_PATTERNS will be
# used.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
INCLUDE_FILE_PATTERNS =
# The PREDEFINED tag can be used to specify one or more macro names that are
# defined before the preprocessor is started (similar to the -D option of e.g.
# gcc). The argument of the tag is a list of macros of the form: name or
# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
# is assumed. To prevent a macro definition from being undefined via #undef or
# recursively expanded use the := operator instead of the = operator.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
PREDEFINED = itkNotUsed(x)= \
"itkSetMacro(name,type)=virtual void Set##name (type _arg);" \
"itkGetMacro(name,type)=virtual type Get##name ();" \
"itkGetConstMacro(name,type)=virtual type Get##name () const;" \
"itkSetStringMacro(name)=virtual void Set##name (const char* _arg);" \
"itkGetStringMacro(name)=virtual const char* Get##name () const;" \
"itkSetClampMacro(name,type,min,max)=virtual void Set##name (type _arg);" \
"itkSetObjectMacro(name,type)=virtual void Set##name (type* _arg);" \
"itkGetObjectMacro(name,type)=virtual type* Get##name ();" \
"itkSetConstObjectMacro(name,type)=virtual void Set##name ( const type* _arg);" \
"itkGetConstObjectMacro(name,type)=virtual const type* Get##name ();" \
"itkGetConstReferenceMacro(name,type)=virtual const type& Get##name ();" \
"itkGetConstReferenceObjectMacro(name,type)=virtual const type::Pointer& Get##name () const;" \
"itkBooleanMacro(name)=virtual void name##On (); virtual void name##Off ();" \
"itkSetVector2Macro(name,type)=virtual void Set##name (type _arg1, type _arg2) virtual void Set##name (type _arg[2]);" \
"itkGetVector2Macro(name,type)=virtual type* Get##name () const; virtual void Get##name (type& _arg1, type& _arg2) const; virtual void Get##name (type _arg[2]) const;" \
"itkSetVector3Macro(name,type)=virtual void Set##name (type _arg1, type _arg2, type _arg3) virtual void Set##name (type _arg[3]);" \
"itkGetVector3Macro(name,type)=virtual type* Get##name () const; virtual void Get##name (type& _arg1, type& _arg2, type& _arg3) const; virtual void Get##name (type _arg[3]) const;" \
"itkSetVector4Macro(name,type)=virtual void Set##name (type _arg1, type _arg2, type _arg3, type _arg4) virtual void Set##name (type _arg[4]);" \
"itkGetVector4Macro(name,type)=virtual type* Get##name () const; virtual void Get##name (type& _arg1, type& _arg2, type& _arg3, type& _arg4) const; virtual void Get##name (type _arg[4]) const;" \
"itkSetVector6Macro(name,type)=virtual void Set##name (type _arg1, type _arg2, type _arg3, type _arg4, type _arg5, type _arg6) virtual void Set##name (type _arg[6]);" \
"itkGetVector6Macro(name,type)=virtual type* Get##name () const; virtual void Get##name (type& _arg1, type& _arg2, type& _arg3, type& _arg4, type& _arg5, type& _arg6) const; virtual void Get##name (type _arg[6]) const;" \
"itkSetVectorMacro(name,type,count)=virtual void Set##name(type data[]);" \
"itkGetVectorMacro(name,type,count)=virtual type* Get##name () const;" \
"itkNewMacro(type)=static Pointer New();" \
"itkFactorylessNewMacro(type)=static Pointer New();" \
"itkCloneMacro(type)=Pointer Clone() const;" \
"itkTypeMacro(thisClass,superclass)=virtual const char *GetClassName() const;" \
"itkConceptMacro(name,concept)=enum { name = 0 };" \
"ITK_NUMERIC_LIMITS=std::numeric_limits" \
"ITK_TYPENAME=typename" \
"FEM_ABSTRACT_CLASS(thisClass,parentClass)=public: /** Standard Self typedef.*/ typedef thisClass Self; /** Standard Superclass typedef. */ typedef parentClass Superclass; /** Pointer or SmartPointer to an object. */ typedef Self* Pointer; /** Const pointer or SmartPointer to an object. */ typedef const Self* ConstPointer; private:" \
"FEM_CLASS(thisClass,parentClass)=FEM_ABSTRACT_CLASS(thisClass,parentClass) public: /** Create a new object from the existing one */ virtual Baseclass::Pointer Clone() const; /** Class ID for FEM object factory */ static const int CLID; /** Virtual function to access the class ID */ virtual int ClassID() const { return CLID; /** Object creation in an itk compatible way */ static Self::Pointer New() { return new Self(); } private:" \
FREEVERSION \
ERROR_CHECKING \
HAS_TIFF \
HAS_JPEG \
HAS_NETLIB \
HAS_PNG \
HAS_ZLIB \
HAS_GLUT \
HAS_QT \
VCL_USE_NATIVE_STL=1 \
VCL_USE_NATIVE_COMPLEX=1 \
VCL_HAS_BOOL=1 \
VXL_BIG_ENDIAN=1 \
VXL_LITTLE_ENDIAN=0 \
VNL_DLL_DATA= \
size_t=vcl_size_t \
"US_PREPEND_NAMESPACE(x)=us::x" \
"US_BEGIN_NAMESPACE= namespace us {" \
"US_END_NAMESPACE=}" \
"US_BASECLASS_NAME=itk::LightObject" \
US_EXPORT= \
"DEPRECATED(func)=func" \
@US_PLATFORM@
# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
# tag can be used to specify a list of macro names that should be expanded. The
# macro definition that is found in the sources will be used. Use the PREDEFINED
# tag if you want to use a different macro definition that overrules the
# definition found in the source code.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
EXPAND_AS_DEFINED =
# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
# remove all references to function-like macros that are alone on a line, have
# an all uppercase name, and do not end with a semicolon. Such function macros
# are typically used for boiler-plate code, and will confuse the parser if not
# removed.
# The default value is: YES.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
SKIP_FUNCTION_MACROS = YES
#---------------------------------------------------------------------------
# Configuration options related to external references
#---------------------------------------------------------------------------
# The TAGFILES tag can be used to specify one or more tag files. For each tag
# file the location of the external documentation should be added. The format of
# a tag file without this location is as follows:
# TAGFILES = file1 file2 ...
# Adding location for the tag files is done as follows:
# TAGFILES = file1=loc1 "file2 = loc2" ...
# where loc1 and loc2 can be relative or absolute paths or URLs. See the
# section "Linking to external documentation" for more information about the use
# of tag files.
# Note: Each tag file must have a unique name (where the name does NOT include
# the path). If a tag file is not located in the directory in which doxygen is
# run, you must also specify the path to the tagfile here.
TAGFILES =
# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
# tag file that is based on the input files it reads. See section "Linking to
# external documentation" for more information about the usage of tag files.
GENERATE_TAGFILE = @MITK_DOXYGEN_TAGFILE_NAME@
# If the ALLEXTERNALS tag is set to YES all external class will be listed in the
# class index. If set to NO only the inherited external classes will be listed.
# The default value is: NO.
ALLEXTERNALS = NO
# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed in
# the modules index. If set to NO, only the current project's groups will be
# listed.
# The default value is: YES.
EXTERNAL_GROUPS = NO
# If the EXTERNAL_PAGES tag is set to YES all external pages will be listed in
# the related pages index. If set to NO, only the current project's pages will
# be listed.
# The default value is: YES.
EXTERNAL_PAGES = YES
#---------------------------------------------------------------------------
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
# If the CLASS_DIAGRAMS tag is set to YES doxygen will generate a class diagram
# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
# NO turns the diagrams off. Note that this option also works with HAVE_DOT
# disabled, but it is recommended to install and use dot, since it yields more
# powerful graphs.
# The default value is: YES.
CLASS_DIAGRAMS = YES
# You can include diagrams made with dia in doxygen documentation. Doxygen will
# then run dia to produce the diagram and insert it in the documentation. The
# DIA_PATH tag allows you to specify the directory where the dia binary resides.
# If left empty dia is assumed to be found in the default search path.
DIA_PATH =
# If set to YES, the inheritance and collaboration graphs will hide inheritance
# and usage relations if the target is undocumented or is not a class.
# The default value is: YES.
HIDE_UNDOC_RELATIONS = YES
# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
# available from the path. This tool is part of Graphviz (see:
# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
# Bell Labs. The other options in this section have no effect if this option is
# set to NO
# The default value is: NO.
HAVE_DOT = @HAVE_DOT@
# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
# to run in parallel. When set to 0 doxygen will base this on the number of
# processors available in the system. You can set it explicitly to a value
# larger than 0 to get control over the balance between CPU load and processing
# speed.
# Minimum value: 0, maximum value: 32, default value: 0.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_NUM_THREADS = @MITK_DOXYGEN_DOT_NUM_THREADS@
# When you want a differently looking font in the dot files that doxygen
# generates you can specify the font name using DOT_FONTNAME. You need to make
# sure dot is able to find the font, which can be done by putting it in a
# standard location or by setting the DOTFONTPATH environment variable or by
# setting DOT_FONTPATH to the directory containing the font.
# The default value is: Helvetica.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTNAME = Helvetica
# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
# dot graphs.
# Minimum value: 4, maximum value: 24, default value: 10.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTSIZE = 10
# By default doxygen will tell dot to use the default font as specified with
# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
# the path where dot can find it using this tag.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTPATH =
# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
# each documented class showing the direct and indirect inheritance relations.
# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
CLASS_GRAPH = YES
# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
# graph for each documented class showing the direct and indirect implementation
# dependencies (inheritance, containment, and class references variables) of the
# class with other documented classes.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
COLLABORATION_GRAPH = YES
# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
# groups, showing the direct groups dependencies.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
GROUP_GRAPHS = YES
# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
# collaboration diagrams in a style similar to the OMG's Unified Modeling
# Language.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
UML_LOOK = @MITK_DOXYGEN_UML_LOOK@
# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
# class node. If there are many fields or methods and many nodes the graph may
# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
# number of items for each type to make the size more manageable. Set this to 0
# for no limit. Note that the threshold may be exceeded by 50% before the limit
# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
# but if the number exceeds 15, the total amount of fields shown is limited to
# 10.
# Minimum value: 0, maximum value: 100, default value: 10.
# This tag requires that the tag HAVE_DOT is set to YES.
UML_LIMIT_NUM_FIELDS = 10
# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
# collaboration graphs will show the relations between templates and their
# instances.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
TEMPLATE_RELATIONS = YES
# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
# YES then doxygen will generate a graph for each documented file showing the
# direct and indirect include dependencies of the file with other documented
# files.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
INCLUDE_GRAPH = NO
# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
# set to YES then doxygen will generate a graph for each documented file showing
# the direct and indirect include dependencies of the file with other documented
# files.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
INCLUDED_BY_GRAPH = NO
# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
# dependency graph for every global function or class method.
#
# Note that enabling this option will significantly increase the time of a run.
# So in most cases it will be better to enable call graphs for selected
# functions only using the \callgraph command.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
CALL_GRAPH = NO
# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
# dependency graph for every global function or class method.
#
# Note that enabling this option will significantly increase the time of a run.
# So in most cases it will be better to enable caller graphs for selected
# functions only using the \callergraph command.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
CALLER_GRAPH = NO
# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
# hierarchy of all classes instead of a textual one.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
GRAPHICAL_HIERARCHY = NO
# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
# dependencies a directory has on other directories in a graphical way. The
# dependency relations are determined by the #include relations between the
# files in the directories.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
DIRECTORY_GRAPH = YES
# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
# generated by dot.
# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
# to make the SVG files visible in IE 9+ (other browsers do not have this
# requirement).
# Possible values are: png, jpg, gif and svg.
# The default value is: png.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_IMAGE_FORMAT = png
# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
# enable generation of interactive SVG images that allow zooming and panning.
#
# Note that this requires a modern browser other than Internet Explorer. Tested
# and working are Firefox, Chrome, Safari, and Opera.
# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
# the SVG files visible. Older versions of IE do not have SVG support.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
INTERACTIVE_SVG = NO
# The DOT_PATH tag can be used to specify the path where the dot tool can be
# found. If left blank, it is assumed the dot tool can be found in the path.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_PATH = "@DOXYGEN_DOT_PATH@"
# The DOTFILE_DIRS tag can be used to specify one or more directories that
# contain dot files that are included in the documentation (see the \dotfile
# command).
# This tag requires that the tag HAVE_DOT is set to YES.
DOTFILE_DIRS =
# The MSCFILE_DIRS tag can be used to specify one or more directories that
# contain msc files that are included in the documentation (see the \mscfile
# command).
MSCFILE_DIRS =
# The DIAFILE_DIRS tag can be used to specify one or more directories that
# contain dia files that are included in the documentation (see the \diafile
# command).
DIAFILE_DIRS =
# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
# path where java can find the plantuml.jar file. If left blank, it is assumed
# PlantUML is not used or called during a preprocessing step. Doxygen will
# generate a warning when it encounters a \startuml command in this case and
# will not generate output for the diagram.
# This tag requires that the tag HAVE_DOT is set to YES.
PLANTUML_JAR_PATH =
# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
# that will be shown in the graph. If the number of nodes in a graph becomes
# larger than this value, doxygen will truncate the graph, which is visualized
# by representing a node as a red box. Note that doxygen if the number of direct
# children of the root node in a graph is already larger than
# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
# Minimum value: 0, maximum value: 10000, default value: 50.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_GRAPH_MAX_NODES = 50
# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
# generated by dot. A depth value of 3 means that only nodes reachable from the
# root by following a path via at most 3 edges will be shown. Nodes that lay
# further from the root node will be omitted. Note that setting this option to 1
# or 2 may greatly reduce the computation time needed for large code bases. Also
# note that the size of a graph can be further restricted by
# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
# Minimum value: 0, maximum value: 1000, default value: 0.
# This tag requires that the tag HAVE_DOT is set to YES.
MAX_DOT_GRAPH_DEPTH = 0
# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
# background. This is disabled by default, because dot on Windows does not seem
# to support this out of the box.
#
# Warning: Depending on the platform used, enabling this option may lead to
# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
# read).
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_TRANSPARENT = NO
# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
# files in one run (i.e. multiple -o and -T options on the command line). This
# makes dot run faster, but since only newer versions of dot (>1.8.10) support
# this, this feature is disabled by default.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_MULTI_TARGETS = NO
# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
# explaining the meaning of the various boxes and arrows in the dot generated
# graphs.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
GENERATE_LEGEND = YES
# If the DOT_CLEANUP tag is set to YES doxygen will remove the intermediate dot
# files that are used to generate the various graphs.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_CLEANUP = YES
diff --git a/Documentation/doxygen_developers_guide.conf.in b/Documentation/doxygen_developers_guide.conf.in
index 2b7d5a1c56..40b23f0bb8 100644
--- a/Documentation/doxygen_developers_guide.conf.in
+++ b/Documentation/doxygen_developers_guide.conf.in
@@ -1,2334 +1,2328 @@
# Doxyfile 1.8.8
# This file describes the settings to be used by the documentation system
# doxygen (www.doxygen.org) for a project.
#
# All text after a double hash (##) is considered a comment and is placed in
# front of the TAG it is preceding.
#
# All text after a single hash (#) is considered a comment and will be ignored.
# The format is:
# TAG = value [value, ...]
# For lists, items can also be appended using:
# TAG += value [value, ...]
# Values that contain spaces should be placed between quotes (\" \").
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
# This tag specifies the encoding used for all characters in the config file
# that follow. The default is UTF-8 which is also the encoding used for all text
# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv
# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv
# for the list of possible encodings.
# The default value is: UTF-8.
DOXYFILE_ENCODING = UTF-8
# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
# double-quotes, unless you are using Doxywizard) that should identify the
# project for which the documentation is generated. This name is used in the
# title of most generated pages and in a few other places.
# The default value is: My Project.
PROJECT_NAME = MITK
# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
# could be handy for archiving the generated documentation or if some version
# control system is used.
PROJECT_NUMBER = @MITK_VERSION_STRING@
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
# quick idea about the purpose of the project. Keep the description short.
PROJECT_BRIEF = "Medical Imaging Interaction Toolkit"
# With the PROJECT_LOGO tag one can specify an logo or icon that is included in
# the documentation. The maximum height of the logo should not exceed 55 pixels
# and the maximum width should not exceed 200 pixels. Doxygen will copy the logo
# to the output directory.
PROJECT_LOGO =
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
# into which the generated documentation will be written. If a relative path is
# entered, it will be relative to the location where doxygen was started. If
# left blank the current directory will be used.
OUTPUT_DIRECTORY = "@MITK_DOXYGEN_OUTPUT_DIR@/Guides/Developers_Guide/"
# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 4096 sub-
# directories (in 2 levels) under the output directory of each output format and
# will distribute the generated files over these directories. Enabling this
# option can be useful when feeding doxygen a huge amount of source files, where
# putting all generated files in the same directory would otherwise causes
# performance problems for the file system.
# The default value is: NO.
CREATE_SUBDIRS = NO
# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
# characters to appear in the names of generated files. If set to NO, non-ASCII
# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
# U+3044.
# The default value is: NO.
ALLOW_UNICODE_NAMES = NO
# The OUTPUT_LANGUAGE tag is used to specify the language in which all
# documentation generated by doxygen is written. Doxygen will use this
# information to generate all constant output in the proper language.
# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
# Ukrainian and Vietnamese.
# The default value is: English.
OUTPUT_LANGUAGE = English
# If the BRIEF_MEMBER_DESC tag is set to YES doxygen will include brief member
# descriptions after the members that are listed in the file and class
# documentation (similar to Javadoc). Set to NO to disable this.
# The default value is: YES.
BRIEF_MEMBER_DESC = YES
# If the REPEAT_BRIEF tag is set to YES doxygen will prepend the brief
# description of a member or function before the detailed description
#
# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
# brief descriptions will be completely suppressed.
# The default value is: YES.
REPEAT_BRIEF = YES
# This tag implements a quasi-intelligent brief description abbreviator that is
# used to form the text in various listings. Each string in this list, if found
# as the leading text of the brief description, will be stripped from the text
# and the result, after processing the whole list, is used as the annotated
# text. Otherwise, the brief description is used as-is. If left blank, the
# following values are used ($name is automatically replaced with the name of
# the entity):The $name class, The $name widget, The $name file, is, provides,
# specifies, contains, represents, a, an and the.
ABBREVIATE_BRIEF =
# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
# doxygen will generate a detailed section even if there is only a brief
# description.
# The default value is: NO.
ALWAYS_DETAILED_SEC = NO
# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
# inherited members of a class in the documentation of that class as if those
# members were ordinary class members. Constructors, destructors and assignment
# operators of the base classes will not be shown.
# The default value is: NO.
INLINE_INHERITED_MEMB = NO
# If the FULL_PATH_NAMES tag is set to YES doxygen will prepend the full path
# before files name in the file list and in the header files. If set to NO the
# shortest path that makes the file name unique will be used
# The default value is: YES.
FULL_PATH_NAMES = NO
# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
# Stripping is only done if one of the specified strings matches the left-hand
# part of the path. The tag can be used to show relative paths in the file list.
# If left blank the directory from which doxygen is run is used as the path to
# strip.
#
# Note that you can specify absolute paths here, but also relative paths, which
# will be relative from the directory where doxygen is started.
# This tag requires that the tag FULL_PATH_NAMES is set to YES.
STRIP_FROM_PATH =
# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
# path mentioned in the documentation of a class, which tells the reader which
# header file to include in order to use a class. If left blank only the name of
# the header file containing the class definition is used. Otherwise one should
# specify the list of include paths that are normally passed to the compiler
# using the -I flag.
STRIP_FROM_INC_PATH =
# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
# less readable) file names. This can be useful is your file systems doesn't
# support long names like on DOS, Mac, or CD-ROM.
# The default value is: NO.
SHORT_NAMES = NO
# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
# first line (until the first dot) of a Javadoc-style comment as the brief
# description. If set to NO, the Javadoc-style will behave just like regular Qt-
# style comments (thus requiring an explicit @brief command for a brief
# description.)
# The default value is: NO.
JAVADOC_AUTOBRIEF = NO
# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
# line (until the first dot) of a Qt-style comment as the brief description. If
# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
# requiring an explicit \brief command for a brief description.)
# The default value is: NO.
QT_AUTOBRIEF = NO
# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
# a brief description. This used to be the default behavior. The new default is
# to treat a multi-line C++ comment block as a detailed description. Set this
# tag to YES if you prefer the old behavior instead.
#
# Note that setting this tag to YES also means that rational rose comments are
# not recognized any more.
# The default value is: NO.
MULTILINE_CPP_IS_BRIEF = NO
# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
# documentation from any documented member that it re-implements.
# The default value is: YES.
INHERIT_DOCS = YES
# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce a
# new page for each member. If set to NO, the documentation of a member will be
# part of the file/class/namespace that contains it.
# The default value is: NO.
SEPARATE_MEMBER_PAGES = NO
# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
# uses this value to replace tabs by spaces in code fragments.
# Minimum value: 1, maximum value: 16, default value: 4.
TAB_SIZE = 8
# This tag can be used to specify a number of aliases that act as commands in
# the documentation. An alias has the form:
# name=value
# For example adding
# "sideeffect=@par Side Effects:\n"
# will allow you to put the command \sideeffect (or @sideeffect) in the
# documentation, which will result in a user-defined paragraph with heading
# "Side Effects:". You can put \n's in the value part of an alias to insert
# newlines.
ALIASES = "FIXME=\par Fix Me's:\n" \
"BlueBerry=\if BLUEBERRY" \
"endBlueBerry=\endif" \
"bundlemainpage{1}=\page \1" \
"embmainpage{1}=\page \1" \
"github{2}=<a href=\"https://github.com/MITK/MITK/blob/master/\1\">\2</a>" \
"deprecatedSince{1}=\xrefitem deprecatedSince\1 \" Deprecated as of \1\" \"Functions deprecated as of \1\" " \
"minimumCMakeVersion=@MITK_CMAKE_MINIMUM_REQUIRED_VERSION@" \
"minimumQt5Version=@MITK_QT5_MINIMUM_VERSION@" \
"imageMacro{3}=\image html \1 \2 \n \image latex \1 \2 width=\3cm" \
"developersguidemainpage{1}=\mainpage " \
"usersguidemainpage{1}=\page \1" \
"nondependentPluginLink{3}= \ref \1 \"\3\" "
-# This tag can be used to specify a number of word-keyword mappings (TCL only).
-# A mapping has the form "name=value". For example adding "class=itcl::class"
-# will allow you to use the command class in the itcl::class meaning.
-
-TCL_SUBST =
-
# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
# only. Doxygen will then generate output that is more tailored for C. For
# instance, some of the names that are used will be different. The list of all
# members will be omitted, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_FOR_C = NO
# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
# Python sources only. Doxygen will then generate output that is more tailored
# for that language. For instance, namespaces will be presented as packages,
# qualified scopes will look different, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_JAVA = NO
# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
# sources. Doxygen will then generate output that is tailored for Fortran.
# The default value is: NO.
OPTIMIZE_FOR_FORTRAN = NO
# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
# sources. Doxygen will then generate output that is tailored for VHDL.
# The default value is: NO.
OPTIMIZE_OUTPUT_VHDL = NO
# Doxygen selects the parser to use depending on the extension of the files it
# parses. With this tag you can assign which parser to use for a given
# extension. Doxygen has a built-in mapping, but you can override or extend it
# using this tag. The format is ext=language, where ext is a file extension, and
# language is one of the parsers supported by doxygen: IDL, Java, Javascript,
# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran:
# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran:
# Fortran. In the later case the parser tries to guess whether the code is fixed
# or free formatted code, this is the default for Fortran type files), VHDL. For
# instance to make doxygen treat .inc files as Fortran files (default is PHP),
# and .f files as C (default is Fortran), use: inc=Fortran f=C.
#
# Note For files without extension you can use no_extension as a placeholder.
#
# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
# the files are not read by doxygen.
EXTENSION_MAPPING =
# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
# according to the Markdown format, which allows for more readable
# documentation. See http://daringfireball.net/projects/markdown/ for details.
# The output of markdown processing is further processed by doxygen, so you can
# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
# case of backward compatibilities issues.
# The default value is: YES.
MARKDOWN_SUPPORT = YES
# When enabled doxygen tries to link words that correspond to documented
# classes, or namespaces to their corresponding documentation. Such a link can
# be prevented in individual cases by by putting a % sign in front of the word
# or globally by setting AUTOLINK_SUPPORT to NO.
# The default value is: YES.
AUTOLINK_SUPPORT = YES
# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
# to include (a tag file for) the STL sources as input, then you should set this
# tag to YES in order to let doxygen match functions declarations and
# definitions whose arguments contain STL classes (e.g. func(std::string);
# versus func(std::string) {}). This also make the inheritance and collaboration
# diagrams that involve STL classes more complete and accurate.
# The default value is: NO.
BUILTIN_STL_SUPPORT = YES
# If you use Microsoft's C++/CLI language, you should set this option to YES to
# enable parsing support.
# The default value is: NO.
CPP_CLI_SUPPORT = NO
# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen
# will parse them like normal C++ but will assume all classes use public instead
# of private inheritance when no explicit protection keyword is present.
# The default value is: NO.
SIP_SUPPORT = NO
# For Microsoft's IDL there are propget and propput attributes to indicate
# getter and setter methods for a property. Setting this option to YES will make
# doxygen to replace the get and set methods by a property in the documentation.
# This will only work if the methods are indeed getting or setting a simple
# type. If this is not the case, or you want to show the methods anyway, you
# should set this option to NO.
# The default value is: YES.
IDL_PROPERTY_SUPPORT = YES
# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
# tag is set to YES, then doxygen will reuse the documentation of the first
# member in the group (if any) for the other members of the group. By default
# all members of a group must be documented explicitly.
# The default value is: NO.
DISTRIBUTE_GROUP_DOC = YES
# Set the SUBGROUPING tag to YES to allow class member groups of the same type
# (for instance a group of public functions) to be put as a subgroup of that
# type (e.g. under the Public Functions section). Set it to NO to prevent
# subgrouping. Alternatively, this can be done per class using the
# \nosubgrouping command.
# The default value is: YES.
SUBGROUPING = YES
# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
# are shown inside the group in which they are included (e.g. using \ingroup)
# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
# and RTF).
#
# Note that this feature does not work in combination with
# SEPARATE_MEMBER_PAGES.
# The default value is: NO.
INLINE_GROUPED_CLASSES = NO
# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
# with only public data fields or simple typedef fields will be shown inline in
# the documentation of the scope in which they are defined (i.e. file,
# namespace, or group documentation), provided this scope is documented. If set
# to NO, structs, classes, and unions are shown on a separate page (for HTML and
# Man pages) or section (for LaTeX and RTF).
# The default value is: NO.
INLINE_SIMPLE_STRUCTS = NO
# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
# enum is documented as struct, union, or enum with the name of the typedef. So
# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
# with name TypeT. When disabled the typedef will appear as a member of a file,
# namespace, or class. And the struct will be named TypeS. This can typically be
# useful for C code in case the coding convention dictates that all compound
# types are typedef'ed and only the typedef is referenced, never the tag name.
# The default value is: NO.
TYPEDEF_HIDES_STRUCT = NO
# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
# cache is used to resolve symbols given their name and scope. Since this can be
# an expensive process and often the same symbol appears multiple times in the
# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
# doxygen will become slower. If the cache is too large, memory is wasted. The
# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
# symbols. At the end of a run doxygen will report the cache usage and suggest
# the optimal cache size from a speed point of view.
# Minimum value: 0, maximum value: 9, default value: 0.
LOOKUP_CACHE_SIZE = 0
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
# documentation are documented, even if no documentation was available. Private
# class members and static file members will be hidden unless the
# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
# Note: This will also disable the warnings about undocumented members that are
# normally produced when WARNINGS is set to YES.
# The default value is: NO.
EXTRACT_ALL = YES
# If the EXTRACT_PRIVATE tag is set to YES all private members of a class will
# be included in the documentation.
# The default value is: NO.
EXTRACT_PRIVATE = NO
# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal
# scope will be included in the documentation.
# The default value is: NO.
EXTRACT_PACKAGE = NO
# If the EXTRACT_STATIC tag is set to YES all static members of a file will be
# included in the documentation.
# The default value is: NO.
EXTRACT_STATIC = YES
# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) defined
# locally in source files will be included in the documentation. If set to NO
# only classes defined in header files are included. Does not have any effect
# for Java sources.
# The default value is: YES.
EXTRACT_LOCAL_CLASSES = @MITK_DOXYGEN_INTERNAL_DOCS@
# This flag is only useful for Objective-C code. When set to YES local methods,
# which are defined in the implementation section but not in the interface are
# included in the documentation. If set to NO only methods in the interface are
# included.
# The default value is: NO.
EXTRACT_LOCAL_METHODS = NO
# If this flag is set to YES, the members of anonymous namespaces will be
# extracted and appear in the documentation as a namespace called
# 'anonymous_namespace{file}', where file will be replaced with the base name of
# the file that contains the anonymous namespace. By default anonymous namespace
# are hidden.
# The default value is: NO.
EXTRACT_ANON_NSPACES = NO
# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
# undocumented members inside documented classes or files. If set to NO these
# members will be included in the various overviews, but no documentation
# section is generated. This option has no effect if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_MEMBERS = NO
# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
# undocumented classes that are normally visible in the class hierarchy. If set
# to NO these classes will be included in the various overviews. This option has
# no effect if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_CLASSES = NO
# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
# (class|struct|union) declarations. If set to NO these declarations will be
# included in the documentation.
# The default value is: NO.
HIDE_FRIEND_COMPOUNDS = @MITK_DOXYGEN_HIDE_FRIEND_COMPOUNDS@
# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
# documentation blocks found inside the body of a function. If set to NO these
# blocks will be appended to the function's detailed documentation block.
# The default value is: NO.
HIDE_IN_BODY_DOCS = NO
# The INTERNAL_DOCS tag determines if documentation that is typed after a
# \internal command is included. If the tag is set to NO then the documentation
# will be excluded. Set it to YES to include the internal documentation.
# The default value is: NO.
INTERNAL_DOCS = @MITK_DOXYGEN_INTERNAL_DOCS@
# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
# names in lower-case letters. If set to YES upper-case letters are also
# allowed. This is useful if you have classes or files whose names only differ
# in case and if your file system supports case sensitive file names. Windows
# and Mac users are advised to set this option to NO.
# The default value is: system dependent.
CASE_SENSE_NAMES = YES
# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
# their full class and namespace scopes in the documentation. If set to YES the
# scope will be hidden.
# The default value is: NO.
HIDE_SCOPE_NAMES = NO
# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
# the files that are included by a file in the documentation of that file.
# The default value is: YES.
SHOW_INCLUDE_FILES = YES
# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
# grouped member an include statement to the documentation, telling the reader
# which file to include in order to use the member.
# The default value is: NO.
SHOW_GROUPED_MEMB_INC = NO
# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
# files with double quotes in the documentation rather than with sharp brackets.
# The default value is: NO.
FORCE_LOCAL_INCLUDES = NO
# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
# documentation for inline members.
# The default value is: YES.
INLINE_INFO = YES
# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
# (detailed) documentation of file and class members alphabetically by member
# name. If set to NO the members will appear in declaration order.
# The default value is: YES.
SORT_MEMBER_DOCS = YES
# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
# descriptions of file, namespace and class members alphabetically by member
# name. If set to NO the members will appear in declaration order. Note that
# this will also influence the order of the classes in the class list.
# The default value is: NO.
SORT_BRIEF_DOCS = NO
# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
# (brief and detailed) documentation of class members so that constructors and
# destructors are listed first. If set to NO the constructors will appear in the
# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
# member documentation.
# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
# detailed member documentation.
# The default value is: NO.
SORT_MEMBERS_CTORS_1ST = NO
# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
# of group names into alphabetical order. If set to NO the group names will
# appear in their defined order.
# The default value is: NO.
SORT_GROUP_NAMES = NO
# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
# fully-qualified names, including namespaces. If set to NO, the class list will
# be sorted only by class name, not including the namespace part.
# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
# Note: This option applies only to the class list, not to the alphabetical
# list.
# The default value is: NO.
SORT_BY_SCOPE_NAME = YES
# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
# type resolution of all parameters of a function it will reject a match between
# the prototype and the implementation of a member function even if there is
# only one candidate or it is obvious which candidate to choose by doing a
# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
# accept a match between prototype and implementation in such cases.
# The default value is: NO.
STRICT_PROTO_MATCHING = NO
# The GENERATE_TODOLIST tag can be used to enable ( YES) or disable ( NO) the
# todo list. This list is created by putting \todo commands in the
# documentation.
# The default value is: YES.
GENERATE_TODOLIST = @MITK_DOXYGEN_GENERATE_TODOLIST@
# The GENERATE_TESTLIST tag can be used to enable ( YES) or disable ( NO) the
# test list. This list is created by putting \test commands in the
# documentation.
# The default value is: YES.
GENERATE_TESTLIST = YES
# The GENERATE_BUGLIST tag can be used to enable ( YES) or disable ( NO) the bug
# list. This list is created by putting \bug commands in the documentation.
# The default value is: YES.
GENERATE_BUGLIST = @MITK_DOXYGEN_GENERATE_BUGLIST@
# The GENERATE_DEPRECATEDLIST tag can be used to enable ( YES) or disable ( NO)
# the deprecated list. This list is created by putting \deprecated commands in
# the documentation.
# The default value is: YES.
GENERATE_DEPRECATEDLIST= @MITK_DOXYGEN_GENERATE_DEPRECATEDLIST@
# The ENABLED_SECTIONS tag can be used to enable conditional documentation
# sections, marked by \if <section_label> ... \endif and \cond <section_label>
# ... \endcond blocks.
ENABLED_SECTIONS = @MITK_DOXYGEN_ENABLED_SECTIONS@
# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
# initial value of a variable or macro / define can have for it to appear in the
# documentation. If the initializer consists of more lines than specified here
# it will be hidden. Use a value of 0 to hide initializers completely. The
# appearance of the value of individual variables and macros / defines can be
# controlled using \showinitializer or \hideinitializer command in the
# documentation regardless of this setting.
# Minimum value: 0, maximum value: 10000, default value: 30.
MAX_INITIALIZER_LINES = 0
# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
# the bottom of the documentation of classes and structs. If set to YES the list
# will mention the files that were used to generate the documentation.
# The default value is: YES.
SHOW_USED_FILES = YES
# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
# will remove the Files entry from the Quick Index and from the Folder Tree View
# (if specified).
# The default value is: YES.
SHOW_FILES = NO
# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
# page. This will remove the Namespaces entry from the Quick Index and from the
# Folder Tree View (if specified).
# The default value is: YES.
SHOW_NAMESPACES = NO
# The FILE_VERSION_FILTER tag can be used to specify a program or script that
# doxygen should invoke to get the current version for each file (typically from
# the version control system). Doxygen will invoke the program by executing (via
# popen()) the command command input-file, where command is the value of the
# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
# by doxygen. Whatever the program writes to standard output is used as the file
# version. For an example see the documentation.
FILE_VERSION_FILTER =
# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
# by doxygen. The layout file controls the global structure of the generated
# output files in an output format independent way. To create the layout file
# that represents doxygen's defaults, run doxygen with the -l option. You can
# optionally specify a file name after the option, if omitted DoxygenLayout.xml
# will be used as the name of the layout file.
#
# Note that if you run doxygen from a directory containing a file called
# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
# tag is left empty.
LAYOUT_FILE =
# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
# the reference definitions. This must be a list of .bib files. The .bib
# extension is automatically appended if omitted. This requires the bibtex tool
# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
# For LaTeX the style of the bibliography can be controlled using
# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
# search path. See also \cite for info how to create references.
CITE_BIB_FILES =
#---------------------------------------------------------------------------
# Configuration options related to warning and progress messages
#---------------------------------------------------------------------------
# The QUIET tag can be used to turn on/off the messages that are generated to
# standard output by doxygen. If QUIET is set to YES this implies that the
# messages are off.
# The default value is: NO.
-QUIET = NO
+QUIET = YES
# The WARNINGS tag can be used to turn on/off the warning messages that are
# generated to standard error ( stderr) by doxygen. If WARNINGS is set to YES
# this implies that the warnings are on.
#
# Tip: Turn warnings on while writing the documentation.
# The default value is: YES.
WARNINGS = YES
# If the WARN_IF_UNDOCUMENTED tag is set to YES, then doxygen will generate
# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
# will automatically be disabled.
# The default value is: YES.
WARN_IF_UNDOCUMENTED = YES
# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
# potential errors in the documentation, such as not documenting some parameters
# in a documented function, or documenting parameters that don't exist or using
# markup commands wrongly.
# The default value is: YES.
WARN_IF_DOC_ERROR = YES
# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
# are documented, but have no documentation for their parameters or return
# value. If set to NO doxygen will only warn about wrong or incomplete parameter
# documentation, but not about the absence of documentation.
# The default value is: NO.
WARN_NO_PARAMDOC = NO
# The WARN_FORMAT tag determines the format of the warning messages that doxygen
# can produce. The string should contain the $file, $line, and $text tags, which
# will be replaced by the file and line number from which the warning originated
# and the warning text. Optionally the format may contain $version, which will
# be replaced by the version of the file (if it could be obtained via
# FILE_VERSION_FILTER)
# The default value is: $file:$line: $text.
WARN_FORMAT = "$file:$line: $text"
# The WARN_LOGFILE tag can be used to specify a file to which warning and error
# messages should be written. If left blank the output is written to standard
# error (stderr).
WARN_LOGFILE =
#---------------------------------------------------------------------------
# Configuration options related to the input files
#---------------------------------------------------------------------------
# The INPUT tag is used to specify the files and/or directories that contain
# documented source files. You may enter file names like myfile.cpp or
# directories like /usr/src/myproject. Separate the files or directories with
# spaces.
# Note: If this tag is empty the current directory is searched.
INPUT = "@MITK_SOURCE_DIR@/Core/Documentation/Doxygen/Concepts/" \
"@MITK_SOURCE_DIR@/Documentation/Doxygen/DeveloperManual/" \
"@MITK_SOURCE_DIR@/Modules/"
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
# documentation (see: http://www.gnu.org/software/libiconv) for the list of
# possible encodings.
# The default value is: UTF-8.
INPUT_ENCODING = UTF-8
# If the value of the INPUT tag contains directories, you can use the
# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
# *.h) to filter out the source-files in the directories. If left blank the
# following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii,
# *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp,
# *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown,
# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
# *.qsf, *.as and *.js.
FILE_PATTERNS = *.dox \
*.md
# The RECURSIVE tag can be used to specify whether or not subdirectories should
# be searched for input files as well.
# The default value is: NO.
RECURSIVE = YES
# The EXCLUDE tag can be used to specify files and/or directories that should be
# excluded from the INPUT source files. This way you can easily exclude a
# subdirectory from a directory tree whose root is specified with the INPUT tag.
#
# Note that relative paths are relative to the directory from which doxygen is
# run.
EXCLUDE =
# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
# directories that are symbolic links (a Unix file system feature) are excluded
# from the input.
# The default value is: NO.
EXCLUDE_SYMLINKS = NO
# If the value of the INPUT tag contains directories, you can use the
# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
# certain files from those directories.
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories for example use the pattern */test/*
EXCLUDE_PATTERNS = modules.dox \
*/Plugins/*/documentation/doxygen/*
# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
# (namespaces, classes, functions, etc.) that should be excluded from the
# output. The symbol name can be a fully qualified name, a word, or if the
# wildcard * is used, a substring. Examples: ANamespace, AClass,
# AClass::ANamespace, ANamespace::*Test
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories use the pattern */test/*
EXCLUDE_SYMBOLS =
# The EXAMPLE_PATH tag can be used to specify one or more files or directories
# that contain example code fragments that are included (see the \include
# command).
EXAMPLE_PATH =
# If the value of the EXAMPLE_PATH tag contains directories, you can use the
# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
# *.h) to filter out the source-files in the directories. If left blank all
# files are included.
EXAMPLE_PATTERNS =
# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
# searched for input files to be used with the \include or \dontinclude commands
# irrespective of the value of the RECURSIVE tag.
# The default value is: NO.
EXAMPLE_RECURSIVE = YES
# The IMAGE_PATH tag can be used to specify one or more files or directories
# that contain images that are to be included in the documentation (see the
# \image command).
IMAGE_PATH = "@MITK_SOURCE_DIR@/Core/Documentation/Doxygen/Concepts/" \
"@MITK_SOURCE_DIR@/Documentation/Doxygen/DeveloperManual/" \
"@MITK_SOURCE_DIR@/Modules/"
# The INPUT_FILTER tag can be used to specify a program that doxygen should
# invoke to filter for each input file. Doxygen will invoke the filter program
# by executing (via popen()) the command:
#
# <filter> <input-file>
#
# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
# name of an input file. Doxygen will then use the output that the filter
# program writes to standard output. If FILTER_PATTERNS is specified, this tag
# will be ignored.
#
# Note that the filter must not add or remove lines; it is applied before the
# code is scanned, but not when the output code is generated. If lines are added
# or removed, the anchors will not be placed correctly.
INPUT_FILTER =
# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
# basis. Doxygen will compare the file name with each pattern and apply the
# filter if there is a match. The filters are a list of the form: pattern=filter
# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
# patterns match the file name, INPUT_FILTER is applied.
FILTER_PATTERNS = *.cmake=@CMakeDoxygenFilter_EXECUTABLE@
# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
# INPUT_FILTER ) will also be used to filter the input files that are used for
# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
# The default value is: NO.
FILTER_SOURCE_FILES = NO
# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
# it is also possible to disable source filtering for a specific pattern using
# *.ext= (so without naming a filter).
# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
FILTER_SOURCE_PATTERNS =
# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
# is part of the input, its contents will be placed on the main page
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.
USE_MDFILE_AS_MAINPAGE =
#---------------------------------------------------------------------------
# Configuration options related to source browsing
#---------------------------------------------------------------------------
# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
# generated. Documented entities will be cross-referenced with these sources.
#
# Note: To get rid of all source code in the generated output, make sure that
# also VERBATIM_HEADERS is set to NO.
# The default value is: NO.
SOURCE_BROWSER = YES
# Setting the INLINE_SOURCES tag to YES will include the body of functions,
# classes and enums directly into the documentation.
# The default value is: NO.
INLINE_SOURCES = NO
# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
# special comment blocks from generated source code fragments. Normal C, C++ and
# Fortran comments will always remain visible.
# The default value is: YES.
STRIP_CODE_COMMENTS = YES
# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
# function all documented functions referencing it will be listed.
# The default value is: NO.
REFERENCED_BY_RELATION = YES
# If the REFERENCES_RELATION tag is set to YES then for each documented function
# all documented entities called/used by that function will be listed.
# The default value is: NO.
REFERENCES_RELATION = YES
# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
# to YES, then the hyperlinks from functions in REFERENCES_RELATION and
# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
# link to the documentation.
# The default value is: YES.
REFERENCES_LINK_SOURCE = YES
# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
# source code will show a tooltip with additional information such as prototype,
# brief description and links to the definition and documentation. Since this
# will make the HTML file larger and loading of large files a bit slower, you
# can opt to disable this feature.
# The default value is: YES.
# This tag requires that the tag SOURCE_BROWSER is set to YES.
SOURCE_TOOLTIPS = YES
# If the USE_HTAGS tag is set to YES then the references to source code will
# point to the HTML generated by the htags(1) tool instead of doxygen built-in
# source browser. The htags tool is part of GNU's global source tagging system
# (see http://www.gnu.org/software/global/global.html). You will need version
# 4.8.6 or higher.
#
# To use it do the following:
# - Install the latest version of global
# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
# - Make sure the INPUT points to the root of the source tree
# - Run doxygen as normal
#
# Doxygen will invoke htags (and that will in turn invoke gtags), so these
# tools must be available from the command line (i.e. in the search path).
#
# The result: instead of the source browser generated by doxygen, the links to
# source code will now point to the output of htags.
# The default value is: NO.
# This tag requires that the tag SOURCE_BROWSER is set to YES.
USE_HTAGS = NO
# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
# verbatim copy of the header file for each class for which an include is
# specified. Set to NO to disable this.
# See also: Section \class.
# The default value is: YES.
VERBATIM_HEADERS = YES
#---------------------------------------------------------------------------
# Configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
# compounds will be generated. Enable this if the project contains a lot of
# classes, structs, unions or interfaces.
# The default value is: YES.
ALPHABETICAL_INDEX = YES
# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
# which the alphabetical index list will be split.
# Minimum value: 1, maximum value: 20, default value: 5.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
COLS_IN_ALPHA_INDEX = 3
# In case all classes in a project start with a common prefix, all classes will
# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
# can be used to specify a prefix (or a list of prefixes) that should be ignored
# while generating the index headers.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
IGNORE_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the HTML output
#---------------------------------------------------------------------------
# If the GENERATE_HTML tag is set to YES doxygen will generate HTML output
# The default value is: YES.
GENERATE_HTML = NO
# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: html.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_OUTPUT = html
# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
# generated HTML page (for example: .htm, .php, .asp).
# The default value is: .html.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FILE_EXTENSION = .html
# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
# each generated HTML page. If the tag is left blank doxygen will generate a
# standard header.
#
# To get valid HTML the header file that includes any scripts and style sheets
# that doxygen needs, which is dependent on the configuration options used (e.g.
# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
# default header using
# doxygen -w html new_header.html new_footer.html new_stylesheet.css
# YourConfigFile
# and then modify the file new_header.html. See also section "Doxygen usage"
# for information on how to generate the default header that doxygen normally
# uses.
# Note: The header is subject to change so you typically have to regenerate the
# default header when upgrading to a newer version of doxygen. For a description
# of the possible markers and block names see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_HEADER =
# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
# generated HTML page. If the tag is left blank doxygen will generate a standard
# footer. See HTML_HEADER for more information on how to generate a default
# footer and what special commands can be used inside the footer. See also
# section "Doxygen usage" for information on how to generate the default footer
# that doxygen normally uses.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FOOTER =
# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
# sheet that is used by each HTML page. It can be used to fine-tune the look of
# the HTML output. If left blank doxygen will generate a default style sheet.
# See also section "Doxygen usage" for information on how to generate the style
# sheet that doxygen normally uses.
# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
# it is more robust and this tag (HTML_STYLESHEET) will in the future become
# obsolete.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_STYLESHEET =
# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
# cascading style sheets that are included after the standard style sheets
# created by doxygen. Using this option one can overrule certain style aspects.
# This is preferred over using HTML_STYLESHEET since it does not replace the
# standard style sheet and is therefor more robust against future updates.
# Doxygen will copy the style sheet files to the output directory.
# Note: The order of the extra stylesheet files is of importance (e.g. the last
# stylesheet in the list overrules the setting of the previous ones in the
# list). For an example see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_STYLESHEET = @MITK_DOXYGEN_STYLESHEET@
# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the HTML output directory. Note
# that these files will be copied to the base HTML output directory. Use the
# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
# files will be copied as-is; there are no commands or markers available.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_FILES =
# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
# will adjust the colors in the stylesheet and background images according to
# this color. Hue is specified as an angle on a colorwheel, see
# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
# purple, and 360 is red again.
# Minimum value: 0, maximum value: 359, default value: 220.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_HUE = 220
# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
# in the HTML output. For a value of 0 the output will use grayscales only. A
# value of 255 will produce the most vivid colors.
# Minimum value: 0, maximum value: 255, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_SAT = 100
# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
# luminance component of the colors in the HTML output. Values below 100
# gradually make the output lighter, whereas values above 100 make the output
# darker. The value divided by 100 is the actual gamma applied, so 80 represents
# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
# change the gamma.
# Minimum value: 40, maximum value: 240, default value: 80.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_GAMMA = 80
# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
# page will contain the date and time when the page was generated. Setting this
# to NO can help when comparing the output of multiple runs.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_TIMESTAMP = YES
# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
# documentation will contain sections that can be hidden and shown after the
# page has loaded.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_DYNAMIC_SECTIONS = @MITK_DOXYGEN_HTML_DYNAMIC_SECTIONS@
# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
# shown in the various tree structured indices initially; the user can expand
# and collapse entries dynamically later on. Doxygen will expand the tree to
# such a level that at most the specified number of entries are visible (unless
# a fully collapsed tree already exceeds this amount). So setting the number of
# entries 1 will produce a full collapsed tree by default. 0 is a special value
# representing an infinite number of entries and will result in a full expanded
# tree by default.
# Minimum value: 0, maximum value: 9999, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_INDEX_NUM_ENTRIES = 100
# If the GENERATE_DOCSET tag is set to YES, additional index files will be
# generated that can be used as input for Apple's Xcode 3 integrated development
# environment (see: http://developer.apple.com/tools/xcode/), introduced with
# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
# Makefile in the HTML output directory. Running make will produce the docset in
# that directory and running make install will install the docset in
# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
# for more information.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_DOCSET = NO
# This tag determines the name of the docset feed. A documentation feed provides
# an umbrella under which multiple documentation sets from a single provider
# (such as a company or product suite) can be grouped.
# The default value is: Doxygen generated docs.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_FEEDNAME = "Doxygen generated docs"
# This tag specifies a string that should uniquely identify the documentation
# set bundle. This should be a reverse domain-name style string, e.g.
# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_BUNDLE_ID = org.doxygen.Project
# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
# the documentation publisher. This should be a reverse domain-name style
# string, e.g. com.mycompany.MyDocSet.documentation.
# The default value is: org.doxygen.Publisher.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_ID = org.doxygen.Publisher
# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
# The default value is: Publisher.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_NAME = Publisher
# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
# Windows.
#
# The HTML Help Workshop contains a compiler that can convert all HTML output
# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
# files are now used as the Windows 98 help format, and will replace the old
# Windows help format (.hlp) on all Windows platforms in the future. Compressed
# HTML files also contain an index, a table of contents, and you can search for
# words in the documentation. The HTML workshop also contains a viewer for
# compressed HTML files.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_HTMLHELP = NO
# The CHM_FILE tag can be used to specify the file name of the resulting .chm
# file. You can add a path in front of the file if the result should not be
# written to the html output directory.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_FILE =
# The HHC_LOCATION tag can be used to specify the location (absolute path
# including file name) of the HTML help compiler ( hhc.exe). If non-empty
# doxygen will try to run the HTML help compiler on the generated index.hhp.
# The file has to be specified with full path.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
HHC_LOCATION =
# The GENERATE_CHI flag controls if a separate .chi index file is generated (
# YES) or that it should be included in the master .chm file ( NO).
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
GENERATE_CHI = NO
# The CHM_INDEX_ENCODING is used to encode HtmlHelp index ( hhk), content ( hhc)
# and project file content.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_INDEX_ENCODING =
# The BINARY_TOC flag controls whether a binary table of contents is generated (
# YES) or a normal table of contents ( NO) in the .chm file. Furthermore it
# enables the Previous and Next buttons.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
BINARY_TOC = NO
# The TOC_EXPAND flag can be set to YES to add extra items for group members to
# the table of contents of the HTML help documentation and to the tree view.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
TOC_EXPAND = NO
# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
# (.qch) of the generated HTML documentation.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_QHP = @MITK_DOXYGEN_GENERATE_QHP@
# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
# the file name of the resulting .qch file. The path specified is relative to
# the HTML output folder.
# This tag requires that the tag GENERATE_QHP is set to YES.
QCH_FILE = @MITK_DOXYGEN_QCH_FILE@
# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
# Project output. For more information please see Qt Help Project / Namespace
# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_NAMESPACE = "org.mitk"
# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
# Help Project output. For more information please see Qt Help Project / Virtual
# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
# folders).
# The default value is: doc.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_VIRTUAL_FOLDER = MITK
# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
# filter to add. For more information please see Qt Help Project / Custom
# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
# filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_NAME =
# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
# custom filter to add. For more information please see Qt Help Project / Custom
# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
# filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_ATTRS =
# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
# project's filter section matches. Qt Help Project / Filter Attributes (see:
# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_SECT_FILTER_ATTRS =
# The QHG_LOCATION tag can be used to specify the location of Qt's
# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
# generated .qhp file.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHG_LOCATION = @QT_HELPGENERATOR_EXECUTABLE@
# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
# generated, together with the HTML files, they form an Eclipse help plugin. To
# install this plugin and make it available under the help contents menu in
# Eclipse, the contents of the directory containing the HTML and XML files needs
# to be copied into the plugins directory of eclipse. The name of the directory
# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
# After copying Eclipse needs to be restarted before the help appears.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_ECLIPSEHELP = NO
# A unique identifier for the Eclipse help plugin. When installing the plugin
# the directory name containing the HTML and XML files should also have this
# name. Each documentation set should have its own identifier.
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
ECLIPSE_DOC_ID = org.doxygen.Project
# If you want full control over the layout of the generated HTML pages it might
# be necessary to disable the index and replace it with your own. The
# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
# of each HTML page. A value of NO enables the index and the value YES disables
# it. Since the tabs in the index contain the same information as the navigation
# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
DISABLE_INDEX = NO
# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
# structure should be generated to display hierarchical information. If the tag
# value is set to YES, a side panel will be generated containing a tree-like
# index structure (just like the one that is generated for HTML Help). For this
# to work a browser that supports JavaScript, DHTML, CSS and frames is required
# (i.e. any modern browser). Windows users are probably better off using the
# HTML help feature. Via custom stylesheets (see HTML_EXTRA_STYLESHEET) one can
# further fine-tune the look of the index. As an example, the default style
# sheet generated by doxygen has an example that shows how to put an image at
# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
# the same information as the tab index, you could consider setting
# DISABLE_INDEX to YES when enabling this option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_TREEVIEW = YES
# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
# doxygen will group on one line in the generated HTML documentation.
#
# Note that a value of 0 will completely suppress the enum values from appearing
# in the overview section.
# Minimum value: 0, maximum value: 20, default value: 4.
# This tag requires that the tag GENERATE_HTML is set to YES.
ENUM_VALUES_PER_LINE = 4
# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
# to set the initial width (in pixels) of the frame in which the tree is shown.
# Minimum value: 0, maximum value: 1500, default value: 250.
# This tag requires that the tag GENERATE_HTML is set to YES.
TREEVIEW_WIDTH = 300
# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open links to
# external symbols imported via tag files in a separate window.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
EXT_LINKS_IN_WINDOW = NO
# Use this tag to change the font size of LaTeX formulas included as images in
# the HTML documentation. When you change the font size after a successful
# doxygen run you need to manually remove any form_*.png images from the HTML
# output directory to force them to be regenerated.
# Minimum value: 8, maximum value: 50, default value: 10.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_FONTSIZE = 10
# Use the FORMULA_TRANPARENT tag to determine whether or not the images
# generated for formulas are transparent PNGs. Transparent PNGs are not
# supported properly for IE 6.0, but are supported on all modern browsers.
#
# Note that when changing this option you need to delete any form_*.png files in
# the HTML output directory before the changes have effect.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_TRANSPARENT = YES
# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
# http://www.mathjax.org) which uses client side Javascript for the rendering
# instead of using prerendered bitmaps. Use this if you do not have LaTeX
# installed or if you want to formulas look prettier in the HTML output. When
# enabled you may also need to install MathJax separately and configure the path
# to it using the MATHJAX_RELPATH option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
USE_MATHJAX = NO
# When MathJax is enabled you can set the default output format to be used for
# the MathJax output. See the MathJax site (see:
# http://docs.mathjax.org/en/latest/output.html) for more details.
# Possible values are: HTML-CSS (which is slower, but has the best
# compatibility), NativeMML (i.e. MathML) and SVG.
# The default value is: HTML-CSS.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_FORMAT = HTML-CSS
# When MathJax is enabled you need to specify the location relative to the HTML
# output directory using the MATHJAX_RELPATH option. The destination directory
# should contain the MathJax.js script. For instance, if the mathjax directory
# is located at the same level as the HTML output directory, then
# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
# Content Delivery Network so you can quickly see the result without installing
# MathJax. However, it is strongly recommended to install a local copy of
# MathJax from http://www.mathjax.org before deployment.
# The default value is: http://cdn.mathjax.org/mathjax/latest.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_RELPATH = http://www.mathjax.org/mathjax
# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
# extension names that should be enabled during MathJax rendering. For example
# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_EXTENSIONS =
# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
# of code that will be used on startup of the MathJax code. See the MathJax site
# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
# example see the documentation.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_CODEFILE =
# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
# the HTML output. The underlying search engine uses javascript and DHTML and
# should work on any modern browser. Note that when using HTML help
# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
# there is already a search function so this one should typically be disabled.
# For large projects the javascript based search engine can be slow, then
# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
# search using the keyboard; to jump to the search box use <access key> + S
# (what the <access key> is depends on the OS and browser, but it is typically
# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
# key> to jump into the search results window, the results can be navigated
# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
# the search. The filter options can be selected when the cursor is inside the
# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
# to select a filter and <Enter> or <escape> to activate or cancel the filter
# option.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
SEARCHENGINE = YES
# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
# implemented using a web server instead of a web client using Javascript. There
# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
# setting. When disabled, doxygen will generate a PHP script for searching and
# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
# and searching needs to be provided by external tools. See the section
# "External Indexing and Searching" for details.
# The default value is: NO.
# This tag requires that the tag SEARCHENGINE is set to YES.
SERVER_BASED_SEARCH = NO
# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
# script for searching. Instead the search results are written to an XML file
# which needs to be processed by an external indexer. Doxygen will invoke an
# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
# search results.
#
# Doxygen ships with an example indexer ( doxyindexer) and search engine
# (doxysearch.cgi) which are based on the open source search engine library
# Xapian (see: http://xapian.org/).
#
# See the section "External Indexing and Searching" for details.
# The default value is: NO.
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTERNAL_SEARCH = NO
# The SEARCHENGINE_URL should point to a search engine hosted by a web server
# which will return the search results when EXTERNAL_SEARCH is enabled.
#
# Doxygen ships with an example indexer ( doxyindexer) and search engine
# (doxysearch.cgi) which are based on the open source search engine library
# Xapian (see: http://xapian.org/). See the section "External Indexing and
# Searching" for details.
# This tag requires that the tag SEARCHENGINE is set to YES.
SEARCHENGINE_URL =
# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
# search data is written to a file for indexing by an external tool. With the
# SEARCHDATA_FILE tag the name of this file can be specified.
# The default file is: searchdata.xml.
# This tag requires that the tag SEARCHENGINE is set to YES.
SEARCHDATA_FILE = searchdata.xml
# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
# projects and redirect the results back to the right project.
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTERNAL_SEARCH_ID =
# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
# projects other than the one defined by this configuration file, but that are
# all added to the same external search index. Each project needs to have a
# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
# to a relative location where the documentation can be found. The format is:
# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTRA_SEARCH_MAPPINGS =
#---------------------------------------------------------------------------
# Configuration options related to the LaTeX output
#---------------------------------------------------------------------------
# If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output.
# The default value is: YES.
GENERATE_LATEX = YES
# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: latex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_OUTPUT = latex
# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
# invoked.
#
# Note that when enabling USE_PDFLATEX this option is only used for generating
# bitmaps for formulas in the HTML output, but not in the Makefile that is
# written to the output directory.
# The default file is: latex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_CMD_NAME = latex
# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
# index for LaTeX.
# The default file is: makeindex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
MAKEINDEX_CMD_NAME = makeindex
# If the COMPACT_LATEX tag is set to YES doxygen generates more compact LaTeX
# documents. This may be useful for small projects and may help to save some
# trees in general.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
COMPACT_LATEX = NO
# The PAPER_TYPE tag can be used to set the paper type that is used by the
# printer.
# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
# 14 inches) and executive (7.25 x 10.5 inches).
# The default value is: a4.
# This tag requires that the tag GENERATE_LATEX is set to YES.
-PAPER_TYPE = a4wide
+PAPER_TYPE = a4
# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
# that should be included in the LaTeX output. To get the times font for
# instance you can specify
# EXTRA_PACKAGES=times
# If left blank no extra packages will be included.
# This tag requires that the tag GENERATE_LATEX is set to YES.
EXTRA_PACKAGES = amssymb
# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
# generated LaTeX document. The header should contain everything until the first
# chapter. If it is left blank doxygen will generate a standard header. See
# section "Doxygen usage" for information on how to let doxygen write the
# default header to a separate file.
#
# Note: Only use a user-defined header if you know what you are doing! The
# following commands have a special meaning inside the header: $title,
# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
# $projectbrief, $projectlogo. Doxygen will replace $title with the empy string,
# for the replacement values of the other commands the user is refered to
# HTML_HEADER.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HEADER =
# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
# generated LaTeX document. The footer should contain everything after the last
# chapter. If it is left blank doxygen will generate a standard footer. See
# LATEX_HEADER for more information on how to generate a default footer and what
# special commands can be used inside the footer.
#
# Note: Only use a user-defined footer if you know what you are doing!
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_FOOTER =
# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the LATEX_OUTPUT output
# directory. Note that the files will be copied as-is; there are no commands or
# markers available.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_EXTRA_FILES =
# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
# contain links (just like the HTML output) instead of page references. This
# makes the output suitable for online browsing using a PDF viewer.
# The default value is: YES.
# This tag requires that the tag GENERATE_LATEX is set to YES.
PDF_HYPERLINKS = YES
# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
# the PDF file directly from the LaTeX files. Set this option to YES to get a
# higher quality PDF documentation.
# The default value is: YES.
# This tag requires that the tag GENERATE_LATEX is set to YES.
USE_PDFLATEX = YES
# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
# command to the generated LaTeX files. This will instruct LaTeX to keep running
# if errors occur, instead of asking the user for help. This option is also used
# when generating formulas in HTML.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_BATCHMODE = YES
# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
# index chapters (such as File Index, Compound Index, etc.) in the output.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HIDE_INDICES = YES
# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
# code with syntax highlighting in the LaTeX output.
#
# Note that which sources are shown also depends on other settings such as
# SOURCE_BROWSER.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_SOURCE_CODE = NO
# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
# bibliography, e.g. plainnat, or ieeetr. See
# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
# The default value is: plain.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_BIB_STYLE = plain
#---------------------------------------------------------------------------
# Configuration options related to the RTF output
#---------------------------------------------------------------------------
# If the GENERATE_RTF tag is set to YES doxygen will generate RTF output. The
# RTF output is optimized for Word 97 and may not look too pretty with other RTF
# readers/editors.
# The default value is: NO.
GENERATE_RTF = NO
# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: rtf.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_OUTPUT = rtf
# If the COMPACT_RTF tag is set to YES doxygen generates more compact RTF
# documents. This may be useful for small projects and may help to save some
# trees in general.
# The default value is: NO.
# This tag requires that the tag GENERATE_RTF is set to YES.
COMPACT_RTF = NO
# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
# contain hyperlink fields. The RTF file will contain links (just like the HTML
# output) instead of page references. This makes the output suitable for online
# browsing using Word or some other Word compatible readers that support those
# fields.
#
# Note: WordPad (write) and others do not support links.
# The default value is: NO.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_HYPERLINKS = NO
# Load stylesheet definitions from file. Syntax is similar to doxygen's config
# file, i.e. a series of assignments. You only have to provide replacements,
# missing definitions are set to their default value.
#
# See also section "Doxygen usage" for information on how to generate the
# default style sheet that doxygen normally uses.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_STYLESHEET_FILE =
# Set optional variables used in the generation of an RTF document. Syntax is
# similar to doxygen's config file. A template extensions file can be generated
# using doxygen -e rtf extensionFile.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_EXTENSIONS_FILE =
#---------------------------------------------------------------------------
# Configuration options related to the man page output
#---------------------------------------------------------------------------
# If the GENERATE_MAN tag is set to YES doxygen will generate man pages for
# classes and files.
# The default value is: NO.
GENERATE_MAN = NO
# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it. A directory man3 will be created inside the directory specified by
# MAN_OUTPUT.
# The default directory is: man.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_OUTPUT = man
# The MAN_EXTENSION tag determines the extension that is added to the generated
# man pages. In case the manual section does not start with a number, the number
# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
# optional.
# The default value is: .3.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_EXTENSION = .3
# The MAN_SUBDIR tag determines the name of the directory created within
# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
# MAN_EXTENSION with the initial . removed.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_SUBDIR =
# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
# will generate one additional man file for each entity documented in the real
# man page(s). These additional files only source the real man page, but without
# them the man command would be unable to find the correct page.
# The default value is: NO.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_LINKS = NO
#---------------------------------------------------------------------------
# Configuration options related to the XML output
#---------------------------------------------------------------------------
# If the GENERATE_XML tag is set to YES doxygen will generate an XML file that
# captures the structure of the code including all documentation.
# The default value is: NO.
GENERATE_XML = NO
# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: xml.
# This tag requires that the tag GENERATE_XML is set to YES.
XML_OUTPUT = xml
# If the XML_PROGRAMLISTING tag is set to YES doxygen will dump the program
# listings (including syntax highlighting and cross-referencing information) to
# the XML output. Note that enabling this will significantly increase the size
# of the XML output.
# The default value is: YES.
# This tag requires that the tag GENERATE_XML is set to YES.
XML_PROGRAMLISTING = YES
#---------------------------------------------------------------------------
# Configuration options related to the DOCBOOK output
#---------------------------------------------------------------------------
# If the GENERATE_DOCBOOK tag is set to YES doxygen will generate Docbook files
# that can be used to generate PDF.
# The default value is: NO.
GENERATE_DOCBOOK = NO
# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
# front of it.
# The default directory is: docbook.
# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
DOCBOOK_OUTPUT = docbook
# If the DOCBOOK_PROGRAMLISTING tag is set to YES doxygen will include the
# program listings (including syntax highlighting and cross-referencing
# information) to the DOCBOOK output. Note that enabling this will significantly
# increase the size of the DOCBOOK output.
# The default value is: NO.
# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
DOCBOOK_PROGRAMLISTING = NO
#---------------------------------------------------------------------------
# Configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
# If the GENERATE_AUTOGEN_DEF tag is set to YES doxygen will generate an AutoGen
# Definitions (see http://autogen.sf.net) file that captures the structure of
# the code including all documentation. Note that this feature is still
# experimental and incomplete at the moment.
# The default value is: NO.
GENERATE_AUTOGEN_DEF = NO
#---------------------------------------------------------------------------
# Configuration options related to the Perl module output
#---------------------------------------------------------------------------
# If the GENERATE_PERLMOD tag is set to YES doxygen will generate a Perl module
# file that captures the structure of the code including all documentation.
#
# Note that this feature is still experimental and incomplete at the moment.
# The default value is: NO.
GENERATE_PERLMOD = NO
# If the PERLMOD_LATEX tag is set to YES doxygen will generate the necessary
# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
# output from the Perl module output.
# The default value is: NO.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_LATEX = NO
# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be nicely
# formatted so it can be parsed by a human reader. This is useful if you want to
# understand what is going on. On the other hand, if this tag is set to NO the
# size of the Perl module output will be much smaller and Perl will parse it
# just the same.
# The default value is: YES.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_PRETTY = YES
# The names of the make variables in the generated doxyrules.make file are
# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
# so different doxyrules.make files included by the same Makefile don't
# overwrite each other's variables.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_MAKEVAR_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
# If the ENABLE_PREPROCESSING tag is set to YES doxygen will evaluate all
# C-preprocessor directives found in the sources and include files.
# The default value is: YES.
ENABLE_PREPROCESSING = YES
# If the MACRO_EXPANSION tag is set to YES doxygen will expand all macro names
# in the source code. If set to NO only conditional compilation will be
# performed. Macro expansion can be done in a controlled way by setting
# EXPAND_ONLY_PREDEF to YES.
# The default value is: NO.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
MACRO_EXPANSION = YES
# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
# the macro expansion is limited to the macros specified with the PREDEFINED and
# EXPAND_AS_DEFINED tags.
# The default value is: NO.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
EXPAND_ONLY_PREDEF = NO
# If the SEARCH_INCLUDES tag is set to YES the includes files in the
# INCLUDE_PATH will be searched if a #include is found.
# The default value is: YES.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
SEARCH_INCLUDES = YES
# The INCLUDE_PATH tag can be used to specify one or more directories that
# contain include files that are not input files but should be processed by the
# preprocessor.
# This tag requires that the tag SEARCH_INCLUDES is set to YES.
INCLUDE_PATH =
# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
# patterns (like *.h and *.hpp) to filter out the header-files in the
# directories. If left blank, the patterns specified with FILE_PATTERNS will be
# used.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
INCLUDE_FILE_PATTERNS =
# The PREDEFINED tag can be used to specify one or more macro names that are
# defined before the preprocessor is started (similar to the -D option of e.g.
# gcc). The argument of the tag is a list of macros of the form: name or
# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
# is assumed. To prevent a macro definition from being undefined via #undef or
# recursively expanded use the := operator instead of the = operator.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
PREDEFINED =
# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
# tag can be used to specify a list of macro names that should be expanded. The
# macro definition that is found in the sources will be used. Use the PREDEFINED
# tag if you want to use a different macro definition that overrules the
# definition found in the source code.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
EXPAND_AS_DEFINED =
# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
# remove all references to function-like macros that are alone on a line, have
# an all uppercase name, and do not end with a semicolon. Such function macros
# are typically used for boiler-plate code, and will confuse the parser if not
# removed.
# The default value is: YES.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
SKIP_FUNCTION_MACROS = YES
#---------------------------------------------------------------------------
# Configuration options related to external references
#---------------------------------------------------------------------------
# The TAGFILES tag can be used to specify one or more tag files. For each tag
# file the location of the external documentation should be added. The format of
# a tag file without this location is as follows:
# TAGFILES = file1 file2 ...
# Adding location for the tag files is done as follows:
# TAGFILES = file1=loc1 "file2 = loc2" ...
# where loc1 and loc2 can be relative or absolute paths or URLs. See the
# section "Linking to external documentation" for more information about the use
# of tag files.
# Note: Each tag file must have a unique name (where the name does NOT include
# the path). If a tag file is not located in the directory in which doxygen is
# run, you must also specify the path to the tagfile here.
TAGFILES = @BLUEBERRY_DOXYGEN_TAGFILE@
# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
# tag file that is based on the input files it reads. See section "Linking to
# external documentation" for more information about the usage of tag files.
GENERATE_TAGFILE = @MITK_DOXYGEN_TAGFILE_NAME@
# If the ALLEXTERNALS tag is set to YES all external class will be listed in the
# class index. If set to NO only the inherited external classes will be listed.
# The default value is: NO.
ALLEXTERNALS = NO
# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed in
# the modules index. If set to NO, only the current project's groups will be
# listed.
# The default value is: YES.
EXTERNAL_GROUPS = NO
# If the EXTERNAL_PAGES tag is set to YES all external pages will be listed in
# the related pages index. If set to NO, only the current project's pages will
# be listed.
# The default value is: YES.
EXTERNAL_PAGES = YES
#---------------------------------------------------------------------------
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
# If the CLASS_DIAGRAMS tag is set to YES doxygen will generate a class diagram
# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
# NO turns the diagrams off. Note that this option also works with HAVE_DOT
# disabled, but it is recommended to install and use dot, since it yields more
# powerful graphs.
# The default value is: YES.
CLASS_DIAGRAMS = YES
# You can include diagrams made with dia in doxygen documentation. Doxygen will
# then run dia to produce the diagram and insert it in the documentation. The
# DIA_PATH tag allows you to specify the directory where the dia binary resides.
# If left empty dia is assumed to be found in the default search path.
DIA_PATH =
# If set to YES, the inheritance and collaboration graphs will hide inheritance
# and usage relations if the target is undocumented or is not a class.
# The default value is: YES.
HIDE_UNDOC_RELATIONS = YES
# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
# available from the path. This tool is part of Graphviz (see:
# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
# Bell Labs. The other options in this section have no effect if this option is
# set to NO
# The default value is: NO.
HAVE_DOT = @HAVE_DOT@
# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
# to run in parallel. When set to 0 doxygen will base this on the number of
# processors available in the system. You can set it explicitly to a value
# larger than 0 to get control over the balance between CPU load and processing
# speed.
# Minimum value: 0, maximum value: 32, default value: 0.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_NUM_THREADS = @MITK_DOXYGEN_DOT_NUM_THREADS@
# When you want a differently looking font in the dot files that doxygen
# generates you can specify the font name using DOT_FONTNAME. You need to make
# sure dot is able to find the font, which can be done by putting it in a
# standard location or by setting the DOTFONTPATH environment variable or by
# setting DOT_FONTPATH to the directory containing the font.
# The default value is: Helvetica.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTNAME = Helvetica
# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
# dot graphs.
# Minimum value: 4, maximum value: 24, default value: 10.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTSIZE = 10
# By default doxygen will tell dot to use the default font as specified with
# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
# the path where dot can find it using this tag.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTPATH =
# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
# each documented class showing the direct and indirect inheritance relations.
# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
CLASS_GRAPH = YES
# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
# graph for each documented class showing the direct and indirect implementation
# dependencies (inheritance, containment, and class references variables) of the
# class with other documented classes.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
COLLABORATION_GRAPH = YES
# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
# groups, showing the direct groups dependencies.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
GROUP_GRAPHS = YES
# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
# collaboration diagrams in a style similar to the OMG's Unified Modeling
# Language.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
UML_LOOK = @MITK_DOXYGEN_UML_LOOK@
# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
# class node. If there are many fields or methods and many nodes the graph may
# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
# number of items for each type to make the size more manageable. Set this to 0
# for no limit. Note that the threshold may be exceeded by 50% before the limit
# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
# but if the number exceeds 15, the total amount of fields shown is limited to
# 10.
# Minimum value: 0, maximum value: 100, default value: 10.
# This tag requires that the tag HAVE_DOT is set to YES.
UML_LIMIT_NUM_FIELDS = 10
# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
# collaboration graphs will show the relations between templates and their
# instances.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
TEMPLATE_RELATIONS = YES
# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
# YES then doxygen will generate a graph for each documented file showing the
# direct and indirect include dependencies of the file with other documented
# files.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
INCLUDE_GRAPH = NO
# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
# set to YES then doxygen will generate a graph for each documented file showing
# the direct and indirect include dependencies of the file with other documented
# files.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
INCLUDED_BY_GRAPH = NO
# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
# dependency graph for every global function or class method.
#
# Note that enabling this option will significantly increase the time of a run.
# So in most cases it will be better to enable call graphs for selected
# functions only using the \callgraph command.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
CALL_GRAPH = NO
# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
# dependency graph for every global function or class method.
#
# Note that enabling this option will significantly increase the time of a run.
# So in most cases it will be better to enable caller graphs for selected
# functions only using the \callergraph command.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
CALLER_GRAPH = NO
# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
# hierarchy of all classes instead of a textual one.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
GRAPHICAL_HIERARCHY = NO
# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
# dependencies a directory has on other directories in a graphical way. The
# dependency relations are determined by the #include relations between the
# files in the directories.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
DIRECTORY_GRAPH = YES
# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
# generated by dot.
# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
# to make the SVG files visible in IE 9+ (other browsers do not have this
# requirement).
# Possible values are: png, jpg, gif and svg.
# The default value is: png.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_IMAGE_FORMAT = png
# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
# enable generation of interactive SVG images that allow zooming and panning.
#
# Note that this requires a modern browser other than Internet Explorer. Tested
# and working are Firefox, Chrome, Safari, and Opera.
# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
# the SVG files visible. Older versions of IE do not have SVG support.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
INTERACTIVE_SVG = NO
# The DOT_PATH tag can be used to specify the path where the dot tool can be
# found. If left blank, it is assumed the dot tool can be found in the path.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_PATH = "@DOXYGEN_DOT_PATH@"
# The DOTFILE_DIRS tag can be used to specify one or more directories that
# contain dot files that are included in the documentation (see the \dotfile
# command).
# This tag requires that the tag HAVE_DOT is set to YES.
DOTFILE_DIRS =
# The MSCFILE_DIRS tag can be used to specify one or more directories that
# contain msc files that are included in the documentation (see the \mscfile
# command).
MSCFILE_DIRS =
# The DIAFILE_DIRS tag can be used to specify one or more directories that
# contain dia files that are included in the documentation (see the \diafile
# command).
DIAFILE_DIRS =
# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
# path where java can find the plantuml.jar file. If left blank, it is assumed
# PlantUML is not used or called during a preprocessing step. Doxygen will
# generate a warning when it encounters a \startuml command in this case and
# will not generate output for the diagram.
# This tag requires that the tag HAVE_DOT is set to YES.
PLANTUML_JAR_PATH =
# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
# that will be shown in the graph. If the number of nodes in a graph becomes
# larger than this value, doxygen will truncate the graph, which is visualized
# by representing a node as a red box. Note that doxygen if the number of direct
# children of the root node in a graph is already larger than
# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
# Minimum value: 0, maximum value: 10000, default value: 50.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_GRAPH_MAX_NODES = 50
# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
# generated by dot. A depth value of 3 means that only nodes reachable from the
# root by following a path via at most 3 edges will be shown. Nodes that lay
# further from the root node will be omitted. Note that setting this option to 1
# or 2 may greatly reduce the computation time needed for large code bases. Also
# note that the size of a graph can be further restricted by
# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
# Minimum value: 0, maximum value: 1000, default value: 0.
# This tag requires that the tag HAVE_DOT is set to YES.
MAX_DOT_GRAPH_DEPTH = 0
# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
# background. This is disabled by default, because dot on Windows does not seem
# to support this out of the box.
#
# Warning: Depending on the platform used, enabling this option may lead to
# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
# read).
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_TRANSPARENT = NO
# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
# files in one run (i.e. multiple -o and -T options on the command line). This
# makes dot run faster, but since only newer versions of dot (>1.8.10) support
# this, this feature is disabled by default.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_MULTI_TARGETS = NO
# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
# explaining the meaning of the various boxes and arrows in the dot generated
# graphs.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
GENERATE_LEGEND = YES
# If the DOT_CLEANUP tag is set to YES doxygen will remove the intermediate dot
# files that are used to generate the various graphs.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_CLEANUP = YES
diff --git a/Documentation/doxygen_plugin_manual.conf.in b/Documentation/doxygen_plugin_manual.conf.in
index 02af836a8b..20d0f84560 100644
--- a/Documentation/doxygen_plugin_manual.conf.in
+++ b/Documentation/doxygen_plugin_manual.conf.in
@@ -1,2322 +1,2317 @@
# Doxyfile 1.8.8
# This file describes the settings to be used by the documentation system
# doxygen (www.doxygen.org) for a project.
#
# All text after a double hash (##) is considered a comment and is placed in
# front of the TAG it is preceding.
#
# All text after a single hash (#) is considered a comment and will be ignored.
# The format is:
# TAG = value [value, ...]
# For lists, items can also be appended using:
# TAG += value [value, ...]
# Values that contain spaces should be placed between quotes (\" \").
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
# This tag specifies the encoding used for all characters in the config file
# that follow. The default is UTF-8 which is also the encoding used for all text
# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv
# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv
# for the list of possible encodings.
# The default value is: UTF-8.
DOXYFILE_ENCODING = UTF-8
# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
# double-quotes, unless you are using Doxywizard) that should identify the
# project for which the documentation is generated. This name is used in the
# title of most generated pages and in a few other places.
# The default value is: My Project.
PROJECT_NAME = "@Plugin-Name@"
# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
# could be handy for archiving the generated documentation or if some version
# control system is used.
PROJECT_NUMBER =
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
# quick idea about the purpose of the project. Keep the description short.
PROJECT_BRIEF =
# With the PROJECT_LOGO tag one can specify an logo or icon that is included in
# the documentation. The maximum height of the logo should not exceed 55 pixels
# and the maximum width should not exceed 200 pixels. Doxygen will copy the logo
# to the output directory.
PROJECT_LOGO =
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
# into which the generated documentation will be written. If a relative path is
# entered, it will be relative to the location where doxygen was started. If
# left blank the current directory will be used.
OUTPUT_DIRECTORY = "@PLUGIN_DOXYGEN_OUTPUT_DIR@"
# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 4096 sub-
# directories (in 2 levels) under the output directory of each output format and
# will distribute the generated files over these directories. Enabling this
# option can be useful when feeding doxygen a huge amount of source files, where
# putting all generated files in the same directory would otherwise causes
# performance problems for the file system.
# The default value is: NO.
CREATE_SUBDIRS = NO
# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
# characters to appear in the names of generated files. If set to NO, non-ASCII
# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
# U+3044.
# The default value is: NO.
ALLOW_UNICODE_NAMES = NO
# The OUTPUT_LANGUAGE tag is used to specify the language in which all
# documentation generated by doxygen is written. Doxygen will use this
# information to generate all constant output in the proper language.
# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
# Ukrainian and Vietnamese.
# The default value is: English.
OUTPUT_LANGUAGE = English
# If the BRIEF_MEMBER_DESC tag is set to YES doxygen will include brief member
# descriptions after the members that are listed in the file and class
# documentation (similar to Javadoc). Set to NO to disable this.
# The default value is: YES.
BRIEF_MEMBER_DESC = YES
# If the REPEAT_BRIEF tag is set to YES doxygen will prepend the brief
# description of a member or function before the detailed description
#
# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
# brief descriptions will be completely suppressed.
# The default value is: YES.
REPEAT_BRIEF = YES
# This tag implements a quasi-intelligent brief description abbreviator that is
# used to form the text in various listings. Each string in this list, if found
# as the leading text of the brief description, will be stripped from the text
# and the result, after processing the whole list, is used as the annotated
# text. Otherwise, the brief description is used as-is. If left blank, the
# following values are used ($name is automatically replaced with the name of
# the entity):The $name class, The $name widget, The $name file, is, provides,
# specifies, contains, represents, a, an and the.
ABBREVIATE_BRIEF =
# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
# doxygen will generate a detailed section even if there is only a brief
# description.
# The default value is: NO.
ALWAYS_DETAILED_SEC = NO
# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
# inherited members of a class in the documentation of that class as if those
# members were ordinary class members. Constructors, destructors and assignment
# operators of the base classes will not be shown.
# The default value is: NO.
INLINE_INHERITED_MEMB = NO
# If the FULL_PATH_NAMES tag is set to YES doxygen will prepend the full path
# before files name in the file list and in the header files. If set to NO the
# shortest path that makes the file name unique will be used
# The default value is: YES.
FULL_PATH_NAMES = NO
# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
# Stripping is only done if one of the specified strings matches the left-hand
# part of the path. The tag can be used to show relative paths in the file list.
# If left blank the directory from which doxygen is run is used as the path to
# strip.
#
# Note that you can specify absolute paths here, but also relative paths, which
# will be relative from the directory where doxygen is started.
# This tag requires that the tag FULL_PATH_NAMES is set to YES.
STRIP_FROM_PATH =
# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
# path mentioned in the documentation of a class, which tells the reader which
# header file to include in order to use a class. If left blank only the name of
# the header file containing the class definition is used. Otherwise one should
# specify the list of include paths that are normally passed to the compiler
# using the -I flag.
STRIP_FROM_INC_PATH =
# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
# less readable) file names. This can be useful is your file systems doesn't
# support long names like on DOS, Mac, or CD-ROM.
# The default value is: NO.
SHORT_NAMES = NO
# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
# first line (until the first dot) of a Javadoc-style comment as the brief
# description. If set to NO, the Javadoc-style will behave just like regular Qt-
# style comments (thus requiring an explicit @brief command for a brief
# description.)
# The default value is: NO.
JAVADOC_AUTOBRIEF = NO
# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
# line (until the first dot) of a Qt-style comment as the brief description. If
# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
# requiring an explicit \brief command for a brief description.)
# The default value is: NO.
QT_AUTOBRIEF = NO
# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
# a brief description. This used to be the default behavior. The new default is
# to treat a multi-line C++ comment block as a detailed description. Set this
# tag to YES if you prefer the old behavior instead.
#
# Note that setting this tag to YES also means that rational rose comments are
# not recognized any more.
# The default value is: NO.
MULTILINE_CPP_IS_BRIEF = NO
# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
# documentation from any documented member that it re-implements.
# The default value is: YES.
INHERIT_DOCS = YES
# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce a
# new page for each member. If set to NO, the documentation of a member will be
# part of the file/class/namespace that contains it.
# The default value is: NO.
SEPARATE_MEMBER_PAGES = NO
# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
# uses this value to replace tabs by spaces in code fragments.
# Minimum value: 1, maximum value: 16, default value: 4.
TAB_SIZE = 8
# This tag can be used to specify a number of aliases that act as commands in
# the documentation. An alias has the form:
# name=value
# For example adding
# "sideeffect=@par Side Effects:\n"
# will allow you to put the command \sideeffect (or @sideeffect) in the
# documentation, which will result in a user-defined paragraph with heading
# "Side Effects:". You can put \n's in the value part of an alias to insert
# newlines.
ALIASES = bundlemainpage{1}=\mainpage \
"isHtml=\if NO_SUCH_THING" \
"isHtmlend=\endif" \
"imageMacro{3}=\image html \1 \2 \n \image latex \1 \2 width=\3cm" \
"developersguidemainpage{1}=\page \1 " \
"usersguidemainpage{1}=\page \1 " \
"nondependentPluginLink{3}= <a href=\"qthelp://\2/bundle/\1.html\"> \3 </a> "
-# This tag can be used to specify a number of word-keyword mappings (TCL only).
-# A mapping has the form "name=value". For example adding "class=itcl::class"
-# will allow you to use the command class in the itcl::class meaning.
-
-TCL_SUBST =
-
# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
# only. Doxygen will then generate output that is more tailored for C. For
# instance, some of the names that are used will be different. The list of all
# members will be omitted, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_FOR_C = NO
# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
# Python sources only. Doxygen will then generate output that is more tailored
# for that language. For instance, namespaces will be presented as packages,
# qualified scopes will look different, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_JAVA = NO
# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
# sources. Doxygen will then generate output that is tailored for Fortran.
# The default value is: NO.
OPTIMIZE_FOR_FORTRAN = NO
# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
# sources. Doxygen will then generate output that is tailored for VHDL.
# The default value is: NO.
OPTIMIZE_OUTPUT_VHDL = NO
# Doxygen selects the parser to use depending on the extension of the files it
# parses. With this tag you can assign which parser to use for a given
# extension. Doxygen has a built-in mapping, but you can override or extend it
# using this tag. The format is ext=language, where ext is a file extension, and
# language is one of the parsers supported by doxygen: IDL, Java, Javascript,
# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran:
# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran:
# Fortran. In the later case the parser tries to guess whether the code is fixed
# or free formatted code, this is the default for Fortran type files), VHDL. For
# instance to make doxygen treat .inc files as Fortran files (default is PHP),
# and .f files as C (default is Fortran), use: inc=Fortran f=C.
#
# Note For files without extension you can use no_extension as a placeholder.
#
# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
# the files are not read by doxygen.
EXTENSION_MAPPING =
# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
# according to the Markdown format, which allows for more readable
# documentation. See http://daringfireball.net/projects/markdown/ for details.
# The output of markdown processing is further processed by doxygen, so you can
# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
# case of backward compatibilities issues.
# The default value is: YES.
MARKDOWN_SUPPORT = YES
# When enabled doxygen tries to link words that correspond to documented
# classes, or namespaces to their corresponding documentation. Such a link can
# be prevented in individual cases by by putting a % sign in front of the word
# or globally by setting AUTOLINK_SUPPORT to NO.
# The default value is: YES.
AUTOLINK_SUPPORT = YES
# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
# to include (a tag file for) the STL sources as input, then you should set this
# tag to YES in order to let doxygen match functions declarations and
# definitions whose arguments contain STL classes (e.g. func(std::string);
# versus func(std::string) {}). This also make the inheritance and collaboration
# diagrams that involve STL classes more complete and accurate.
# The default value is: NO.
BUILTIN_STL_SUPPORT = NO
# If you use Microsoft's C++/CLI language, you should set this option to YES to
# enable parsing support.
# The default value is: NO.
CPP_CLI_SUPPORT = NO
# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen
# will parse them like normal C++ but will assume all classes use public instead
# of private inheritance when no explicit protection keyword is present.
# The default value is: NO.
SIP_SUPPORT = NO
# For Microsoft's IDL there are propget and propput attributes to indicate
# getter and setter methods for a property. Setting this option to YES will make
# doxygen to replace the get and set methods by a property in the documentation.
# This will only work if the methods are indeed getting or setting a simple
# type. If this is not the case, or you want to show the methods anyway, you
# should set this option to NO.
# The default value is: YES.
IDL_PROPERTY_SUPPORT = YES
# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
# tag is set to YES, then doxygen will reuse the documentation of the first
# member in the group (if any) for the other members of the group. By default
# all members of a group must be documented explicitly.
# The default value is: NO.
DISTRIBUTE_GROUP_DOC = NO
# Set the SUBGROUPING tag to YES to allow class member groups of the same type
# (for instance a group of public functions) to be put as a subgroup of that
# type (e.g. under the Public Functions section). Set it to NO to prevent
# subgrouping. Alternatively, this can be done per class using the
# \nosubgrouping command.
# The default value is: YES.
SUBGROUPING = YES
# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
# are shown inside the group in which they are included (e.g. using \ingroup)
# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
# and RTF).
#
# Note that this feature does not work in combination with
# SEPARATE_MEMBER_PAGES.
# The default value is: NO.
INLINE_GROUPED_CLASSES = NO
# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
# with only public data fields or simple typedef fields will be shown inline in
# the documentation of the scope in which they are defined (i.e. file,
# namespace, or group documentation), provided this scope is documented. If set
# to NO, structs, classes, and unions are shown on a separate page (for HTML and
# Man pages) or section (for LaTeX and RTF).
# The default value is: NO.
INLINE_SIMPLE_STRUCTS = NO
# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
# enum is documented as struct, union, or enum with the name of the typedef. So
# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
# with name TypeT. When disabled the typedef will appear as a member of a file,
# namespace, or class. And the struct will be named TypeS. This can typically be
# useful for C code in case the coding convention dictates that all compound
# types are typedef'ed and only the typedef is referenced, never the tag name.
# The default value is: NO.
TYPEDEF_HIDES_STRUCT = NO
# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
# cache is used to resolve symbols given their name and scope. Since this can be
# an expensive process and often the same symbol appears multiple times in the
# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
# doxygen will become slower. If the cache is too large, memory is wasted. The
# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
# symbols. At the end of a run doxygen will report the cache usage and suggest
# the optimal cache size from a speed point of view.
# Minimum value: 0, maximum value: 9, default value: 0.
LOOKUP_CACHE_SIZE = 0
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
# documentation are documented, even if no documentation was available. Private
# class members and static file members will be hidden unless the
# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
# Note: This will also disable the warnings about undocumented members that are
# normally produced when WARNINGS is set to YES.
# The default value is: NO.
EXTRACT_ALL = YES
# If the EXTRACT_PRIVATE tag is set to YES all private members of a class will
# be included in the documentation.
# The default value is: NO.
EXTRACT_PRIVATE = NO
# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal
# scope will be included in the documentation.
# The default value is: NO.
EXTRACT_PACKAGE = NO
# If the EXTRACT_STATIC tag is set to YES all static members of a file will be
# included in the documentation.
# The default value is: NO.
EXTRACT_STATIC = YES
# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) defined
# locally in source files will be included in the documentation. If set to NO
# only classes defined in header files are included. Does not have any effect
# for Java sources.
# The default value is: YES.
EXTRACT_LOCAL_CLASSES = YES
# This flag is only useful for Objective-C code. When set to YES local methods,
# which are defined in the implementation section but not in the interface are
# included in the documentation. If set to NO only methods in the interface are
# included.
# The default value is: NO.
EXTRACT_LOCAL_METHODS = NO
# If this flag is set to YES, the members of anonymous namespaces will be
# extracted and appear in the documentation as a namespace called
# 'anonymous_namespace{file}', where file will be replaced with the base name of
# the file that contains the anonymous namespace. By default anonymous namespace
# are hidden.
# The default value is: NO.
EXTRACT_ANON_NSPACES = NO
# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
# undocumented members inside documented classes or files. If set to NO these
# members will be included in the various overviews, but no documentation
# section is generated. This option has no effect if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_MEMBERS = NO
# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
# undocumented classes that are normally visible in the class hierarchy. If set
# to NO these classes will be included in the various overviews. This option has
# no effect if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_CLASSES = NO
# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
# (class|struct|union) declarations. If set to NO these declarations will be
# included in the documentation.
# The default value is: NO.
HIDE_FRIEND_COMPOUNDS = NO
# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
# documentation blocks found inside the body of a function. If set to NO these
# blocks will be appended to the function's detailed documentation block.
# The default value is: NO.
HIDE_IN_BODY_DOCS = NO
# The INTERNAL_DOCS tag determines if documentation that is typed after a
# \internal command is included. If the tag is set to NO then the documentation
# will be excluded. Set it to YES to include the internal documentation.
# The default value is: NO.
INTERNAL_DOCS = NO
# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
# names in lower-case letters. If set to YES upper-case letters are also
# allowed. This is useful if you have classes or files whose names only differ
# in case and if your file system supports case sensitive file names. Windows
# and Mac users are advised to set this option to NO.
# The default value is: system dependent.
CASE_SENSE_NAMES = YES
# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
# their full class and namespace scopes in the documentation. If set to YES the
# scope will be hidden.
# The default value is: NO.
HIDE_SCOPE_NAMES = NO
# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
# the files that are included by a file in the documentation of that file.
# The default value is: YES.
SHOW_INCLUDE_FILES = YES
# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
# grouped member an include statement to the documentation, telling the reader
# which file to include in order to use the member.
# The default value is: NO.
SHOW_GROUPED_MEMB_INC = NO
# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
# files with double quotes in the documentation rather than with sharp brackets.
# The default value is: NO.
FORCE_LOCAL_INCLUDES = NO
# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
# documentation for inline members.
# The default value is: YES.
INLINE_INFO = YES
# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
# (detailed) documentation of file and class members alphabetically by member
# name. If set to NO the members will appear in declaration order.
# The default value is: YES.
SORT_MEMBER_DOCS = YES
# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
# descriptions of file, namespace and class members alphabetically by member
# name. If set to NO the members will appear in declaration order. Note that
# this will also influence the order of the classes in the class list.
# The default value is: NO.
SORT_BRIEF_DOCS = NO
# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
# (brief and detailed) documentation of class members so that constructors and
# destructors are listed first. If set to NO the constructors will appear in the
# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
# member documentation.
# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
# detailed member documentation.
# The default value is: NO.
SORT_MEMBERS_CTORS_1ST = NO
# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
# of group names into alphabetical order. If set to NO the group names will
# appear in their defined order.
# The default value is: NO.
SORT_GROUP_NAMES = NO
# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
# fully-qualified names, including namespaces. If set to NO, the class list will
# be sorted only by class name, not including the namespace part.
# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
# Note: This option applies only to the class list, not to the alphabetical
# list.
# The default value is: NO.
SORT_BY_SCOPE_NAME = NO
# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
# type resolution of all parameters of a function it will reject a match between
# the prototype and the implementation of a member function even if there is
# only one candidate or it is obvious which candidate to choose by doing a
# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
# accept a match between prototype and implementation in such cases.
# The default value is: NO.
STRICT_PROTO_MATCHING = NO
# The GENERATE_TODOLIST tag can be used to enable ( YES) or disable ( NO) the
# todo list. This list is created by putting \todo commands in the
# documentation.
# The default value is: YES.
GENERATE_TODOLIST = NO
# The GENERATE_TESTLIST tag can be used to enable ( YES) or disable ( NO) the
# test list. This list is created by putting \test commands in the
# documentation.
# The default value is: YES.
GENERATE_TESTLIST = NO
# The GENERATE_BUGLIST tag can be used to enable ( YES) or disable ( NO) the bug
# list. This list is created by putting \bug commands in the documentation.
# The default value is: YES.
GENERATE_BUGLIST = NO
# The GENERATE_DEPRECATEDLIST tag can be used to enable ( YES) or disable ( NO)
# the deprecated list. This list is created by putting \deprecated commands in
# the documentation.
# The default value is: YES.
GENERATE_DEPRECATEDLIST= NO
# The ENABLED_SECTIONS tag can be used to enable conditional documentation
# sections, marked by \if <section_label> ... \endif and \cond <section_label>
# ... \endcond blocks.
ENABLED_SECTIONS =
# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
# initial value of a variable or macro / define can have for it to appear in the
# documentation. If the initializer consists of more lines than specified here
# it will be hidden. Use a value of 0 to hide initializers completely. The
# appearance of the value of individual variables and macros / defines can be
# controlled using \showinitializer or \hideinitializer command in the
# documentation regardless of this setting.
# Minimum value: 0, maximum value: 10000, default value: 30.
MAX_INITIALIZER_LINES = 30
# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
# the bottom of the documentation of classes and structs. If set to YES the list
# will mention the files that were used to generate the documentation.
# The default value is: YES.
SHOW_USED_FILES = YES
# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
# will remove the Files entry from the Quick Index and from the Folder Tree View
# (if specified).
# The default value is: YES.
SHOW_FILES = YES
# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
# page. This will remove the Namespaces entry from the Quick Index and from the
# Folder Tree View (if specified).
# The default value is: YES.
SHOW_NAMESPACES = NO
# The FILE_VERSION_FILTER tag can be used to specify a program or script that
# doxygen should invoke to get the current version for each file (typically from
# the version control system). Doxygen will invoke the program by executing (via
# popen()) the command command input-file, where command is the value of the
# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
# by doxygen. Whatever the program writes to standard output is used as the file
# version. For an example see the documentation.
FILE_VERSION_FILTER =
# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
# by doxygen. The layout file controls the global structure of the generated
# output files in an output format independent way. To create the layout file
# that represents doxygen's defaults, run doxygen with the -l option. You can
# optionally specify a file name after the option, if omitted DoxygenLayout.xml
# will be used as the name of the layout file.
#
# Note that if you run doxygen from a directory containing a file called
# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
# tag is left empty.
LAYOUT_FILE =
# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
# the reference definitions. This must be a list of .bib files. The .bib
# extension is automatically appended if omitted. This requires the bibtex tool
# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
# For LaTeX the style of the bibliography can be controlled using
# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
# search path. See also \cite for info how to create references.
CITE_BIB_FILES =
#---------------------------------------------------------------------------
# Configuration options related to warning and progress messages
#---------------------------------------------------------------------------
# The QUIET tag can be used to turn on/off the messages that are generated to
# standard output by doxygen. If QUIET is set to YES this implies that the
# messages are off.
# The default value is: NO.
QUIET = YES
# The WARNINGS tag can be used to turn on/off the warning messages that are
# generated to standard error ( stderr) by doxygen. If WARNINGS is set to YES
# this implies that the warnings are on.
#
# Tip: Turn warnings on while writing the documentation.
# The default value is: YES.
WARNINGS = YES
# If the WARN_IF_UNDOCUMENTED tag is set to YES, then doxygen will generate
# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
# will automatically be disabled.
# The default value is: YES.
WARN_IF_UNDOCUMENTED = YES
# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
# potential errors in the documentation, such as not documenting some parameters
# in a documented function, or documenting parameters that don't exist or using
# markup commands wrongly.
# The default value is: YES.
WARN_IF_DOC_ERROR = YES
# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
# are documented, but have no documentation for their parameters or return
# value. If set to NO doxygen will only warn about wrong or incomplete parameter
# documentation, but not about the absence of documentation.
# The default value is: NO.
WARN_NO_PARAMDOC = NO
# The WARN_FORMAT tag determines the format of the warning messages that doxygen
# can produce. The string should contain the $file, $line, and $text tags, which
# will be replaced by the file and line number from which the warning originated
# and the warning text. Optionally the format may contain $version, which will
# be replaced by the version of the file (if it could be obtained via
# FILE_VERSION_FILTER)
# The default value is: $file:$line: $text.
WARN_FORMAT = "$file:$line: $text"
# The WARN_LOGFILE tag can be used to specify a file to which warning and error
# messages should be written. If left blank the output is written to standard
# error (stderr).
WARN_LOGFILE =
#---------------------------------------------------------------------------
# Configuration options related to the input files
#---------------------------------------------------------------------------
# The INPUT tag is used to specify the files and/or directories that contain
# documented source files. You may enter file names like myfile.cpp or
# directories like /usr/src/myproject. Separate the files or directories with
# spaces.
# Note: If this tag is empty the current directory is searched.
INPUT = "@PLUGIN_DOXYGEN_INPUT_DIR@"
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
# documentation (see: http://www.gnu.org/software/libiconv) for the list of
# possible encodings.
# The default value is: UTF-8.
INPUT_ENCODING = UTF-8
# If the value of the INPUT tag contains directories, you can use the
# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
# *.h) to filter out the source-files in the directories. If left blank the
# following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii,
# *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp,
# *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown,
# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
# *.qsf, *.as and *.js.
-FILE_PATTERNS = *.dox
+FILE_PATTERNS = *.dox \
+ *.md
# The RECURSIVE tag can be used to specify whether or not subdirectories should
# be searched for input files as well.
# The default value is: NO.
RECURSIVE = YES
# The EXCLUDE tag can be used to specify files and/or directories that should be
# excluded from the INPUT source files. This way you can easily exclude a
# subdirectory from a directory tree whose root is specified with the INPUT tag.
#
# Note that relative paths are relative to the directory from which doxygen is
# run.
EXCLUDE =
# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
# directories that are symbolic links (a Unix file system feature) are excluded
# from the input.
# The default value is: NO.
EXCLUDE_SYMLINKS = NO
# If the value of the INPUT tag contains directories, you can use the
# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
# certain files from those directories.
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories for example use the pattern */test/*
EXCLUDE_PATTERNS =
# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
# (namespaces, classes, functions, etc.) that should be excluded from the
# output. The symbol name can be a fully qualified name, a word, or if the
# wildcard * is used, a substring. Examples: ANamespace, AClass,
# AClass::ANamespace, ANamespace::*Test
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories use the pattern */test/*
EXCLUDE_SYMBOLS =
# The EXAMPLE_PATH tag can be used to specify one or more files or directories
# that contain example code fragments that are included (see the \include
# command).
EXAMPLE_PATH =
# If the value of the EXAMPLE_PATH tag contains directories, you can use the
# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
# *.h) to filter out the source-files in the directories. If left blank all
# files are included.
EXAMPLE_PATTERNS =
# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
# searched for input files to be used with the \include or \dontinclude commands
# irrespective of the value of the RECURSIVE tag.
# The default value is: NO.
EXAMPLE_RECURSIVE = NO
# The IMAGE_PATH tag can be used to specify one or more files or directories
# that contain images that are to be included in the documentation (see the
# \image command).
IMAGE_PATH = "@PLUGIN_DOXYGEN_INPUT_DIR@"
# The INPUT_FILTER tag can be used to specify a program that doxygen should
# invoke to filter for each input file. Doxygen will invoke the filter program
# by executing (via popen()) the command:
#
# <filter> <input-file>
#
# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
# name of an input file. Doxygen will then use the output that the filter
# program writes to standard output. If FILTER_PATTERNS is specified, this tag
# will be ignored.
#
# Note that the filter must not add or remove lines; it is applied before the
# code is scanned, but not when the output code is generated. If lines are added
# or removed, the anchors will not be placed correctly.
INPUT_FILTER =
# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
# basis. Doxygen will compare the file name with each pattern and apply the
# filter if there is a match. The filters are a list of the form: pattern=filter
# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
# patterns match the file name, INPUT_FILTER is applied.
FILTER_PATTERNS =
# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
# INPUT_FILTER ) will also be used to filter the input files that are used for
# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
# The default value is: NO.
FILTER_SOURCE_FILES = NO
# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
# it is also possible to disable source filtering for a specific pattern using
# *.ext= (so without naming a filter).
# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
FILTER_SOURCE_PATTERNS =
# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
# is part of the input, its contents will be placed on the main page
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.
USE_MDFILE_AS_MAINPAGE =
#---------------------------------------------------------------------------
# Configuration options related to source browsing
#---------------------------------------------------------------------------
# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
# generated. Documented entities will be cross-referenced with these sources.
#
# Note: To get rid of all source code in the generated output, make sure that
# also VERBATIM_HEADERS is set to NO.
# The default value is: NO.
SOURCE_BROWSER = NO
# Setting the INLINE_SOURCES tag to YES will include the body of functions,
# classes and enums directly into the documentation.
# The default value is: NO.
INLINE_SOURCES = YES
# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
# special comment blocks from generated source code fragments. Normal C, C++ and
# Fortran comments will always remain visible.
# The default value is: YES.
STRIP_CODE_COMMENTS = YES
# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
# function all documented functions referencing it will be listed.
# The default value is: NO.
REFERENCED_BY_RELATION = YES
# If the REFERENCES_RELATION tag is set to YES then for each documented function
# all documented entities called/used by that function will be listed.
# The default value is: NO.
REFERENCES_RELATION = YES
# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
# to YES, then the hyperlinks from functions in REFERENCES_RELATION and
# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
# link to the documentation.
# The default value is: YES.
REFERENCES_LINK_SOURCE = YES
# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
# source code will show a tooltip with additional information such as prototype,
# brief description and links to the definition and documentation. Since this
# will make the HTML file larger and loading of large files a bit slower, you
# can opt to disable this feature.
# The default value is: YES.
# This tag requires that the tag SOURCE_BROWSER is set to YES.
SOURCE_TOOLTIPS = YES
# If the USE_HTAGS tag is set to YES then the references to source code will
# point to the HTML generated by the htags(1) tool instead of doxygen built-in
# source browser. The htags tool is part of GNU's global source tagging system
# (see http://www.gnu.org/software/global/global.html). You will need version
# 4.8.6 or higher.
#
# To use it do the following:
# - Install the latest version of global
# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
# - Make sure the INPUT points to the root of the source tree
# - Run doxygen as normal
#
# Doxygen will invoke htags (and that will in turn invoke gtags), so these
# tools must be available from the command line (i.e. in the search path).
#
# The result: instead of the source browser generated by doxygen, the links to
# source code will now point to the output of htags.
# The default value is: NO.
# This tag requires that the tag SOURCE_BROWSER is set to YES.
USE_HTAGS = NO
# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
# verbatim copy of the header file for each class for which an include is
# specified. Set to NO to disable this.
# See also: Section \class.
# The default value is: YES.
VERBATIM_HEADERS = YES
#---------------------------------------------------------------------------
# Configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
# compounds will be generated. Enable this if the project contains a lot of
# classes, structs, unions or interfaces.
# The default value is: YES.
ALPHABETICAL_INDEX = NO
# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
# which the alphabetical index list will be split.
# Minimum value: 1, maximum value: 20, default value: 5.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
COLS_IN_ALPHA_INDEX = 3
# In case all classes in a project start with a common prefix, all classes will
# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
# can be used to specify a prefix (or a list of prefixes) that should be ignored
# while generating the index headers.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
IGNORE_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the HTML output
#---------------------------------------------------------------------------
# If the GENERATE_HTML tag is set to YES doxygen will generate HTML output
# The default value is: YES.
GENERATE_HTML = YES
# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: html.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_OUTPUT = html
# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
# generated HTML page (for example: .htm, .php, .asp).
# The default value is: .html.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FILE_EXTENSION = .html
# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
# each generated HTML page. If the tag is left blank doxygen will generate a
# standard header.
#
# To get valid HTML the header file that includes any scripts and style sheets
# that doxygen needs, which is dependent on the configuration options used (e.g.
# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
# default header using
# doxygen -w html new_header.html new_footer.html new_stylesheet.css
# YourConfigFile
# and then modify the file new_header.html. See also section "Doxygen usage"
# for information on how to generate the default header that doxygen normally
# uses.
# Note: The header is subject to change so you typically have to regenerate the
# default header when upgrading to a newer version of doxygen. For a description
# of the possible markers and block names see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_HEADER =
# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
# generated HTML page. If the tag is left blank doxygen will generate a standard
# footer. See HTML_HEADER for more information on how to generate a default
# footer and what special commands can be used inside the footer. See also
# section "Doxygen usage" for information on how to generate the default footer
# that doxygen normally uses.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FOOTER =
# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
# sheet that is used by each HTML page. It can be used to fine-tune the look of
# the HTML output. If left blank doxygen will generate a default style sheet.
# See also section "Doxygen usage" for information on how to generate the style
# sheet that doxygen normally uses.
# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
# it is more robust and this tag (HTML_STYLESHEET) will in the future become
# obsolete.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_STYLESHEET =
# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
# cascading style sheets that are included after the standard style sheets
# created by doxygen. Using this option one can overrule certain style aspects.
# This is preferred over using HTML_STYLESHEET since it does not replace the
# standard style sheet and is therefor more robust against future updates.
# Doxygen will copy the style sheet files to the output directory.
# Note: The order of the extra stylesheet files is of importance (e.g. the last
# stylesheet in the list overrules the setting of the previous ones in the
# list). For an example see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_STYLESHEET =
# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the HTML output directory. Note
# that these files will be copied to the base HTML output directory. Use the
# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
# files will be copied as-is; there are no commands or markers available.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_FILES =
# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
# will adjust the colors in the stylesheet and background images according to
# this color. Hue is specified as an angle on a colorwheel, see
# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
# purple, and 360 is red again.
# Minimum value: 0, maximum value: 359, default value: 220.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_HUE = 220
# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
# in the HTML output. For a value of 0 the output will use grayscales only. A
# value of 255 will produce the most vivid colors.
# Minimum value: 0, maximum value: 255, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_SAT = 100
# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
# luminance component of the colors in the HTML output. Values below 100
# gradually make the output lighter, whereas values above 100 make the output
# darker. The value divided by 100 is the actual gamma applied, so 80 represents
# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
# change the gamma.
# Minimum value: 40, maximum value: 240, default value: 80.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_GAMMA = 80
# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
# page will contain the date and time when the page was generated. Setting this
# to NO can help when comparing the output of multiple runs.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_TIMESTAMP = YES
# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
# documentation will contain sections that can be hidden and shown after the
# page has loaded.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_DYNAMIC_SECTIONS = NO
# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
# shown in the various tree structured indices initially; the user can expand
# and collapse entries dynamically later on. Doxygen will expand the tree to
# such a level that at most the specified number of entries are visible (unless
# a fully collapsed tree already exceeds this amount). So setting the number of
# entries 1 will produce a full collapsed tree by default. 0 is a special value
# representing an infinite number of entries and will result in a full expanded
# tree by default.
# Minimum value: 0, maximum value: 9999, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_INDEX_NUM_ENTRIES = 100
# If the GENERATE_DOCSET tag is set to YES, additional index files will be
# generated that can be used as input for Apple's Xcode 3 integrated development
# environment (see: http://developer.apple.com/tools/xcode/), introduced with
# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
# Makefile in the HTML output directory. Running make will produce the docset in
# that directory and running make install will install the docset in
# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
# for more information.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_DOCSET = NO
# This tag determines the name of the docset feed. A documentation feed provides
# an umbrella under which multiple documentation sets from a single provider
# (such as a company or product suite) can be grouped.
# The default value is: Doxygen generated docs.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_FEEDNAME = "Doxygen generated docs"
# This tag specifies a string that should uniquely identify the documentation
# set bundle. This should be a reverse domain-name style string, e.g.
# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_BUNDLE_ID = org.doxygen.Project
# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
# the documentation publisher. This should be a reverse domain-name style
# string, e.g. com.mycompany.MyDocSet.documentation.
# The default value is: org.doxygen.Publisher.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_ID = org.doxygen.Publisher
# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
# The default value is: Publisher.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_NAME = Publisher
# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
# Windows.
#
# The HTML Help Workshop contains a compiler that can convert all HTML output
# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
# files are now used as the Windows 98 help format, and will replace the old
# Windows help format (.hlp) on all Windows platforms in the future. Compressed
# HTML files also contain an index, a table of contents, and you can search for
# words in the documentation. The HTML workshop also contains a viewer for
# compressed HTML files.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_HTMLHELP = NO
# The CHM_FILE tag can be used to specify the file name of the resulting .chm
# file. You can add a path in front of the file if the result should not be
# written to the html output directory.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_FILE =
# The HHC_LOCATION tag can be used to specify the location (absolute path
# including file name) of the HTML help compiler ( hhc.exe). If non-empty
# doxygen will try to run the HTML help compiler on the generated index.hhp.
# The file has to be specified with full path.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
HHC_LOCATION =
# The GENERATE_CHI flag controls if a separate .chi index file is generated (
# YES) or that it should be included in the master .chm file ( NO).
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
GENERATE_CHI = NO
# The CHM_INDEX_ENCODING is used to encode HtmlHelp index ( hhk), content ( hhc)
# and project file content.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_INDEX_ENCODING =
# The BINARY_TOC flag controls whether a binary table of contents is generated (
# YES) or a normal table of contents ( NO) in the .chm file. Furthermore it
# enables the Previous and Next buttons.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
BINARY_TOC = NO
# The TOC_EXPAND flag can be set to YES to add extra items for group members to
# the table of contents of the HTML help documentation and to the tree view.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
TOC_EXPAND = NO
# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
# (.qch) of the generated HTML documentation.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_QHP = YES
# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
# the file name of the resulting .qch file. The path specified is relative to
# the HTML output folder.
# This tag requires that the tag GENERATE_QHP is set to YES.
QCH_FILE =
# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
# Project output. For more information please see Qt Help Project / Namespace
# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_NAMESPACE = @Plugin-SymbolicName@
# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
# Help Project output. For more information please see Qt Help Project / Virtual
# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
# folders).
# The default value is: doc.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_VIRTUAL_FOLDER = bundle
# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
# filter to add. For more information please see Qt Help Project / Custom
# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
# filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_NAME = @PLUGIN_QHP_CUST_FILTER_NAME@
# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
# custom filter to add. For more information please see Qt Help Project / Custom
# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
# filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_ATTRS = @PLUGIN_QHP_CUST_FILTER_ATTRS@
# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
# project's filter section matches. Qt Help Project / Filter Attributes (see:
# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_SECT_FILTER_ATTRS = @PLUGIN_QHP_SECT_FILTER_ATTRS@
# The QHG_LOCATION tag can be used to specify the location of Qt's
# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
# generated .qhp file.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHG_LOCATION =
# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
# generated, together with the HTML files, they form an Eclipse help plugin. To
# install this plugin and make it available under the help contents menu in
# Eclipse, the contents of the directory containing the HTML and XML files needs
# to be copied into the plugins directory of eclipse. The name of the directory
# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
# After copying Eclipse needs to be restarted before the help appears.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_ECLIPSEHELP = NO
# A unique identifier for the Eclipse help plugin. When installing the plugin
# the directory name containing the HTML and XML files should also have this
# name. Each documentation set should have its own identifier.
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
ECLIPSE_DOC_ID = org.doxygen.Project
# If you want full control over the layout of the generated HTML pages it might
# be necessary to disable the index and replace it with your own. The
# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
# of each HTML page. A value of NO enables the index and the value YES disables
# it. Since the tabs in the index contain the same information as the navigation
# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
DISABLE_INDEX = YES
# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
# structure should be generated to display hierarchical information. If the tag
# value is set to YES, a side panel will be generated containing a tree-like
# index structure (just like the one that is generated for HTML Help). For this
# to work a browser that supports JavaScript, DHTML, CSS and frames is required
# (i.e. any modern browser). Windows users are probably better off using the
# HTML help feature. Via custom stylesheets (see HTML_EXTRA_STYLESHEET) one can
# further fine-tune the look of the index. As an example, the default style
# sheet generated by doxygen has an example that shows how to put an image at
# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
# the same information as the tab index, you could consider setting
# DISABLE_INDEX to YES when enabling this option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_TREEVIEW = NO
# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
# doxygen will group on one line in the generated HTML documentation.
#
# Note that a value of 0 will completely suppress the enum values from appearing
# in the overview section.
# Minimum value: 0, maximum value: 20, default value: 4.
# This tag requires that the tag GENERATE_HTML is set to YES.
ENUM_VALUES_PER_LINE = 4
# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
# to set the initial width (in pixels) of the frame in which the tree is shown.
# Minimum value: 0, maximum value: 1500, default value: 250.
# This tag requires that the tag GENERATE_HTML is set to YES.
TREEVIEW_WIDTH = 250
# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open links to
# external symbols imported via tag files in a separate window.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
EXT_LINKS_IN_WINDOW = NO
# Use this tag to change the font size of LaTeX formulas included as images in
# the HTML documentation. When you change the font size after a successful
# doxygen run you need to manually remove any form_*.png images from the HTML
# output directory to force them to be regenerated.
# Minimum value: 8, maximum value: 50, default value: 10.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_FONTSIZE = 10
# Use the FORMULA_TRANPARENT tag to determine whether or not the images
# generated for formulas are transparent PNGs. Transparent PNGs are not
# supported properly for IE 6.0, but are supported on all modern browsers.
#
# Note that when changing this option you need to delete any form_*.png files in
# the HTML output directory before the changes have effect.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_TRANSPARENT = YES
# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
# http://www.mathjax.org) which uses client side Javascript for the rendering
# instead of using prerendered bitmaps. Use this if you do not have LaTeX
# installed or if you want to formulas look prettier in the HTML output. When
# enabled you may also need to install MathJax separately and configure the path
# to it using the MATHJAX_RELPATH option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
USE_MATHJAX = NO
# When MathJax is enabled you can set the default output format to be used for
# the MathJax output. See the MathJax site (see:
# http://docs.mathjax.org/en/latest/output.html) for more details.
# Possible values are: HTML-CSS (which is slower, but has the best
# compatibility), NativeMML (i.e. MathML) and SVG.
# The default value is: HTML-CSS.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_FORMAT = HTML-CSS
# When MathJax is enabled you need to specify the location relative to the HTML
# output directory using the MATHJAX_RELPATH option. The destination directory
# should contain the MathJax.js script. For instance, if the mathjax directory
# is located at the same level as the HTML output directory, then
# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
# Content Delivery Network so you can quickly see the result without installing
# MathJax. However, it is strongly recommended to install a local copy of
# MathJax from http://www.mathjax.org before deployment.
# The default value is: http://cdn.mathjax.org/mathjax/latest.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest
# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
# extension names that should be enabled during MathJax rendering. For example
# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_EXTENSIONS =
# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
# of code that will be used on startup of the MathJax code. See the MathJax site
# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
# example see the documentation.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_CODEFILE =
# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
# the HTML output. The underlying search engine uses javascript and DHTML and
# should work on any modern browser. Note that when using HTML help
# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
# there is already a search function so this one should typically be disabled.
# For large projects the javascript based search engine can be slow, then
# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
# search using the keyboard; to jump to the search box use <access key> + S
# (what the <access key> is depends on the OS and browser, but it is typically
# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
# key> to jump into the search results window, the results can be navigated
# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
# the search. The filter options can be selected when the cursor is inside the
# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
# to select a filter and <Enter> or <escape> to activate or cancel the filter
# option.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
SEARCHENGINE = NO
# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
# implemented using a web server instead of a web client using Javascript. There
# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
# setting. When disabled, doxygen will generate a PHP script for searching and
# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
# and searching needs to be provided by external tools. See the section
# "External Indexing and Searching" for details.
# The default value is: NO.
# This tag requires that the tag SEARCHENGINE is set to YES.
SERVER_BASED_SEARCH = NO
# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
# script for searching. Instead the search results are written to an XML file
# which needs to be processed by an external indexer. Doxygen will invoke an
# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
# search results.
#
# Doxygen ships with an example indexer ( doxyindexer) and search engine
# (doxysearch.cgi) which are based on the open source search engine library
# Xapian (see: http://xapian.org/).
#
# See the section "External Indexing and Searching" for details.
# The default value is: NO.
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTERNAL_SEARCH = NO
# The SEARCHENGINE_URL should point to a search engine hosted by a web server
# which will return the search results when EXTERNAL_SEARCH is enabled.
#
# Doxygen ships with an example indexer ( doxyindexer) and search engine
# (doxysearch.cgi) which are based on the open source search engine library
# Xapian (see: http://xapian.org/). See the section "External Indexing and
# Searching" for details.
# This tag requires that the tag SEARCHENGINE is set to YES.
SEARCHENGINE_URL =
# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
# search data is written to a file for indexing by an external tool. With the
# SEARCHDATA_FILE tag the name of this file can be specified.
# The default file is: searchdata.xml.
# This tag requires that the tag SEARCHENGINE is set to YES.
SEARCHDATA_FILE = searchdata.xml
# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
# projects and redirect the results back to the right project.
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTERNAL_SEARCH_ID =
# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
# projects other than the one defined by this configuration file, but that are
# all added to the same external search index. Each project needs to have a
# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
# to a relative location where the documentation can be found. The format is:
# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTRA_SEARCH_MAPPINGS =
#---------------------------------------------------------------------------
# Configuration options related to the LaTeX output
#---------------------------------------------------------------------------
# If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output.
# The default value is: YES.
GENERATE_LATEX = NO
# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: latex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_OUTPUT = latex
# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
# invoked.
#
# Note that when enabling USE_PDFLATEX this option is only used for generating
# bitmaps for formulas in the HTML output, but not in the Makefile that is
# written to the output directory.
# The default file is: latex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_CMD_NAME = latex
# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
# index for LaTeX.
# The default file is: makeindex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
MAKEINDEX_CMD_NAME = makeindex
# If the COMPACT_LATEX tag is set to YES doxygen generates more compact LaTeX
# documents. This may be useful for small projects and may help to save some
# trees in general.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
COMPACT_LATEX = NO
# The PAPER_TYPE tag can be used to set the paper type that is used by the
# printer.
# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
# 14 inches) and executive (7.25 x 10.5 inches).
# The default value is: a4.
# This tag requires that the tag GENERATE_LATEX is set to YES.
-PAPER_TYPE = a4wide
+PAPER_TYPE = a4
# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
# that should be included in the LaTeX output. To get the times font for
# instance you can specify
# EXTRA_PACKAGES=times
# If left blank no extra packages will be included.
# This tag requires that the tag GENERATE_LATEX is set to YES.
EXTRA_PACKAGES =
# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
# generated LaTeX document. The header should contain everything until the first
# chapter. If it is left blank doxygen will generate a standard header. See
# section "Doxygen usage" for information on how to let doxygen write the
# default header to a separate file.
#
# Note: Only use a user-defined header if you know what you are doing! The
# following commands have a special meaning inside the header: $title,
# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
# $projectbrief, $projectlogo. Doxygen will replace $title with the empy string,
# for the replacement values of the other commands the user is refered to
# HTML_HEADER.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HEADER =
# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
# generated LaTeX document. The footer should contain everything after the last
# chapter. If it is left blank doxygen will generate a standard footer. See
# LATEX_HEADER for more information on how to generate a default footer and what
# special commands can be used inside the footer.
#
# Note: Only use a user-defined footer if you know what you are doing!
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_FOOTER =
# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the LATEX_OUTPUT output
# directory. Note that the files will be copied as-is; there are no commands or
# markers available.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_EXTRA_FILES =
# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
# contain links (just like the HTML output) instead of page references. This
# makes the output suitable for online browsing using a PDF viewer.
# The default value is: YES.
# This tag requires that the tag GENERATE_LATEX is set to YES.
PDF_HYPERLINKS = NO
# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
# the PDF file directly from the LaTeX files. Set this option to YES to get a
# higher quality PDF documentation.
# The default value is: YES.
# This tag requires that the tag GENERATE_LATEX is set to YES.
USE_PDFLATEX = NO
# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
# command to the generated LaTeX files. This will instruct LaTeX to keep running
# if errors occur, instead of asking the user for help. This option is also used
# when generating formulas in HTML.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_BATCHMODE = NO
# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
# index chapters (such as File Index, Compound Index, etc.) in the output.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HIDE_INDICES = NO
# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
# code with syntax highlighting in the LaTeX output.
#
# Note that which sources are shown also depends on other settings such as
# SOURCE_BROWSER.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_SOURCE_CODE = NO
# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
# bibliography, e.g. plainnat, or ieeetr. See
# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
# The default value is: plain.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_BIB_STYLE = plain
#---------------------------------------------------------------------------
# Configuration options related to the RTF output
#---------------------------------------------------------------------------
# If the GENERATE_RTF tag is set to YES doxygen will generate RTF output. The
# RTF output is optimized for Word 97 and may not look too pretty with other RTF
# readers/editors.
# The default value is: NO.
GENERATE_RTF = NO
# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: rtf.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_OUTPUT = rtf
# If the COMPACT_RTF tag is set to YES doxygen generates more compact RTF
# documents. This may be useful for small projects and may help to save some
# trees in general.
# The default value is: NO.
# This tag requires that the tag GENERATE_RTF is set to YES.
COMPACT_RTF = NO
# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
# contain hyperlink fields. The RTF file will contain links (just like the HTML
# output) instead of page references. This makes the output suitable for online
# browsing using Word or some other Word compatible readers that support those
# fields.
#
# Note: WordPad (write) and others do not support links.
# The default value is: NO.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_HYPERLINKS = NO
# Load stylesheet definitions from file. Syntax is similar to doxygen's config
# file, i.e. a series of assignments. You only have to provide replacements,
# missing definitions are set to their default value.
#
# See also section "Doxygen usage" for information on how to generate the
# default style sheet that doxygen normally uses.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_STYLESHEET_FILE =
# Set optional variables used in the generation of an RTF document. Syntax is
# similar to doxygen's config file. A template extensions file can be generated
# using doxygen -e rtf extensionFile.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_EXTENSIONS_FILE =
#---------------------------------------------------------------------------
# Configuration options related to the man page output
#---------------------------------------------------------------------------
# If the GENERATE_MAN tag is set to YES doxygen will generate man pages for
# classes and files.
# The default value is: NO.
GENERATE_MAN = NO
# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it. A directory man3 will be created inside the directory specified by
# MAN_OUTPUT.
# The default directory is: man.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_OUTPUT = man
# The MAN_EXTENSION tag determines the extension that is added to the generated
# man pages. In case the manual section does not start with a number, the number
# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
# optional.
# The default value is: .3.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_EXTENSION = .3
# The MAN_SUBDIR tag determines the name of the directory created within
# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
# MAN_EXTENSION with the initial . removed.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_SUBDIR =
# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
# will generate one additional man file for each entity documented in the real
# man page(s). These additional files only source the real man page, but without
# them the man command would be unable to find the correct page.
# The default value is: NO.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_LINKS = NO
#---------------------------------------------------------------------------
# Configuration options related to the XML output
#---------------------------------------------------------------------------
# If the GENERATE_XML tag is set to YES doxygen will generate an XML file that
# captures the structure of the code including all documentation.
# The default value is: NO.
GENERATE_XML = NO
# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: xml.
# This tag requires that the tag GENERATE_XML is set to YES.
XML_OUTPUT = xml
# If the XML_PROGRAMLISTING tag is set to YES doxygen will dump the program
# listings (including syntax highlighting and cross-referencing information) to
# the XML output. Note that enabling this will significantly increase the size
# of the XML output.
# The default value is: YES.
# This tag requires that the tag GENERATE_XML is set to YES.
XML_PROGRAMLISTING = YES
#---------------------------------------------------------------------------
# Configuration options related to the DOCBOOK output
#---------------------------------------------------------------------------
# If the GENERATE_DOCBOOK tag is set to YES doxygen will generate Docbook files
# that can be used to generate PDF.
# The default value is: NO.
GENERATE_DOCBOOK = NO
# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
# front of it.
# The default directory is: docbook.
# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
DOCBOOK_OUTPUT = docbook
# If the DOCBOOK_PROGRAMLISTING tag is set to YES doxygen will include the
# program listings (including syntax highlighting and cross-referencing
# information) to the DOCBOOK output. Note that enabling this will significantly
# increase the size of the DOCBOOK output.
# The default value is: NO.
# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
DOCBOOK_PROGRAMLISTING = NO
#---------------------------------------------------------------------------
# Configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
# If the GENERATE_AUTOGEN_DEF tag is set to YES doxygen will generate an AutoGen
# Definitions (see http://autogen.sf.net) file that captures the structure of
# the code including all documentation. Note that this feature is still
# experimental and incomplete at the moment.
# The default value is: NO.
GENERATE_AUTOGEN_DEF = NO
#---------------------------------------------------------------------------
# Configuration options related to the Perl module output
#---------------------------------------------------------------------------
# If the GENERATE_PERLMOD tag is set to YES doxygen will generate a Perl module
# file that captures the structure of the code including all documentation.
#
# Note that this feature is still experimental and incomplete at the moment.
# The default value is: NO.
GENERATE_PERLMOD = NO
# If the PERLMOD_LATEX tag is set to YES doxygen will generate the necessary
# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
# output from the Perl module output.
# The default value is: NO.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_LATEX = NO
# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be nicely
# formatted so it can be parsed by a human reader. This is useful if you want to
# understand what is going on. On the other hand, if this tag is set to NO the
# size of the Perl module output will be much smaller and Perl will parse it
# just the same.
# The default value is: YES.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_PRETTY = YES
# The names of the make variables in the generated doxyrules.make file are
# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
# so different doxyrules.make files included by the same Makefile don't
# overwrite each other's variables.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_MAKEVAR_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
# If the ENABLE_PREPROCESSING tag is set to YES doxygen will evaluate all
# C-preprocessor directives found in the sources and include files.
# The default value is: YES.
ENABLE_PREPROCESSING = YES
# If the MACRO_EXPANSION tag is set to YES doxygen will expand all macro names
# in the source code. If set to NO only conditional compilation will be
# performed. Macro expansion can be done in a controlled way by setting
# EXPAND_ONLY_PREDEF to YES.
# The default value is: NO.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
MACRO_EXPANSION = YES
# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
# the macro expansion is limited to the macros specified with the PREDEFINED and
# EXPAND_AS_DEFINED tags.
# The default value is: NO.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
EXPAND_ONLY_PREDEF = NO
# If the SEARCH_INCLUDES tag is set to YES the includes files in the
# INCLUDE_PATH will be searched if a #include is found.
# The default value is: YES.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
SEARCH_INCLUDES = YES
# The INCLUDE_PATH tag can be used to specify one or more directories that
# contain include files that are not input files but should be processed by the
# preprocessor.
# This tag requires that the tag SEARCH_INCLUDES is set to YES.
INCLUDE_PATH =
# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
# patterns (like *.h and *.hpp) to filter out the header-files in the
# directories. If left blank, the patterns specified with FILE_PATTERNS will be
# used.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
INCLUDE_FILE_PATTERNS =
# The PREDEFINED tag can be used to specify one or more macro names that are
# defined before the preprocessor is started (similar to the -D option of e.g.
# gcc). The argument of the tag is a list of macros of the form: name or
# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
# is assumed. To prevent a macro definition from being undefined via #undef or
# recursively expanded use the := operator instead of the = operator.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
PREDEFINED =
# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
# tag can be used to specify a list of macro names that should be expanded. The
# macro definition that is found in the sources will be used. Use the PREDEFINED
# tag if you want to use a different macro definition that overrules the
# definition found in the source code.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
EXPAND_AS_DEFINED =
# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
# remove all references to function-like macros that are alone on a line, have
# an all uppercase name, and do not end with a semicolon. Such function macros
# are typically used for boiler-plate code, and will confuse the parser if not
# removed.
# The default value is: YES.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
SKIP_FUNCTION_MACROS = YES
#---------------------------------------------------------------------------
# Configuration options related to external references
#---------------------------------------------------------------------------
# The TAGFILES tag can be used to specify one or more tag files. For each tag
# file the location of the external documentation should be added. The format of
# a tag file without this location is as follows:
# TAGFILES = file1 file2 ...
# Adding location for the tag files is done as follows:
# TAGFILES = file1=loc1 "file2 = loc2" ...
# where loc1 and loc2 can be relative or absolute paths or URLs. See the
# section "Linking to external documentation" for more information about the use
# of tag files.
# Note: Each tag file must have a unique name (where the name does NOT include
# the path). If a tag file is not located in the directory in which doxygen is
# run, you must also specify the path to the tagfile here.
TAGFILES = @PLUGIN_DOXYGEN_TAGFILES@
# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
# tag file that is based on the input files it reads. See section "Linking to
# external documentation" for more information about the usage of tag files.
GENERATE_TAGFILE = "@PLUGIN_DOXYGEN_OUTPUT_DIR@/@PROJECT_NAME@.tag"
# If the ALLEXTERNALS tag is set to YES all external class will be listed in the
# class index. If set to NO only the inherited external classes will be listed.
# The default value is: NO.
ALLEXTERNALS = NO
# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed in
# the modules index. If set to NO, only the current project's groups will be
# listed.
# The default value is: YES.
EXTERNAL_GROUPS = YES
# If the EXTERNAL_PAGES tag is set to YES all external pages will be listed in
# the related pages index. If set to NO, only the current project's pages will
# be listed.
# The default value is: YES.
EXTERNAL_PAGES = YES
#---------------------------------------------------------------------------
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
# If the CLASS_DIAGRAMS tag is set to YES doxygen will generate a class diagram
# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
# NO turns the diagrams off. Note that this option also works with HAVE_DOT
# disabled, but it is recommended to install and use dot, since it yields more
# powerful graphs.
# The default value is: YES.
CLASS_DIAGRAMS = YES
# You can include diagrams made with dia in doxygen documentation. Doxygen will
# then run dia to produce the diagram and insert it in the documentation. The
# DIA_PATH tag allows you to specify the directory where the dia binary resides.
# If left empty dia is assumed to be found in the default search path.
DIA_PATH =
# If set to YES, the inheritance and collaboration graphs will hide inheritance
# and usage relations if the target is undocumented or is not a class.
# The default value is: YES.
HIDE_UNDOC_RELATIONS = YES
# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
# available from the path. This tool is part of Graphviz (see:
# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
# Bell Labs. The other options in this section have no effect if this option is
# set to NO
# The default value is: NO.
HAVE_DOT = NO
# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
# to run in parallel. When set to 0 doxygen will base this on the number of
# processors available in the system. You can set it explicitly to a value
# larger than 0 to get control over the balance between CPU load and processing
# speed.
# Minimum value: 0, maximum value: 32, default value: 0.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_NUM_THREADS = 0
# When you want a differently looking font in the dot files that doxygen
# generates you can specify the font name using DOT_FONTNAME. You need to make
# sure dot is able to find the font, which can be done by putting it in a
# standard location or by setting the DOTFONTPATH environment variable or by
# setting DOT_FONTPATH to the directory containing the font.
# The default value is: Helvetica.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTNAME = Helvetica
# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
# dot graphs.
# Minimum value: 4, maximum value: 24, default value: 10.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTSIZE = 10
# By default doxygen will tell dot to use the default font as specified with
# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
# the path where dot can find it using this tag.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTPATH =
# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
# each documented class showing the direct and indirect inheritance relations.
# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
CLASS_GRAPH = YES
# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
# graph for each documented class showing the direct and indirect implementation
# dependencies (inheritance, containment, and class references variables) of the
# class with other documented classes.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
COLLABORATION_GRAPH = YES
# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
# groups, showing the direct groups dependencies.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
GROUP_GRAPHS = YES
# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
# collaboration diagrams in a style similar to the OMG's Unified Modeling
# Language.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
UML_LOOK = NO
# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
# class node. If there are many fields or methods and many nodes the graph may
# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
# number of items for each type to make the size more manageable. Set this to 0
# for no limit. Note that the threshold may be exceeded by 50% before the limit
# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
# but if the number exceeds 15, the total amount of fields shown is limited to
# 10.
# Minimum value: 0, maximum value: 100, default value: 10.
# This tag requires that the tag HAVE_DOT is set to YES.
UML_LIMIT_NUM_FIELDS = 10
# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
# collaboration graphs will show the relations between templates and their
# instances.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
TEMPLATE_RELATIONS = YES
# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
# YES then doxygen will generate a graph for each documented file showing the
# direct and indirect include dependencies of the file with other documented
# files.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
INCLUDE_GRAPH = YES
# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
# set to YES then doxygen will generate a graph for each documented file showing
# the direct and indirect include dependencies of the file with other documented
# files.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
INCLUDED_BY_GRAPH = YES
# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
# dependency graph for every global function or class method.
#
# Note that enabling this option will significantly increase the time of a run.
# So in most cases it will be better to enable call graphs for selected
# functions only using the \callgraph command.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
CALL_GRAPH = NO
# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
# dependency graph for every global function or class method.
#
# Note that enabling this option will significantly increase the time of a run.
# So in most cases it will be better to enable caller graphs for selected
# functions only using the \callergraph command.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
CALLER_GRAPH = NO
# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
# hierarchy of all classes instead of a textual one.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
GRAPHICAL_HIERARCHY = YES
# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
# dependencies a directory has on other directories in a graphical way. The
# dependency relations are determined by the #include relations between the
# files in the directories.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
DIRECTORY_GRAPH = YES
# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
# generated by dot.
# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
# to make the SVG files visible in IE 9+ (other browsers do not have this
# requirement).
# Possible values are: png, jpg, gif and svg.
# The default value is: png.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_IMAGE_FORMAT = png
# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
# enable generation of interactive SVG images that allow zooming and panning.
#
# Note that this requires a modern browser other than Internet Explorer. Tested
# and working are Firefox, Chrome, Safari, and Opera.
# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
# the SVG files visible. Older versions of IE do not have SVG support.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
INTERACTIVE_SVG = NO
# The DOT_PATH tag can be used to specify the path where the dot tool can be
# found. If left blank, it is assumed the dot tool can be found in the path.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_PATH =
# The DOTFILE_DIRS tag can be used to specify one or more directories that
# contain dot files that are included in the documentation (see the \dotfile
# command).
# This tag requires that the tag HAVE_DOT is set to YES.
DOTFILE_DIRS =
# The MSCFILE_DIRS tag can be used to specify one or more directories that
# contain msc files that are included in the documentation (see the \mscfile
# command).
MSCFILE_DIRS =
# The DIAFILE_DIRS tag can be used to specify one or more directories that
# contain dia files that are included in the documentation (see the \diafile
# command).
DIAFILE_DIRS =
# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
# path where java can find the plantuml.jar file. If left blank, it is assumed
# PlantUML is not used or called during a preprocessing step. Doxygen will
# generate a warning when it encounters a \startuml command in this case and
# will not generate output for the diagram.
# This tag requires that the tag HAVE_DOT is set to YES.
PLANTUML_JAR_PATH =
# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
# that will be shown in the graph. If the number of nodes in a graph becomes
# larger than this value, doxygen will truncate the graph, which is visualized
# by representing a node as a red box. Note that doxygen if the number of direct
# children of the root node in a graph is already larger than
# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
# Minimum value: 0, maximum value: 10000, default value: 50.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_GRAPH_MAX_NODES = 50
# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
# generated by dot. A depth value of 3 means that only nodes reachable from the
# root by following a path via at most 3 edges will be shown. Nodes that lay
# further from the root node will be omitted. Note that setting this option to 1
# or 2 may greatly reduce the computation time needed for large code bases. Also
# note that the size of a graph can be further restricted by
# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
# Minimum value: 0, maximum value: 1000, default value: 0.
# This tag requires that the tag HAVE_DOT is set to YES.
MAX_DOT_GRAPH_DEPTH = 0
# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
# background. This is disabled by default, because dot on Windows does not seem
# to support this out of the box.
#
# Warning: Depending on the platform used, enabling this option may lead to
# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
# read).
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_TRANSPARENT = NO
# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
# files in one run (i.e. multiple -o and -T options on the command line). This
# makes dot run faster, but since only newer versions of dot (>1.8.10) support
# this, this feature is disabled by default.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_MULTI_TARGETS = YES
# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
# explaining the meaning of the various boxes and arrows in the dot generated
# graphs.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
GENERATE_LEGEND = YES
# If the DOT_CLEANUP tag is set to YES doxygen will remove the intermediate dot
# files that are used to generate the various graphs.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_CLEANUP = YES
diff --git a/Documentation/doxygen_users_guide.conf.in b/Documentation/doxygen_users_guide.conf.in
index 4cc098ed88..9d35050568 100644
--- a/Documentation/doxygen_users_guide.conf.in
+++ b/Documentation/doxygen_users_guide.conf.in
@@ -1,2332 +1,2326 @@
# Doxyfile 1.8.8
# This file describes the settings to be used by the documentation system
# doxygen (www.doxygen.org) for a project.
#
# All text after a double hash (##) is considered a comment and is placed in
# front of the TAG it is preceding.
#
# All text after a single hash (#) is considered a comment and will be ignored.
# The format is:
# TAG = value [value, ...]
# For lists, items can also be appended using:
# TAG += value [value, ...]
# Values that contain spaces should be placed between quotes (\" \").
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
# This tag specifies the encoding used for all characters in the config file
# that follow. The default is UTF-8 which is also the encoding used for all text
# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv
# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv
# for the list of possible encodings.
# The default value is: UTF-8.
DOXYFILE_ENCODING = UTF-8
# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
# double-quotes, unless you are using Doxywizard) that should identify the
# project for which the documentation is generated. This name is used in the
# title of most generated pages and in a few other places.
# The default value is: My Project.
PROJECT_NAME = MITK
# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
# could be handy for archiving the generated documentation or if some version
# control system is used.
PROJECT_NUMBER = @MITK_VERSION_STRING@
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
# quick idea about the purpose of the project. Keep the description short.
PROJECT_BRIEF = "Medical Imaging Interaction Toolkit"
# With the PROJECT_LOGO tag one can specify an logo or icon that is included in
# the documentation. The maximum height of the logo should not exceed 55 pixels
# and the maximum width should not exceed 200 pixels. Doxygen will copy the logo
# to the output directory.
PROJECT_LOGO =
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
# into which the generated documentation will be written. If a relative path is
# entered, it will be relative to the location where doxygen was started. If
# left blank the current directory will be used.
OUTPUT_DIRECTORY = "@MITK_DOXYGEN_OUTPUT_DIR@/Guides/Users_Guide/"
# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 4096 sub-
# directories (in 2 levels) under the output directory of each output format and
# will distribute the generated files over these directories. Enabling this
# option can be useful when feeding doxygen a huge amount of source files, where
# putting all generated files in the same directory would otherwise causes
# performance problems for the file system.
# The default value is: NO.
CREATE_SUBDIRS = NO
# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
# characters to appear in the names of generated files. If set to NO, non-ASCII
# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
# U+3044.
# The default value is: NO.
ALLOW_UNICODE_NAMES = NO
# The OUTPUT_LANGUAGE tag is used to specify the language in which all
# documentation generated by doxygen is written. Doxygen will use this
# information to generate all constant output in the proper language.
# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
# Ukrainian and Vietnamese.
# The default value is: English.
OUTPUT_LANGUAGE = English
# If the BRIEF_MEMBER_DESC tag is set to YES doxygen will include brief member
# descriptions after the members that are listed in the file and class
# documentation (similar to Javadoc). Set to NO to disable this.
# The default value is: YES.
BRIEF_MEMBER_DESC = YES
# If the REPEAT_BRIEF tag is set to YES doxygen will prepend the brief
# description of a member or function before the detailed description
#
# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
# brief descriptions will be completely suppressed.
# The default value is: YES.
REPEAT_BRIEF = YES
# This tag implements a quasi-intelligent brief description abbreviator that is
# used to form the text in various listings. Each string in this list, if found
# as the leading text of the brief description, will be stripped from the text
# and the result, after processing the whole list, is used as the annotated
# text. Otherwise, the brief description is used as-is. If left blank, the
# following values are used ($name is automatically replaced with the name of
# the entity):The $name class, The $name widget, The $name file, is, provides,
# specifies, contains, represents, a, an and the.
ABBREVIATE_BRIEF =
# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
# doxygen will generate a detailed section even if there is only a brief
# description.
# The default value is: NO.
ALWAYS_DETAILED_SEC = NO
# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
# inherited members of a class in the documentation of that class as if those
# members were ordinary class members. Constructors, destructors and assignment
# operators of the base classes will not be shown.
# The default value is: NO.
INLINE_INHERITED_MEMB = NO
# If the FULL_PATH_NAMES tag is set to YES doxygen will prepend the full path
# before files name in the file list and in the header files. If set to NO the
# shortest path that makes the file name unique will be used
# The default value is: YES.
FULL_PATH_NAMES = NO
# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
# Stripping is only done if one of the specified strings matches the left-hand
# part of the path. The tag can be used to show relative paths in the file list.
# If left blank the directory from which doxygen is run is used as the path to
# strip.
#
# Note that you can specify absolute paths here, but also relative paths, which
# will be relative from the directory where doxygen is started.
# This tag requires that the tag FULL_PATH_NAMES is set to YES.
STRIP_FROM_PATH =
# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
# path mentioned in the documentation of a class, which tells the reader which
# header file to include in order to use a class. If left blank only the name of
# the header file containing the class definition is used. Otherwise one should
# specify the list of include paths that are normally passed to the compiler
# using the -I flag.
STRIP_FROM_INC_PATH =
# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
# less readable) file names. This can be useful is your file systems doesn't
# support long names like on DOS, Mac, or CD-ROM.
# The default value is: NO.
SHORT_NAMES = NO
# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
# first line (until the first dot) of a Javadoc-style comment as the brief
# description. If set to NO, the Javadoc-style will behave just like regular Qt-
# style comments (thus requiring an explicit @brief command for a brief
# description.)
# The default value is: NO.
JAVADOC_AUTOBRIEF = NO
# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
# line (until the first dot) of a Qt-style comment as the brief description. If
# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
# requiring an explicit \brief command for a brief description.)
# The default value is: NO.
QT_AUTOBRIEF = NO
# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
# a brief description. This used to be the default behavior. The new default is
# to treat a multi-line C++ comment block as a detailed description. Set this
# tag to YES if you prefer the old behavior instead.
#
# Note that setting this tag to YES also means that rational rose comments are
# not recognized any more.
# The default value is: NO.
MULTILINE_CPP_IS_BRIEF = NO
# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
# documentation from any documented member that it re-implements.
# The default value is: YES.
INHERIT_DOCS = YES
# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce a
# new page for each member. If set to NO, the documentation of a member will be
# part of the file/class/namespace that contains it.
# The default value is: NO.
SEPARATE_MEMBER_PAGES = NO
# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
# uses this value to replace tabs by spaces in code fragments.
# Minimum value: 1, maximum value: 16, default value: 4.
TAB_SIZE = 8
# This tag can be used to specify a number of aliases that act as commands in
# the documentation. An alias has the form:
# name=value
# For example adding
# "sideeffect=@par Side Effects:\n"
# will allow you to put the command \sideeffect (or @sideeffect) in the
# documentation, which will result in a user-defined paragraph with heading
# "Side Effects:". You can put \n's in the value part of an alias to insert
# newlines.
ALIASES = "FIXME=\par Fix Me's:\n" \
"BlueBerry=\if BLUEBERRY" \
"endBlueBerry=\endif" \
"bundlemainpage{1}=\page \1" \
"embmainpage{1}=\page \1" \
"github{2}=<a href=\"https://github.com/MITK/MITK/blob/master/\1\">\2</a>" \
"deprecatedSince{1}=\xrefitem deprecatedSince\1 \" Deprecated as of \1\" \"Functions deprecated as of \1\" " \
"minimumCMakeVersion=@MITK_CMAKE_MINIMUM_REQUIRED_VERSION@" \
"minimumQt5Version=@MITK_QT5_MINIMUM_VERSION@" \
"imageMacro{3}=\image html \1 \2 \n \image latex \1 \2 width=\3cm" \
"developersguidemainpage{1}=\page \1 " \
"usersguidemainpage{1}=\mainpage " \
"nondependentPluginLink{3}= \ref \1 \"\3\" "
-# This tag can be used to specify a number of word-keyword mappings (TCL only).
-# A mapping has the form "name=value". For example adding "class=itcl::class"
-# will allow you to use the command class in the itcl::class meaning.
-
-TCL_SUBST =
-
# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
# only. Doxygen will then generate output that is more tailored for C. For
# instance, some of the names that are used will be different. The list of all
# members will be omitted, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_FOR_C = NO
# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
# Python sources only. Doxygen will then generate output that is more tailored
# for that language. For instance, namespaces will be presented as packages,
# qualified scopes will look different, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_JAVA = NO
# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
# sources. Doxygen will then generate output that is tailored for Fortran.
# The default value is: NO.
OPTIMIZE_FOR_FORTRAN = NO
# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
# sources. Doxygen will then generate output that is tailored for VHDL.
# The default value is: NO.
OPTIMIZE_OUTPUT_VHDL = NO
# Doxygen selects the parser to use depending on the extension of the files it
# parses. With this tag you can assign which parser to use for a given
# extension. Doxygen has a built-in mapping, but you can override or extend it
# using this tag. The format is ext=language, where ext is a file extension, and
# language is one of the parsers supported by doxygen: IDL, Java, Javascript,
# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran:
# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran:
# Fortran. In the later case the parser tries to guess whether the code is fixed
# or free formatted code, this is the default for Fortran type files), VHDL. For
# instance to make doxygen treat .inc files as Fortran files (default is PHP),
# and .f files as C (default is Fortran), use: inc=Fortran f=C.
#
# Note For files without extension you can use no_extension as a placeholder.
#
# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
# the files are not read by doxygen.
EXTENSION_MAPPING =
# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
# according to the Markdown format, which allows for more readable
# documentation. See http://daringfireball.net/projects/markdown/ for details.
# The output of markdown processing is further processed by doxygen, so you can
# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
# case of backward compatibilities issues.
# The default value is: YES.
MARKDOWN_SUPPORT = YES
# When enabled doxygen tries to link words that correspond to documented
# classes, or namespaces to their corresponding documentation. Such a link can
# be prevented in individual cases by by putting a % sign in front of the word
# or globally by setting AUTOLINK_SUPPORT to NO.
# The default value is: YES.
AUTOLINK_SUPPORT = YES
# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
# to include (a tag file for) the STL sources as input, then you should set this
# tag to YES in order to let doxygen match functions declarations and
# definitions whose arguments contain STL classes (e.g. func(std::string);
# versus func(std::string) {}). This also make the inheritance and collaboration
# diagrams that involve STL classes more complete and accurate.
# The default value is: NO.
BUILTIN_STL_SUPPORT = YES
# If you use Microsoft's C++/CLI language, you should set this option to YES to
# enable parsing support.
# The default value is: NO.
CPP_CLI_SUPPORT = NO
# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen
# will parse them like normal C++ but will assume all classes use public instead
# of private inheritance when no explicit protection keyword is present.
# The default value is: NO.
SIP_SUPPORT = NO
# For Microsoft's IDL there are propget and propput attributes to indicate
# getter and setter methods for a property. Setting this option to YES will make
# doxygen to replace the get and set methods by a property in the documentation.
# This will only work if the methods are indeed getting or setting a simple
# type. If this is not the case, or you want to show the methods anyway, you
# should set this option to NO.
# The default value is: YES.
IDL_PROPERTY_SUPPORT = YES
# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
# tag is set to YES, then doxygen will reuse the documentation of the first
# member in the group (if any) for the other members of the group. By default
# all members of a group must be documented explicitly.
# The default value is: NO.
DISTRIBUTE_GROUP_DOC = YES
# Set the SUBGROUPING tag to YES to allow class member groups of the same type
# (for instance a group of public functions) to be put as a subgroup of that
# type (e.g. under the Public Functions section). Set it to NO to prevent
# subgrouping. Alternatively, this can be done per class using the
# \nosubgrouping command.
# The default value is: YES.
SUBGROUPING = YES
# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
# are shown inside the group in which they are included (e.g. using \ingroup)
# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
# and RTF).
#
# Note that this feature does not work in combination with
# SEPARATE_MEMBER_PAGES.
# The default value is: NO.
INLINE_GROUPED_CLASSES = NO
# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
# with only public data fields or simple typedef fields will be shown inline in
# the documentation of the scope in which they are defined (i.e. file,
# namespace, or group documentation), provided this scope is documented. If set
# to NO, structs, classes, and unions are shown on a separate page (for HTML and
# Man pages) or section (for LaTeX and RTF).
# The default value is: NO.
INLINE_SIMPLE_STRUCTS = NO
# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
# enum is documented as struct, union, or enum with the name of the typedef. So
# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
# with name TypeT. When disabled the typedef will appear as a member of a file,
# namespace, or class. And the struct will be named TypeS. This can typically be
# useful for C code in case the coding convention dictates that all compound
# types are typedef'ed and only the typedef is referenced, never the tag name.
# The default value is: NO.
TYPEDEF_HIDES_STRUCT = NO
# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
# cache is used to resolve symbols given their name and scope. Since this can be
# an expensive process and often the same symbol appears multiple times in the
# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
# doxygen will become slower. If the cache is too large, memory is wasted. The
# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
# symbols. At the end of a run doxygen will report the cache usage and suggest
# the optimal cache size from a speed point of view.
# Minimum value: 0, maximum value: 9, default value: 0.
LOOKUP_CACHE_SIZE = 0
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
# documentation are documented, even if no documentation was available. Private
# class members and static file members will be hidden unless the
# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
# Note: This will also disable the warnings about undocumented members that are
# normally produced when WARNINGS is set to YES.
# The default value is: NO.
EXTRACT_ALL = YES
# If the EXTRACT_PRIVATE tag is set to YES all private members of a class will
# be included in the documentation.
# The default value is: NO.
EXTRACT_PRIVATE = NO
# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal
# scope will be included in the documentation.
# The default value is: NO.
EXTRACT_PACKAGE = NO
# If the EXTRACT_STATIC tag is set to YES all static members of a file will be
# included in the documentation.
# The default value is: NO.
EXTRACT_STATIC = YES
# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) defined
# locally in source files will be included in the documentation. If set to NO
# only classes defined in header files are included. Does not have any effect
# for Java sources.
# The default value is: YES.
EXTRACT_LOCAL_CLASSES = @MITK_DOXYGEN_INTERNAL_DOCS@
# This flag is only useful for Objective-C code. When set to YES local methods,
# which are defined in the implementation section but not in the interface are
# included in the documentation. If set to NO only methods in the interface are
# included.
# The default value is: NO.
EXTRACT_LOCAL_METHODS = NO
# If this flag is set to YES, the members of anonymous namespaces will be
# extracted and appear in the documentation as a namespace called
# 'anonymous_namespace{file}', where file will be replaced with the base name of
# the file that contains the anonymous namespace. By default anonymous namespace
# are hidden.
# The default value is: NO.
EXTRACT_ANON_NSPACES = NO
# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
# undocumented members inside documented classes or files. If set to NO these
# members will be included in the various overviews, but no documentation
# section is generated. This option has no effect if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_MEMBERS = NO
# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
# undocumented classes that are normally visible in the class hierarchy. If set
# to NO these classes will be included in the various overviews. This option has
# no effect if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_CLASSES = NO
# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
# (class|struct|union) declarations. If set to NO these declarations will be
# included in the documentation.
# The default value is: NO.
HIDE_FRIEND_COMPOUNDS = @MITK_DOXYGEN_HIDE_FRIEND_COMPOUNDS@
# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
# documentation blocks found inside the body of a function. If set to NO these
# blocks will be appended to the function's detailed documentation block.
# The default value is: NO.
HIDE_IN_BODY_DOCS = NO
# The INTERNAL_DOCS tag determines if documentation that is typed after a
# \internal command is included. If the tag is set to NO then the documentation
# will be excluded. Set it to YES to include the internal documentation.
# The default value is: NO.
INTERNAL_DOCS = @MITK_DOXYGEN_INTERNAL_DOCS@
# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
# names in lower-case letters. If set to YES upper-case letters are also
# allowed. This is useful if you have classes or files whose names only differ
# in case and if your file system supports case sensitive file names. Windows
# and Mac users are advised to set this option to NO.
# The default value is: system dependent.
CASE_SENSE_NAMES = YES
# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
# their full class and namespace scopes in the documentation. If set to YES the
# scope will be hidden.
# The default value is: NO.
HIDE_SCOPE_NAMES = NO
# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
# the files that are included by a file in the documentation of that file.
# The default value is: YES.
SHOW_INCLUDE_FILES = YES
# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
# grouped member an include statement to the documentation, telling the reader
# which file to include in order to use the member.
# The default value is: NO.
SHOW_GROUPED_MEMB_INC = NO
# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
# files with double quotes in the documentation rather than with sharp brackets.
# The default value is: NO.
FORCE_LOCAL_INCLUDES = NO
# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
# documentation for inline members.
# The default value is: YES.
INLINE_INFO = YES
# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
# (detailed) documentation of file and class members alphabetically by member
# name. If set to NO the members will appear in declaration order.
# The default value is: YES.
SORT_MEMBER_DOCS = YES
# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
# descriptions of file, namespace and class members alphabetically by member
# name. If set to NO the members will appear in declaration order. Note that
# this will also influence the order of the classes in the class list.
# The default value is: NO.
SORT_BRIEF_DOCS = NO
# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
# (brief and detailed) documentation of class members so that constructors and
# destructors are listed first. If set to NO the constructors will appear in the
# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
# member documentation.
# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
# detailed member documentation.
# The default value is: NO.
SORT_MEMBERS_CTORS_1ST = NO
# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
# of group names into alphabetical order. If set to NO the group names will
# appear in their defined order.
# The default value is: NO.
SORT_GROUP_NAMES = NO
# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
# fully-qualified names, including namespaces. If set to NO, the class list will
# be sorted only by class name, not including the namespace part.
# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
# Note: This option applies only to the class list, not to the alphabetical
# list.
# The default value is: NO.
SORT_BY_SCOPE_NAME = YES
# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
# type resolution of all parameters of a function it will reject a match between
# the prototype and the implementation of a member function even if there is
# only one candidate or it is obvious which candidate to choose by doing a
# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
# accept a match between prototype and implementation in such cases.
# The default value is: NO.
STRICT_PROTO_MATCHING = NO
# The GENERATE_TODOLIST tag can be used to enable ( YES) or disable ( NO) the
# todo list. This list is created by putting \todo commands in the
# documentation.
# The default value is: YES.
GENERATE_TODOLIST = @MITK_DOXYGEN_GENERATE_TODOLIST@
# The GENERATE_TESTLIST tag can be used to enable ( YES) or disable ( NO) the
# test list. This list is created by putting \test commands in the
# documentation.
# The default value is: YES.
GENERATE_TESTLIST = YES
# The GENERATE_BUGLIST tag can be used to enable ( YES) or disable ( NO) the bug
# list. This list is created by putting \bug commands in the documentation.
# The default value is: YES.
GENERATE_BUGLIST = @MITK_DOXYGEN_GENERATE_BUGLIST@
# The GENERATE_DEPRECATEDLIST tag can be used to enable ( YES) or disable ( NO)
# the deprecated list. This list is created by putting \deprecated commands in
# the documentation.
# The default value is: YES.
GENERATE_DEPRECATEDLIST= @MITK_DOXYGEN_GENERATE_DEPRECATEDLIST@
# The ENABLED_SECTIONS tag can be used to enable conditional documentation
# sections, marked by \if <section_label> ... \endif and \cond <section_label>
# ... \endcond blocks.
ENABLED_SECTIONS = @MITK_DOXYGEN_ENABLED_SECTIONS@
# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
# initial value of a variable or macro / define can have for it to appear in the
# documentation. If the initializer consists of more lines than specified here
# it will be hidden. Use a value of 0 to hide initializers completely. The
# appearance of the value of individual variables and macros / defines can be
# controlled using \showinitializer or \hideinitializer command in the
# documentation regardless of this setting.
# Minimum value: 0, maximum value: 10000, default value: 30.
MAX_INITIALIZER_LINES = 0
# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
# the bottom of the documentation of classes and structs. If set to YES the list
# will mention the files that were used to generate the documentation.
# The default value is: YES.
SHOW_USED_FILES = YES
# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
# will remove the Files entry from the Quick Index and from the Folder Tree View
# (if specified).
# The default value is: YES.
SHOW_FILES = YES
# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
# page. This will remove the Namespaces entry from the Quick Index and from the
# Folder Tree View (if specified).
# The default value is: YES.
SHOW_NAMESPACES = YES
# The FILE_VERSION_FILTER tag can be used to specify a program or script that
# doxygen should invoke to get the current version for each file (typically from
# the version control system). Doxygen will invoke the program by executing (via
# popen()) the command command input-file, where command is the value of the
# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
# by doxygen. Whatever the program writes to standard output is used as the file
# version. For an example see the documentation.
FILE_VERSION_FILTER =
# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
# by doxygen. The layout file controls the global structure of the generated
# output files in an output format independent way. To create the layout file
# that represents doxygen's defaults, run doxygen with the -l option. You can
# optionally specify a file name after the option, if omitted DoxygenLayout.xml
# will be used as the name of the layout file.
#
# Note that if you run doxygen from a directory containing a file called
# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
# tag is left empty.
LAYOUT_FILE =
# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
# the reference definitions. This must be a list of .bib files. The .bib
# extension is automatically appended if omitted. This requires the bibtex tool
# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
# For LaTeX the style of the bibliography can be controlled using
# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
# search path. See also \cite for info how to create references.
CITE_BIB_FILES =
#---------------------------------------------------------------------------
# Configuration options related to warning and progress messages
#---------------------------------------------------------------------------
# The QUIET tag can be used to turn on/off the messages that are generated to
# standard output by doxygen. If QUIET is set to YES this implies that the
# messages are off.
# The default value is: NO.
-QUIET = NO
+QUIET = YES
# The WARNINGS tag can be used to turn on/off the warning messages that are
# generated to standard error ( stderr) by doxygen. If WARNINGS is set to YES
# this implies that the warnings are on.
#
# Tip: Turn warnings on while writing the documentation.
# The default value is: YES.
WARNINGS = YES
# If the WARN_IF_UNDOCUMENTED tag is set to YES, then doxygen will generate
# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
# will automatically be disabled.
# The default value is: YES.
WARN_IF_UNDOCUMENTED = YES
# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
# potential errors in the documentation, such as not documenting some parameters
# in a documented function, or documenting parameters that don't exist or using
# markup commands wrongly.
# The default value is: YES.
WARN_IF_DOC_ERROR = YES
# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
# are documented, but have no documentation for their parameters or return
# value. If set to NO doxygen will only warn about wrong or incomplete parameter
# documentation, but not about the absence of documentation.
# The default value is: NO.
WARN_NO_PARAMDOC = NO
# The WARN_FORMAT tag determines the format of the warning messages that doxygen
# can produce. The string should contain the $file, $line, and $text tags, which
# will be replaced by the file and line number from which the warning originated
# and the warning text. Optionally the format may contain $version, which will
# be replaced by the version of the file (if it could be obtained via
# FILE_VERSION_FILTER)
# The default value is: $file:$line: $text.
WARN_FORMAT = "$file:$line: $text"
# The WARN_LOGFILE tag can be used to specify a file to which warning and error
# messages should be written. If left blank the output is written to standard
# error (stderr).
WARN_LOGFILE =
#---------------------------------------------------------------------------
# Configuration options related to the input files
#---------------------------------------------------------------------------
# The INPUT tag is used to specify the files and/or directories that contain
# documented source files. You may enter file names like myfile.cpp or
# directories like /usr/src/myproject. Separate the files or directories with
# spaces.
# Note: If this tag is empty the current directory is searched.
INPUT = @USERS_GUIDE_INPUT@
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
# documentation (see: http://www.gnu.org/software/libiconv) for the list of
# possible encodings.
# The default value is: UTF-8.
INPUT_ENCODING = UTF-8
# If the value of the INPUT tag contains directories, you can use the
# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
# *.h) to filter out the source-files in the directories. If left blank the
# following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii,
# *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp,
# *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown,
# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
# *.qsf, *.as and *.js.
FILE_PATTERNS = *.dox \
*.md
# The RECURSIVE tag can be used to specify whether or not subdirectories should
# be searched for input files as well.
# The default value is: NO.
RECURSIVE = YES
# The EXCLUDE tag can be used to specify files and/or directories that should be
# excluded from the INPUT source files. This way you can easily exclude a
# subdirectory from a directory tree whose root is specified with the INPUT tag.
#
# Note that relative paths are relative to the directory from which doxygen is
# run.
EXCLUDE =
# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
# directories that are symbolic links (a Unix file system feature) are excluded
# from the input.
# The default value is: NO.
EXCLUDE_SYMLINKS = NO
# If the value of the INPUT tag contains directories, you can use the
# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
# certain files from those directories.
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories for example use the pattern */test/*
EXCLUDE_PATTERNS = modules.dox \
*/Plugins/*/documentation/doxygen/*
# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
# (namespaces, classes, functions, etc.) that should be excluded from the
# output. The symbol name can be a fully qualified name, a word, or if the
# wildcard * is used, a substring. Examples: ANamespace, AClass,
# AClass::ANamespace, ANamespace::*Test
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories use the pattern */test/*
EXCLUDE_SYMBOLS =
# The EXAMPLE_PATH tag can be used to specify one or more files or directories
# that contain example code fragments that are included (see the \include
# command).
EXAMPLE_PATH =
# If the value of the EXAMPLE_PATH tag contains directories, you can use the
# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
# *.h) to filter out the source-files in the directories. If left blank all
# files are included.
EXAMPLE_PATTERNS =
# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
# searched for input files to be used with the \include or \dontinclude commands
# irrespective of the value of the RECURSIVE tag.
# The default value is: NO.
EXAMPLE_RECURSIVE = YES
# The IMAGE_PATH tag can be used to specify one or more files or directories
# that contain images that are to be included in the documentation (see the
# \image command).
IMAGE_PATH = "@MITK_SOURCE_DIR@/Documentation/Doxygen/UserManual/" \
"@MITK_SOURCE_DIR@/Plugins/" \
"@MITK_SOURCE_DIR@/Examples/Plugins/"
# The INPUT_FILTER tag can be used to specify a program that doxygen should
# invoke to filter for each input file. Doxygen will invoke the filter program
# by executing (via popen()) the command:
#
# <filter> <input-file>
#
# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
# name of an input file. Doxygen will then use the output that the filter
# program writes to standard output. If FILTER_PATTERNS is specified, this tag
# will be ignored.
#
# Note that the filter must not add or remove lines; it is applied before the
# code is scanned, but not when the output code is generated. If lines are added
# or removed, the anchors will not be placed correctly.
INPUT_FILTER =
# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
# basis. Doxygen will compare the file name with each pattern and apply the
# filter if there is a match. The filters are a list of the form: pattern=filter
# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
# patterns match the file name, INPUT_FILTER is applied.
FILTER_PATTERNS = *.cmake=@CMakeDoxygenFilter_EXECUTABLE@
# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
# INPUT_FILTER ) will also be used to filter the input files that are used for
# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
# The default value is: NO.
FILTER_SOURCE_FILES = NO
# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
# it is also possible to disable source filtering for a specific pattern using
# *.ext= (so without naming a filter).
# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
FILTER_SOURCE_PATTERNS =
# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
# is part of the input, its contents will be placed on the main page
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.
USE_MDFILE_AS_MAINPAGE =
#---------------------------------------------------------------------------
# Configuration options related to source browsing
#---------------------------------------------------------------------------
# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
# generated. Documented entities will be cross-referenced with these sources.
#
# Note: To get rid of all source code in the generated output, make sure that
# also VERBATIM_HEADERS is set to NO.
# The default value is: NO.
SOURCE_BROWSER = YES
# Setting the INLINE_SOURCES tag to YES will include the body of functions,
# classes and enums directly into the documentation.
# The default value is: NO.
INLINE_SOURCES = NO
# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
# special comment blocks from generated source code fragments. Normal C, C++ and
# Fortran comments will always remain visible.
# The default value is: YES.
STRIP_CODE_COMMENTS = YES
# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
# function all documented functions referencing it will be listed.
# The default value is: NO.
REFERENCED_BY_RELATION = YES
# If the REFERENCES_RELATION tag is set to YES then for each documented function
# all documented entities called/used by that function will be listed.
# The default value is: NO.
REFERENCES_RELATION = YES
# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
# to YES, then the hyperlinks from functions in REFERENCES_RELATION and
# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
# link to the documentation.
# The default value is: YES.
REFERENCES_LINK_SOURCE = YES
# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
# source code will show a tooltip with additional information such as prototype,
# brief description and links to the definition and documentation. Since this
# will make the HTML file larger and loading of large files a bit slower, you
# can opt to disable this feature.
# The default value is: YES.
# This tag requires that the tag SOURCE_BROWSER is set to YES.
SOURCE_TOOLTIPS = YES
# If the USE_HTAGS tag is set to YES then the references to source code will
# point to the HTML generated by the htags(1) tool instead of doxygen built-in
# source browser. The htags tool is part of GNU's global source tagging system
# (see http://www.gnu.org/software/global/global.html). You will need version
# 4.8.6 or higher.
#
# To use it do the following:
# - Install the latest version of global
# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
# - Make sure the INPUT points to the root of the source tree
# - Run doxygen as normal
#
# Doxygen will invoke htags (and that will in turn invoke gtags), so these
# tools must be available from the command line (i.e. in the search path).
#
# The result: instead of the source browser generated by doxygen, the links to
# source code will now point to the output of htags.
# The default value is: NO.
# This tag requires that the tag SOURCE_BROWSER is set to YES.
USE_HTAGS = NO
# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
# verbatim copy of the header file for each class for which an include is
# specified. Set to NO to disable this.
# See also: Section \class.
# The default value is: YES.
VERBATIM_HEADERS = YES
#---------------------------------------------------------------------------
# Configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
# compounds will be generated. Enable this if the project contains a lot of
# classes, structs, unions or interfaces.
# The default value is: YES.
ALPHABETICAL_INDEX = YES
# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
# which the alphabetical index list will be split.
# Minimum value: 1, maximum value: 20, default value: 5.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
COLS_IN_ALPHA_INDEX = 3
# In case all classes in a project start with a common prefix, all classes will
# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
# can be used to specify a prefix (or a list of prefixes) that should be ignored
# while generating the index headers.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
IGNORE_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the HTML output
#---------------------------------------------------------------------------
# If the GENERATE_HTML tag is set to YES doxygen will generate HTML output
# The default value is: YES.
GENERATE_HTML = NO
# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: html.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_OUTPUT = html
# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
# generated HTML page (for example: .htm, .php, .asp).
# The default value is: .html.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FILE_EXTENSION = .html
# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
# each generated HTML page. If the tag is left blank doxygen will generate a
# standard header.
#
# To get valid HTML the header file that includes any scripts and style sheets
# that doxygen needs, which is dependent on the configuration options used (e.g.
# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
# default header using
# doxygen -w html new_header.html new_footer.html new_stylesheet.css
# YourConfigFile
# and then modify the file new_header.html. See also section "Doxygen usage"
# for information on how to generate the default header that doxygen normally
# uses.
# Note: The header is subject to change so you typically have to regenerate the
# default header when upgrading to a newer version of doxygen. For a description
# of the possible markers and block names see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_HEADER =
# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
# generated HTML page. If the tag is left blank doxygen will generate a standard
# footer. See HTML_HEADER for more information on how to generate a default
# footer and what special commands can be used inside the footer. See also
# section "Doxygen usage" for information on how to generate the default footer
# that doxygen normally uses.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FOOTER =
# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
# sheet that is used by each HTML page. It can be used to fine-tune the look of
# the HTML output. If left blank doxygen will generate a default style sheet.
# See also section "Doxygen usage" for information on how to generate the style
# sheet that doxygen normally uses.
# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
# it is more robust and this tag (HTML_STYLESHEET) will in the future become
# obsolete.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_STYLESHEET =
# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
# cascading style sheets that are included after the standard style sheets
# created by doxygen. Using this option one can overrule certain style aspects.
# This is preferred over using HTML_STYLESHEET since it does not replace the
# standard style sheet and is therefor more robust against future updates.
# Doxygen will copy the style sheet files to the output directory.
# Note: The order of the extra stylesheet files is of importance (e.g. the last
# stylesheet in the list overrules the setting of the previous ones in the
# list). For an example see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_STYLESHEET = @MITK_DOXYGEN_STYLESHEET@
# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the HTML output directory. Note
# that these files will be copied to the base HTML output directory. Use the
# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
# files will be copied as-is; there are no commands or markers available.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_FILES =
# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
# will adjust the colors in the stylesheet and background images according to
# this color. Hue is specified as an angle on a colorwheel, see
# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
# purple, and 360 is red again.
# Minimum value: 0, maximum value: 359, default value: 220.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_HUE = 220
# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
# in the HTML output. For a value of 0 the output will use grayscales only. A
# value of 255 will produce the most vivid colors.
# Minimum value: 0, maximum value: 255, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_SAT = 100
# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
# luminance component of the colors in the HTML output. Values below 100
# gradually make the output lighter, whereas values above 100 make the output
# darker. The value divided by 100 is the actual gamma applied, so 80 represents
# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
# change the gamma.
# Minimum value: 40, maximum value: 240, default value: 80.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_GAMMA = 80
# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
# page will contain the date and time when the page was generated. Setting this
# to NO can help when comparing the output of multiple runs.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_TIMESTAMP = YES
# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
# documentation will contain sections that can be hidden and shown after the
# page has loaded.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_DYNAMIC_SECTIONS = @MITK_DOXYGEN_HTML_DYNAMIC_SECTIONS@
# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
# shown in the various tree structured indices initially; the user can expand
# and collapse entries dynamically later on. Doxygen will expand the tree to
# such a level that at most the specified number of entries are visible (unless
# a fully collapsed tree already exceeds this amount). So setting the number of
# entries 1 will produce a full collapsed tree by default. 0 is a special value
# representing an infinite number of entries and will result in a full expanded
# tree by default.
# Minimum value: 0, maximum value: 9999, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_INDEX_NUM_ENTRIES = 100
# If the GENERATE_DOCSET tag is set to YES, additional index files will be
# generated that can be used as input for Apple's Xcode 3 integrated development
# environment (see: http://developer.apple.com/tools/xcode/), introduced with
# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
# Makefile in the HTML output directory. Running make will produce the docset in
# that directory and running make install will install the docset in
# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
# for more information.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_DOCSET = NO
# This tag determines the name of the docset feed. A documentation feed provides
# an umbrella under which multiple documentation sets from a single provider
# (such as a company or product suite) can be grouped.
# The default value is: Doxygen generated docs.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_FEEDNAME = "Doxygen generated docs"
# This tag specifies a string that should uniquely identify the documentation
# set bundle. This should be a reverse domain-name style string, e.g.
# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_BUNDLE_ID = org.doxygen.Project
# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
# the documentation publisher. This should be a reverse domain-name style
# string, e.g. com.mycompany.MyDocSet.documentation.
# The default value is: org.doxygen.Publisher.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_ID = org.doxygen.Publisher
# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
# The default value is: Publisher.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_NAME = Publisher
# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
# Windows.
#
# The HTML Help Workshop contains a compiler that can convert all HTML output
# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
# files are now used as the Windows 98 help format, and will replace the old
# Windows help format (.hlp) on all Windows platforms in the future. Compressed
# HTML files also contain an index, a table of contents, and you can search for
# words in the documentation. The HTML workshop also contains a viewer for
# compressed HTML files.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_HTMLHELP = NO
# The CHM_FILE tag can be used to specify the file name of the resulting .chm
# file. You can add a path in front of the file if the result should not be
# written to the html output directory.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_FILE =
# The HHC_LOCATION tag can be used to specify the location (absolute path
# including file name) of the HTML help compiler ( hhc.exe). If non-empty
# doxygen will try to run the HTML help compiler on the generated index.hhp.
# The file has to be specified with full path.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
HHC_LOCATION =
# The GENERATE_CHI flag controls if a separate .chi index file is generated (
# YES) or that it should be included in the master .chm file ( NO).
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
GENERATE_CHI = NO
# The CHM_INDEX_ENCODING is used to encode HtmlHelp index ( hhk), content ( hhc)
# and project file content.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_INDEX_ENCODING =
# The BINARY_TOC flag controls whether a binary table of contents is generated (
# YES) or a normal table of contents ( NO) in the .chm file. Furthermore it
# enables the Previous and Next buttons.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
BINARY_TOC = NO
# The TOC_EXPAND flag can be set to YES to add extra items for group members to
# the table of contents of the HTML help documentation and to the tree view.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
TOC_EXPAND = NO
# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
# (.qch) of the generated HTML documentation.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_QHP = @MITK_DOXYGEN_GENERATE_QHP@
# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
# the file name of the resulting .qch file. The path specified is relative to
# the HTML output folder.
# This tag requires that the tag GENERATE_QHP is set to YES.
QCH_FILE = @MITK_DOXYGEN_QCH_FILE@
# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
# Project output. For more information please see Qt Help Project / Namespace
# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_NAMESPACE = "org.mitk"
# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
# Help Project output. For more information please see Qt Help Project / Virtual
# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
# folders).
# The default value is: doc.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_VIRTUAL_FOLDER = MITK
# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
# filter to add. For more information please see Qt Help Project / Custom
# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
# filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_NAME =
# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
# custom filter to add. For more information please see Qt Help Project / Custom
# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
# filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_ATTRS =
# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
# project's filter section matches. Qt Help Project / Filter Attributes (see:
# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_SECT_FILTER_ATTRS =
# The QHG_LOCATION tag can be used to specify the location of Qt's
# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
# generated .qhp file.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHG_LOCATION = @QT_HELPGENERATOR_EXECUTABLE@
# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
# generated, together with the HTML files, they form an Eclipse help plugin. To
# install this plugin and make it available under the help contents menu in
# Eclipse, the contents of the directory containing the HTML and XML files needs
# to be copied into the plugins directory of eclipse. The name of the directory
# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
# After copying Eclipse needs to be restarted before the help appears.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_ECLIPSEHELP = NO
# A unique identifier for the Eclipse help plugin. When installing the plugin
# the directory name containing the HTML and XML files should also have this
# name. Each documentation set should have its own identifier.
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
ECLIPSE_DOC_ID = org.doxygen.Project
# If you want full control over the layout of the generated HTML pages it might
# be necessary to disable the index and replace it with your own. The
# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
# of each HTML page. A value of NO enables the index and the value YES disables
# it. Since the tabs in the index contain the same information as the navigation
# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
DISABLE_INDEX = NO
# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
# structure should be generated to display hierarchical information. If the tag
# value is set to YES, a side panel will be generated containing a tree-like
# index structure (just like the one that is generated for HTML Help). For this
# to work a browser that supports JavaScript, DHTML, CSS and frames is required
# (i.e. any modern browser). Windows users are probably better off using the
# HTML help feature. Via custom stylesheets (see HTML_EXTRA_STYLESHEET) one can
# further fine-tune the look of the index. As an example, the default style
# sheet generated by doxygen has an example that shows how to put an image at
# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
# the same information as the tab index, you could consider setting
# DISABLE_INDEX to YES when enabling this option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_TREEVIEW = YES
# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
# doxygen will group on one line in the generated HTML documentation.
#
# Note that a value of 0 will completely suppress the enum values from appearing
# in the overview section.
# Minimum value: 0, maximum value: 20, default value: 4.
# This tag requires that the tag GENERATE_HTML is set to YES.
ENUM_VALUES_PER_LINE = 4
# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
# to set the initial width (in pixels) of the frame in which the tree is shown.
# Minimum value: 0, maximum value: 1500, default value: 250.
# This tag requires that the tag GENERATE_HTML is set to YES.
TREEVIEW_WIDTH = 300
# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open links to
# external symbols imported via tag files in a separate window.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
EXT_LINKS_IN_WINDOW = NO
# Use this tag to change the font size of LaTeX formulas included as images in
# the HTML documentation. When you change the font size after a successful
# doxygen run you need to manually remove any form_*.png images from the HTML
# output directory to force them to be regenerated.
# Minimum value: 8, maximum value: 50, default value: 10.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_FONTSIZE = 10
# Use the FORMULA_TRANPARENT tag to determine whether or not the images
# generated for formulas are transparent PNGs. Transparent PNGs are not
# supported properly for IE 6.0, but are supported on all modern browsers.
#
# Note that when changing this option you need to delete any form_*.png files in
# the HTML output directory before the changes have effect.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_TRANSPARENT = YES
# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
# http://www.mathjax.org) which uses client side Javascript for the rendering
# instead of using prerendered bitmaps. Use this if you do not have LaTeX
# installed or if you want to formulas look prettier in the HTML output. When
# enabled you may also need to install MathJax separately and configure the path
# to it using the MATHJAX_RELPATH option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
USE_MATHJAX = NO
# When MathJax is enabled you can set the default output format to be used for
# the MathJax output. See the MathJax site (see:
# http://docs.mathjax.org/en/latest/output.html) for more details.
# Possible values are: HTML-CSS (which is slower, but has the best
# compatibility), NativeMML (i.e. MathML) and SVG.
# The default value is: HTML-CSS.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_FORMAT = HTML-CSS
# When MathJax is enabled you need to specify the location relative to the HTML
# output directory using the MATHJAX_RELPATH option. The destination directory
# should contain the MathJax.js script. For instance, if the mathjax directory
# is located at the same level as the HTML output directory, then
# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
# Content Delivery Network so you can quickly see the result without installing
# MathJax. However, it is strongly recommended to install a local copy of
# MathJax from http://www.mathjax.org before deployment.
# The default value is: http://cdn.mathjax.org/mathjax/latest.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_RELPATH = http://www.mathjax.org/mathjax
# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
# extension names that should be enabled during MathJax rendering. For example
# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_EXTENSIONS =
# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
# of code that will be used on startup of the MathJax code. See the MathJax site
# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
# example see the documentation.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_CODEFILE =
# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
# the HTML output. The underlying search engine uses javascript and DHTML and
# should work on any modern browser. Note that when using HTML help
# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
# there is already a search function so this one should typically be disabled.
# For large projects the javascript based search engine can be slow, then
# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
# search using the keyboard; to jump to the search box use <access key> + S
# (what the <access key> is depends on the OS and browser, but it is typically
# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
# key> to jump into the search results window, the results can be navigated
# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
# the search. The filter options can be selected when the cursor is inside the
# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
# to select a filter and <Enter> or <escape> to activate or cancel the filter
# option.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
SEARCHENGINE = YES
# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
# implemented using a web server instead of a web client using Javascript. There
# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
# setting. When disabled, doxygen will generate a PHP script for searching and
# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
# and searching needs to be provided by external tools. See the section
# "External Indexing and Searching" for details.
# The default value is: NO.
# This tag requires that the tag SEARCHENGINE is set to YES.
SERVER_BASED_SEARCH = NO
# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
# script for searching. Instead the search results are written to an XML file
# which needs to be processed by an external indexer. Doxygen will invoke an
# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
# search results.
#
# Doxygen ships with an example indexer ( doxyindexer) and search engine
# (doxysearch.cgi) which are based on the open source search engine library
# Xapian (see: http://xapian.org/).
#
# See the section "External Indexing and Searching" for details.
# The default value is: NO.
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTERNAL_SEARCH = NO
# The SEARCHENGINE_URL should point to a search engine hosted by a web server
# which will return the search results when EXTERNAL_SEARCH is enabled.
#
# Doxygen ships with an example indexer ( doxyindexer) and search engine
# (doxysearch.cgi) which are based on the open source search engine library
# Xapian (see: http://xapian.org/). See the section "External Indexing and
# Searching" for details.
# This tag requires that the tag SEARCHENGINE is set to YES.
SEARCHENGINE_URL =
# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
# search data is written to a file for indexing by an external tool. With the
# SEARCHDATA_FILE tag the name of this file can be specified.
# The default file is: searchdata.xml.
# This tag requires that the tag SEARCHENGINE is set to YES.
SEARCHDATA_FILE = searchdata.xml
# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
# projects and redirect the results back to the right project.
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTERNAL_SEARCH_ID =
# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
# projects other than the one defined by this configuration file, but that are
# all added to the same external search index. Each project needs to have a
# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
# to a relative location where the documentation can be found. The format is:
# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTRA_SEARCH_MAPPINGS =
#---------------------------------------------------------------------------
# Configuration options related to the LaTeX output
#---------------------------------------------------------------------------
# If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output.
# The default value is: YES.
GENERATE_LATEX = YES
# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: latex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_OUTPUT = latex
# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
# invoked.
#
# Note that when enabling USE_PDFLATEX this option is only used for generating
# bitmaps for formulas in the HTML output, but not in the Makefile that is
# written to the output directory.
# The default file is: latex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_CMD_NAME = latex
# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
# index for LaTeX.
# The default file is: makeindex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
MAKEINDEX_CMD_NAME = makeindex
# If the COMPACT_LATEX tag is set to YES doxygen generates more compact LaTeX
# documents. This may be useful for small projects and may help to save some
# trees in general.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
COMPACT_LATEX = NO
# The PAPER_TYPE tag can be used to set the paper type that is used by the
# printer.
# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
# 14 inches) and executive (7.25 x 10.5 inches).
# The default value is: a4.
# This tag requires that the tag GENERATE_LATEX is set to YES.
-PAPER_TYPE = a4wide
+PAPER_TYPE = a4
# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
# that should be included in the LaTeX output. To get the times font for
# instance you can specify
# EXTRA_PACKAGES=times
# If left blank no extra packages will be included.
# This tag requires that the tag GENERATE_LATEX is set to YES.
EXTRA_PACKAGES = amssymb
# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
# generated LaTeX document. The header should contain everything until the first
# chapter. If it is left blank doxygen will generate a standard header. See
# section "Doxygen usage" for information on how to let doxygen write the
# default header to a separate file.
#
# Note: Only use a user-defined header if you know what you are doing! The
# following commands have a special meaning inside the header: $title,
# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
# $projectbrief, $projectlogo. Doxygen will replace $title with the empy string,
# for the replacement values of the other commands the user is refered to
# HTML_HEADER.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HEADER =
# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
# generated LaTeX document. The footer should contain everything after the last
# chapter. If it is left blank doxygen will generate a standard footer. See
# LATEX_HEADER for more information on how to generate a default footer and what
# special commands can be used inside the footer.
#
# Note: Only use a user-defined footer if you know what you are doing!
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_FOOTER =
# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the LATEX_OUTPUT output
# directory. Note that the files will be copied as-is; there are no commands or
# markers available.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_EXTRA_FILES =
# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
# contain links (just like the HTML output) instead of page references. This
# makes the output suitable for online browsing using a PDF viewer.
# The default value is: YES.
# This tag requires that the tag GENERATE_LATEX is set to YES.
PDF_HYPERLINKS = YES
# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
# the PDF file directly from the LaTeX files. Set this option to YES to get a
# higher quality PDF documentation.
# The default value is: YES.
# This tag requires that the tag GENERATE_LATEX is set to YES.
USE_PDFLATEX = YES
# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
# command to the generated LaTeX files. This will instruct LaTeX to keep running
# if errors occur, instead of asking the user for help. This option is also used
# when generating formulas in HTML.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_BATCHMODE = YES
# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
# index chapters (such as File Index, Compound Index, etc.) in the output.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HIDE_INDICES = NO
# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
# code with syntax highlighting in the LaTeX output.
#
# Note that which sources are shown also depends on other settings such as
# SOURCE_BROWSER.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_SOURCE_CODE = NO
# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
# bibliography, e.g. plainnat, or ieeetr. See
# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
# The default value is: plain.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_BIB_STYLE = plain
#---------------------------------------------------------------------------
# Configuration options related to the RTF output
#---------------------------------------------------------------------------
# If the GENERATE_RTF tag is set to YES doxygen will generate RTF output. The
# RTF output is optimized for Word 97 and may not look too pretty with other RTF
# readers/editors.
# The default value is: NO.
GENERATE_RTF = NO
# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: rtf.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_OUTPUT = rtf
# If the COMPACT_RTF tag is set to YES doxygen generates more compact RTF
# documents. This may be useful for small projects and may help to save some
# trees in general.
# The default value is: NO.
# This tag requires that the tag GENERATE_RTF is set to YES.
COMPACT_RTF = NO
# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
# contain hyperlink fields. The RTF file will contain links (just like the HTML
# output) instead of page references. This makes the output suitable for online
# browsing using Word or some other Word compatible readers that support those
# fields.
#
# Note: WordPad (write) and others do not support links.
# The default value is: NO.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_HYPERLINKS = NO
# Load stylesheet definitions from file. Syntax is similar to doxygen's config
# file, i.e. a series of assignments. You only have to provide replacements,
# missing definitions are set to their default value.
#
# See also section "Doxygen usage" for information on how to generate the
# default style sheet that doxygen normally uses.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_STYLESHEET_FILE =
# Set optional variables used in the generation of an RTF document. Syntax is
# similar to doxygen's config file. A template extensions file can be generated
# using doxygen -e rtf extensionFile.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_EXTENSIONS_FILE =
#---------------------------------------------------------------------------
# Configuration options related to the man page output
#---------------------------------------------------------------------------
# If the GENERATE_MAN tag is set to YES doxygen will generate man pages for
# classes and files.
# The default value is: NO.
GENERATE_MAN = NO
# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it. A directory man3 will be created inside the directory specified by
# MAN_OUTPUT.
# The default directory is: man.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_OUTPUT = man
# The MAN_EXTENSION tag determines the extension that is added to the generated
# man pages. In case the manual section does not start with a number, the number
# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
# optional.
# The default value is: .3.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_EXTENSION = .3
# The MAN_SUBDIR tag determines the name of the directory created within
# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
# MAN_EXTENSION with the initial . removed.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_SUBDIR =
# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
# will generate one additional man file for each entity documented in the real
# man page(s). These additional files only source the real man page, but without
# them the man command would be unable to find the correct page.
# The default value is: NO.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_LINKS = NO
#---------------------------------------------------------------------------
# Configuration options related to the XML output
#---------------------------------------------------------------------------
# If the GENERATE_XML tag is set to YES doxygen will generate an XML file that
# captures the structure of the code including all documentation.
# The default value is: NO.
GENERATE_XML = NO
# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: xml.
# This tag requires that the tag GENERATE_XML is set to YES.
XML_OUTPUT = xml
# If the XML_PROGRAMLISTING tag is set to YES doxygen will dump the program
# listings (including syntax highlighting and cross-referencing information) to
# the XML output. Note that enabling this will significantly increase the size
# of the XML output.
# The default value is: YES.
# This tag requires that the tag GENERATE_XML is set to YES.
XML_PROGRAMLISTING = YES
#---------------------------------------------------------------------------
# Configuration options related to the DOCBOOK output
#---------------------------------------------------------------------------
# If the GENERATE_DOCBOOK tag is set to YES doxygen will generate Docbook files
# that can be used to generate PDF.
# The default value is: NO.
GENERATE_DOCBOOK = NO
# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
# front of it.
# The default directory is: docbook.
# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
DOCBOOK_OUTPUT = docbook
# If the DOCBOOK_PROGRAMLISTING tag is set to YES doxygen will include the
# program listings (including syntax highlighting and cross-referencing
# information) to the DOCBOOK output. Note that enabling this will significantly
# increase the size of the DOCBOOK output.
# The default value is: NO.
# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
DOCBOOK_PROGRAMLISTING = NO
#---------------------------------------------------------------------------
# Configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
# If the GENERATE_AUTOGEN_DEF tag is set to YES doxygen will generate an AutoGen
# Definitions (see http://autogen.sf.net) file that captures the structure of
# the code including all documentation. Note that this feature is still
# experimental and incomplete at the moment.
# The default value is: NO.
GENERATE_AUTOGEN_DEF = NO
#---------------------------------------------------------------------------
# Configuration options related to the Perl module output
#---------------------------------------------------------------------------
# If the GENERATE_PERLMOD tag is set to YES doxygen will generate a Perl module
# file that captures the structure of the code including all documentation.
#
# Note that this feature is still experimental and incomplete at the moment.
# The default value is: NO.
GENERATE_PERLMOD = NO
# If the PERLMOD_LATEX tag is set to YES doxygen will generate the necessary
# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
# output from the Perl module output.
# The default value is: NO.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_LATEX = NO
# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be nicely
# formatted so it can be parsed by a human reader. This is useful if you want to
# understand what is going on. On the other hand, if this tag is set to NO the
# size of the Perl module output will be much smaller and Perl will parse it
# just the same.
# The default value is: YES.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_PRETTY = YES
# The names of the make variables in the generated doxyrules.make file are
# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
# so different doxyrules.make files included by the same Makefile don't
# overwrite each other's variables.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_MAKEVAR_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
# If the ENABLE_PREPROCESSING tag is set to YES doxygen will evaluate all
# C-preprocessor directives found in the sources and include files.
# The default value is: YES.
ENABLE_PREPROCESSING = YES
# If the MACRO_EXPANSION tag is set to YES doxygen will expand all macro names
# in the source code. If set to NO only conditional compilation will be
# performed. Macro expansion can be done in a controlled way by setting
# EXPAND_ONLY_PREDEF to YES.
# The default value is: NO.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
MACRO_EXPANSION = YES
# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
# the macro expansion is limited to the macros specified with the PREDEFINED and
# EXPAND_AS_DEFINED tags.
# The default value is: NO.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
EXPAND_ONLY_PREDEF = NO
# If the SEARCH_INCLUDES tag is set to YES the includes files in the
# INCLUDE_PATH will be searched if a #include is found.
# The default value is: YES.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
SEARCH_INCLUDES = YES
# The INCLUDE_PATH tag can be used to specify one or more directories that
# contain include files that are not input files but should be processed by the
# preprocessor.
# This tag requires that the tag SEARCH_INCLUDES is set to YES.
INCLUDE_PATH =
# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
# patterns (like *.h and *.hpp) to filter out the header-files in the
# directories. If left blank, the patterns specified with FILE_PATTERNS will be
# used.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
INCLUDE_FILE_PATTERNS =
# The PREDEFINED tag can be used to specify one or more macro names that are
# defined before the preprocessor is started (similar to the -D option of e.g.
# gcc). The argument of the tag is a list of macros of the form: name or
# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
# is assumed. To prevent a macro definition from being undefined via #undef or
# recursively expanded use the := operator instead of the = operator.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
PREDEFINED =
# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
# tag can be used to specify a list of macro names that should be expanded. The
# macro definition that is found in the sources will be used. Use the PREDEFINED
# tag if you want to use a different macro definition that overrules the
# definition found in the source code.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
EXPAND_AS_DEFINED =
# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
# remove all references to function-like macros that are alone on a line, have
# an all uppercase name, and do not end with a semicolon. Such function macros
# are typically used for boiler-plate code, and will confuse the parser if not
# removed.
# The default value is: YES.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
SKIP_FUNCTION_MACROS = YES
#---------------------------------------------------------------------------
# Configuration options related to external references
#---------------------------------------------------------------------------
# The TAGFILES tag can be used to specify one or more tag files. For each tag
# file the location of the external documentation should be added. The format of
# a tag file without this location is as follows:
# TAGFILES = file1 file2 ...
# Adding location for the tag files is done as follows:
# TAGFILES = file1=loc1 "file2 = loc2" ...
# where loc1 and loc2 can be relative or absolute paths or URLs. See the
# section "Linking to external documentation" for more information about the use
# of tag files.
# Note: Each tag file must have a unique name (where the name does NOT include
# the path). If a tag file is not located in the directory in which doxygen is
# run, you must also specify the path to the tagfile here.
TAGFILES = @BLUEBERRY_DOXYGEN_TAGFILE@
# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
# tag file that is based on the input files it reads. See section "Linking to
# external documentation" for more information about the usage of tag files.
GENERATE_TAGFILE = @MITK_DOXYGEN_TAGFILE_NAME@
# If the ALLEXTERNALS tag is set to YES all external class will be listed in the
# class index. If set to NO only the inherited external classes will be listed.
# The default value is: NO.
ALLEXTERNALS = NO
# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed in
# the modules index. If set to NO, only the current project's groups will be
# listed.
# The default value is: YES.
EXTERNAL_GROUPS = NO
# If the EXTERNAL_PAGES tag is set to YES all external pages will be listed in
# the related pages index. If set to NO, only the current project's pages will
# be listed.
# The default value is: YES.
EXTERNAL_PAGES = YES
#---------------------------------------------------------------------------
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
# If the CLASS_DIAGRAMS tag is set to YES doxygen will generate a class diagram
# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
# NO turns the diagrams off. Note that this option also works with HAVE_DOT
# disabled, but it is recommended to install and use dot, since it yields more
# powerful graphs.
# The default value is: YES.
CLASS_DIAGRAMS = YES
# You can include diagrams made with dia in doxygen documentation. Doxygen will
# then run dia to produce the diagram and insert it in the documentation. The
# DIA_PATH tag allows you to specify the directory where the dia binary resides.
# If left empty dia is assumed to be found in the default search path.
DIA_PATH =
# If set to YES, the inheritance and collaboration graphs will hide inheritance
# and usage relations if the target is undocumented or is not a class.
# The default value is: YES.
HIDE_UNDOC_RELATIONS = YES
# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
# available from the path. This tool is part of Graphviz (see:
# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
# Bell Labs. The other options in this section have no effect if this option is
# set to NO
# The default value is: NO.
HAVE_DOT = @HAVE_DOT@
# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
# to run in parallel. When set to 0 doxygen will base this on the number of
# processors available in the system. You can set it explicitly to a value
# larger than 0 to get control over the balance between CPU load and processing
# speed.
# Minimum value: 0, maximum value: 32, default value: 0.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_NUM_THREADS = @MITK_DOXYGEN_DOT_NUM_THREADS@
# When you want a differently looking font in the dot files that doxygen
# generates you can specify the font name using DOT_FONTNAME. You need to make
# sure dot is able to find the font, which can be done by putting it in a
# standard location or by setting the DOTFONTPATH environment variable or by
# setting DOT_FONTPATH to the directory containing the font.
# The default value is: Helvetica.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTNAME = Helvetica
# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
# dot graphs.
# Minimum value: 4, maximum value: 24, default value: 10.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTSIZE = 10
# By default doxygen will tell dot to use the default font as specified with
# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
# the path where dot can find it using this tag.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTPATH =
# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
# each documented class showing the direct and indirect inheritance relations.
# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
CLASS_GRAPH = YES
# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
# graph for each documented class showing the direct and indirect implementation
# dependencies (inheritance, containment, and class references variables) of the
# class with other documented classes.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
COLLABORATION_GRAPH = YES
# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
# groups, showing the direct groups dependencies.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
GROUP_GRAPHS = YES
# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
# collaboration diagrams in a style similar to the OMG's Unified Modeling
# Language.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
UML_LOOK = @MITK_DOXYGEN_UML_LOOK@
# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
# class node. If there are many fields or methods and many nodes the graph may
# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
# number of items for each type to make the size more manageable. Set this to 0
# for no limit. Note that the threshold may be exceeded by 50% before the limit
# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
# but if the number exceeds 15, the total amount of fields shown is limited to
# 10.
# Minimum value: 0, maximum value: 100, default value: 10.
# This tag requires that the tag HAVE_DOT is set to YES.
UML_LIMIT_NUM_FIELDS = 10
# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
# collaboration graphs will show the relations between templates and their
# instances.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
TEMPLATE_RELATIONS = YES
# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
# YES then doxygen will generate a graph for each documented file showing the
# direct and indirect include dependencies of the file with other documented
# files.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
INCLUDE_GRAPH = NO
# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
# set to YES then doxygen will generate a graph for each documented file showing
# the direct and indirect include dependencies of the file with other documented
# files.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
INCLUDED_BY_GRAPH = NO
# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
# dependency graph for every global function or class method.
#
# Note that enabling this option will significantly increase the time of a run.
# So in most cases it will be better to enable call graphs for selected
# functions only using the \callgraph command.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
CALL_GRAPH = NO
# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
# dependency graph for every global function or class method.
#
# Note that enabling this option will significantly increase the time of a run.
# So in most cases it will be better to enable caller graphs for selected
# functions only using the \callergraph command.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
CALLER_GRAPH = NO
# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
# hierarchy of all classes instead of a textual one.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
GRAPHICAL_HIERARCHY = NO
# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
# dependencies a directory has on other directories in a graphical way. The
# dependency relations are determined by the #include relations between the
# files in the directories.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
DIRECTORY_GRAPH = YES
# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
# generated by dot.
# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
# to make the SVG files visible in IE 9+ (other browsers do not have this
# requirement).
# Possible values are: png, jpg, gif and svg.
# The default value is: png.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_IMAGE_FORMAT = png
# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
# enable generation of interactive SVG images that allow zooming and panning.
#
# Note that this requires a modern browser other than Internet Explorer. Tested
# and working are Firefox, Chrome, Safari, and Opera.
# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
# the SVG files visible. Older versions of IE do not have SVG support.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
INTERACTIVE_SVG = NO
# The DOT_PATH tag can be used to specify the path where the dot tool can be
# found. If left blank, it is assumed the dot tool can be found in the path.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_PATH = "@DOXYGEN_DOT_PATH@"
# The DOTFILE_DIRS tag can be used to specify one or more directories that
# contain dot files that are included in the documentation (see the \dotfile
# command).
# This tag requires that the tag HAVE_DOT is set to YES.
DOTFILE_DIRS =
# The MSCFILE_DIRS tag can be used to specify one or more directories that
# contain msc files that are included in the documentation (see the \mscfile
# command).
MSCFILE_DIRS =
# The DIAFILE_DIRS tag can be used to specify one or more directories that
# contain dia files that are included in the documentation (see the \diafile
# command).
DIAFILE_DIRS =
# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
# path where java can find the plantuml.jar file. If left blank, it is assumed
# PlantUML is not used or called during a preprocessing step. Doxygen will
# generate a warning when it encounters a \startuml command in this case and
# will not generate output for the diagram.
# This tag requires that the tag HAVE_DOT is set to YES.
PLANTUML_JAR_PATH =
# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
# that will be shown in the graph. If the number of nodes in a graph becomes
# larger than this value, doxygen will truncate the graph, which is visualized
# by representing a node as a red box. Note that doxygen if the number of direct
# children of the root node in a graph is already larger than
# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
# Minimum value: 0, maximum value: 10000, default value: 50.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_GRAPH_MAX_NODES = 50
# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
# generated by dot. A depth value of 3 means that only nodes reachable from the
# root by following a path via at most 3 edges will be shown. Nodes that lay
# further from the root node will be omitted. Note that setting this option to 1
# or 2 may greatly reduce the computation time needed for large code bases. Also
# note that the size of a graph can be further restricted by
# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
# Minimum value: 0, maximum value: 1000, default value: 0.
# This tag requires that the tag HAVE_DOT is set to YES.
MAX_DOT_GRAPH_DEPTH = 0
# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
# background. This is disabled by default, because dot on Windows does not seem
# to support this out of the box.
#
# Warning: Depending on the platform used, enabling this option may lead to
# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
# read).
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_TRANSPARENT = NO
# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
# files in one run (i.e. multiple -o and -T options on the command line). This
# makes dot run faster, but since only newer versions of dot (>1.8.10) support
# this, this feature is disabled by default.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_MULTI_TARGETS = NO
# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
# explaining the meaning of the various boxes and arrows in the dot generated
# graphs.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
GENERATE_LEGEND = YES
# If the DOT_CLEANUP tag is set to YES doxygen will remove the intermediate dot
# files that are used to generate the various graphs.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_CLEANUP = YES
diff --git a/Examples/BlueBerryExampleLauncher/CMakeLists.txt b/Examples/BlueBerryExampleLauncher/CMakeLists.txt
index 06111f4d8c..6890323b01 100644
--- a/Examples/BlueBerryExampleLauncher/CMakeLists.txt
+++ b/Examples/BlueBerryExampleLauncher/CMakeLists.txt
@@ -1,82 +1,76 @@
project(BlueBerryExampleLauncher)
set(_source_files
BlueBerryExampleLauncher.cpp
BlueBerryExampleLauncherDialog.cpp
)
set(_source_moc_h_files
BlueBerryExampleLauncherDialog.h
)
set(_source_ui_files
BlueBerryExampleLauncherDialog.ui
)
# this is a workaround for Visual Studio. The relative include paths in the generated
# moc files can get very long and can't be resolved by the MSVC compiler.
foreach(_moc_src ${_source_moc_h_files})
qt5_wrap_cpp(_source_files ${_moc_src} OPTIONS -f${_moc_src})
endforeach()
qt5_wrap_ui(_source_files ${_source_ui_files})
include_directories(${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_BINARY_DIR}
)
#-----------------------------------------------------------------------------
# Create provisioning files
#-----------------------------------------------------------------------------
set(_plugins_for_all_demos
)
file(GLOB _demo_configurations Configurations/*.cmake)
set(ALL_REQUIRED_PLUGINS ${_plugins_for_all_demos})
foreach(_demo_config_file ${_demo_configurations})
set(REQUIRED_PLUGINS )
set(DESCRIPTION )
include(${_demo_config_file})
get_filename_component(_name ${_demo_config_file} NAME_WE)
mitkFunctionCreateProvisioningFile(FILE ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${PROJECT_NAME}_${_name}.provisioning
PLUGINS ${REQUIRED_PLUGINS} ${_plugins_for_all_demos}
NO_INSTALL
)
if(DESCRIPTION)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/BlueBerryExampleDescription.txt
${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${PROJECT_NAME}_${_name}.txt @ONLY)
endif()
list(APPEND ALL_REQUIRED_PLUGINS ${REQUIRED_PLUGINS})
endforeach()
list(REMOVE_DUPLICATES ALL_REQUIRED_PLUGINS)
set(ALL_REQUIRED_PLUGIN_TARGETS )
foreach(req_plugin ${ALL_REQUIRED_PLUGINS})
string(REPLACE "." "_" _plugin_target ${req_plugin})
if(TARGET ${_plugin_target})
list(APPEND ALL_REQUIRED_PLUGIN_TARGETS ${_plugin_target})
endif()
endforeach()
#-----------------------------------------------------------------------------
# Create the example launcher
#-----------------------------------------------------------------------------
mitkFunctionCreateBlueBerryApplication(
NAME ${PROJECT_NAME}
DESCRIPTION "MITK Application Framework Demo"
SOURCES ${_source_files}
# PLUGINS ${ALL_REQUIRED_PLUGIN_TARGETS}
NO_PROVISIONING
NO_INSTALL
)
add_dependencies(${PROJECT_NAME} ${ALL_REQUIRED_PLUGIN_TARGETS})
-
-# subproject support
-set_property(TARGET ${PROJECT_NAME} PROPERTY LABELS ${MITK_DEFAULT_SUBPROJECTS})
-foreach(subproject ${MITK_DEFAULT_SUBPROJECTS})
- add_dependencies(${subproject} ${PROJECT_NAME})
-endforeach()
diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt
index e14eb0f581..870475f3a0 100644
--- a/Examples/CMakeLists.txt
+++ b/Examples/CMakeLists.txt
@@ -1,52 +1,49 @@
-
-set(MITK_DEFAULT_SUBPROJECTS MITK-Examples)
-
#-----------------------------------------------------------------------------
# Set-up example plugins
#-----------------------------------------------------------------------------
if(MITK_USE_BLUEBERRY)
# Specify which plug-ins belong to this project
macro(GetMyTargetLibraries all_target_libraries varname)
set(re_ctkplugin_mitk "^org_mitk_example_[a-zA-Z0-9_]+$")
set(_tmp_list)
list(APPEND _tmp_list ${all_target_libraries})
ctkMacroListFilter(_tmp_list re_ctkplugin_mitk OUTPUT_VARIABLE ${varname})
endmacro()
set(MITK_EXAMPLE_PLUGIN_TARGETS )
foreach(mitk_example_plugin ${MITK_EXAMPLE_PLUGINS})
ctkFunctionExtractOptionNameAndValue(${mitk_example_plugin} plugin_name plugin_value)
string(REPLACE "." "_" _plugin_target ${plugin_name})
list(APPEND MITK_EXAMPLE_PLUGIN_TARGETS ${_plugin_target})
mark_as_advanced(${${_plugin_target}_option_name})
endforeach()
endif()
#-----------------------------------------------------------------------------
# Add example executables
#-----------------------------------------------------------------------------
set(MITK_DIR ${PROJECT_BINARY_DIR})
set(MITK_EXPORTS_FILE_INCLUDED 1)
set(_example_dirs
Dump
MbiLog
QtFreeRender
Tutorial
FirstSteps
Annotation
)
if(MITK_USE_BLUEBERRY)
list(APPEND _example_dirs
BlueBerryExampleLauncher
)
endif()
foreach(_example_dir ${_example_dirs})
add_subdirectory(${_example_dir})
endforeach()
diff --git a/Examples/FirstSteps/NewModule/CMakeLists.txt b/Examples/FirstSteps/NewModule/CMakeLists.txt
index 9fd2803595..12f4c6f71e 100644
--- a/Examples/FirstSteps/NewModule/CMakeLists.txt
+++ b/Examples/FirstSteps/NewModule/CMakeLists.txt
@@ -1,11 +1,10 @@
MITK_CREATE_MODULE(
INCLUDE_DIRS
PUBLIC ${MITK_BINARY_DIR}
PRIVATE src/DataManagement
DEPENDS PUBLIC MitkCore
- SUBPROJECTS MITK-Examples
)
add_subdirectory(autoload/IO)
add_subdirectory(cmdapps)
add_subdirectory(test)
diff --git a/Examples/FirstSteps/NewModule/autoload/IO/CMakeLists.txt b/Examples/FirstSteps/NewModule/autoload/IO/CMakeLists.txt
index c9c1d4d72b..24b2612a99 100644
--- a/Examples/FirstSteps/NewModule/autoload/IO/CMakeLists.txt
+++ b/Examples/FirstSteps/NewModule/autoload/IO/CMakeLists.txt
@@ -1,9 +1,8 @@
MITK_CREATE_MODULE( NewModuleIO
INCLUDE_DIRS
PRIVATE src/IO
DEPENDS PUBLIC MitkNewModule MitkSceneSerialization
PACKAGE_DEPENDS
PRIVATE tinyxml
AUTOLOAD_WITH MitkCore
- SUBPROJECTS MITK-Examples
-)
\ No newline at end of file
+)
diff --git a/Modules/Classification/CLMiniApps/CMakeLists.txt b/Modules/Classification/CLMiniApps/CMakeLists.txt
index 162e071d36..3755b73a83 100644
--- a/Modules/Classification/CLMiniApps/CMakeLists.txt
+++ b/Modules/Classification/CLMiniApps/CMakeLists.txt
@@ -1,120 +1,117 @@
option(BUILD_ClassificationMiniApps "Build commandline tools for classification" OFF)
if(BUILD_ClassificationMiniApps OR MITK_BUILD_ALL_APPS)
-
include_directories(
${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_BINARY_DIR}
)
# list of miniapps
# if an app requires additional dependencies
# they are added after a "^^" and separated by "_"
set( classificationminiapps
RandomForestTraining^^MitkCLVigraRandomForest
NativeHeadCTSegmentation^^MitkCLVigraRandomForest
ManualSegmentationEvaluation^^MitkCLVigraRandomForest
CLScreenshot^^MitkCore_MitkQtWidgetsExt_MitkCLUtilities
CLDicom2Nrrd^^MitkCore
CLResampleImageToReference^^MitkCore
CLGlobalImageFeatures^^MitkCLUtilities_MitkQtWidgetsExt
CLMRNormalization^^MitkCLUtilities_MitkCLMRUtilities
CLStaple^^MitkCLUtilities
CLVoxelFeatures^^MitkCLUtilities
CLPolyToNrrd^^
CLPlanarFigureToNrrd^^MitkCore_MitkSegmentation_MitkMultilabel
CLSimpleVoxelClassification^^MitkDataCollection_MitkCLVigraRandomForest
CLVoxelClassification^^MitkDataCollection_MitkCLImportanceWeighting_MitkCLVigraRandomForest
CLBrainMask^^MitkCLUtilities
XRaxSimulationFromCT^^MitkCLUtilities
CLRandomSampling^^MitkCore_MitkCLUtilities
CLRemoveEmptyVoxels^^MitkCore
CLN4^^MitkCore
CLSkullMask^^MitkCore
CLPointSetToSegmentation^^
CLMultiForestPrediction^^MitkDataCollection_MitkCLVigraRandomForest
CLNrrdToPoly^^MitkCore
CL2Dto3DImage^^MitkCore
CLWeighting^^MitkCore_MitkCLImportanceWeighting_MitkCLUtilities
CLOverlayRoiCenterOfMass^^MitkCore_MitkCLUtilities_MitkQtWidgetsExt
CLLungSegmentation^^MitkCore_MitkSegmentation_MitkMultilabel
- # RandomForestPrediction^^MitkCLVigraRandomForest
)
foreach(classificationminiapps ${classificationminiapps})
# extract mini app name and dependencies
string(REPLACE "^^" "\\;" miniapp_info ${classificationminiapps})
set(miniapp_info_list ${miniapp_info})
list(GET miniapp_info_list 0 appname)
list(GET miniapp_info_list 1 raw_dependencies)
string(REPLACE "_" "\\;" dependencies "${raw_dependencies}")
set(dependencies_list ${dependencies})
mitk_create_executable(${appname}
DEPENDS MitkCore MitkCLCore MitkCommandLine ${dependencies_list}
PACKAGE_DEPENDS ITK Qt5|Core Vigra
CPP_FILES ${appname}.cpp
)
- # CPP_FILES ${appname}.cpp mitkCommandLineParser.cpp
if(EXECUTABLE_IS_ENABLED)
# On Linux, create a shell script to start a relocatable application
if(UNIX AND NOT APPLE)
install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.sh" DESTINATION "." RENAME ${EXECUTABLE_TARGET}.sh)
endif()
get_target_property(_is_bundle ${EXECUTABLE_TARGET} MACOSX_BUNDLE)
if(APPLE)
if(_is_bundle)
set(_target_locations ${EXECUTABLE_TARGET}.app)
set(${_target_locations}_qt_plugins_install_dir ${EXECUTABLE_TARGET}.app/Contents/MacOS)
set(_bundle_dest_dir ${EXECUTABLE_TARGET}.app/Contents/MacOS)
set(_qt_plugins_for_current_bundle ${EXECUTABLE_TARGET}.app/Contents/MacOS)
set(_qt_conf_install_dirs ${EXECUTABLE_TARGET}.app/Contents/Resources)
install(TARGETS ${EXECUTABLE_TARGET} BUNDLE DESTINATION . )
else()
if(NOT MACOSX_BUNDLE_NAMES)
set(_qt_conf_install_dirs bin)
set(_target_locations bin/${EXECUTABLE_TARGET})
set(${_target_locations}_qt_plugins_install_dir bin)
install(TARGETS ${EXECUTABLE_TARGET} RUNTIME DESTINATION bin)
else()
foreach(bundle_name ${MACOSX_BUNDLE_NAMES})
list(APPEND _qt_conf_install_dirs ${bundle_name}.app/Contents/Resources)
set(_current_target_location ${bundle_name}.app/Contents/MacOS/${EXECUTABLE_TARGET})
list(APPEND _target_locations ${_current_target_location})
set(${_current_target_location}_qt_plugins_install_dir ${bundle_name}.app/Contents/MacOS)
message( " set(${_current_target_location}_qt_plugins_install_dir ${bundle_name}.app/Contents/MacOS) ")
install(TARGETS ${EXECUTABLE_TARGET} RUNTIME DESTINATION ${bundle_name}.app/Contents/MacOS/)
endforeach()
endif()
endif()
else()
set(_target_locations bin/${EXECUTABLE_TARGET}${CMAKE_EXECUTABLE_SUFFIX})
set(${_target_locations}_qt_plugins_install_dir bin)
set(_qt_conf_install_dirs bin)
install(TARGETS ${EXECUTABLE_TARGET} RUNTIME DESTINATION bin)
endif()
endif()
endforeach()
mitk_create_executable(CLMatchPointReg
DEPENDS MitkCore MitkCLUtilities MitkMatchPointRegistration MitkCommandLine MitkMatchPointRegistrationUI
PACKAGE_DEPENDS ITK Qt5|Core Vigra MatchPoint
CPP_FILES CLMatchPointReg.cpp
)
- # On Linux, create a shell script to start a relocatable application
- if(UNIX AND NOT APPLE)
- install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.sh" DESTINATION "." RENAME ${EXECUTABLE_TARGET}.sh)
- endif()
+ # On Linux, create a shell script to start a relocatable application
+ if(UNIX AND NOT APPLE)
+ install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.sh" DESTINATION "." RENAME ${EXECUTABLE_TARGET}.sh)
+ endif()
if(EXECUTABLE_IS_ENABLED)
MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET})
endif()
endif()
diff --git a/Modules/Classification/DataCollection/DataHolder/mitkDataCollection.cpp.i14783 b/Modules/Classification/DataCollection/DataHolder/mitkDataCollection.cpp.i14783
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/Modules/CommandLine/CMakeLists.txt b/Modules/CommandLine/CMakeLists.txt
index 716f698871..5f101a602e 100644
--- a/Modules/CommandLine/CMakeLists.txt
+++ b/Modules/CommandLine/CMakeLists.txt
@@ -1,7 +1,6 @@
MITK_CREATE_MODULE(
INCLUDE_DIRS
PUBLIC include/
PRIVATE src/
- SUBPROJECTS MITK-Modules
DEPENDS MitkCore
)
diff --git a/Modules/Core/CMakeLists.txt b/Modules/Core/CMakeLists.txt
index bae8a92060..9443972b06 100644
--- a/Modules/Core/CMakeLists.txt
+++ b/Modules/Core/CMakeLists.txt
@@ -1,66 +1,65 @@
set(TOOL_CPPS "")
# temporary suppress warnings in the following files until image accessors are fully integrated.
set_source_files_properties( src/DataManagement/mitkImage.cpp COMPILE_FLAGS -DMITK_NO_DEPRECATED_WARNINGS )
set_source_files_properties( src/Controllers/mitkSliceNavigationController.cpp COMPILE_FLAGS -DMITK_NO_DEPRECATED_WARNINGS )
MITK_CREATE_MODULE(
INCLUDE_DIRS
PUBLIC ${MITK_BINARY_DIR}
PRIVATE src/Algorithms src/Controllers src/DataManagement src/Interactions src/IO src/Rendering ${OPENGL_INCLUDE_DIR}
DEPENDS PUBLIC mbilog CppMicroServices
PACKAGE_DEPENDS
PRIVATE tinyxml OpenGL
PUBLIC ITK|ITKTransform+ITKImageGrid+ITKImageFeature+ITKIOImageBase+ITKIOHDF5+ITKIOLSM+ITKIOMRC+ITKIOBioRad+ITKIOGE+ITKIOStimulate+ITKIOBruker+ITKIOMINC
# We privately use/link all ITK modules in order to support all IO, Transform, etc.
# factories from ITK which are registered "automatically" via a factory manager.
PRIVATE ITK
PUBLIC VTK|vtkFiltersTexture+vtkFiltersParallel+vtkImagingStencil+vtkImagingMath+vtkInteractionStyle+vtkRenderingOpenGL2+vtkRenderingContextOpenGL2+vtkRenderingVolumeOpenGL2+vtkRenderingFreeType+vtkRenderingLabel+vtkInteractionWidgets+vtkIOGeometry+vtkIOXML
PUBLIC Boost|boost
- SUBPROJECTS MITK-Core
# Do not automatically create CppMicroServices initialization code.
# Because the VTK 6 "auto-init" functionality injects file-local static
# initialization code in every cpp file which includes a VTK header,
# static initialization order becomes an issue again. For the Mitk
# core library, we need to ensure that the VTK static initialization stuff
# happens before the CppMicroServices initialization, since the latter
# might already use VTK code which needs to access VTK object factories.
# Hence, CppMicroServices initialization code is placed manually within
# the mitkCoreActivator.cpp file.
NO_INIT
)
if(NOT TARGET ${MODULE_TARGET})
message(SEND_ERROR "Core target ${MODULE_TARGET} does not exist")
endif()
function(_itk_create_factory_register_manager)
# In MITK_ITK_Config.cmake, we do *not* include ITK_USE_FILE, which
# prevents multiple registrations/unregistrations of ITK IO factories
# during library loading/unloading (of MITK libraries). However, we need
# "one" place where the IO factories are registered at
# least once. This could be the application executable, but every executable would
# need to take care of that itself. Instead, we allow the auto registration in the
# Mitk Core library.
set(NO_DIRECTORY_SCOPED_ITK_COMPILE_DEFINITION 1)
find_package(ITK)
include(${ITK_USE_FILE})
if(NOT ITK_NO_IO_FACTORY_REGISTER_MANAGER)
# We manually add the define which will be of target scope. MITK
# patches ITK_USE_FILE to remove the directory scoped compile
# definition since it would be propagated to other targets in the
# same directory scope but these targets might want to *not*
# use the ITK factory manager stuff.
target_compile_definitions(${MODULE_TARGET} PRIVATE ITK_IO_FACTORY_REGISTER_MANAGER)
endif()
endfunction()
_itk_create_factory_register_manager()
if(MSVC_IDE OR MSVC_VERSION)
target_link_libraries(${MODULE_TARGET} PRIVATE psapi.lib)
endif()
if(BUILD_TESTING)
add_subdirectory(TestingHelper)
add_subdirectory(test)
endif()
diff --git a/Modules/CppMicroServices/cmake/usFunctionCompileSnippets.cmake b/Modules/CppMicroServices/cmake/usFunctionCompileSnippets.cmake
index 2df8c74a4d..1fd333819b 100644
--- a/Modules/CppMicroServices/cmake/usFunctionCompileSnippets.cmake
+++ b/Modules/CppMicroServices/cmake/usFunctionCompileSnippets.cmake
@@ -1,51 +1,50 @@
function(usFunctionCompileSnippets snippet_path)
# get all files called "main.cpp"
file(GLOB_RECURSE main_cpp_list "${snippet_path}/main.cpp")
foreach(main_cpp_file ${main_cpp_list})
# get the directory containing the main.cpp file
get_filename_component(main_cpp_dir "${main_cpp_file}" PATH)
set(snippet_src_files )
# If there exists a "files.cmake" file in the snippet directory,
# include it and assume it sets the variable "snippet_src_files"
# to a list of source files for the snippet.
if(EXISTS "${main_cpp_dir}/files.cmake")
include("${main_cpp_dir}/files.cmake")
set(_tmp_src_files ${snippet_src_files})
set(snippet_src_files )
foreach(_src_file ${_tmp_src_files})
if(IS_ABSOLUTE ${_src_file})
list(APPEND snippet_src_files ${_src_file})
else()
list(APPEND snippet_src_files ${main_cpp_dir}/${_src_file})
endif()
endforeach()
else()
# glob all files in the directory and add them to the snippet src list
file(GLOB_RECURSE snippet_src_files "${main_cpp_dir}/*")
endif()
# Uset the top-level directory name as the executable name
string(REPLACE "/" ";" main_cpp_dir_tokens "${main_cpp_dir}")
list(GET main_cpp_dir_tokens -1 snippet_exec_name)
set(snippet_target_name "Snippet-${snippet_exec_name}")
add_executable(${snippet_target_name} ${snippet_src_files})
target_link_libraries(${snippet_target_name} ${PROJECT_TARGET} ${snippet_link_libraries})
set_property(TARGET ${snippet_target_name} APPEND PROPERTY COMPILE_DEFINITIONS US_MODULE_NAME=main)
set_property(TARGET ${snippet_target_name} PROPERTY US_MODULE_NAME main)
set_property(TARGET ${snippet_target_name} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/CppMicroServices/Snippets")
set_target_properties(${snippet_target_name} PROPERTIES
- LABELS Documentation
RUNTIME_OUTPUT_DIRECTORY "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/snippets"
ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_ARCHIVE_OUTPUT_DIRECTORY}/snippets"
LIBRARY_OUTPUT_DIRECTORY "${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/snippets"
OUTPUT_NAME ${snippet_exec_name}
)
endforeach()
endfunction()
diff --git a/Modules/CppMicroServices/core/doc/snippets/uServices-resources-cmake/CMakeLists.txt b/Modules/CppMicroServices/core/doc/snippets/uServices-resources-cmake/CMakeLists.txt
index d1ab01f6f0..9d41b1df2e 100644
--- a/Modules/CppMicroServices/core/doc/snippets/uServices-resources-cmake/CMakeLists.txt
+++ b/Modules/CppMicroServices/core/doc/snippets/uServices-resources-cmake/CMakeLists.txt
@@ -1,9 +1,8 @@
include(${CMAKE_CURRENT_LIST_DIR}/CMakeLists_example.txt)
set_target_properties(mymodule PROPERTIES
- LABELS Documentation
RUNTIME_OUTPUT_DIRECTORY "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/snippets"
ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_ARCHIVE_OUTPUT_DIRECTORY}/snippets"
LIBRARY_OUTPUT_DIRECTORY "${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/snippets"
OUTPUT_NAME Snippet-mymodule
)
diff --git a/Modules/CppMicroServices/core/examples/CMakeLists.txt b/Modules/CppMicroServices/core/examples/CMakeLists.txt
index 1144b939be..96b99784f8 100644
--- a/Modules/CppMicroServices/core/examples/CMakeLists.txt
+++ b/Modules/CppMicroServices/core/examples/CMakeLists.txt
@@ -1,176 +1,169 @@
project(CoreExamples)
cmake_minimum_required(VERSION 2.8)
find_package(CppMicroServices NO_MODULE REQUIRED)
include_directories(${CppMicroServices_INCLUDE_DIRS})
#-----------------------------------------------------------------------------
# Set C/CXX flags
#-----------------------------------------------------------------------------
#if(${CMAKE_PROJECT_NAME} STREQUAL ${PROJECT_NAME})
# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CppMicroServices_CXX_FLAGS}")
# set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} ${CppMicroServices_CXX_FLAGS_RELEASE}")
# set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} ${CppMicroServices_CXX_FLAGS_DEBUG}")
# set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${CppMicroServices_C_FLAGS}")
# set(CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} ${CppMicroServices_C_FLAGS_RELEASE}")
# set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} ${CppMicroServices_C_FLAGS_DEBUG}")
#endif()
#-----------------------------------------------------------------------------
# Init output directories
#-----------------------------------------------------------------------------
set(CoreExamples_ARCHIVE_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/lib")
set(CoreExamples_LIBRARY_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/lib")
set(CoreExamples_RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/bin")
foreach(_type ARCHIVE LIBRARY RUNTIME)
if(NOT CMAKE_${_type}_OUTPUT_DIRECTORY)
set(CMAKE_${_type}_OUTPUT_DIRECTORY ${CoreExamples_${_type}_OUTPUT_DIRECTORY})
endif()
endforeach()
function(CreateExample _name)
add_library(Example-${_name} ${ARGN})
set_property(TARGET Example-${_name} APPEND PROPERTY COMPILE_DEFINITIONS US_MODULE_NAME=${_name})
if(NOT US_BUILD_SHARED_LIBS)
set_property(TARGET Example-${_name} APPEND PROPERTY COMPILE_DEFINITIONS US_STATIC_MODULE)
endif()
if(${_name}_DEPENDS)
foreach(_dep ${${_name}_DEPENDS})
include_directories(${PROJECT_SOURCE_DIR}/${_dep})
target_link_libraries(Example-${_name} Example-${_dep})
endforeach()
endif()
target_link_libraries(Example-${_name} ${CppMicroServices_LIBRARIES})
- set_target_properties(Example-${_name} PROPERTIES
- LABELS Examples
- OUTPUT_NAME ${_name}
- )
+ set_target_properties(Example-${_name} PROPERTIES OUTPUT_NAME ${_name})
endfunction()
add_subdirectory(eventlistener)
add_subdirectory(dictionaryservice)
add_subdirectory(frenchdictionary)
add_subdirectory(dictionaryclient)
add_subdirectory(dictionaryclient2)
add_subdirectory(dictionaryclient3)
add_subdirectory(spellcheckservice)
add_subdirectory(spellcheckclient)
add_subdirectory(driver)
#-----------------------------------------------------------------------------
# Test if examples compile against an install tree and if the
# Makefile example compiles
#-----------------------------------------------------------------------------
if(US_BUILD_TESTING)
enable_testing()
set(_example_tests )
if(WIN32)
string(REGEX REPLACE "^.:" "" _install_prefix ${CMAKE_INSTALL_PREFIX})
else()
set(_install_prefix ${CMAKE_INSTALL_PREFIX})
endif()
set(_install_dir "${CppMicroServices_BINARY_DIR}/install_test/${_install_prefix}")
add_test(NAME usInstallCleanTest
COMMAND ${CMAKE_COMMAND} -E remove_directory "${_install_dir}")
add_test(NAME usInstallTest
WORKING_DIRECTORY ${CppMicroServices_BINARY_DIR}
COMMAND ${CMAKE_COMMAND} --build ${CppMicroServices_BINARY_DIR} --config $<CONFIGURATION> --target install)
set_tests_properties(usInstallTest PROPERTIES
ENVIRONMENT "DESTDIR=${CppMicroServices_BINARY_DIR}/install_test"
DEPENDS usInstallCleanTest)
set(_examples_binary_dir "${CppMicroServices_BINARY_DIR}/examples_build")
add_test(NAME usExamplesCleanTest
COMMAND ${CMAKE_COMMAND} -E remove_directory "${_examples_binary_dir}")
add_test(NAME usExamplesCreateDirTest
COMMAND ${CMAKE_COMMAND} -E make_directory "${_examples_binary_dir}")
set_tests_properties(usExamplesCreateDirTest PROPERTIES
DEPENDS usExamplesCleanTest)
list(APPEND _example_tests usInstallCleanTest usInstallTest usExamplesCleanTest
usExamplesCreateDirTest)
if(CMAKE_CONFIGURATION_TYPES)
foreach(config ${CMAKE_CONFIGURATION_TYPES})
add_test(NAME usExamplesConfigureTest-${config} CONFIGURATIONS ${config}
WORKING_DIRECTORY ${_examples_binary_dir}
COMMAND ${CMAKE_COMMAND}
-D CMAKE_C_COMPILER:STRING=${CMAKE_C_COMPILER}
-D CMAKE_CXX_COMPILER:STRING=${CMAKE_CXX_COMPILER}
-D BUILD_SHARED_LIBS:BOOL=${US_BUILD_SHARED_LIBS}
-G ${CMAKE_GENERATOR}
"-DCppMicroServices_DIR:PATH=${_install_dir}/${AUXILIARY_CMAKE_INSTALL_DIR}"
"${CMAKE_CURRENT_LIST_DIR}")
set_tests_properties(usExamplesConfigureTest-${config} PROPERTIES
DEPENDS "usInstallTest;usExamplesCreateDirTest")
add_test(NAME usExamplesBuildTest-${config} CONFIGURATIONS ${config}
WORKING_DIRECTORY ${_examples_binary_dir}
COMMAND ${CMAKE_COMMAND} --build . --config ${config})
set_tests_properties(usExamplesBuildTest-${config} PROPERTIES
DEPENDS usExamplesConfigureTest-${config})
list(APPEND _example_tests usExamplesConfigureTest-${config} usExamplesBuildTest-${config})
endforeach()
else()
add_test(NAME usExamplesConfigureTest-${CMAKE_BUILD_TYPE}
WORKING_DIRECTORY ${_examples_binary_dir}
COMMAND ${CMAKE_COMMAND}
-D CMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
-D CMAKE_C_COMPILER:STRING=${CMAKE_C_COMPILER}
-D CMAKE_CXX_COMPILER:STRING=${CMAKE_CXX_COMPILER}
-D BUILD_SHARED_LIBS:BOOL=${US_BUILD_SHARED_LIBS}
-G ${CMAKE_GENERATOR}
"-DCppMicroServices_DIR:PATH=${_install_dir}/${AUXILIARY_CMAKE_INSTALL_DIR}"
"${CMAKE_CURRENT_LIST_DIR}")
set_tests_properties(usExamplesConfigureTest-${CMAKE_BUILD_TYPE} PROPERTIES
DEPENDS "usInstallTest;usExamplesCreateDirTest")
add_test(NAME usExamplesBuildTest-${CMAKE_BUILD_TYPE}
WORKING_DIRECTORY ${_examples_binary_dir}
COMMAND ${CMAKE_COMMAND} --build . --config ${CMAKE_BUILD_TYPE})
set_tests_properties(usExamplesBuildTest-${CMAKE_BUILD_TYPE} PROPERTIES
DEPENDS usExamplesConfigureTest-${CMAKE_BUILD_TYPE})
list(APPEND _example_tests usExamplesConfigureTest-${CMAKE_BUILD_TYPE} usExamplesBuildTest-${CMAKE_BUILD_TYPE})
endif()
# The makefile is Linux specific, so only try to build the Makefile example
# if we are on a proper system
if(UNIX AND NOT APPLE AND US_BUILD_SHARED_LIBS)
find_program(MAKE_COMMAND NAMES make gmake)
find_program(CXX_COMMAND NAMES g++)
mark_as_advanced(MAKE_COMMAND CXX_COMMAND)
if(MAKE_COMMAND AND CXX_COMMAND)
add_test(NAME usMakefileExampleCleanTest
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/makefile
COMMAND ${MAKE_COMMAND} clean)
add_test(NAME usMakefileExampleTest
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/makefile
COMMAND ${MAKE_COMMAND})
set_tests_properties(usMakefileExampleTest PROPERTIES
DEPENDS "usMakefileExampleCleanTest;usInstallTest"
ENVIRONMENT "CppMicroServices_ROOT=${CppMicroServices_BINARY_DIR}/install_test${CMAKE_INSTALL_PREFIX};US_CXX_FLAGS=${US_CXX_FLAGS}")
list(APPEND _example_tests usMakefileExampleCleanTest usMakefileExampleTest)
endif()
endif()
- if(US_TEST_LABELS)
- set_tests_properties(${_example_tests} PROPERTIES LABELS "${US_TEST_LABELS}")
- endif()
-
endif()
diff --git a/Modules/CppMicroServices/core/examples/dictionaryservice/CMakeLists.txt b/Modules/CppMicroServices/core/examples/dictionaryservice/CMakeLists.txt
index c904b4e9ac..25e76663ff 100644
--- a/Modules/CppMicroServices/core/examples/dictionaryservice/CMakeLists.txt
+++ b/Modules/CppMicroServices/core/examples/dictionaryservice/CMakeLists.txt
@@ -1,31 +1,28 @@
# The library name for the module
set(_lib_name dictionaryservice)
# A list of source code files
set(_srcs
Activator.cpp
IDictionaryService.cpp
)
# Generate module initialization code
usFunctionGenerateModuleInit(_srcs)
# Create the library
add_library(Example-${_lib_name} ${_srcs})
# Add the required compile definitions
set_property(TARGET Example-${_lib_name} APPEND PROPERTY COMPILE_DEFINITIONS US_MODULE_NAME=${_lib_name})
if(NOT US_BUILD_SHARED_LIBS)
set_property(TARGET Example-${_lib_name} APPEND PROPERTY COMPILE_DEFINITIONS US_STATIC_MODULE)
endif()
# Link the CppMicroServices library
target_link_libraries(Example-${_lib_name} ${CppMicroServices_LIBRARIES})
-set_target_properties(Example-${_lib_name} PROPERTIES
- LABELS Examples
- OUTPUT_NAME ${_lib_name}
-)
+set_target_properties(Example-${_lib_name} PROPERTIES OUTPUT_NAME ${_lib_name})
#CreateExample(dictionaryservice ${_srcs})
diff --git a/Modules/CppMicroServices/core/test/CMakeLists.txt b/Modules/CppMicroServices/core/test/CMakeLists.txt
index 612276d86c..6a763a0fa7 100644
--- a/Modules/CppMicroServices/core/test/CMakeLists.txt
+++ b/Modules/CppMicroServices/core/test/CMakeLists.txt
@@ -1,102 +1,98 @@
#-----------------------------------------------------------------------------
# Configure files, include dirs, etc.
#-----------------------------------------------------------------------------
configure_file("${CMAKE_CURRENT_SOURCE_DIR}/usTestingConfig.h.in" "${PROJECT_BINARY_DIR}/include/usTestingConfig.h")
include_directories(${CMAKE_CURRENT_SOURCE_DIR})
#-----------------------------------------------------------------------------
# Create test modules
#-----------------------------------------------------------------------------
include(usFunctionCreateTestModule)
set(_us_test_module_libs "" CACHE INTERNAL "" FORCE)
add_subdirectory(modules)
#-----------------------------------------------------------------------------
# Add unit tests
#-----------------------------------------------------------------------------
set(_tests
usAnyTest
usLDAPFilterTest
usLogTest
usModuleHooksTest
usModuleManifestTest
usModuleTest
usModuleResourceTest
usServiceFactoryTest
usServiceHooksTest
usServiceRegistryPerformanceTest
usServiceRegistryTest
usServiceTemplateTest
usServiceTrackerTest
usStaticModuleResourceTest
usStaticModuleTest
)
if(US_BUILD_SHARED_LIBS)
list(APPEND _tests
usServiceListenerTest
usSharedLibraryTest
)
if(US_ENABLE_AUTOLOADING_SUPPORT)
list(APPEND _tests usModuleAutoLoadTest)
endif()
endif()
set(_additional_srcs
usTestDriverActivator.cpp
usTestManager.cpp
usTestUtilModuleListener.cpp
)
set(_test_driver us${PROJECT_NAME}TestDriver)
set(_test_sourcelist_extra_args )
create_test_sourcelist(_srcs ${_test_driver}.cpp ${_tests} ${_test_sourcelist_extra_args})
# Generate a custom "module init" file for the test driver executable
usFunctionGenerateModuleInit(_srcs)
usFunctionGetResourceSource(TARGET ${_test_driver} OUT _srcs)
add_executable(${_test_driver} ${_srcs} ${_additional_srcs})
set_property(TARGET ${_test_driver} APPEND PROPERTY COMPILE_DEFINITIONS US_MODULE_NAME=main)
set_property(TARGET ${_test_driver} PROPERTY US_MODULE_NAME main)
set_property(TARGET ${_test_driver} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/CppMicroServices/Tests")
if(NOT US_BUILD_SHARED_LIBS)
set_property(TARGET ${_test_driver} APPEND PROPERTY COMPILE_DEFINITIONS US_STATIC_MODULE)
target_link_libraries(${_test_driver} ${_us_test_module_libs})
endif()
target_link_libraries(${_test_driver} ${Core_TARGET})
if(UNIX AND NOT APPLE)
target_link_libraries(${_test_driver} rt)
endif()
# Add resources
usFunctionEmbedResources(TARGET ${_test_driver}
FILES usTestResource.txt manifest.json
ZIP_ARCHIVES ${Core_TARGET} ${_us_test_module_libs})
# Register tests
foreach(_test ${_tests})
add_test(NAME ${_test} COMMAND ${_test_driver} ${_test})
endforeach()
-if(US_TEST_LABELS)
- set_tests_properties(${_tests} PROPERTIES LABELS "${US_TEST_LABELS}")
-endif()
-
#-----------------------------------------------------------------------------
# Add dependencies for shared libraries
#-----------------------------------------------------------------------------
if(US_BUILD_SHARED_LIBS)
foreach(_test_module ${_us_test_module_libs})
add_dependencies(${_test_driver} ${_test_module})
endforeach()
endif()
diff --git a/Modules/DICOMTesting/test/CMakeLists.txt b/Modules/DICOMTesting/test/CMakeLists.txt
index 6bb2f72b2b..5912e42626 100644
--- a/Modules/DICOMTesting/test/CMakeLists.txt
+++ b/Modules/DICOMTesting/test/CMakeLists.txt
@@ -1,87 +1,89 @@
-
-MITK_CREATE_MODULE_TESTS(LABELS)
-
-include(mitkFunctionAddTestLabel)
+MITK_CREATE_MODULE_TESTS()
# verify minimum expectations:
# files are recognized as DICOM
# loading files results in a given number of images
mitkAddCustomModuleTest(mitkDICOMTestingSanityTest_NoFiles mitkDICOMTestingSanityTest 0)
mitkAddCustomModuleTest(mitkDICOMTestingSanityTest_CTImage mitkDICOMTestingSanityTest 1 ${MITK_DATA_DIR}/spacing-ok-ct.dcm)
mitkAddCustomModuleTest(mitkDICOMTestingSanityTest_MRImage mitkDICOMTestingSanityTest 1 ${MITK_DATA_DIR}/spacing-ok-mr.dcm)
mitkAddCustomModuleTest(mitkDICOMTestingSanityTest_SCImage mitkDICOMTestingSanityTest 1 ${MITK_DATA_DIR}/spacing-ok-sc.dcm)
mitkAddCustomModuleTest(mitkDICOMTestingSanityTest_NoImagePositionPatient mitkDICOMTestingSanityTest 1 ${MITK_DATA_DIR}/spacing-ok-sc-no2032.dcm)
# verifies that the loader can also be used to just scan for tags and provide them in mitk::Properties (parameter preLoadedVolume)
mitkAddCustomModuleTest(mitkDICOMPreloadedVolumeTest_Slice mitkDICOMPreloadedVolumeTest ${MITK_DATA_DIR}/spacing-ok-ct.dcm)
set(VERIFY_DUMP_CMD ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/VerifyDICOMMitkImageDump)
set(CT_ABDOMEN_DIR ${MITK_DATA_DIR}/TinyCTAbdomen_DICOMReader)
set(MR_HEART_DIR ${MITK_DATA_DIR}/3D+t-Heart)
set(CT_TILT_HEAD_DIR ${MITK_DATA_DIR}/TiltHead)
set(CT_TILT_DIR ${MITK_DATA_DIR}/TiltedData)
set(SOP_CLASSES_DIR ${MITK_DATA_DIR}/DICOMReader)
# these variables could be passed as parameters to a generic test creation function
set(TESTS_DIR Tests)
set(INPUT_LISTNAME input)
set(EXPECTED_DUMP expected.dump)
function(AddDicomTestsFromDataRepository CURRENT_DATASET_DIR TESTS_DIR INPUT_LISTNAME EXPECTED_DUMP)
# find all test input lists
file(GLOB_RECURSE allInputs ${CURRENT_DATASET_DIR}/${TESTS_DIR}/*/${INPUT_LISTNAME})
function(expectFileExists filename)
if(NOT EXISTS ${filename})
message(SEND_ERROR "Test case expected file ${filename} which does not exist! Please fix your CMake code or file layout.")
endif(NOT EXISTS ${filename})
endfunction(expectFileExists)
foreach(input ${allInputs})
# extract only the name of the directory of this very test case
string(REGEX REPLACE ".*${TESTS_DIR}/([^/]+)/.*" "\\1" input ${input})
set(inputfilelist "${CURRENT_DATASET_DIR}/${TESTS_DIR}/${input}/${INPUT_LISTNAME}")
set(expecteddump "${CURRENT_DATASET_DIR}/${TESTS_DIR}/${input}/${EXPECTED_DUMP}")
- set(testname "DICOM_Load_${input}")
+ set(test_name "DICOM_Load_${input}")
#message(STATUS "DICOM loading test case '${input}'")
expectFileExists(${inputfilelist})
expectFileExists(${expecteddump})
# TODO provide error messages if input not valid
set(dicomFiles) # clear list
# read list of file names from file "input"
file(STRINGS ${inputfilelist} rawDicomFiles)
foreach(raw ${rawDicomFiles})
# prepend each file with an abosolute path
set(fileWithFullPath ${CURRENT_DATASET_DIR}/${raw})
list(APPEND dicomFiles ${fileWithFullPath})
endforeach(raw ${rawDicomFiles})
#message(STATUS " Load ${dicomFiles}")
- add_test(${testname}
- ${VERIFY_DUMP_CMD} ${expecteddump} ${dicomFiles})
- mitkFunctionAddTestLabel(${testname})
+ add_test(${test_name} ${VERIFY_DUMP_CMD} ${expecteddump} ${dicomFiles})
+ mitkFunctionGetLibrarySearchPaths(MITK_RUNTIME_PATH_RELEASE release RELEASE)
+ mitkFunctionGetLibrarySearchPaths(MITK_RUNTIME_PATH_DEBUG debug DEBUG)
+ set(test_env_path ${MITK_RUNTIME_PATH_RELEASE} ${MITK_RUNTIME_PATH_DEBUG} $ENV{PATH})
+ list(REMOVE_DUPLICATES test_env_path)
+ string (REGEX REPLACE "\;" "\\\;" test_env_path "${test_env_path}")
+ set_property(TEST ${test_name} PROPERTY ENVIRONMENT "PATH=${test_env_path}" APPEND)
+ set_property(TEST ${test_name} PROPERTY SKIP_RETURN_CODE 77)
endforeach(input allInputs)
endfunction(AddDicomTestsFromDataRepository CURRENT_DATASET_DIR TESTS_DIR INPUT_LISTNAME EXPECTED_DUMP)
AddDicomTestsFromDataRepository(${CT_ABDOMEN_DIR} ${TESTS_DIR} ${INPUT_LISTNAME} ${EXPECTED_DUMP})
AddDicomTestsFromDataRepository(${CT_TILT_HEAD_DIR} ${TESTS_DIR} ${INPUT_LISTNAME} ${EXPECTED_DUMP})
AddDicomTestsFromDataRepository(${CT_TILT_DIR} ${TESTS_DIR} ${INPUT_LISTNAME} ${EXPECTED_DUMP})
AddDicomTestsFromDataRepository(${MR_HEART_DIR} ${TESTS_DIR} ${INPUT_LISTNAME} ${EXPECTED_DUMP})
AddDicomTestsFromDataRepository(${SOP_CLASSES_DIR} ${TESTS_DIR} ${INPUT_LISTNAME} ${EXPECTED_DUMP})
# use one more realistic series for testing property lists
file(GLOB_RECURSE abdomenImages ${CT_ABDOMEN_DIR}/14?) # this is just one small volume
mitkAddCustomModuleTest(mitkDICOMPreloadedVolumeTest_Abdomen mitkDICOMPreloadedVolumeTest ${abdomenImages})
diff --git a/Modules/IGT/CMakeLists.txt b/Modules/IGT/CMakeLists.txt
index 79cb9fd186..760efba59f 100644
--- a/Modules/IGT/CMakeLists.txt
+++ b/Modules/IGT/CMakeLists.txt
@@ -1,64 +1,63 @@
include(MITKIGTHardware.cmake)
if(MITK_USE_MICRON_TRACKER)
set(ADDITIONAL_INCLUDE_DIRS ${ADDITIONAL_INCLUDE_DIRS} ${MITK_MICRON_TRACKER_INCLUDE_DIR})
set(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_MICRON_TRACKER_LIB})
endif(MITK_USE_MICRON_TRACKER)
if(MITK_USE_OPTITRACK_TRACKER)
set(ADDITIONAL_INCLUDE_DIRS ${ADDITIONAL_INCLUDE_DIRS} ${MITK_OPTITRACK_TRACKER_INCLUDE_DIR})
set(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_OPTITRACK_TRACKER_LIB})
add_definitions( -DMITK_USE_OPTITRACK_TRACKER )
endif(MITK_USE_OPTITRACK_TRACKER)
if(MITK_USE_MICROBIRD_TRACKER)
set(ADDITIONAL_INCLUDE_DIRS ${ADDITIONAL_INCLUDE_DIRS} ${MITK_USE_MICROBIRD_TRACKER_INCLUDE_DIR})
set(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_USE_MICROBIRD_TRACKER_LIB})
endif(MITK_USE_MICROBIRD_TRACKER)
if(MITK_USE_POLHEMUS_TRACKER)
set(ADDITIONAL_INCLUDE_DIRS ${ADDITIONAL_INCLUDE_DIRS} ${MITK_POLHEMUS_TRACKER_INCLUDE_DIR})
set(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_POLHEMUS_TRACKER_LIB})
endif(MITK_USE_POLHEMUS_TRACKER)
MITK_CREATE_MODULE(
- SUBPROJECTS MITK-IGT
INCLUDE_DIRS
PUBLIC Algorithms Common DataManagement ExceptionHandling IO Rendering TrackingDevices TestingHelper
PRIVATE ${ADDITIONAL_INCLUDE_DIRS}
DEPENDS PUBLIC MitkImageStatistics MitkSceneSerialization MitkIGTBase MitkOpenIGTLink
PACKAGE_DEPENDS ITK|ITKRegistrationCommon tinyxml OpenIGTLink
ADDITIONAL_LIBS "${ADDITIONAL_LIBS}"
)
if(MitkIGT_IS_ENABLED)
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/ClaronMicron.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/IntuitiveDaVinci.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAurora.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAurora_Dome.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAuroraCompactFG_Dome.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAuroraPlanarFG_Dome.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAuroraTabletopFG_Dome.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAuroraTabletopFG_Prototype_Dome.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIPolarisOldModel.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIPolarisSpectra.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIPolarisSpectraExtendedPyramid.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIPolarisVicra.stl )
endif()
if(NOT MODULE_IS_ENABLED)
message(STATUS "IGTTutorialStep1 won't be built. Missing: ${_RESULT}")
else()
## create IGT config
configure_file(mitkIGTConfig.h.in ${PROJECT_BINARY_DIR}/mitkIGTConfig.h @ONLY)
# add test programm for serial communication classADD_EXECUTABLE(SerialCommunicationTest IGTTrackingDevices/mitkSerialCommunicationTest.cpp)target_link_libraries(SerialCommunicationTest mitkIGT Mitk tinyxml PocoXML)
add_subdirectory(autoload/DeviceRegistry)
add_subdirectory(Tutorial)
add_subdirectory(Testing)
endif()
diff --git a/Modules/IGTUI/CMakeLists.txt b/Modules/IGTUI/CMakeLists.txt
index d37c9b60a3..dc3353f397 100644
--- a/Modules/IGTUI/CMakeLists.txt
+++ b/Modules/IGTUI/CMakeLists.txt
@@ -1,12 +1,11 @@
MITK_CREATE_MODULE(
- SUBPROJECTS MITK-IGT
INCLUDE_DIRS Qmitk
DEPENDS MitkIGT MitkQtWidgetsExt MitkPersistence
)
add_subdirectory(autoload/ConfigurationWidgetRegistry)
## create IGTUI config
configure_file(mitkIGTUIConfig.h.in ${PROJECT_BINARY_DIR}/mitkIGTUIConfig.h @ONLY)
diff --git a/Modules/IpPicSupportIO/Testing/CMakeLists.txt b/Modules/IpPicSupportIO/Testing/CMakeLists.txt
index 930c090bf0..9e874e1ea1 100644
--- a/Modules/IpPicSupportIO/Testing/CMakeLists.txt
+++ b/Modules/IpPicSupportIO/Testing/CMakeLists.txt
@@ -1,4 +1,4 @@
-MITK_CREATE_MODULE_TESTS(LABELS MITK-Modules)
+MITK_CREATE_MODULE_TESTS()
mitkAddCustomModuleTest(mitkPicFileReaderTest_emptyFile mitkPicFileReaderTest ${CMAKE_CURRENT_SOURCE_DIR}/Data/emptyFile.pic)
mitkAddCustomModuleTest(mitkPicFileReaderTest_emptyGzipFile mitkPicFileReaderTest ${CMAKE_CURRENT_SOURCE_DIR}/Data/emptyFile.pic.gz)
diff --git a/Modules/OpenIGTLink/CMakeLists.txt b/Modules/OpenIGTLink/CMakeLists.txt
index ac6c973d10..882e3a92f7 100644
--- a/Modules/OpenIGTLink/CMakeLists.txt
+++ b/Modules/OpenIGTLink/CMakeLists.txt
@@ -1,9 +1,8 @@
mitk_create_module(
- SUBPROJECTS MITK-IGT
DEPENDS MitkCore
PACKAGE_DEPENDS PUBLIC OpenIGTLink
INCLUDE_DIRS Filters DeviceSources
)
add_subdirectory(Testing)
diff --git a/Modules/QtWidgets/CMakeLists.txt b/Modules/QtWidgets/CMakeLists.txt
index 08c2333393..1938494ee8 100644
--- a/Modules/QtWidgets/CMakeLists.txt
+++ b/Modules/QtWidgets/CMakeLists.txt
@@ -1,9 +1,8 @@
MITK_CREATE_MODULE(
INCLUDE_DIRS PRIVATE resource # for xpm includes
DEPENDS MitkPlanarFigure MitkAnnotation
PACKAGE_DEPENDS
PUBLIC ITK|ITKIOImageBase VTK|vtkGUISupportQt+vtkRenderingQt Qt5|Widgets+OpenGL+Core
- SUBPROJECTS MITK-CoreUI
)
add_subdirectory(test)
diff --git a/Modules/SceneSerialization/test/CMakeLists.txt b/Modules/SceneSerialization/test/CMakeLists.txt
index 07a93f524e..62a7032a54 100644
--- a/Modules/SceneSerialization/test/CMakeLists.txt
+++ b/Modules/SceneSerialization/test/CMakeLists.txt
@@ -1,25 +1,32 @@
-MITK_CREATE_MODULE_TESTS(LABELS MITK-Modules)
+MITK_CREATE_MODULE_TESTS()
if(TARGET ${TESTDRIVER})
if(BUILD_TESTING AND MODULE_IS_ENABLED)
add_test(mitkSceneIOTest_Pic3D.nrrd_binary.stl
${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TESTDRIVER}
mitkSceneIOTest
${MITK_DATA_DIR}/Pic3D.nrrd
${MITK_DATA_DIR}/binary.stl
)
- set_property(TEST mitkSceneIOTest_Pic3D.nrrd_binary.stl PROPERTY LABELS MITK-Modules)
+
+ mitkFunctionGetLibrarySearchPaths(MITK_RUNTIME_PATH_RELEASE release RELEASE)
+ mitkFunctionGetLibrarySearchPaths(MITK_RUNTIME_PATH_DEBUG debug DEBUG)
+ set(test_env_path ${MITK_RUNTIME_PATH_RELEASE} ${MITK_RUNTIME_PATH_DEBUG} $ENV{PATH})
+ list(REMOVE_DUPLICATES test_env_path)
+ string (REGEX REPLACE "\;" "\\\;" test_env_path "${test_env_path}")
+ set_property(TEST mitkSceneIOTest_Pic3D.nrrd_binary.stl APPEND PROPERTY ENVIRONMENT "PATH=${test_env_path}")
+ set_property(TEST mitkSceneIOTest_Pic3D.nrrd_binary.stl PROPERTY SKIP_RETURN_CODE 77)
mitkAddCustomModuleTest(mitkSceneIOCompatibility_NoRainbowCT mitkSceneIOCompatibilityTest
${MITK_DATA_DIR}/RenderingTestData/SceneFiles/rainbows-post-17547.mitk # scene to load
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/rainbows-post-17547.png) # reference rendering
if (FALSE) # fix not yet integrated
mitkAddCustomModuleTest(mitkSceneIOCompatibility_SurfaceIntLineWidth mitkSceneIOCompatibilityTest
${MITK_DATA_DIR}/RenderingTestData/SceneFiles/surface-pre-18528.mitk # scene to load
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/surface-pre-18528.png) # reference rendering
endif()
endif()
endif()
diff --git a/Modules/Segmentation/Interactions/mitkAutoMLSegmentationWithPreviewTool.cpp b/Modules/Segmentation/Interactions/mitkAutoMLSegmentationWithPreviewTool.cpp
new file mode 100644
index 0000000000..5451a67f34
--- /dev/null
+++ b/Modules/Segmentation/Interactions/mitkAutoMLSegmentationWithPreviewTool.cpp
@@ -0,0 +1,204 @@
+/*============================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center (DKFZ)
+All rights reserved.
+
+Use of this source code is governed by a 3-clause BSD license that can be
+found in the LICENSE file.
+
+============================================================================*/
+
+// MITK
+#include "mitkAutoMLSegmentationWithPreviewTool.h"
+#include "mitkImageAccessByItk.h"
+#include "mitkToolManager.h"
+#include <mitkITKImageImport.h>
+#include <mitkImageCast.h>
+#include <mitkLevelWindowProperty.h>
+#include <mitkLookupTableProperty.h>
+#include <mitkRenderingModeProperty.h>
+#include <mitkSliceNavigationController.h>
+
+// ITK
+#include <itkBinaryThresholdImageFilter.h>
+#include <itkOrImageFilter.h>
+
+mitk::AutoMLSegmentationWithPreviewTool::AutoMLSegmentationWithPreviewTool() : AutoSegmentationWithPreviewTool(true)
+{
+}
+
+void mitk::AutoMLSegmentationWithPreviewTool::SetSelectedLabels(const SelectedLabelVectorType& regions)
+{
+ if (m_SelectedLabels != regions)
+ {
+ m_SelectedLabels = regions;
+ //Note: we do not call this->Modified() on puprose. Reason: changing the
+ //selected regions should not force to run otsu filter in DoUpdatePreview due to changed MTime.
+ }
+}
+
+const mitk::LabelSetImage* mitk::AutoMLSegmentationWithPreviewTool::GetMLPreview() const
+{
+ if (m_MLPreviewNode.IsNotNull())
+ {
+ const auto mlPreviewImage = dynamic_cast<const LabelSetImage*>(this->m_MLPreviewNode->GetData());
+ return mlPreviewImage;
+ }
+
+ return nullptr;
+}
+
+mitk::AutoMLSegmentationWithPreviewTool::SelectedLabelVectorType mitk::AutoMLSegmentationWithPreviewTool::GetSelectedLabels() const
+{
+ return this->m_SelectedLabels;
+}
+
+void mitk::AutoMLSegmentationWithPreviewTool::Activated()
+{
+ Superclass::Activated();
+
+ m_SelectedLabels = {};
+
+ m_MLPreviewNode = mitk::DataNode::New();
+ m_MLPreviewNode->SetProperty("name", StringProperty::New(std::string(this->GetName()) + "ML preview"));
+ m_MLPreviewNode->SetProperty("helper object", BoolProperty::New(true));
+ m_MLPreviewNode->SetVisibility(true);
+ m_MLPreviewNode->SetOpacity(1.0);
+
+ m_ToolManager->GetDataStorage()->Add(m_MLPreviewNode);
+}
+
+void mitk::AutoMLSegmentationWithPreviewTool::Deactivated()
+{
+ m_ToolManager->GetDataStorage()->Remove(m_MLPreviewNode);
+ m_MLPreviewNode = nullptr;
+
+ Superclass::Deactivated();
+}
+
+void mitk::AutoMLSegmentationWithPreviewTool::UpdateCleanUp()
+{
+ if (m_MLPreviewNode.IsNotNull())
+ m_MLPreviewNode->SetVisibility(m_SelectedLabels.empty());
+
+ if (nullptr != this->GetPreviewSegmentationNode())
+ this->GetPreviewSegmentationNode()->SetVisibility(!m_SelectedLabels.empty());
+
+ if (m_SelectedLabels.empty())
+ {
+ this->ResetPreviewNode();
+ }
+}
+
+void mitk::AutoMLSegmentationWithPreviewTool::DoUpdatePreview(const Image* inputAtTimeStep, Image* previewImage, TimeStepType timeStep)
+{
+ const auto timePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint();
+
+ if (nullptr == m_MLPreviewNode->GetData()
+ || this->GetMTime() > m_MLPreviewNode->GetData()->GetMTime()
+ || this->m_LastMLTimeStep != timeStep //this covers the case where dynamic
+ //segmentations have to compute a preview
+ //for all time steps on confirmation
+ || this->GetLastTimePointOfUpdate() != timePoint //this ensures that static seg
+ //previews work with dynamic images
+ //with avoiding unnecessary other computations
+ )
+ {
+ if (nullptr == inputAtTimeStep)
+ {
+ MITK_WARN << "Cannot run segementation. Currently selected input image is not set.";
+ return;
+ }
+
+ this->m_LastMLTimeStep = timeStep;
+
+ auto newMLPreview = ComputeMLPreview(inputAtTimeStep, timeStep);
+
+ if (newMLPreview.IsNotNull())
+ {
+ this->m_MLPreviewNode->SetData(newMLPreview);
+ this->m_MLPreviewNode->SetProperty("binary", mitk::BoolProperty::New(false));
+ mitk::RenderingModeProperty::Pointer renderingMode = mitk::RenderingModeProperty::New();
+ renderingMode->SetValue(mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR);
+ this->m_MLPreviewNode->SetProperty("Image Rendering.Mode", renderingMode);
+ mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
+ mitk::LookupTableProperty::Pointer prop = mitk::LookupTableProperty::New(lut);
+ vtkSmartPointer<vtkLookupTable> lookupTable = vtkSmartPointer<vtkLookupTable>::New();
+ lookupTable->SetHueRange(1.0, 0.0);
+ lookupTable->SetSaturationRange(1.0, 1.0);
+ lookupTable->SetValueRange(1.0, 1.0);
+ lookupTable->SetTableRange(-1.0, 1.0);
+ lookupTable->Build();
+ lut->SetVtkLookupTable(lookupTable);
+ prop->SetLookupTable(lut);
+ this->m_MLPreviewNode->SetProperty("LookupTable", prop);
+ mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New();
+ mitk::LevelWindow levelwindow;
+ levelwindow.SetRangeMinMax(0, newMLPreview->GetScalarValueMax());
+ levWinProp->SetLevelWindow(levelwindow);
+ this->m_MLPreviewNode->SetProperty("levelwindow", levWinProp);
+ }
+ }
+
+ if (!m_SelectedLabels.empty())
+ {
+ const auto mlPreviewImage = this->GetMLPreview();
+ if (nullptr != mlPreviewImage)
+ {
+ AccessByItk_n(mlPreviewImage, CalculateMergedSimplePreview, (previewImage, timeStep));
+ }
+ }
+}
+
+template <typename TPixel, unsigned int VImageDimension>
+void mitk::AutoMLSegmentationWithPreviewTool::CalculateMergedSimplePreview(const itk::Image<TPixel, VImageDimension>* itkImage, mitk::Image* segmentation, unsigned int timeStep)
+{
+ typedef itk::Image<TPixel, VImageDimension> InputImageType;
+ typedef itk::Image<mitk::Tool::DefaultSegmentationDataType, VImageDimension> OutputImageType;
+
+ typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> FilterType;
+
+ typename FilterType::Pointer filter = FilterType::New();
+
+ // InputImageType::Pointer itkImage;
+ typename OutputImageType::Pointer itkBinaryResultImage;
+
+ filter->SetInput(itkImage);
+ filter->SetLowerThreshold(m_SelectedLabels[0]);
+ filter->SetUpperThreshold(m_SelectedLabels[0]);
+ filter->SetInsideValue(1);
+ filter->SetOutsideValue(0);
+ filter->AddObserver(itk::ProgressEvent(), m_ProgressCommand);
+ filter->Update();
+ itkBinaryResultImage = filter->GetOutput();
+ itkBinaryResultImage->DisconnectPipeline();
+
+ // if more than one region id is used compute the union of all given binary regions
+ for (const auto labelID : m_SelectedLabels)
+ {
+ if (labelID != m_SelectedLabels[0])
+ {
+ filter->SetLowerThreshold(labelID);
+ filter->SetUpperThreshold(labelID);
+ filter->SetInsideValue(1);
+ filter->SetOutsideValue(0);
+ filter->Update();
+
+ typename OutputImageType::Pointer tempImage = filter->GetOutput();
+
+ typename itk::OrImageFilter<OutputImageType, OutputImageType>::Pointer orFilter =
+ itk::OrImageFilter<OutputImageType, OutputImageType>::New();
+ orFilter->SetInput1(tempImage);
+ orFilter->SetInput2(itkBinaryResultImage);
+ orFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand);
+
+ orFilter->UpdateLargestPossibleRegion();
+ itkBinaryResultImage = orFilter->GetOutput();
+ }
+ }
+ //----------------------------------------------------------------------------------------------------
+
+ segmentation->SetVolume((void*)(itkBinaryResultImage->GetPixelContainer()->GetBufferPointer()), timeStep);
+}
diff --git a/Modules/Segmentation/Interactions/mitkAutoMLSegmentationWithPreviewTool.h b/Modules/Segmentation/Interactions/mitkAutoMLSegmentationWithPreviewTool.h
new file mode 100644
index 0000000000..94163df1ad
--- /dev/null
+++ b/Modules/Segmentation/Interactions/mitkAutoMLSegmentationWithPreviewTool.h
@@ -0,0 +1,82 @@
+/*============================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center (DKFZ)
+All rights reserved.
+
+Use of this source code is governed by a 3-clause BSD license that can be
+found in the LICENSE file.
+
+============================================================================*/
+#ifndef MITK_AUTO_ML_SEGMENTATION_WITH_PREVIEW_TOOL_H
+#define MITK_AUTO_ML_SEGMENTATION_WITH_PREVIEW_TOOL_H
+
+#include "mitkAutoSegmentationWithPreviewTool.h"
+#include "mitkDataNode.h"
+#include "mitkLabelSetImage.h"
+
+#include <MitkSegmentationExports.h>
+
+namespace mitk
+{
+ /**
+ \brief Base class for any auto segmentation tool that provides a preview of the new segmentation and generates
+ segmentations with multiple labels.
+
+ This tool class implements the basic logic to handle previews of multi label segmentations and
+ to allow to pick arbitrary labels as selected and merge them to a single segmentation to store this
+ segmentation as confirmed segmentation.
+
+ \ingroup ToolManagerEtAl
+ \sa mitk::Tool
+ \sa QmitkInteractiveSegmentation
+ */
+ class MITKSEGMENTATION_EXPORT AutoMLSegmentationWithPreviewTool : public AutoSegmentationWithPreviewTool
+ {
+ public:
+ mitkClassMacro(AutoMLSegmentationWithPreviewTool, AutoSegmentationWithPreviewTool);
+
+ void Activated() override;
+ void Deactivated() override;
+
+ using SelectedLabelVectorType = std::vector<Label::PixelType>;
+ void SetSelectedLabels(const SelectedLabelVectorType& regions);
+ SelectedLabelVectorType GetSelectedLabels() const;
+
+ const LabelSetImage* GetMLPreview() const;
+
+ protected:
+ AutoMLSegmentationWithPreviewTool();
+ ~AutoMLSegmentationWithPreviewTool() = default;
+
+ void UpdateCleanUp() override;
+ void DoUpdatePreview(const Image* inputAtTimeStep, Image* previewImage, TimeStepType timeStep) override;
+
+ /** Function to generate the new multi lable preview for a given time step input image.
+ * The function must be implemented by derived tools.
+ * This function is called by DoUpdatePreview if needed.
+ * Reasons are:
+ * - ML preview does not exist
+ * - Modify time of tools is newer then of ML preview
+ * - ML preview was not generated for the current selected timestep of input image or for the current selected timepoint.*/
+ virtual LabelSetImage::Pointer ComputeMLPreview(const Image* inputAtTimeStep, TimeStepType timeStep) = 0;
+
+ private:
+ /** Function to generate a simple (single lable) preview by merging all labels of the ML preview that are selected and
+ * copies that single label preview to the passed previewImage.
+ * This function is called by DoUpdatePreview if needed.
+ * @param mlPreviewImage Multi label preview that is the source.
+ * @param previewImage Pointer to the single label preview image that should receive the merged selected labels.
+ * @timeStep Time step of the previewImage that should be filled.*/
+ template <typename TPixel, unsigned int VImageDimension>
+ void CalculateMergedSimplePreview(const itk::Image<TPixel, VImageDimension>* mlImage, mitk::Image* segmentation, unsigned int timeStep);
+
+ SelectedLabelVectorType m_SelectedLabels = {};
+
+ // holds the multilabel result as a preview image
+ mitk::DataNode::Pointer m_MLPreviewNode;
+ TimeStepType m_LastMLTimeStep = 0;
+ };
+}
+#endif
diff --git a/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.cpp b/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.cpp
index 8e9b4291f7..e8554c2228 100644
--- a/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.cpp
+++ b/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.cpp
@@ -1,474 +1,478 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkAutoSegmentationWithPreviewTool.h"
#include "mitkToolManager.h"
#include "mitkColorProperty.h"
#include "mitkLevelWindowProperty.h"
#include "mitkProperties.h"
#include "mitkDataStorage.h"
#include "mitkRenderingManager.h"
#include <mitkSliceNavigationController.h>
#include "mitkImageAccessByItk.h"
#include "mitkImageCast.h"
#include "mitkImageStatisticsHolder.h"
#include "mitkImageTimeSelector.h"
#include "mitkLabelSetImage.h"
#include "mitkMaskAndCutRoiImageFilter.h"
#include "mitkPadImageFilter.h"
#include "mitkNodePredicateGeometry.h"
mitk::AutoSegmentationWithPreviewTool::AutoSegmentationWithPreviewTool(bool lazyDynamicPreviews): m_LazyDynamicPreviews(lazyDynamicPreviews)
{
m_ProgressCommand = mitk::ToolCommand::New();
}
mitk::AutoSegmentationWithPreviewTool::~AutoSegmentationWithPreviewTool()
{
}
bool mitk::AutoSegmentationWithPreviewTool::CanHandle(const BaseData* referenceData, const BaseData* workingData) const
{
if (!Superclass::CanHandle(referenceData, workingData))
return false;
if (workingData == nullptr)
return true;
auto* labelSet = dynamic_cast<const LabelSetImage*>(workingData);
if (labelSet != nullptr)
return true;
auto* image = dynamic_cast<const Image*>(workingData);
if (image == nullptr)
return false;
//if it is a normal image and not a label set image is used as working data
//it must have the same pixel type as a label set.
return MakeScalarPixelType< DefaultSegmentationDataType >() == image->GetPixelType();
}
void mitk::AutoSegmentationWithPreviewTool::Activated()
{
Superclass::Activated();
m_ToolManager->RoiDataChanged +=
mitk::MessageDelegate<mitk::AutoSegmentationWithPreviewTool>(this, &mitk::AutoSegmentationWithPreviewTool::OnRoiDataChanged);
m_ToolManager->SelectedTimePointChanged +=
mitk::MessageDelegate<mitk::AutoSegmentationWithPreviewTool>(this, &mitk::AutoSegmentationWithPreviewTool::OnTimePointChanged);
m_ReferenceDataNode = m_ToolManager->GetReferenceData(0);
m_SegmentationInputNode = m_ReferenceDataNode;
m_LastTimePointOfUpdate = 0;
if (m_PreviewSegmentationNode.IsNull())
{
m_PreviewSegmentationNode = DataNode::New();
m_PreviewSegmentationNode->SetProperty("color", ColorProperty::New(0.0, 1.0, 0.0));
m_PreviewSegmentationNode->SetProperty("name", StringProperty::New(std::string(this->GetName())+" preview"));
m_PreviewSegmentationNode->SetProperty("opacity", FloatProperty::New(0.3));
m_PreviewSegmentationNode->SetProperty("binary", BoolProperty::New(true));
m_PreviewSegmentationNode->SetProperty("helper object", BoolProperty::New(true));
}
if (m_SegmentationInputNode.IsNotNull())
{
this->ResetPreviewNode();
this->InitiateToolByInput();
}
else
{
m_ToolManager->ActivateTool(-1);
}
}
void mitk::AutoSegmentationWithPreviewTool::Deactivated()
{
m_ToolManager->RoiDataChanged -=
mitk::MessageDelegate<mitk::AutoSegmentationWithPreviewTool>(this, &mitk::AutoSegmentationWithPreviewTool::OnRoiDataChanged);
m_ToolManager->SelectedTimePointChanged -=
mitk::MessageDelegate<mitk::AutoSegmentationWithPreviewTool>(this, &mitk::AutoSegmentationWithPreviewTool::OnTimePointChanged);
m_SegmentationInputNode = nullptr;
m_ReferenceDataNode = nullptr;
try
{
if (DataStorage *storage = m_ToolManager->GetDataStorage())
{
storage->Remove(m_PreviewSegmentationNode);
RenderingManager::GetInstance()->RequestUpdateAll();
}
}
catch (...)
{
// don't care
}
- m_PreviewSegmentationNode->SetData(nullptr);
+ if (m_PreviewSegmentationNode.IsNotNull())
+ {
+ m_PreviewSegmentationNode->SetData(nullptr);
+ }
Superclass::Deactivated();
}
void mitk::AutoSegmentationWithPreviewTool::ConfirmSegmentation()
{
if (m_LazyDynamicPreviews && m_CreateAllTimeSteps)
{ // The tool should create all time steps but is currently in lazy mode,
// thus ensure that a preview for all time steps is available.
this->UpdatePreview(true);
}
CreateResultSegmentationFromPreview();
RenderingManager::GetInstance()->RequestUpdateAll();
if (!m_KeepActiveAfterAccept)
{
m_ToolManager->ActivateTool(-1);
}
}
void mitk::AutoSegmentationWithPreviewTool::InitiateToolByInput()
{
//default implementation does nothing.
//implement in derived classes to change behavior
}
mitk::Image* mitk::AutoSegmentationWithPreviewTool::GetPreviewSegmentation()
{
if (m_PreviewSegmentationNode.IsNull())
{
return nullptr;
}
return dynamic_cast<Image*>(m_PreviewSegmentationNode->GetData());
}
mitk::DataNode* mitk::AutoSegmentationWithPreviewTool::GetPreviewSegmentationNode()
{
return m_PreviewSegmentationNode;
}
const mitk::Image* mitk::AutoSegmentationWithPreviewTool::GetSegmentationInput() const
{
if (m_SegmentationInputNode.IsNull())
{
return nullptr;
}
return dynamic_cast<const Image*>(m_SegmentationInputNode->GetData());
}
const mitk::Image* mitk::AutoSegmentationWithPreviewTool::GetReferenceData() const
{
if (m_ReferenceDataNode.IsNull())
{
return nullptr;
}
return dynamic_cast<const Image*>(m_ReferenceDataNode->GetData());
}
void mitk::AutoSegmentationWithPreviewTool::ResetPreviewNode()
{
itk::RGBPixel<float> previewColor;
previewColor[0] = 0.0f;
previewColor[1] = 1.0f;
previewColor[2] = 0.0f;
const auto image = this->GetSegmentationInput();
if (nullptr != image)
{
mitk::LabelSetImage::ConstPointer workingImage =
dynamic_cast<const mitk::LabelSetImage *>(m_ToolManager->GetWorkingData(0)->GetData());
if (workingImage.IsNotNull())
{
auto newPreviewImage = workingImage->Clone();
if (newPreviewImage.IsNull())
{
MITK_ERROR << "Cannot create preview helper objects. Unable to clone working image";
return;
}
m_PreviewSegmentationNode->SetData(newPreviewImage);
// Let's paint the feedback node green...
newPreviewImage->GetActiveLabel()->SetColor(previewColor);
newPreviewImage->GetActiveLabelSet()->UpdateLookupTable(newPreviewImage->GetActiveLabel()->GetValue());
}
else
{
mitk::Image::ConstPointer workingImageBin = dynamic_cast<const mitk::Image*>(m_ToolManager->GetWorkingData(0)->GetData());
if (workingImageBin.IsNotNull())
{
auto newPreviewImage = workingImageBin->Clone();
if (newPreviewImage.IsNull())
{
MITK_ERROR << "Cannot create preview helper objects. Unable to clone working image";
return;
}
m_PreviewSegmentationNode->SetData(newPreviewImage->Clone());
}
else
{
mitkThrow() << "Tool is an invalid state. Cannot setup preview node. Working data is an unsupported class and should have not been accepted by CanHandle().";
}
}
m_PreviewSegmentationNode->SetColor(previewColor);
m_PreviewSegmentationNode->SetOpacity(0.5);
int layer(50);
m_ReferenceDataNode->GetIntProperty("layer", layer);
m_PreviewSegmentationNode->SetIntProperty("layer", layer + 1);
if (DataStorage *ds = m_ToolManager->GetDataStorage())
{
if (!ds->Exists(m_PreviewSegmentationNode))
ds->Add(m_PreviewSegmentationNode, m_ReferenceDataNode);
}
}
}
template <typename TPixel, unsigned int VImageDimension>
static void ITKSetVolume(const itk::Image<TPixel, VImageDimension> *originalImage,
mitk::Image *segmentation,
unsigned int timeStep)
{
auto constPixelContainer = originalImage->GetPixelContainer();
//have to make a const cast because itk::PixelContainer does not provide a const correct access :(
auto pixelContainer = const_cast<typename itk::Image<TPixel, VImageDimension>::PixelContainer*>(constPixelContainer);
segmentation->SetVolume((void *)pixelContainer->GetBufferPointer(), timeStep);
}
void mitk::AutoSegmentationWithPreviewTool::TransferImageAtTimeStep(const Image* sourceImage, Image* destinationImage, const TimeStepType timeStep)
{
try
{
Image::ConstPointer image3D = this->GetImageByTimeStep(sourceImage, timeStep);
if (image3D->GetPixelType() != destinationImage->GetPixelType())
{
mitkThrow() << "Cannot transfer images. Tool is in an invalid state, source image and destination image do not have the same pixel type. "
<< "Source pixel type: " << sourceImage->GetPixelType().GetTypeAsString()
<< "; destination pixel type: " << destinationImage->GetPixelType().GetTypeAsString();
}
if (!Equal(*(sourceImage->GetGeometry(timeStep)), *(destinationImage->GetGeometry(timeStep)), NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_PRECISION, false))
{
mitkThrow() << "Cannot transfer images. Tool is in an invalid state, source image and destination image do not have the same geometry.";
}
if (image3D->GetDimension() == 2)
{
AccessFixedDimensionByItk_2(
image3D, ITKSetVolume, 2, destinationImage, timeStep);
}
else
{
AccessFixedDimensionByItk_2(
image3D, ITKSetVolume, 3, destinationImage, timeStep);
}
}
catch (...)
{
Tool::ErrorMessage("Error accessing single time steps of the original image. Cannot create segmentation.");
throw;
}
}
void mitk::AutoSegmentationWithPreviewTool::CreateResultSegmentationFromPreview()
{
const auto segInput = this->GetSegmentationInput();
auto previewImage = this->GetPreviewSegmentation();
if (nullptr != segInput && nullptr != previewImage)
{
DataNode::Pointer resultSegmentationNode = GetTargetSegmentationNode();
if (resultSegmentationNode.IsNotNull())
{
const auto timePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint();
auto resultSegmentation = dynamic_cast<Image*>(resultSegmentationNode->GetData());
// REMARK: the following code in this scope assumes that previewImage and resultSegmentation
// are clones of the working image (segmentation provided to the tool). Therefore they have
// the same time geometry.
if (previewImage->GetTimeSteps() != resultSegmentation->GetTimeSteps())
{
mitkThrow() << "Cannot perform threshold. Internal tool state is invalid."
<< " Preview segmentation and segmentation result image have different time geometries.";
}
if (m_CreateAllTimeSteps)
{
for (unsigned int timeStep = 0; timeStep < previewImage->GetTimeSteps(); ++timeStep)
{
TransferImageAtTimeStep(previewImage, resultSegmentation, timeStep);
}
}
else
{
const auto timeStep = resultSegmentation->GetTimeGeometry()->TimePointToTimeStep(timePoint);
TransferImageAtTimeStep(previewImage, resultSegmentation, timeStep);
}
// since we are maybe working on a smaller image, pad it to the size of the original image
if (m_ReferenceDataNode.GetPointer() != m_SegmentationInputNode.GetPointer())
{
mitk::PadImageFilter::Pointer padFilter = mitk::PadImageFilter::New();
padFilter->SetInput(0, resultSegmentation);
padFilter->SetInput(1, dynamic_cast<mitk::Image*>(m_ReferenceDataNode->GetData()));
padFilter->SetBinaryFilter(true);
padFilter->SetUpperThreshold(1);
padFilter->SetLowerThreshold(1);
padFilter->Update();
resultSegmentationNode->SetData(padFilter->GetOutput());
}
m_ToolManager->SetWorkingData(resultSegmentationNode);
m_ToolManager->GetWorkingData(0)->Modified();
}
}
}
void mitk::AutoSegmentationWithPreviewTool::OnRoiDataChanged()
{
mitk::DataNode::ConstPointer node = m_ToolManager->GetRoiData(0);
if (node.IsNotNull())
{
mitk::MaskAndCutRoiImageFilter::Pointer roiFilter = mitk::MaskAndCutRoiImageFilter::New();
mitk::Image::Pointer image = dynamic_cast<mitk::Image *>(m_SegmentationInputNode->GetData());
if (image.IsNull())
return;
roiFilter->SetInput(image);
roiFilter->SetRegionOfInterest(node->GetData());
roiFilter->Update();
mitk::DataNode::Pointer tmpNode = mitk::DataNode::New();
tmpNode->SetData(roiFilter->GetOutput());
m_SegmentationInputNode = tmpNode;
}
else
m_SegmentationInputNode = m_ReferenceDataNode;
this->ResetPreviewNode();
this->InitiateToolByInput();
this->UpdatePreview();
}
void mitk::AutoSegmentationWithPreviewTool::OnTimePointChanged()
{
if (m_IsTimePointChangeAware && m_PreviewSegmentationNode.IsNotNull() && m_SegmentationInputNode.IsNotNull())
{
const auto timePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint();
const bool isStaticSegOnDynamicImage = m_PreviewSegmentationNode->GetData()->GetTimeSteps() == 1 && m_SegmentationInputNode->GetData()->GetTimeSteps() > 1;
if (timePoint!=m_LastTimePointOfUpdate && (isStaticSegOnDynamicImage || m_LazyDynamicPreviews))
{ //we only need to update either because we are lazzy
//or because we have a static segmentation with a dynamic image
this->UpdatePreview();
}
}
}
void mitk::AutoSegmentationWithPreviewTool::UpdatePreview(bool ignoreLazyPreviewSetting)
{
const auto inputImage = this->GetSegmentationInput();
auto previewImage = this->GetPreviewSegmentation();
int progress_steps = 200;
+ this->CurrentlyBusy.Send(true);
+
this->UpdatePrepare();
const auto timePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint();
try
{
- this->CurrentlyBusy.Send(true);
if (nullptr != inputImage && nullptr != previewImage)
{
m_ProgressCommand->AddStepsToDo(progress_steps);
if (previewImage->GetTimeSteps() > 1 && (ignoreLazyPreviewSetting || !m_LazyDynamicPreviews))
{
for (unsigned int timeStep = 0; timeStep < inputImage->GetTimeSteps(); ++timeStep)
{
auto feedBackImage3D = this->GetImageByTimeStep(inputImage, timeStep);
this->DoUpdatePreview(feedBackImage3D, previewImage, timeStep);
}
}
else
{
auto feedBackImage3D = this->GetImageByTimePoint(inputImage, timePoint);
auto timeStep = previewImage->GetTimeGeometry()->TimePointToTimeStep(timePoint);
this->DoUpdatePreview(feedBackImage3D, previewImage, timeStep);
}
RenderingManager::GetInstance()->RequestUpdateAll();
}
}
catch (itk::ExceptionObject & excep)
{
MITK_ERROR << "Exception caught: " << excep.GetDescription();
m_ProgressCommand->SetProgress(progress_steps);
std::string msg = excep.GetDescription();
ErrorMessage.Send(msg);
}
catch (...)
{
m_ProgressCommand->SetProgress(progress_steps);
CurrentlyBusy.Send(false);
throw;
}
this->UpdateCleanUp();
m_LastTimePointOfUpdate = timePoint;
m_ProgressCommand->SetProgress(progress_steps);
CurrentlyBusy.Send(false);
}
void mitk::AutoSegmentationWithPreviewTool::UpdatePrepare()
{
// default implementation does nothing
//reimplement in derived classes for special behavior
}
void mitk::AutoSegmentationWithPreviewTool::UpdateCleanUp()
{
// default implementation does nothing
//reimplement in derived classes for special behavior
}
mitk::TimePointType mitk::AutoSegmentationWithPreviewTool::GetLastTimePointOfUpdate() const
{
return m_LastTimePointOfUpdate;
}
diff --git a/Modules/Segmentation/Interactions/mitkOtsuTool3D.cpp b/Modules/Segmentation/Interactions/mitkOtsuTool3D.cpp
index 9a5f4cc388..ec02f6a346 100644
--- a/Modules/Segmentation/Interactions/mitkOtsuTool3D.cpp
+++ b/Modules/Segmentation/Interactions/mitkOtsuTool3D.cpp
@@ -1,253 +1,86 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
// MITK
#include "mitkOtsuTool3D.h"
-#include "mitkImageAccessByItk.h"
-#include "mitkLabelSetImage.h"
#include "mitkOtsuSegmentationFilter.h"
-#include "mitkRenderingManager.h"
-#include "mitkToolManager.h"
-#include <mitkITKImageImport.h>
-#include <mitkImageCast.h>
-#include <mitkLevelWindowProperty.h>
-#include <mitkLookupTableProperty.h>
-#include <mitkRenderingModeProperty.h>
-#include <mitkSliceNavigationController.h>
-
-// ITK
-#include <itkBinaryThresholdImageFilter.h>
-#include <itkOrImageFilter.h>
-#include <itkOtsuMultipleThresholdsImageFilter.h>
// us
#include <usGetModuleContext.h>
#include <usModule.h>
#include <usModuleContext.h>
#include <usModuleResource.h>
#include <mitkImageStatisticsHolder.h>
namespace mitk
{
MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, OtsuTool3D, "Otsu Segmentation");
}
-mitk::OtsuTool3D::OtsuTool3D() : AutoSegmentationWithPreviewTool(true)
-{
-}
-
-mitk::OtsuTool3D::~OtsuTool3D()
-{
-}
-
-void mitk::OtsuTool3D::SetSelectedRegions(const SelectedRegionVectorType& regions)
-{
- if (m_SelectedRegions != regions)
- {
- m_SelectedRegions = regions;
- //Note: we do not call this->Modified() on puprose. Reason: changing the
- //selected regions should not force to run otsu filter in DoUpdatePreview due to changed MTime.
- }
-}
-
-mitk::OtsuTool3D::SelectedRegionVectorType mitk::OtsuTool3D::GetSelectedRegions() const
-{
- return this->m_SelectedRegions;
-}
-
void mitk::OtsuTool3D::Activated()
{
Superclass::Activated();
- m_SelectedRegions = {};
m_NumberOfBins = 128;
m_NumberOfRegions = 2;
m_UseValley = false;
-
- m_OtsuResultNode = mitk::DataNode::New();
- m_OtsuResultNode->SetName("Otsu_Preview");
- // m_MultiLabelResultNode->SetBoolProperty("helper object", true);
- m_OtsuResultNode->SetVisibility(true);
- m_OtsuResultNode->SetOpacity(1.0);
-
- m_ToolManager->GetDataStorage()->Add(m_OtsuResultNode);
-}
-
-void mitk::OtsuTool3D::Deactivated()
-{
- m_ToolManager->GetDataStorage()->Remove(m_OtsuResultNode);
- m_OtsuResultNode = nullptr;
-
- Superclass::Deactivated();
}
const char **mitk::OtsuTool3D::GetXPM() const
{
return nullptr;
}
us::ModuleResource mitk::OtsuTool3D::GetIconResource() const
{
us::Module *module = us::GetModuleContext()->GetModule();
us::ModuleResource resource = module->GetResource("Otsu_48x48.png");
return resource;
}
const char* mitk::OtsuTool3D::GetName() const
{
return "Otsu";
}
-void mitk::OtsuTool3D::UpdateCleanUp()
-{
- if (m_OtsuResultNode.IsNotNull())
- m_OtsuResultNode->SetVisibility(m_SelectedRegions.empty());
-
- if (nullptr != this->GetPreviewSegmentationNode())
- this->GetPreviewSegmentationNode()->SetVisibility(!m_SelectedRegions.empty());
-
- if (m_SelectedRegions.empty())
- {
- this->ResetPreviewNode();
- }
-}
-
-void mitk::OtsuTool3D::DoUpdatePreview(const Image* inputAtTimeStep, Image* previewImage, TimeStepType timeStep)
+mitk::LabelSetImage::Pointer mitk::OtsuTool3D::ComputeMLPreview(const Image* inputAtTimeStep, TimeStepType /*timeStep*/)
{
int numberOfThresholds = m_NumberOfRegions - 1;
- const auto timePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint();
- mitk::LabelSetImage::Pointer otsuResultImage = dynamic_cast<LabelSetImage*>(this->m_OtsuResultNode->GetData());
-
- if (nullptr == m_OtsuResultNode->GetData()
- || this->GetMTime() > m_OtsuResultNode->GetData()->GetMTime()
- || this->m_LastOtsuTimeStep != timeStep //this covers the case where dynamic
- //segmentations have to compute a preview
- //for all time steps on confirmation
- || this->GetLastTimePointOfUpdate() != timePoint //this ensures that static seg
- //previews work with dynamic images
- //with avoiding unnecessary other otsu computations
- )
- {
- if (nullptr == inputAtTimeStep)
- {
- MITK_WARN << "Cannot run segementation. Currently selected input image is not set.";
- return;
- }
-
- this->m_LastOtsuTimeStep = timeStep;
-
- mitk::OtsuSegmentationFilter::Pointer otsuFilter = mitk::OtsuSegmentationFilter::New();
- otsuFilter->SetNumberOfThresholds(numberOfThresholds);
- otsuFilter->SetValleyEmphasis(m_UseValley);
- otsuFilter->SetNumberOfBins(m_NumberOfBins);
- otsuFilter->SetInput(inputAtTimeStep);
- otsuFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand);
-
- try
- {
- otsuFilter->Update();
- }
- catch (...)
- {
- mitkThrow() << "itkOtsuFilter error (image dimension must be in {2, 3} and image must not be RGB)";
- }
-
- otsuResultImage = mitk::LabelSetImage::New();
- otsuResultImage->InitializeByLabeledImage(otsuFilter->GetOutput());
- this->m_OtsuResultNode->SetData(otsuResultImage);
- this->m_OtsuResultNode->SetProperty("binary", mitk::BoolProperty::New(false));
- mitk::RenderingModeProperty::Pointer renderingMode = mitk::RenderingModeProperty::New();
- renderingMode->SetValue(mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR);
- this->m_OtsuResultNode->SetProperty("Image Rendering.Mode", renderingMode);
- mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
- mitk::LookupTableProperty::Pointer prop = mitk::LookupTableProperty::New(lut);
- vtkSmartPointer<vtkLookupTable> lookupTable = vtkSmartPointer<vtkLookupTable>::New();
- lookupTable->SetHueRange(1.0, 0.0);
- lookupTable->SetSaturationRange(1.0, 1.0);
- lookupTable->SetValueRange(1.0, 1.0);
- lookupTable->SetTableRange(-1.0, 1.0);
- lookupTable->Build();
- lut->SetVtkLookupTable(lookupTable);
- prop->SetLookupTable(lut);
- this->m_OtsuResultNode->SetProperty("LookupTable", prop);
- mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New();
- mitk::LevelWindow levelwindow;
- levelwindow.SetRangeMinMax(0, numberOfThresholds + 1);
- levWinProp->SetLevelWindow(levelwindow);
- this->m_OtsuResultNode->SetProperty("levelwindow", levWinProp);
- }
+ mitk::OtsuSegmentationFilter::Pointer otsuFilter = mitk::OtsuSegmentationFilter::New();
+ otsuFilter->SetNumberOfThresholds(numberOfThresholds);
+ otsuFilter->SetValleyEmphasis(m_UseValley);
+ otsuFilter->SetNumberOfBins(m_NumberOfBins);
+ otsuFilter->SetInput(inputAtTimeStep);
+ otsuFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand);
- if (!m_SelectedRegions.empty())
+ try
{
- AccessByItk_n(otsuResultImage, CalculatePreview, (previewImage, timeStep));
+ otsuFilter->Update();
}
-}
-
-template <typename TPixel, unsigned int VImageDimension>
-void mitk::OtsuTool3D::CalculatePreview(itk::Image<TPixel, VImageDimension> *itkImage, mitk::Image* segmentation, unsigned int timeStep)
-{
- typedef itk::Image<TPixel, VImageDimension> InputImageType;
- typedef itk::Image<mitk::Tool::DefaultSegmentationDataType, VImageDimension> OutputImageType;
-
- typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> FilterType;
-
- typename FilterType::Pointer filter = FilterType::New();
-
- // InputImageType::Pointer itkImage;
- typename OutputImageType::Pointer itkBinaryResultImage;
-
- filter->SetInput(itkImage);
- filter->SetLowerThreshold(m_SelectedRegions[0]);
- filter->SetUpperThreshold(m_SelectedRegions[0]);
- filter->SetInsideValue(1);
- filter->SetOutsideValue(0);
- filter->AddObserver(itk::ProgressEvent(), m_ProgressCommand);
- filter->Update();
- itkBinaryResultImage = filter->GetOutput();
- itkBinaryResultImage->DisconnectPipeline();
-
- // if more than one region id is used compute the union of all given binary regions
- for (const auto regionID : m_SelectedRegions)
+ catch (...)
{
- if (regionID != m_SelectedRegions[0])
- {
- filter->SetLowerThreshold(regionID);
- filter->SetUpperThreshold(regionID);
- filter->SetInsideValue(1);
- filter->SetOutsideValue(0);
- filter->Update();
-
- typename OutputImageType::Pointer tempImage = filter->GetOutput();
-
- typename itk::OrImageFilter<OutputImageType, OutputImageType>::Pointer orFilter =
- itk::OrImageFilter<OutputImageType, OutputImageType>::New();
- orFilter->SetInput1(tempImage);
- orFilter->SetInput2(itkBinaryResultImage);
- orFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand);
-
- orFilter->UpdateLargestPossibleRegion();
- itkBinaryResultImage = orFilter->GetOutput();
- }
+ mitkThrow() << "itkOtsuFilter error (image dimension must be in {2, 3} and image must not be RGB)";
}
- //----------------------------------------------------------------------------------------------------
- segmentation->SetVolume((void*)(itkBinaryResultImage->GetPixelContainer()->GetBufferPointer()), timeStep);
+ auto otsuResultImage = mitk::LabelSetImage::New();
+ otsuResultImage->InitializeByLabeledImage(otsuFilter->GetOutput());
+ return otsuResultImage;
}
unsigned int mitk::OtsuTool3D::GetMaxNumberOfBins() const
{
const auto min = this->GetReferenceData()->GetStatistics()->GetScalarValueMin();
const auto max = this->GetReferenceData()->GetStatistics()->GetScalarValueMaxNoRecompute();
return static_cast<unsigned int>(max - min) + 1;
}
diff --git a/Modules/Segmentation/Interactions/mitkOtsuTool3D.h b/Modules/Segmentation/Interactions/mitkOtsuTool3D.h
index 7761ec60dd..3703b237a6 100644
--- a/Modules/Segmentation/Interactions/mitkOtsuTool3D.h
+++ b/Modules/Segmentation/Interactions/mitkOtsuTool3D.h
@@ -1,80 +1,64 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef MITKOTSUTOOL3D_H
#define MITKOTSUTOOL3D_H
-#include "itkImage.h"
-#include "mitkAutoSegmentationWithPreviewTool.h"
-#include "mitkDataNode.h"
+#include "mitkAutoMLSegmentationWithPreviewTool.h"
#include <MitkSegmentationExports.h>
namespace us
{
class ModuleResource;
}
namespace mitk
{
class Image;
- class MITKSEGMENTATION_EXPORT OtsuTool3D : public AutoSegmentationWithPreviewTool
+ class MITKSEGMENTATION_EXPORT OtsuTool3D : public AutoMLSegmentationWithPreviewTool
{
public:
- mitkClassMacro(OtsuTool3D, AutoSegmentationWithPreviewTool);
+ mitkClassMacro(OtsuTool3D, AutoMLSegmentationWithPreviewTool);
itkFactorylessNewMacro(Self);
itkCloneMacro(Self);
const char *GetName() const override;
const char **GetXPM() const override;
us::ModuleResource GetIconResource() const override;
void Activated() override;
- void Deactivated() override;
itkSetMacro(NumberOfBins, unsigned int);
itkGetConstMacro(NumberOfBins, unsigned int);
itkSetMacro(NumberOfRegions, unsigned int);
itkGetConstMacro(NumberOfRegions, unsigned int);
itkSetMacro(UseValley, bool);
itkGetConstMacro(UseValley, bool);
itkBooleanMacro(UseValley);
- using SelectedRegionVectorType = std::vector<int>;
- void SetSelectedRegions(const SelectedRegionVectorType& regions);
- SelectedRegionVectorType GetSelectedRegions() const;
-
/**Returns the number of max bins based on the current input image.*/
unsigned int GetMaxNumberOfBins() const;
protected:
- OtsuTool3D();
- ~OtsuTool3D() override;
-
- void UpdateCleanUp() override;
- void DoUpdatePreview(const Image* inputAtTimeStep, Image* previewImage, TimeStepType timeStep) override;
+ OtsuTool3D() = default;
+ ~OtsuTool3D() = default;
- template <typename TPixel, unsigned int VImageDimension>
- void CalculatePreview(itk::Image<TPixel, VImageDimension> *itkImage, mitk::Image* segmentation, unsigned int timeStep);
+ LabelSetImage::Pointer ComputeMLPreview(const Image* inputAtTimeStep, TimeStepType timeStep) override;
unsigned int m_NumberOfBins = 128;
unsigned int m_NumberOfRegions = 2;
bool m_UseValley = false;
- SelectedRegionVectorType m_SelectedRegions = {};
-
- // holds the multilabel result as a preview image
- mitk::DataNode::Pointer m_OtsuResultNode;
- TimeStepType m_LastOtsuTimeStep = 0;
}; // class
} // namespace
#endif
diff --git a/Modules/Segmentation/Interactions/mitkSegmentationInteractor.cpp b/Modules/Segmentation/Interactions/mitkSegmentationInteractor.cpp
index bdb6497405..4aec82aba5 100644
--- a/Modules/Segmentation/Interactions/mitkSegmentationInteractor.cpp
+++ b/Modules/Segmentation/Interactions/mitkSegmentationInteractor.cpp
@@ -1,61 +1,63 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkSegmentationInteractor.h"
#include "mitkInteractionPositionEvent.h"
#include "mitkLabelSetImage.h"
#include "mitkToolManager.h"
#include "mitkToolManagerProvider.h"
#include <mitkImagePixelReadAccessor.h>
#include <cstring>
void mitk::SegmentationInteractor::ConnectActionsAndFunctions()
{
Superclass::ConnectActionsAndFunctions();
// CONNECT_FUNCTION("change_active_label", ChangeActiveLabel);
}
bool mitk::SegmentationInteractor::ChangeActiveLabel(StateMachineAction *, InteractionEvent *interactionEvent)
{
BaseRenderer::Pointer sender = interactionEvent->GetSender();
auto *positionEvent = static_cast<InteractionPositionEvent *>(interactionEvent);
// MLI TODO
// m_LastDisplayCoordinate = m_CurrentDisplayCoordinate;
// m_CurrentDisplayCoordinate = positionEvent->GetPointerPositionOnScreen();
- mitk::ToolManager *toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager();
+ auto *toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(
+ mitk::ToolManagerProvider::MULTILABEL_SEGMENTATION);
+
assert(toolManager);
DataNode *workingNode(toolManager->GetWorkingData(0));
if (workingNode)
{
auto *workingImage = dynamic_cast<mitk::LabelSetImage *>(workingNode->GetData());
assert(workingImage);
int timestep = positionEvent->GetSender()->GetTimeStep();
int pixelValue = static_cast<int>(workingImage->GetPixelValueByWorldCoordinate(positionEvent->GetPositionInWorld(), timestep));
workingImage->GetActiveLabelSet()->SetActiveLabel(pixelValue); // can be the background
// Call Events
// workingImage->ActiveLabelEvent.Send(pixelValue);
// MLI TODO
// toolManager->WorkingDataModified.Send();
}
RenderingManager::GetInstance()->RequestUpdateAll();
return true;
}
diff --git a/Modules/Segmentation/Interactions/mitkSegmentationInteractor.h b/Modules/Segmentation/Interactions/mitkSegmentationInteractor.h
index 700f51751a..b5fcb1f559 100644
--- a/Modules/Segmentation/Interactions/mitkSegmentationInteractor.h
+++ b/Modules/Segmentation/Interactions/mitkSegmentationInteractor.h
@@ -1,51 +1,51 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkSegmentationInteractor_h
#define mitkSegmentationInteractor_h
#include "MitkSegmentationExports.h"
#include "mitkDisplayInteractor.h"
namespace mitk
{
/**
*\class SegmentationInteractor
- *@brief Observer that adds interaction with a segmentation session to the default display interaction.
+ *@brief Observer that adds interaction with a multi-label segmentation session to the default display interaction.
*
* At the moment, this includes changing the active label.
*
* @ingroup Interaction
**/
class MITKSEGMENTATION_EXPORT SegmentationInteractor : public DisplayInteractor
{
public:
mitkClassMacro(SegmentationInteractor, DisplayInteractor);
itkNewMacro(Self);
protected : SegmentationInteractor(){};
~SegmentationInteractor() override{};
/**
* Derived function.
* Connects the action names used in the state machine pattern with functions implemented within
* this InteractionEventObserver. This is only necessary here because the events are processed by the state machine.
*/
void ConnectActionsAndFunctions() override;
/**
* Changes the active label.
*/
bool ChangeActiveLabel(StateMachineAction *, InteractionEvent *);
};
}
#endif
diff --git a/Modules/Segmentation/Interactions/mitkWatershedTool.cpp b/Modules/Segmentation/Interactions/mitkWatershedTool.cpp
index 47e29e4da4..b533bbe242 100644
--- a/Modules/Segmentation/Interactions/mitkWatershedTool.cpp
+++ b/Modules/Segmentation/Interactions/mitkWatershedTool.cpp
@@ -1,188 +1,163 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkWatershedTool.h"
#include "mitkIOUtil.h"
#include "mitkITKImageImport.h"
#include "mitkImage.h"
#include "mitkLabelSetImage.h"
#include "mitkImageAccessByItk.h"
#include "mitkImageCast.h"
#include "mitkImageStatisticsHolder.h"
#include "mitkLevelWindowManager.h"
#include "mitkLookupTable.h"
#include "mitkLookupTableProperty.h"
#include "mitkProgressBar.h"
#include "mitkRenderingManager.h"
#include "mitkRenderingModeProperty.h"
#include "mitkToolCommand.h"
#include "mitkToolManager.h"
#include <mitkSliceNavigationController.h>
#include <usGetModuleContext.h>
#include <usModule.h>
#include <usModuleContext.h>
#include <usModuleResource.h>
#include <vtkLookupTable.h>
#include <itkExceptionObject.h>
#include <itkGradientMagnitudeRecursiveGaussianImageFilter.h>
#include <itkWatershedImageFilter.h>
namespace mitk
{
MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, WatershedTool, "Watershed tool");
}
-mitk::WatershedTool::WatershedTool() : m_Threshold(0.0), m_Level(0.0)
-{
-}
-
-mitk::WatershedTool::~WatershedTool()
-{
-}
void mitk::WatershedTool::Activated()
{
Superclass::Activated();
-}
-void mitk::WatershedTool::Deactivated()
-{
- Superclass::Deactivated();
+ m_Level = 0.0;
+ m_Threshold = 0.0;
+
+ m_MagFilter = nullptr;
+ m_WatershedFilter = nullptr;
+ m_LastFilterInput = nullptr;
}
us::ModuleResource mitk::WatershedTool::GetIconResource() const
{
us::Module *module = us::GetModuleContext()->GetModule();
us::ModuleResource resource = module->GetResource("Watershed_48x48.png");
return resource;
}
const char **mitk::WatershedTool::GetXPM() const
{
return nullptr;
}
const char *mitk::WatershedTool::GetName() const
{
return "Watershed";
}
-void mitk::WatershedTool::DoIt()
+mitk::LabelSetImage::Pointer mitk::WatershedTool::ComputeMLPreview(const Image* inputAtTimeStep, TimeStepType /*timeStep*/)
{
- // get image from tool manager
- mitk::DataNode::Pointer referenceData = m_ToolManager->GetReferenceData(0);
- mitk::Image::ConstPointer input = dynamic_cast<const mitk::Image *>(referenceData->GetData());
- if (input.IsNull())
- return;
-
- const auto timePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint();
- input = GetImageByTimePoint(input, timePoint);
-
- if (nullptr == input)
- {
- MITK_WARN << "Cannot run segementation. Currently selected timepoint is not in the time bounds of the selected reference image. Time point: " << timePoint;
- return;
- }
-
- mitk::Image::Pointer output;
+ mitk::LabelSetImage::Pointer labelSetOutput;
try
{
+ mitk::Image::Pointer output;
+ bool inputChanged = inputAtTimeStep != m_LastFilterInput;
// create and run itk filter pipeline
- AccessByItk_1(input.GetPointer(), ITKWatershed, output);
+ AccessByItk_2(inputAtTimeStep, ITKWatershed, output, inputChanged);
- mitk::LabelSetImage::Pointer labelSetOutput = mitk::LabelSetImage::New();
+ labelSetOutput = mitk::LabelSetImage::New();
labelSetOutput->InitializeByLabeledImage(output);
-
- // create a new datanode for output
- mitk::DataNode::Pointer dataNode = mitk::DataNode::New();
- dataNode->SetData(labelSetOutput);
-
- // set name of data node
- std::string name = referenceData->GetName() + "_Watershed";
- dataNode->SetName(name);
-
- // look, if there is already a node with this name
- mitk::DataStorage::SetOfObjects::ConstPointer children =
- m_ToolManager->GetDataStorage()->GetDerivations(referenceData);
- mitk::DataStorage::SetOfObjects::ConstIterator currentNode = children->Begin();
- mitk::DataNode::Pointer removeNode;
- while (currentNode != children->End())
- {
- if (dataNode->GetName().compare(currentNode->Value()->GetName()) == 0)
- {
- removeNode = currentNode->Value();
- }
- currentNode++;
- }
- // remove node with same name
- if (removeNode.IsNotNull())
- m_ToolManager->GetDataStorage()->Remove(removeNode);
-
- // add output to the data storage
- m_ToolManager->GetDataStorage()->Add(dataNode, referenceData);
}
- catch (itk::ExceptionObject &e)
+ catch (itk::ExceptionObject & e)
{
+ //force reset of filters as they might be in an invalid state now.
+ m_MagFilter = nullptr;
+ m_WatershedFilter = nullptr;
+ m_LastFilterInput = nullptr;
+
MITK_ERROR << "Watershed Filter Error: " << e.GetDescription();
}
+
+ m_LastFilterInput = inputAtTimeStep;
- RenderingManager::GetInstance()->RequestUpdateAll();
+ return labelSetOutput;
}
template <typename TPixel, unsigned int VImageDimension>
-void mitk::WatershedTool::ITKWatershed(const itk::Image<TPixel, VImageDimension> *originalImage,
- mitk::Image::Pointer &segmentation)
+void mitk::WatershedTool::ITKWatershed(const itk::Image<TPixel, VImageDimension>* originalImage,
+ mitk::Image::Pointer& segmentation, bool inputChanged)
{
typedef itk::WatershedImageFilter<itk::Image<float, VImageDimension>> WatershedFilter;
typedef itk::GradientMagnitudeRecursiveGaussianImageFilter<itk::Image<TPixel, VImageDimension>,
- itk::Image<float, VImageDimension>>
+ itk::Image<float, VImageDimension>>
MagnitudeFilter;
+ // We create the filter pipeline only once (if needed) and not everytime we
+ // generate the ml image preview.
+ // Reason: If only the levels are changed the update of the pipe line is very
+ // fast and we want to profit from this feature.
+
// at first add a gradient magnitude filter
- typename MagnitudeFilter::Pointer magnitude = MagnitudeFilter::New();
- magnitude->SetInput(originalImage);
- magnitude->SetSigma(1.0);
+ typename MagnitudeFilter::Pointer magnitude = dynamic_cast<MagnitudeFilter*>(m_MagFilter.GetPointer());
+ if (magnitude.IsNull())
+ {
+ magnitude = MagnitudeFilter::New();
+ magnitude->SetSigma(1.0);
+ magnitude->AddObserver(itk::ProgressEvent(), m_ProgressCommand);
+ m_MagFilter = magnitude.GetPointer();
+ }
- // use the progress bar
- mitk::ToolCommand::Pointer command = mitk::ToolCommand::New();
- command->AddStepsToDo(60);
+ if (inputChanged)
+ {
+ magnitude->SetInput(originalImage);
+ }
// then add the watershed filter to the pipeline
- typename WatershedFilter::Pointer watershed = WatershedFilter::New();
- watershed->SetInput(magnitude->GetOutput());
+ typename WatershedFilter::Pointer watershed = dynamic_cast<WatershedFilter*>(m_WatershedFilter.GetPointer());
+ if (watershed.IsNull())
+ {
+ watershed = WatershedFilter::New();
+ watershed->SetInput(magnitude->GetOutput());
+ watershed->AddObserver(itk::ProgressEvent(), m_ProgressCommand);
+ m_WatershedFilter = watershed.GetPointer();
+ }
+
watershed->SetThreshold(m_Threshold);
watershed->SetLevel(m_Level);
- watershed->AddObserver(itk::ProgressEvent(), command);
watershed->Update();
// then make sure, that the output has the desired pixel type
typedef itk::CastImageFilter<typename WatershedFilter::OutputImageType,
- itk::Image<Tool::DefaultSegmentationDataType, VImageDimension>>
+ itk::Image<Tool::DefaultSegmentationDataType, VImageDimension>>
CastFilter;
typename CastFilter::Pointer cast = CastFilter::New();
cast->SetInput(watershed->GetOutput());
// start the whole pipeline
cast->Update();
- // reset the progress bar by setting progress
- command->SetProgress(10);
-
// since we obtain a new image from our pipeline, we have to make sure, that our mitk::Image::Pointer
// is responsible for the memory management of the output image
segmentation = mitk::GrabItkImageMemory(cast->GetOutput());
}
diff --git a/Modules/Segmentation/Interactions/mitkWatershedTool.h b/Modules/Segmentation/Interactions/mitkWatershedTool.h
index f50734141b..a4bea005ec 100644
--- a/Modules/Segmentation/Interactions/mitkWatershedTool.h
+++ b/Modules/Segmentation/Interactions/mitkWatershedTool.h
@@ -1,88 +1,84 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkWatershedTool_h_Included
#define mitkWatershedTool_h_Included
-#include "mitkAutoSegmentationTool.h"
+#include "mitkAutoMLSegmentationWithPreviewTool.h"
#include "mitkCommon.h"
#include <MitkSegmentationExports.h>
-#include <itkImage.h>
namespace us
{
class ModuleResource;
}
namespace mitk
{
- class Image;
-
/**
\brief Simple watershed segmentation tool.
\ingroup Interaction
\ingroup ToolManagerEtAl
Wraps ITK Watershed Filter into tool concept of MITK. For more information look into ITK documentation.
\warning Only to be instantiated by mitk::ToolManager.
-
- $Darth Vader$
*/
- class MITKSEGMENTATION_EXPORT WatershedTool : public AutoSegmentationTool
+ class MITKSEGMENTATION_EXPORT WatershedTool : public AutoMLSegmentationWithPreviewTool
{
public:
- mitkClassMacro(WatershedTool, AutoSegmentationTool);
+ mitkClassMacro(WatershedTool, AutoMLSegmentationWithPreviewTool);
itkFactorylessNewMacro(Self);
itkCloneMacro(Self);
- void SetThreshold(double t)
- {
- m_Threshold = t;
- }
+ const char** GetXPM() const override;
+ const char* GetName() const override;
+ us::ModuleResource GetIconResource() const override;
+
+ void Activated() override;
+
+ itkSetMacro(Threshold, double);
+ itkGetConstMacro(Threshold, double);
+
+ itkSetMacro(Level, double);
+ itkGetConstMacro(Level, double);
+
+ protected:
+ WatershedTool() = default;
+ ~WatershedTool() = default;
+
+ LabelSetImage::Pointer ComputeMLPreview(const Image* inputAtTimeStep, TimeStepType timeStep) override;
- void SetLevel(double l) { m_Level = l; }
- /** \brief Grabs the tool reference data and creates an ITK pipeline consisting of a GradientMagnitude
- * image filter followed by a Watershed image filter. The output of the filter pipeline is then added
- * to the data storage. */
- void DoIt();
+ /** \brief Threshold parameter of the ITK Watershed Image Filter. See ITK Documentation for more information. */
+ double m_Threshold = 0.0;
+ /** \brief Threshold parameter of the ITK Watershed Image Filter. See ITK Documentation for more information. */
+ double m_Level = 0.0;
+private:
/** \brief Creates and runs an ITK filter pipeline consisting of the filters: GradientMagnitude-, Watershed- and
* CastImageFilter.
*
* \param originalImage The input image, which is delivered by the AccessByItk macro.
* \param segmentation A pointer to the output image, which will point to the pipeline output after execution.
*/
template <typename TPixel, unsigned int VImageDimension>
- void ITKWatershed(const itk::Image<TPixel, VImageDimension> *originalImage, itk::SmartPointer<mitk::Image> &segmentation);
-
- const char **GetXPM() const override;
- const char *GetName() const override;
- us::ModuleResource GetIconResource() const override;
-
- protected:
- WatershedTool(); // purposely hidden
- ~WatershedTool() override;
-
- void Activated() override;
- void Deactivated() override;
+ void ITKWatershed(const itk::Image<TPixel, VImageDimension>* originalImage, itk::SmartPointer<mitk::Image>& segmentation, bool inputChanged);
- /** \brief Threshold parameter of the ITK Watershed Image Filter. See ITK Documentation for more information. */
- double m_Threshold;
- /** \brief Threshold parameter of the ITK Watershed Image Filter. See ITK Documentation for more information. */
- double m_Level;
+ itk::ProcessObject::Pointer m_MagFilter;
+ itk::ProcessObject::Pointer m_WatershedFilter;
+ mitk::Image::ConstPointer m_LastFilterInput;
};
} // namespace
#endif
diff --git a/Modules/Segmentation/files.cmake b/Modules/Segmentation/files.cmake
index 1deb993fd5..3bce31c9b5 100644
--- a/Modules/Segmentation/files.cmake
+++ b/Modules/Segmentation/files.cmake
@@ -1,117 +1,118 @@
set(CPP_FILES
Algorithms/mitkCalculateSegmentationVolume.cpp
Algorithms/mitkContourModelSetToImageFilter.cpp
Algorithms/mitkContourSetToPointSetFilter.cpp
Algorithms/mitkContourUtils.cpp
Algorithms/mitkCorrectorAlgorithm.cpp
Algorithms/mitkDiffImageApplier.cpp
Algorithms/mitkDiffSliceOperation.cpp
Algorithms/mitkDiffSliceOperationApplier.cpp
Algorithms/mitkFeatureBasedEdgeDetectionFilter.cpp
Algorithms/mitkImageLiveWireContourModelFilter.cpp
Algorithms/mitkImageToContourFilter.cpp
#Algorithms/mitkImageToContourModelFilter.cpp
Algorithms/mitkImageToLiveWireContourFilter.cpp
Algorithms/mitkManualSegmentationToSurfaceFilter.cpp
Algorithms/mitkOtsuSegmentationFilter.cpp
Algorithms/mitkOverwriteDirectedPlaneImageFilter.cpp
Algorithms/mitkOverwriteSliceImageFilter.cpp
Algorithms/mitkSegmentationObjectFactory.cpp
Algorithms/mitkShapeBasedInterpolationAlgorithm.cpp
Algorithms/mitkShowSegmentationAsSmoothedSurface.cpp
Algorithms/mitkShowSegmentationAsSurface.cpp
Algorithms/mitkVtkImageOverwrite.cpp
Controllers/mitkSegmentationInterpolationController.cpp
Controllers/mitkToolManager.cpp
Controllers/mitkSegmentationModuleActivator.cpp
Controllers/mitkToolManagerProvider.cpp
DataManagement/mitkContour.cpp
DataManagement/mitkContourSet.cpp
DataManagement/mitkExtrudedContour.cpp
Interactions/mitkAdaptiveRegionGrowingTool.cpp
Interactions/mitkAddContourTool.cpp
Interactions/mitkAutoCropTool.cpp
Interactions/mitkAutoSegmentationTool.cpp
Interactions/mitkAutoSegmentationWithPreviewTool.cpp
+ Interactions/mitkAutoMLSegmentationWithPreviewTool.cpp
Interactions/mitkBinaryThresholdBaseTool.cpp
Interactions/mitkBinaryThresholdTool.cpp
Interactions/mitkBinaryThresholdULTool.cpp
Interactions/mitkCalculateGrayValueStatisticsTool.cpp
Interactions/mitkCalculateVolumetryTool.cpp
Interactions/mitkContourModelInteractor.cpp
Interactions/mitkContourModelLiveWireInteractor.cpp
Interactions/mitkLiveWireTool2D.cpp
Interactions/mitkContourTool.cpp
Interactions/mitkCorrectorTool2D.cpp
Interactions/mitkCreateSurfaceTool.cpp
Interactions/mitkDrawPaintbrushTool.cpp
Interactions/mitkErasePaintbrushTool.cpp
Interactions/mitkEraseRegionTool.cpp
Interactions/mitkFastMarchingTool.cpp
Interactions/mitkFastMarchingTool3D.cpp
Interactions/mitkFeedbackContourTool.cpp
Interactions/mitkFillRegionTool.cpp
Interactions/mitkOtsuTool3D.cpp
Interactions/mitkPaintbrushTool.cpp
Interactions/mitkPixelManipulationTool.cpp
Interactions/mitkRegionGrowingTool.cpp
Interactions/mitkSegmentationsProcessingTool.cpp
Interactions/mitkSetRegionTool.cpp
Interactions/mitkSegTool2D.cpp
Interactions/mitkSubtractContourTool.cpp
Interactions/mitkTool.cpp
Interactions/mitkToolCommand.cpp
Interactions/mitkWatershedTool.cpp
Interactions/mitkPickingTool.cpp
Interactions/mitkSegmentationInteractor.cpp #SO
Rendering/mitkContourMapper2D.cpp
Rendering/mitkContourSetMapper2D.cpp
Rendering/mitkContourSetVtkMapper3D.cpp
Rendering/mitkContourVtkMapper3D.cpp
SegmentationUtilities/BooleanOperations/mitkBooleanOperation.cpp
SegmentationUtilities/MorphologicalOperations/mitkMorphologicalOperations.cpp
#Added from ML
Controllers/mitkSliceBasedInterpolationController.cpp
Algorithms/mitkSurfaceStampImageFilter.cpp
)
set(RESOURCE_FILES
Add_48x48.png
Add_Cursor_32x32.png
Correction_48x48.png
Correction_Cursor_32x32.png
Erase_48x48.png
Erase_Cursor_32x32.png
FastMarching_48x48.png
FastMarching_Cursor_32x32.png
Fill_48x48.png
Fill_Cursor_32x32.png
LiveWire_48x48.png
LiveWire_Cursor_32x32.png
Otsu_48x48.png
Paint_48x48.png
Paint_Cursor_32x32.png
Pick_48x48.png
RegionGrowing_48x48.png
RegionGrowing_Cursor_32x32.png
Subtract_48x48.png
Subtract_Cursor_32x32.png
Threshold_48x48.png
TwoThresholds_48x48.png
Watershed_48x48.png
Watershed_Cursor_32x32.png
Wipe_48x48.png
Wipe_Cursor_32x32.png
Interactions/dummy.xml
Interactions/LiveWireTool.xml
Interactions/FastMarchingTool.xml
Interactions/PressMoveRelease.xml
Interactions/PressMoveReleaseAndPointSetting.xml
Interactions/PressMoveReleaseWithCTRLInversion.xml
Interactions/PressMoveReleaseWithCTRLInversionAllMouseMoves.xml
Interactions/SegmentationToolsConfig.xml
Interactions/ContourModelModificationConfig.xml
Interactions/ContourModelModificationInteractor.xml
)
diff --git a/Modules/SegmentationUI/Qmitk/QmitkMaskStampWidget.h b/Modules/SegmentationUI/Qmitk/QmitkMaskStampWidget.h
index 456a6f1cc4..e75f8c8adf 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkMaskStampWidget.h
+++ b/Modules/SegmentationUI/Qmitk/QmitkMaskStampWidget.h
@@ -1,59 +1,61 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef QmitkMaskStampWidget_h_Included
#define QmitkMaskStampWidget_h_Included
#include "MitkSegmentationUIExports.h"
#include "mitkDataNode.h"
#include <QWidget>
#include "ui_QmitkMaskStampWidgetGUIControls.h"
namespace mitk
{
class ToolManager;
}
/**
\brief GUI for mask stamp functionality
+ This class uses the mitk::ToolManagerProvider::MULTILABEL_SEGMENTATION context.
+
\ingroup ToolManagerEtAl
\ingroup Widgets
*/
class MITKSEGMENTATIONUI_EXPORT QmitkMaskStampWidget : public QWidget
{
Q_OBJECT
public:
QmitkMaskStampWidget(QWidget *parent = nullptr, const char *name = nullptr);
~QmitkMaskStampWidget() override;
void SetDataStorage(mitk::DataStorage *storage);
protected slots:
void OnShowInformation(bool);
void OnStamp();
private:
mitk::ToolManager *m_ToolManager;
mitk::DataStorage *m_DataStorage;
Ui::QmitkMaskStampWidgetGUIControls m_Controls;
};
#endif
diff --git a/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.cpp
index 031b353dab..9e925b66ba 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.cpp
+++ b/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.cpp
@@ -1,214 +1,194 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "QmitkOtsuTool3DGUI.h"
-#include "QmitkConfirmSegmentationDialog.h"
#include <QMessageBox>
-#include <qlabel.h>
-#include <qlayout.h>
-#include <qlistwidget.h>
-#include <qpushbutton.h>
-#include <qspinbox.h>
MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitkOtsuTool3DGUI, "")
QmitkOtsuTool3DGUI::QmitkOtsuTool3DGUI() : QmitkToolGUI(), m_NumberOfRegions(0)
{
m_Controls.setupUi(this);
connect(m_Controls.previewButton, SIGNAL(clicked()), this, SLOT(OnSpinboxValueAccept()));
- connect(m_Controls.m_selectionListWidget, SIGNAL(itemSelectionChanged()), this, SLOT(OnRegionSelectionChanged()));
+ connect(m_Controls.m_selectionListWidget, &QmitkSimpleLabelSetListWidget::SelectedLabelsChanged, this, &QmitkOtsuTool3DGUI::OnRegionSelectionChanged);
connect(m_Controls.m_Spinbox, SIGNAL(valueChanged(int)), this, SLOT(OnRegionSpinboxChanged(int)));
connect(m_Controls.m_ConfSegButton, SIGNAL(clicked()), this, SLOT(OnSegmentationRegionAccept()));
connect(this, SIGNAL(NewToolAssociated(mitk::Tool *)), this, SLOT(OnNewToolAssociated(mitk::Tool *)));
connect(m_Controls.advancedSettingsButton, SIGNAL(toggled(bool)), this, SLOT(OnAdvancedSettingsButtonToggled(bool)));
this->OnAdvancedSettingsButtonToggled(false);
}
QmitkOtsuTool3DGUI::~QmitkOtsuTool3DGUI()
{
if (m_OtsuTool3DTool.IsNotNull())
{
m_OtsuTool3DTool->CurrentlyBusy -=
mitk::MessageDelegate1<QmitkOtsuTool3DGUI, bool>(this, &QmitkOtsuTool3DGUI::BusyStateChanged);
}
}
void QmitkOtsuTool3DGUI::OnRegionSpinboxChanged(int numberOfRegions)
{
// we have to change to minimum number of histogram bins accordingly
int curBinValue = m_Controls.m_BinsSpinBox->value();
if (curBinValue < numberOfRegions)
m_Controls.m_BinsSpinBox->setValue(numberOfRegions);
}
-void QmitkOtsuTool3DGUI::OnRegionSelectionChanged()
+void QmitkOtsuTool3DGUI::OnRegionSelectionChanged(const QmitkSimpleLabelSetListWidget::LabelVectorType& selectedLabels)
{
- m_SelectedItems = m_Controls.m_selectionListWidget->selectedItems();
-
if (m_OtsuTool3DTool.IsNotNull())
{
- // update preview of region
- QList<QListWidgetItem *>::Iterator it;
- std::vector<int> regionIDs;
- for (it = m_SelectedItems.begin(); it != m_SelectedItems.end(); ++it)
- regionIDs.push_back((*it)->text().toInt());
+ mitk::AutoMLSegmentationWithPreviewTool::SelectedLabelVectorType labelIDs;
+ for (const auto& label : selectedLabels)
+ {
+ labelIDs.push_back(label->GetValue());
+ }
- m_OtsuTool3DTool->SetSelectedRegions(regionIDs);
+ m_OtsuTool3DTool->SetSelectedLabels(labelIDs);
m_OtsuTool3DTool->UpdatePreview();
- m_Controls.m_ConfSegButton->setEnabled(!regionIDs.empty());
+ m_Controls.m_ConfSegButton->setEnabled(!labelIDs.empty());
}
}
void QmitkOtsuTool3DGUI::OnAdvancedSettingsButtonToggled(bool toggled)
{
m_Controls.m_ValleyCheckbox->setVisible(toggled);
m_Controls.binLabel->setVisible(toggled);
m_Controls.m_BinsSpinBox->setVisible(toggled);
if (toggled)
{
int max = m_OtsuTool3DTool->GetMaxNumberOfBins();
if (max >= m_Controls.m_BinsSpinBox->minimum())
{
m_Controls.m_BinsSpinBox->setMaximum(max);
}
}
}
void QmitkOtsuTool3DGUI::OnNewToolAssociated(mitk::Tool *tool)
{
if (m_OtsuTool3DTool.IsNotNull())
{
m_OtsuTool3DTool->CurrentlyBusy -=
mitk::MessageDelegate1<QmitkOtsuTool3DGUI, bool>(this, &QmitkOtsuTool3DGUI::BusyStateChanged);
}
m_OtsuTool3DTool = dynamic_cast<mitk::OtsuTool3D *>(tool);
if (m_OtsuTool3DTool.IsNotNull())
{
m_OtsuTool3DTool->CurrentlyBusy +=
mitk::MessageDelegate1<QmitkOtsuTool3DGUI, bool>(this, &QmitkOtsuTool3DGUI::BusyStateChanged);
m_OtsuTool3DTool->SetOverwriteExistingSegmentation(true);
m_OtsuTool3DTool->IsTimePointChangeAwareOff();
m_Controls.m_CheckProcessAll->setVisible(m_OtsuTool3DTool->GetTargetSegmentationNode()->GetData()->GetTimeSteps() > 1);
}
}
void QmitkOtsuTool3DGUI::OnSegmentationRegionAccept()
{
- QmitkConfirmSegmentationDialog dialog;
QString segName = QString::fromStdString(m_OtsuTool3DTool->GetCurrentSegmentationName());
if (m_OtsuTool3DTool.IsNotNull())
{
if (this->m_Controls.m_CheckCreateNew->isChecked())
{
m_OtsuTool3DTool->SetOverwriteExistingSegmentation(false);
}
else
{
m_OtsuTool3DTool->SetOverwriteExistingSegmentation(true);
}
m_OtsuTool3DTool->SetCreateAllTimeSteps(this->m_Controls.m_CheckProcessAll->isChecked());
this->m_Controls.m_ConfSegButton->setEnabled(false);
m_OtsuTool3DTool->ConfirmSegmentation();
}
}
void QmitkOtsuTool3DGUI::OnSpinboxValueAccept()
{
if (m_NumberOfRegions == m_Controls.m_Spinbox->value() &&
m_UseValleyEmphasis == m_Controls.m_ValleyCheckbox->isChecked() &&
m_NumberOfBins == m_Controls.m_BinsSpinBox->value())
return;
if (m_OtsuTool3DTool.IsNotNull())
{
try
{
int proceed;
QMessageBox *messageBox = new QMessageBox(QMessageBox::Question,
nullptr,
"The otsu segmentation computation may take several minutes depending "
"on the number of Regions you selected. Proceed anyway?",
QMessageBox::Ok | QMessageBox::Cancel);
if (m_Controls.m_Spinbox->value() >= 5)
{
proceed = messageBox->exec();
if (proceed != QMessageBox::Ok)
return;
}
m_NumberOfRegions = m_Controls.m_Spinbox->value();
m_UseValleyEmphasis = m_Controls.m_ValleyCheckbox->isChecked();
m_NumberOfBins = m_Controls.m_BinsSpinBox->value();
m_OtsuTool3DTool->SetNumberOfRegions(m_NumberOfRegions);
m_OtsuTool3DTool->SetUseValley(m_UseValleyEmphasis);
m_OtsuTool3DTool->SetNumberOfBins(m_NumberOfBins);
m_OtsuTool3DTool->UpdatePreview();
}
catch (...)
{
this->setCursor(Qt::ArrowCursor);
QMessageBox *messageBox =
new QMessageBox(QMessageBox::Critical,
nullptr,
"itkOtsuFilter error: image dimension must be in {2, 3} and no RGB images can be handled.");
messageBox->exec();
delete messageBox;
return;
}
- // insert regions into widget
- QString itemName;
- QListWidgetItem *item;
- m_Controls.m_selectionListWidget->clear();
- for (int i = 0; i < m_Controls.m_Spinbox->value(); ++i)
- {
- itemName = QString::number(i);
- item = new QListWidgetItem(itemName);
- m_Controls.m_selectionListWidget->addItem(item);
- }
- // deactivate 'confirm segmentation'-button
- m_Controls.m_ConfSegButton->setEnabled(false);
+ m_Controls.m_selectionListWidget->SetLabelSetImage(m_OtsuTool3DTool->GetMLPreview());
m_OtsuTool3DTool->IsTimePointChangeAwareOn();
}
}
void QmitkOtsuTool3DGUI::BusyStateChanged(bool value)
{
if (value)
{
QApplication::setOverrideCursor(QCursor(Qt::BusyCursor));
}
else
{
QApplication::restoreOverrideCursor();
}
m_Controls.m_ValleyCheckbox->setEnabled(!value);
m_Controls.binLabel->setEnabled(!value);
m_Controls.m_BinsSpinBox->setEnabled(!value);
- m_Controls.m_ConfSegButton->setEnabled(!m_OtsuTool3DTool->GetSelectedRegions().empty() && !value);
+ m_Controls.m_ConfSegButton->setEnabled(!m_OtsuTool3DTool->GetSelectedLabels().empty() && !value);
m_Controls.m_CheckProcessAll->setEnabled(!value);
m_Controls.m_CheckCreateNew->setEnabled(!value);
m_Controls.previewButton->setEnabled(!value);
}
diff --git a/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.h b/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.h
index ce2ad862fe..e7a3762c43 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.h
+++ b/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.h
@@ -1,83 +1,75 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef QmitkOtsuTool3DGUI_h_Included
#define QmitkOtsuTool3DGUI_h_Included
#include "QmitkToolGUI.h"
#include "mitkOtsuTool3D.h"
+
#include "ui_QmitkOtsuToolWidgetControls.h"
+
#include <MitkSegmentationUIExports.h>
-#include <QListWidget>
#include <QPushButton>
-class QSpinBox;
-class QLabel;
-
/**
\ingroup org_mitk_gui_qt_interactivesegmentation_internal
\brief GUI for mitk::.
\sa mitk::
This GUI shows ...
Last contributor: $Author$
*/
class MITKSEGMENTATIONUI_EXPORT QmitkOtsuTool3DGUI : public QmitkToolGUI
{
Q_OBJECT
public:
mitkClassMacro(QmitkOtsuTool3DGUI, QmitkToolGUI);
itkFactorylessNewMacro(Self);
itkCloneMacro(Self);
- signals :
+protected slots :
- public slots :
-
- protected slots :
-
- void OnNewToolAssociated(mitk::Tool *);
+ void OnNewToolAssociated(mitk::Tool *);
void OnSpinboxValueAccept();
void OnSegmentationRegionAccept();
- void OnRegionSelectionChanged();
+ void OnRegionSelectionChanged(const QmitkSimpleLabelSetListWidget::LabelVectorType& selectedLabels);
void OnRegionSpinboxChanged(int);
private slots:
void OnAdvancedSettingsButtonToggled(bool toggled);
protected:
QmitkOtsuTool3DGUI();
~QmitkOtsuTool3DGUI() override;
void BusyStateChanged(bool value) override;
mitk::OtsuTool3D::Pointer m_OtsuTool3DTool;
Ui_QmitkOtsuToolWidgetControls m_Controls;
int m_NumberOfRegions;
bool m_UseValleyEmphasis;
int m_NumberOfBins;
-
- QList<QListWidgetItem *> m_SelectedItems;
};
#endif
diff --git a/Modules/SegmentationUI/Qmitk/QmitkOtsuToolWidgetControls.ui b/Modules/SegmentationUI/Qmitk/QmitkOtsuToolWidgetControls.ui
index 27e1d87ff8..d01d26178d 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkOtsuToolWidgetControls.ui
+++ b/Modules/SegmentationUI/Qmitk/QmitkOtsuToolWidgetControls.ui
@@ -1,234 +1,253 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>QmitkOtsuToolWidgetControls</class>
<widget class="QWidget" name="QmitkOtsuToolWidgetControls">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
- <width>192</width>
- <height>300</height>
+ <width>699</width>
+ <height>352</height>
</rect>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Ignored" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>100</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>100000</width>
<height>100000</height>
</size>
</property>
<property name="windowTitle">
<string>QmitkOtsuToolWidget</string>
</property>
- <property name="toolTip">
- <string>Move to adjust the segmentation</string>
- </property>
<layout class="QVBoxLayout" name="verticalLayout">
<item>
<layout class="QHBoxLayout" name="horizontalLayout">
<property name="sizeConstraint">
<enum>QLayout::SetNoConstraint</enum>
</property>
<item>
<widget class="QLabel" name="numberOfRegionsLabel">
<property name="sizePolicy">
- <sizepolicy hsizetype="Ignored" vsizetype="Minimum">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="text">
<string>Number of Regions:</string>
</property>
</widget>
</item>
<item>
<widget class="QSpinBox" name="m_Spinbox">
<property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Minimum">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="maximumSize">
<size>
<width>40</width>
<height>16777215</height>
</size>
</property>
<property name="minimum">
<number>2</number>
</property>
<property name="maximum">
<number>32</number>
</property>
</widget>
</item>
+ <item>
+ <spacer name="horizontalSpacer">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
</layout>
</item>
<item>
<widget class="ctkExpandButton" name="advancedSettingsButton">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>0</width>
<height>32</height>
</size>
</property>
<property name="text">
<string>Advanced settings</string>
</property>
<property name="toolButtonStyle">
<enum>Qt::ToolButtonTextBesideIcon</enum>
</property>
<property name="mirrorOnExpand" stdset="0">
<bool>true</bool>
</property>
</widget>
</item>
<item>
- <layout class="QGridLayout" name="advancedSettingsLayout">
+ <layout class="QGridLayout" name="advancedSettingsLayout" rowstretch="0,0" columnstretch="0,0,0">
+ <item row="1" column="1">
+ <widget class="QSpinBox" name="m_BinsSpinBox">
+ <property name="minimum">
+ <number>2</number>
+ </property>
+ <property name="maximum">
+ <number>4096</number>
+ </property>
+ <property name="value">
+ <number>128</number>
+ </property>
+ </widget>
+ </item>
<item row="0" column="0">
<widget class="QCheckBox" name="m_ValleyCheckbox">
<property name="text">
<string>Use Valley Emphasis</string>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QLabel" name="binLabel">
<property name="text">
<string>Number of Histogram Bins:</string>
</property>
</widget>
</item>
- <item row="1" column="1">
- <widget class="QSpinBox" name="m_BinsSpinBox">
- <property name="minimum">
- <number>2</number>
- </property>
- <property name="maximum">
- <number>4096</number>
+ <item row="1" column="2">
+ <spacer name="horizontalSpacer_2">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
</property>
- <property name="value">
- <number>128</number>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
</property>
- </widget>
+ </spacer>
</item>
</layout>
</item>
<item>
- <widget class="QListWidget" name="m_selectionListWidget">
+ <widget class="QmitkSimpleLabelSetListWidget" name="m_selectionListWidget" native="true">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="maximumSize">
<size>
<width>10000000</width>
- <height>100</height>
+ <height>10000000</height>
</size>
</property>
- <property name="autoScrollMargin">
- <number>0</number>
- </property>
- <property name="selectionMode">
- <enum>QAbstractItemView::MultiSelection</enum>
- </property>
- <property name="resizeMode">
- <enum>QListView::Adjust</enum>
- </property>
</widget>
</item>
<item>
<widget class="QPushButton" name="previewButton">
<property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Minimum">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="maximumSize">
<size>
<width>100000</width>
<height>16777215</height>
</size>
</property>
<property name="text">
<string>Preview</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="m_ConfSegButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Minimum">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="maximumSize">
<size>
<width>100000</width>
<height>16777215</height>
</size>
</property>
<property name="text">
<string>Confirm Segmentation</string>
</property>
</widget>
</item>
<item>
<widget class="QCheckBox" name="m_CheckProcessAll">
<property name="toolTip">
<string>Process/overwrite all time steps of the dynamic segmentation and not just the currently visible time step.</string>
</property>
<property name="text">
<string>Process all time steps</string>
</property>
</widget>
</item>
<item>
<widget class="QCheckBox" name="m_CheckCreateNew">
<property name="toolTip">
<string>Add the confirmed segmentation as a new segmentation instead of overwriting the currently selected.</string>
</property>
<property name="text">
<string>Create as new segmentation</string>
</property>
</widget>
</item>
</layout>
</widget>
<layoutdefault spacing="6" margin="11"/>
<customwidgets>
<customwidget>
<class>ctkExpandButton</class>
<extends>QToolButton</extends>
<header>ctkExpandButton.h</header>
</customwidget>
+ <customwidget>
+ <class>QmitkSimpleLabelSetListWidget</class>
+ <extends>QWidget</extends>
+ <header>QmitkSimpleLabelSetListWidget.h</header>
+ </customwidget>
</customwidgets>
<resources/>
<connections/>
</ui>
diff --git a/Modules/SegmentationUI/Qmitk/QmitkSimpleLabelSetListWidget.cpp b/Modules/SegmentationUI/Qmitk/QmitkSimpleLabelSetListWidget.cpp
new file mode 100644
index 0000000000..8d6f3215f9
--- /dev/null
+++ b/Modules/SegmentationUI/Qmitk/QmitkSimpleLabelSetListWidget.cpp
@@ -0,0 +1,182 @@
+/*============================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center (DKFZ)
+All rights reserved.
+
+Use of this source code is governed by a 3-clause BSD license that can be
+found in the LICENSE file.
+
+============================================================================*/
+
+#include "QmitkSimpleLabelSetListWidget.h"
+
+#include "mitkMessage.h"
+
+#include <qlayout.h>
+
+QmitkSimpleLabelSetListWidget::QmitkSimpleLabelSetListWidget(QWidget* parent) : QWidget(parent), m_LabelList(nullptr)
+{
+ QGridLayout* layout = new QGridLayout(this);
+ this->setContentsMargins(0, 0, 0, 0);
+
+ m_LabelList = new QListWidget(this);
+ m_LabelList->setSelectionMode(QAbstractItemView::MultiSelection);
+ m_LabelList->setResizeMode(QListView::Adjust);
+ m_LabelList->setAutoScrollMargin(0);
+ layout->addWidget(m_LabelList);
+
+ connect(m_LabelList, SIGNAL(itemSelectionChanged()), this, SLOT(OnLabelSelectionChanged()));
+}
+
+QmitkSimpleLabelSetListWidget::~QmitkSimpleLabelSetListWidget()
+{
+ if (m_LabelSetImage.IsNotNull())
+ {
+ m_LabelSetImage->BeforeChangeLayerEvent -= mitk::MessageDelegate<QmitkSimpleLabelSetListWidget>(
+ this, &QmitkSimpleLabelSetListWidget::OnLooseLabelSetConnection);
+ m_LabelSetImage->AfterChangeLayerEvent -= mitk::MessageDelegate<QmitkSimpleLabelSetListWidget>(
+ this, &QmitkSimpleLabelSetListWidget::OnEstablishLabelSetConnection);
+ OnLooseLabelSetConnection();
+ }
+}
+
+QmitkSimpleLabelSetListWidget::LabelVectorType QmitkSimpleLabelSetListWidget::SelectedLabels() const
+{
+ auto selectedItems = m_LabelList->selectedItems();
+ LabelVectorType result;
+
+ QList<QListWidgetItem*>::Iterator it;
+ for (it = selectedItems.begin(); it != selectedItems.end(); ++it)
+ {
+ auto labelValue = (*it)->data(Qt::UserRole).toUInt();
+
+
+ auto activeLayerID = m_LabelSetImage->GetActiveLayer();
+ auto labelSet = m_LabelSetImage->GetLabelSet(activeLayerID);
+
+ result.push_back(labelSet->GetLabel(labelValue));
+ }
+
+ return result;
+}
+
+const mitk::LabelSetImage* QmitkSimpleLabelSetListWidget::GetLabelSetImage() const
+{
+ return m_LabelSetImage;
+}
+
+void QmitkSimpleLabelSetListWidget::SetLabelSetImage(const mitk::LabelSetImage* image)
+{
+ if (image != m_LabelSetImage)
+ {
+ if (m_LabelSetImage.IsNotNull())
+ {
+ m_LabelSetImage->BeforeChangeLayerEvent -= mitk::MessageDelegate<QmitkSimpleLabelSetListWidget>(
+ this, &QmitkSimpleLabelSetListWidget::OnLooseLabelSetConnection);
+ m_LabelSetImage->AfterChangeLayerEvent -= mitk::MessageDelegate<QmitkSimpleLabelSetListWidget>(
+ this, &QmitkSimpleLabelSetListWidget::OnLayerChanged);
+ this->OnLooseLabelSetConnection();
+ }
+
+ m_LabelSetImage = image;
+
+ if (m_LabelSetImage.IsNotNull())
+ {
+ m_LabelSetImage->BeforeChangeLayerEvent += mitk::MessageDelegate<QmitkSimpleLabelSetListWidget>(
+ this, &QmitkSimpleLabelSetListWidget::OnLooseLabelSetConnection);
+ m_LabelSetImage->AfterChangeLayerEvent += mitk::MessageDelegate<QmitkSimpleLabelSetListWidget>(
+ this, &QmitkSimpleLabelSetListWidget::OnLayerChanged);
+ this->OnLayerChanged();
+ }
+ }
+}
+
+void QmitkSimpleLabelSetListWidget::OnLooseLabelSetConnection()
+{
+ if (m_LabelSetImage.IsNull())
+ return;
+
+ auto activeLayerID = m_LabelSetImage->GetActiveLayer();
+ auto labelSet = m_LabelSetImage->GetLabelSet(activeLayerID);
+
+ // Reset LabelSetWidget Events
+ labelSet->AddLabelEvent -= mitk::MessageDelegate<QmitkSimpleLabelSetListWidget>(
+ this, &QmitkSimpleLabelSetListWidget::OnLabelChanged);
+ labelSet->RemoveLabelEvent -= mitk::MessageDelegate<QmitkSimpleLabelSetListWidget>(
+ this, &QmitkSimpleLabelSetListWidget::OnLabelChanged);
+ labelSet->ModifyLabelEvent -= mitk::MessageDelegate<QmitkSimpleLabelSetListWidget>(
+ this, &QmitkSimpleLabelSetListWidget::OnLabelChanged);
+}
+
+void QmitkSimpleLabelSetListWidget::OnEstablishLabelSetConnection()
+{
+ if (m_LabelSetImage.IsNull())
+ return;
+
+ auto activeLayerID = m_LabelSetImage->GetActiveLayer();
+ auto labelSet = m_LabelSetImage->GetLabelSet(activeLayerID);
+
+ // Reset LabelSetWidget Events
+ labelSet->AddLabelEvent += mitk::MessageDelegate<QmitkSimpleLabelSetListWidget>(
+ this, &QmitkSimpleLabelSetListWidget::OnLabelChanged);
+ labelSet->RemoveLabelEvent += mitk::MessageDelegate<QmitkSimpleLabelSetListWidget>(
+ this, &QmitkSimpleLabelSetListWidget::OnLabelChanged);
+ labelSet->ModifyLabelEvent += mitk::MessageDelegate<QmitkSimpleLabelSetListWidget>(
+ this, &QmitkSimpleLabelSetListWidget::OnLabelChanged);
+}
+
+void QmitkSimpleLabelSetListWidget::OnLayerChanged()
+{
+ this->OnEstablishLabelSetConnection();
+ this->ResetList();
+ emit ActiveLayerChanged();
+ emit SelectedLabelsChanged(this->SelectedLabels());
+}
+
+void QmitkSimpleLabelSetListWidget::OnLabelChanged()
+{
+ this->ResetList();
+ emit ActiveLayerChanged();
+ emit SelectedLabelsChanged(this->SelectedLabels());
+}
+
+void QmitkSimpleLabelSetListWidget::OnLabelSelectionChanged()
+{
+ emit SelectedLabelsChanged(this->SelectedLabels());
+}
+
+void QmitkSimpleLabelSetListWidget::ResetList()
+{
+ m_LabelList->clear();
+
+ auto activeLayerID = m_LabelSetImage->GetActiveLayer();
+ auto labelSet = m_LabelSetImage->GetLabelSet(activeLayerID);
+
+ auto iter = labelSet->IteratorConstBegin();
+ for (; iter != labelSet->IteratorConstEnd(); ++iter)
+ {
+ auto color = iter->second->GetColor();
+ QPixmap pixmap(10, 10);
+ pixmap.fill(QColor(color[0] * 255, color[1] * 255, color[2] * 255));
+ QIcon icon(pixmap);
+
+ QListWidgetItem* item = new QListWidgetItem(icon, QString::fromStdString(iter->second->GetName()));
+ item->setData(Qt::UserRole, QVariant(iter->second->GetValue()));
+ m_LabelList->addItem(item);
+ }
+}
+
+void QmitkSimpleLabelSetListWidget::SetSelectedLabels(const LabelVectorType& selectedLabels)
+{
+ for (int i = 0; i < m_LabelList->count(); ++i)
+ {
+ QListWidgetItem* item = m_LabelList->item(i);
+ auto labelValue = item->data(Qt::UserRole).toUInt();
+
+ auto finding = std::find_if(selectedLabels.begin(), selectedLabels.end(), [labelValue](const mitk::Label* label) {return label->GetValue() == labelValue; });
+ item->setSelected(finding != selectedLabels.end());
+ }
+}
+
diff --git a/Modules/SegmentationUI/Qmitk/QmitkSimpleLabelSetListWidget.h b/Modules/SegmentationUI/Qmitk/QmitkSimpleLabelSetListWidget.h
new file mode 100644
index 0000000000..88c716ff0c
--- /dev/null
+++ b/Modules/SegmentationUI/Qmitk/QmitkSimpleLabelSetListWidget.h
@@ -0,0 +1,63 @@
+/*============================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center (DKFZ)
+All rights reserved.
+
+Use of this source code is governed by a 3-clause BSD license that can be
+found in the LICENSE file.
+
+============================================================================*/
+
+#ifndef QmitkSimpleLabelSetListWidget_h_Included
+#define QmitkSimpleLabelSetListWidget_h_Included
+
+#include "mitkLabel.h"
+#include "mitkLabelSetImage.h"
+#include <MitkSegmentationUIExports.h>
+#include <QListWidget>
+
+/**
+ \brief Widget that offers a simple list that displays all labels (color and name) in the active
+ layer of a LabelSetImage.
+*/
+class MITKSEGMENTATIONUI_EXPORT QmitkSimpleLabelSetListWidget : public QWidget
+{
+ Q_OBJECT
+
+public:
+ QmitkSimpleLabelSetListWidget(QWidget* parent = nullptr);
+ ~QmitkSimpleLabelSetListWidget() override;
+
+ using LabelVectorType = std::vector<mitk::Label::ConstPointer>;
+
+ LabelVectorType SelectedLabels() const;
+ const mitk::LabelSetImage* GetLabelSetImage() const;
+
+signals:
+ void SelectedLabelsChanged(const LabelVectorType& selectedLabels);
+ void ActiveLayerChanged();
+
+public slots :
+ void SetLabelSetImage(const mitk::LabelSetImage* image);
+ void SetSelectedLabels(const LabelVectorType& selectedLabels);
+
+protected slots:
+
+ void OnLabelSelectionChanged();
+
+protected:
+ void OnLayerChanged();
+ void OnLabelChanged();
+
+ void OnLooseLabelSetConnection();
+ void OnEstablishLabelSetConnection();
+
+ void ResetList();
+
+ mitk::LabelSetImage::ConstPointer m_LabelSetImage;
+ QListWidget* m_LabelList;
+};
+
+#endif
diff --git a/Modules/SegmentationUI/Qmitk/QmitkSliceBasedInterpolatorWidget.h b/Modules/SegmentationUI/Qmitk/QmitkSliceBasedInterpolatorWidget.h
index c23db6bcf3..f33ab64114 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkSliceBasedInterpolatorWidget.h
+++ b/Modules/SegmentationUI/Qmitk/QmitkSliceBasedInterpolatorWidget.h
@@ -1,195 +1,197 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef QmitkSliceBasedInterpolatorWidget_h_Included
#define QmitkSliceBasedInterpolatorWidget_h_Included
#include "MitkSegmentationUIExports.h"
#include "mitkDataStorage.h"
#include "mitkSliceBasedInterpolationController.h"
#include <map>
#include <QWidget>
#include "ui_QmitkSliceBasedInterpolatorWidgetGUIControls.h"
namespace mitk
{
class PlaneGeometry;
class SliceNavigationController;
class LabelSetImage;
class ToolManager;
class DiffSliceOperation;
}
/**
\brief GUI for slices interpolation.
\ingroup ToolManagerEtAl
\ingroup Widgets
\sa QmitkInteractiveSegmentation
\sa mitk::SegmentationInterpolation
While mitk::SegmentationInterpolation does the bookkeeping of interpolation
(keeping track of which slices contain how much segmentation) and the algorithmic work,
QmitkSliceBasedInterpolatorWidget is responsible to watch the GUI, to notice, which slice is currently
visible. It triggers generation of interpolation suggestions and also triggers acception of
suggestions.
+ This class uses the mitk::ToolManagerProvider::MULTILABEL_SEGMENTATION context.
+
\todo show/hide feedback on demand
Last contributor: $Author: maleike $
*/
class MITKSEGMENTATIONUI_EXPORT QmitkSliceBasedInterpolatorWidget : public QWidget
{
Q_OBJECT
public:
QmitkSliceBasedInterpolatorWidget(QWidget *parent = nullptr, const char *name = nullptr);
~QmitkSliceBasedInterpolatorWidget() override;
void SetDataStorage(mitk::DataStorage &storage);
/**
Sets the slice navigation controllers for getting slice changed events from the views.
*/
void SetSliceNavigationControllers(const QList<mitk::SliceNavigationController *> &controllers);
void OnToolManagerWorkingDataModified();
void OnTimeChanged(itk::Object *sender, const itk::EventObject &);
void OnSliceChanged(itk::Object *sender, const itk::EventObject &);
void OnSliceNavigationControllerDeleted(const itk::Object *sender, const itk::EventObject &);
/**
Just public because it is called by itk::Commands. You should not need to call this.
*/
void OnSliceInterpolationInfoChanged(const itk::EventObject &);
Ui::QmitkSliceBasedInterpolatorWidgetGUIControls m_Controls;
signals:
void signalSliceBasedInterpolationEnabled(bool);
public slots:
/**
\brief Reaction to "Start/Stop" button click
*/
void OnToggleWidgetActivation(bool);
protected slots:
/**
\brief Reaction to "Accept Current Slice" button click.
*/
void OnAcceptInterpolationClicked();
/*
\brief Reaction to "Accept All Slices" button click.
Opens popup to ask about which orientation should be interpolated
*/
void OnAcceptAllInterpolationsClicked();
/*
\brief Called from popup menu of OnAcceptAllInterpolationsClicked()
Will trigger interpolation for all slices in given orientation
*/
void OnAcceptAllPopupActivated(QAction *action);
protected:
typedef std::map<QAction *, mitk::SliceNavigationController *> ActionToSliceDimensionMapType;
const ActionToSliceDimensionMapType CreateActionToSliceDimension();
ActionToSliceDimensionMapType m_ActionToSliceDimensionMap;
void AcceptAllInterpolations(mitk::SliceNavigationController *slicer);
void WaitCursorOn();
void WaitCursorOff();
void RestoreOverrideCursor();
/**
Gets the working slice based on the given plane geometry and last saved interaction
\param planeGeometry a plane geometry
*/
mitk::Image::Pointer GetWorkingSlice(const mitk::PlaneGeometry *planeGeometry);
/**
Retrieves the currently selected PlaneGeometry from a SlicedGeometry3D that is generated by a
SliceNavigationController
and calls Interpolate to further process this PlaneGeometry into an interpolation.
\param e is a actually a mitk::SliceNavigationController::GeometrySliceEvent, sent by a SliceNavigationController
\param slice the SliceNavigationController
*/
void TranslateAndInterpolateChangedSlice(const itk::EventObject &e, mitk::SliceNavigationController *slicer);
/**
Given a PlaneGeometry, this method figures out which slice of the first working image (of the associated
ToolManager)
should be interpolated. The actual work is then done by our SegmentationInterpolation object.
*/
void Interpolate(mitk::PlaneGeometry *plane, mitk::TimePointType timePoint, mitk::SliceNavigationController *slicer);
/**
Called internally to update the interpolation suggestion. Finds out about the focused render window and requests an
interpolation.
*/
void UpdateVisibleSuggestion();
private:
mitk::SliceBasedInterpolationController::Pointer m_SliceInterpolatorController;
mitk::ToolManager *m_ToolManager;
bool m_Activated;
template <typename TPixel, unsigned int VImageDimension>
void WritePreviewOnWorkingImage(itk::Image<TPixel, VImageDimension> *target,
const mitk::Image *source,
int overwritevalue);
QHash<mitk::SliceNavigationController *, int> m_ControllerToTimeObserverTag;
QHash<mitk::SliceNavigationController *, int> m_ControllerToSliceObserverTag;
QHash<mitk::SliceNavigationController *, int> m_ControllerToDeleteObserverTag;
unsigned int m_InterpolationInfoChangedObserverTag;
mitk::DiffSliceOperation *m_doOperation;
mitk::DiffSliceOperation *m_undoOperation;
mitk::DataNode::Pointer m_PreviewNode;
mitk::Image::Pointer m_PreviewImage;
mitk::LabelSetImage::Pointer m_WorkingImage;
QHash<mitk::SliceNavigationController *, mitk::TimePointType> m_TimePoints;
mitk::DataStorage::Pointer m_DataStorage;
mitk::SliceNavigationController *m_LastSNC;
unsigned int m_LastSliceIndex;
};
#endif
diff --git a/Modules/SegmentationUI/Qmitk/QmitkSurfaceBasedInterpolatorWidget.h b/Modules/SegmentationUI/Qmitk/QmitkSurfaceBasedInterpolatorWidget.h
index a4582310dc..fb16e7f7b0 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkSurfaceBasedInterpolatorWidget.h
+++ b/Modules/SegmentationUI/Qmitk/QmitkSurfaceBasedInterpolatorWidget.h
@@ -1,119 +1,121 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef QmitkSurfaceBasedInterpolatorWidgetWidget_h_Included
#define QmitkSurfaceBasedInterpolatorWidgetWidget_h_Included
#include "MitkSegmentationUIExports.h"
#include "mitkDataNode.h"
#include "mitkDataStorage.h"
#include "mitkLabelSetImage.h"
#include "mitkSurfaceBasedInterpolationController.h"
#include <map>
#include <QWidget>
// For running 3D interpolation in background
#include <QFuture>
#include <QFutureWatcher>
#include <QTimer>
#include <QtConcurrentRun>
#include "ui_QmitkSurfaceBasedInterpolatorWidgetGUIControls.h"
namespace mitk
{
class ToolManager;
}
/**
\brief GUI for surface-based interpolation.
\ingroup ToolManagerEtAl
\ingroup Widgets
\sa QmitkInteractiveSegmentation
\sa mitk::SurfaceBasedInterpolationController
QmitkSurfaceBasedInterpolatorWidgetController is responsible to watch the GUI, to notice, which slice is currently
visible. It triggers generation of interpolation suggestions and also triggers acception of suggestions.
+
+ This class uses the mitk::ToolManagerProvider::MULTILABEL_SEGMENTATION context.
*/
class MITKSEGMENTATIONUI_EXPORT QmitkSurfaceBasedInterpolatorWidget : public QWidget
{
Q_OBJECT
public:
QmitkSurfaceBasedInterpolatorWidget(QWidget *parent = nullptr, const char *name = nullptr);
~QmitkSurfaceBasedInterpolatorWidget() override;
void SetDataStorage(mitk::DataStorage &storage);
void OnToolManagerWorkingDataModified();
/**
Just public because it is called by itk::Commands. You should not need to call this.
*/
void OnSurfaceInterpolationInfoChanged(const itk::EventObject &);
/**
* @brief Set the visibility of the interpolation
*/
void ShowInterpolationResult(bool);
Ui::QmitkSurfaceBasedInterpolatorWidgetGUIControls m_Controls;
public slots:
/**
\brief Reaction to "Start/Stop" button click
*/
void OnToggleWidgetActivation(bool);
protected slots:
void OnAcceptInterpolationClicked();
void OnSurfaceInterpolationFinished();
void OnRunInterpolation();
void OnShowMarkers(bool);
void StartUpdateInterpolationTimer();
void StopUpdateInterpolationTimer();
void ChangeSurfaceColor();
private:
mitk::SurfaceBasedInterpolationController::Pointer m_SurfaceBasedInterpolatorController;
mitk::ToolManager *m_ToolManager;
bool m_Activated;
unsigned int m_SurfaceInterpolationInfoChangedObserverTag;
mitk::DataNode::Pointer m_InterpolatedSurfaceNode;
mitk::DataNode::Pointer m_3DContourNode;
mitk::DataStorage::Pointer m_DataStorage;
mitk::LabelSetImage::Pointer m_WorkingImage;
QFuture<void> m_Future;
QFutureWatcher<void> m_Watcher;
QTimer *m_Timer;
};
#endif
diff --git a/Modules/SegmentationUI/Qmitk/QmitkSurfaceStampWidget.cpp b/Modules/SegmentationUI/Qmitk/QmitkSurfaceStampWidget.cpp
index 05be2aa182..ad9a9a0f92 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkSurfaceStampWidget.cpp
+++ b/Modules/SegmentationUI/Qmitk/QmitkSurfaceStampWidget.cpp
@@ -1,117 +1,117 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "QmitkSurfaceStampWidget.h"
#include <mitkLabelSetImage.h>
#include <mitkRenderingManager.h>
#include <mitkSurface.h>
#include <mitkToolManagerProvider.h>
#include <QMessageBox>
QmitkSurfaceStampWidget::QmitkSurfaceStampWidget(QWidget *parent, const char * /*name*/)
: QWidget(parent), m_ToolManager(nullptr), m_DataStorage(nullptr)
{
m_Controls.setupUi(this);
m_Controls.m_InformationWidget->hide();
m_ToolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(mitk::ToolManagerProvider::MULTILABEL_SEGMENTATION);
m_ToolManager->ActivateTool(-1);
mitk::NodePredicateAnd::Pointer m_SurfacePredicate = mitk::NodePredicateAnd::New();
m_SurfacePredicate->AddPredicate(mitk::NodePredicateDataType::New("Surface"));
m_SurfacePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object")));
m_Controls.m_cbSurfaceNodeSelector->SetPredicate(m_SurfacePredicate);
connect(m_Controls.m_pbStamp, SIGNAL(clicked()), this, SLOT(OnStamp()));
connect(m_Controls.m_cbShowInformation, SIGNAL(toggled(bool)), this, SLOT(OnShowInformation(bool)));
m_Controls.m_InformationWidget->hide();
}
QmitkSurfaceStampWidget::~QmitkSurfaceStampWidget()
{
}
void QmitkSurfaceStampWidget::SetDataStorage(mitk::DataStorage *storage)
{
m_DataStorage = storage;
m_Controls.m_cbSurfaceNodeSelector->SetDataStorage(m_DataStorage);
}
void QmitkSurfaceStampWidget::OnStamp()
{
mitk::DataNode *surfaceNode = m_Controls.m_cbSurfaceNodeSelector->GetSelectedNode();
if (!surfaceNode)
{
QMessageBox::information(this, "Surface Stamp", "Please load and select a surface before starting some action.");
return;
}
- m_ToolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager();
+ m_ToolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(mitk::ToolManagerProvider::MULTILABEL_SEGMENTATION);
assert(m_ToolManager);
m_ToolManager->ActivateTool(-1);
mitk::Surface *surface = dynamic_cast<mitk::Surface *>(surfaceNode->GetData());
if (!surface)
{
QMessageBox::information(this, "Surface Stamp", "Please load and select a surface before starting some action.");
return;
}
mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0);
if (!workingNode)
{
QMessageBox::information(
this, "Surface Stamp", "Please load and select a segmentation before starting some action.");
return;
}
mitk::LabelSetImage *workingImage = dynamic_cast<mitk::LabelSetImage *>(workingNode->GetData());
if (!workingImage)
{
QMessageBox::information(
this, "Surface Stamp", "Please load and select a segmentation before starting some action.");
return;
}
QApplication::setOverrideCursor(QCursor(Qt::BusyCursor));
try
{
// workingImage->SurfaceStamp( surface, m_Controls.m_chkOverwrite->isChecked() );
}
catch (mitk::Exception &e)
{
QApplication::restoreOverrideCursor();
MITK_ERROR << "Exception caught: " << e.GetDescription();
QMessageBox::information(
this, "Surface Stamp", "Could not stamp the selected surface.\n See error log for details.\n");
return;
}
QApplication::restoreOverrideCursor();
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void QmitkSurfaceStampWidget::OnShowInformation(bool on)
{
if (on)
m_Controls.m_InformationWidget->show();
else
m_Controls.m_InformationWidget->hide();
}
diff --git a/Modules/SegmentationUI/Qmitk/QmitkSurfaceStampWidget.h b/Modules/SegmentationUI/Qmitk/QmitkSurfaceStampWidget.h
index 6320838ba2..852eced247 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkSurfaceStampWidget.h
+++ b/Modules/SegmentationUI/Qmitk/QmitkSurfaceStampWidget.h
@@ -1,58 +1,60 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef QmitkSurfaceStampWidget_h_Included
#define QmitkSurfaceStampWidget_h_Included
#include "MitkSegmentationUIExports.h"
#include <QWidget>
#include "ui_QmitkSurfaceStampWidgetGUIControls.h"
namespace mitk
{
class ToolManager;
}
/**
\brief GUI for surface-based interpolation.
+ This class uses the mitk::ToolManagerProvider::MULTILABEL_SEGMENTATION context.
+
\ingroup ToolManagerEtAl
\ingroup Widgets
*/
class MITKSEGMENTATIONUI_EXPORT QmitkSurfaceStampWidget : public QWidget
{
Q_OBJECT
public:
QmitkSurfaceStampWidget(QWidget *parent = nullptr, const char *name = nullptr);
~QmitkSurfaceStampWidget() override;
void SetDataStorage(mitk::DataStorage *storage);
protected slots:
void OnShowInformation(bool);
void OnStamp();
private:
mitk::ToolManager *m_ToolManager;
mitk::DataStorage *m_DataStorage;
Ui::QmitkSurfaceStampWidgetGUIControls m_Controls;
};
#endif
diff --git a/Modules/SegmentationUI/Qmitk/QmitkToolSelectionBox.cpp b/Modules/SegmentationUI/Qmitk/QmitkToolSelectionBox.cpp
index 43ca2e2c15..2036ea6b67 100755
--- a/Modules/SegmentationUI/Qmitk/QmitkToolSelectionBox.cpp
+++ b/Modules/SegmentationUI/Qmitk/QmitkToolSelectionBox.cpp
@@ -1,722 +1,683 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
//#define MBILOG_ENABLE_DEBUG 1
#include <QmitkStyleManager.h>
#include "QmitkToolSelectionBox.h"
#include "QmitkToolGUI.h"
#include "mitkBaseRenderer.h"
#include <QList>
#include <qapplication.h>
#include <qlayout.h>
#include <qmessagebox.h>
#include <qtoolbutton.h>
#include <qtooltip.h>
#include <queue>
#include "usModuleResource.h"
#include "usModuleResourceStream.h"
#include "mitkToolManagerProvider.h"
QmitkToolSelectionBox::QmitkToolSelectionBox(QWidget *parent, mitk::DataStorage *)
: QWidget(parent),
m_SelfCall(false),
m_DisplayedGroups("default"),
m_LayoutColumns(2),
m_ShowNames(true),
m_GenerateAccelerators(false),
m_ToolGUIWidget(nullptr),
m_LastToolGUI(nullptr),
m_ToolButtonGroup(nullptr),
m_ButtonLayout(nullptr),
m_EnabledMode(EnabledWithReferenceAndWorkingDataVisible)
{
QFont currentFont = QWidget::font();
currentFont.setBold(true);
QWidget::setFont(currentFont);
m_ToolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager();
- // muellerm
// QButtonGroup
m_ToolButtonGroup = new QButtonGroup(this);
// some features of QButtonGroup
m_ToolButtonGroup->setExclusive(false); // mutually exclusive toggle buttons
RecreateButtons();
QWidget::setContentsMargins(0, 0, 0, 0);
if (layout() != nullptr)
{
layout()->setContentsMargins(0, 0, 0, 0);
}
// reactions to signals
connect(m_ToolButtonGroup, SIGNAL(buttonClicked(int)), this, SLOT(toolButtonClicked(int)));
// reactions to ToolManager events
m_ToolManager->ActiveToolChanged +=
mitk::MessageDelegate<QmitkToolSelectionBox>(this, &QmitkToolSelectionBox::OnToolManagerToolModified);
m_ToolManager->ReferenceDataChanged +=
mitk::MessageDelegate<QmitkToolSelectionBox>(this, &QmitkToolSelectionBox::OnToolManagerReferenceDataModified);
m_ToolManager->WorkingDataChanged +=
mitk::MessageDelegate<QmitkToolSelectionBox>(this, &QmitkToolSelectionBox::OnToolManagerWorkingDataModified);
// show active tool
SetOrUnsetButtonForActiveTool();
QWidget::setEnabled(false);
}
QmitkToolSelectionBox::~QmitkToolSelectionBox()
{
m_ToolManager->ActiveToolChanged -=
mitk::MessageDelegate<QmitkToolSelectionBox>(this, &QmitkToolSelectionBox::OnToolManagerToolModified);
m_ToolManager->ReferenceDataChanged -=
mitk::MessageDelegate<QmitkToolSelectionBox>(this, &QmitkToolSelectionBox::OnToolManagerReferenceDataModified);
m_ToolManager->WorkingDataChanged -=
mitk::MessageDelegate<QmitkToolSelectionBox>(this, &QmitkToolSelectionBox::OnToolManagerWorkingDataModified);
}
void QmitkToolSelectionBox::SetEnabledMode(EnabledMode mode)
{
m_EnabledMode = mode;
SetGUIEnabledAccordingToToolManagerState();
}
mitk::ToolManager *QmitkToolSelectionBox::GetToolManager()
{
return m_ToolManager;
}
void QmitkToolSelectionBox::SetToolManager(
mitk::ToolManager &newManager) // no nullptr pointer allowed here, a manager is required
{
// say bye to the old manager
m_ToolManager->ActiveToolChanged -=
mitk::MessageDelegate<QmitkToolSelectionBox>(this, &QmitkToolSelectionBox::OnToolManagerToolModified);
m_ToolManager->ReferenceDataChanged -=
mitk::MessageDelegate<QmitkToolSelectionBox>(this, &QmitkToolSelectionBox::OnToolManagerReferenceDataModified);
m_ToolManager->WorkingDataChanged -=
mitk::MessageDelegate<QmitkToolSelectionBox>(this, &QmitkToolSelectionBox::OnToolManagerWorkingDataModified);
if (QWidget::isEnabled())
{
m_ToolManager->UnregisterClient();
}
m_ToolManager = &newManager;
RecreateButtons();
// greet the new one
m_ToolManager->ActiveToolChanged +=
mitk::MessageDelegate<QmitkToolSelectionBox>(this, &QmitkToolSelectionBox::OnToolManagerToolModified);
m_ToolManager->ReferenceDataChanged +=
mitk::MessageDelegate<QmitkToolSelectionBox>(this, &QmitkToolSelectionBox::OnToolManagerReferenceDataModified);
m_ToolManager->WorkingDataChanged +=
mitk::MessageDelegate<QmitkToolSelectionBox>(this, &QmitkToolSelectionBox::OnToolManagerWorkingDataModified);
if (QWidget::isEnabled())
{
m_ToolManager->RegisterClient();
}
// ask the new one what the situation is like
SetOrUnsetButtonForActiveTool();
}
void QmitkToolSelectionBox::toolButtonClicked(int id)
{
if (!QWidget::isEnabled())
return; // this method could be triggered from the constructor, when we are still disabled
MITK_DEBUG << "toolButtonClicked(" << id << "): id translates to tool ID " << m_ToolIDForButtonID[id];
- // QToolButton* toolButton = dynamic_cast<QToolButton*>( Q3ButtonGroup::find(id) );
QToolButton *toolButton = dynamic_cast<QToolButton *>(m_ToolButtonGroup->buttons().at(id));
if (toolButton)
{
if ((m_ButtonIDForToolID.find(m_ToolManager->GetActiveToolID()) !=
m_ButtonIDForToolID.end()) // if we have this tool in our box
&&
(m_ButtonIDForToolID[m_ToolManager->GetActiveToolID()] ==
id)) // the tool corresponding to this button is already active
{
// disable this button, disable all tools
- // mmueller
toolButton->setChecked(false);
m_ToolManager->ActivateTool(-1); // disable everything
}
else
{
// enable the corresponding tool
m_SelfCall = true;
m_ToolManager->ActivateTool(m_ToolIDForButtonID[id]);
m_SelfCall = false;
}
}
}
void QmitkToolSelectionBox::OnToolManagerToolModified()
{
SetOrUnsetButtonForActiveTool();
}
void QmitkToolSelectionBox::SetOrUnsetButtonForActiveTool()
{
// we want to emit a signal in any case, whether we selected ourselves or somebody else changes "our" tool manager.
// --> emit before check on m_SelfCall
int id = m_ToolManager->GetActiveToolID();
// don't emit signal for shape model tools
bool emitSignal = true;
mitk::Tool *tool = m_ToolManager->GetActiveTool();
if (tool && std::string(tool->GetGroup()) == "organ_segmentation")
emitSignal = false;
if (emitSignal)
emit ToolSelected(id);
// delete old GUI (if any)
if (m_LastToolGUI && m_ToolGUIWidget)
{
if (m_ToolGUIWidget->layout())
{
m_ToolGUIWidget->layout()->removeWidget(m_LastToolGUI);
}
- // m_LastToolGUI->reparent(nullptr, QPoint(0,0));
- // TODO: reparent <-> setParent, Daniel fragen
m_LastToolGUI->setParent(nullptr);
delete m_LastToolGUI; // will hopefully notify parent and layouts
m_LastToolGUI = nullptr;
QLayout *layout = m_ToolGUIWidget->layout();
if (layout)
{
layout->activate();
}
}
QToolButton *toolButton(nullptr);
- // mitk::Tool* tool = m_ToolManager->GetActiveTool();
if (m_ButtonIDForToolID.find(id) != m_ButtonIDForToolID.end()) // if this tool is in our box
{
- // toolButton = dynamic_cast<QToolButton*>( Q3ButtonGroup::find( m_ButtonIDForToolID[id] ) );
toolButton = dynamic_cast<QToolButton *>(m_ToolButtonGroup->buttons().at(m_ButtonIDForToolID[id]));
}
if (toolButton)
{
// mmueller
// uncheck all other buttons
QAbstractButton *tmpBtn = nullptr;
QList<QAbstractButton *>::iterator it;
for (int i = 0; i < m_ToolButtonGroup->buttons().size(); ++i)
{
tmpBtn = m_ToolButtonGroup->buttons().at(i);
if (tmpBtn != toolButton)
dynamic_cast<QToolButton *>(tmpBtn)->setChecked(false);
}
toolButton->setChecked(true);
if (m_ToolGUIWidget && tool)
{
// create and reparent new GUI (if any)
itk::Object::Pointer possibleGUI = tool->GetGUI("Qmitk", "GUI").GetPointer(); // prefix and postfix
if (possibleGUI.IsNull())
possibleGUI = tool->GetGUI("", "GUI").GetPointer();
QmitkToolGUI *gui = dynamic_cast<QmitkToolGUI *>(possibleGUI.GetPointer());
//!
m_LastToolGUI = gui;
if (gui)
{
gui->SetTool(tool);
- // mmueller
- // gui->reparent(m_ToolGUIWidget, gui->geometry().topLeft(), true );
gui->setParent(m_ToolGUIWidget);
gui->move(gui->geometry().topLeft());
gui->show();
QLayout *layout = m_ToolGUIWidget->layout();
if (!layout)
{
layout = new QVBoxLayout(m_ToolGUIWidget);
}
if (layout)
{
- // mmueller
layout->addWidget(gui);
- // layout->add( gui );
layout->activate();
}
}
}
}
else
{
// disable all buttons
QToolButton *selectedToolButton = dynamic_cast<QToolButton *>(m_ToolButtonGroup->checkedButton());
- // QToolButton* selectedToolButton = dynamic_cast<QToolButton*>( Q3ButtonGroup::find( Q3ButtonGroup::selectedId() )
- // );
if (selectedToolButton)
{
- // mmueller
selectedToolButton->setChecked(false);
- // selectedToolButton->setOn(false);
}
}
}
void QmitkToolSelectionBox::OnToolManagerReferenceDataModified()
{
if (m_SelfCall)
return;
MITK_DEBUG << "OnToolManagerReferenceDataModified()";
- SetGUIEnabledAccordingToToolManagerState();
+ this->UpdateButtonsEnabledState();
+ this->SetGUIEnabledAccordingToToolManagerState();
}
void QmitkToolSelectionBox::OnToolManagerWorkingDataModified()
{
if (m_SelfCall)
return;
MITK_DEBUG << "OnToolManagerWorkingDataModified()";
- SetGUIEnabledAccordingToToolManagerState();
+ this->UpdateButtonsEnabledState();
+ this->SetGUIEnabledAccordingToToolManagerState();
}
/**
Implementes the logic, which decides, when tools are activated/deactivated.
*/
void QmitkToolSelectionBox::SetGUIEnabledAccordingToToolManagerState()
{
mitk::DataNode *referenceNode = m_ToolManager->GetReferenceData(0);
mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0);
- // MITK_DEBUG << this->name() << ": SetGUIEnabledAccordingToToolManagerState: referenceNode " << (void*)referenceNode
- // << " workingNode " << (void*)workingNode << " isVisible() " << isVisible();
-
bool enabled = true;
switch (m_EnabledMode)
{
default:
case EnabledWithReferenceAndWorkingDataVisible:
enabled = referenceNode && workingNode &&
referenceNode->IsVisible(
mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget0"))) &&
workingNode->IsVisible(
mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget0"))) &&
isVisible();
break;
case EnabledWithReferenceData:
enabled = referenceNode && isVisible();
break;
case EnabledWithWorkingData:
enabled = workingNode && isVisible();
break;
case AlwaysEnabled:
enabled = isVisible();
break;
}
if (QWidget::isEnabled() == enabled)
return; // nothing to change
QWidget::setEnabled(enabled);
if (enabled)
{
m_ToolManager->RegisterClient();
int id = m_ToolManager->GetActiveToolID();
emit ToolSelected(id);
}
else
{
m_ToolManager->ActivateTool(-1);
m_ToolManager->UnregisterClient();
emit ToolSelected(-1);
}
}
/**
External enableization...
*/
void QmitkToolSelectionBox::setEnabled(bool /*enable*/)
{
SetGUIEnabledAccordingToToolManagerState();
}
-void QmitkToolSelectionBox::RecreateButtons()
+void QmitkToolSelectionBox::UpdateButtonsEnabledState()
{
- if (m_ToolManager.IsNull())
- return;
+ auto buttons = m_ToolButtonGroup->buttons();
- /*
- // remove all buttons that are there
- QObjectList *l = Q3ButtonGroup::queryList( "QButton" );
- QObjectListIt it( *l ); // iterate over all buttons
- QObject *obj;
+ const auto refDataNode = m_ToolManager->GetReferenceData(0);
+ const mitk::BaseData* refData = nullptr;
+ if (nullptr != refDataNode)
+ {
+ refData = refDataNode->GetData();
+ }
- while ( (obj = it.current()) != 0 )
+ const auto workingDataNode = m_ToolManager->GetWorkingData(0);
+ const mitk::BaseData* workingData = nullptr;
+ if (nullptr != workingDataNode)
{
- ++it;
- QButton* button = dynamic_cast<QButton*>(obj);
- if (button)
- {
- Q3ButtonGroup::remove(button);
- delete button;
- }
+ workingData = workingDataNode->GetData();
+ }
+
+ for (const auto& button : buttons)
+ {
+ const auto buttonID = m_ToolButtonGroup->id(button);
+ const auto toolID = m_ToolIDForButtonID[buttonID];
+ const auto tool = m_ToolManager->GetToolById(toolID);
+
+ button->setEnabled(tool->CanHandle(refData, workingData));
}
- delete l; // delete the list, not the objects
- */
+}
+
+void QmitkToolSelectionBox::RecreateButtons()
+{
+ if (m_ToolManager.IsNull())
+ return;
- // mmueller Qt impl
QList<QAbstractButton *> l = m_ToolButtonGroup->buttons();
// remove all buttons that are there
QList<QAbstractButton *>::iterator it;
QAbstractButton *btn;
for (it = l.begin(); it != l.end(); ++it)
{
btn = *it;
m_ToolButtonGroup->removeButton(btn);
- // this->removeChild(btn);
delete btn;
}
- // end mmueller Qt impl
mitk::ToolManager::ToolVectorTypeConst allPossibleTools = m_ToolManager->GetTools();
mitk::ToolManager::ToolVectorTypeConst allTools;
typedef std::pair<std::string::size_type, const mitk::Tool *> SortPairType;
typedef std::priority_queue<SortPairType> SortedToolQueueType;
SortedToolQueueType toolPositions;
// clear and sort all tools
// step one: find name/group of all tools in m_DisplayedGroups string. remember these positions for all tools.
for (mitk::ToolManager::ToolVectorTypeConst::const_iterator iter = allPossibleTools.begin();
iter != allPossibleTools.end();
++iter)
{
const mitk::Tool *tool = *iter;
std::string::size_type namePos = m_DisplayedGroups.find(std::string("'") + tool->GetName() + "'");
std::string::size_type groupPos = m_DisplayedGroups.find(std::string("'") + tool->GetGroup() + "'");
if (!m_DisplayedGroups.empty() && namePos == std::string::npos && groupPos == std::string::npos)
continue; // skip
if (m_DisplayedGroups.empty() && std::string(tool->GetName()).length() > 0)
{
namePos = static_cast<std::string::size_type>(tool->GetName()[0]);
}
SortPairType thisPair = std::make_pair(namePos < groupPos ? namePos : groupPos, *iter);
toolPositions.push(thisPair);
}
// step two: sort tools according to previously found positions in m_DisplayedGroups
MITK_DEBUG << "Sorting order of tools (lower number --> earlier in button group)";
while (!toolPositions.empty())
{
SortPairType thisPair = toolPositions.top();
MITK_DEBUG << "Position " << thisPair.first << " : " << thisPair.second->GetName();
allTools.push_back(thisPair.second);
toolPositions.pop();
}
std::reverse(allTools.begin(), allTools.end());
MITK_DEBUG << "Sorted tools:";
for (mitk::ToolManager::ToolVectorTypeConst::const_iterator iter = allTools.begin(); iter != allTools.end(); ++iter)
{
MITK_DEBUG << (*iter)->GetName();
}
- // try to change layout... bad?
- // Q3GroupBox::setColumnLayout ( m_LayoutColumns, Qt::Horizontal );
- // mmueller using gridlayout instead of Q3GroupBox
- // this->setLayout(0);
if (m_ButtonLayout == nullptr)
m_ButtonLayout = new QGridLayout;
- /*else
- delete m_ButtonLayout;*/
int row(0);
int column(-1);
int currentButtonID(0);
m_ButtonIDForToolID.clear();
m_ToolIDForButtonID.clear();
QToolButton *button = nullptr;
MITK_DEBUG << "Creating buttons for tools";
// fill group box with buttons
for (mitk::ToolManager::ToolVectorTypeConst::const_iterator iter = allTools.begin(); iter != allTools.end(); ++iter)
{
const mitk::Tool *tool = *iter;
int currentToolID(m_ToolManager->GetToolID(tool));
++column;
// new line if we are at the maximum columns
if (column == m_LayoutColumns)
{
++row;
column = 0;
}
button = new QToolButton;
button->setSizePolicy(QSizePolicy(QSizePolicy::Minimum, QSizePolicy::Minimum));
// add new button to the group
MITK_DEBUG << "Adding button with ID " << currentToolID;
m_ToolButtonGroup->addButton(button, currentButtonID);
// ... and to the layout
MITK_DEBUG << "Adding button in row/column " << row << "/" << column;
m_ButtonLayout->addWidget(button, row, column);
if (m_LayoutColumns == 1)
{
- // button->setTextPosition( QToolButton::BesideIcon );
- // mmueller
button->setToolButtonStyle(Qt::ToolButtonTextBesideIcon);
}
else
{
- // button->setTextPosition( QToolButton::BelowIcon );
- // mmueller
button->setToolButtonStyle(Qt::ToolButtonTextUnderIcon);
}
- // button->setToggleButton( true );
- // mmueller
button->setCheckable(true);
if (currentToolID == m_ToolManager->GetActiveToolID())
button->setChecked(true);
QString label;
if (m_GenerateAccelerators)
{
label += "&";
}
label += tool->GetName();
QString tooltip = tool->GetName();
MITK_DEBUG << tool->GetName() << ", " << label.toLocal8Bit().constData() << ", '"
<< tooltip.toLocal8Bit().constData();
if (m_ShowNames)
{
- /*
- button->setUsesTextLabel(true);
- button->setTextLabel( label ); // a label
- QToolTip::add( button, tooltip );
- */
- // mmueller Qt
button->setText(label); // a label
button->setToolTip(tooltip);
- // mmueller
QFont currentFont = button->font();
currentFont.setBold(false);
button->setFont(currentFont);
}
us::ModuleResource iconResource = tool->GetIconResource();
if (!iconResource.IsValid())
{
button->setIcon(QIcon(QPixmap(tool->GetXPM())));
}
else
{
auto isSVG = "svg" == iconResource.GetSuffix();
auto openmode = isSVG ? std::ios_base::in : std::ios_base::binary;
us::ModuleResourceStream resourceStream(iconResource, openmode);
resourceStream.seekg(0, std::ios::end);
std::ios::pos_type length = resourceStream.tellg();
resourceStream.seekg(0, std::ios::beg);
char *data = new char[length];
resourceStream.read(data, length);
if (isSVG)
{
button->setIcon(QmitkStyleManager::ThemeIcon(QByteArray::fromRawData(data, length)));
}
else
{
QPixmap pixmap;
pixmap.loadFromData(QByteArray::fromRawData(data, length));
button->setIcon(QIcon(pixmap));
}
delete[] data;
if (m_ShowNames)
{
if (m_LayoutColumns == 1)
button->setToolButtonStyle(Qt::ToolButtonTextBesideIcon);
else
button->setToolButtonStyle(Qt::ToolButtonTextUnderIcon);
button->setIconSize(QSize(24, 24));
}
else
{
button->setToolButtonStyle(Qt::ToolButtonIconOnly);
button->setIconSize(QSize(32, 32));
button->setToolTip(tooltip);
}
}
if (m_GenerateAccelerators)
{
QString firstLetter = QString(tool->GetName());
firstLetter.truncate(1);
button->setShortcut(
firstLetter); // a keyboard shortcut (just the first letter of the given name w/o any CTRL or something)
}
- mitk::DataNode *dataNode = m_ToolManager->GetReferenceData(0);
- const auto workingDataNode = m_ToolManager->GetWorkingData(0);
- const mitk::BaseData* workingData = nullptr;
- if (nullptr != workingDataNode)
- {
- workingData = workingDataNode->GetData();
- }
-
- if (nullptr == dataNode || !tool->CanHandle(dataNode->GetData(), workingData))
- button->setEnabled(false);
-
m_ButtonIDForToolID[currentToolID] = currentButtonID;
m_ToolIDForButtonID[currentButtonID] = currentToolID;
MITK_DEBUG << "m_ButtonIDForToolID[" << currentToolID << "] == " << currentButtonID;
MITK_DEBUG << "m_ToolIDForButtonID[" << currentButtonID << "] == " << currentToolID;
tool->GUIProcessEventsMessage += mitk::MessageDelegate<QmitkToolSelectionBox>(
this, &QmitkToolSelectionBox::OnToolGUIProcessEventsMessage); // will never add a listener twice, so we don't have
// to check here
tool->ErrorMessage += mitk::MessageDelegate1<QmitkToolSelectionBox, std::string>(
this,
&QmitkToolSelectionBox::OnToolErrorMessage); // will never add a listener twice, so we don't have to check here
tool->GeneralMessage +=
mitk::MessageDelegate1<QmitkToolSelectionBox, std::string>(this, &QmitkToolSelectionBox::OnGeneralToolMessage);
++currentButtonID;
}
// setting grid layout for this groupbox
this->setLayout(m_ButtonLayout);
+ this->UpdateButtonsEnabledState();
// this->update();
}
void QmitkToolSelectionBox::OnToolGUIProcessEventsMessage()
{
qApp->processEvents();
}
void QmitkToolSelectionBox::OnToolErrorMessage(std::string s)
{
QMessageBox::critical(
this, "MITK", QString(s.c_str()), QMessageBox::Ok, QMessageBox::NoButton, QMessageBox::NoButton);
}
void QmitkToolSelectionBox::OnGeneralToolMessage(std::string s)
{
QMessageBox::information(
this, "MITK", QString(s.c_str()), QMessageBox::Ok, QMessageBox::NoButton, QMessageBox::NoButton);
}
void QmitkToolSelectionBox::SetDisplayedToolGroups(const std::string &toolGroups)
{
if (m_DisplayedGroups != toolGroups)
{
QString q_DisplayedGroups = toolGroups.c_str();
// quote all unquoted single words
q_DisplayedGroups = q_DisplayedGroups.replace(QRegExp("\\b(\\w+)\\b|'([^']+)'"), "'\\1\\2'");
MITK_DEBUG << "m_DisplayedGroups was \"" << toolGroups << "\"";
m_DisplayedGroups = q_DisplayedGroups.toLocal8Bit().constData();
MITK_DEBUG << "m_DisplayedGroups is \"" << m_DisplayedGroups << "\"";
RecreateButtons();
SetOrUnsetButtonForActiveTool();
}
}
void QmitkToolSelectionBox::SetLayoutColumns(int columns)
{
if (columns > 0 && columns != m_LayoutColumns)
{
m_LayoutColumns = columns;
RecreateButtons();
}
}
void QmitkToolSelectionBox::SetShowNames(bool show)
{
if (show != m_ShowNames)
{
m_ShowNames = show;
RecreateButtons();
}
}
void QmitkToolSelectionBox::SetGenerateAccelerators(bool accel)
{
if (accel != m_GenerateAccelerators)
{
m_GenerateAccelerators = accel;
RecreateButtons();
}
}
void QmitkToolSelectionBox::SetToolGUIArea(QWidget *parentWidget)
{
m_ToolGUIWidget = parentWidget;
}
void QmitkToolSelectionBox::setTitle(const QString & /*title*/)
{
}
void QmitkToolSelectionBox::showEvent(QShowEvent *e)
{
QWidget::showEvent(e);
SetGUIEnabledAccordingToToolManagerState();
}
void QmitkToolSelectionBox::hideEvent(QHideEvent *e)
{
QWidget::hideEvent(e);
SetGUIEnabledAccordingToToolManagerState();
}
diff --git a/Modules/SegmentationUI/Qmitk/QmitkToolSelectionBox.h b/Modules/SegmentationUI/Qmitk/QmitkToolSelectionBox.h
index 643e32bd71..2afc06ce0f 100755
--- a/Modules/SegmentationUI/Qmitk/QmitkToolSelectionBox.h
+++ b/Modules/SegmentationUI/Qmitk/QmitkToolSelectionBox.h
@@ -1,147 +1,148 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef QmitkToolSelectionBox_h_Included
#define QmitkToolSelectionBox_h_Included
#include "QmitkToolGUIArea.h"
#include <MitkSegmentationUIExports.h>
#include "mitkToolManager.h"
#include <QButtonGroup>
#include <QGridLayout>
#include <QWidget>
#include <map>
class QmitkToolGUI;
/**
\brief Display the tool selection state of a mitk::ToolManager
\sa mitk::ToolManager
\ingroup org_mitk_gui_qt_interactivesegmentation
\ingroup ToolManagerEtAl
This widget graphically displays the active tool of a mitk::ToolManager as a set
of toggle buttons. Each button show the identification of a Tool (icon and name).
When a button's toggle state is "down", the tool is activated. When a different button
is clicked, the active tool is switched. When you click an already active button, the
associated tool is deactivated with no replacement, which means that no tool is active
then.
When this widget is enabled/disabled it (normally) also enables/disables the tools. There
could be cases where two QmitkToolSelectionBox widgets are associated to the same ToolManager,
but if this happens, please look deeply into the code.
Last contributor: $Author: maleike $
*/
class MITKSEGMENTATIONUI_EXPORT QmitkToolSelectionBox : public QWidget
//!
{
Q_OBJECT
public:
enum EnabledMode
{
EnabledWithReferenceAndWorkingDataVisible,
EnabledWithReferenceData,
EnabledWithWorkingData,
AlwaysEnabled
};
QmitkToolSelectionBox(QWidget *parent = nullptr, mitk::DataStorage *storage = nullptr);
~QmitkToolSelectionBox() override;
mitk::ToolManager *GetToolManager();
void SetToolManager(mitk::ToolManager &); // no nullptr pointer allowed here, a manager is required
void setTitle(const QString &title);
/**
You may specify a list of tool "groups" that should be displayed in this widget. Every Tool can report its group
as a string. This method will try to find the tool's group inside the supplied string \param toolGroups. If there is
a match,
the tool is displayed. Effectively, you can provide a human readable list like "default, lymphnodevolumetry,
oldERISstuff".
*/
void SetDisplayedToolGroups(const std::string &toolGroups = nullptr);
void OnToolManagerToolModified();
void OnToolManagerReferenceDataModified();
void OnToolManagerWorkingDataModified();
void OnToolGUIProcessEventsMessage();
void OnToolErrorMessage(std::string s);
void OnGeneralToolMessage(std::string s);
void RecreateButtons();
signals:
/// Whenever a tool is activated. id is the index of the active tool. Counting starts at 0, -1 indicates "no tool
/// selected"
/// This signal is also emitted, when the whole QmitkToolSelectionBox get disabled. Then it will claim
/// ToolSelected(-1)
/// When it is enabled again, there will be another ToolSelected event with the tool that is currently selected
void ToolSelected(int id);
public slots:
virtual void setEnabled(bool);
virtual void SetEnabledMode(EnabledMode mode);
virtual void SetLayoutColumns(int);
virtual void SetShowNames(bool);
virtual void SetGenerateAccelerators(bool);
virtual void SetToolGUIArea(QWidget *parentWidget);
protected slots:
void toolButtonClicked(int id);
void SetGUIEnabledAccordingToToolManagerState();
+ void UpdateButtonsEnabledState();
protected:
void showEvent(QShowEvent *) override;
void hideEvent(QHideEvent *) override;
void SetOrUnsetButtonForActiveTool();
mitk::ToolManager::Pointer m_ToolManager;
bool m_SelfCall;
std::string m_DisplayedGroups;
/// stores relationship between button IDs of the Qt widget and tool IDs of ToolManager
std::map<int, int> m_ButtonIDForToolID;
/// stores relationship between button IDs of the Qt widget and tool IDs of ToolManager
std::map<int, int> m_ToolIDForButtonID;
int m_LayoutColumns;
bool m_ShowNames;
bool m_GenerateAccelerators;
QWidget *m_ToolGUIWidget;
QmitkToolGUI *m_LastToolGUI;
// store buttons in this group
QButtonGroup *m_ToolButtonGroup;
QGridLayout *m_ButtonLayout;
EnabledMode m_EnabledMode;
};
#endif
diff --git a/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUI.cpp
index a6f7763f5c..41c3151292 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUI.cpp
+++ b/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUI.cpp
@@ -1,150 +1,199 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "QmitkWatershedToolGUI.h"
-#include "QmitkNewSegmentationDialog.h"
-#include "mitkProgressBar.h"
-
-#include <qapplication.h>
-#include <qlabel.h>
-#include <qlayout.h>
-#include <qpainter.h>
-#include <qpushbutton.h>
-#include <qslider.h>
+#include <QMessageBox>
MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitkWatershedToolGUI, "")
-QmitkWatershedToolGUI::QmitkWatershedToolGUI() : QmitkToolGUI(), m_SliderThreshold(nullptr), m_SliderLevel(nullptr)
+QmitkWatershedToolGUI::QmitkWatershedToolGUI() : QmitkToolGUI()
{
- // create the visible widgets
- QGridLayout *layout = new QGridLayout(this);
- this->setContentsMargins(0, 0, 0, 0);
-
- QLabel *label = new QLabel("Threshold ", this);
- QFont f = label->font();
- f.setBold(false);
- label->setFont(f);
- layout->addWidget(label, 0, 0);
-
- QLabel *label2 = new QLabel("Level ", this);
- f = label2->font();
- f.setBold(false);
- label2->setFont(f);
- layout->addWidget(label2, 2, 0);
-
- m_ThresholdLabel = new QLabel(" 0.04", this);
- f = m_ThresholdLabel->font();
- f.setBold(false);
- m_ThresholdLabel->setFont(f);
- layout->addWidget(m_ThresholdLabel, 0, 1);
-
- m_SliderThreshold = new QSlider(Qt::Horizontal, this);
- m_SliderThreshold->setMinimum(0);
- m_SliderThreshold->setMaximum(100);
- m_SliderThreshold->setPageStep(1);
- m_SliderThreshold->setValue(4);
- connect(m_SliderThreshold, SIGNAL(valueChanged(int)), this, SLOT(OnSliderValueThresholdChanged(int)));
- layout->addWidget(m_SliderThreshold, 1, 0, 1, 2);
-
- m_LevelLabel = new QLabel(" 0.35", this);
- f = m_LevelLabel->font();
- f.setBold(false);
- m_LevelLabel->setFont(f);
- layout->addWidget(m_LevelLabel, 2, 1);
-
- m_SliderLevel = new QSlider(Qt::Horizontal, this);
- m_SliderLevel->setMinimum(0);
- m_SliderLevel->setMaximum(100);
- m_SliderLevel->setPageStep(1);
- m_SliderLevel->setValue(35);
- connect(m_SliderLevel, SIGNAL(valueChanged(int)), this, SLOT(OnSliderValueLevelChanged(int)));
- layout->addWidget(m_SliderLevel, 3, 0, 1, 2);
-
- QPushButton *okButton = new QPushButton("Run Segmentation", this);
- connect(okButton, SIGNAL(clicked()), this, SLOT(OnCreateSegmentation()));
- okButton->setFont(f);
- layout->addWidget(okButton, 4, 0, 1, 2);
-
- m_InformationLabel = new QLabel("", this);
- f = m_InformationLabel->font();
- f.setBold(false);
- m_InformationLabel->setFont(f);
- layout->addWidget(m_InformationLabel, 5, 0, 1, 2);
-
+ m_Controls.setupUi(this);
+
+ m_Controls.thresholdSlider->setMinimum(0);
+ //We set the threshold maximum to 0.5 to avoid crashes in the watershed filter
+ //see T27703 for more details.
+ m_Controls.thresholdSlider->setMaximum(0.5);
+ m_Controls.thresholdSlider->setValue(m_Threshold);
+ m_Controls.thresholdSlider->setPageStep(0.01);
+ m_Controls.thresholdSlider->setSingleStep(0.001);
+ m_Controls.thresholdSlider->setDecimals(4);
+
+ m_Controls.levelSlider->setMinimum(0);
+ m_Controls.levelSlider->setMaximum(1);
+ m_Controls.levelSlider->setValue(m_Level);
+ m_Controls.levelSlider->setPageStep(0.1);
+ m_Controls.levelSlider->setSingleStep(0.01);
+
+ connect(m_Controls.previewButton, SIGNAL(clicked()), this, SLOT(OnSettingsAccept()));
+ connect(m_Controls.m_selectionListWidget, &QmitkSimpleLabelSetListWidget::SelectedLabelsChanged, this, &QmitkWatershedToolGUI::OnRegionSelectionChanged);
+ connect(m_Controls.levelSlider, SIGNAL(valueChanged(double)), this, SLOT(OnLevelChanged(double)));
+ connect(m_Controls.thresholdSlider, SIGNAL(valueChanged(double)), this, SLOT(OnThresholdChanged(double)));
+ connect(m_Controls.m_ConfSegButton, SIGNAL(clicked()), this, SLOT(OnSegmentationRegionAccept()));
connect(this, SIGNAL(NewToolAssociated(mitk::Tool *)), this, SLOT(OnNewToolAssociated(mitk::Tool *)));
}
QmitkWatershedToolGUI::~QmitkWatershedToolGUI()
{
if (m_WatershedTool.IsNotNull())
{
- // m_WatershedTool->SizeChanged -= mitk::MessageDelegate1<QmitkWatershedToolGUI, int>( this,
- // &QmitkWatershedToolGUI::OnSizeChanged );
+ m_WatershedTool->CurrentlyBusy -=
+ mitk::MessageDelegate1<QmitkWatershedToolGUI, bool>(this, &QmitkWatershedToolGUI::BusyStateChanged);
+ }
+}
+
+void QmitkWatershedToolGUI::OnRegionSelectionChanged(const QmitkSimpleLabelSetListWidget::LabelVectorType& selectedLabels)
+{
+ if (m_WatershedTool.IsNotNull())
+ {
+ mitk::AutoMLSegmentationWithPreviewTool::SelectedLabelVectorType labelIDs;
+ for (const auto& label : selectedLabels)
+ {
+ labelIDs.push_back(label->GetValue());
+ }
+
+ m_WatershedTool->SetSelectedLabels(labelIDs);
+ m_WatershedTool->UpdatePreview();
+
+ m_Controls.m_ConfSegButton->setEnabled(!labelIDs.empty());
}
}
void QmitkWatershedToolGUI::OnNewToolAssociated(mitk::Tool *tool)
{
if (m_WatershedTool.IsNotNull())
{
- // m_WatershedTool->SizeChanged -= mitk::MessageDelegate1<QmitkWatershedToolGUI, int>( this,
- // &QmitkWatershedToolGUI::OnSizeChanged );
+ m_WatershedTool->CurrentlyBusy -=
+ mitk::MessageDelegate1<QmitkWatershedToolGUI, bool>(this, &QmitkWatershedToolGUI::BusyStateChanged);
}
m_WatershedTool = dynamic_cast<mitk::WatershedTool *>(tool);
- OnSliderValueLevelChanged(35);
- OnSliderValueThresholdChanged(4);
if (m_WatershedTool.IsNotNull())
{
- // m_WatershedTool->SizeChanged += mitk::MessageDelegate1<QmitkWatershedToolGUI, int>( this,
- // &QmitkWatershedToolGUI::OnSizeChanged );
+ m_WatershedTool->CurrentlyBusy +=
+ mitk::MessageDelegate1<QmitkWatershedToolGUI, bool>(this, &QmitkWatershedToolGUI::BusyStateChanged);
+
+ m_WatershedTool->SetLevel(m_Level);
+ m_WatershedTool->SetThreshold(m_Threshold);
+
+ m_WatershedTool->SetOverwriteExistingSegmentation(true);
+ m_WatershedTool->IsTimePointChangeAwareOff();
+ m_Controls.m_CheckProcessAll->setVisible(m_WatershedTool->GetTargetSegmentationNode()->GetData()->GetTimeSteps() > 1);
}
}
-void QmitkWatershedToolGUI::OnSliderValueThresholdChanged(int value)
+void QmitkWatershedToolGUI::OnSegmentationRegionAccept()
{
+ QString segName = QString::fromStdString(m_WatershedTool->GetCurrentSegmentationName());
+
if (m_WatershedTool.IsNotNull())
{
- double realValue = value / 100.;
- m_WatershedTool->SetThreshold(realValue);
- m_ThresholdLabel->setText(QString::number(realValue));
+ if (this->m_Controls.m_CheckCreateNew->isChecked())
+ {
+ m_WatershedTool->SetOverwriteExistingSegmentation(false);
+ }
+ else
+ {
+ m_WatershedTool->SetOverwriteExistingSegmentation(true);
+ }
+
+ m_WatershedTool->SetCreateAllTimeSteps(this->m_Controls.m_CheckProcessAll->isChecked());
+
+ this->m_Controls.m_ConfSegButton->setEnabled(false);
+ m_WatershedTool->ConfirmSegmentation();
}
}
-void QmitkWatershedToolGUI::OnSliderValueLevelChanged(int value)
+void QmitkWatershedToolGUI::OnSettingsAccept()
{
if (m_WatershedTool.IsNotNull())
{
- double realValue = value / 100.;
- m_WatershedTool->SetLevel(realValue);
- m_LevelLabel->setText(QString::number(realValue));
+ try
+ {
+ m_Threshold = m_Controls.thresholdSlider->value();
+ m_Level = m_Controls.levelSlider->value();
+ m_WatershedTool->SetThreshold(m_Threshold);
+ m_WatershedTool->SetLevel(m_Level);
+
+ m_WatershedTool->UpdatePreview();
+ }
+ catch (const std::exception& e)
+ {
+ this->setCursor(Qt::ArrowCursor);
+ std::stringstream stream;
+ stream << "Error while generation watershed segmentation. Reason: " << e.what();
+
+ QMessageBox* messageBox =
+ new QMessageBox(QMessageBox::Critical,
+ nullptr, stream.str().c_str());
+ messageBox->exec();
+ delete messageBox;
+ MITK_ERROR << stream.str();
+ return;
+ }
+ catch (...)
+ {
+ this->setCursor(Qt::ArrowCursor);
+ std::stringstream stream;
+ stream << "Unkown error occured while generation watershed segmentation.";
+
+ QMessageBox* messageBox =
+ new QMessageBox(QMessageBox::Critical,
+ nullptr, stream.str().c_str());
+ messageBox->exec();
+ delete messageBox;
+ MITK_ERROR << stream.str();
+ return;
+ }
+
+ m_Controls.m_selectionListWidget->SetLabelSetImage(m_WatershedTool->GetMLPreview());
+ m_WatershedTool->IsTimePointChangeAwareOn();
}
}
-void QmitkWatershedToolGUI::OnCreateSegmentation()
+void QmitkWatershedToolGUI::BusyStateChanged(bool value)
{
- QApplication::setOverrideCursor(Qt::BusyCursor);
- m_InformationLabel->setText(QString("Please wait some time for computation..."));
- m_InformationLabel->repaint();
- QApplication::processEvents();
+ if (value)
+ {
+ QApplication::setOverrideCursor(QCursor(Qt::BusyCursor));
+ }
+ else
+ {
+ QApplication::restoreOverrideCursor();
+ }
- m_WatershedTool->DoIt();
- m_InformationLabel->setText(QString(""));
- QApplication::setOverrideCursor(Qt::ArrowCursor);
+ m_Controls.levelSlider->setEnabled(!value);
+ m_Controls.thresholdSlider->setEnabled(!value);
+ m_Controls.m_ConfSegButton->setEnabled(!m_WatershedTool->GetSelectedLabels().empty() && !value);
+ m_Controls.m_CheckProcessAll->setEnabled(!value);
+ m_Controls.m_CheckCreateNew->setEnabled(!value);
+ m_Controls.previewButton->setEnabled(!value);
+}
- for (int i = 0; i < 60; ++i)
+
+void QmitkWatershedToolGUI::OnLevelChanged(double value)
+{
+ if (m_WatershedTool.IsNotNull())
+ {
+ m_WatershedTool->SetLevel(value);
+ }
+}
+
+void QmitkWatershedToolGUI::OnThresholdChanged(double value)
+{
+ if (m_WatershedTool.IsNotNull())
{
- mitk::ProgressBar::GetInstance()->Progress();
+ m_WatershedTool->SetThreshold(value);
}
}
diff --git a/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUI.h b/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUI.h
index 23c40cab24..c5b8bbe5f1 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUI.h
+++ b/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUI.h
@@ -1,72 +1,71 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef QmitkWatershedToolGUI_h_Included
#define QmitkWatershedToolGUI_h_Included
#include "QmitkToolGUI.h"
#include "mitkWatershedTool.h"
-#include <MitkSegmentationUIExports.h>
-class QSlider;
-class QLabel;
-class QFrame;
+#include "ui_QmitkWatershedToolGUIControls.h"
+
+#include <MitkSegmentationUIExports.h>
/**
\ingroup org_mitk_gui_qt_interactivesegmentation_internal
\brief GUI for mitk::WatershedTool.
\sa mitk::WatershedTool
This GUI shows two sliders to change the watershed parameters. It executes the watershed algorithm by clicking on the
button.
*/
class MITKSEGMENTATIONUI_EXPORT QmitkWatershedToolGUI : public QmitkToolGUI
{
Q_OBJECT
public:
mitkClassMacro(QmitkWatershedToolGUI, QmitkToolGUI);
itkFactorylessNewMacro(Self);
itkCloneMacro(Self);
- protected slots :
+protected slots :
+
+ void OnNewToolAssociated(mitk::Tool *);
- void OnNewToolAssociated(mitk::Tool *);
+ void OnSettingsAccept();
- /** \brief Passes the chosen threshold value directly to the watershed tool */
- void OnSliderValueThresholdChanged(int value);
- /** \brief Passes the chosen level value directly to the watershed tool */
- void OnSliderValueLevelChanged(int value);
- /** \brief Starts segmentation algorithm in the watershed tool */
- void OnCreateSegmentation();
+ void OnSegmentationRegionAccept();
+
+ void OnRegionSelectionChanged(const QmitkSimpleLabelSetListWidget::LabelVectorType& selectedLabels);
+
+ void OnLevelChanged(double value);
+ void OnThresholdChanged(double value);
protected:
QmitkWatershedToolGUI();
~QmitkWatershedToolGUI() override;
- QSlider *m_SliderThreshold;
- QSlider *m_SliderLevel;
-
- /** \brief Label showing the current threshold value. */
- QLabel *m_ThresholdLabel;
- /** \brief Label showing the current level value. */
- QLabel *m_LevelLabel;
- /** \brief Label showing additional informations. */
- QLabel *m_InformationLabel;
+ void BusyStateChanged(bool value) override;
- QFrame *m_Frame;
+ //Recommendation from ITK is to have a threshold:level ration around 1:100
+ //we set Level a bit higher. This provokes more oversegmentation,
+ //but produces less objects in the first run and profits form the fact that
+ //decreasing level is quite fast in the filter.
+ double m_Level = 0.6;
+ double m_Threshold = 0.004;
+ Ui_QmitkWatershedToolGUIControls m_Controls;
mitk::WatershedTool::Pointer m_WatershedTool;
};
#endif
diff --git a/Modules/SegmentationUI/Qmitk/QmitkOtsuToolWidgetControls.ui b/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUIControls.ui
similarity index 52%
copy from Modules/SegmentationUI/Qmitk/QmitkOtsuToolWidgetControls.ui
copy to Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUIControls.ui
index 27e1d87ff8..4c4931c08a 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkOtsuToolWidgetControls.ui
+++ b/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUIControls.ui
@@ -1,234 +1,160 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
- <class>QmitkOtsuToolWidgetControls</class>
- <widget class="QWidget" name="QmitkOtsuToolWidgetControls">
+ <class>QmitkWatershedToolGUIControls</class>
+ <widget class="QWidget" name="QmitkWatershedToolGUIControls">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>192</width>
- <height>300</height>
+ <height>352</height>
</rect>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Ignored" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>100</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>100000</width>
<height>100000</height>
</size>
</property>
<property name="windowTitle">
<string>QmitkOtsuToolWidget</string>
</property>
- <property name="toolTip">
- <string>Move to adjust the segmentation</string>
- </property>
<layout class="QVBoxLayout" name="verticalLayout">
<item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <property name="sizeConstraint">
- <enum>QLayout::SetNoConstraint</enum>
- </property>
- <item>
- <widget class="QLabel" name="numberOfRegionsLabel">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Ignored" vsizetype="Minimum">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
+ <layout class="QGridLayout" name="advancedSettingsLayout">
+ <item row="1" column="0">
+ <widget class="QLabel" name="levelLabel">
<property name="text">
- <string>Number of Regions:</string>
+ <string>Level:</string>
</property>
</widget>
</item>
- <item>
- <widget class="QSpinBox" name="m_Spinbox">
+ <item row="0" column="0">
+ <widget class="QLabel" name="thresholdLabel">
<property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Minimum">
+ <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
- <property name="maximumSize">
- <size>
- <width>40</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="minimum">
- <number>2</number>
- </property>
- <property name="maximum">
- <number>32</number>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="ctkExpandButton" name="advancedSettingsButton">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>32</height>
- </size>
- </property>
- <property name="text">
- <string>Advanced settings</string>
- </property>
- <property name="toolButtonStyle">
- <enum>Qt::ToolButtonTextBesideIcon</enum>
- </property>
- <property name="mirrorOnExpand" stdset="0">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QGridLayout" name="advancedSettingsLayout">
- <item row="0" column="0">
- <widget class="QCheckBox" name="m_ValleyCheckbox">
<property name="text">
- <string>Use Valley Emphasis</string>
+ <string>Threshold:</string>
</property>
</widget>
</item>
- <item row="1" column="0">
- <widget class="QLabel" name="binLabel">
- <property name="text">
- <string>Number of Histogram Bins:</string>
- </property>
- </widget>
+ <item row="0" column="1">
+ <widget class="ctkSliderWidget" name="thresholdSlider" native="true"/>
</item>
<item row="1" column="1">
- <widget class="QSpinBox" name="m_BinsSpinBox">
- <property name="minimum">
- <number>2</number>
- </property>
- <property name="maximum">
- <number>4096</number>
- </property>
- <property name="value">
- <number>128</number>
- </property>
- </widget>
+ <widget class="ctkSliderWidget" name="levelSlider" native="true"/>
</item>
</layout>
</item>
<item>
- <widget class="QListWidget" name="m_selectionListWidget">
+ <widget class="QmitkSimpleLabelSetListWidget" name="m_selectionListWidget" native="true">
<property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Minimum">
+ <sizepolicy hsizetype="Minimum" vsizetype="MinimumExpanding">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="maximumSize">
<size>
<width>10000000</width>
- <height>100</height>
+ <height>10000000</height>
</size>
</property>
- <property name="autoScrollMargin">
- <number>0</number>
- </property>
- <property name="selectionMode">
- <enum>QAbstractItemView::MultiSelection</enum>
- </property>
- <property name="resizeMode">
- <enum>QListView::Adjust</enum>
- </property>
</widget>
</item>
<item>
<widget class="QPushButton" name="previewButton">
<property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Minimum">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="maximumSize">
<size>
<width>100000</width>
<height>16777215</height>
</size>
</property>
<property name="text">
<string>Preview</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="m_ConfSegButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Minimum">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="maximumSize">
<size>
<width>100000</width>
<height>16777215</height>
</size>
</property>
<property name="text">
<string>Confirm Segmentation</string>
</property>
</widget>
</item>
<item>
<widget class="QCheckBox" name="m_CheckProcessAll">
<property name="toolTip">
<string>Process/overwrite all time steps of the dynamic segmentation and not just the currently visible time step.</string>
</property>
<property name="text">
<string>Process all time steps</string>
</property>
</widget>
</item>
<item>
<widget class="QCheckBox" name="m_CheckCreateNew">
<property name="toolTip">
<string>Add the confirmed segmentation as a new segmentation instead of overwriting the currently selected.</string>
</property>
<property name="text">
<string>Create as new segmentation</string>
</property>
</widget>
</item>
</layout>
</widget>
<layoutdefault spacing="6" margin="11"/>
<customwidgets>
<customwidget>
- <class>ctkExpandButton</class>
- <extends>QToolButton</extends>
- <header>ctkExpandButton.h</header>
+ <class>QmitkSimpleLabelSetListWidget</class>
+ <extends>QWidget</extends>
+ <header>QmitkSimpleLabelSetListWidget.h</header>
+ </customwidget>
+ <customwidget>
+ <class>ctkSliderWidget</class>
+ <extends>QWidget</extends>
+ <header location="global">ctkSliderWidget.h</header>
+ <container>1</container>
</customwidget>
</customwidgets>
<resources/>
<connections/>
</ui>
diff --git a/Modules/SegmentationUI/files.cmake b/Modules/SegmentationUI/files.cmake
index a7ba3f718d..d84231e8a4 100644
--- a/Modules/SegmentationUI/files.cmake
+++ b/Modules/SegmentationUI/files.cmake
@@ -1,81 +1,84 @@
set( CPP_FILES
Qmitk/QmitkAdaptiveRegionGrowingToolGUI.cpp
Qmitk/QmitkBinaryThresholdToolGUI.cpp
Qmitk/QmitkBinaryThresholdULToolGUI.cpp
Qmitk/QmitkCalculateGrayValueStatisticsToolGUI.cpp
Qmitk/QmitkConfirmSegmentationDialog.cpp
Qmitk/QmitkCopyToClipBoardDialog.cpp
Qmitk/QmitkDrawPaintbrushToolGUI.cpp
Qmitk/QmitkErasePaintbrushToolGUI.cpp
Qmitk/QmitkFastMarchingTool3DGUI.cpp
Qmitk/QmitkFastMarchingToolGUI.cpp
Qmitk/QmitkLiveWireTool2DGUI.cpp
Qmitk/QmitkNewSegmentationDialog.cpp
Qmitk/QmitkOtsuTool3DGUI.cpp
Qmitk/QmitkPaintbrushToolGUI.cpp
Qmitk/QmitkPickingToolGUI.cpp
Qmitk/QmitkPixelManipulationToolGUI.cpp
Qmitk/QmitkSlicesInterpolator.cpp
Qmitk/QmitkToolGUI.cpp
Qmitk/QmitkToolGUIArea.cpp
Qmitk/QmitkToolSelectionBox.cpp
Qmitk/QmitkWatershedToolGUI.cpp
#Added from ML
Qmitk/QmitkLabelSetWidget.cpp
Qmitk/QmitkSurfaceStampWidget.cpp
Qmitk/QmitkMaskStampWidget.cpp
Qmitk/QmitkSliceBasedInterpolatorWidget.cpp
Qmitk/QmitkSurfaceBasedInterpolatorWidget.cpp
Qmitk/QmitkSearchLabelDialog.cpp
+Qmitk/QmitkSimpleLabelSetListWidget.cpp
)
set(MOC_H_FILES
Qmitk/QmitkAdaptiveRegionGrowingToolGUI.h
Qmitk/QmitkBinaryThresholdToolGUI.h
Qmitk/QmitkBinaryThresholdULToolGUI.h
Qmitk/QmitkCalculateGrayValueStatisticsToolGUI.h
Qmitk/QmitkConfirmSegmentationDialog.h
Qmitk/QmitkCopyToClipBoardDialog.h
Qmitk/QmitkDrawPaintbrushToolGUI.h
Qmitk/QmitkErasePaintbrushToolGUI.h
Qmitk/QmitkFastMarchingTool3DGUI.h
Qmitk/QmitkFastMarchingToolGUI.h
Qmitk/QmitkLiveWireTool2DGUI.h
Qmitk/QmitkNewSegmentationDialog.h
Qmitk/QmitkOtsuTool3DGUI.h
Qmitk/QmitkPaintbrushToolGUI.h
Qmitk/QmitkPickingToolGUI.h
Qmitk/QmitkPixelManipulationToolGUI.h
Qmitk/QmitkSlicesInterpolator.h
Qmitk/QmitkToolGUI.h
Qmitk/QmitkToolGUIArea.h
Qmitk/QmitkToolSelectionBox.h
Qmitk/QmitkWatershedToolGUI.h
#Added from ML
Qmitk/QmitkLabelSetWidget.h
Qmitk/QmitkSurfaceStampWidget.h
Qmitk/QmitkMaskStampWidget.h
Qmitk/QmitkSliceBasedInterpolatorWidget.h
Qmitk/QmitkSurfaceBasedInterpolatorWidget.h
Qmitk/QmitkSearchLabelDialog.h
+Qmitk/QmitkSimpleLabelSetListWidget.h
)
set(UI_FILES
Qmitk/QmitkAdaptiveRegionGrowingToolGUIControls.ui
Qmitk/QmitkConfirmSegmentationDialog.ui
Qmitk/QmitkOtsuToolWidgetControls.ui
Qmitk/QmitkPickingToolGUIControls.ui
Qmitk/QmitkLiveWireTool2DGUIControls.ui
+Qmitk/QmitkWatershedToolGUIControls.ui
#Added from ML
Qmitk/QmitkLabelSetWidgetControls.ui
Qmitk/QmitkSurfaceStampWidgetGUIControls.ui
Qmitk/QmitkMaskStampWidgetGUIControls.ui
Qmitk/QmitkSliceBasedInterpolatorWidgetGUIControls.ui
Qmitk/QmitkSurfaceBasedInterpolatorWidgetGUIControls.ui
Qmitk/QmitkSearchLabelDialogGUI.ui
)
set(QRC_FILES
resources/SegmentationUI.qrc
)
diff --git a/Modules/ToFHardware/CMakeLists.txt b/Modules/ToFHardware/CMakeLists.txt
index 45414ffffe..3c591fa061 100644
--- a/Modules/ToFHardware/CMakeLists.txt
+++ b/Modules/ToFHardware/CMakeLists.txt
@@ -1,33 +1,32 @@
#Define the platform string
mitkMacroGetPMDPlatformString(_PLATFORM_STRING)
MITK_CREATE_MODULE(
- SUBPROJECTS MITK-ToF
DEPENDS MitkOpenCVVideoSupport MitkIGTBase MitkCameraCalibration MitkIpPic
PACKAGE_DEPENDS ITK|ITKIONRRD
ADDITIONAL_LIBS ${ADDITIONAL_LIBS}
)
# set(tofHardware_srcs )
# usFunctionEmbedResources(tofHardware_srcs
# LIBRARY_NAME mitkToFHardware
# ROOT_DIR ${MITK_DATA_DIR}/ToF-Data/CalibrationFiles
# FILES Default_Parameters.xml Kinect_IR_camera.xml Kinect_RGB_camera.xml Mesa-SR4000_Camera.xml PMDCamBoard_camera.xml PMDCamCube2_camera.xml PMDCamCube3_camera.xml
# )
add_subdirectory(Testing)
add_subdirectory(Kinect)
add_subdirectory(KinectV2)
add_subdirectory(PMD)
add_subdirectory(MesaSR4000)
# Install external libraries which are not directly linked to a MITK module
include(${CMAKE_CURRENT_SOURCE_DIR}/mitkToFHardwareInstallRules.cmake)
CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/mitkToFHardwareInstallRules.cmake
${PROJECT_BINARY_DIR}/mitkToFHardwareInstallRules.cmake COPYONLY)
CONFIGURE_FILE(mitkToFConfig.h.in ${PROJECT_BINARY_DIR}/mitkToFConfig.h @ONLY)
#foreach(tofhardwaresubfolder_dir ${tofhardwaresubfolder_dirs})
# add_subdirectory(${tofhardwaresubfolder_dirs})
#endforeach()
diff --git a/Modules/ToFHardware/Kinect/CMakeLists.txt b/Modules/ToFHardware/Kinect/CMakeLists.txt
index e4342230e2..a7c5376a0c 100644
--- a/Modules/ToFHardware/Kinect/CMakeLists.txt
+++ b/Modules/ToFHardware/Kinect/CMakeLists.txt
@@ -1,26 +1,25 @@
#Begin Kinect hardware
OPTION(MITK_USE_TOF_KINECT "Enable support for Kinect camera" OFF)
IF(MITK_USE_TOF_KINECT)
mitkFunctionCheckCompilerFlags("-Wno-error=unknown-pragmas" CMAKE_CXX_FLAGS)
mitkFunctionCheckCompilerFlags("-Wno-error=reorder" CMAKE_CXX_FLAGS)
FIND_LIBRARY(MITK_KINECT_LIB libOpenNI DOC "Kinect access library.")
FIND_PATH(MITK_KINECT_INCLUDE_DIR XnCppWrapper.h DOC "Include directory of Kinect camera.")
SET(MITK_TOF_AVAILABLE_CAMERAS ${MITK_TOF_AVAILABLE_CAMERAS},Microsoft Kinect)
SET(INCLUDE_DIRS_INTERNAL ${INCLUDE_DIRS_INTERNAL} ${MITK_KINECT_INCLUDE_DIR})
SET(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_KINECT_LIB})
MITK_CREATE_MODULE(
- SUBPROJECTS MITK-ToF
INCLUDE_DIRS
PUBLIC ${MITK_BIN_DIR}
PRIVATE ${INCLUDE_DIRS_INTERNAL}
DEPENDS MitkToFHardware
ADDITIONAL_LIBS ${ADDITIONAL_LIBS}
AUTOLOAD_WITH MitkToFHardware
)
Message("Kinect Module generated")
add_subdirectory(Testing)
ENDIF(MITK_USE_TOF_KINECT)
#End Kinect Hardware
diff --git a/Modules/ToFHardware/KinectV2/CMakeLists.txt b/Modules/ToFHardware/KinectV2/CMakeLists.txt
index e1b35b9d9f..fcfab10ee9 100644
--- a/Modules/ToFHardware/KinectV2/CMakeLists.txt
+++ b/Modules/ToFHardware/KinectV2/CMakeLists.txt
@@ -1,21 +1,20 @@
OPTION(MITK_USE_TOF_KINECTV2 "Enable support for Kinect V2 camera" OFF)
IF(MITK_USE_TOF_KINECTV2)
FIND_LIBRARY(MITK_KINECTV2_LIB KinectV20.lib DOC "Kinect V2 access library.")
FIND_PATH(MITK_KINECTV2_INCLUDE_DIR Kinect.h DOC "Include directory of Kinect V2 camera.")
SET(MITK_TOF_AVAILABLE_CAMERAS ${MITK_TOF_AVAILABLE_CAMERAS},Microsoft Kinect V2)
SET(INCLUDE_DIRS_INTERNAL ${INCLUDE_DIRS_INTERNAL} ${MITK_KINECTV2_INCLUDE_DIR})
SET(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_KINECTV2_LIB})
MITK_CREATE_MODULE(
- SUBPROJECTS MITK-ToF
INCLUDE_DIRS ${MITK_BIN_DIR}
INTERNAL_INCLUDE_DIRS ${INCLUDE_DIRS_INTERNAL}
DEPENDS MitkToFHardware MitkOpenCVVideoSupport
ADDITIONAL_LIBS ${ADDITIONAL_LIBS}
AUTOLOAD_WITH MitkToFHardware
)
Message("Kinect V2 Module generated")
add_subdirectory(Testing)
ENDIF(MITK_USE_TOF_KINECTV2)
diff --git a/Modules/ToFHardware/MesaSR4000/CMakeLists.txt b/Modules/ToFHardware/MesaSR4000/CMakeLists.txt
index fb5efc890c..80575d9ddd 100644
--- a/Modules/ToFHardware/MesaSR4000/CMakeLists.txt
+++ b/Modules/ToFHardware/MesaSR4000/CMakeLists.txt
@@ -1,28 +1,27 @@
#Begin MESA SR4000 hardware
OPTION(MITK_USE_TOF_MESASR4000 "Enable support for MESA SR4000" OFF)
IF(MITK_USE_TOF_MESASR4000)
FIND_LIBRARY(MITK_MESA_LIB libMesaSR DOC "MESA access library.")
GET_FILENAME_COMPONENT(MITK_MESA_SDK_DIR ${MITK_MESA_LIB} PATH)
SET(MITK_MESA_SDK_DIR ${MITK_MESA_SDK_DIR}/..)
FIND_PATH(MITK_MESA_INCLUDE_DIR libMesaSR.h ${MITK_MESA_SDK_DIR}/include DOC "Include directory of MESA-SDK.")
SET(MITK_TOF_AVAILABLE_CAMERAS ${MITK_TOF_AVAILABLE_CAMERAS},MESA Swissranger 4000)
IF(WIN32)
INSTALL(FILES ${MITK_MESA_SDK_DIR}/bin/libMesaSR.dll DESTINATION bin CONFIGURATIONS Release)
ENDIf(WIN32)
set(INCLUDE_DIRS_INTERNAL ${INCLUDE_DIRS_INTERNAL} ${MITK_MESA_SDK_DIR}/include)
set(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_MESA_LIB})
MITK_CREATE_MODULE(
- SUBPROJECTS MITK-ToF
INCLUDE_DIRS ${MITK_BIN_DIR}
INTERNAL_INCLUDE_DIRS ${INCLUDE_DIRS_INTERNAL}
DEPENDS MitkToFHardware
ADDITIONAL_LIBS ${ADDITIONAL_LIBS}
AUTOLOAD_WITH MitkToFHardware
)
Message("MESASR4000 Module generated")
add_subdirectory(Testing)
ENDIF(MITK_USE_TOF_MESASR4000)
#End MESA SR4000 Hardware
diff --git a/Modules/ToFHardware/PMD/CMakeLists.txt b/Modules/ToFHardware/PMD/CMakeLists.txt
index 0e2aaca2cd..baddf03e07 100644
--- a/Modules/ToFHardware/PMD/CMakeLists.txt
+++ b/Modules/ToFHardware/PMD/CMakeLists.txt
@@ -1,102 +1,101 @@
#Begin PMD Module
OPTION(MITK_USE_TOF_PMDCAMCUBE "Enable support for Cam Cube camera" OFF)
IF(WIN32)
IF(_PLATFORM_STRING MATCHES "W32")
OPTION(MITK_USE_TOF_PMDCAMBOARD "Enable support for PMD camboard" OFF)
ENDIF(_PLATFORM_STRING MATCHES "W32")
ElSE(WIN32)
OPTION(MITK_USE_TOF_PMDCAMBOARD "Enable support for PMD camboard" OFF)
ENDIF(WIN32)
IF(WIN32)
IF(_PLATFORM_STRING MATCHES "W32")
OPTION(MITK_USE_TOF_PMDO3 "Enable support for PMD O3" OFF)
ENDIF(_PLATFORM_STRING MATCHES "W32")
ENDIF(WIN32)
SET(MITK_USE_PMD OFF)
IF(MITK_USE_TOF_PMDO3 OR MITK_USE_TOF_PMDCAMCUBE OR MITK_USE_TOF_PMDCAMBOARD)
SET(MITK_USE_PMD ON)
ENDIF(MITK_USE_TOF_PMDO3 OR MITK_USE_TOF_PMDCAMCUBE OR MITK_USE_TOF_PMDCAMBOARD)
#Creating Basics for all PMD devices
IF(MITK_USE_PMD)
#-----Setting generall Path-----
FIND_LIBRARY(MITK_PMD_LIB pmdaccess2 DOC "PMD access library.")
GET_FILENAME_COMPONENT(MITK_PMD_SDK_DIR ${MITK_PMD_LIB} PATH)
SET(MITK_PMD_SDK_DIR ${MITK_PMD_SDK_DIR}/.. CACHE INTERNAL "PMD SDK directory")
FIND_PATH(MITK_PMD_INCLUDE_DIR pmdsdk2.h ${MITK_PMD_SDK_DIR}/include DOC "Include directory of PMD-SDK.")
Set(INCLUDE_DIRS_INTERNAL ${INCLUDE_DIRS_INTERNAL} ${MITK_PMD_SDK_DIR}/include)
Set(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_PMD_LIB})
#-----Creating the PMD-Module itself-----
MITK_CREATE_MODULE(
- SUBPROJECTS MITK-ToF
INCLUDE_DIRS ${MITK_BINARY_DIR}
INTERNAL_INCLUDE_DIRS ${INCLUDE_DIRS_INTERNAL}
DEPENDS MitkToFHardware
ADDITIONAL_LIBS ${ADDITIONAL_LIBS}
AUTOLOAD_WITH MitkToFHardware
)
Message("PMD Module generated")
add_subdirectory(Testing)
ENDIF(MITK_USE_PMD)
#Only for CamCube
IF(MITK_USE_TOF_PMDCAMCUBE)
# message(${MITK_BINARY_DIR})
# message(${MITK_PMD_SDK_DIR})
# message(${_PLATFORM_STRING})
configure_file(${MITK_PMD_SDK_DIR}/plugins/camcube3.${_PLATFORM_STRING}.pap ${MITK_BINARY_DIR}/bin/camcube3.${_PLATFORM_STRING}.pap COPYONLY)
configure_file(${MITK_PMD_SDK_DIR}/plugins/camcubeproc.${_PLATFORM_STRING}.ppp ${MITK_BINARY_DIR}/bin/camcubeproc.${_PLATFORM_STRING}.ppp COPYONLY)
IF(_PLATFORM_STRING MATCHES "W32")
configure_file(${MITK_PMD_SDK_DIR}/plugins/pmdfile.${_PLATFORM_STRING}.pcp ${MITK_BINARY_DIR}/bin/pmdfile.${_PLATFORM_STRING}.pap COPYONLY)
ENDIF()
SET(MITK_TOF_PMD_CAMCUBE_SOURCE camcube3.${_PLATFORM_STRING}.pap)
SET(MITK_TOF_PMD_CAMCUBE_PROC camcubeproc.${_PLATFORM_STRING}.ppp)
IF(_PLATFORM_STRING MATCHES "W32")
SET(MITK_TOF_PMD_FILE_SOURCE pmdfile.${_PLATFORM_STRING}.pcp)
ENDIF()
SET(MITK_TOF_AVAILABLE_CAMERAS ${MITK_TOF_AVAILABLE_CAMERAS},PMD CamCube 2.0/3.0,PMD CamCubeRaw 2.0/3.0,PMD Player,PMD Raw Data Player)
Message("PMDCamCube activated")
ENDIF(MITK_USE_TOF_PMDCAMCUBE)
#-------------------------------Begin CamBoard hardware-------------------------------------------
IF(MITK_USE_TOF_PMDCAMBOARD)
IF(_PLATFORM_STRING MATCHES "W32")
configure_file(${MITK_PMD_SDK_DIR}/plugins/camboard.${_PLATFORM_STRING}.pap ${MITK_BINARY_DIR}/bin/camboard.${_PLATFORM_STRING}.pap COPYONLY)
configure_file(${MITK_PMD_SDK_DIR}/plugins/camboardproc.${_PLATFORM_STRING}.ppp ${MITK_BINARY_DIR}/bin/camboardproc.${_PLATFORM_STRING}.ppp COPYONLY)
ENDIF()
SET(MITK_TOF_PMD_CAMBOARD_SOURCE camboard.${_PLATFORM_STRING}.pap)
SET(MITK_TOF_PMD_CAMBOARD_PROC camboardproc.${_PLATFORM_STRING}.ppp)
SET(MITK_TOF_AVAILABLE_CAMERAS ${MITK_TOF_AVAILABLE_CAMERAS},PMD CamBoard,PMD CamBoardRaw)
# FILE(GLOB MITK_TOF_PMD_CAMBOARD_SOURCE camboard.${_PLATFORM_STRING}.pap)
# FILE(GLOB MITK_TOF_PMD_CAMBOARD_PROC camboardproc.${_PLATFORM_STRING}.ppp)
# FILE(GLOB MITK_TOF_PMD_FILE_SOURCE ${MITK_PMD_SDK_DIR}/plugins/pmdfile.${_PLATFORM_STRING}.pcp)
Message("PMDCamBoard activated")
ENDIF(MITK_USE_TOF_PMDCAMBOARD)
#----------------------------------------Begin PMD O3 hardware--------------------------------------------
# only if PMD O3 is enabled
IF(WIN32 AND MITK_USE_TOF_PMDO3)
Message("PMDO3 is activated")
configure_file(${MITK_PMD_SDK_DIR}/plugins/o3d.${_PLATFORM_STRING}.pcp ${MITK_BINARY_DIR}/bin/o3d.${_PLATFORM_STRING}.pcp COPYONLY)
configure_file(${MITK_PMD_SDK_DIR}/plugins/o3d.${_PLATFORM_STRING}.pcp ${MITK_BINARY_DIR}/bin/o3d.${_PLATFORM_STRING}.pcp COPYONLY)
SET(MITK_TOF_PMD_O3D_SOURCE o3d.${_PLATFORM_STRING}.pcp)
SET(MITK_TOF_PMD_O3D_PROC o3d.${_PLATFORM_STRING}.pcp)
SET(MITK_TOF_AVAILABLE_CAMERAS ${MITK_TOF_AVAILABLE_CAMERAS},PMD O3D)
ENDIF()
#Generate the mitkToFPMDConfig.h file which is used internally
CONFIGURE_FILE(mitkToFPMDConfig.h.in ${PROJECT_BINARY_DIR}/mitkToFPMDConfig.h @ONLY)
diff --git a/Modules/ToFProcessing/CMakeLists.txt b/Modules/ToFProcessing/CMakeLists.txt
index 51c57e409b..5e2e9cc973 100644
--- a/Modules/ToFProcessing/CMakeLists.txt
+++ b/Modules/ToFProcessing/CMakeLists.txt
@@ -1,13 +1,12 @@
MITK_CREATE_MODULE(
- SUBPROJECTS MITK-ToF
DEPENDS MitkCameraCalibration
PACKAGE_DEPENDS OpenCV
WARNINGS_NO_ERRORS
)
if(BUILD_TESTING)
add_subdirectory(Testing)
endif(BUILD_TESTING)
diff --git a/Modules/ToFUI/CMakeLists.txt b/Modules/ToFUI/CMakeLists.txt
index 2eaf906d34..c625537b6a 100644
--- a/Modules/ToFUI/CMakeLists.txt
+++ b/Modules/ToFUI/CMakeLists.txt
@@ -1,7 +1,6 @@
MITK_CREATE_MODULE(
- SUBPROJECTS MITK-ToF
INCLUDE_DIRS Qmitk
DEPENDS MitkToFHardware MitkToFProcessing MitkQtWidgetsExt
PACKAGE_DEPENDS CTK|CTKWidgets
)
diff --git a/Plugins/org.blueberry.ui.qt.log/documentation/UserManual/blueberrylogview.dox b/Plugins/org.blueberry.ui.qt.log/documentation/UserManual/blueberrylogview.dox
index 34290412a6..4f4fa8fde2 100644
--- a/Plugins/org.blueberry.ui.qt.log/documentation/UserManual/blueberrylogview.dox
+++ b/Plugins/org.blueberry.ui.qt.log/documentation/UserManual/blueberrylogview.dox
@@ -1,16 +1,16 @@
/**
-\page org_blueberry_ui_qt_log The Logging Plugin
+\page org_blueberry_views_logview The Logging Plugin
\imageMacro{logging.svg,"Icon of the Logging Plugin",2.00}
-This plug-in records all logging output of events and progress as specified in the source code with time of occurence, level of importance (Info, Warning, Error, Fatal, Debug), the message given and where it happens. The logging starts once the plug-is started. A screenshot of the provided Logging view is shown next.
+This plug-in records all logging output of events and progress as specified in the source code with time of occurrence, level of importance (Info, Warning, Error, Fatal, Debug), the message given and the origin of the message (source code section).
-\imageMacro{LogView.png,"Screenshot of the Logging Module",16.00}
+\imageMacro{LogView.png,"Screenshot of the Logging Plugin",16.00}
-There are different features available in the view. The "Filter" text field allows for searching all log events containing a certain substring. Using the button "Copy to clipboard" on the bottom right you can copy the current content of the logging view to your clipboard. This enables you to insert the logging information to any text processing application.
+There are different features available in the view. The 'Filter' text field provides the possibility to search for all log events containing a certain substring. The 'Copy to clipboard' button allows you to copy the current content of the logging view to your clipboard. This enables you to insert the logging information to any text processing application.
-You can also show more information on every logging message by activating the two checkboxes. In the simple view, leaving both checkboxes unchecked, you'll see logging messages and logging levels. A brief description of the logging levels can be found in the \ref LoggingPage "logging concept documentation". The checkbox "Categories" adds a column for the category. The checkbox "Advanced Fields" shows method, filename and linenumber where the logging message was emitted as well as the running time of the application. The next figure shows all information which can be shown in the Logging Module.
+In the simple logging view, you'll see logging messages and logging levels. A brief description of the logging levels can be found in the \ref LoggingPage "logging concept documentation". With two checkboxes more information on every logging message can be activated. The checkbox 'categories' adds a column for the category. The checkbox 'advanced fields' additionally displays the time from application start to the log message entry and the function, filename and line number of the logging message origin.
\imageMacro{LogViewExplain.png,"Details on the Vizualized Logging Information",16.00}
*/
diff --git a/Plugins/org.mitk.core.services/CMakeLists.txt b/Plugins/org.mitk.core.services/CMakeLists.txt
index ab0342e947..b490a1a9cb 100644
--- a/Plugins/org.mitk.core.services/CMakeLists.txt
+++ b/Plugins/org.mitk.core.services/CMakeLists.txt
@@ -1,8 +1,7 @@
project(org_mitk_core_services)
mitk_create_plugin(
EXPORT_DIRECTIVE MITK_CORE_SERVICES_PLUGIN
EXPORTED_INCLUDE_SUFFIXES src
- SUBPROJECTS MITK-CoreUI
MODULE_DEPENDS PUBLIC MitkCore
)
diff --git a/Plugins/org.mitk.gui.common/CMakeLists.txt b/Plugins/org.mitk.gui.common/CMakeLists.txt
index 4708013faa..3c3fcd88a7 100644
--- a/Plugins/org.mitk.gui.common/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.common/CMakeLists.txt
@@ -1,9 +1,8 @@
project(org_mitk_gui_common)
mitk_create_plugin(
EXPORT_DIRECTIVE MITK_GUI_COMMON_PLUGIN
EXPORTED_INCLUDE_SUFFIXES src
MODULE_DEPENDS MitkQtWidgets
- SUBPROJECTS MITK-CoreUI
)
diff --git a/Plugins/org.mitk.gui.qt.application/CMakeLists.txt b/Plugins/org.mitk.gui.qt.application/CMakeLists.txt
index 04efa26bd0..5790187d9c 100644
--- a/Plugins/org.mitk.gui.qt.application/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.qt.application/CMakeLists.txt
@@ -1,9 +1,8 @@
project(org_mitk_gui_qt_application)
mitk_create_plugin(
EXPORT_DIRECTIVE MITK_QT_APP
EXPORTED_INCLUDE_SUFFIXES src
MODULE_DEPENDS MitkQtWidgets MitkQtWidgetsExt
PACKAGE_DEPENDS Qt5|OpenGL+Xml
- SUBPROJECTS MITK-CoreUI
)
diff --git a/Plugins/org.mitk.gui.qt.basicimageprocessing/src/internal/QmitkBasicImageProcessingView.cpp b/Plugins/org.mitk.gui.qt.basicimageprocessing/src/internal/QmitkBasicImageProcessingView.cpp
index 521b2da18a..1790e3da27 100644
--- a/Plugins/org.mitk.gui.qt.basicimageprocessing/src/internal/QmitkBasicImageProcessingView.cpp
+++ b/Plugins/org.mitk.gui.qt.basicimageprocessing/src/internal/QmitkBasicImageProcessingView.cpp
@@ -1,1427 +1,1345 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "QmitkBasicImageProcessingView.h"
// QT includes (GUI)
#include <qlabel.h>
#include <qspinbox.h>
#include <qpushbutton.h>
#include <qcheckbox.h>
#include <qgroupbox.h>
#include <qradiobutton.h>
#include <qmessagebox.h>
-// Berry includes (selection service)
-#include <berryISelectionService.h>
-#include <berryIWorkbenchWindow.h>
-
-// MITK includes (GUI)
-#include "QmitkDataNodeSelectionProvider.h"
-#include "mitkDataNodeObject.h"
-
// MITK includes (general)
#include <mitkNodePredicateDataType.h>
#include <mitkNodePredicateDimension.h>
-#include <mitkNodePredicateAnd.h>
+#include <mitkNodePredicateNot.h>
+#include <mitkNodePredicateOr.h>
+#include <mitkNodePredicateProperty.h>
#include <mitkImageTimeSelector.h>
#include <mitkVectorImageMapper2D.h>
#include <mitkProperties.h>
#include <mitkLevelWindowProperty.h>
#include <mitkImageStatisticsHolder.h>
// Includes for image casting between ITK and MITK
#include <mitkImageCast.h>
#include <mitkITKImageImport.h>
// ITK includes (general)
#include <itkVectorImage.h>
#include <itkImageFileWriter.h>
// Morphological Operations
#include <itkBinaryBallStructuringElement.h>
#include <itkGrayscaleDilateImageFilter.h>
#include <itkGrayscaleErodeImageFilter.h>
#include <itkGrayscaleMorphologicalOpeningImageFilter.h>
#include <itkGrayscaleMorphologicalClosingImageFilter.h>
// Smoothing
#include <itkMedianImageFilter.h>
#include <itkDiscreteGaussianImageFilter.h>
#include <itkTotalVariationDenoisingImageFilter.h>
// Threshold
#include <itkBinaryThresholdImageFilter.h>
// Inversion
#include <itkInvertIntensityImageFilter.h>
// Derivatives
#include <itkGradientMagnitudeRecursiveGaussianImageFilter.h>
#include <itkLaplacianImageFilter.h>
#include <itkSobelEdgeDetectionImageFilter.h>
// Resampling
#include <itkResampleImageFilter.h>
#include <itkNearestNeighborInterpolateImageFunction.h>
#include <itkBSplineInterpolateImageFunction.h>
#include <itkCastImageFilter.h>
#include <itkLinearInterpolateImageFunction.h>
// Image Arithmetics
#include <itkAddImageFilter.h>
#include <itkSubtractImageFilter.h>
#include <itkMultiplyImageFilter.h>
#include <itkDivideImageFilter.h>
// Boolean operations
#include <itkOrImageFilter.h>
#include <itkAndImageFilter.h>
#include <itkXorImageFilter.h>
// Flip Image
#include <itkFlipImageFilter.h>
#include <itkRescaleIntensityImageFilter.h>
#include <itkShiftScaleImageFilter.h>
-
// Convenient Definitions
typedef itk::Image<short, 3> ImageType;
typedef itk::Image<unsigned char, 3> SegmentationImageType;
typedef itk::Image<double, 3> DoubleImageType;
typedef itk::Image<itk::Vector<float,3>, 3> VectorImageType;
typedef itk::BinaryBallStructuringElement<ImageType::PixelType, 3> BallType;
typedef itk::GrayscaleDilateImageFilter<ImageType, ImageType, BallType> DilationFilterType;
typedef itk::GrayscaleErodeImageFilter<ImageType, ImageType, BallType> ErosionFilterType;
typedef itk::GrayscaleMorphologicalOpeningImageFilter<ImageType, ImageType, BallType> OpeningFilterType;
typedef itk::GrayscaleMorphologicalClosingImageFilter<ImageType, ImageType, BallType> ClosingFilterType;
typedef itk::MedianImageFilter< ImageType, ImageType > MedianFilterType;
typedef itk::DiscreteGaussianImageFilter< ImageType, ImageType> GaussianFilterType;
-typedef itk::TotalVariationDenoisingImageFilter<DoubleImageType, DoubleImageType> TotalVariationFilterType;
+typedef itk::TotalVariationDenoisingImageFilter<DoubleImageType, DoubleImageType> TotalVariationFilterType;
typedef itk::TotalVariationDenoisingImageFilter<VectorImageType, VectorImageType> VectorTotalVariationFilterType;
typedef itk::BinaryThresholdImageFilter< ImageType, ImageType > ThresholdFilterType;
typedef itk::InvertIntensityImageFilter< ImageType, ImageType > InversionFilterType;
typedef itk::GradientMagnitudeRecursiveGaussianImageFilter< ImageType, ImageType > GradientFilterType;
-typedef itk::LaplacianImageFilter< DoubleImageType, DoubleImageType > LaplacianFilterType;
-typedef itk::SobelEdgeDetectionImageFilter< DoubleImageType, DoubleImageType > SobelFilterType;
+typedef itk::LaplacianImageFilter< DoubleImageType, DoubleImageType > LaplacianFilterType;
+typedef itk::SobelEdgeDetectionImageFilter< DoubleImageType, DoubleImageType > SobelFilterType;
typedef itk::ResampleImageFilter< ImageType, ImageType > ResampleImageFilterType;
typedef itk::ResampleImageFilter< ImageType, ImageType > ResampleImageFilterType2;
-typedef itk::CastImageFilter< ImageType, DoubleImageType > ImagePTypeToFloatPTypeCasterType;
+typedef itk::CastImageFilter< ImageType, DoubleImageType > ImagePTypeToFloatPTypeCasterType;
typedef itk::AddImageFilter< ImageType, ImageType, ImageType > AddFilterType;
typedef itk::SubtractImageFilter< ImageType, ImageType, ImageType > SubtractFilterType;
typedef itk::MultiplyImageFilter< ImageType, ImageType, ImageType > MultiplyFilterType;
-typedef itk::DivideImageFilter< ImageType, ImageType, DoubleImageType > DivideFilterType;
+typedef itk::DivideImageFilter< ImageType, ImageType, DoubleImageType > DivideFilterType;
typedef itk::OrImageFilter< ImageType, ImageType > OrImageFilterType;
typedef itk::AndImageFilter< ImageType, ImageType > AndImageFilterType;
typedef itk::XorImageFilter< ImageType, ImageType > XorImageFilterType;
typedef itk::FlipImageFilter< ImageType > FlipImageFilterType;
typedef itk::LinearInterpolateImageFunction< ImageType, double > LinearInterpolatorType;
typedef itk::NearestNeighborInterpolateImageFunction< ImageType, double > NearestInterpolatorType;
+const std::string QmitkBasicImageProcessing::VIEW_ID = "org.mitk.views.basicimageprocessing";
QmitkBasicImageProcessing::QmitkBasicImageProcessing()
-: QmitkAbstractView(),
- m_Controls(nullptr),
- m_SelectedImageNode(nullptr),
- m_TimeStepperAdapter(nullptr)
+ : QmitkAbstractView()
+ , m_Controls(new Ui::QmitkBasicImageProcessingViewControls)
+ , m_TimeStepperAdapter(nullptr)
{
+ auto isImage = mitk::TNodePredicateDataType<mitk::Image>::New();
+ auto isNotHelperObject = mitk::NodePredicateNot::New(
+ mitk::NodePredicateProperty::New("helper object", mitk::BoolProperty::New(true)));
+ auto dimensionPredicate = mitk::NodePredicateOr::New(
+ mitk::NodePredicateDimension::New(3), mitk::NodePredicateDimension::New(4));
+
+ m_IsImagePredicate = mitk::NodePredicateAnd::New(
+ isImage, isNotHelperObject, dimensionPredicate);
}
QmitkBasicImageProcessing::~QmitkBasicImageProcessing()
{
- //berry::ISelectionService* s = GetSite()->GetWorkbenchWindow()->GetSelectionService();
- //if(s)
- // s->RemoveSelectionListener(m_SelectionListener);
+
}
void QmitkBasicImageProcessing::CreateQtPartControl(QWidget *parent)
{
- if (m_Controls == nullptr)
- {
- m_Controls = new Ui::QmitkBasicImageProcessingViewControls;
- m_Controls->setupUi(parent);
- this->CreateConnections();
-
+ m_Controls->setupUi(parent);
+
+ m_Controls->selectedImageWidget->SetDataStorage(this->GetDataStorage());
+ m_Controls->selectedImageWidget->SetNodePredicate(m_IsImagePredicate);
+ m_Controls->selectedImageWidget->SetSelectionIsOptional(true);
+ m_Controls->selectedImageWidget->SetAutoSelectNewNodes(true);
+ m_Controls->selectedImageWidget->SetEmptyInfo(QString("Please select a 3D / 4D image"));
+ m_Controls->selectedImageWidget->SetPopUpTitel(QString("Select an image"));
+
+ m_Controls->selectedImageWidget_2->SetDataStorage(this->GetDataStorage());
+ m_Controls->selectedImageWidget_2->SetNodePredicate(m_IsImagePredicate);
+ m_Controls->selectedImageWidget_2->SetSelectionIsOptional(true);
+ m_Controls->selectedImageWidget_2->SetAutoSelectNewNodes(true);
+ m_Controls->selectedImageWidget_2->SetEmptyInfo(QString("Please select a 3D / 4D image"));
+ m_Controls->selectedImageWidget_2->SetPopUpTitel(QString("Select an image"));
- //setup predictaes for combobox
-
- mitk::NodePredicateDimension::Pointer dimensionPredicate = mitk::NodePredicateDimension::New(3);
- mitk::NodePredicateDataType::Pointer imagePredicate = mitk::NodePredicateDataType::New("Image");
- m_Controls->m_ImageSelector2->SetDataStorage(this->GetDataStorage());
- m_Controls->m_ImageSelector2->SetPredicate(mitk::NodePredicateAnd::New(dimensionPredicate, imagePredicate));
- }
m_Controls->gbTwoImageOps->hide();
- m_SelectedImageNode = mitk::DataStorageSelection::New(this->GetDataStorage(), false);
-
- // Setup Controls
-
- this->m_Controls->cbWhat1->clear();
- this->m_Controls->cbWhat1->insertItem(NOACTIONSELECTED, "Please select operation");
- this->m_Controls->cbWhat1->insertItem(CATEGORY_DENOISING, "--- Denoising ---");
- this->m_Controls->cbWhat1->insertItem(GAUSSIAN, "Gaussian");
- this->m_Controls->cbWhat1->insertItem(MEDIAN, "Median");
- this->m_Controls->cbWhat1->insertItem(TOTALVARIATION, "Total Variation");
- this->m_Controls->cbWhat1->insertItem(CATEGORY_MORPHOLOGICAL, "--- Morphological ---");
- this->m_Controls->cbWhat1->insertItem(DILATION, "Dilation");
- this->m_Controls->cbWhat1->insertItem(EROSION, "Erosion");
- this->m_Controls->cbWhat1->insertItem(OPENING, "Opening");
- this->m_Controls->cbWhat1->insertItem(CLOSING, "Closing");
- this->m_Controls->cbWhat1->insertItem(CATEGORY_EDGE_DETECTION, "--- Edge Detection ---");
- this->m_Controls->cbWhat1->insertItem(GRADIENT, "Gradient");
- this->m_Controls->cbWhat1->insertItem(LAPLACIAN, "Laplacian (2nd Derivative)");
- this->m_Controls->cbWhat1->insertItem(SOBEL, "Sobel Operator");
- this->m_Controls->cbWhat1->insertItem(CATEGORY_MISC, "--- Misc ---");
- this->m_Controls->cbWhat1->insertItem(THRESHOLD, "Threshold");
- this->m_Controls->cbWhat1->insertItem(INVERSION, "Image Inversion");
- this->m_Controls->cbWhat1->insertItem(DOWNSAMPLING, "Downsampling");
- this->m_Controls->cbWhat1->insertItem(FLIPPING, "Flipping");
- this->m_Controls->cbWhat1->insertItem(RESAMPLING, "Resample to");
- this->m_Controls->cbWhat1->insertItem(RESCALE, "Rescale values to interval");
- this->m_Controls->cbWhat1->insertItem(RESCALE2, "Rescale values by scalar");
-
- this->m_Controls->cbWhat2->clear();
- this->m_Controls->cbWhat2->insertItem(TWOIMAGESNOACTIONSELECTED, "Please select on operation");
- this->m_Controls->cbWhat2->insertItem(CATEGORY_ARITHMETIC, "--- Arithmetric operations ---");
- this->m_Controls->cbWhat2->insertItem(ADD, "Add to Image 1:");
- this->m_Controls->cbWhat2->insertItem(SUBTRACT, "Subtract from Image 1:");
- this->m_Controls->cbWhat2->insertItem(MULTIPLY, "Multiply with Image 1:");
- this->m_Controls->cbWhat2->insertItem(RESAMPLE_TO, "Resample Image 1 to fit geometry:");
- this->m_Controls->cbWhat2->insertItem(DIVIDE, "Divide Image 1 by:");
- this->m_Controls->cbWhat2->insertItem(CATEGORY_BOOLEAN, "--- Boolean operations ---");
- this->m_Controls->cbWhat2->insertItem(AND, "AND");
- this->m_Controls->cbWhat2->insertItem(OR, "OR");
- this->m_Controls->cbWhat2->insertItem(XOR, "XOR");
-
- this->m_Controls->cbParam4->clear();
- this->m_Controls->cbParam4->insertItem(LINEAR, "Linear");
- this->m_Controls->cbParam4->insertItem(NEAREST, "Nearest neighbor");
+ m_Controls->cbWhat1->clear();
+ m_Controls->cbWhat1->insertItem(NOACTIONSELECTED, "Please select an operation");
+ m_Controls->cbWhat1->insertItem(CATEGORY_DENOISING, "--- Denoising ---");
+ m_Controls->cbWhat1->insertItem(GAUSSIAN, "Gaussian");
+ m_Controls->cbWhat1->insertItem(MEDIAN, "Median");
+ m_Controls->cbWhat1->insertItem(TOTALVARIATION, "Total Variation");
+ m_Controls->cbWhat1->insertItem(CATEGORY_MORPHOLOGICAL, "--- Morphological ---");
+ m_Controls->cbWhat1->insertItem(DILATION, "Dilation");
+ m_Controls->cbWhat1->insertItem(EROSION, "Erosion");
+ m_Controls->cbWhat1->insertItem(OPENING, "Opening");
+ m_Controls->cbWhat1->insertItem(CLOSING, "Closing");
+ m_Controls->cbWhat1->insertItem(CATEGORY_EDGE_DETECTION, "--- Edge Detection ---");
+ m_Controls->cbWhat1->insertItem(GRADIENT, "Gradient");
+ m_Controls->cbWhat1->insertItem(LAPLACIAN, "Laplacian (2nd Derivative)");
+ m_Controls->cbWhat1->insertItem(SOBEL, "Sobel Operator");
+ m_Controls->cbWhat1->insertItem(CATEGORY_MISC, "--- Misc ---");
+ m_Controls->cbWhat1->insertItem(THRESHOLD, "Threshold");
+ m_Controls->cbWhat1->insertItem(INVERSION, "Image Inversion");
+ m_Controls->cbWhat1->insertItem(DOWNSAMPLING, "Downsampling");
+ m_Controls->cbWhat1->insertItem(FLIPPING, "Flipping");
+ m_Controls->cbWhat1->insertItem(RESAMPLING, "Resample to");
+ m_Controls->cbWhat1->insertItem(RESCALE, "Rescale values to interval");
+ m_Controls->cbWhat1->insertItem(RESCALE2, "Rescale values by scalar");
+
+ m_Controls->cbWhat2->clear();
+ m_Controls->cbWhat2->insertItem(TWOIMAGESNOACTIONSELECTED, "Please select an operation");
+ m_Controls->cbWhat2->insertItem(CATEGORY_ARITHMETIC, "--- Arithmetric operations ---");
+ m_Controls->cbWhat2->insertItem(ADD, "Add to Image 1:");
+ m_Controls->cbWhat2->insertItem(SUBTRACT, "Subtract from Image 1:");
+ m_Controls->cbWhat2->insertItem(MULTIPLY, "Multiply with Image 1:");
+ m_Controls->cbWhat2->insertItem(RESAMPLE_TO, "Resample Image 1 to fit geometry:");
+ m_Controls->cbWhat2->insertItem(DIVIDE, "Divide Image 1 by:");
+ m_Controls->cbWhat2->insertItem(CATEGORY_BOOLEAN, "--- Boolean operations ---");
+ m_Controls->cbWhat2->insertItem(AND, "AND");
+ m_Controls->cbWhat2->insertItem(OR, "OR");
+ m_Controls->cbWhat2->insertItem(XOR, "XOR");
+
+ m_Controls->cbParam4->clear();
+ m_Controls->cbParam4->insertItem(LINEAR, "Linear");
+ m_Controls->cbParam4->insertItem(NEAREST, "Nearest neighbor");
m_Controls->dsbParam1->hide();
m_Controls->dsbParam2->hide();
m_Controls->dsbParam3->hide();
m_Controls->tlParam3->hide();
m_Controls->tlParam4->hide();
m_Controls->cbParam4->hide();
+
+ this->CreateConnections();
}
void QmitkBasicImageProcessing::CreateConnections()
{
- if ( m_Controls )
- {
- connect( (QObject*)(m_Controls->cbWhat1), SIGNAL( activated(int) ), this, SLOT( SelectAction(int) ) );
- connect( (QObject*)(m_Controls->btnDoIt), SIGNAL(clicked()),(QObject*) this, SLOT(StartButtonClicked()));
- connect( (QObject*)(m_Controls->cbWhat2), SIGNAL( activated(int) ), this, SLOT( SelectAction2(int) ) );
- connect( (QObject*)(m_Controls->btnDoIt2), SIGNAL(clicked()),(QObject*) this, SLOT(StartButton2Clicked()));
- connect( (QObject*)(m_Controls->rBOneImOp), SIGNAL( clicked() ), this, SLOT( ChangeGUI() ) );
- connect( (QObject*)(m_Controls->rBTwoImOp), SIGNAL( clicked() ), this, SLOT( ChangeGUI() ) );
- connect( (QObject*)(m_Controls->cbParam4), SIGNAL( activated(int) ), this, SLOT( SelectInterpolator(int) ) );
- }
+ connect(m_Controls->cbWhat1, QOverload<int>::of(&QComboBox::activated), this, &QmitkBasicImageProcessing::SelectAction);
+ connect(m_Controls->btnDoIt, &QPushButton::clicked, this, &QmitkBasicImageProcessing::StartButtonClicked);
+ connect(m_Controls->cbWhat2, QOverload<int>::of(&QComboBox::activated), this, &QmitkBasicImageProcessing::SelectAction2);
+ connect(m_Controls->btnDoIt2, &QPushButton::clicked, this, &QmitkBasicImageProcessing::StartButton2Clicked);
+ connect(m_Controls->rBOneImOp, &QRadioButton::clicked, this, &QmitkBasicImageProcessing::ChangeGUI);
+ connect(m_Controls->rBTwoImOp, &QRadioButton::clicked, this, &QmitkBasicImageProcessing::ChangeGUI);
+ connect(m_Controls->cbParam4, QOverload<int>::of(&QComboBox::activated), this, &QmitkBasicImageProcessing::SelectInterpolator);
+ connect(m_Controls->selectedImageWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged,
+ this, &QmitkBasicImageProcessing::OnCurrentSelectionChanged);
+ connect(m_Controls->selectedImageWidget_2, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged,
+ this, &QmitkBasicImageProcessing::OnCurrentSelectionChanged);
}
void QmitkBasicImageProcessing::InternalGetTimeNavigationController()
{
auto renwin_part = GetRenderWindowPart();
if( renwin_part != nullptr )
{
auto tnc = renwin_part->GetTimeNavigationController();
if( tnc != nullptr )
{
m_TimeStepperAdapter = new QmitkStepperAdapter((QObject*) m_Controls->sliceNavigatorTime, tnc->GetTime(), "sliceNavigatorTimeFromBIP");
}
}
}
void QmitkBasicImageProcessing::SetFocus()
{
m_Controls->rBOneImOp->setFocus();
}
-//datamanager selection changed
-void QmitkBasicImageProcessing::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList<mitk::DataNode::Pointer>& nodes)
+void QmitkBasicImageProcessing::OnCurrentSelectionChanged(const QList<mitk::DataNode::Pointer>& nodes)
{
- //any nodes there?
- if (!nodes.empty())
+ if (nodes.empty() || nodes.front().IsNull())
{
- // reset GUI
-// this->ResetOneImageOpPanel();
- m_Controls->sliceNavigatorTime->setEnabled(false);
- m_Controls->leImage1->setText(tr("Select an Image in Data Manager"));
- m_Controls->tlWhat1->setEnabled(false);
- m_Controls->cbWhat1->setEnabled(false);
- m_Controls->tlWhat2->setEnabled(false);
- m_Controls->cbWhat2->setEnabled(false);
-
- m_SelectedImageNode->RemoveAllNodes();
- //get the selected Node
- mitk::DataNode* _DataNode = nodes.front();
- *m_SelectedImageNode = _DataNode;
- //try to cast to image
- mitk::Image::Pointer tempImage = dynamic_cast<mitk::Image*>(m_SelectedImageNode->GetNode()->GetData());
-
- //no image
- if( tempImage.IsNull() || (tempImage->IsInitialized() == false) )
- {
- m_Controls->leImage1->setText(tr("Not an image."));
- return;
- }
-
- //2D image
- if( tempImage->GetDimension() < 3)
- {
- m_Controls->leImage1->setText(tr("2D images are not supported."));
- return;
- }
+ m_Controls->sliceNavigatorTime->setEnabled(false);
+ m_Controls->tlTime->setEnabled(false);
+ m_Controls->tlWhat1->setEnabled(false);
+ m_Controls->cbWhat1->setEnabled(false);
+ m_Controls->tlWhat2->setEnabled(false);
+ m_Controls->cbWhat2->setEnabled(false);
+ return;
+ }
- //image
- m_Controls->leImage1->setText(QString(m_SelectedImageNode->GetNode()->GetName().c_str()));
+ auto selectedImage = dynamic_cast<mitk::Image*>(nodes.front()->GetData());
+ if (nullptr == selectedImage)
+ {
+ return;
+ }
- // button coding
- if ( tempImage->GetDimension() > 3 )
- {
- // try to retrieve the TNC (for 4-D Processing )
- this->InternalGetTimeNavigationController();
+ if (selectedImage->GetDimension() > 3)
+ {
+ // try to retrieve the TNC (for 4-D Processing )
+ this->InternalGetTimeNavigationController();
- m_Controls->sliceNavigatorTime->setEnabled(true);
- m_Controls->tlTime->setEnabled(true);
- }
- m_Controls->tlWhat1->setEnabled(true);
- m_Controls->cbWhat1->setEnabled(true);
- m_Controls->tlWhat2->setEnabled(true);
- m_Controls->cbWhat2->setEnabled(true);
+ m_Controls->sliceNavigatorTime->setEnabled(true);
+ m_Controls->tlTime->setEnabled(true);
}
+
+ m_Controls->tlWhat1->setEnabled(true);
+ m_Controls->cbWhat1->setEnabled(true);
+ m_Controls->tlWhat2->setEnabled(true);
+ m_Controls->cbWhat2->setEnabled(true);
}
void QmitkBasicImageProcessing::ChangeGUI()
{
if(m_Controls->rBOneImOp->isChecked())
{
m_Controls->gbTwoImageOps->hide();
m_Controls->gbOneImageOps->show();
}
else if(m_Controls->rBTwoImOp->isChecked())
{
m_Controls->gbOneImageOps->hide();
m_Controls->gbTwoImageOps->show();
}
}
-void QmitkBasicImageProcessing::ResetOneImageOpPanel()
-{
- m_Controls->tlParam1->setText(tr("Param1"));
- m_Controls->tlParam2->setText(tr("Param2"));
-
- m_Controls->cbWhat1->setCurrentIndex(0);
-
- m_Controls->tlTime->setEnabled(false);
-
- this->ResetParameterPanel();
-
- m_Controls->btnDoIt->setEnabled(false);
- m_Controls->cbHideOrig->setEnabled(false);
-}
-
void QmitkBasicImageProcessing::ResetParameterPanel()
{
m_Controls->tlParam->setEnabled(false);
m_Controls->tlParam1->setEnabled(false);
m_Controls->tlParam2->setEnabled(false);
m_Controls->tlParam3->setEnabled(false);
m_Controls->tlParam4->setEnabled(false);
m_Controls->sbParam1->setEnabled(false);
m_Controls->sbParam2->setEnabled(false);
m_Controls->dsbParam1->setEnabled(false);
m_Controls->dsbParam2->setEnabled(false);
m_Controls->dsbParam3->setEnabled(false);
m_Controls->cbParam4->setEnabled(false);
m_Controls->sbParam1->setValue(0);
m_Controls->sbParam2->setValue(0);
m_Controls->dsbParam1->setValue(0);
m_Controls->dsbParam2->setValue(0);
m_Controls->dsbParam3->setValue(0);
m_Controls->sbParam1->show();
m_Controls->sbParam2->show();
m_Controls->dsbParam1->hide();
m_Controls->dsbParam2->hide();
m_Controls->dsbParam3->hide();
m_Controls->cbParam4->hide();
m_Controls->tlParam3->hide();
m_Controls->tlParam4->hide();
}
-void QmitkBasicImageProcessing::ResetTwoImageOpPanel()
-{
- m_Controls->cbWhat2->setCurrentIndex(0);
-
- m_Controls->tlImage2->setEnabled(false);
- m_Controls->m_ImageSelector2->setEnabled(false);
-
- m_Controls->btnDoIt2->setEnabled(false);
-}
-
void QmitkBasicImageProcessing::SelectAction(int action)
{
- if ( ! m_SelectedImageNode->GetNode() ) return;
+ auto selectedImage = m_Controls->selectedImageWidget->GetSelectedNode();
+ if (selectedImage.IsNull())
+ {
+ return;
+ }
// Prepare GUI
this->ResetParameterPanel();
m_Controls->btnDoIt->setEnabled(false);
m_Controls->cbHideOrig->setEnabled(false);
QString text1 = tr("No Parameters");
QString text2 = text1;
QString text3 = text1;
QString text4 = text1;
if (action != 19)
{
m_Controls->dsbParam1->hide();
m_Controls->dsbParam2->hide();
m_Controls->dsbParam3->hide();
m_Controls->tlParam1->show();
m_Controls->tlParam2->show();
m_Controls->tlParam3->hide();
m_Controls->tlParam4->hide();
m_Controls->sbParam1->show();
m_Controls->sbParam2->show();
m_Controls->cbParam4->hide();
}
- // check which operation the user has selected and set parameters and GUI accordingly
+
switch (action)
{
case 2:
{
m_SelectedAction = GAUSSIAN;
m_Controls->tlParam1->setEnabled(true);
m_Controls->sbParam1->hide();
m_Controls->dsbParam1->show();
m_Controls->dsbParam1->setEnabled(true);
text1 = tr("&Variance:");
m_Controls->tlParam2->hide();
m_Controls->sbParam2->hide();
m_Controls->dsbParam1->setMinimum( 0 );
m_Controls->dsbParam1->setMaximum( 200 );
m_Controls->dsbParam1->setValue( 2 );
break;
}
-
case 3:
{
m_SelectedAction = MEDIAN;
m_Controls->tlParam1->setEnabled(true);
m_Controls->sbParam1->setEnabled(true);
text1 = tr("&Radius:");
m_Controls->sbParam1->setMinimum( 0 );
m_Controls->sbParam1->setMaximum( 200 );
m_Controls->sbParam1->setValue( 3 );
break;
}
-
case 4:
{
m_SelectedAction = TOTALVARIATION;
m_Controls->tlParam1->setEnabled(true);
m_Controls->sbParam1->setEnabled(true);
m_Controls->tlParam2->setEnabled(true);
m_Controls->sbParam2->setEnabled(true);
text1 = tr("Number Iterations:");
text2 = tr("Regularization\n(Lambda/1000):");
m_Controls->sbParam1->setMinimum( 1 );
m_Controls->sbParam1->setMaximum( 1000 );
m_Controls->sbParam1->setValue( 40 );
m_Controls->sbParam2->setMinimum( 0 );
m_Controls->sbParam2->setMaximum( 100000 );
m_Controls->sbParam2->setValue( 1 );
break;
}
-
case 6:
{
m_SelectedAction = DILATION;
m_Controls->tlParam1->setEnabled(true);
m_Controls->sbParam1->setEnabled(true);
text1 = tr("&Radius:");
m_Controls->sbParam1->setMinimum( 0 );
m_Controls->sbParam1->setMaximum( 200 );
m_Controls->sbParam1->setValue( 3 );
break;
}
-
case 7:
{
m_SelectedAction = EROSION;
m_Controls->tlParam1->setEnabled(true);
m_Controls->sbParam1->setEnabled(true);
text1 = tr("&Radius:");
m_Controls->sbParam1->setMinimum( 0 );
m_Controls->sbParam1->setMaximum( 200 );
m_Controls->sbParam1->setValue( 3 );
break;
}
-
case 8:
{
m_SelectedAction = OPENING;
m_Controls->tlParam1->setEnabled(true);
m_Controls->sbParam1->setEnabled(true);
text1 = tr("&Radius:");
m_Controls->sbParam1->setMinimum( 0 );
m_Controls->sbParam1->setMaximum( 200 );
m_Controls->sbParam1->setValue( 3 );
break;
}
-
case 9:
{
m_SelectedAction = CLOSING;
m_Controls->tlParam1->setEnabled(true);
m_Controls->sbParam1->setEnabled(true);
text1 = tr("&Radius:");
m_Controls->sbParam1->setMinimum( 0 );
m_Controls->sbParam1->setMaximum( 200 );
m_Controls->sbParam1->setValue( 3 );
break;
}
-
case 11:
{
m_SelectedAction = GRADIENT;
m_Controls->tlParam1->setEnabled(true);
m_Controls->sbParam1->hide();
m_Controls->dsbParam1->show();
m_Controls->dsbParam1->setEnabled(true);
text1 = tr("Sigma of Gaussian Kernel:\n(in Image Spacing Units)");
m_Controls->tlParam2->hide();
m_Controls->sbParam2->hide();
m_Controls->dsbParam1->setMinimum( 0 );
m_Controls->dsbParam1->setMaximum( 200 );
m_Controls->dsbParam1->setValue( 2 );
break;
}
-
case 12:
{
m_SelectedAction = LAPLACIAN;
break;
}
-
case 13:
{
m_SelectedAction = SOBEL;
break;
}
-
case 15:
{
m_SelectedAction = THRESHOLD;
m_Controls->tlParam1->setEnabled(true);
m_Controls->sbParam1->setEnabled(true);
m_Controls->tlParam2->setEnabled(true);
m_Controls->sbParam2->setEnabled(true);
text1 = tr("Lower threshold:");
text2 = tr("Upper threshold:");
m_Controls->sbParam1->setMinimum( -100000 );
m_Controls->sbParam1->setMaximum( 100000 );
m_Controls->sbParam1->setValue( 0 );
m_Controls->sbParam2->setMinimum( -100000 );
m_Controls->sbParam2->setMaximum( 100000 );
m_Controls->sbParam2->setValue( 300 );
break;
}
-
case 16:
{
m_SelectedAction = INVERSION;
break;
}
-
case 17:
{
m_SelectedAction = DOWNSAMPLING;
m_Controls->tlParam1->setEnabled(true);
m_Controls->sbParam1->setEnabled(true);
text1 = tr("Downsampling by Factor:");
m_Controls->sbParam1->setMinimum( 1 );
m_Controls->sbParam1->setMaximum( 100 );
m_Controls->sbParam1->setValue( 2 );
break;
}
-
case 18:
{
m_SelectedAction = FLIPPING;
m_Controls->tlParam1->setEnabled(true);
m_Controls->sbParam1->setEnabled(true);
text1 = tr("Flip across axis:");
m_Controls->sbParam1->setMinimum( 0 );
m_Controls->sbParam1->setMaximum( 2 );
m_Controls->sbParam1->setValue( 1 );
break;
}
-
case 19:
{
m_SelectedAction = RESAMPLING;
m_Controls->tlParam1->setEnabled(true);
m_Controls->sbParam1->setEnabled(false);
m_Controls->sbParam1->hide();
m_Controls->dsbParam1->show();
m_Controls->dsbParam1->setEnabled(true);
m_Controls->tlParam2->setEnabled(true);
m_Controls->sbParam2->setEnabled(false);
m_Controls->sbParam2->hide();
m_Controls->dsbParam2->show();
m_Controls->dsbParam2->setEnabled(true);
m_Controls->tlParam3->show();
m_Controls->tlParam3->setEnabled(true);
m_Controls->dsbParam3->show();
m_Controls->dsbParam3->setEnabled(true);
m_Controls->tlParam4->show();
m_Controls->tlParam4->setEnabled(true);
m_Controls->cbParam4->show();
m_Controls->cbParam4->setEnabled(true);
m_Controls->dsbParam1->setMinimum(0.01);
m_Controls->dsbParam1->setMaximum(10.0);
m_Controls->dsbParam1->setSingleStep(0.1);
m_Controls->dsbParam1->setValue(0.3);
m_Controls->dsbParam2->setMinimum(0.01);
m_Controls->dsbParam2->setMaximum(10.0);
m_Controls->dsbParam2->setSingleStep(0.1);
m_Controls->dsbParam2->setValue(0.3);
m_Controls->dsbParam3->setMinimum(0.01);
m_Controls->dsbParam3->setMaximum(10.0);
m_Controls->dsbParam3->setSingleStep(0.1);
m_Controls->dsbParam3->setValue(1.5);
text1 = tr("x-spacing:");
text2 = tr("y-spacing:");
text3 = tr("z-spacing:");
text4 = tr("Interplation:");
break;
}
-
case 20:
{
m_SelectedAction = RESCALE;
m_Controls->dsbParam1->show();
m_Controls->tlParam1->show();
m_Controls->dsbParam1->setEnabled(true);
m_Controls->tlParam1->setEnabled(true);
m_Controls->dsbParam2->show();
m_Controls->tlParam2->show();
m_Controls->dsbParam2->setEnabled(true);
m_Controls->tlParam2->setEnabled(true);
text1 = tr("Output minimum:");
text2 = tr("Output maximum:");
break;
}
case 21:
{
m_SelectedAction = RESCALE2;
m_Controls->dsbParam1->show();
m_Controls->tlParam1->show();
m_Controls->dsbParam1->setEnabled(true);
m_Controls->tlParam1->setEnabled(true);
text1 = tr("Scaling value:");
break;
}
-
- default: return;
+ default:
+ return;
}
m_Controls->tlParam->setEnabled(true);
m_Controls->tlParam1->setText(text1);
m_Controls->tlParam2->setText(text2);
m_Controls->tlParam3->setText(text3);
m_Controls->tlParam4->setText(text4);
m_Controls->btnDoIt->setEnabled(true);
m_Controls->cbHideOrig->setEnabled(true);
}
void QmitkBasicImageProcessing::StartButtonClicked()
{
- if(!m_SelectedImageNode->GetNode()) return;
+ auto selectedNode = m_Controls->selectedImageWidget->GetSelectedNode();
+ if (selectedNode.IsNull())
+ {
+ return;
+ }
this->BusyCursorOn();
mitk::Image::Pointer newImage;
-
try
{
- newImage = dynamic_cast<mitk::Image*>(m_SelectedImageNode->GetNode()->GetData());
+ newImage = dynamic_cast<mitk::Image*>(selectedNode->GetData());
}
catch ( std::exception &e )
{
QString exceptionString = tr("An error occured during image loading:\n");
exceptionString.append( e.what() );
QMessageBox::warning( nullptr, "Basic Image Processing", exceptionString , QMessageBox::Ok, QMessageBox::NoButton );
this->BusyCursorOff();
return;
}
// check if input image is valid, casting does not throw exception when casting from 'nullptr-Object'
if ( (! newImage) || (newImage->IsInitialized() == false) )
{
this->BusyCursorOff();
QMessageBox::warning( nullptr, "Basic Image Processing", tr("Input image is broken or not initialized. Returning."), QMessageBox::Ok, QMessageBox::NoButton );
return;
}
// check if operation is done on 4D a image time step
if(newImage->GetDimension() > 3)
{
- mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
+ auto timeSelector = mitk::ImageTimeSelector::New();
timeSelector->SetInput(newImage);
timeSelector->SetTimeNr( ((QmitkSliderNavigatorWidget*)m_Controls->sliceNavigatorTime)->GetPos() );
timeSelector->Update();
newImage = timeSelector->GetOutput();
}
-
-
// check if image or vector image
- ImageType::Pointer itkImage = ImageType::New();
- VectorImageType::Pointer itkVecImage = VectorImageType::New();
+ auto itkImage = ImageType::New();
+ auto itkVecImage = VectorImageType::New();
int isVectorImage = newImage->GetPixelType().GetNumberOfComponents();
if(isVectorImage > 1)
{
CastToItkImage( newImage, itkVecImage );
}
else
{
CastToItkImage( newImage, itkImage );
}
std::stringstream nameAddition("");
int param1 = m_Controls->sbParam1->value();
int param2 = m_Controls->sbParam2->value();
double dparam1 = m_Controls->dsbParam1->value();
double dparam2 = m_Controls->dsbParam2->value();
double dparam3 = m_Controls->dsbParam3->value();
- try{
-
+ try
+ {
switch (m_SelectedAction)
{
-
case GAUSSIAN:
{
GaussianFilterType::Pointer gaussianFilter = GaussianFilterType::New();
gaussianFilter->SetInput( itkImage );
gaussianFilter->SetVariance( dparam1 );
gaussianFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(gaussianFilter->GetOutput())->Clone();
nameAddition << "_Gaussian_var_" << dparam1;
std::cout << "Gaussian filtering successful." << std::endl;
break;
}
-
case MEDIAN:
{
MedianFilterType::Pointer medianFilter = MedianFilterType::New();
MedianFilterType::InputSizeType size;
size.Fill(param1);
medianFilter->SetRadius( size );
medianFilter->SetInput(itkImage);
medianFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(medianFilter->GetOutput())->Clone();
nameAddition << "_Median_radius_" << param1;
std::cout << "Median Filtering successful." << std::endl;
break;
}
-
case TOTALVARIATION:
{
if(isVectorImage > 1)
{
VectorTotalVariationFilterType::Pointer TVFilter
= VectorTotalVariationFilterType::New();
TVFilter->SetInput( itkVecImage.GetPointer() );
TVFilter->SetNumberIterations(param1);
TVFilter->SetLambda(double(param2)/1000.);
TVFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(TVFilter->GetOutput())->Clone();
}
else
{
ImagePTypeToFloatPTypeCasterType::Pointer floatCaster = ImagePTypeToFloatPTypeCasterType::New();
floatCaster->SetInput( itkImage );
floatCaster->Update();
DoubleImageType::Pointer fImage = floatCaster->GetOutput();
TotalVariationFilterType::Pointer TVFilter
= TotalVariationFilterType::New();
TVFilter->SetInput( fImage.GetPointer() );
TVFilter->SetNumberIterations(param1);
TVFilter->SetLambda(double(param2)/1000.);
TVFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(TVFilter->GetOutput())->Clone();
}
nameAddition << "_TV_Iter_" << param1 << "_L_" << param2;
std::cout << "Total Variation Filtering successful." << std::endl;
break;
}
-
case DILATION:
{
BallType binaryBall;
binaryBall.SetRadius( param1 );
binaryBall.CreateStructuringElement();
DilationFilterType::Pointer dilationFilter = DilationFilterType::New();
dilationFilter->SetInput( itkImage );
dilationFilter->SetKernel( binaryBall );
dilationFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(dilationFilter->GetOutput())->Clone();
nameAddition << "_Dilated_by_" << param1;
std::cout << "Dilation successful." << std::endl;
break;
}
-
case EROSION:
{
BallType binaryBall;
binaryBall.SetRadius( param1 );
binaryBall.CreateStructuringElement();
ErosionFilterType::Pointer erosionFilter = ErosionFilterType::New();
erosionFilter->SetInput( itkImage );
erosionFilter->SetKernel( binaryBall );
erosionFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(erosionFilter->GetOutput())->Clone();
nameAddition << "_Eroded_by_" << param1;
std::cout << "Erosion successful." << std::endl;
break;
}
-
case OPENING:
{
BallType binaryBall;
binaryBall.SetRadius( param1 );
binaryBall.CreateStructuringElement();
OpeningFilterType::Pointer openFilter = OpeningFilterType::New();
openFilter->SetInput( itkImage );
openFilter->SetKernel( binaryBall );
openFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(openFilter->GetOutput())->Clone();
nameAddition << "_Opened_by_" << param1;
std::cout << "Opening successful." << std::endl;
break;
}
-
case CLOSING:
{
BallType binaryBall;
binaryBall.SetRadius( param1 );
binaryBall.CreateStructuringElement();
ClosingFilterType::Pointer closeFilter = ClosingFilterType::New();
closeFilter->SetInput( itkImage );
closeFilter->SetKernel( binaryBall );
closeFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(closeFilter->GetOutput())->Clone();
nameAddition << "_Closed_by_" << param1;
std::cout << "Closing successful." << std::endl;
break;
}
-
case GRADIENT:
{
GradientFilterType::Pointer gradientFilter = GradientFilterType::New();
gradientFilter->SetInput( itkImage );
gradientFilter->SetSigma( dparam1 );
gradientFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(gradientFilter->GetOutput())->Clone();
nameAddition << "_Gradient_sigma_" << dparam1;
std::cout << "Gradient calculation successful." << std::endl;
break;
}
-
case LAPLACIAN:
{
// the laplace filter requires a float type image as input, we need to cast the itkImage
// to correct type
ImagePTypeToFloatPTypeCasterType::Pointer caster = ImagePTypeToFloatPTypeCasterType::New();
caster->SetInput( itkImage );
caster->Update();
DoubleImageType::Pointer fImage = caster->GetOutput();
LaplacianFilterType::Pointer laplacianFilter = LaplacianFilterType::New();
laplacianFilter->SetInput( fImage );
laplacianFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(laplacianFilter->GetOutput())->Clone();
nameAddition << "_Second_Derivative";
std::cout << "Laplacian filtering successful." << std::endl;
break;
}
-
case SOBEL:
{
// the sobel filter requires a float type image as input, we need to cast the itkImage
// to correct type
ImagePTypeToFloatPTypeCasterType::Pointer caster = ImagePTypeToFloatPTypeCasterType::New();
caster->SetInput( itkImage );
caster->Update();
DoubleImageType::Pointer fImage = caster->GetOutput();
SobelFilterType::Pointer sobelFilter = SobelFilterType::New();
sobelFilter->SetInput( fImage );
sobelFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(sobelFilter->GetOutput())->Clone();
nameAddition << "_Sobel";
std::cout << "Edge Detection successful." << std::endl;
break;
}
-
case THRESHOLD:
{
ThresholdFilterType::Pointer thFilter = ThresholdFilterType::New();
thFilter->SetLowerThreshold(param1 < param2 ? param1 : param2);
thFilter->SetUpperThreshold(param2 > param1 ? param2 : param1);
thFilter->SetInsideValue(1);
thFilter->SetOutsideValue(0);
thFilter->SetInput(itkImage);
thFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(thFilter->GetOutput())->Clone();
nameAddition << "_Threshold";
std::cout << "Thresholding successful." << std::endl;
break;
}
-
case INVERSION:
{
InversionFilterType::Pointer invFilter = InversionFilterType::New();
mitk::ScalarType min = newImage->GetStatistics()->GetScalarValueMin();
mitk::ScalarType max = newImage->GetStatistics()->GetScalarValueMax();
invFilter->SetMaximum( max + min );
invFilter->SetInput(itkImage);
invFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(invFilter->GetOutput())->Clone();
nameAddition << "_Inverted";
std::cout << "Image inversion successful." << std::endl;
break;
}
-
case DOWNSAMPLING:
{
ResampleImageFilterType::Pointer downsampler = ResampleImageFilterType::New();
downsampler->SetInput( itkImage );
NearestInterpolatorType::Pointer interpolator = NearestInterpolatorType::New();
downsampler->SetInterpolator( interpolator );
downsampler->SetDefaultPixelValue( 0 );
ResampleImageFilterType::SpacingType spacing = itkImage->GetSpacing();
spacing *= (double) param1;
downsampler->SetOutputSpacing( spacing );
downsampler->SetOutputOrigin( itkImage->GetOrigin() );
downsampler->SetOutputDirection( itkImage->GetDirection() );
ResampleImageFilterType::SizeType size = itkImage->GetLargestPossibleRegion().GetSize();
for ( int i = 0; i < 3; ++i )
{
size[i] /= param1;
}
downsampler->SetSize( size );
downsampler->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(downsampler->GetOutput())->Clone();
nameAddition << "_Downsampled_by_" << param1;
std::cout << "Downsampling successful." << std::endl;
break;
}
-
case FLIPPING:
{
FlipImageFilterType::Pointer flipper = FlipImageFilterType::New();
flipper->SetInput( itkImage );
itk::FixedArray<bool, 3> flipAxes;
for(int i=0; i<3; ++i)
{
if(i == param1)
{
flipAxes[i] = true;
}
else
{
flipAxes[i] = false;
}
}
flipper->SetFlipAxes(flipAxes);
flipper->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(flipper->GetOutput())->Clone();
std::cout << "Image flipping successful." << std::endl;
break;
}
-
case RESAMPLING:
{
std::string selectedInterpolator;
ResampleImageFilterType::Pointer resampler = ResampleImageFilterType::New();
switch (m_SelectedInterpolation)
{
case LINEAR:
{
LinearInterpolatorType::Pointer interpolator = LinearInterpolatorType::New();
resampler->SetInterpolator(interpolator);
selectedInterpolator = "Linear";
break;
}
case NEAREST:
{
NearestInterpolatorType::Pointer interpolator = NearestInterpolatorType::New();
resampler->SetInterpolator(interpolator);
selectedInterpolator = "Nearest";
break;
}
default:
{
LinearInterpolatorType::Pointer interpolator = LinearInterpolatorType::New();
resampler->SetInterpolator(interpolator);
selectedInterpolator = "Linear";
break;
}
}
resampler->SetInput( itkImage );
resampler->SetOutputOrigin( itkImage->GetOrigin() );
ImageType::SizeType input_size = itkImage->GetLargestPossibleRegion().GetSize();
ImageType::SpacingType input_spacing = itkImage->GetSpacing();
ImageType::SizeType output_size;
ImageType::SpacingType output_spacing;
output_size[0] = input_size[0] * (input_spacing[0] / dparam1);
output_size[1] = input_size[1] * (input_spacing[1] / dparam2);
output_size[2] = input_size[2] * (input_spacing[2] / dparam3);
output_spacing [0] = dparam1;
output_spacing [1] = dparam2;
output_spacing [2] = dparam3;
resampler->SetSize( output_size );
resampler->SetOutputSpacing( output_spacing );
resampler->SetOutputDirection( itkImage->GetDirection() );
resampler->UpdateLargestPossibleRegion();
ImageType::Pointer resampledImage = resampler->GetOutput();
newImage = mitk::ImportItkImage( resampledImage )->Clone();
nameAddition << "_Resampled_" << selectedInterpolator;
std::cout << "Resampling successful." << std::endl;
break;
}
-
-
case RESCALE:
{
DoubleImageType::Pointer floatImage = DoubleImageType::New();
CastToItkImage( newImage, floatImage );
itk::RescaleIntensityImageFilter<DoubleImageType,DoubleImageType>::Pointer filter = itk::RescaleIntensityImageFilter<DoubleImageType,DoubleImageType>::New();
filter->SetInput(0, floatImage);
filter->SetOutputMinimum(dparam1);
filter->SetOutputMaximum(dparam2);
filter->Update();
floatImage = filter->GetOutput();
newImage = mitk::Image::New();
newImage->InitializeByItk(floatImage.GetPointer());
newImage->SetVolume(floatImage->GetBufferPointer());
nameAddition << "_Rescaled";
std::cout << "Rescaling successful." << std::endl;
break;
}
case RESCALE2:
{
DoubleImageType::Pointer floatImage = DoubleImageType::New();
CastToItkImage( newImage, floatImage );
itk::ShiftScaleImageFilter<DoubleImageType,DoubleImageType>::Pointer filter = itk::ShiftScaleImageFilter<DoubleImageType,DoubleImageType>::New();
filter->SetInput(0, floatImage);
filter->SetScale(dparam1);
filter->Update();
floatImage = filter->GetOutput();
newImage = mitk::Image::New();
newImage->InitializeByItk(floatImage.GetPointer());
newImage->SetVolume(floatImage->GetBufferPointer());
nameAddition << "_Rescaled";
std::cout << "Rescaling successful." << std::endl;
break;
}
default:
this->BusyCursorOff();
return;
}
}
catch (...)
{
this->BusyCursorOff();
QMessageBox::warning(nullptr, "Warning", "Problem when applying filter operation. Check your input...");
return;
}
newImage->DisconnectPipeline();
// adjust level/window to new image
mitk::LevelWindow levelwindow;
levelwindow.SetAuto( newImage );
- mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New();
+ auto levWinProp = mitk::LevelWindowProperty::New();
levWinProp->SetLevelWindow( levelwindow );
// compose new image name
- std::string name = m_SelectedImageNode->GetNode()->GetName();
+ std::string name = selectedNode->GetName();
if (name.find(".pic.gz") == name.size() -7 )
{
name = name.substr(0,name.size() -7);
}
name.append( nameAddition.str() );
// create final result MITK data storage node
- mitk::DataNode::Pointer result = mitk::DataNode::New();
+ auto result = mitk::DataNode::New();
result->SetProperty( "levelwindow", levWinProp );
result->SetProperty( "name", mitk::StringProperty::New( name.c_str() ) );
result->SetData( newImage );
// for vector images, a different mapper is needed
if(isVectorImage > 1)
{
- mitk::VectorImageMapper2D::Pointer mapper =
- mitk::VectorImageMapper2D::New();
+ auto mapper = mitk::VectorImageMapper2D::New();
result->SetMapper(1,mapper);
}
- // reset GUI to ease further processing
-// this->ResetOneImageOpPanel();
-
// add new image to data storage and set as active to ease further processing
- GetDataStorage()->Add( result, m_SelectedImageNode->GetNode() );
- if ( m_Controls->cbHideOrig->isChecked() == true )
- m_SelectedImageNode->GetNode()->SetProperty( "visible", mitk::BoolProperty::New(false) );
- // TODO!! m_Controls->m_ImageSelector1->SetSelectedNode(result);
+ GetDataStorage()->Add(result, selectedNode);
+ if (m_Controls->cbHideOrig->isChecked() == true)
+ {
+ selectedNode->SetProperty("visible", mitk::BoolProperty::New(false));
+ }
// show the results
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
this->BusyCursorOff();
}
void QmitkBasicImageProcessing::SelectAction2(int operation)
{
- // check which operation the user has selected and set parameters and GUI accordingly
switch (operation)
{
case 2:
m_SelectedOperation = ADD;
break;
case 3:
m_SelectedOperation = SUBTRACT;
break;
case 4:
m_SelectedOperation = MULTIPLY;
break;
case 5:
m_SelectedOperation = DIVIDE;
break;
case 6:
m_SelectedOperation = RESAMPLE_TO;
break;
case 8:
m_SelectedOperation = AND;
break;
case 9:
m_SelectedOperation = OR;
break;
case 10:
m_SelectedOperation = XOR;
break;
default:
-// this->ResetTwoImageOpPanel();
return;
}
- m_Controls->tlImage2->setEnabled(true);
- m_Controls->m_ImageSelector2->setEnabled(true);
+
+ m_Controls->selectedImageLabel_2->setEnabled(true);
+ m_Controls->selectedImageWidget_2->setEnabled(true);
m_Controls->btnDoIt2->setEnabled(true);
}
void QmitkBasicImageProcessing::StartButton2Clicked()
{
- mitk::Image::Pointer newImage1 = dynamic_cast<mitk::Image*>
- (m_SelectedImageNode->GetNode()->GetData());
- mitk::Image::Pointer newImage2 = dynamic_cast<mitk::Image*>
- (m_Controls->m_ImageSelector2->GetSelectedNode()->GetData());
+ auto selectedNode = m_Controls->selectedImageWidget->GetSelectedNode();
+ if (selectedNode.IsNull())
+ {
+ return;
+ }
+
+ auto selectedNode2 = m_Controls->selectedImageWidget_2->GetSelectedNode();
+ if (selectedNode2.IsNull())
+ {
+ return;
+ }
+
+ mitk::Image::Pointer newImage1 = dynamic_cast<mitk::Image*>(selectedNode->GetData());
+ mitk::Image::Pointer newImage2 = dynamic_cast<mitk::Image*>(selectedNode2->GetData());
// check if images are valid
- if( (!newImage1) || (!newImage2) || (newImage1->IsInitialized() == false) || (newImage2->IsInitialized() == false) )
+ if(newImage1.IsNull() || newImage2.IsNull() || false == newImage1->IsInitialized() || false == newImage2->IsInitialized())
{
- itkGenericExceptionMacro(<< "At least one of the input images are broken or not initialized. Returning");
+ itkGenericExceptionMacro(<< "At least one of the input images is broken or not initialized.");
return;
}
this->BusyCursorOn();
-// this->ResetTwoImageOpPanel();
// check if 4D image and use filter on correct time step
if(newImage1->GetDimension() > 3)
{
- mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
+ auto timeSelector = mitk::ImageTimeSelector::New();
auto sn_widget = static_cast<QmitkSliderNavigatorWidget*>( m_Controls->sliceNavigatorTime );
int time = 0;
if( sn_widget != nullptr )
time = sn_widget->GetPos();
timeSelector->SetInput(newImage1);
timeSelector->SetTimeNr( time );
timeSelector->UpdateLargestPossibleRegion();
newImage1 = timeSelector->GetOutput();
newImage1->DisconnectPipeline();
timeSelector->SetInput(newImage2);
timeSelector->SetTimeNr( time );
timeSelector->UpdateLargestPossibleRegion();
newImage2 = timeSelector->GetOutput();
newImage2->DisconnectPipeline();
}
- // reset GUI for better usability
-// this->ResetTwoImageOpPanel();
-
- ImageType::Pointer itkImage1 = ImageType::New();
- ImageType::Pointer itkImage2 = ImageType::New();
+ auto itkImage1 = ImageType::New();
+ auto itkImage2 = ImageType::New();
CastToItkImage( newImage1, itkImage1 );
CastToItkImage( newImage2, itkImage2 );
- // Remove temp image
-// newImage2 = nullptr;
-
std::string nameAddition = "";
-
try
{
switch (m_SelectedOperation)
{
case ADD:
{
AddFilterType::Pointer addFilter = AddFilterType::New();
addFilter->SetInput1( itkImage1 );
addFilter->SetInput2( itkImage2 );
addFilter->UpdateLargestPossibleRegion();
newImage1 = mitk::ImportItkImage(addFilter->GetOutput())->Clone();
nameAddition = "_Added";
}
break;
-
case SUBTRACT:
{
SubtractFilterType::Pointer subFilter = SubtractFilterType::New();
subFilter->SetInput1( itkImage1 );
subFilter->SetInput2( itkImage2 );
subFilter->UpdateLargestPossibleRegion();
newImage1 = mitk::ImportItkImage(subFilter->GetOutput())->Clone();
nameAddition = "_Subtracted";
}
break;
-
case MULTIPLY:
{
MultiplyFilterType::Pointer multFilter = MultiplyFilterType::New();
multFilter->SetInput1( itkImage1 );
multFilter->SetInput2( itkImage2 );
multFilter->UpdateLargestPossibleRegion();
newImage1 = mitk::ImportItkImage(multFilter->GetOutput())->Clone();
nameAddition = "_Multiplied";
}
break;
-
case DIVIDE:
{
DivideFilterType::Pointer divFilter = DivideFilterType::New();
divFilter->SetInput1( itkImage1 );
divFilter->SetInput2( itkImage2 );
divFilter->UpdateLargestPossibleRegion();
newImage1 = mitk::ImportItkImage<DoubleImageType>(divFilter->GetOutput())->Clone();
nameAddition = "_Divided";
}
break;
-
case AND:
{
AndImageFilterType::Pointer andFilter = AndImageFilterType::New();
andFilter->SetInput1( itkImage1 );
andFilter->SetInput2( itkImage2 );
andFilter->UpdateLargestPossibleRegion();
newImage1 = mitk::ImportItkImage(andFilter->GetOutput())->Clone();
nameAddition = "_AND";
break;
}
-
case OR:
{
OrImageFilterType::Pointer orFilter = OrImageFilterType::New();
orFilter->SetInput1( itkImage1 );
orFilter->SetInput2( itkImage2 );
orFilter->UpdateLargestPossibleRegion();
newImage1 = mitk::ImportItkImage(orFilter->GetOutput())->Clone();
nameAddition = "_OR";
break;
}
-
case XOR:
{
XorImageFilterType::Pointer xorFilter = XorImageFilterType::New();
xorFilter->SetInput1( itkImage1 );
xorFilter->SetInput2( itkImage2 );
xorFilter->UpdateLargestPossibleRegion();
newImage1 = mitk::ImportItkImage(xorFilter->GetOutput())->Clone();
nameAddition = "_XOR";
break;
}
-
case RESAMPLE_TO:
{
-
-
itk::BSplineInterpolateImageFunction<DoubleImageType, double>::Pointer bspl_interpolator
= itk::BSplineInterpolateImageFunction<DoubleImageType, double>::New();
bspl_interpolator->SetSplineOrder( 3 );
itk::NearestNeighborInterpolateImageFunction< DoubleImageType >::Pointer nn_interpolator
= itk::NearestNeighborInterpolateImageFunction< DoubleImageType>::New();
DoubleImageType::Pointer itkImage1 = DoubleImageType::New();
DoubleImageType::Pointer itkImage2 = DoubleImageType::New();
CastToItkImage( newImage1, itkImage1 );
CastToItkImage( newImage2, itkImage2 );
itk::ResampleImageFilter< DoubleImageType, DoubleImageType >::Pointer resampleFilter = itk::ResampleImageFilter< DoubleImageType, DoubleImageType >::New();
resampleFilter->SetInput( itkImage1 );
resampleFilter->SetReferenceImage( itkImage2 );
resampleFilter->SetUseReferenceImage( true );
// use NN interp with binary images
- if( m_SelectedImageNode->GetNode()->GetProperty("binary") )
+ if(selectedNode->GetProperty("binary") )
resampleFilter->SetInterpolator( nn_interpolator );
else
resampleFilter->SetInterpolator( bspl_interpolator );
resampleFilter->SetDefaultPixelValue( 0 );
try
{
resampleFilter->UpdateLargestPossibleRegion();
}
catch( const itk::ExceptionObject &e)
{
MITK_WARN << "Updating resampling filter failed. ";
MITK_WARN << "REASON: " << e.what();
}
DoubleImageType::Pointer resampledImage = resampleFilter->GetOutput();
newImage1 = mitk::ImportItkImage( resampledImage )->Clone();
nameAddition = "_Resampled";
break;
}
default:
std::cout << "Something went wrong..." << std::endl;
this->BusyCursorOff();
return;
}
}
catch (const itk::ExceptionObject& e )
{
this->BusyCursorOff();
QMessageBox::warning(nullptr, "ITK Exception", e.what() );
QMessageBox::warning(nullptr, "Warning", tr("Problem when applying arithmetic operation to two images. Check dimensions of input images."));
return;
}
// disconnect pipeline; images will not be reused
newImage1->DisconnectPipeline();
itkImage1 = nullptr;
itkImage2 = nullptr;
// adjust level/window to new image and compose new image name
mitk::LevelWindow levelwindow;
levelwindow.SetAuto( newImage1 );
- mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New();
+ auto levWinProp = mitk::LevelWindowProperty::New();
levWinProp->SetLevelWindow( levelwindow );
- std::string name = m_SelectedImageNode->GetNode()->GetName();
+ std::string name = selectedNode->GetName();
if (name.find(".pic.gz") == name.size() -7 )
{
name = name.substr(0,name.size() -7);
}
// create final result MITK data storage node
- mitk::DataNode::Pointer result = mitk::DataNode::New();
+ auto result = mitk::DataNode::New();
result->SetProperty( "levelwindow", levWinProp );
result->SetProperty( "name", mitk::StringProperty::New( (name + nameAddition ).c_str() ));
result->SetData( newImage1 );
- GetDataStorage()->Add( result, m_SelectedImageNode->GetNode() );
+ this->GetDataStorage()->Add(result, selectedNode);
- // show only the newly created image
- m_SelectedImageNode->GetNode()->SetProperty( "visible", mitk::BoolProperty::New(false) );
- m_Controls->m_ImageSelector2->GetSelectedNode()->SetProperty( "visible", mitk::BoolProperty::New(false) );
+ if (m_Controls->cbHideOrig->isChecked() == true)
+ {
+ selectedNode->SetProperty("visible", mitk::BoolProperty::New(false));
+ selectedNode2->SetProperty("visible", mitk::BoolProperty::New(false));
+ }
// show the newly created image
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
this->BusyCursorOff();
}
void QmitkBasicImageProcessing::SelectInterpolator(int interpolator)
{
switch (interpolator)
{
case 0:
{
m_SelectedInterpolation = LINEAR;
break;
}
case 1:
{
m_SelectedInterpolation = NEAREST;
break;
}
}
}
diff --git a/Plugins/org.mitk.gui.qt.basicimageprocessing/src/internal/QmitkBasicImageProcessingView.h b/Plugins/org.mitk.gui.qt.basicimageprocessing/src/internal/QmitkBasicImageProcessingView.h
index b25c6f7448..a750463193 100644
--- a/Plugins/org.mitk.gui.qt.basicimageprocessing/src/internal/QmitkBasicImageProcessingView.h
+++ b/Plugins/org.mitk.gui.qt.basicimageprocessing/src/internal/QmitkBasicImageProcessingView.h
@@ -1,183 +1,154 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
-#if !defined(QmitkBasicImageProcessingView_H__INCLUDED)
-#define QmitkBasicImageProcessingView_H__INCLUDED
+#ifndef QMITKBASICIMAGEPROCESSINGVIEW_H
+#define QMITKBASICIMAGEPROCESSINGVIEW_H
-#include <QmitkAbstractView.h>
-#include <org_mitk_gui_qt_basicimageprocessing_Export.h>
-#include "ui_QmitkBasicImageProcessingViewControls.h"
+#include <ui_QmitkBasicImageProcessingViewControls.h>
-#include "QmitkStepperAdapter.h"
+#include <org_mitk_gui_qt_basicimageprocessing_Export.h>
-#include <mitkDataStorageSelection.h>
+#include <mitkNodePredicateAnd.h>
+#include <QmitkStepperAdapter.h>
+#include <QmitkAbstractView.h>
/*!
\brief This module allows to use some basic image processing filters for preprocessing, image enhancement and testing purposes
Several basic ITK image processing filters, like denoising, morphological and edge detection
are encapsulated in this module and can be selected via a list and an intuitive parameter input.
The selected filter will be applied on the image, and a new image showing the output is displayed
as result.
Also, some image arithmetic operations are available.
Images can be 3D or 4D.
In the 4D case, the filters work on the 3D image selected via the
time slider. The result is also a 3D image.
\class QmitkBasicImageProcessing
\author Tobias Schwarz
\version 1.0 (3M3)
\date 2009-05-10
\ingroup Bundles
*/
class BASICIMAGEPROCESSING_EXPORT QmitkBasicImageProcessing : public QmitkAbstractView
{
Q_OBJECT
public:
+ static const std::string VIEW_ID;
- /*!
- \brief default constructor
- */
QmitkBasicImageProcessing();
-
- /*!
- \brief default destructor
- */
~QmitkBasicImageProcessing() override;
- /*!
- \brief method for creating the widget containing the application controls, like sliders, buttons etc.
- */
- void CreateQtPartControl(QWidget *parent) override;
-
void SetFocus() override;
- /*!
- \brief method for creating the connections of main and control widget
- */
- virtual void CreateConnections();
-
- /*!
- \brief Invoked when the DataManager selection changed
- */
- void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
-
+private Q_SLOTS:
- protected slots:
+ void OnCurrentSelectionChanged(const QList<mitk::DataNode::Pointer>& nodes);
/*
- * When an action is selected in the "one image ops" list box
- */
- void SelectAction(int action);
+ * When an action is selected in the "one image ops" list box
+ */
+ void SelectAction(int action);
- /*
- * When an action is selected in the "two image ops" list box
- */
- void SelectAction2(int operation);
+ /*
+ * When an action is selected in the "two image ops" list box
+ */
+ void SelectAction2(int operation);
- /*
- * The "Execute" button in the "one image ops" box was triggered
- */
- void StartButtonClicked();
+ /*
+ * The "Execute" button in the "one image ops" box was triggered
+ */
+ void StartButtonClicked();
- /*
- * The "Execute" button in the "two image ops" box was triggered
- */
- void StartButton2Clicked();
+ /*
+ * The "Execute" button in the "two image ops" box was triggered
+ */
+ void StartButton2Clicked();
- /*
- * Switch between the one and the two image operations GUI
- */
- void ChangeGUI();
+ /*
+ * Switch between the one and the two image operations GUI
+ */
+ void ChangeGUI();
- void SelectInterpolator(int interpolator);
+ void SelectInterpolator(int interpolator);
private:
- /*
- * After a one image operation, reset the "one image ops" panel
- */
- void ResetOneImageOpPanel();
+ void CreateQtPartControl(QWidget *parent) override;
+ virtual void CreateConnections();
/*
* Helper method to reset the parameter set panel
*/
void ResetParameterPanel();
- /*
- * After a two image operation, reset the "two image ops" panel
- */
- void ResetTwoImageOpPanel();
-
/** retrieve the tnc from renderwindow part */
void InternalGetTimeNavigationController();
- /*!
- * controls containing sliders for scrolling through the slices
- */
- Ui::QmitkBasicImageProcessingViewControls *m_Controls;
+ Ui::QmitkBasicImageProcessingViewControls* m_Controls;
+
+ QmitkStepperAdapter* m_TimeStepperAdapter;
- //mitk::DataNode* m_SelectedImageNode;
- mitk::DataStorageSelection::Pointer m_SelectedImageNode;
- QmitkStepperAdapter* m_TimeStepperAdapter;
+ mitk::NodePredicateAnd::Pointer m_IsImagePredicate;
- enum ActionType {
+ enum ActionType
+ {
NOACTIONSELECTED,
CATEGORY_DENOISING,
GAUSSIAN,
MEDIAN,
TOTALVARIATION,
CATEGORY_MORPHOLOGICAL,
DILATION,
EROSION,
OPENING,
CLOSING,
CATEGORY_EDGE_DETECTION,
GRADIENT,
LAPLACIAN,
SOBEL,
CATEGORY_MISC,
THRESHOLD,
INVERSION,
DOWNSAMPLING,
FLIPPING,
RESAMPLING,
RESCALE,
RESCALE2
} m_SelectedAction;
- enum OperationType{
+ enum OperationType
+ {
TWOIMAGESNOACTIONSELECTED,
CATEGORY_ARITHMETIC,
ADD,
SUBTRACT,
MULTIPLY,
DIVIDE,
RESAMPLE_TO,
CATEGORY_BOOLEAN,
AND,
OR,
XOR
} m_SelectedOperation;
- enum InterpolationType{
+ enum InterpolationType
+ {
LINEAR,
NEAREST
} m_SelectedInterpolation;
};
-#endif // !defined(QmitkBasicImageProcessing_H__INCLUDED)
-
-
+#endif // !defined(QmitkBasicImageProcessing_H__INCLUDED)QMITKBASICIMAGEPROCESSINGVIEW_H
diff --git a/Plugins/org.mitk.gui.qt.basicimageprocessing/src/internal/QmitkBasicImageProcessingViewControls.ui b/Plugins/org.mitk.gui.qt.basicimageprocessing/src/internal/QmitkBasicImageProcessingViewControls.ui
index b6a6c4dd2b..abb43d9246 100644
--- a/Plugins/org.mitk.gui.qt.basicimageprocessing/src/internal/QmitkBasicImageProcessingViewControls.ui
+++ b/Plugins/org.mitk.gui.qt.basicimageprocessing/src/internal/QmitkBasicImageProcessingViewControls.ui
@@ -1,428 +1,447 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>QmitkBasicImageProcessingViewControls</class>
<widget class="QWidget" name="QmitkBasicImageProcessingViewControls">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
- <width>448</width>
- <height>980</height>
+ <width>370</width>
+ <height>620</height>
</rect>
</property>
<property name="windowTitle">
- <string>Form</string>
+ <string>Basic Image Processing</string>
</property>
<layout class="QGridLayout" name="gridLayout_4">
<item row="0" column="0">
<widget class="QGroupBox" name="groupBox">
- <property name="title">
- <string/>
- </property>
- <property name="flat">
- <bool>false</bool>
- </property>
<layout class="QGridLayout" name="gridLayout_3">
<item row="0" column="0">
<widget class="QRadioButton" name="rBOneImOp">
<property name="text">
<string>Filters
(One Image)</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QRadioButton" name="rBTwoImOp">
<property name="text">
<string>Arithmetic
(Two Images)</string>
</property>
</widget>
</item>
- <item row="1" column="0" colspan="2">
- <widget class="QLineEdit" name="leImage1">
+ <item row="1" column="0">
+ <widget class="QLabel" name="selectedImageLabel">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
<property name="text">
- <string>Select an image in the Data Manager</string>
+ <string>Selected image</string>
</property>
- <property name="readOnly">
- <bool>true</bool>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QmitkSingleNodeSelectionWidget" name="selectedImageWidget" native="true">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>0</width>
+ <height>40</height>
+ </size>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QLabel" name="tlTime">
<property name="enabled">
<bool>false</bool>
</property>
<property name="toolTip">
<string>Output image will be 3D</string>
</property>
<property name="text">
<string>Choose time step if 4D
(Slider for both images)</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="1">
<widget class="QmitkSliderNavigatorWidget" name="sliceNavigatorTime" native="true">
<property name="enabled">
<bool>false</bool>
</property>
<property name="toolTip">
<string>Output image will be 3D</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
- <item row="2" column="0">
- <widget class="QGroupBox" name="gbTwoImageOps">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="title">
- <string/>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- <layout class="QGridLayout" name="gridLayout_2">
- <item row="2" column="0" colspan="2">
- <widget class="QLabel" name="tlImage2">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Select second image:</string>
- </property>
- <property name="wordWrap">
- <bool>false</bool>
- </property>
- <property name="buddy">
- <cstring>m_ImageSelector2</cstring>
- </property>
- </widget>
- </item>
- <item row="3" column="0" colspan="3">
- <widget class="QmitkDataStorageComboBox" name="m_ImageSelector2">
- <property name="enabled">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item row="6" column="0" colspan="3">
- <widget class="QPushButton" name="btnDoIt2">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>E&xecute</string>
- </property>
- </widget>
- </item>
- <item row="0" column="0">
- <widget class="QLabel" name="tlWhat2">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Select an operation:</string>
- </property>
- <property name="wordWrap">
- <bool>false</bool>
- </property>
- <property name="buddy">
- <cstring>cbWhat2</cstring>
- </property>
- </widget>
- </item>
- <item row="1" column="0" colspan="3">
- <widget class="QComboBox" name="cbWhat2">
- <property name="enabled">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item row="3" column="0">
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>254</width>
- <height>403</height>
- </size>
- </property>
- </spacer>
- </item>
<item row="1" column="0">
<widget class="QGroupBox" name="gbOneImageOps">
- <property name="title">
- <string/>
- </property>
<layout class="QGridLayout" name="gridLayout">
<item row="0" column="0" colspan="3">
<widget class="QLabel" name="tlWhat1">
<property name="enabled">
<bool>false</bool>
</property>
<property name="text">
<string>Select an operation:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
<property name="buddy">
<cstring>cbWhat1</cstring>
</property>
</widget>
</item>
<item row="1" column="0" colspan="3">
<widget class="QComboBox" name="cbWhat1">
<property name="enabled">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="0" colspan="3">
<widget class="QLabel" name="tlParam">
<property name="enabled">
<bool>false</bool>
</property>
<property name="text">
<string>... and parameters:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="3" column="0">
<widget class="QLabel" name="tlParam1">
<property name="enabled">
<bool>false</bool>
</property>
<property name="text">
<string>Parameter 1:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
<property name="buddy">
<cstring>sbParam1</cstring>
</property>
</widget>
</item>
- <item row="4" column="0">
- <widget class="QLabel" name="tlParam2">
+ <item row="3" column="1">
+ <widget class="QSpinBox" name="sbParam1">
<property name="enabled">
<bool>false</bool>
</property>
- <property name="text">
- <string>Parameter 2:</string>
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
</property>
- <property name="wordWrap">
- <bool>false</bool>
+ <property name="minimum">
+ <number>-999999999</number>
</property>
- <property name="buddy">
- <cstring>sbParam2</cstring>
+ <property name="maximum">
+ <number>999999999</number>
</property>
</widget>
</item>
- <item row="8" column="0" colspan="3">
- <widget class="QPushButton" name="btnDoIt">
+ <item row="3" column="2">
+ <widget class="QDoubleSpinBox" name="dsbParam1">
<property name="enabled">
<bool>false</bool>
</property>
- <property name="text">
- <string>&Execute</string>
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
</property>
- </widget>
- </item>
- <item row="7" column="0">
- <widget class="QCheckBox" name="cbHideOrig">
- <property name="enabled">
- <bool>false</bool>
+ <property name="decimals">
+ <number>4</number>
</property>
- <property name="text">
- <string>Hide Original Image</string>
+ <property name="minimum">
+ <double>-999999999.000000000000000</double>
</property>
- <property name="checked">
- <bool>true</bool>
+ <property name="maximum">
+ <double>999999999.000000000000000</double>
</property>
</widget>
</item>
- <item row="5" column="0">
- <widget class="QLabel" name="tlParam3">
+ <item row="4" column="0">
+ <widget class="QLabel" name="tlParam2">
<property name="enabled">
<bool>false</bool>
</property>
<property name="text">
- <string>Parameter 3:</string>
+ <string>Parameter 2:</string>
</property>
- </widget>
- </item>
- <item row="6" column="0">
- <widget class="QLabel" name="tlParam4">
- <property name="enabled">
+ <property name="wordWrap">
<bool>false</bool>
</property>
- <property name="text">
- <string>Parameter 4:</string>
+ <property name="buddy">
+ <cstring>sbParam2</cstring>
</property>
</widget>
</item>
- <item row="6" column="2">
- <widget class="QComboBox" name="cbParam4">
+ <item row="4" column="1">
+ <widget class="QSpinBox" name="sbParam2">
<property name="enabled">
<bool>false</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
+ <property name="minimum">
+ <number>-999999999</number>
+ </property>
+ <property name="maximum">
+ <number>999999999</number>
+ </property>
</widget>
</item>
- <item row="5" column="2">
- <widget class="QDoubleSpinBox" name="dsbParam3">
+ <item row="4" column="2">
+ <widget class="QDoubleSpinBox" name="dsbParam2">
<property name="enabled">
<bool>false</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
- <property name="layoutDirection">
- <enum>Qt::LeftToRight</enum>
- </property>
- <property name="alignment">
- <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
- </property>
<property name="decimals">
<number>4</number>
</property>
<property name="minimum">
<double>-999999999.000000000000000</double>
</property>
<property name="maximum">
<double>999999999.000000000000000</double>
</property>
</widget>
</item>
- <item row="4" column="2">
- <widget class="QDoubleSpinBox" name="dsbParam2">
+ <item row="5" column="0">
+ <widget class="QLabel" name="tlParam3">
+ <property name="enabled">
+ <bool>false</bool>
+ </property>
+ <property name="text">
+ <string>Parameter 3:</string>
+ </property>
+ </widget>
+ </item>
+ <item row="5" column="2">
+ <widget class="QDoubleSpinBox" name="dsbParam3">
<property name="enabled">
<bool>false</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
+ <property name="layoutDirection">
+ <enum>Qt::LeftToRight</enum>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
+ </property>
<property name="decimals">
<number>4</number>
</property>
<property name="minimum">
<double>-999999999.000000000000000</double>
</property>
<property name="maximum">
<double>999999999.000000000000000</double>
</property>
</widget>
</item>
- <item row="3" column="2">
- <widget class="QDoubleSpinBox" name="dsbParam1">
+ <item row="6" column="0">
+ <widget class="QLabel" name="tlParam4">
+ <property name="enabled">
+ <bool>false</bool>
+ </property>
+ <property name="text">
+ <string>Parameter 4:</string>
+ </property>
+ </widget>
+ </item>
+ <item row="6" column="2">
+ <widget class="QComboBox" name="cbParam4">
<property name="enabled">
<bool>false</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
- <property name="decimals">
- <number>4</number>
+ </widget>
+ </item>
+ <item row="7" column="0">
+ <widget class="QCheckBox" name="cbHideOrig">
+ <property name="enabled">
+ <bool>false</bool>
</property>
- <property name="minimum">
- <double>-999999999.000000000000000</double>
+ <property name="text">
+ <string>Hide Original Image</string>
</property>
- <property name="maximum">
- <double>999999999.000000000000000</double>
+ <property name="checked">
+ <bool>true</bool>
</property>
</widget>
</item>
- <item row="3" column="1">
- <widget class="QSpinBox" name="sbParam1">
+ <item row="8" column="0" colspan="3">
+ <widget class="QPushButton" name="btnDoIt">
<property name="enabled">
<bool>false</bool>
</property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
+ <property name="text">
+ <string>&Execute</string>
</property>
- <property name="minimum">
- <number>-999999999</number>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item row="2" column="0">
+ <widget class="QGroupBox" name="gbTwoImageOps">
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
+ <property name="checked">
+ <bool>false</bool>
+ </property>
+ <layout class="QGridLayout" name="gridLayout_2">
+ <item row="0" column="0">
+ <widget class="QLabel" name="tlWhat2">
+ <property name="enabled">
+ <bool>false</bool>
</property>
- <property name="maximum">
- <number>999999999</number>
+ <property name="text">
+ <string>Select an operation:</string>
+ </property>
+ <property name="wordWrap">
+ <bool>false</bool>
+ </property>
+ <property name="buddy">
+ <cstring>cbWhat2</cstring>
</property>
</widget>
</item>
- <item row="4" column="1">
- <widget class="QSpinBox" name="sbParam2">
+ <item row="1" column="0" colspan="2">
+ <widget class="QComboBox" name="cbWhat2">
<property name="enabled">
<bool>false</bool>
</property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+ </widget>
+ </item>
+ <item row="2" column="0">
+ <widget class="QLabel" name="selectedImageLabel_2">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
- <property name="minimum">
- <number>-999999999</number>
+ <property name="enabled">
+ <bool>false</bool>
</property>
- <property name="maximum">
- <number>999999999</number>
+ <property name="text">
+ <string>Selected second image</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="1">
+ <widget class="QmitkSingleNodeSelectionWidget" name="selectedImageWidget_2" native="true">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="enabled">
+ <bool>false</bool>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>0</width>
+ <height>40</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="0" colspan="2">
+ <widget class="QPushButton" name="btnDoIt2">
+ <property name="enabled">
+ <bool>false</bool>
+ </property>
+ <property name="text">
+ <string>E&xecute</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
+ <item row="3" column="0">
+ <spacer name="verticalSpacer">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>254</width>
+ <height>403</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
</layout>
</widget>
<customwidgets>
<customwidget>
- <class>QmitkDataStorageComboBox</class>
- <extends>QComboBox</extends>
- <header location="global">QmitkDataStorageComboBox.h</header>
+ <class>QmitkSingleNodeSelectionWidget</class>
+ <extends>QWidget</extends>
+ <header location="global">QmitkSingleNodeSelectionWidget.h</header>
</customwidget>
<customwidget>
<class>QmitkSliderNavigatorWidget</class>
<extends>QWidget</extends>
<header location="global">QmitkSliderNavigatorWidget.h</header>
</customwidget>
</customwidgets>
<resources/>
<connections/>
</ui>
diff --git a/Plugins/org.mitk.gui.qt.cmdlinemodules/documentation/UserManual/cmdlinemodules.dox b/Plugins/org.mitk.gui.qt.cmdlinemodules/documentation/UserManual/cmdlinemodules.dox
index 9e485fd10f..ea56159ff5 100644
--- a/Plugins/org.mitk.gui.qt.cmdlinemodules/documentation/UserManual/cmdlinemodules.dox
+++ b/Plugins/org.mitk.gui.qt.cmdlinemodules/documentation/UserManual/cmdlinemodules.dox
@@ -1,172 +1,168 @@
/**
\page org_mitk_views_cmdlinemodules The Command Line Modules View
\imageMacro{cmdlinemodules_Icon.png,"Icon of the Command Line Modules View",2.00}
\tableofcontents
\section CLIPrefix Contribution
This plugin was developed at the <a href="http://cmic.cs.ucl.ac.uk/">Centre For Medical Image Computing</a> (CMIC),
part of <a href="http://www.ucl.ac.uk/">University College London</a> (UCL) and contributed back to the
<a href="http://www.mitk.org">MITK</a> community with thanks.
\section CLIIntroduction Introduction
This view provides the facility to run third party command line programs, and load the data back
-into the <a href="qthelp://org.mitk.gui.qt.datamanager/bundle/index.html">DataManager</a> for
-immediate visualisation. All that is required is that the command line application can be called
+into the DataManager for immediate visualisation. All that is required is that the command line application can be called
with an argument of --xml and respond with a valid XML description of the necessary parameters,
and currently, that if the program requires images, they must be NifTI images.
This view can then generate a Graphical User Interface (GUI) dynamically from the XML to enable the
user to interact with the command line application. This provides an easy to use, and potentially
very flexible way to integrate almost any third party, medical imaging, command line application.
As a high level introduction, this view performs the following steps:
\li The view searches for available programs to run, and for each valid module, stores the XML document describing
the interface, and populates a searchable list of available programs.
\li When a program is selected, the GUI is generated.
\li The user can then set the necessary parameters and run the program.
\li Multiple programs can be launched in succession and run simultaneously, and where available on the host platform,
the user can pause, resume or cancel running jobs and see console output for each job.
As a consequence of the very flexible nature of this plugin, these instructions can only describe how to launch
-command line modules in a general sense. The examples shown have been constructed by downloading the latest version (subversion commit 329)
-of the NiftyReg package, available <a href="http://sourceforge.net/projects/niftyreg/">here</a>, and described further
-<a href="http://www.cmpbjournal.com/article/S0169-2607(09)00253-3/abstract">here</a>. NiftyReg provides valid XML descriptors
-to enable the integration of the NiftyReg affine (RegAladin) and and non-rigid (RegF3D) image registration algorithms, as well
+command line modules in a general sense. The examples shown have been constructed by the latest version of the NiftyReg package.
+Futher information on the NiftyReg package, including links to the source code, can be found on the wiki page <a href="http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftyReg">here</a>.
+NiftyReg provides valid XML descriptors to enable the integration of the NiftyReg affine (RegAladin) and and non-rigid (RegF3D) image registration algorithms, as well
as utility programs to resample an image, and calculate a Jacobian image. These same XML descriptors work within
<a href="http://www.slicer.org/">Slicer</a> and <a href="http://www.mitk.org/">MITK</a> based applications.
\section CLIPreferences Preferences
The first time that the Command Line Modules View is launched, it is advisable to set the user preferences for the view. Please refer
to Figure 1.
\imageMacro{cmdlinemodules_Preferences.png,"Figure 1. The Command Line Modules Preferences Page",16.00}
Each of these preferences is now explained in some detail.
\li show debug output: If checked will output more messages to the console for debugging purposes.
+\li show advanced widgets: If selected, additional widgets appear in the front-end for advanced users.
+\li XML time-out (secs): Sets the time-out for the retrieval of the XML.
\li XML validation mode: The user may select a different mode for XML validation. If this is changed, the application will
need to be restarted. There are 3 modes available. If the user selects "strict" mode, the XML schema produced by the
command line application must exactly conform to <a href="http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation">
this definition</a>. For "none", there will be no validation. For "weak" validation, the application will report errors,
but try to carry on and load as many modules as possible. The XML validation errors are available as tool-tips on
the tab widget when the module is launched. Many third party modules included with Slicer currently have
incorrect XML (typically, mis-ordered XML tags), and so the "weak" or "none" mode may assist in loading them.
By default the "weak" mode is chosen so that only valid modules are loaded.
\li max concurrent processes: Sets the maximum number of concurrent jobs that can be run via this interface. The default is 4.
When the maximum number is reached, the green "Run" button is disabled until a job finishes.
The next 7 preferences are to control where the view will search for valid command line programs. By default these are off
as the searching process can take a long time and slow down the startup time of the GUI. The options provided are:
-\li scan home directory: Scan the users home directory. (See QDir::homePath().)
-\li scan home directory/cli-modules: Scans the sub-directory called cli-modules under the users home directory.
-\li scan current directory: Scan the current working directory. (See QDir::homePath().)
-\li scan current directory/cli-modules: Scans the sub-directory called cli-modules under the current working directory.
-\li scan installation directory: This is the directory where the actual application is stored.
-\li scan installation directory/cli-modules: Scans the sub-directory called cli-modules under the application installation directory.
+\li scan installation dir: This is the directory where the actual application is stored.
+\li scan installation dir/cli-modules: Scans the sub-directory called cli-modules under the application installation directory.
+\li scan home dir: Scan the users home directory. (See QDir::homePath().)
+\li scan home dir/cli-modules: Scans the sub-directory called cli-modules under the users home directory.
+\li scan current dir: Scan the current working directory. (See QDir::homePath().)
+\li scan current dir/cli-modules: Scans the sub-directory called cli-modules under the current working directory.
\li scan CTK_MODULE_LOAD_PATH: Scans the directory or list of directories defined by the environment variable CTK_MODULE_LOAD_PATH.
A list is colon separated on Linux/Mac, and semi-colon separated on Windows.
In most cases, it is suggested that the user will leave these options unchecked, as the user can also
specify custom directories, and even cherry-pick specific command line programs to load. Figure 2 shows
a selection box that enables the user to specify custom directories to scan, and Figure 3. shows a selection
box that enables the user to select specific modules. Picking specific directories, and specific executables
will most likely make the application quicker to launch.
-\imageMacro{cmdlinemodules_PreferencesAdditionalDirectories.png,"Figure 2. The User can specify specific directories to scan".",7.90}
-\imageMacro{cmdlinemodules_PreferencesAdditionalModules.png,"Figure 3. The User can specify specific command line programs to load".",7.92}
+\imageMacro{cmdlinemodules_PreferencesAdditionalDirectories.png,"Figure 2. The User can specify specific directories to scan.",7.90}
+\imageMacro{cmdlinemodules_PreferencesAdditionalModules.png,"Figure 3. The User can specify specific command line programs to load.",7.92}
These directory and file selection boxes enable directories or files to be added, removed and updated in a similar fashion.
The user must make sure that the list of files selected in the "additional modules" section are not already contained within
the directories specified in the "additional module directories" section.
In addition, the preferences page provides:
\li temporary directory: Images stored in the DataManager are first written to a temporary folder as
<a href="http://niftilib.sourceforge.net/">Nifti</a> images before being passed to each command line program.
This temporary directory will default to a platform specific temporary folder, but the user may select their preferred choice
of temporary workspace.
\section CLIUsage Usage
When the view is launched, a simple interface is presented, as shown in Figure 4.
\imageMacro{cmdlinemodules_Initial.png,"Figure 4. The initial interface\, with no command line programs available.",8.66}
In this example, all the above check-box preferences were off, and the "additional module directories"
was empty, and the "additional modules" list was empty so no command line applications were found.
The "Search" box displays zero entries, and there is nothing to search.
If the available search paths contain programs that are compatible (i.e. runnable) with this view,
the name of the programs are displayed in the "Search" box in a nested menu, shown in Figure 5.
\imageMacro{cmdlinemodules_WithPrograms.png,"Figure 5. When valid paths are set\, and programs are discovered\, the menu is recalculated to show available programs.",10.54}
When a program is selected, the relevant interface is displayed, by default as collapsed group boxes to save space.
Each section can be individually expanded if necessary to see the parameters.
\imageMacro{cmdlinemodules_NiftyReg.png,"Figure 6. An example program\, showing parameters for NiftyReg's program RegAladin.",10.24}
-In this example, the parameters are displayed for <a href="http://www0.cs.ucl.ac.uk/staff/m.modat/Marcs_Page/Software.html">NiftyReg</a>
+In this example, the parameters are displayed for <a href="https://sourceforge.net/projects/niftyreg/">NiftyReg</a>
produced at <a href="http://www.ucl.ac.uk">UCL</a>, and more specifically for the affine registration program called
RegAladin. The interface can contain a wide variety of controls. If a parameter for a command line program is an input image,
then the widget displayed is linked to the DataManager, so that as new images are loaded, the correct image can be easily
selected from the combo box.
At this stage, multiple tabs can be opened, with one tab for each command line program. Figure 7 shows 2 tabs,
for the RegAladin and RegF3D programs.
\imageMacro{cmdlinemodules_F3D.png,"Figure 7. Multiple tabs can be opened\, one for each command line program.",10.24}
The main view provides some simple controls:
\li Green arrow: Launch (run) the command line executable of the currently selected tab.
\li Yellow undo arrow: Resets the GUI controls of the currently selected tab to default values, if and only if the original XML specified a default value.
At this stage, nothing has been launched. When the user hits the green arrow button, a job is launched.
Each running job is shown as a new progress reporting widget under the main tabbed widget, as shown in Figure 8.
\imageMacro{cmdlinemodules_NiftyRegRunning2.png,"Figure 8. Multiple programs can be run\, each with individual controls and console output.",10.24}
The controls for each running job are:
\li Blue pause button: If supported on the host platform, this button will be enabled and can be toggled off (pause) or on (resume).
\li Red square: If supported on the host platform, this button will kill the command line program.
\li Black cross: Will remove the progress reporting widget from the GUI.
When the user hits the green arrow in the main view:
\li The currently selected tab is designated the "current" job, and contains the "current" set of parameters.
\li A new progress reporting widget is created.
\li The current parameters are copied to the progress reporting widget. In Figure 8. a parameters section
is visible, and by default is collapsed, as they are simply for referring back to.
\li All the output for the command line program is shown in the console widget, with a separate console for each job.
\li Each new progress reporting widget is simply stacked vertically (newest is top-most), and it is up to the
user to delete them when they are finished.
It is easy to run multiple jobs. The green button simply launches the job corresponding to the current tab repeatedly.
It is up to the user to make sure that any output file names are changed between successive invocations of the same command
line module to avoid overwritting output data.
In addition, each set of parameters contains an "About" section containing details of the contributors, the licence and acknowledgements and also
-a "Help" section containing a description and a link to any on-line documentation.
+a "Help" section containing a description and a link to any online documentation.
These documentation features are provided by the developers of the third party plugin, and not by the host program.
If information is missing, the user must contact the third party developers.
\section CLITechnicalNotes Technical Notes
From a technical perspective, the Command Line Modules View is a simple view, harnessing the power of the CTK
-command line modules framework. For technical information see:
-
-\li The doxygen generated <a href="http://www.commontk.org/docs/html/CommandLineModules_Page.html">manual page</a>.
-\li The <a href="http://www.commontk.org/index.php/Documentation/Command_Line_Interface">wiki page</a>.
-
+command line modules framework. For technical information see the <a href="http://www.commontk.org/index.php/Documentation/Command_Line_Interface">CTK wiki page</a>
and obviously the CTK code base.
*/
diff --git a/Plugins/org.mitk.gui.qt.cmdlinemodules/documentation/UserManual/cmdlinemodules_Preferences.png b/Plugins/org.mitk.gui.qt.cmdlinemodules/documentation/UserManual/cmdlinemodules_Preferences.png
index 84ee80bb59..6b311789a1 100644
Binary files a/Plugins/org.mitk.gui.qt.cmdlinemodules/documentation/UserManual/cmdlinemodules_Preferences.png and b/Plugins/org.mitk.gui.qt.cmdlinemodules/documentation/UserManual/cmdlinemodules_Preferences.png differ
diff --git a/Plugins/org.mitk.gui.qt.cmdlinemodules/plugin.xml b/Plugins/org.mitk.gui.qt.cmdlinemodules/plugin.xml
index 7cc2548e7f..4c29515213 100644
--- a/Plugins/org.mitk.gui.qt.cmdlinemodules/plugin.xml
+++ b/Plugins/org.mitk.gui.qt.cmdlinemodules/plugin.xml
@@ -1,28 +1,28 @@
<?xml version="1.0" encoding="UTF-8"?>
<plugin>
<extension point="org.blueberry.ui.views">
- <view id="org.mitk.gui.qt.cmdlinemodules"
+ <view id="org.mitk.views.cmdlinemodules"
name="Command Line Modules"
class="CommandLineModulesView"
icon="resources/icon.xpm" >
<description>Control the execution of Commandline-Tools</description>
<keywordReference id="org.mitk.views.cmdlinemodules.ViewKeyword"/>
</view>
</extension>
<extension point="org.blueberry.ui.preferencePages">
<page id="org.mitk.gui.qt.cmdlinemodules.CommandLineModulesPreferencesPage" name="Command Line Modules" class="CommandLineModulesPreferencesPage">
<keywordreference id="org.mitk.gui.qt.cmdlinemodules.CommandLineModulesPreferencesPageKeywords"></keywordreference>
</page>
</extension>
<extension point="org.blueberry.ui.keywords">
<keyword id="org.mitk.views.cmdlinemodules.ViewKeyword" label="CTK-Apps" />
<keyword id="org.mitk.views.cmdlinemodules.ViewKeyword" label="Apps" />
<keyword id="org.mitk.views.cmdlinemodules.ViewKeyword" label="Commandline" />
<keyword id="org.mitk.views.cmdlinemodules.ViewKeyword" label="CMD" />
<keyword id="org.mitk.views.cmdlinemodules.ViewKeyword" label="Smalltools" />
</extension>
</plugin>
diff --git a/Plugins/org.mitk.gui.qt.common.legacy/CMakeLists.txt b/Plugins/org.mitk.gui.qt.common.legacy/CMakeLists.txt
index 720f7b98a3..50b2016664 100755
--- a/Plugins/org.mitk.gui.qt.common.legacy/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.qt.common.legacy/CMakeLists.txt
@@ -1,8 +1,7 @@
project(org_mitk_gui_qt_common_legacy)
mitk_create_plugin(
EXPORT_DIRECTIVE MITK_QT_COMMON_LEGACY
EXPORTED_INCLUDE_SUFFIXES src
MODULE_DEPENDS MitkQtWidgets
- SUBPROJECTS MITK-CoreUI
)
diff --git a/Plugins/org.mitk.gui.qt.common/CMakeLists.txt b/Plugins/org.mitk.gui.qt.common/CMakeLists.txt
index d30d57f00e..7211d902fb 100755
--- a/Plugins/org.mitk.gui.qt.common/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.qt.common/CMakeLists.txt
@@ -1,8 +1,7 @@
project(org_mitk_gui_qt_common)
mitk_create_plugin(
EXPORT_DIRECTIVE MITK_QT_COMMON
EXPORTED_INCLUDE_SUFFIXES src
MODULE_DEPENDS MitkQtWidgets
- SUBPROJECTS MITK-CoreUI
)
diff --git a/Plugins/org.mitk.gui.qt.common/src/QmitkSingleNodeSelectionWidget.h b/Plugins/org.mitk.gui.qt.common/src/QmitkSingleNodeSelectionWidget.h
index 3c4571eb93..ed0edc443b 100644
--- a/Plugins/org.mitk.gui.qt.common/src/QmitkSingleNodeSelectionWidget.h
+++ b/Plugins/org.mitk.gui.qt.common/src/QmitkSingleNodeSelectionWidget.h
@@ -1,79 +1,94 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef QMITK_SINGLE_NODE_SELECTION_WIDGET_H
#define QMITK_SINGLE_NODE_SELECTION_WIDGET_H
#include <mitkDataStorage.h>
#include <mitkWeakPointer.h>
#include <mitkNodePredicateBase.h>
#include "org_mitk_gui_qt_common_Export.h"
#include "ui_QmitkSingleNodeSelectionWidget.h"
#include <QmitkAbstractNodeSelectionWidget.h>
#include <QmitkNodeSelectionButton.h>
class QmitkAbstractDataStorageModel;
/**
* @class QmitkSingleNodeSelectionWidget
* @brief Widget that represents a node selection of (max) one node. It acts like a button. Clicking on it
* allows to change the selection.
+*
+* @remark This class provides a public function 'SetAutoSelectNewNodes' that can be used to enable
+* the auto selection mode (default is false).
+* The user of this class calling this function has to make sure that the base-class Q_SIGNAL
+* 'CurrentSelectionChanged', which will be emitted by this function, is already
+* connected to a receiving slot, if the initial valid auto selection should not get lost.
*/
class MITK_QT_COMMON QmitkSingleNodeSelectionWidget : public QmitkAbstractNodeSelectionWidget
{
Q_OBJECT
public:
explicit QmitkSingleNodeSelectionWidget(QWidget* parent = nullptr);
mitk::DataNode::Pointer GetSelectedNode() const;
bool GetAutoSelectNewNodes() const;
using NodeList = QmitkAbstractNodeSelectionWidget::NodeList;
public Q_SLOTS:
void SetCurrentSelectedNode(mitk::DataNode* selectedNode);
- /** Sets the auto selection mode (Default is false).
- If auto select is true and the following conditions are fullfilled, the widget will
- select a node automatically from the data storage:
- - a data storage is set
- - data storage contains at least one node that matches the given predicate
- - no selection is set.*/
+ /**
+ * Sets the auto selection mode (default is false).
+ * If auto select is true and the following conditions are fullfilled, the widget will
+ * select a node automatically from the data storage:
+ * - a data storage is set
+ * - data storage contains at least one node that matches the given predicate
+ * - no selection is set
+ *
+ * @remark Enabling the auto selection mode by calling 'SetAutoSelectNewNodes(true)'
+ * will directly emit a 'QmitkSingleNodeSelectionWidget::CurrentSelectionChanged' Q_SIGNAL
+ * if a valid auto selection was made.
+ * If this initial emission should not get lost, auto selection mode needs to be enabled after this
+ * selection widget has been connected via the 'QmitkSingleNodeSelectionWidget::CurrentSelectionChanged'
+ * Q_SIGNAL to a receiving function.
+ */
void SetAutoSelectNewNodes(bool autoSelect);
protected Q_SLOTS:
virtual void OnClearSelection();
protected:
void ReviseSelectionChanged(const NodeList& oldInternalSelection, NodeList& newInternalSelection) override;
bool eventFilter(QObject *obj, QEvent *ev) override;
void EditSelection();
void UpdateInfo() override;
void OnNodeAddedToStorage(const mitk::DataNode* node) override;
/** Helper function that gets a suitable auto selected node from the datastorage that fits to the predicate settings.
@param ignoreNodes You may pass a list of nodes that must not be choosen as auto selected node. */
mitk::DataNode::Pointer DetermineAutoSelectNode(const NodeList& ignoreNodes = {});
/** See documentation of SetAutoSelectNewNodes for details*/
bool m_AutoSelectNewNodes;
Ui_QmitkSingleNodeSelectionWidget m_Controls;
};
#endif // QMITK_SINGLE_NODE_SELECTION_WIDGET_H
diff --git a/Plugins/org.mitk.gui.qt.fit.demo/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.fit.demo/documentation/UserManual/Manual.dox
index 9460060acb..8b785a0367 100644
--- a/Plugins/org.mitk.gui.qt.fit.demo/documentation/UserManual/Manual.dox
+++ b/Plugins/org.mitk.gui.qt.fit.demo/documentation/UserManual/Manual.dox
@@ -1,17 +1,22 @@
/**
-\page org_mitk_gui_qt_fit_demo The Model Fit Demo View
+\page org_mitk_views_fit_demo The Fit Generator Demo View
\imageMacro{fit_demo_doc.svg,"Icon of the Fit Demo View",3.0}
\tableofcontents
\section FIT_DEMO_Introduction Introduction
-This plugin is a very simple demo plugin that allows 1) to generate a demo 3D+t image (with linear increasing values) and 2) to perform a linear fit on a selected node.
-It was/is use to demonstrate basic principle and to generate example fit sessions for demo and testing purposes (e.g. functionality of the fit inspector).
+The <i>Fit Generator Demo View</i> is a very simple demo view that allows 1) to generate a demo 3D+t image (with linear increasing values, model parameters are slope and offset) and 2) to perform a linear fit on a selected node.
+The purpose of this view is to demonstrate the basic principle of MITK's model fit functionality and to generate example fit sessions for demo and testing purposes (e.g. the functionality of the fit inspector).
+
+\section FIT_DEMO_Usage Usage
+
+To run the demo please follow these steps:\n
+
+1. Press the button <i>Generate test data</i> to create 3D+t demo data. Alternatively, you can also load a different data set of your choice.
+2. Choose the data node that should be used as <i>Selected Time Series</i> input. You can optionally create a mask on the data set and select it by pressing "CTRL" and the selected mask node.
+3. Press <i>Start Modelling</i> to start the fitting process and wait for it to finish.
+4. The output nodes <i>slope</i>, <i>offset</i>, <i>x-intercept</i> and fit evaluation parameters can be found as child nodes of the chosen input.
-\section FIT_DEMO_Contact Contact information
-This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics
-and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support,
-find a bug or have a feature request, feel free to contact us at www.mitk.org.
*/
diff --git a/Plugins/org.mitk.gui.qt.fit.demo/plugin.xml b/Plugins/org.mitk.gui.qt.fit.demo/plugin.xml
index 1ac84c636b..f428eeb193 100644
--- a/Plugins/org.mitk.gui.qt.fit.demo/plugin.xml
+++ b/Plugins/org.mitk.gui.qt.fit.demo/plugin.xml
@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<plugin>
<extension point="org.blueberry.ui.views">
- <view id="org.mitk.gui.qt.fit.demo"
+ <view id="org.mitk.views.fit.demo"
name="Fit Generator Demo"
category="Fitting"
class="FitGeneratorDemoView"
icon="resources/icon.svg" />
</extension>
</plugin>
diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/MFI_DataExport.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/MFI_DataExport.png
deleted file mode 100644
index 6caf5dafe0..0000000000
Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/MFI_DataExport.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/Manual.dox
index 4abb6951fd..561288c80a 100644
--- a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/Manual.dox
+++ b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/Manual.dox
@@ -1,78 +1,72 @@
/**
-\page org_mitk_gui_qt_fit_inspector The Model Fit Inspector View
+\page org_mitk_views_fit_inspector The Model Fit Inspector View
\imageMacro{fit_inspector_doc.svg,"Icon of the Model Fit Inspector View",3.0}
\tableofcontents
\section FIT_INSPECTOR_Introduction Introduction
-This view (Model Fit Inspector; MFI) offers the possibility to display the time course of the signal within an individual
+The Model Fit Inspector (MFI) View offers the possibility to display the time course of the signal within an individual
voxel (with or without fit).
-\section FIT_INSPECTOR_Contact Contact information
-This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics
-and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support,
-find a bug or have a feature request, feel free to contact us at www.mitk.org.
-
\section FIT_INSPECTOR_Raw Viewing without a model fit
\imageMacro{fit_inspect_raw.png, "Example screen shot showing the inspection of raw dynamic data without a fit.", 10}
-Open the view and select the dynamic image in the data manager.
+Open the view and choose the dynamic image via the <i>Input</i> selection widget from the available data selection in the data manager.
The graph plot will show the time course of image intensities (signal) in the selected voxel (cross hair) as red data points.
-The blue point indicates the frame currently displayed in the 4-window view.
-\section FIT_INSPECTOR_Fit Viewing without a model fit
+\section FIT_INSPECTOR_Fit Viewing with a model fit
\imageMacro{fit_inspect_fit.png, "Example screen shot showing the inspection of dynamic data and an associated fit.", 10}
-Selecting a parameter map of the fit of interest in the Data Manager will display the raw data curve in red dots with
-corresponding fit as black line in the selected cross-hair position. If an AIF-based model was used,
-the utilized AIF (averaged over AIF mask) is also displayed (default in green). The color of the AIF display can be adjusted.
+Selecting a parameter map of interest using the <i>Input</i> selection widget from the data selection available in the data manager will display the raw data curve as red data points along with
+the corresponding fit as black line in the selected cross-hair position. If an AIF-based model was used,
+the utilized AIF (averaged over AIF mask) is also displayed (default in green). The color of the AIF display can be adjusted (\ref FIT_INSPECTOR_Fit_Settings).
For ROI based fits, the MFI will display both the current data curve in the selected voxel (in red)
-and the ROI-averaged fitted curve (in dark green, can be adjusted). Scrolling through the individual voxels will change
-the current data curve, but the ROI-based curve remains the same. If voxels outside the fitted area defined by the mask
+and the ROI-averaged fitted curve (in dark green, color can be adjusted). Scrolling through the individual voxels will change
+the current data curve, but the ROI-based curve and the fit remain the same. If voxels outside the fitting mask
are selected, the raw data voxel values will be displayed, however no black fit line is visualized.
Below the data plot, several options for data visualization can be selected:
\subsection FIT_INSPECTOR_Fit_info Fit info tab
\imageMacro{fit_inspect_info.png, "Details of the fit info tab.", 5}
-The Fit info tab displays meta-data for selected fits performed on the displayed data set. If no fit was performed and only raw data is visualized, the fields are empty.
+The <i>Fit info</i> tab displays meta-data for selected fits performed on the displayed data set. If no fit was performed and only raw data is visualized, these fields are empty.
\subsection FIT_INSPECTOR_Fit_Parameter Fit parameter tab
\imageMacro{fit_inspect_results.png, "Details of the fit parameter tab.", 5}
-The "fit parameter" tab shows fit related parameter estimate values, derived parameters, fit criterion values and (optional) debug parameter maps
+The <i>Fit parameter</i> tab shows fit related parameter estimates, derived parameters, fit criterion values and (optional) debug parameter maps
in the selected voxel (and all inspection positions; see also \ref FIT_INSPECTOR_Inspect "inspection positions") listed as a table.
If no fit was performed and only raw data is visualized, the table is empty.
-The content of the table may by copied to clipboard or exported as csv file, by clicking the respective button below the table.
+The content of the table may be copied to the clipboard or exported as csv file, by clicking the respective button below the table.
\subsection FIT_INSPECTOR_Fit_Inspection Inspection positions tab
\imageMacro{fit_inspect_positions.png, "Details of the inspection position tab.", 5}
-The tab allows to manage inspection positions (see here for more about \ref FIT_INSPECTOR_Inspect "inspection positions").
+The <i>Inspection position</i> tab allows to manage inspection positions (see here for more about \ref FIT_INSPECTOR_Inspect "inspection positions").
- (1) Shows the coordinates of the current selected position in the workbench.
-- (2) Press to make the current position a inspected position. It will be added at the bottom of the list (3).
+- (2) Click the <i>Add as bookmark</i> button to make the current position an inspected position. It will be added to the bottom of the list (3).
- (3) List of all inspection positions
- (4) Toggle adding mode on/off. If on, you can add new positions by clicking into render windows with "SHIFT + left mouse button".
- (5) Manually adding inspection positions by entering the coordinates.
- (6) Remove the selected inspection positions. (Hot key: Del)
- (7) Move the selected inspection position up in the list (3).
- (8) Move the selected inspection position down in the list (3).
- (9) Save inspection points to a file.
- (10) Load inspection points from a file.
\subsection FIT_INSPECTOR_Fit_Settings Settings tab
\imageMacro{fit_inspect_settings.png, "Details of the settings tab.", 5}
-The View settings tab is used to adjust the plot display, namely, x and y axis scales and colors of displayed data plots (i.e. AIF).
+The <i>View settings</i> tab is used to adjust the plot display, namely, x and y axis scaling and colors of displayed data plots (i.e. AIF).
\subsection FIT_INSPECTOR_Fit_Export Plot data export tab
-\imageMacro{fit_inspect_export.png, "Details of the plot data export tab.", 5}
-Displays voxel data (input image) and corresponding time grid together with model fit values and additional curves (like AIF values) for each time point.
-The table will contain the position depended values of the current selected position as well as of all inspection positions (see also \ref FIT_INSPECTOR_Inspect "inspection positions").
+\imageMacro{fit_inspect_plotDataExport.png, "Details of the plot data export tab.", 5}
+The <i>Plot data export</i> displays voxel data (<i>Sample</i>) and corresponding time grid (<i>Time [s]</i>) together with model fit values (<i>Signal</i>) and additional curves (like AIF values) for each time point.
+The table will contain the values of the current selected position as well as of all inspection positions (see also \ref FIT_INSPECTOR_Inspect "inspection positions").
The data in the table can also be copied to clipboard or exported to csv files, by clicking the respective button below the table.
\section FIT_INSPECTOR_Inspect Inspection positions
-\imageMacro{fit_inspect_positions_example.png, "Example of the usage of inspection positions.", 5}
+\imageMacro{fit_inspect_positions_example.png, "Example usage of inspection positions.", 5}
The fit inspector allows to define positions in the world coordinate system that will be constantly displayed in addition to the current selected position.
These inspected position will be shown in the following parts of the view:
-- The plot windows. See example image above; the plot shows the current position (raw data: red dots, fit: black line) and an additional inspection position (green).
-- The fit parameter tab (see example image above)
-- The plot data export tab.
+- The plot window. See example image above; the plot shows the current position (raw data: red dots, fit: black line) and an additional inspection position (turquoise).
+- The <i>Fit parameter</i> tab (see example image above).
+- The <i>plot data export</i> tab.
It will work with dynamic data with and without an model fit. See the \ref FIT_INSPECTOR_Fit_Inspection "inspection positions tab section" for more details on how to manage inspection positions.
*/
diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_export.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_export.png
deleted file mode 100644
index c6e28b8504..0000000000
Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_export.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_fit.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_fit.png
index 39135d7a61..904edd93fe 100644
Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_fit.png and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_fit.png differ
diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_info.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_info.png
index db85415509..dd80bd85f8 100644
Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_info.png and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_info.png differ
diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_plotDataExport.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_plotDataExport.png
new file mode 100644
index 0000000000..77eddfcc4b
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_plotDataExport.png differ
diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions.png
index 6d5c46c456..630665a304 100644
Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions.png and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions.png differ
diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions_example.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions_example.png
index ddfef4b2c1..c851ab7cfe 100644
Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions_example.png and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions_example.png differ
diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_raw.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_raw.png
index c333213f75..cf3213c9a3 100644
Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_raw.png and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_raw.png differ
diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_results.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_results.png
index 49a74507ce..65154c8600 100644
Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_results.png and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_results.png differ
diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_settings.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_settings.png
index ffedbddbfe..69cb6065b4 100644
Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_settings.png and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_settings.png differ
diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/plugin.xml b/Plugins/org.mitk.gui.qt.fit.inspector/plugin.xml
index 3a24f2ddb5..69d4996bf2 100644
--- a/Plugins/org.mitk.gui.qt.fit.inspector/plugin.xml
+++ b/Plugins/org.mitk.gui.qt.fit.inspector/plugin.xml
@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<plugin>
<extension point="org.blueberry.ui.views">
- <view id="org.mitk.gui.qt.fit.inspector"
+ <view id="org.mitk.views.fit.inspector"
name="ModelFit Inspector View"
category="Fitting"
class="ModelFitInspectorView"
icon="resources/icon.svg" />
</extension>
</plugin>
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/Manual.dox
index 3d911805f2..4307dc669c 100644
--- a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/Manual.dox
+++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/Manual.dox
@@ -1,46 +1,68 @@
/**
-\page org_mitk_gui_qt_matchpoint_algorithm_browser The MatchPoint Algorithm Browser View
+\page org_mitk_views_matchpoint_algorithm_browser The MatchPoint Algorithm Browser View
\imageMacro{map_icon_browser_doc.svg, "Icon of the MatchPoint Algorithm Browser", 3}
\tableofcontents
\section MAP_BROWSER_Introduction Introduction
This view offers the user a way to search for available registration algorithms and select them for
-further usage by other views (e.g. MatchPoint Algorithm Control \ref org_mitk_gui_qt_algorithm_control).
+further usage by other views (e.g. \ref org_mitk_views_matchpoint_algorithm_control).
\section MAP_BROWSER_Usage Usage
-\remark If you see no algorithms available by the browser, please check the search paths which can be configured at the MatchPoint preference page (Ctrl+P).
+\remark If you see no algorithms available by the browser, please check the search path which can be configured at the MatchPoint preference page (Ctrl+P).
+\imageMacro{map_browser_preferencesPath.png, "Matchpoint preferences",14}
-The basic idea of the browser is that you can use this view as central place to search for suitable algorithms. If you select an algorithm you can see its profile in the lower part of the view.
-If a algorithm is selected all other views (e.g. \ref org_mitk_gui_qt_algorithm_control) which use registration algorithms will be notified and allow to choose the selected algorithm for usage.
-\imageMacro{map_browser.png, "View of the browser with the list of available algorithm and the profile area",14}
+The basic idea of the browser is that you can use this view as central place to search for suitable registration algorithms.
+If an algorithm is selected, all other views (e.g. \ref org_mitk_views_matchpoint_algorithm_control) which use registration algorithms will be notified and allow to choose the selected algorithm for usage.
+If you select an algorithm you can see its profile in the lower part of the view.
+\imageMacro{map_browser_viewScreenshot.png, "View of the browser with the list of available algorithms and the profile area",14}
\section MAP_BROWSER_Profile Profile info
-In the following a short information about the different properties classified in the profile.\n
+In the following, a short description of the properties classified in the profile is given.\n
+\subsection MAP_BROWSER_Profile_Identification Identification
<ul>
-<li><b>UID</b> Unique identifier for the registration algorithm (e.g. used in the library; may not be "human readable/understandable")</li>
-<li><b>Author</b> Name of the author(s) that has (have) developed the algorithm.</li>
-<li><b>Terms</b> Terms of usage for the algorithm.</li>
-<li><b>Data</b> type The type of date which is used by the algorithm to determine the registration. E.g. Image, point set, contour or surface</li>
-<li><b>Computation style</b> Specifies of the algorithm determines the registration by an iterative optimization process or analytically (e.g. closed form solution).
-Deterministic Specifies if the algorithm is deterministic (same input -> same output) or stochastic (e.g. by sampling the image while determining the registration). Results of stochastic algorithm may vary (slightly) because of their random aspect.
-Resolution style Defines if the algorithm uses a multi resolution/scale approach.</li>
-<li><b>Dim (Moving)</b> Number of dimensions of the frame of reference within which the data is defined that should be registered.</li>
-<li><b>Modality (Moving)</b> Modality of the moving entity (image). Thus the frame of reference where the registration should map from. E.g. CT, MRI, PET </li>
-<li><b>Dim (Target)</b> Number of dimensions of the frame of reference into which the data should be mapped. </li>
-<li><b>Modality (Target)</b> Modality of the target entity (image). Thus the frame of reference where the registration should map into. E.g. CT, MRI, PET </li>
-<li><b>Subject</b> Defines if the algorithm was developed to register data of the same subject (intrasubject), to register two subjects (intersubject) or to register onto an atlas. </li>
-<li><b>Object</b> Specifies for which "part" of the anatomy the algorithm was developed for. </li>
-<li><b>Transformation model</b> Specifies the type of transformation used by the algorithm. E.g.: affine, b-spline, non-rigid. </li>
-<li><b>Transformation domain</b> Defines it the transformation operates globally (e.g. Matrix) or locally (e.g. vector field). </li>
-<li><b>Optimization strategy</b> The used optimization strategy (if an optimizer is used). </li>
+<li><b>Namespace</b> Namespace in which the registration name is defined. </li>
+<li><b>Name</b> Identifies the name of the registration algorithm. The name is unique within the specified namespace.</li>
+<li><b>Version</b> Specifies the version of the registration algorithm.</li>
+<li><b>BuildTag</b> Additional information specifying the build (e.g. the build-date and -time of the so-/dll-file, the Matchpoint and the ITK version).</li>
+<li><b>Location</b> Specifies the path where the so-/dll-file of the registration implementation can be found.</li>
+</ul>
+\subsection MAP_BROWSER_Profile_Description Description
+A short description of the chosen registration algorithm.
+
+\subsection MAP_BROWSER_Profile_Keywords Keywords
+Typical keywords associated with the selected algorithm. They can i.e. be used in the search field.
+
+\subsection MAP_BROWSER_Profile_Characteristics Characteristics
+<ul>
+<li><b>Data type(s)</b> The type(s) of date which is used by the algorithm to determine the registration, e.g. image, point set, contour or surface.</li>
+<li><b>Computational style</b> Specifies if the registration is determined by an iterative optimization process or analytically (e.g. closed form solution). </li>
+<li><b>Deterministic</b> Specifies if the algorithm is deterministic (same input -> same output) or stochastic (e.g. by sampling the image while determining the registration).
+Results of stochastic algorithm may vary (slightly) because of their random aspect.</li>
+<li><b>Resolution style</b> Defines if the algorithm uses a multi resolution/scale approach.</li>
+<li><b>Moving dim</b> Number of dimensions of the frame of reference within which the data is defined that should be registered. </li>
+<li><b>Moving modality</b> Modality of the moving entity (image). Thus the frame of reference where the registration should map from, e.g. CT, MRI, PET. </li>
+<li><b>Target dim</b> Number of dimensions of the frame of reference into which the data should be mapped.</li>
+<li><b>Target modality</b> Modality of the target entity (image). Thus the frame of reference where the registration should map into, e.g. CT, MRI, PET. </li>
+<li><b>Subject</b> Defines if the algorithm was developed to register data of the same subject (intra-subject), to register two subjects (inter-subject) or to register onto an atlas. </li>
+<li><b>Object</b> Specifies which "part" of the anatomy the algorithm was developed for. </li>
+<li><b>Transformation model</b> Specifies the type of transformation used by the algorithm, e.g. affine, b-spline, non-rigid.</li>
+<li><b>Transformation domain</b> Defines if the transformation operates globally (e.g. Matrix) or locally (e.g. vector field).</li>
<li><b>Metric</b> The cost function/metric that is used by the optimizer (if an optimizer is used). </li>
-<li><b>Citation/Reference</b> Reference to literature that contains information about the algorithm and should be used to cite the algorithm.</li>
-<li><b>Literature</b> Secondary literature regarding the algorithm or used concepts in the algorithm. Use the field "Citation/Reference" for the literature that should be cited when using the algorithm.</li>
-<li><b>Contact</b> Internal contact for questions regarding the algorithm. </li>
+<li><b>Optimization</b> The used optimization strategy (if an optimizer is used). </li>
+<li><b>Interaction</b> Style of interaction. Currently only fully automatic registration algorithms are supported by MITK. </li>
+</ul>
+
+\subsection MAP_BROWSER_Profile_ContactAndUsage Contact & Usage
+<ul>
+<li><b>Contact</b> Name of the author(s) that has (have) developed the algorithm and an email address for further questions regarding the algorithm.</li>
+<li><b>Terms</b> Terms of usage for the algorithm.</li>
+<li><b>Citation</b> Reference to the literature that contains information about the algorithm and should be used to cite the algorithm. </li>
</ul>
*/
+
+
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/map_browser.png b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/map_browser.png
deleted file mode 100644
index ab3922c518..0000000000
Binary files a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/map_browser.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/map_browser_preferencesPath.png b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/map_browser_preferencesPath.png
new file mode 100644
index 0000000000..145132e3fa
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/map_browser_preferencesPath.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/map_browser_viewScreenshot.png b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/map_browser_viewScreenshot.png
new file mode 100644
index 0000000000..ab19f1dc70
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/map_browser_viewScreenshot.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/Manual.dox
index 93f1b219bb..2e852eeafa 100644
--- a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/Manual.dox
+++ b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/Manual.dox
@@ -1,50 +1,56 @@
/**
-\page org_mitk_gui_qt_matchpoint_evaluator The MatchPoint Registration Evaluation View
+\page org_mitk_views_matchpoint_evaluator The MatchPoint Registration Evaluation View
\imageMacro{map_evaluator_doc.svg, "Icon of the MatchPoint Registration Evaluator", 3}
\tableofcontents
\section MAP_REGEVAL_Introduction Introduction
This view offers the possibility to evaluate the quality of the registration/mapping of two given images by visual inspection.
-One may select no registration. Then the images will be displayed in evaluation mode assuming an identity transform (so no mapping).
+This can either by used to assess the visual quality of a registration or to assess how well the image contents are already aligned
+by default. To achieve the latter, one may select no registration. Then the images will be displayed in evaluation mode assuming an identity transform (so no mapping).
It is one of several MatchPoint registration plug-ins.\n
-\section MAP_REGEVAL_Contact Contact information
-This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics
-and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support,
-find a bug or have a feature request, feel free to contact us at www.mitk.org.
-
\section MAP_REGEVAL_Usage Usage
-\imageMacro{map_view_example.png, "Example screenshot showing the plug-in in use.", 14}
-To use the evaluation view you must have selected at least the moving and the target image you want to use to evaluate.
-If you select a registration with referenced target and moving image (the normal state if you generate registrations with the MatchPoint plugins)
-these images will be auto selected by just clicking on the registration.
-If you select no registration the view will assume that an identity transform should be used.\n
-As long as no valid set of data is selected the "Start evaluation" button will be disabled. If its enabled you may start the evaluation mode with it.
-
-\imageMacro{map_no_data_selected.png, "Example screenshot showing the state if no data is selected", 5}
+\imageMacro{map_view_evaluator_example.png, "Example screenshot showing the main elements of the view.", 14}
+(1) The currently selected registration that should be used to map the moving image for evaluation. Click to change. If no registration is selected, a direct evaluation will be performed.\n
+(2) Reset button will remove the currently selected registration.\n
+(3) Auto select option. If active the view will try to deduce and automatically select (if loaded in the application) the moving and target image when the registration changes. The view assumes that the moving and target images used to determine the registration should be used.\n
+(4) The currently selected moving data. Click to change.\n
+(5) The currently selected target data. Click to change.\n
+(6) Start/Stop button used to activate/deactivate the evaluation. This button become active when at least the moving and the target image are selected.\n
+(7) Selection of the visualization style. (only visible if evaluation is active)\n
+(8) Style specific settings. (only visible if evaluation is active)\n
If the evaluation view is active you can choose between different modes of visualization. For more details see \ref MAP_REGEVAL_Styles.\n
To stop the evaluation mode, you may use the "Stop evaluation" button or just close the evaluation view.
-\remark The evaluation view will use the level window settings of the used images. So to changes the level windowing of the evaluation view, you must change the
-level windowing of the respective images.
+\remark The evaluation view will use the level window settings of the used images. So to change the level windowing of the evaluation view, you must change the
+level windowing of the respective input images (moving image and target image).
+
+\section MAP_REGEVAL_Accuracy Evaluating accuracy
+<b>Important note:</b> Please be aware, that a visual inspection of registration quality is only a weak surrogate for a thorough accuracy analysis based on representative and suitable ground truth data. From a visually good mapping you can not deduce a correct registration. This is especially true if the degrees of freedom of the registration increases. For a rigid registration it might by feasible to discern correct and incorrect registration. But for none rigid registrations you definitely you should use this view only for first visual inspection (to check if it SEEMS to do the right thing and is worth further exploration) or illustrating the registration effect for registration you have assessed in a sound way.
\section MAP_REGEVAL_Styles Visualization styles
You can choose from the following visualization styles to evaluate the registration/mapping quality:\n
\li "Blend": Blends the images with a user defined weight. Default is 50:50.
-\imageMacro{map_style_blend.png, "Example for mode: Blend", 5}
-\li "Checkerboard": Checkerboard style that composes both images. You may define the resolution of the checkerboard.
+\imageMacro{map_view_blend_settings.png, "Settings of the Blend style", 8}
+(1) Click to set the weights to 100% target image.\n
+(2) Click to set the weights to 50:50 (equal blend).\n
+(3) Slider to adjust the weights between target image and the mapped input image. The spin box shows the weight of the mapped input image.\n
+(4) Click to set the weights to 100% mapped input image.\n
+(5) Click to toggle the weight between both images.\n
+\imageMacro{map_style_blend.png, "Example for mode: Blend (50:50)", 5}
+\li "Checkerboard": Checkerboard style that composes both images by showing image 1 in all light squares and image 2 in all dark squares. You can define the resolution/number of squares of the checkerboard.
\imageMacro{map_style_checkerboard.png, "Example for mode: Checkerboard", 5}
\li "Color blend": Color blend of the images (blue: target image; yellow: moving). Areas where you see no color implies good intensity matchings.
\imageMacro{map_style_color_blend.png, "Example for mode: Color blend", 5}
-\li "Contour": Blend mode that display one image as blue "background" and the other image in yellow contours. You may choose the role of the images.
+\li "Contour": Blend mode that displays one image as blue "background" and the other image in yellow contours. You can choose the role of the images.
\imageMacro{map_style_contour.png, "Example for mode: Contour", 5}
\li "Difference": Displays the absolute difference of both images.
\li "Wipe": Blend mode that makes a rectilinear combination of the images. You can choose the mode how the images are splitted. The split is synchronized with the current selection. So you may interact with the split border to position it on interesting areas.
\imageMacro{map_style_wipe_cross.png, "Example for mode: Wipe cross", 5}
\imageMacro{map_style_wipe_horizontal.png, "Example for mode: Wipe horizontal", 5}
*/
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_no_data_selected.png b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_no_data_selected.png
deleted file mode 100644
index 2a72cfa281..0000000000
Binary files a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_no_data_selected.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_blend_settings.png b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_blend_settings.png
new file mode 100644
index 0000000000..ff4c1c314a
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_blend_settings.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_blend_settings.svg b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_blend_settings.svg
new file mode 100644
index 0000000000..91573fb6d3
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_blend_settings.svg
@@ -0,0 +1,398 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:cc="http://creativecommons.org/ns#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:svg="http://www.w3.org/2000/svg"
+ xmlns="http://www.w3.org/2000/svg"
+ xmlns:xlink="http://www.w3.org/1999/xlink"
+ xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+ xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+ version="1.1"
+ id="svg4485"
+ width="748.53125"
+ height="174.21954"
+ viewBox="0 0 748.53125 174.21954"
+ sodipodi:docname="map_view_blend_settings.svg"
+ inkscape:version="0.92.3 (2405546, 2018-03-11)"
+ inkscape:export-filename="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.evaluator\documentation\UserManual\map_view_example.png"
+ inkscape:export-xdpi="96"
+ inkscape:export-ydpi="96">
+ <metadata
+ id="metadata4491">
+ <rdf:RDF>
+ <cc:Work
+ rdf:about="">
+ <dc:format>image/svg+xml</dc:format>
+ <dc:type
+ rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+ <dc:title />
+ </cc:Work>
+ </rdf:RDF>
+ </metadata>
+ <defs
+ id="defs4489">
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5474"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5472"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotM"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker4945"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4943"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.4,0,0,0.4,2.96,0.4)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotS"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4564"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotM"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotM"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4561"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.4,0,0,0.4,2.96,0.4)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-5"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-0"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-0"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-3"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-01"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-7"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562-8"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560-3"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9-8"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1-6"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath5294">
+ <rect
+ y="297.78046"
+ x="-56.937675"
+ height="175.15721"
+ width="484.87534"
+ id="rect5296"
+ style="opacity:1;fill:#800000;fill-opacity:1;stroke:#000000;stroke-width:3.80894065;stroke-linecap:butt;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:0" />
+ </clipPath>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562-7"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560-9"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562-6"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560-90"
+ inkscape:connector-curvature="0" />
+ </marker>
+ </defs>
+ <sodipodi:namedview
+ pagecolor="#ffffff"
+ bordercolor="#666666"
+ borderopacity="1"
+ objecttolerance="10"
+ gridtolerance="10"
+ guidetolerance="10"
+ inkscape:pageopacity="0"
+ inkscape:pageshadow="2"
+ inkscape:window-width="1680"
+ inkscape:window-height="1017"
+ id="namedview4487"
+ showgrid="false"
+ inkscape:zoom="1"
+ inkscape:cx="76.38541"
+ inkscape:cy="266.99957"
+ inkscape:window-x="249"
+ inkscape:window-y="97"
+ inkscape:window-maximized="0"
+ inkscape:current-layer="svg4485" />
+ <image
+ sodipodi:absref="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.evaluator\documentation\UserManual\map_view_evaluator_example_raw.png"
+ xlink:href="map_view_evaluator_example_raw.png"
+ width="427"
+ height="471"
+ preserveAspectRatio="none"
+ id="image4493"
+ x="0"
+ y="1"
+ clip-path="url(#clipPath5294)"
+ transform="translate(0,-297.78046)" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-0)"
+ d="m 396.13594,118.55192 h 38.53626 -0.76851"
+ id="path4495-7-2"
+ inkscape:connector-curvature="0"
+ sodipodi:nodetypes="ccc" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-01)"
+ d="M 314.07217,149.68209 H 434.6722 430.36508"
+ id="path4495-7-8"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:none;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5562)"
+ d="M 280.40049,106.15195 V 83.031946 H 434.6722"
+ id="path5464"
+ inkscape:connector-curvature="0"
+ sodipodi:nodetypes="ccc" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="89.219543"
+ id="text9677"><tspan
+ sodipodi:role="line"
+ id="tspan9675"
+ x="437.88541"
+ y="89.219543"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(3) Slider to adjust weighting</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="124.74039"
+ id="text9677-0"><tspan
+ sodipodi:role="line"
+ id="tspan9675-2"
+ x="437.88541"
+ y="124.74039"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(4) Set to 100% mapped visibility</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="154.74039"
+ id="text9677-3"
+ inkscape:export-xdpi="96"
+ inkscape:export-ydpi="96"><tspan
+ sodipodi:role="line"
+ id="tspan9675-91"
+ x="437.88541"
+ y="154.74039"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(5) Toggle weighting</tspan></text>
+ <flowRoot
+ xml:space="preserve"
+ id="flowRoot4717"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ transform="translate(0,-297.78046)"><flowRegion
+ id="flowRegion4719"><rect
+ id="rect4721"
+ width="337"
+ height="48"
+ x="353"
+ y="188" /></flowRegion><flowPara
+ id="flowPara4723" /></flowRoot> <path
+ style="fill:none;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5562-7)"
+ d="M 208.88504,77.775776 V 48.448036 H 434.6722"
+ id="path5464-3"
+ inkscape:connector-curvature="0"
+ sodipodi:nodetypes="ccc" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="54.635624"
+ id="text9677-7"><tspan
+ sodipodi:role="line"
+ id="tspan9675-7"
+ x="437.88541"
+ y="54.635624"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(2) Set to 50:50 visibility</tspan></text>
+ <path
+ style="fill:none;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5562-6)"
+ d="M 53.437255,103.402 V 13.448036 H 434.6722"
+ id="path5464-9"
+ inkscape:connector-curvature="0"
+ sodipodi:nodetypes="ccc" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="19.635624"
+ id="text9677-6"><tspan
+ sodipodi:role="line"
+ id="tspan9675-26"
+ x="437.88541"
+ y="19.635624"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(1) Set to 100% target visibility</tspan></text>
+ <flowRoot
+ xml:space="preserve"
+ id="flowRoot8271"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ transform="translate(0,3.4570313e-6)"><flowRegion
+ id="flowRegion8273"><rect
+ id="rect8275"
+ width="996"
+ height="349"
+ x="-160"
+ y="-82.780457" /></flowRegion><flowPara
+ id="flowPara8277" /></flowRoot></svg>
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_evaluator_example.png b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_evaluator_example.png
new file mode 100644
index 0000000000..e29f63b0d9
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_evaluator_example.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_evaluator_example.svg b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_evaluator_example.svg
new file mode 100644
index 0000000000..ae70bf0a5b
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_evaluator_example.svg
@@ -0,0 +1,409 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:cc="http://creativecommons.org/ns#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:svg="http://www.w3.org/2000/svg"
+ xmlns="http://www.w3.org/2000/svg"
+ xmlns:xlink="http://www.w3.org/1999/xlink"
+ xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+ xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+ version="1.1"
+ id="svg4485"
+ width="700"
+ height="471"
+ viewBox="0 0 700 471"
+ sodipodi:docname="map_view_evaluator_example.svg"
+ inkscape:version="0.92.3 (2405546, 2018-03-11)"
+ inkscape:export-filename="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.evaluator\documentation\UserManual\map_view_evaluator_example.png"
+ inkscape:export-xdpi="96"
+ inkscape:export-ydpi="96">
+ <metadata
+ id="metadata4491">
+ <rdf:RDF>
+ <cc:Work
+ rdf:about="">
+ <dc:format>image/svg+xml</dc:format>
+ <dc:type
+ rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+ <dc:title />
+ </cc:Work>
+ </rdf:RDF>
+ </metadata>
+ <defs
+ id="defs4489">
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5474"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5472"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotM"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker4945"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4943"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.4,0,0,0.4,2.96,0.4)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotS"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4564"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotM"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotM"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4561"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.4,0,0,0.4,2.96,0.4)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-6"
+ style="overflow:visible"
+ inkscape:isstock="true"
+ inkscape:collect="always">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-4"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-5"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-0"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-0"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-3"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-01"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-7"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562-8"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560-3"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9-8"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1-6"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ </defs>
+ <sodipodi:namedview
+ pagecolor="#ffffff"
+ bordercolor="#666666"
+ borderopacity="1"
+ objecttolerance="10"
+ gridtolerance="10"
+ guidetolerance="10"
+ inkscape:pageopacity="0"
+ inkscape:pageshadow="2"
+ inkscape:window-width="1680"
+ inkscape:window-height="1017"
+ id="namedview4487"
+ showgrid="false"
+ inkscape:zoom="1"
+ inkscape:cx="-26.78125"
+ inkscape:cy="265.99957"
+ inkscape:window-x="65"
+ inkscape:window-y="55"
+ inkscape:window-maximized="0"
+ inkscape:current-layer="svg4485" />
+ <image
+ sodipodi:absref="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.evaluator\documentation\UserManual\map_view_evaluator_example_raw.png"
+ xlink:href="map_view_evaluator_example_raw.png"
+ width="427"
+ height="471"
+ preserveAspectRatio="none"
+ id="image4493"
+ x="0"
+ y="1" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-6)"
+ d="m 405.59771,169.14016 h 29.07449 -1.03837"
+ id="path4495-3"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0)"
+ d="m 405.59771,236.00464 h 29.07449 -1.03837"
+ id="path4495-7"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:4.92934513;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-5)"
+ d="m 382.27704,275.06062 h 52.39516 -1.00923"
+ id="path4495-7-1"
+ inkscape:connector-curvature="0"
+ sodipodi:nodetypes="ccc" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5.00747824;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-0)"
+ d="m 382.4479,334.33238 h 52.2243 -1.04148"
+ id="path4495-7-2"
+ inkscape:connector-curvature="0"
+ sodipodi:nodetypes="ccc" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-01)"
+ d="m 405.59771,373.46255 h 29.07449 -1.03837"
+ id="path4495-7-8"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-9)"
+ d="m 405.59771,80.479309 h 29.07449 -1.03837"
+ id="path4495-7-6"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:none;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5562)"
+ d="M 362.01135,69.48537 V 42.812402 h 72.66085"
+ id="path5464"
+ inkscape:connector-curvature="0"
+ sodipodi:nodetypes="ccc" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="49"
+ id="text9677"><tspan
+ sodipodi:role="line"
+ id="tspan9675"
+ x="437.88541"
+ y="49"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(1) Registration slot</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="340.52084"
+ id="text9677-0"><tspan
+ sodipodi:role="line"
+ id="tspan9675-2"
+ x="437.88541"
+ y="340.52084"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(7) Evaluation styles</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="86.520828"
+ id="text9677-5"><tspan
+ sodipodi:role="line"
+ id="tspan9675-8"
+ x="437.88541"
+ y="86.520828"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(2) Registration reset</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="175.52083"
+ id="text9677-1"><tspan
+ sodipodi:role="line"
+ id="tspan9675-1"
+ x="437.88541"
+ y="175.52083"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(4) Moving image slot</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="241.52083"
+ id="text9677-09"><tspan
+ sodipodi:role="line"
+ id="tspan9675-0"
+ x="437.88541"
+ y="241.52083"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(5) Target image slot</tspan><tspan
+ sodipodi:role="line"
+ x="437.88541"
+ y="291.52081"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000"
+ id="tspan4725" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="279.52084"
+ id="text9677-50"><tspan
+ sodipodi:role="line"
+ id="tspan9675-6"
+ x="437.88541"
+ y="279.52084"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(6) Start/Stop button</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="378.52084"
+ id="text9677-3"><tspan
+ sodipodi:role="line"
+ id="tspan9675-91"
+ x="437.88541"
+ y="378.52084"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(8) Style specific settings</tspan></text>
+ <flowRoot
+ xml:space="preserve"
+ id="flowRoot4717"
+ style="fill:black;stroke:none;stroke-opacity:1;stroke-width:1px;stroke-linejoin:miter;stroke-linecap:butt;fill-opacity:1;font-family:sans-serif;font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;letter-spacing:0px;word-spacing:0px"><flowRegion
+ id="flowRegion4719"><rect
+ id="rect4721"
+ width="337"
+ height="48"
+ x="353"
+ y="188" /></flowRegion><flowPara
+ id="flowPara4723" /></flowRoot> <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-9-8)"
+ d="M 233.34176,115.47931 H 434.6722 427.48186"
+ id="path4495-7-6-1"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="121.52084"
+ id="text9677-5-0"><tspan
+ sodipodi:role="line"
+ id="tspan9675-8-4"
+ x="437.88541"
+ y="121.52084"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(3) Auto select option</tspan></text>
+</svg>
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_evaluator_example_raw.png b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_evaluator_example_raw.png
new file mode 100644
index 0000000000..ce373edb1b
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_evaluator_example_raw.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_example.png b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_example.png
deleted file mode 100644
index 496925adee..0000000000
Binary files a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_example.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/plugin.xml b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/plugin.xml
index 015b7372b2..ab99f800b2 100644
--- a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/plugin.xml
+++ b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/plugin.xml
@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<plugin>
<extension point="org.blueberry.ui.views">
- <view id="org.mitk.views.matchpoint.evaluation.editor"
+ <view id="org.mitk.views.matchpoint.evaluator"
name="MatchPoint Registration Evaluator"
class="QmitkMatchPointRegistrationEvaluator"
category="Registration"
icon="resources/evaluator.svg" />
</extension>
</plugin>
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/Manual.dox
index ac1d07d340..39073f4f70 100644
--- a/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/Manual.dox
+++ b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/Manual.dox
@@ -1,64 +1,55 @@
/**
-\page org_mitk_gui_qt_matchpoint_framereg The MatchPoint Motion/Frame Correction View
+\page org_mitk_views_matchpoint_framereg The MatchPoint Frame Correction View
\imageMacro{"map_framereg_icon_doc.svg", "Icon of the MatchPoint Algorithm Control", 3}
\tableofcontents
\section MAP_FRAME_Introduction Introduction
-This plugin offers the user a way to use a selected registration algorithm in order to make a frame/motion correction
-for a selected 3D+t images. The plugin is for example helpfull if you have a dynamic image with motion artifacts in same
-time points and you want to reduce/remove this motion artifacts.
-For the selection of an algorithm please see MatchPoint Algorithm Browser (\ref de_dkfz_matchpoint_mitk_gui_qt_algorithm_browser).
+This view offers the user a way to use a selected registration algorithm in order to apply a frame correction to a selected 3D+t image.
+This is for example useful if you have a dynamic image with motion artifacts in some time points and you want to reduce/remove these motion artifacts.
-\section MAP_FRAME_Contact Contact information
-This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics
-and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support,
-find a bug or have a feature request, feel free to contact us at www.mitk.org.
\section MAP_FRAME_Usage Usage
-\imageMacro{"map_framereg_example.png" , "Example screenshot showing the plugin in use.", 15}
-To use the plugin a registration algorithm must be loaded and the image must be selected, that should be corrected.\n
-The correction is performed that every frame/timpoint of the image is registered to the first frame. And the corrected frames
-is mapped in the same geometry then the first frame.\n
-If an algorithm is loaded and input images are selected, the plugin will automatically switch to the "Execution" tab.
+\imageMacro{"map_framereg_example.png" , "Example screenshot of the view.", 15}
+To use the view, a 3D+t image must be selected and a registration algorithm must be loaded. For the selection of an algorithm please see \ref org_mitk_views_matchpoint_algorithm_browser.\n
+The correction is performed such that every time frame of the image is registered to the first time frame. And the corrected time frames are mapped to the same geometry as the first frame.\n
+If an algorithm is loaded and an input images is selected, the view will automatically switch to the <i>Execution</i> tab.
\subsection MAP_FRAME_Usage_selection Algorithm selection tab
\imageMacro{map_step1_selection.png, "Details of the algorithm selection tab.", 6}
-In this tab you can load/"book" the algorithm selected in the MatchPoint Algorithm Browser. In the tab you see the ID of the algorithm
-selected by the browser and its profile information.\n
-If you press "Load selected algorithm", the algorithm will be used by the plugin for the frame correction and the name of the algorithm occurs
-in the text field "Loaded algorithm" (at the top of the plugin view).\n
-At this point, it has no effect if you change the the selection in the browser. The plugin will keep the loaded algorithm until
-you choose to load another one.
+In this tab, you can load the algorithm selected in the MatchPoint Algorithm Browser. In the area below the selection button the profile information of the registration algorithm is displayed.
+For a detailed description of the profile characteristics the user is referred to \ref org_mitk_views_matchpoint_algorithm_browser .\n
+When clicking the <i>Load selected algorithm</i> button, the selected algorithm will be used by the view for the frame correction and the name of the algorithm will be displayed in the text field <i>Loaded algorithm</i> at the top of the view.\n
+At this point, it has no effect if you change the the selection in the algorithm browser. The view will keep the loaded algorithm until you choose to load another one.
\subsection MAP_FRAME_Usage_exec Execution tab
\imageMacro{map_step2_execution.png, "Details of the execution tab.", 6}
In this tab you can specify a name for the correction job (this will determine the names of the result nodes in the data manager).\n
-"Start" will trigger the correction process.
+Clicking the <i>Start</i> button will trigger the correction process.
\subsection MAP_FRAME_Usage_settings Settings tab
\imageMacro{map_step3_settings.png, "Details of the settings tab.", 6}
-In this tab, you can (1) define the mapping settings \ref MAP_FRAME_Mapper_Settings "(See details)", used for the corrected frames, or (2) parametrize the loaded algorithm (before it starts), if it offers any possibility to do so.
+In this tab, you can configure the \ref MAP_FRAME_Mapper_Settings which are used for the corrected frames, or parameterize the loaded algorithm (before it starts), if it offers any possibility to do so.
-\subsubsection MAP_FRAME_Mapper_Settings Mapper settings
+\subsubsection MAP_FRAME_Mapper_Settings Mapping settings
For the mapping of corrected images, you have several settings available:\n
-\li "Allow undefined pixels": Activate to handle pixels of the result image that are not in the field of view of the input image. This pixel will get the "padding value".
-\li "Allow error pixels": Activate to handle pixels of the result image that can not be mapped because the registration does not support this part of the output image. This pixel will get the "error value".
-\li "Interpolator": Set to choose the interpolation strategy that should be used for mapping. \ref MAP_FRAME_Interpolation "(see details)"
+\li <b>Allow undefined pixels</b> Activate to handle pixels of the result image that are not in the field of view of the input image. These pixels will get the <i>padding value</i>.
+\li <b>Allow error pixels</b> Activate to handle pixels of the result image that can not be mapped because the registration does not support this part of the output image. These pixels will get the <i>error value</i>.
+\li <b>Interpolator</b> Set to choose the interpolation strategy that should be used for mapping. See details at \ref MAP_FRAME_Interpolation .
\subsubsection MAP_FRAME_Interpolation Interpolation
You can choose from the following interpolation strategies:\n
-\li "nearest neighbour": Use the value of the nearest pixel. Fastest, but high interpolation errors for gray value images. Right choice for label images or masks.
-\li "Linear": Fast linear interpolation with often sufficient quality. Tends to blur edges.
-\li "BSpline (3rd order)": Good trade off between time and quality.
-\li "Windowed Sinc (Hamming)": Good interpolation quality but very time consuming.
-\li "Windowed Sinc (Welch)": Good interpolation quality but very time consuming.
+\li <b>Nearest Neighbour</b> Use the value of the nearest pixel. Fastest, but high interpolation errors for gray value images. Right choice for label images or masks.
+\li <b>Linear"</b> Fast linear interpolation with often sufficient quality. Tends to blur edges.
+\li <b>BSpline (3rd order)</b> Good trade off between time and quality.
+\li <b>Windowed Sinc (Hamming)</b> Good interpolation quality but very time consuming.
+\li <b>Windowed Sinc (Welch)</b> Good interpolation quality but very time consuming.
\subsection MAP_FRAME_Usage_frame_selection Frame selection tab
\imageMacro{map_step4_frameselection.png, "Details of the frame selection tab.", 6}
-In this tab you can specify the frames of the currently selected image that should be corrected. As default all frames of an image will be corrected.
-If you only select specific frames, these frames will be corrected all other frames will be just copied unchanged.
+In this tab you can specify the frames of the currently selected image that should be corrected. As default all frames of an image will be selected.
+If you only select specific frames, these frames will be corrected whilst all other frames will be just copied unchanged.
*/
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_framereg_example.png b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_framereg_example.png
index 239a753a9b..ba24c8c777 100644
Binary files a/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_framereg_example.png and b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_framereg_example.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_step1_selection.png b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_step1_selection.png
index 0996b98c1e..61c45463ae 100644
Binary files a/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_step1_selection.png and b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_step1_selection.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_step2_execution.png b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_step2_execution.png
index 500141580c..bf7ba62daf 100644
Binary files a/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_step2_execution.png and b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_step2_execution.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_step3_settings.png b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_step3_settings.png
index 4e5bbad475..cfac4acd7b 100644
Binary files a/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_step3_settings.png and b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_step3_settings.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_step4_frameselection.png b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_step4_frameselection.png
index 9a1747713f..bc48d796f1 100644
Binary files a/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_step4_frameselection.png and b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map_step4_frameselection.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.framereg/plugin.xml b/Plugins/org.mitk.gui.qt.matchpoint.framereg/plugin.xml
index 0386b0c385..92f222248b 100644
--- a/Plugins/org.mitk.gui.qt.matchpoint.framereg/plugin.xml
+++ b/Plugins/org.mitk.gui.qt.matchpoint.framereg/plugin.xml
@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<plugin>
<extension point="org.blueberry.ui.views">
- <view id="org.mitk.views.matchpoint.algorithm.framereg"
+ <view id="org.mitk.views.matchpoint.framereg"
name="MatchPoint Frame Correction"
class="QmitkMatchPointFrameCorrection"
category="Registration"
icon="resources/icon.svg" />
</extension>
</plugin>
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/Manual.dox
index d4af889568..3eb87ca121 100644
--- a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/Manual.dox
+++ b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/Manual.dox
@@ -1,69 +1,77 @@
/**
-\page org_mitk_gui_qt_matchpoint_manipulator The MatchPoint Registration Manipulator View
+\page org_mitk_views_matchpoint_manipulator The MatchPoint Registration Manipulator View
\imageMacro{map_manipulator_icon_doc.svg, "Icon of the MatchPoint Registration Manipulator", 3}
\tableofcontents
\section MAP_REGMANIP_Introduction Introduction
This view offers the possibility to manually manipulate a registration to establish a good mapping between data.
-The effect of manipulation is visualized with to user defined images to allow visual inspection.\n
+The effect of manipulation is visualized with two user defined images to allow for visual inspection.\n
It is one of several MatchPoint registration plug-ins.\n
-\imageMacro{map_view_example.png, "Example screenshot showing the plug-in in use", 10}
-
-\section MAP_REGMANIP_Contact Contact information
-This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics
-and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support,
-find a bug or have a feature request, feel free to contact us at www.mitk.org.
\section MAP_REGMANIP_Usage Usage
-\imageMacro{map_view_steps.png, "Illustration of the workflow steps.", 7}
-The typical workflow with the manipulator has following steps/sections:
-1. <b>Source selection</b>: You can choose between starting a new registration and using a selected registration. For later option,
-the registration must be selected in the data manager.
+\imageMacro{map_view_manipulator_example.png, "Example screenshot showing the main elements of the view used to start a manipulation.", 14}
+The typical workflow with the manipulator has following steps/sections:\n\n
+(1) <b>Source selection</b>: You can choose between starting a new registration and using a selected registration. For latter option,
+the registration must be selected (see (2)).
\remark If you choose a new registration, the manipulator will automatically pre initialize this new transform
to align the centers of the used images and therefore starts with sensible settings.
\remark If you choose an existing registration, the registration will *not* be altered. It serves as template/baseline
for the manipulation, which will be "on top" of the existing registration.
-2. <b>Image selection</b>: To allow visual inspection of the manipulation to images are needed. If you have selected a registration
-(independent from the source selection mode) the manipulator will use the moving and target images used to determine the selected
-registration as images for the manipulation. You can also explicitly select images in the data manager (press shift while
-selecting for multi select).
-3. <b>Start manual registration</b>: If all settings are valid, you can start the manipulation. The render windows will automatically
-switch to the visual inspection mode. The views will be reinitialized to the field of view of the target image.
+(2) <b>Registration slot</b>: Shows the currently selected registration that serves as baseline. Only active if (1) is selected appropriately. Click to change.\n\n
+
+(3) <b>Auto select option</b>: If active the view will try to deduce and automatically select (if loaded in the application) the moving and target image when the baseline registration changes. The view assumes that the moving and target images used to determine the registration should be used to illustrate the effects of the manipulation.\n\n
+
+(4) <b>Moving image slot</b>: To allow for visual inspection of the manipulation a moving image must be specified. This image is mapped by the manipulated registration to illustrate the effects of the manipulation. Click to change the image.\n\n
+
+(5) <b>Target image slot</b>: To allow for visual inspection of the manipulation a target image must be specified. This image is used to compare against the mapped moving image to illustrate the effects of the manipulation. Click to change the image.\n\n
+
+(6) <b>Start manual registration</b>: If all settings are valid, you can start the manipulation. The render windows will automatically
+switch to the visual inspection mode. The views will be reinitialized to the field of view of the target image.\n\n\n
+
+\imageMacro{map_view_manipulator_started.png, "Controls after the manipulation session is started.", 14}
+
+(7) <b>New registration name</b>: You may choose to give the resulting registration a special name.\n\n
+
+(8) Additionally you can choose the convenience
+option to map the moving image with the confirmed registration automatically and also store the mapped image.\n\n
+
+(9) <b>Settings</b>: You can alter the settings of the transform (\ref MAP_REGMANIP_TransSettings) and the rendering settings (\ref MAP_REGMANIP_EvalSettings) for the visual inspection.\n\n
+
+(10) <b>Translation parameters</b>: You can alter the translation parameter of the transform by using the sliders or the spinboxes. For more details see transform settings section (\ref MAP_REGMANIP_TransSettings).\n\n
+
+(11) <b>Rotation parameters</b>: You can alter the rotation parameter of the transform by using the sliders or the spinboxes. For more details see transform settings section (\ref MAP_REGMANIP_TransSettings).\n\n
-4. <b>Generation settings</b>: You may choose to give the resulting registration a special name. Additionally you can choose the convenience
-option to map the moving image with the confirmed registration automatically.
+(12) <b>Center of rotation</b>: You may choose the center of rotation for your manipulation. For more details see transform settings section (\ref MAP_REGMANIP_TransSettings).\n\n
-5. <b>Settings</b>: You can alter the settings of the transform (\ref MAP_REGMANIP_TransSettings) and the rendering settings (\ref MAP_REGMANIP_EvalSettings)
-for the visual inspection.
+(13) <b>Confirmation</b>: You may confirm the determined registration and store it in the data storage with the given name. The manipulation session will be automatically closed.\n\n
-6. <b>Cancel or confirmation</b>: You may cancel the manipulation process (Closing the view equals cancelation) or confirm the determined registration
-and store it in the data storage with the given name.\n
+(14) <b>Cancel</b>: You may cancel the session any time. No changes will be stored and the manipulation session will be automatically closed.\n
\section MAP_REGMANIP_TransSettings Transformation settings
You can alter the translation and the rotation of the transform. In addition you may choose the center of rotation type.
You have the following options:\n
- <b>Moving image center</b>: Rotate around the center of the moving image.
- <b>World origin</b>: Rotate around (0.0,0.0,0.0), the world origin.
- <b>Current navigator position</b>: Rotate around the current navigator position in the render views.
\remark <em>FAQ: Why are the translation values "jumping" when I change the center mode or when I am rotating?</em>\n
The reason is the relation between center, rotation, and translation.\n
A transformation is defined as x' = R (x - C) + C + T\n
where x': transformed point; x: point to transform; R: rotation matrix; C: center point; T: translation vector.\n
The offset of a transform is defined as O = -RC + C + T\n
The offset as well as the rotation matrix stay constant if the center point changes, therefore the translation has to be altered.
-\note To ease the orientation, the edit fields have background colours which resemble the colours of the plane the changes will
+\note To ease the orientation, the edit fields have background colors which resemble the colors of the plane the changes will
"happen".\n
For translation, the translation vector will be perpendicular to the indicated plane (The image moves "through" the plane).
For rotation, the rotation axis will be perpendicular to the indicated plane.
\section MAP_REGMANIP_EvalSettings Evaluation settings
-The settings you can choose are equal to the settings of the evaluation view (\ref org_mitk_gui_qt_matchpoint_evaluator).
+The settings you can choose are equal to the settings of the evaluation view (\ref org_mitk_views_matchpoint_evaluator).
Please see the documentation of the MatchPoint Registration Evaluator view for more details.
*/
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_example.png b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_example.png
deleted file mode 100644
index ab8d6e5d1f..0000000000
Binary files a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_example.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example.png b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example.png
new file mode 100644
index 0000000000..d3dbb5e430
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example.svg b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example.svg
new file mode 100644
index 0000000000..cf290b44e4
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example.svg
@@ -0,0 +1,377 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:cc="http://creativecommons.org/ns#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:svg="http://www.w3.org/2000/svg"
+ xmlns="http://www.w3.org/2000/svg"
+ xmlns:xlink="http://www.w3.org/1999/xlink"
+ xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+ xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+ version="1.1"
+ id="svg4485"
+ width="641.82294"
+ height="751"
+ viewBox="0 0 641.82294 751"
+ sodipodi:docname="map_view_manipulator_example.svg"
+ inkscape:version="0.92.3 (2405546, 2018-03-11)"
+ inkscape:export-filename="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.manipulator\documentation\UserManual\map_view_manipulator_example.png"
+ inkscape:export-xdpi="96"
+ inkscape:export-ydpi="96">
+ <metadata
+ id="metadata4491">
+ <rdf:RDF>
+ <cc:Work
+ rdf:about="">
+ <dc:format>image/svg+xml</dc:format>
+ <dc:type
+ rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+ <dc:title />
+ </cc:Work>
+ </rdf:RDF>
+ </metadata>
+ <defs
+ id="defs4489">
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5474"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5472"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotM"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker4945"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4943"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.4,0,0,0.4,2.96,0.4)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotS"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4564"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotM"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotM"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4561"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.4,0,0,0.4,2.96,0.4)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-6"
+ style="overflow:visible"
+ inkscape:isstock="true"
+ inkscape:collect="always">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-4"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-5"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-0"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-0"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-3"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-01"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-7"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562-8"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560-3"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9-8"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1-6"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ </defs>
+ <sodipodi:namedview
+ pagecolor="#ffffff"
+ bordercolor="#666666"
+ borderopacity="1"
+ objecttolerance="10"
+ gridtolerance="10"
+ guidetolerance="10"
+ inkscape:pageopacity="0"
+ inkscape:pageshadow="2"
+ inkscape:window-width="1680"
+ inkscape:window-height="987"
+ id="namedview4487"
+ showgrid="false"
+ inkscape:zoom="1"
+ inkscape:cx="275.35097"
+ inkscape:cy="364.89936"
+ inkscape:window-x="-8"
+ inkscape:window-y="-8"
+ inkscape:window-maximized="1"
+ inkscape:current-layer="svg4485" />
+ <image
+ sodipodi:absref="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.manipulator\documentation\UserManual\map_view_manipulator_example_raw.png"
+ xlink:href="map_view_manipulator_example_raw.png"
+ y="0"
+ x="0"
+ id="image4493"
+ preserveAspectRatio="none"
+ height="751"
+ width="426" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-6)"
+ d="m 405.59771,228.14016 h 29.07449 -1.03837"
+ id="path4495-3"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0)"
+ d="m 405.59771,295.00464 h 29.07449 -1.03837"
+ id="path4495-7"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:4.92934513;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-5)"
+ d="m 382.27704,334.06062 h 52.39516 -1.00923"
+ id="path4495-7-1"
+ inkscape:connector-curvature="0"
+ sodipodi:nodetypes="ccc" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5.00747824;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-0)"
+ d="m 382.4479,81.33238 h 52.2243 -1.04148"
+ id="path4495-7-2"
+ inkscape:connector-curvature="0"
+ sodipodi:nodetypes="ccc" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-9)"
+ d="m 405.59771,127.47931 h 29.07449 -1.03837"
+ id="path4495-7-6"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="87.520844"
+ id="text9677-0"><tspan
+ sodipodi:role="line"
+ id="tspan9675-2"
+ x="437.88541"
+ y="87.520844"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(1) Source selection</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="133.52083"
+ id="text9677-5"><tspan
+ sodipodi:role="line"
+ id="tspan9675-8"
+ x="437.88541"
+ y="133.52083"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(2) Registration slot</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="234.52083"
+ id="text9677-1"><tspan
+ sodipodi:role="line"
+ id="tspan9675-1"
+ x="437.88541"
+ y="234.52083"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(4) Moving image slot</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="300.52081"
+ id="text9677-09"><tspan
+ sodipodi:role="line"
+ id="tspan9675-0"
+ x="437.88541"
+ y="300.52081"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(5) Target image slot</tspan><tspan
+ sodipodi:role="line"
+ x="437.88541"
+ y="350.52081"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000"
+ id="tspan4725" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="338.52084"
+ id="text9677-50"><tspan
+ sodipodi:role="line"
+ id="tspan9675-6"
+ x="437.88541"
+ y="338.52084"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(6) Start button</tspan></text>
+ <flowRoot
+ xml:space="preserve"
+ id="flowRoot4717"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ transform="translate(0,-1)"><flowRegion
+ id="flowRegion4719"><rect
+ id="rect4721"
+ width="337"
+ height="48"
+ x="353"
+ y="188" /></flowRegion><flowPara
+ id="flowPara4723" /></flowRoot> <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-9-8)"
+ d="M 233.34176,164.47931 H 434.6722 427.48186"
+ id="path4495-7-6-1"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="170.52084"
+ id="text9677-5-0"><tspan
+ sodipodi:role="line"
+ id="tspan9675-8-4"
+ x="437.88541"
+ y="170.52084"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(3) Auto select option</tspan></text>
+</svg>
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example_raw.png b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example_raw.png
new file mode 100644
index 0000000000..b3afbb095f
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example_raw.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started.png b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started.png
new file mode 100644
index 0000000000..b467ba42bc
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started.svg b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started.svg
new file mode 100644
index 0000000000..ee1a78f1dc
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started.svg
@@ -0,0 +1,455 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:cc="http://creativecommons.org/ns#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:svg="http://www.w3.org/2000/svg"
+ xmlns="http://www.w3.org/2000/svg"
+ xmlns:xlink="http://www.w3.org/1999/xlink"
+ xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+ xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+ version="1.1"
+ id="svg4485"
+ width="699.35419"
+ height="416.01044"
+ viewBox="0 0 699.35419 416.01044"
+ sodipodi:docname="map_view_manipulator_started.svg"
+ inkscape:version="0.92.3 (2405546, 2018-03-11)"
+ inkscape:export-filename="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.manipulator\documentation\UserManual\map_view_manipulator_started.png"
+ inkscape:export-xdpi="96"
+ inkscape:export-ydpi="96">
+ <metadata
+ id="metadata4491">
+ <rdf:RDF>
+ <cc:Work
+ rdf:about="">
+ <dc:format>image/svg+xml</dc:format>
+ <dc:type
+ rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+ <dc:title />
+ </cc:Work>
+ </rdf:RDF>
+ </metadata>
+ <defs
+ id="defs4489">
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5474"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5472"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotM"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker4945"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4943"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.4,0,0,0.4,2.96,0.4)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotS"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4564"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotM"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotM"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4561"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.4,0,0,0.4,2.96,0.4)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-6"
+ style="overflow:visible"
+ inkscape:isstock="true"
+ inkscape:collect="always">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-4"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-5"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-0"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-0"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-3"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-01"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-7"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562-8"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560-3"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9-8"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1-6"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9-8-3"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1-6-3"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-58"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-19"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ </defs>
+ <sodipodi:namedview
+ pagecolor="#ffffff"
+ bordercolor="#666666"
+ borderopacity="1"
+ objecttolerance="10"
+ gridtolerance="10"
+ guidetolerance="10"
+ inkscape:pageopacity="0"
+ inkscape:pageshadow="2"
+ inkscape:window-width="1680"
+ inkscape:window-height="987"
+ id="namedview4487"
+ showgrid="false"
+ inkscape:zoom="1"
+ inkscape:cx="240.60215"
+ inkscape:cy="29.909777"
+ inkscape:window-x="-8"
+ inkscape:window-y="-8"
+ inkscape:window-maximized="1"
+ inkscape:current-layer="svg4485" />
+ <image
+ sodipodi:absref="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.manipulator\documentation\UserManual\map_view_manipulator_started_raw.png"
+ xlink:href="map_view_manipulator_started_raw.png"
+ width="426"
+ height="400"
+ preserveAspectRatio="none"
+ id="image4493"
+ x="0"
+ y="0" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-6)"
+ d="m 405.59771,228.14016 h 29.07449 -1.03837"
+ id="path4495-3"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0)"
+ d="m 405.59771,379.00464 h 29.07449 -1.03837"
+ id="path4495-7"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:4.92934513;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-5)"
+ d="m 382.27704,344.06062 h 52.39516 -1.00923"
+ id="path4495-7-1"
+ inkscape:connector-curvature="0"
+ sodipodi:nodetypes="ccc" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5.00747824;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-0)"
+ d="m 382.4479,33.33238 h 52.2243 -1.04148"
+ id="path4495-7-2"
+ inkscape:connector-curvature="0"
+ sodipodi:nodetypes="ccc" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-9)"
+ d="m 405.59771,123.47931 h 29.07449 -1.03837"
+ id="path4495-7-6"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="39.520844"
+ id="text9677-0"><tspan
+ sodipodi:role="line"
+ id="tspan9675-2"
+ x="437.88541"
+ y="39.520844"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(7) New registration name</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="129.52083"
+ id="text9677-5"><tspan
+ sodipodi:role="line"
+ id="tspan9675-8"
+ x="437.88541"
+ y="129.52083"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(10) Translation parameters</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="234.52083"
+ id="text9677-1"><tspan
+ sodipodi:role="line"
+ id="tspan9675-1"
+ x="437.88541"
+ y="234.52083"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(11) Rotation parameters</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="384.52081"
+ id="text9677-09"><tspan
+ sodipodi:role="line"
+ id="tspan9675-0"
+ x="437.88541"
+ y="384.52081"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(13) Confirm registration</tspan><tspan
+ sodipodi:role="line"
+ x="437.88541"
+ y="434.52081"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000"
+ id="tspan4725" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="348.52084"
+ id="text9677-50"><tspan
+ sodipodi:role="line"
+ id="tspan9675-6"
+ x="437.88541"
+ y="348.52084"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(12) Center of rotation type</tspan></text>
+ <flowRoot
+ xml:space="preserve"
+ id="flowRoot4717"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ transform="translate(0,-1)"><flowRegion
+ id="flowRegion4719"><rect
+ id="rect4721"
+ width="337"
+ height="48"
+ x="353"
+ y="188" /></flowRegion><flowPara
+ id="flowPara4723" /></flowRoot> <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-9-8)"
+ d="M 233.34176,58.47931 H 434.6722 427.48186"
+ id="path4495-7-6-1"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="64.520844"
+ id="text9677-5-0"><tspan
+ sodipodi:role="line"
+ id="tspan9675-8-4"
+ x="437.88541"
+ y="64.520844"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(8) Auto image mapping</tspan></text>
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-9-8-3)"
+ d="M 274.59782,84.4793 H 434.6722 428.95528"
+ id="path4495-7-6-1-5"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="90.520836"
+ id="text9677-5-0-6"><tspan
+ sodipodi:role="line"
+ id="tspan9675-8-4-6"
+ x="437.88541"
+ y="90.520836"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(9) Setting tabs</tspan></text>
+ <path
+ style="fill:none;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-58)"
+ d="m 182.433,380.8786 v 25.12606 h 252.2392 -8.61565"
+ id="path4495-7-7"
+ inkscape:connector-curvature="0"
+ sodipodi:nodetypes="cccc" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="437.88541"
+ y="411.52084"
+ id="text9677-09-1"><tspan
+ sodipodi:role="line"
+ id="tspan9675-0-9"
+ x="437.88541"
+ y="411.52084"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(14) Cancel manipulation</tspan><tspan
+ sodipodi:role="line"
+ x="437.88541"
+ y="461.52084"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000"
+ id="tspan4725-3" /></text>
+ <flowRoot
+ xml:space="preserve"
+ id="flowRoot962"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"><flowRegion
+ id="flowRegion964"><rect
+ id="rect966"
+ width="807"
+ height="661"
+ x="-64"
+ y="-26.989563" /></flowRegion><flowPara
+ id="flowPara968"></flowPara></flowRoot></svg>
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started_raw.png b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started_raw.png
new file mode 100644
index 0000000000..ffac708563
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started_raw.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_steps.png b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_steps.png
deleted file mode 100644
index 1ddf20fc83..0000000000
Binary files a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_steps.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/Manual.dox
index 1a23e3e98a..ede511a3e5 100644
--- a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/Manual.dox
+++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/Manual.dox
@@ -1,21 +1,88 @@
/**
-\page org_mitk_gui_qt_matchpoint_visualizer The MatchPoint Registration Visualizer View
+\page org_mitk_views_matchpoint_visualizer The MatchPoint Registration Visualizer View
\imageMacro{map_vis_icon_doc.svg, "Icon of the Registration Visualizer",3}
\tableofcontents
\section MAP_VIS_Introduction Introduction
-This view is in development to offer the user a way to visualize MatchPoint registrations in a MITK scene.
-Currently only a simple grid visualization and glyph visualization is implemented.\n
-\remark <b>This is an experimental version and work in progress.</b> So please excuse errors or usage issues and report them. This view will be improved and polished with the next releases.
-
-\section MAP_VIS_Contact Contact information
-This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics
-and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support,
-find a bug or have a feature request, feel free to contact us at www.mitk.org.
+This view is in development to offer the user a way to visualize MatchPoint registrations (so the transformation/deformation field they represent) in a MITK scene.
+Currently, a simple grid visualization and glyph visualization is implemented.\n
+\remark <b>This is an experimental version and work in progress.</b> So please excuse errors or usage issues and report them at https://phabricator.mitk.org.
\section MAP_VIS_Usage Usage
-Oops. Documentation is missing and to be done.
-*/
+\imageMacro{map_view_visualizer_example.png, "Example screenshot showing the main elements of the view used to visualize a registration.", 14}
+The view has following steps/sections:\n\n
+(1) <b>Registration slot</b>: Shows the currently selected registration which is visualized and whose visualization settings should be altered. Click to change.\n\n
+
+(2) <b>Registration information</b>: General information on the selected registration.\n\n
+
+(3) <b>Update visual settings</b>: By clicking the button the current settings will be accepted and the visualization of the registration will be updated accordingly.\n\n
+
+(4) <b>Mapping direction</b>: Allows to select the mapping direction that should be visualized (more details see below \ref MAP_VIS_Direction).\n\n
+
+(5) <b>Visualization style</b>: Select how the registration should be visualized. Currently two options are available.:
+- Grid: Visualize as a wire frame grid that is deformed by the registration. The magnitude of deformation can be encoded in the grid color (cf style example "a)" below).
+- Glyph: Visualize as a cloud of arrows that follow the deformation vectors of the registrations. The magnitude of deformation can be encoded in the glyph color (cf style example "f)" below).
+
+More details can be found in the settings and style section below.
+
+\imageMacro{map_view_visualizer_style_example.png, "Example of the appearance of different style settings: a) grid style; b) grid with no color interpolation; c) grid in unicolor; d) grid with different grid frequency (frequency=1); e) grid also showing start grid (in gray); f) glyph style.", 14}
+
+\section MAP_VIS_Settings_vis Visualization settings
+\imageMacro{map_view_visualizer_vis_settings.png, "Visualization settings offered by view.", 8}
+(6) <b>Color style</b>: The following color styles are available:
+- uni color: everything painted in the selected color (cf style example "c)"). Click on the color button to change the used color.
+- vector magnitode: the color is depending on the respective vector magnitude of the deformation field (cf style example "a)" and "b)"). See (7) for instructions to change the used color encoding for the magnitude.
+
+(7) <b>Color coding settings</b>: One can change the color and associated vector length (in mm) for 4 classes of magnitude (negligible, small, medium and large). The color is encoded accordingly.\n\n
+
+(8) <b>Interpolate colors</b>: By default activated, the colors between to magnitude classes (see (7)) will be linear interpolated (e.g. with the settings given in the example shifts of 5 mm will be yellow, 10 mm will be orange and >=15 mm will be red). If interpolation is deactivated the color of one class is used till a next higher class is reached. Cf style example "a)" and "b)", in "b)" no red color can be seen because no shift was 15 mm or greater (magnitude class "large").
+
+\section MAP_VIS_Settings_grid Grid settings
+\imageMacro{map_view_visualizer_grid_settings.png, "Grid settings offered by view.", 8}
+These are only available for style "grid".\n\n
+(9) <b>Grid frequency</b>: Allows to control how spares the grid frame should be. With a frequency n only each n-th element of the frame will be visualized, so the visual grid has n-times the spacing of the FOV. One can also achieve something similar with just changing the FOV spacing (see below), but using the frequency allows for a sparse frame and still having a high resolution in the frame deformation. The latter one would loose if just using a low FOV spacing. Style example "a)" and "d)" illustrate different frequency settings and there effect.\n\n
+
+(10) <b>Start grid</b>: If activated also the start grid of the registration will (for the chosen direction) will be visible. This is another grid specific possibility to illustrate the amount of deformation (cf style example "e)").\n\n
+
+(11) <b>Start grid color</b>: Select the color that should be used for the start grid. Click on the color button to change the used color.
+
+\section MAP_VIS_Settings_FOV Field of view (FOV) settings
+\imageMacro{map_view_visualizer_FOV_settings.png, "FOV settings offered by view.", 8}
+The field of view defines the area of space (grid) that should be used for the visualization of the registration.\n\n
+
+(12) <b>Size</b>: Size of the FOV in mm.\n\n
+
+(13) <b>Origin</b>: Origin of the FOV in mm.\n\n
+
+(14) <b>Spacing</b>: Spacing of the FOV in mm. This directly impact the visualization's level of detail. IMPORTANT: Please be careful with setting small spacings, as it can lead to computational very expensive visualizations.\n\n
+
+(15) <b>Orientation</b>: Orientation matrix of the FOV (only readable).\n\n
+
+(16) <b>FOV Reference slot</b>: Select an image that should be used to define the geometric properties of the FOV. By default (and available) the target image used to determine the registration will be used. Click slot to change the FOV reference.\n\n
+
+(17) <b>Relevant FOV reference properties</b>: One can select which properties of the reference image will be used to specify the FOV.\n\n
+
+\section MAP_VIS_Direction Information regarding the directions
+
+Registrations can have two supported directions (direct and inverse). The direct kernel maps from the moving space into the target space, so this is the direction that "naively" people assume when they think about registrations. But practically it is only used to map continuous data like point sets. The inverse kernel maps from the target space into the moving space and is used to map images by so called inverse mapping. The effect is most obvious in the glyph style, where the glyphs points from the mapped space to the point in the moving space.
+
+\section MAP_VIS_used_data Data reference
+The data visible in the visualization styles images is part of the Patient 1 of the DIR_validation_data data set.
+For further information:
+https://www.creatis.insa-lyon.fr/rio/dir_validation_data
+
+--------------
+
+ By downloading this data, you agreeing to follow these guidelines. When using any of the data provided for publications, please make reference to:
+
+ The institution from which they were obtained: the Léon Bérard Cancer Center & CREATIS lab, Lyon, France.
+ The article containing the description of this data:
+
+ J. Vandemeulebroucke, S. Rit, J. Kybic, P. Clarysse, and D. Sarrut. Spatiotemporal motion estimation for respiratory-correlated imaging of the lungs. In Med Phys, 2011, 38(1), 166-178. pdf
+
+---------------
+
+*/
\ No newline at end of file
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings.png
new file mode 100644
index 0000000000..7de94d99f5
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings.svg b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings.svg
new file mode 100644
index 0000000000..bf6621589a
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings.svg
@@ -0,0 +1,472 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:cc="http://creativecommons.org/ns#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:svg="http://www.w3.org/2000/svg"
+ xmlns="http://www.w3.org/2000/svg"
+ xmlns:xlink="http://www.w3.org/1999/xlink"
+ xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+ xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+ version="1.1"
+ id="svg4485"
+ width="804.48956"
+ height="124"
+ viewBox="0 0 804.48956 124"
+ sodipodi:docname="map_view_visualizer_FOV_settings.svg"
+ inkscape:version="0.92.3 (2405546, 2018-03-11)"
+ inkscape:export-filename="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.visualizer\documentation\UserManual\map_view_visualizer_FOV_settings.png"
+ inkscape:export-xdpi="96"
+ inkscape:export-ydpi="96">
+ <metadata
+ id="metadata4491">
+ <rdf:RDF>
+ <cc:Work
+ rdf:about="">
+ <dc:format>image/svg+xml</dc:format>
+ <dc:type
+ rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+ <dc:title></dc:title>
+ </cc:Work>
+ </rdf:RDF>
+ </metadata>
+ <defs
+ id="defs4489">
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5474"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5472"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotM"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker4945"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4943"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.4,0,0,0.4,2.96,0.4)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotS"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4564"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotM"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotM"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4561"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.4,0,0,0.4,2.96,0.4)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-6"
+ style="overflow:visible"
+ inkscape:isstock="true"
+ inkscape:collect="always">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-4"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-5"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-0"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-0"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-3"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-01"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-7"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562-8"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560-3"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9-8"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1-6"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-3"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-31"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-4"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-16"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9-1"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1-60"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9-5"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1-7"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9-80"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1-2"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ </defs>
+ <sodipodi:namedview
+ pagecolor="#ffffff"
+ bordercolor="#666666"
+ borderopacity="1"
+ objecttolerance="10"
+ gridtolerance="10"
+ guidetolerance="10"
+ inkscape:pageopacity="0"
+ inkscape:pageshadow="2"
+ inkscape:window-width="1680"
+ inkscape:window-height="987"
+ id="namedview4487"
+ showgrid="false"
+ inkscape:zoom="1"
+ inkscape:cx="444.82306"
+ inkscape:cy="7.1012534"
+ inkscape:window-x="-8"
+ inkscape:window-y="-8"
+ inkscape:window-maximized="1"
+ inkscape:current-layer="svg4485" />
+ <image
+ sodipodi:absref="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.visualizer\documentation\UserManual\map_view_visualizer_FOV_settings_raw.png"
+ xlink:href="map_view_visualizer_FOV_settings_raw.png"
+ mask="none"
+ width="331"
+ height="367"
+ preserveAspectRatio="none"
+ id="image4493"
+ x="0"
+ y="0" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-6)"
+ d="m 302.13739,298.1402 h 35.53481 -1.2691"
+ id="path4495-3"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-9)"
+ d="M 125.15508,44.4793 H 337.6722 330.08234"
+ id="path4495-7-6"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="340.88538"
+ y="50.520752"
+ id="text9677-5"><tspan
+ sodipodi:role="line"
+ id="tspan9675-8"
+ x="340.88538"
+ y="50.520752"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(12) Setting the size of the visualization</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="340.88538"
+ y="304.52075"
+ id="text9677-1"><tspan
+ sodipodi:role="line"
+ id="tspan9675-1"
+ x="340.88538"
+ y="304.52075"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(16) Optional slot of a FOV reference</tspan></text>
+ <flowRoot
+ xml:space="preserve"
+ id="flowRoot4717"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ transform="translate(0,-393)"><flowRegion
+ id="flowRegion4719"><rect
+ id="rect4721"
+ width="337"
+ height="48"
+ x="353"
+ y="188" /></flowRegion><flowPara
+ id="flowPara4723" /></flowRoot> <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-4)"
+ d="m 269.75874,343.0047 h 67.91346 -2.42547"
+ id="path4495-7-5"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="340.88538"
+ y="348.521"
+ id="text9677-09-9"><tspan
+ sodipodi:role="line"
+ id="tspan9675-0-2"
+ x="340.88538"
+ y="348.521"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(17) Set relevant FOV reference properties</tspan><tspan
+ sodipodi:role="line"
+ x="340.88538"
+ y="398.521"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000"
+ id="tspan4725-7" /></text>
+ <flowRoot
+ xml:space="preserve"
+ id="flowRoot6290"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ transform="translate(0,-392)"><flowRegion
+ id="flowRegion6292"><rect
+ id="rect6294"
+ width="839"
+ height="562"
+ x="-158"
+ y="273" /></flowRegion><flowPara
+ id="flowPara6296"></flowPara></flowRoot> <flowRoot
+ xml:space="preserve"
+ id="flowRoot6719"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"><flowRegion
+ id="flowRegion6721"><rect
+ id="rect6723"
+ width="620"
+ height="252"
+ x="-129"
+ y="-103" /></flowRegion><flowPara
+ id="flowPara6725"></flowPara></flowRoot> <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-9-1)"
+ d="M 125.15508,91.479382 H 337.6722 330.08234"
+ id="path4495-7-6-0"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="340.88538"
+ y="97.520836"
+ id="text9677-5-1"><tspan
+ sodipodi:role="line"
+ id="tspan9675-8-6"
+ x="340.88538"
+ y="97.520836"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(13) Setting the origin of the visualization</tspan></text>
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-9-5)"
+ d="M 125.15508,140.47938 H 337.6722 330.08234"
+ id="path4495-7-6-4"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="340.88538"
+ y="146.52084"
+ id="text9677-5-12"><tspan
+ sodipodi:role="line"
+ id="tspan9675-8-1"
+ x="340.88538"
+ y="146.52084"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(14) Setting the spacing of the visualization</tspan></text>
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-9-80)"
+ d="M 149.02514,214.47938 H 337.6722 330.93484"
+ id="path4495-7-6-3"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="340.88538"
+ y="220.52083"
+ id="text9677-5-15"><tspan
+ sodipodi:role="line"
+ id="tspan9675-8-5"
+ x="340.88538"
+ y="220.52083"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(15) Displaying the orientation of the visualization</tspan></text>
+</svg>
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings_raw.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings_raw.png
new file mode 100644
index 0000000000..2764ba009f
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings_raw.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_example.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_example.png
new file mode 100644
index 0000000000..cbee7fa9b4
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_example.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_example.svg b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_example.svg
new file mode 100644
index 0000000000..92c711068f
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_example.svg
@@ -0,0 +1,399 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:cc="http://creativecommons.org/ns#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:svg="http://www.w3.org/2000/svg"
+ xmlns="http://www.w3.org/2000/svg"
+ xmlns:xlink="http://www.w3.org/1999/xlink"
+ xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+ xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+ version="1.1"
+ id="svg4485"
+ width="678.44788"
+ height="707"
+ viewBox="0 0 678.44788 707"
+ sodipodi:docname="map_view_visualizer_example.svg"
+ inkscape:version="0.92.3 (2405546, 2018-03-11)"
+ inkscape:export-filename="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.manipulator\documentation\UserManual\map_view_manipulator_example.png"
+ inkscape:export-xdpi="96"
+ inkscape:export-ydpi="96">
+ <metadata
+ id="metadata4491">
+ <rdf:RDF>
+ <cc:Work
+ rdf:about="">
+ <dc:format>image/svg+xml</dc:format>
+ <dc:type
+ rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+ <dc:title />
+ </cc:Work>
+ </rdf:RDF>
+ </metadata>
+ <defs
+ id="defs4489">
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5474"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5472"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotM"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker4945"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4943"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.4,0,0,0.4,2.96,0.4)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotS"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4564"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotM"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotM"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4561"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.4,0,0,0.4,2.96,0.4)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-6"
+ style="overflow:visible"
+ inkscape:isstock="true"
+ inkscape:collect="always">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-4"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-5"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-0"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-0"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-3"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-01"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-7"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562-8"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560-3"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9-8"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1-6"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-3"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-31"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-4"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-16"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ </defs>
+ <sodipodi:namedview
+ pagecolor="#ffffff"
+ bordercolor="#666666"
+ borderopacity="1"
+ objecttolerance="10"
+ gridtolerance="10"
+ guidetolerance="10"
+ inkscape:pageopacity="0"
+ inkscape:pageshadow="2"
+ inkscape:window-width="1680"
+ inkscape:window-height="987"
+ id="namedview4487"
+ showgrid="false"
+ inkscape:zoom="1"
+ inkscape:cx="278.46875"
+ inkscape:cy="320.89936"
+ inkscape:window-x="-8"
+ inkscape:window-y="-8"
+ inkscape:window-maximized="1"
+ inkscape:current-layer="svg4485" />
+ <image
+ sodipodi:absref="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.visualizer\documentation\UserManual\map_view_visualizer_example_raw.png"
+ xlink:href="map_view_visualizer_example_raw.png"
+ width="353"
+ height="707"
+ preserveAspectRatio="none"
+ id="image4493"
+ x="0"
+ y="0" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-6)"
+ d="m 329.59771,196.14016 h 29.07449 -1.03837"
+ id="path4495-3"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0)"
+ d="m 329.59771,295.00464 h 29.07449 -1.03837"
+ id="path4495-7"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-9)"
+ d="m 329.59771,99.47931 h 29.07449 -1.03837"
+ id="path4495-7-6"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="361.88541"
+ y="105.52083"
+ id="text9677-5"><tspan
+ sodipodi:role="line"
+ id="tspan9675-8"
+ x="361.88541"
+ y="105.52083"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(1) Registration slot</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="361.88541"
+ y="202.52083"
+ id="text9677-1"><tspan
+ sodipodi:role="line"
+ id="tspan9675-1"
+ x="361.88541"
+ y="202.52083"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(2) Registation information</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="361.88541"
+ y="300.52081"
+ id="text9677-09"><tspan
+ sodipodi:role="line"
+ id="tspan9675-0"
+ x="361.88541"
+ y="300.52081"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(3) Update visual settings</tspan><tspan
+ sodipodi:role="line"
+ x="361.88541"
+ y="350.52081"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000"
+ id="tspan4725" /></text>
+ <flowRoot
+ xml:space="preserve"
+ id="flowRoot4717"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ transform="translate(0,-1)"><flowRegion
+ id="flowRegion4719"><rect
+ id="rect4721"
+ width="337"
+ height="48"
+ x="353"
+ y="188" /></flowRegion><flowPara
+ id="flowPara4723" /></flowRoot> <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-3)"
+ d="m 329.59771,345.00466 h 29.07449 -1.03837"
+ id="path4495-7-8"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="361.88541"
+ y="350.52081"
+ id="text9677-09-1"><tspan
+ sodipodi:role="line"
+ id="tspan9675-0-1"
+ x="361.88541"
+ y="350.52081"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(4) Selection of mapping direction</tspan><tspan
+ sodipodi:role="line"
+ x="361.88541"
+ y="400.52081"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000"
+ id="tspan4725-9" /></text>
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-4)"
+ d="m 329.59771,377.00466 h 29.07449 -1.03837"
+ id="path4495-7-5"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="361.88541"
+ y="382.52084"
+ id="text9677-09-9"><tspan
+ sodipodi:role="line"
+ id="tspan9675-0-2"
+ x="361.88541"
+ y="382.52084"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(5) Selection of visualization style</tspan><tspan
+ sodipodi:role="line"
+ x="361.88541"
+ y="432.52084"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000"
+ id="tspan4725-7" /></text>
+</svg>
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_example_raw.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_example_raw.png
new file mode 100644
index 0000000000..af0074d0ec
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_example_raw.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_grid_settings.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_grid_settings.png
new file mode 100644
index 0000000000..f05aee5b51
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_grid_settings.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_grid_settings.svg b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_grid_settings.svg
new file mode 100644
index 0000000000..22ad383050
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_grid_settings.svg
@@ -0,0 +1,379 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:cc="http://creativecommons.org/ns#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:svg="http://www.w3.org/2000/svg"
+ xmlns="http://www.w3.org/2000/svg"
+ xmlns:xlink="http://www.w3.org/1999/xlink"
+ xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+ xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+ version="1.1"
+ id="svg4485"
+ width="804.48956"
+ height="124"
+ viewBox="0 0 804.48956 124"
+ sodipodi:docname="map_view_visualizer_grid_settings.svg"
+ inkscape:version="0.92.3 (2405546, 2018-03-11)"
+ inkscape:export-filename="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.visualizer\documentation\UserManual\map_view_visualizer_vis_settings.png"
+ inkscape:export-xdpi="96"
+ inkscape:export-ydpi="96">
+ <metadata
+ id="metadata4491">
+ <rdf:RDF>
+ <cc:Work
+ rdf:about="">
+ <dc:format>image/svg+xml</dc:format>
+ <dc:type
+ rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+ <dc:title />
+ </cc:Work>
+ </rdf:RDF>
+ </metadata>
+ <defs
+ id="defs4489">
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5474"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5472"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotM"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker4945"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4943"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.4,0,0,0.4,2.96,0.4)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotS"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4564"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotM"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotM"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4561"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.4,0,0,0.4,2.96,0.4)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-6"
+ style="overflow:visible"
+ inkscape:isstock="true"
+ inkscape:collect="always">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-4"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-5"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-0"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-0"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-3"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-01"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-7"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562-8"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560-3"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9-8"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1-6"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-3"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-31"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-4"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-16"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ </defs>
+ <sodipodi:namedview
+ pagecolor="#ffffff"
+ bordercolor="#666666"
+ borderopacity="1"
+ objecttolerance="10"
+ gridtolerance="10"
+ guidetolerance="10"
+ inkscape:pageopacity="0"
+ inkscape:pageshadow="2"
+ inkscape:window-width="1680"
+ inkscape:window-height="987"
+ id="namedview4487"
+ showgrid="false"
+ inkscape:zoom="1"
+ inkscape:cx="226.92706"
+ inkscape:cy="7.1012534"
+ inkscape:window-x="-8"
+ inkscape:window-y="-8"
+ inkscape:window-maximized="1"
+ inkscape:current-layer="svg4485" />
+ <image
+ sodipodi:absref="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.visualizer\documentation\UserManual\map_view_visualizer_grid_settings_raw.png"
+ xlink:href="map_view_visualizer_grid_settings_raw.png"
+ y="0"
+ x="0"
+ id="image4493"
+ preserveAspectRatio="none"
+ height="124"
+ width="329"
+ mask="none" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-6)"
+ d="M 224.61004,71.1402 H 335.6722 331.70571"
+ id="path4495-3"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-9)"
+ d="M 147.02514,44.4793 H 335.6722 328.93484"
+ id="path4495-7-6"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="338.88538"
+ y="50.520752"
+ id="text9677-5"><tspan
+ sodipodi:role="line"
+ id="tspan9675-8"
+ x="338.88538"
+ y="50.520752"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(9) Set freqency of visible gride frames</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="338.88538"
+ y="77.520752"
+ id="text9677-1"><tspan
+ sodipodi:role="line"
+ id="tspan9675-1"
+ x="338.88538"
+ y="77.520752"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(10) Visibility of start grid of the mapping direction</tspan></text>
+ <flowRoot
+ xml:space="preserve"
+ id="flowRoot4717"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ transform="translate(0,-393)"><flowRegion
+ id="flowRegion4719"><rect
+ id="rect4721"
+ width="337"
+ height="48"
+ x="353"
+ y="188" /></flowRegion><flowPara
+ id="flowPara4723" /></flowRoot> <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-4)"
+ d="M 105.40533,98.0047 H 335.6722 327.44843"
+ id="path4495-7-5"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="338.88538"
+ y="103.521"
+ id="text9677-09-9"><tspan
+ sodipodi:role="line"
+ id="tspan9675-0-2"
+ x="338.88538"
+ y="103.521"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(11) Color of the start grid</tspan><tspan
+ sodipodi:role="line"
+ x="338.88538"
+ y="153.521"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000"
+ id="tspan4725-7" /></text>
+ <flowRoot
+ xml:space="preserve"
+ id="flowRoot6290"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ transform="translate(0,-392)"><flowRegion
+ id="flowRegion6292"><rect
+ id="rect6294"
+ width="839"
+ height="562"
+ x="-158"
+ y="273" /></flowRegion><flowPara
+ id="flowPara6296" /></flowRoot> <flowRoot
+ xml:space="preserve"
+ id="flowRoot6719"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"><flowRegion
+ id="flowRegion6721"><rect
+ id="rect6723"
+ width="620"
+ height="252"
+ x="-129"
+ y="-103" /></flowRegion><flowPara
+ id="flowPara6725" /></flowRoot></svg>
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_grid_settings_raw.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_grid_settings_raw.png
new file mode 100644
index 0000000000..67aadc7732
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_grid_settings_raw.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_example.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_example.png
new file mode 100644
index 0000000000..8a8c7c833c
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_example.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_example.xcf b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_example.xcf
new file mode 100644
index 0000000000..a454c8d494
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_example.xcf differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_glyph.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_glyph.png
new file mode 100644
index 0000000000..98ed770fd8
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_glyph.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_grid.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_grid.png
new file mode 100644
index 0000000000..6b1c06f2b5
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_grid.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_grid_hiresgrid.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_grid_hiresgrid.png
new file mode 100644
index 0000000000..b2e08b5038
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_grid_hiresgrid.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_grid_nointerpolate.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_grid_nointerpolate.png
new file mode 100644
index 0000000000..18350aef8c
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_grid_nointerpolate.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_grid_startgrid.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_grid_startgrid.png
new file mode 100644
index 0000000000..84e10022b7
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_grid_startgrid.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_grid_unicolor.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_grid_unicolor.png
new file mode 100644
index 0000000000..820b8fc174
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_style_grid_unicolor.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_vis_settings.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_vis_settings.png
new file mode 100644
index 0000000000..ddbd427c72
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_vis_settings.png differ
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_vis_settings.svg b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_vis_settings.svg
new file mode 100644
index 0000000000..d4e6134939
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_vis_settings.svg
@@ -0,0 +1,381 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:cc="http://creativecommons.org/ns#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:svg="http://www.w3.org/2000/svg"
+ xmlns="http://www.w3.org/2000/svg"
+ xmlns:xlink="http://www.w3.org/1999/xlink"
+ xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+ xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+ version="1.1"
+ id="svg4485"
+ width="593.4375"
+ height="315"
+ viewBox="0 0 593.4375 315"
+ sodipodi:docname="map_view_visualizer_vis_settings.svg"
+ inkscape:version="0.92.3 (2405546, 2018-03-11)"
+ inkscape:export-filename="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.visualizer\documentation\UserManual\map_view_visualizer_vis_settings.png"
+ inkscape:export-xdpi="96"
+ inkscape:export-ydpi="96">
+ <metadata
+ id="metadata4491">
+ <rdf:RDF>
+ <cc:Work
+ rdf:about="">
+ <dc:format>image/svg+xml</dc:format>
+ <dc:type
+ rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+ <dc:title></dc:title>
+ </cc:Work>
+ </rdf:RDF>
+ </metadata>
+ <defs
+ id="defs4489">
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5474"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5472"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotM"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker4945"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4943"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.4,0,0,0.4,2.96,0.4)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotS"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4564"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotM"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotM"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4561"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.4,0,0,0.4,2.96,0.4)"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-6"
+ style="overflow:visible"
+ inkscape:isstock="true"
+ inkscape:collect="always">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-4"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-5"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-0"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-0"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-3"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-01"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-7"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker5562-8"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="DotS">
+ <path
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ id="path5560-3"
+ inkscape:connector-curvature="0" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-9-8"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-1-6"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-3"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-31"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <marker
+ inkscape:stockid="DotS"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker5281-0-4"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path5279-5-16"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1"
+ transform="matrix(0.2,0,0,0.2,1.48,0.2)" />
+ </marker>
+ <mask
+ maskUnits="userSpaceOnUse"
+ id="mask5650">
+ <rect
+ style="opacity:1;fill:#ffffff;fill-opacity:1;stroke:#000000;stroke-width:5;stroke-linecap:butt;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:0"
+ id="rect5652"
+ width="368"
+ height="323"
+ x="-5"
+ y="392" />
+ </mask>
+ </defs>
+ <sodipodi:namedview
+ pagecolor="#ffffff"
+ bordercolor="#666666"
+ borderopacity="1"
+ objecttolerance="10"
+ gridtolerance="10"
+ guidetolerance="10"
+ inkscape:pageopacity="0"
+ inkscape:pageshadow="2"
+ inkscape:window-width="1680"
+ inkscape:window-height="987"
+ id="namedview4487"
+ showgrid="false"
+ inkscape:zoom="1"
+ inkscape:cx="332.55734"
+ inkscape:cy="359.07708"
+ inkscape:window-x="-8"
+ inkscape:window-y="-8"
+ inkscape:window-maximized="1"
+ inkscape:current-layer="svg4485" />
+ <image
+ sodipodi:absref="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.visualizer\documentation\UserManual\map_view_visualizer_example_raw.png"
+ xlink:href="map_view_visualizer_example_raw.png"
+ transform="translate(0,-392)"
+ mask="url(#mask5650)"
+ width="353"
+ height="707"
+ preserveAspectRatio="none"
+ id="image4493"
+ x="0"
+ y="0" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-6)"
+ d="M 258.68105,151.1402 H 359.6722 356.06539"
+ id="path4495-3"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-9)"
+ d="M 171.02514,88.4793 H 359.6722 352.93484"
+ id="path4495-7-6"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="362.88538"
+ y="94.520752"
+ id="text9677-5"><tspan
+ sodipodi:role="line"
+ id="tspan9675-8"
+ x="362.88538"
+ y="94.520752"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(6) Color style</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="362.88538"
+ y="157.52075"
+ id="text9677-1"><tspan
+ sodipodi:role="line"
+ id="tspan9675-1"
+ x="362.88538"
+ y="157.52075"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(7) Color coding settings</tspan></text>
+ <flowRoot
+ xml:space="preserve"
+ id="flowRoot4717"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ transform="translate(0,-393)"><flowRegion
+ id="flowRegion4719"><rect
+ id="rect4721"
+ width="337"
+ height="48"
+ x="353"
+ y="188" /></flowRegion><flowPara
+ id="flowPara4723" /></flowRoot> <path
+ style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-4)"
+ d="M 167.19587,286.0047 H 359.6722 352.79808"
+ id="path4495-7-5"
+ inkscape:connector-curvature="0" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none"
+ x="362.88538"
+ y="291.521"
+ id="text9677-09-9"><tspan
+ sodipodi:role="line"
+ id="tspan9675-0-2"
+ x="362.88538"
+ y="291.521"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(8) Interpolation style</tspan><tspan
+ sodipodi:role="line"
+ x="362.88538"
+ y="341.521"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000"
+ id="tspan4725-7" /></text>
+ <flowRoot
+ xml:space="preserve"
+ id="flowRoot6290"
+ style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ transform="translate(0,-392)"><flowRegion
+ id="flowRegion6292"><rect
+ id="rect6294"
+ width="839"
+ height="562"
+ x="-158"
+ y="273" /></flowRegion><flowPara
+ id="flowPara6296"></flowPara></flowRoot></svg>
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.cpp b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.cpp
index b264d54c9f..49fdf85bc0 100644
--- a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.cpp
+++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.cpp
@@ -1,795 +1,798 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "org_mitk_gui_qt_matchpoint_visualizer_Activator.h"
// Blueberry
#include <berryISelectionService.h>
#include <berryIWorkbenchWindow.h>
// Mitk
#include <mitkStatusBar.h>
#include <mitkProperties.h>
#include <mitkColorProperty.h>
#include <mitkNodePredicateDataType.h>
#include <mitkNodePredicateAnd.h>
#include <mitkNodePredicateDataProperty.h>
#include <mitkNodePredicateFunction.h>
#include "mitkRegVisDirectionProperty.h"
#include "mitkRegVisStyleProperty.h"
#include "mitkRegVisColorStyleProperty.h"
#include "mitkRegVisPropertyTags.h"
#include "mitkRegVisHelper.h"
#include "mitkMatchPointPropertyTags.h"
#include "mitkRegistrationHelper.h"
// Qmitk
#include "QmitkMatchPointRegistrationVisualizer.h"
// Qt
#include <QMessageBox>
#include <QErrorMessage>
const std::string QmitkMatchPointRegistrationVisualizer::VIEW_ID =
"org.mitk.views.matchpoint.visualizer";
QmitkMatchPointRegistrationVisualizer::QmitkMatchPointRegistrationVisualizer()
: m_Parent(nullptr), m_internalUpdateGuard(false), m_spSelectedFOVRefNode(nullptr),
m_spSelectedRegNode(nullptr)
{
}
void QmitkMatchPointRegistrationVisualizer::SetFocus()
{
}
void QmitkMatchPointRegistrationVisualizer::CreateConnections()
{
connect(m_Controls->registrationNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkMatchPointRegistrationVisualizer::OnNodeSelectionChanged);
connect(m_Controls->fovReferenceNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkMatchPointRegistrationVisualizer::OnNodeSelectionChanged);
connect(m_Controls->m_pbStyleGrid, SIGNAL(clicked()), this, SLOT(OnStyleButtonPushed()));
connect(m_Controls->m_pbStyleGlyph, SIGNAL(clicked()), this, SLOT(OnStyleButtonPushed()));
connect(m_Controls->m_pbStylePoints, SIGNAL(clicked()), this, SLOT(OnStyleButtonPushed()));
connect(m_Controls->m_comboDirection, SIGNAL(currentIndexChanged(int)), this,
SLOT(OnDirectionChanged(int)));
connect(m_Controls->m_pbUpdateViz, SIGNAL(clicked()), this, SLOT(OnUpdateBtnPushed()));
connect(m_Controls->radioColorUni, SIGNAL(toggled(bool)), m_Controls->btnUniColor,
SLOT(setEnabled(bool)));
connect(m_Controls->radioColorVecMag, SIGNAL(toggled(bool)), m_Controls->groupColorCoding,
SLOT(setEnabled(bool)));
connect(m_Controls->m_pbStyleGrid, SIGNAL(toggled(bool)), m_Controls->tabGrid,
SLOT(setEnabled(bool)));
connect(m_Controls->cbVevMagInterlolate, SIGNAL(toggled(bool)), this,
SLOT(OnColorInterpolationChecked(bool)));
connect(m_Controls->m_checkUseRefSize, SIGNAL(clicked()), this, SLOT(TransferFOVRefGeometry()));
connect(m_Controls->m_checkUseRefSpacing, SIGNAL(clicked()), this, SLOT(TransferFOVRefGeometry()));
connect(m_Controls->m_checkUseRefOrigin, SIGNAL(clicked()), this, SLOT(TransferFOVRefGeometry()));
connect(m_Controls->m_checkUseRefOrientation, SIGNAL(clicked()), this, SLOT(TransferFOVRefGeometry()));
}
void QmitkMatchPointRegistrationVisualizer::Error(QString msg)
{
mitk::StatusBar::GetInstance()->DisplayErrorText(msg.toLatin1());
MITK_ERROR << msg.toStdString().c_str();
}
void QmitkMatchPointRegistrationVisualizer::CreateQtPartControl(QWidget* parent)
{
m_Controls = new Ui::MatchPointRegVisControls;
// create GUI widgets from the Qt Designer's .ui file
m_Controls->setupUi(parent);
m_Parent = parent;
this->m_Controls->registrationNodeSelector->SetDataStorage(this->GetDataStorage());
this->m_Controls->registrationNodeSelector->SetSelectionIsOptional(false);
this->m_Controls->fovReferenceNodeSelector->SetDataStorage(this->GetDataStorage());
this->m_Controls->fovReferenceNodeSelector->SetSelectionIsOptional(false);
m_Controls->registrationNodeSelector->SetInvalidInfo("Select registration.");
m_Controls->registrationNodeSelector->SetPopUpTitel("Select registration.");
m_Controls->registrationNodeSelector->SetPopUpHint("Select the registration object whose registration visualization should be edited.");
m_Controls->fovReferenceNodeSelector->SetInvalidInfo("Select a FOV reference image.");
m_Controls->fovReferenceNodeSelector->SetPopUpTitel("Select a FOV reference image.");
m_Controls->fovReferenceNodeSelector->SetPopUpHint("Select the the image that should be used to define the field of view (FOV) for the registration visualization. The visualization will use the image geometry (size, orientation, spacing...).");
this->ConfigureNodePredicates();
this->m_Controls->btnVecMagColorSmall->setDisplayColorName(false);
this->m_Controls->btnVecMagColorMedium->setDisplayColorName(false);
this->m_Controls->btnVecMagColorLarge->setDisplayColorName(false);
this->m_Controls->btnVecMagColorNeg->setDisplayColorName(false);
this->m_Controls->btnUniColor->setDisplayColorName(false);
this->m_Controls->btnStartGridColor->setDisplayColorName(false);
this->CreateConnections();
this->m_Controls->radioColorUni->setChecked(false);
this->m_Controls->radioColorVecMag->setChecked(true);
this->CheckInputs();
this->LoadStateFromNode();
this->ConfigureVisualizationControls();
+
+ //deactivate because currently not an implemented style
+ this->m_Controls->m_pbStylePoints->setVisible(false);
}
void QmitkMatchPointRegistrationVisualizer::ConfigureNodePredicates()
{
m_Controls->registrationNodeSelector->SetNodePredicate(mitk::MITKRegistrationHelper::RegNodePredicate());
auto geometryCheck = [](const mitk::DataNode * node)
{
return node->GetData() && node->GetData()->GetGeometry();
};
mitk::NodePredicateFunction::Pointer hasGeometry = mitk::NodePredicateFunction::New(geometryCheck);
auto nodePredicate = mitk::NodePredicateAnd::New(mitk::MITKRegistrationHelper::ImageNodePredicate().GetPointer(), hasGeometry.GetPointer());
m_Controls->fovReferenceNodeSelector->SetNodePredicate(nodePredicate.GetPointer());
}
mitk::MAPRegistrationWrapper* QmitkMatchPointRegistrationVisualizer::GetCurrentRegistration()
{
mitk::MAPRegistrationWrapper* result = nullptr;
if (this->m_spSelectedRegNode.IsNotNull())
{
result = dynamic_cast<mitk::MAPRegistrationWrapper*>(this->m_spSelectedRegNode->GetData());
assert(result);
}
return result;
}
mitk::DataNode::Pointer QmitkMatchPointRegistrationVisualizer::GetSelectedRegNode() const
{
return m_Controls->registrationNodeSelector->GetSelectedNode();
}
mitk::DataNode::Pointer QmitkMatchPointRegistrationVisualizer::GetRefNodeOfReg(bool target) const
{
mitk::DataNode::Pointer spResult = nullptr;
if (this->m_spSelectedRegNode.IsNotNull() && m_spSelectedRegNode->GetData())
{
std::string nodeName;
mitk::BaseProperty* uidProp;
if (target)
{
uidProp = m_spSelectedRegNode->GetData()->GetProperty(mitk::Prop_RegAlgTargetData);
}
else
{
uidProp = m_spSelectedRegNode->GetData()->GetProperty(mitk::Prop_RegAlgMovingData);
}
if (uidProp)
{
//search for the target node
mitk::NodePredicateDataProperty::Pointer predicate = mitk::NodePredicateDataProperty::New(mitk::Prop_UID,
uidProp);
spResult = this->GetDataStorage()->GetNode(predicate);
}
}
return spResult;
}
mitk::DataNode::Pointer QmitkMatchPointRegistrationVisualizer::GetSelectedDataNode()
{
return m_Controls->fovReferenceNodeSelector->GetSelectedNode();
}
void QmitkMatchPointRegistrationVisualizer::CheckInputs()
{
this->m_spSelectedRegNode = this->GetSelectedRegNode();
this->InitRegNode();
this->m_spSelectedFOVRefNode = this->GetSelectedDataNode();
}
void QmitkMatchPointRegistrationVisualizer::ConfigureVisualizationControls()
{
if (!m_internalUpdateGuard)
{
m_internalUpdateGuard = true;
m_Controls->groupViz->setVisible(this->m_spSelectedRegNode.IsNotNull());
m_Controls->m_pbUpdateViz->setEnabled(this->m_spSelectedRegNode.IsNotNull());
m_Controls->m_boxSettings->setEnabled(this->m_spSelectedRegNode.IsNotNull());
m_Controls->m_boxStyles->setEnabled(this->m_spSelectedRegNode.IsNotNull());
this->ActualizeRegInfo(this->GetCurrentRegistration());
this->m_Controls->m_checkUseRefSize->setEnabled(this->m_spSelectedRegNode.IsNotNull()
&& this->m_spSelectedFOVRefNode.IsNotNull());
this->m_Controls->m_checkUseRefOrigin->setEnabled(this->m_spSelectedRegNode.IsNotNull()
&& this->m_spSelectedFOVRefNode.IsNotNull());
this->m_Controls->m_checkUseRefSpacing->setEnabled(this->m_spSelectedRegNode.IsNotNull()
&& this->m_spSelectedFOVRefNode.IsNotNull());
m_internalUpdateGuard = false;
}
}
void QmitkMatchPointRegistrationVisualizer::StoreStateInNode()
{
if (this->m_spSelectedRegNode.IsNotNull())
{
//general
this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisDirection,
mitk::RegVisDirectionProperty::New(this->m_Controls->m_comboDirection->currentIndex()));
this->m_spSelectedRegNode->SetBoolProperty(mitk::nodeProp_RegVisGrid,
this->m_Controls->m_pbStyleGrid->isChecked());
this->m_spSelectedRegNode->SetBoolProperty(mitk::nodeProp_RegVisGlyph,
this->m_Controls->m_pbStyleGlyph->isChecked());
this->m_spSelectedRegNode->SetBoolProperty(mitk::nodeProp_RegVisPoints,
this->m_Controls->m_pbStylePoints->isChecked());
//Visualization
if (this->m_Controls->radioColorUni->isChecked())
{
this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisColorStyle,
mitk::RegVisColorStyleProperty::New(0));
}
else
{
this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisColorStyle,
mitk::RegVisColorStyleProperty::New(1));
}
float tmpColor[3];
tmpColor[0] = this->m_Controls->btnUniColor->color().redF();
tmpColor[1] = this->m_Controls->btnUniColor->color().greenF();
tmpColor[2] = this->m_Controls->btnUniColor->color().blueF();
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColorUni,
mitk::ColorProperty::New(tmpColor), nullptr, true);
tmpColor[0] = this->m_Controls->btnVecMagColorNeg->color().redF();
tmpColor[1] = this->m_Controls->btnVecMagColorNeg->color().greenF();
tmpColor[2] = this->m_Controls->btnVecMagColorNeg->color().blueF();
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor1Value,
mitk::ColorProperty::New(tmpColor), nullptr, true);
tmpColor[0] = this->m_Controls->btnVecMagColorSmall->color().redF();
tmpColor[1] = this->m_Controls->btnVecMagColorSmall->color().greenF();
tmpColor[2] = this->m_Controls->btnVecMagColorSmall->color().blueF();
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor2Value,
mitk::ColorProperty::New(tmpColor), nullptr, true);
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor2Magnitude,
mitk::DoubleProperty::New(this->m_Controls->sbVecMagSmall->value()), nullptr, true);
tmpColor[0] = this->m_Controls->btnVecMagColorMedium->color().redF();
tmpColor[1] = this->m_Controls->btnVecMagColorMedium->color().greenF();
tmpColor[2] = this->m_Controls->btnVecMagColorMedium->color().blueF();
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor3Value,
mitk::ColorProperty::New(tmpColor), nullptr, true);
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor3Magnitude,
mitk::DoubleProperty::New(this->m_Controls->sbVecMagMedium->value()), nullptr, true);
tmpColor[0] = this->m_Controls->btnVecMagColorLarge->color().redF();
tmpColor[1] = this->m_Controls->btnVecMagColorLarge->color().greenF();
tmpColor[2] = this->m_Controls->btnVecMagColorLarge->color().blueF();
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor4Value,
mitk::ColorProperty::New(tmpColor), nullptr, true);
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor4Magnitude,
mitk::DoubleProperty::New(this->m_Controls->sbVecMagLarge->value()), nullptr, true);
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColorInterpolate,
mitk::BoolProperty::New(this->m_Controls->cbVevMagInterlolate->isChecked()), nullptr, true);
//Grid Settings
this->m_spSelectedRegNode->SetIntProperty(mitk::nodeProp_RegVisGridFrequence,
this->m_Controls->m_sbGridFrequency->value());
this->m_spSelectedRegNode->SetBoolProperty(mitk::nodeProp_RegVisGridShowStart,
this->m_Controls->m_groupShowStartGrid->isChecked());
tmpColor[0] = this->m_Controls->btnStartGridColor->color().redF();
tmpColor[1] = this->m_Controls->btnStartGridColor->color().greenF();
tmpColor[2] = this->m_Controls->btnStartGridColor->color().blueF();
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisGridStartColor,
mitk::ColorProperty::New(tmpColor), nullptr, true);
//FOV
mitk::Vector3D value;
value[0] = this->m_Controls->m_sbFOVSizeX->value();
value[1] = this->m_Controls->m_sbFOVSizeY->value();
value[2] = this->m_Controls->m_sbFOVSizeZ->value();
this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisFOVSize,
mitk::Vector3DProperty::New(value));
value[0] = this->m_Controls->m_sbGridSpX->value();
value[1] = this->m_Controls->m_sbGridSpY->value();
value[2] = this->m_Controls->m_sbGridSpZ->value();
this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisFOVSpacing,
mitk::Vector3DProperty::New(value));
mitk::Point3D origin;
origin[0] = this->m_Controls->m_sbFOVOriginX->value();
origin[1] = this->m_Controls->m_sbFOVOriginY->value();
origin[2] = this->m_Controls->m_sbFOVOriginZ->value();
this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisFOVOrigin,
mitk::Point3dProperty::New(origin));
mitk::Vector3D orientationRow1;
mitk::Vector3D orientationRow2;
mitk::Vector3D orientationRow3;
orientationRow1.SetVnlVector(m_FOVRefOrientation.GetVnlMatrix().get_row(0));
orientationRow2.SetVnlVector(m_FOVRefOrientation.GetVnlMatrix().get_row(1));
orientationRow3.SetVnlVector(m_FOVRefOrientation.GetVnlMatrix().get_row(2));
this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisFOVOrientation1,
mitk::Vector3DProperty::New(orientationRow1));
this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisFOVOrientation2,
mitk::Vector3DProperty::New(orientationRow2));
this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisFOVOrientation3,
mitk::Vector3DProperty::New(orientationRow3));
}
}
void QmitkMatchPointRegistrationVisualizer::LoadStateFromNode()
{
if (this->m_spSelectedRegNode.IsNotNull())
{
mitk::RegVisDirectionProperty* directionProp = nullptr;
if (this->m_spSelectedRegNode->GetProperty(directionProp, mitk::nodeProp_RegVisDirection))
{
this->m_Controls->m_comboDirection->setCurrentIndex(directionProp->GetValueAsId());
}
else
{
this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString(
mitk::nodeProp_RegVisDirection) + QStringLiteral(" has not the assumed type."));
}
bool styleActive = false;
if (this->m_spSelectedRegNode->GetBoolProperty(mitk::nodeProp_RegVisGrid, styleActive))
{
this->m_Controls->m_pbStyleGrid->setChecked(styleActive);
this->m_Controls->tabGrid->setEnabled(styleActive);
}
else
{
this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString(
mitk::nodeProp_RegVisGrid) + QStringLiteral(" has not the assumed type."));
}
if (this->m_spSelectedRegNode->GetBoolProperty(mitk::nodeProp_RegVisGlyph, styleActive))
{
this->m_Controls->m_pbStyleGlyph->setChecked(styleActive);
}
else
{
this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString(
mitk::nodeProp_RegVisGlyph) + QStringLiteral(" has not the assumed type."));
}
if (this->m_spSelectedRegNode->GetBoolProperty(mitk::nodeProp_RegVisPoints, styleActive))
{
this->m_Controls->m_pbStylePoints->setChecked(styleActive);
}
else
{
this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString(
mitk::nodeProp_RegVisPoints) + QStringLiteral(" has not the assumed type."));
}
///////////////////////////////////////////////////////
//visualization
mitk::RegVisColorStyleProperty* colorStyleProp = nullptr;
if (this->m_spSelectedRegNode->GetProperty(colorStyleProp, mitk::nodeProp_RegVisColorStyle))
{
this->m_Controls->radioColorUni->setChecked(colorStyleProp->GetValueAsId() == 0);
this->m_Controls->radioColorVecMag->setChecked(colorStyleProp->GetValueAsId() == 1);
}
else
{
this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString(
mitk::nodeProp_RegVisColorStyle) + QStringLiteral(" has not the assumed type."));
}
QColor tmpColor;
float colorUni[3] = { 0.0, 0.0, 0.0 };
this->m_spSelectedRegNode->GetColor(colorUni, nullptr, mitk::nodeProp_RegVisColorUni);
tmpColor.setRgbF(colorUni[0], colorUni[1], colorUni[2]);
this->m_Controls->btnUniColor->setColor(tmpColor);
float color1[3] = { 0.0, 0.0, 0.0 };
this->m_spSelectedRegNode->GetColor(color1, nullptr, mitk::nodeProp_RegVisColor1Value);
tmpColor.setRgbF(color1[0], color1[1], color1[2]);
this->m_Controls->btnVecMagColorNeg->setColor(tmpColor);
float color2[3] = { 0.25, 0.25, 0.25 };
this->m_spSelectedRegNode->GetColor(color2, nullptr, mitk::nodeProp_RegVisColor2Value);
tmpColor.setRgbF(color2[0], color2[1], color2[2]);
this->m_Controls->btnVecMagColorSmall->setColor(tmpColor);
float color3[3] = { 0.5, 0.5, 0.5 };
this->m_spSelectedRegNode->GetColor(color3, nullptr, mitk::nodeProp_RegVisColor3Value);
tmpColor.setRgbF(color3[0], color3[1], color3[2]);
this->m_Controls->btnVecMagColorMedium->setColor(tmpColor);
float color4[3] = { 1.0, 1.0, 1.0 };
this->m_spSelectedRegNode->GetColor(color4, nullptr, mitk::nodeProp_RegVisColor4Value);
tmpColor.setRgbF(color4[0], color4[1], color4[2]);
this->m_Controls->btnVecMagColorLarge->setColor(tmpColor);
double mag2 = 0;
this->m_spSelectedRegNode->GetPropertyValue(mitk::nodeProp_RegVisColor2Magnitude, mag2);
double mag3 = 0;
this->m_spSelectedRegNode->GetPropertyValue(mitk::nodeProp_RegVisColor3Magnitude, mag3);
double mag4 = 0;
this->m_spSelectedRegNode->GetPropertyValue(mitk::nodeProp_RegVisColor4Magnitude, mag4);
bool interpolate = true;
this->m_spSelectedRegNode->GetBoolProperty(mitk::nodeProp_RegVisColorInterpolate, interpolate);
this->m_Controls->sbVecMagSmall->setValue(mag2);
this->m_Controls->sbVecMagMedium->setValue(mag3);
this->m_Controls->sbVecMagLarge->setValue(mag4);
this->m_Controls->cbVevMagInterlolate->setChecked(interpolate);
///////////////////////////////////////////////////////
//Grid general
bool showStart = false;
if (this->m_spSelectedRegNode->GetBoolProperty(mitk::nodeProp_RegVisGridShowStart, showStart))
{
this->m_Controls->m_groupShowStartGrid->setChecked(showStart);
}
else
{
this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString(
mitk::nodeProp_RegVisGridShowStart) + QStringLiteral(" is not correctly defined."));
}
int gridFrequ = 5;
if (this->m_spSelectedRegNode->GetIntProperty(mitk::nodeProp_RegVisGridFrequence, gridFrequ))
{
this->m_Controls->m_sbGridFrequency->setValue(gridFrequ);
}
else
{
this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString(
mitk::nodeProp_RegVisGridFrequence) + QStringLiteral(" is not correctly defined."));
}
float colorStart[3] = { 0.0, 0.0, 0.0 };
this->m_spSelectedRegNode->GetColor(colorStart, nullptr, mitk::nodeProp_RegVisGridStartColor);
tmpColor.setRgbF(colorStart[0], colorStart[1], colorStart[2]);
this->m_Controls->btnStartGridColor->setColor(tmpColor);
///////////////////////////////////////////////////////
//FOV
mitk::Vector3DProperty* valueProp = nullptr;
if (this->m_spSelectedRegNode->GetProperty(valueProp, mitk::nodeProp_RegVisFOVSize))
{
this->m_Controls->m_sbFOVSizeX->setValue(valueProp->GetValue()[0]);
this->m_Controls->m_sbFOVSizeY->setValue(valueProp->GetValue()[1]);
this->m_Controls->m_sbFOVSizeZ->setValue(valueProp->GetValue()[2]);
}
else
{
this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString(
mitk::nodeProp_RegVisFOVSize) + QStringLiteral(" is not correctly defined."));
}
if (this->m_spSelectedRegNode->GetProperty(valueProp, mitk::nodeProp_RegVisFOVSpacing))
{
this->m_Controls->m_sbGridSpX->setValue(valueProp->GetValue()[0]);
this->m_Controls->m_sbGridSpY->setValue(valueProp->GetValue()[1]);
this->m_Controls->m_sbGridSpZ->setValue(valueProp->GetValue()[2]);
}
else
{
this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString(
mitk::nodeProp_RegVisFOVSpacing) + QStringLiteral(" is not correctly defined."));
}
mitk::Point3dProperty* originProp = nullptr;
if (this->m_spSelectedRegNode->GetProperty(originProp, mitk::nodeProp_RegVisFOVOrigin))
{
this->m_Controls->m_sbFOVOriginX->setValue(originProp->GetValue()[0]);
this->m_Controls->m_sbFOVOriginY->setValue(originProp->GetValue()[1]);
this->m_Controls->m_sbFOVOriginZ->setValue(originProp->GetValue()[2]);
}
else
{
this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString(
mitk::nodeProp_RegVisFOVOrigin) + QStringLiteral(" is not correctly defined."));
}
mitk::Vector3DProperty* orientationProp1;
mitk::Vector3DProperty* orientationProp2;
mitk::Vector3DProperty* orientationProp3;
if (this->m_spSelectedRegNode->GetProperty(orientationProp1, mitk::nodeProp_RegVisFOVOrientation1) &&
this->m_spSelectedRegNode->GetProperty(orientationProp2, mitk::nodeProp_RegVisFOVOrientation2) &&
this->m_spSelectedRegNode->GetProperty(orientationProp3, mitk::nodeProp_RegVisFOVOrientation3))
{
this->m_Controls->m_sbFOVOriginX->setValue(originProp->GetValue()[0]);
this->m_Controls->m_sbFOVOriginY->setValue(originProp->GetValue()[1]);
this->m_Controls->m_sbFOVOriginZ->setValue(originProp->GetValue()[2]);
m_FOVRefOrientation.GetVnlMatrix().set_row(0, orientationProp1->GetValue().GetVnlVector());
m_FOVRefOrientation.GetVnlMatrix().set_row(1, orientationProp2->GetValue().GetVnlVector());
m_FOVRefOrientation.GetVnlMatrix().set_row(2, orientationProp3->GetValue().GetVnlVector());
}
else
{
m_FOVRefOrientation.SetIdentity();
this->Error(QStringLiteral("Cannot configure plugin controlls correctly. One of the node propertiesy ") +
QString(mitk::nodeProp_RegVisFOVOrientation1) + QString(mitk::nodeProp_RegVisFOVOrientation2) +
QString(mitk::nodeProp_RegVisFOVOrientation3) + QStringLiteral(" is not correctly defined."));
}
this->UpdateOrientationMatrixWidget();
}
}
void QmitkMatchPointRegistrationVisualizer::CheckAndSetDefaultFOVRef()
{
//check if node has a default reference node.
mitk::DataNode::Pointer defaultRef = this->GetRefNodeOfReg(
this->m_Controls->m_comboDirection->currentIndex() ==
1); //direction value 1 = show inverse mapping -> we need the target image used for the registration.
//if there is a default node and no m_spSelectedFOVRefNode is set -> set default node and transfer values
if (defaultRef.IsNotNull() && this->m_spSelectedFOVRefNode.IsNull())
{
//there is a default ref and no ref lock -> select default ref and transfer its values
this->m_spSelectedFOVRefNode = defaultRef;
QmitkSingleNodeSelectionWidget::NodeList selection({ defaultRef });
this->m_Controls->fovReferenceNodeSelector->SetCurrentSelection(selection);
this->m_Controls->m_checkUseRefSize->setChecked(true);
this->m_Controls->m_checkUseRefOrigin->setChecked(true);
this->m_Controls->m_checkUseRefSpacing->setChecked(true);
this->m_Controls->m_checkUseRefOrientation->setChecked(true);
}
if (this->m_spSelectedFOVRefNode.IsNotNull())
{
//auto transfere values
this->TransferFOVRefGeometry();
}
}
void QmitkMatchPointRegistrationVisualizer::OnNodeSelectionChanged(QList<mitk::DataNode::Pointer> /*nodes*/)
{
this->CheckInputs();
this->LoadStateFromNode();
this->CheckAndSetDefaultFOVRef();
this->ConfigureVisualizationControls();
}
void QmitkMatchPointRegistrationVisualizer::ActualizeRegInfo(mitk::MAPRegistrationWrapper*
currentReg)
{
std::stringstream descriptionString;
m_Controls->m_teRegInfo->clear();
if (currentReg)
{
descriptionString << "Moving dimension: " << currentReg->GetMovingDimensions() << "<br/>";
descriptionString << "Target dimension: " << currentReg->GetTargetDimensions() << "<br/>";
descriptionString << "Limited moving representation: " <<
currentReg->HasLimitedMovingRepresentation() << "<br/>";
descriptionString << "Limited target representation: " <<
currentReg->HasLimitedTargetRepresentation() << "<br/>";
mitk::MAPRegistrationWrapper::TagMapType tagMap = currentReg->GetTags();
descriptionString << "<br/><b>Tags:</b><br/>";
for (mitk::MAPRegistrationWrapper::TagMapType::const_iterator pos = tagMap.begin();
pos != tagMap.end(); ++pos)
{
descriptionString << pos->first << " : " << pos->second << "<br/>";
}
}
else
{
descriptionString << "<font color='red'>no registration selected!</font>";
}
m_Controls->m_teRegInfo->insertHtml(QString::fromStdString(descriptionString.str()));
}
void QmitkMatchPointRegistrationVisualizer::OnDirectionChanged(int)
{
this->CheckAndSetDefaultFOVRef();
this->ConfigureVisualizationControls();
}
void QmitkMatchPointRegistrationVisualizer::OnUpdateBtnPushed()
{
this->StoreStateInNode();
mitk::Geometry3D::Pointer gridDesc;
unsigned int gridFrequ = 5;
mitk::GetGridGeometryFromNode(this->m_spSelectedRegNode, gridDesc, gridFrequ);
this->GetCurrentRegistration()->SetGeometry(gridDesc);
mitk::RenderingManager::GetInstance()->ForceImmediateUpdateAll();
}
void QmitkMatchPointRegistrationVisualizer::OnStyleButtonPushed()
{
}
void QmitkMatchPointRegistrationVisualizer::OnColorInterpolationChecked(bool checked)
{
if (checked)
{
this->m_Controls->labelVecMagSmall->setText(QStringLiteral("="));
this->m_Controls->labelVecMagMedium->setText(QStringLiteral("="));
this->m_Controls->labelVecMagLarge->setText(QStringLiteral("="));
}
else
{
this->m_Controls->labelVecMagSmall->setText(QStringLiteral(">"));
this->m_Controls->labelVecMagMedium->setText(QStringLiteral(">"));
this->m_Controls->labelVecMagLarge->setText(QStringLiteral(">"));
}
}
mitk::ScalarType QmitkMatchPointRegistrationVisualizer::GetSaveSpacing(mitk::ScalarType gridRes,
mitk::ScalarType spacing, unsigned int maxGridRes) const
{
mitk::ScalarType newSpacing = spacing;
mitk::ScalarType scaling = gridRes / maxGridRes;
if (scaling > 1.0)
{
newSpacing = spacing * scaling;
}
return newSpacing;
}
void QmitkMatchPointRegistrationVisualizer::TransferFOVRefGeometry()
{
if (this->m_spSelectedFOVRefNode.IsNotNull())
{
assert(this->m_spSelectedFOVRefNode->GetData());
assert(this->m_spSelectedFOVRefNode->GetData()->GetGeometry());
mitk::BaseGeometry* gridRef = this->m_spSelectedFOVRefNode->GetData()->GetGeometry();
mitk::Vector3D spacing = gridRef->GetSpacing();
mitk::Point3D origin = gridRef->GetOrigin();
mitk::Geometry3D::BoundsArrayType bounds = gridRef->GetBounds();
mitk::AffineTransform3D::ConstPointer fovTransform = gridRef->GetIndexToWorldTransform();
if (this->m_Controls->m_checkUseRefSize->isChecked())
{
this->m_Controls->m_sbFOVSizeX->setValue((bounds[1] - bounds[0])*spacing[0]);
this->m_Controls->m_sbFOVSizeY->setValue((bounds[3] - bounds[2])*spacing[1]);
this->m_Controls->m_sbFOVSizeZ->setValue((bounds[5] - bounds[4])*spacing[2]);
}
if (this->m_Controls->m_checkUseRefSpacing->isChecked())
{
this->m_Controls->m_sbGridSpX->setValue(GetSaveSpacing((bounds[1] - bounds[0]), spacing[0], 20));
this->m_Controls->m_sbGridSpY->setValue(GetSaveSpacing((bounds[3] - bounds[2]), spacing[1], 20));
this->m_Controls->m_sbGridSpZ->setValue(GetSaveSpacing((bounds[5] - bounds[4]), spacing[2], 20));
}
if (this->m_Controls->m_checkUseRefOrigin->isChecked())
{
this->m_Controls->m_sbFOVOriginX->setValue(origin[0]);
this->m_Controls->m_sbFOVOriginY->setValue(origin[1]);
this->m_Controls->m_sbFOVOriginZ->setValue(origin[2]);
}
if (this->m_Controls->m_checkUseRefOrientation->isChecked())
{
this->m_FOVRefOrientation = fovTransform->GetMatrix();
this->UpdateOrientationMatrixWidget();
}
}
}
void QmitkMatchPointRegistrationVisualizer::UpdateOrientationMatrixWidget()
{
for (unsigned int r = 0; r < 3; ++r)
{
for (unsigned int c = 0; c < 3; ++c)
{
this->m_Controls->m_tableOrientation->item(r,
c)->setText(QString::number(this->m_FOVRefOrientation.GetVnlMatrix().get(r, c)));
}
}
}
void QmitkMatchPointRegistrationVisualizer::InitRegNode()
{
if (this->m_spSelectedRegNode.IsNotNull())
{
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisGrid, mitk::BoolProperty::New(true));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisGlyph, mitk::BoolProperty::New(false));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisPoints, mitk::BoolProperty::New(false));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisDirection,
mitk::RegVisDirectionProperty::New());
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColorStyle,
mitk::RegVisColorStyleProperty::New(1));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColorUni, mitk::ColorProperty::New(0,
0.5, 0));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisGridFrequence,
mitk::IntProperty::New(3));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisGridShowStart,
mitk::BoolProperty::New(false));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisGridStartColor,
mitk::ColorProperty::New(0.5, 0, 0));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisFOVSize,
mitk::Vector3DProperty::New(mitk::Vector3D(100.0)));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisFOVSpacing,
mitk::Vector3DProperty::New(mitk::Vector3D(5.0)));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor1Value, mitk::ColorProperty::New(0,
0, 0.5));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor2Value, mitk::ColorProperty::New(0,
0.7, 0));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor2Magnitude,
mitk::DoubleProperty::New(1));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor3Value, mitk::ColorProperty::New(1,
1, 0));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor3Magnitude,
mitk::DoubleProperty::New(5));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor4Value, mitk::ColorProperty::New(1,
0, 0));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor4Magnitude,
mitk::DoubleProperty::New(15));
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColorInterpolate,
mitk::BoolProperty::New(true));
mitk::Point3D origin;
origin.Fill(0.0);
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisFOVOrigin,
mitk::Point3dProperty::New(mitk::Point3D(origin)));
mitk::Vector3D vec(0.0);
vec.SetElement(0, 1.0);
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisFOVOrientation1,
mitk::Vector3DProperty::New(vec));
vec.Fill(0.0);
vec.SetElement(1, 1.0);
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisFOVOrientation2,
mitk::Vector3DProperty::New(vec));
vec.Fill(0.0);
vec.SetElement(2, 1.0);
this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisFOVOrientation3,
mitk::Vector3DProperty::New(vec));
}
}
diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.ui b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.ui
index 3c550db5e9..899b10bbc1 100644
--- a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.ui
+++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.ui
@@ -1,1570 +1,1570 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>MatchPointRegVisControls</class>
<widget class="QWidget" name="MatchPointRegVisControls">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>332</width>
<height>738</height>
</rect>
</property>
<layout class="QVBoxLayout" name="verticalLayout">
<property name="spacing">
<number>5</number>
</property>
<property name="leftMargin">
<number>5</number>
</property>
<property name="topMargin">
<number>5</number>
</property>
<property name="rightMargin">
<number>5</number>
</property>
<property name="bottomMargin">
<number>5</number>
</property>
<item>
<widget class="QLabel" name="label">
<property name="palette">
<palette>
<active>
<colorrole role="WindowText">
<brush brushstyle="SolidPattern">
<color alpha="255">
<red>255</red>
<green>0</green>
<blue>0</blue>
</color>
</brush>
</colorrole>
</active>
<inactive>
<colorrole role="WindowText">
<brush brushstyle="SolidPattern">
<color alpha="255">
<red>255</red>
<green>0</green>
<blue>0</blue>
</color>
</brush>
</colorrole>
</inactive>
<disabled>
<colorrole role="WindowText">
<brush brushstyle="SolidPattern">
<color alpha="255">
<red>120</red>
<green>120</green>
<blue>120</blue>
</color>
</brush>
</colorrole>
</disabled>
</palette>
</property>
<property name="text">
<string>Warning: This plugin is in an experimental state!</string>
</property>
</widget>
</item>
<item>
<widget class="QLabel" name="label_4">
<property name="text">
<string>Registration:</string>
</property>
</widget>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout">
<property name="spacing">
<number>3</number>
</property>
<item>
<widget class="QmitkSingleNodeSelectionWidget" name="registrationNodeSelector" native="true">
<property name="minimumSize">
<size>
<width>0</width>
<height>40</height>
</size>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget class="QLabel" name="label_5">
<property name="text">
<string>Info:</string>
</property>
</widget>
</item>
<item>
<widget class="QTextEdit" name="m_teRegInfo">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Maximum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>0</width>
<height>75</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>16777215</width>
<height>130</height>
</size>
</property>
<property name="readOnly">
<bool>true</bool>
</property>
</widget>
</item>
<item>
<widget class="QGroupBox" name="groupViz">
<property name="sizePolicy">
<sizepolicy hsizetype="MinimumExpanding" vsizetype="Preferred">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="title">
<string/>
</property>
<property name="flat">
<bool>false</bool>
</property>
<layout class="QVBoxLayout" name="verticalLayout_2">
<property name="spacing">
<number>5</number>
</property>
<property name="leftMargin">
<number>5</number>
</property>
<property name="topMargin">
<number>5</number>
</property>
<property name="rightMargin">
<number>5</number>
</property>
<property name="bottomMargin">
<number>5</number>
</property>
<item>
<widget class="QPushButton" name="m_pbUpdateViz">
<property name="toolTip">
<string><html><head/><body><p>Updates the visualization with the current settings.</p></body></html></string>
</property>
<property name="text">
<string>Update visualization</string>
</property>
<property name="checkable">
<bool>false</bool>
</property>
</widget>
</item>
<item>
<widget class="QLabel" name="label_13">
<property name="text">
<string>Show mapping direction:</string>
</property>
</widget>
</item>
<item>
<widget class="QComboBox" name="m_comboDirection">
<property name="toolTip">
<string><html><head/><body><p>Select the direction/kernel of the registration you want to visualize:</p><p>- &quot;direct&quot;: select to show the direct mapping kernel (used for continuous spaced data like point sets).</p><p>- &quot;inverse&quot;: select to show the inverse mapping kernel (used for discrete spaced data like voxel images).</p><p><br/></p><p>If the selected registration does not support a direction, you cannot select it.</p></body></html></string>
</property>
<item>
<property name="text">
<string>Direct</string>
</property>
</item>
<item>
<property name="text">
<string>Inverse</string>
</property>
</item>
</widget>
</item>
<item>
<widget class="QWidget" name="m_boxStyles" native="true">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>0</width>
<height>30</height>
</size>
</property>
<layout class="QHBoxLayout" name="horizontalLayout_2">
<property name="spacing">
<number>5</number>
</property>
<property name="leftMargin">
<number>0</number>
</property>
<property name="topMargin">
<number>5</number>
</property>
<property name="rightMargin">
<number>0</number>
</property>
<property name="bottomMargin">
<number>5</number>
</property>
<item>
<widget class="QPushButton" name="m_pbStyleGrid">
<property name="toolTip">
<string><html><head/><body><p>Select to vizualize registration via grid(s).</p></body></html></string>
</property>
<property name="text">
<string>Grid</string>
</property>
<property name="checkable">
<bool>true</bool>
</property>
<property name="checked">
<bool>true</bool>
</property>
<property name="autoExclusive">
<bool>true</bool>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="m_pbStyleGlyph">
<property name="enabled">
<bool>true</bool>
</property>
<property name="toolTip">
<string>Select to vizualize registration via glyphs.</string>
</property>
<property name="text">
<string>Glyph</string>
</property>
<property name="checkable">
<bool>true</bool>
</property>
<property name="autoExclusive">
<bool>true</bool>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="m_pbStylePoints">
<property name="enabled">
<bool>false</bool>
</property>
<property name="toolTip">
<string>Select to vizualize registration via a pointset selected from the data manager...</string>
</property>
<property name="text">
<string>Points</string>
</property>
<property name="checkable">
<bool>true</bool>
</property>
<property name="autoExclusive">
<bool>true</bool>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item>
<widget class="QTabWidget" name="m_boxSettings">
<property name="currentIndex">
<number>2</number>
</property>
<widget class="QWidget" name="tabViz">
<attribute name="title">
<string>Visualization</string>
</attribute>
<layout class="QVBoxLayout" name="verticalLayout_5">
<property name="leftMargin">
<number>5</number>
</property>
<property name="topMargin">
<number>5</number>
</property>
<property name="rightMargin">
<number>5</number>
</property>
<item>
<layout class="QVBoxLayout" name="verticalLayout_7">
<item>
<widget class="QLabel" name="label_15">
<property name="text">
<string>Color style:</string>
</property>
</widget>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_8">
<item>
<widget class="QRadioButton" name="radioColorUni">
<property name="text">
<string>uni color:</string>
</property>
</widget>
</item>
<item>
<widget class="ctkColorPickerButton" name="btnUniColor">
<property name="enabled">
<bool>false</bool>
</property>
<property name="minimumSize">
<size>
<width>60</width>
<height>0</height>
</size>
</property>
<property name="autoFillBackground">
<bool>false</bool>
</property>
<property name="text">
<string/>
</property>
</widget>
</item>
<item>
<spacer name="horizontalSpacer_6">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>40</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
</layout>
</item>
<item>
<widget class="QRadioButton" name="radioColorVecMag">
<property name="text">
<string>vector magnitude:</string>
</property>
</widget>
</item>
<item>
<widget class="QGroupBox" name="groupColorCoding">
<property name="title">
<string>Color coding:</string>
</property>
<layout class="QVBoxLayout" name="verticalLayout_8">
<item>
<layout class="QGridLayout" name="gridLayout_3">
<property name="leftMargin">
<number>0</number>
</property>
<property name="rightMargin">
<number>0</number>
</property>
<property name="horizontalSpacing">
<number>7</number>
</property>
<property name="verticalSpacing">
<number>3</number>
</property>
<item row="3" column="7">
<spacer name="horizontalSpacer_4">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>40</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
<item row="2" column="7">
<spacer name="horizontalSpacer_3">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>40</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
<item row="1" column="7">
<spacer name="horizontalSpacer_2">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>40</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
<item row="0" column="7">
<spacer name="horizontalSpacer">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>40</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
<item row="1" column="5">
<widget class="QLabel" name="label_29">
<property name="text">
<string>mm</string>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="QLabel" name="label_3">
<property name="text">
<string>small:</string>
</property>
</widget>
</item>
<item row="2" column="1">
<widget class="QLabel" name="label_2">
<property name="text">
<string>medium:</string>
</property>
</widget>
</item>
<item row="2" column="3">
<widget class="QLabel" name="labelVecMagMedium">
<property name="maximumSize">
<size>
<width>30</width>
<height>16777215</height>
</size>
</property>
<property name="text">
<string>></string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
</widget>
</item>
<item row="1" column="4">
<widget class="QDoubleSpinBox" name="sbVecMagSmall">
<property name="maximum">
<double>999.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
</widget>
</item>
<item row="3" column="4">
<widget class="QDoubleSpinBox" name="sbVecMagLarge">
<property name="maximum">
<double>999.000000000000000</double>
</property>
</widget>
</item>
<item row="3" column="1">
<widget class="QLabel" name="label_9">
<property name="text">
<string>large:</string>
</property>
</widget>
</item>
<item row="3" column="3">
<widget class="QLabel" name="labelVecMagLarge">
<property name="maximumSize">
<size>
<width>30</width>
<height>16777215</height>
</size>
</property>
<property name="text">
<string>></string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
</widget>
</item>
<item row="3" column="5">
<widget class="QLabel" name="label_30">
<property name="text">
<string>mm</string>
</property>
</widget>
</item>
<item row="2" column="4">
<widget class="QDoubleSpinBox" name="sbVecMagMedium">
<property name="maximum">
<double>999.000000000000000</double>
</property>
</widget>
</item>
<item row="2" column="5">
<widget class="QLabel" name="label_31">
<property name="text">
<string>mm</string>
</property>
</widget>
</item>
<item row="1" column="3">
<widget class="QLabel" name="labelVecMagSmall">
<property name="maximumSize">
<size>
<width>30</width>
<height>16777215</height>
</size>
</property>
<property name="text">
<string>></string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QLabel" name="label_6">
<property name="text">
<string>negligible:</string>
</property>
</widget>
</item>
<item row="3" column="2">
<widget class="ctkColorPickerButton" name="btnVecMagColorLarge">
<property name="minimumSize">
<size>
<width>50</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>40</width>
<height>16777215</height>
</size>
</property>
<property name="text">
<string/>
</property>
</widget>
</item>
<item row="2" column="2">
<widget class="ctkColorPickerButton" name="btnVecMagColorMedium">
<property name="minimumSize">
<size>
<width>50</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>40</width>
<height>16777215</height>
</size>
</property>
<property name="text">
<string/>
</property>
</widget>
</item>
<item row="1" column="2">
<widget class="ctkColorPickerButton" name="btnVecMagColorSmall">
<property name="minimumSize">
<size>
<width>50</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>40</width>
<height>16777215</height>
</size>
</property>
<property name="text">
<string/>
</property>
</widget>
</item>
<item row="0" column="2">
<widget class="ctkColorPickerButton" name="btnVecMagColorNeg">
<property name="minimumSize">
<size>
<width>50</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>40</width>
<height>16777215</height>
</size>
</property>
<property name="text">
<string/>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget class="QCheckBox" name="cbVevMagInterlolate">
<property name="text">
<string>interpolate colors</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
</layout>
</item>
<item>
<spacer name="verticalSpacer_3">
<property name="orientation">
<enum>Qt::Vertical</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>20</width>
<height>40</height>
</size>
</property>
</spacer>
</item>
</layout>
</widget>
<widget class="QWidget" name="tabGrid">
<property name="enabled">
<bool>true</bool>
</property>
<attribute name="title">
<string>Grid</string>
</attribute>
<attribute name="toolTip">
<string><html><head/><body><p>General grid visualization settings.</p></body></html></string>
</attribute>
<layout class="QVBoxLayout" name="verticalLayout_3">
<property name="spacing">
<number>5</number>
</property>
<property name="leftMargin">
<number>5</number>
</property>
<property name="topMargin">
<number>5</number>
</property>
<property name="rightMargin">
<number>5</number>
</property>
<property name="bottomMargin">
<number>5</number>
</property>
<item>
<layout class="QFormLayout" name="formLayout">
<property name="fieldGrowthPolicy">
<enum>QFormLayout::AllNonFixedFieldsGrow</enum>
</property>
<property name="horizontalSpacing">
<number>5</number>
</property>
<property name="verticalSpacing">
<number>5</number>
</property>
<item row="0" column="0">
<widget class="QLabel" name="label_16">
<property name="text">
<string>Grid frequency:</string>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QSpinBox" name="m_sbGridFrequency">
<property name="toolTip">
<string><html><head/><body><p>Indicate the frequency of visible gridlines used for visualization.</p><p>e.g. 1: every line of the grid is visible; 2: only every second line is visible ...</p></body></html></string>
</property>
<property name="maximum">
<number>200</number>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget class="QGroupBox" name="m_groupShowStartGrid">
<property name="font">
<font>
<weight>50</weight>
<bold>false</bold>
</font>
</property>
<property name="toolTip">
<string><html><head/><body><p>Allows that pixels may not be defined in the mapped image because they are outside of the field of view of the used input image.</p><p>The pixels will be marked with the given padding value.</p><p>If unchecked the mapping will be aborted in a case of undefined pixels.</p></body></html></string>
</property>
<property name="title">
<string>Show start grid</string>
</property>
<property name="flat">
<bool>false</bool>
</property>
<property name="checkable">
<bool>true</bool>
</property>
<property name="checked">
<bool>false</bool>
</property>
<layout class="QHBoxLayout" name="horizontalLayout_3">
<property name="leftMargin">
<number>11</number>
</property>
<property name="topMargin">
<number>5</number>
</property>
<property name="rightMargin">
<number>11</number>
</property>
<property name="bottomMargin">
<number>5</number>
</property>
<item>
<widget class="QLabel" name="label_14">
<property name="text">
<string>Color</string>
</property>
</widget>
</item>
<item>
<widget class="ctkColorPickerButton" name="btnStartGridColor">
<property name="minimumSize">
<size>
<width>60</width>
<height>0</height>
</size>
</property>
<property name="autoFillBackground">
<bool>false</bool>
</property>
<property name="text">
<string/>
</property>
</widget>
</item>
<item>
<spacer name="horizontalSpacer_5">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>40</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
</layout>
</widget>
</item>
<item>
<spacer name="verticalSpacer">
<property name="orientation">
<enum>Qt::Vertical</enum>
</property>
<property name="sizeType">
<enum>QSizePolicy::Expanding</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>20</width>
<height>300</height>
</size>
</property>
</spacer>
</item>
</layout>
</widget>
<widget class="QWidget" name="tabFOV">
<attribute name="title">
<string>FOV</string>
</attribute>
<attribute name="toolTip">
<string><html><head/><body><p>Field of view settings (FOV) for vizualizing the grid correctly (its origin, size and orientation).</p></body></html></string>
</attribute>
<layout class="QVBoxLayout" name="verticalLayout_4">
<property name="spacing">
<number>5</number>
</property>
<property name="leftMargin">
<number>5</number>
</property>
<property name="topMargin">
<number>5</number>
</property>
<property name="rightMargin">
<number>5</number>
</property>
<property name="bottomMargin">
<number>5</number>
</property>
<item>
<widget class="QLabel" name="label_18">
<property name="text">
<string>Size (in mm):</string>
</property>
</widget>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_4">
<property name="spacing">
<number>0</number>
</property>
<item>
<widget class="QLabel" name="label_20">
<property name="sizePolicy">
<sizepolicy hsizetype="Maximum" vsizetype="Preferred">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="text">
<string>x:</string>
</property>
</widget>
</item>
<item>
<widget class="QDoubleSpinBox" name="m_sbFOVSizeX">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>10</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>50</width>
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string><html><head/><body><p>Indicate the size (in mm) of the grid in the x direction.</p></body></html></string>
</property>
<property name="decimals">
<number>2</number>
</property>
<property name="minimum">
<double>0.010000000000000</double>
</property>
<property name="maximum">
<double>9999.000000000000000</double>
</property>
</widget>
</item>
<item>
<widget class="QLabel" name="label_21">
<property name="text">
<string>y:</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
</widget>
</item>
<item>
<widget class="QDoubleSpinBox" name="m_sbFOVSizeY">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>10</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>50</width>
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string><html><head/><body><p>Indicate the size (in mm) of the grid in the y direction.</p></body></html></string>
</property>
<property name="decimals">
<number>2</number>
</property>
<property name="minimum">
<double>0.010000000000000</double>
</property>
<property name="maximum">
<double>9999.000000000000000</double>
</property>
</widget>
</item>
<item>
<widget class="QLabel" name="label_19">
<property name="text">
<string>z:</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
</widget>
</item>
<item>
<widget class="QDoubleSpinBox" name="m_sbFOVSizeZ">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>10</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>50</width>
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string><html><head/><body><p>Indicate the size (in mm) of the grid in the z direction.</p></body></html></string>
</property>
<property name="decimals">
<number>2</number>
</property>
<property name="minimum">
<double>0.010000000000000</double>
</property>
<property name="maximum">
<double>9999.000000000000000</double>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget class="QLabel" name="label_24">
<property name="text">
<string>Origin (in mm):</string>
</property>
</widget>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_5">
<property name="spacing">
<number>0</number>
</property>
<item>
<widget class="QLabel" name="label_25">
<property name="sizePolicy">
<sizepolicy hsizetype="Maximum" vsizetype="Preferred">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="text">
<string>x:</string>
</property>
</widget>
</item>
<item>
<widget class="QDoubleSpinBox" name="m_sbFOVOriginX">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>10</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>50</width>
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string><html><head/><body><p>Indicate the origin (in mm) of the grid in the x direction.</p></body></html></string>
</property>
<property name="minimum">
<double>-99999.000000000000000</double>
</property>
<property name="maximum">
<double>99999.000000000000000</double>
</property>
</widget>
</item>
<item>
<widget class="QLabel" name="label_22">
<property name="text">
<string>y:</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
</widget>
</item>
<item>
<widget class="QDoubleSpinBox" name="m_sbFOVOriginY">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>10</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>50</width>
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string><html><head/><body><p>Indicate the origin (in mm) of the grid in the y direction.</p></body></html></string>
</property>
<property name="minimum">
<double>-99999.000000000000000</double>
</property>
<property name="maximum">
<double>99999.000000000000000</double>
</property>
</widget>
</item>
<item>
<widget class="QLabel" name="label_23">
<property name="text">
<string>z:</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
</widget>
</item>
<item>
<widget class="QDoubleSpinBox" name="m_sbFOVOriginZ">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>10</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>50</width>
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string><html><head/><body><p>Indicate the origin (in mm) of the grid in the z direction.</p></body></html></string>
</property>
<property name="minimum">
<double>-99999.000000000000000</double>
</property>
<property name="maximum">
<double>99999.000000000000000</double>
</property>
<property name="value">
<double>0.000000000000000</double>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget class="QLabel" name="label_17">
<property name="text">
<string>Spacing (in mm):</string>
</property>
</widget>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_6">
<property name="spacing">
<number>0</number>
</property>
<item>
<widget class="QLabel" name="label_10">
<property name="sizePolicy">
<sizepolicy hsizetype="Maximum" vsizetype="Preferred">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="text">
<string>x:</string>
</property>
</widget>
</item>
<item>
<widget class="QDoubleSpinBox" name="m_sbGridSpX">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>10</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>50</width>
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string><html><head/><body><p>Indicate the spacing/resolution of the grid in the x direction.</p></body></html></string>
</property>
<property name="minimum">
<double>0.010000000000000</double>
</property>
<property name="maximum">
<double>9999.000000000000000</double>
</property>
<property name="value">
<double>0.010000000000000</double>
</property>
</widget>
</item>
<item>
<widget class="QLabel" name="label_12">
<property name="text">
<string>y:</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
</widget>
</item>
<item>
<widget class="QDoubleSpinBox" name="m_sbGridSpY">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>10</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>50</width>
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string><html><head/><body><p>Indicate the spacing/resolution of the grid in the y direction.</p></body></html></string>
</property>
<property name="minimum">
<double>0.010000000000000</double>
</property>
<property name="maximum">
<double>9999.000000000000000</double>
</property>
<property name="value">
<double>0.010000000000000</double>
</property>
</widget>
</item>
<item>
<widget class="QLabel" name="label_11">
<property name="text">
<string>z:</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
</widget>
</item>
<item>
<widget class="QDoubleSpinBox" name="m_sbGridSpZ">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>10</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>50</width>
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string><html><head/><body><p>Indicate the spacing/resolution of the grid in the z direction.</p></body></html></string>
</property>
<property name="minimum">
<double>0.010000000000000</double>
</property>
<property name="maximum">
<double>9999.000000000000000</double>
</property>
<property name="value">
<double>0.010000000000000</double>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget class="QLabel" name="label_27">
<property name="text">
<string>Orientation:</string>
</property>
</widget>
</item>
<item>
<widget class="QTableWidget" name="m_tableOrientation">
<property name="enabled">
<bool>true</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Maximum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="maximumSize">
<size>
<width>160</width>
<height>50</height>
</size>
</property>
<property name="font">
<font>
<pointsize>7</pointsize>
</font>
</property>
<property name="showDropIndicator" stdset="0">
<bool>false</bool>
</property>
<property name="dragDropOverwriteMode">
<bool>false</bool>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
<property name="cornerButtonEnabled">
<bool>false</bool>
</property>
<attribute name="horizontalHeaderVisible">
<bool>false</bool>
</attribute>
<attribute name="horizontalHeaderMinimumSectionSize">
<number>20</number>
</attribute>
<attribute name="horizontalHeaderDefaultSectionSize">
<number>50</number>
</attribute>
<attribute name="verticalHeaderVisible">
<bool>false</bool>
</attribute>
<attribute name="verticalHeaderDefaultSectionSize">
<number>20</number>
</attribute>
<row>
<property name="text">
<string>R1</string>
</property>
</row>
<row>
<property name="text">
<string>R2</string>
</property>
</row>
<row>
<property name="text">
<string>R3</string>
</property>
</row>
<column>
<property name="text">
<string>C1</string>
</property>
</column>
<column>
<property name="text">
<string>C2</string>
</property>
</column>
<column>
<property name="text">
<string>C3</string>
</property>
</column>
<item row="0" column="0">
<property name="text">
<string>0</string>
</property>
<property name="flags">
<set>ItemIsEnabled</set>
</property>
</item>
<item row="0" column="1">
<property name="text">
<string>0</string>
</property>
<property name="flags">
<set>ItemIsEnabled</set>
</property>
</item>
<item row="0" column="2">
<property name="text">
<string>0</string>
</property>
<property name="flags">
<set>ItemIsEnabled</set>
</property>
</item>
<item row="1" column="0">
<property name="text">
<string>0</string>
</property>
<property name="flags">
<set>ItemIsEnabled</set>
</property>
</item>
<item row="1" column="1">
<property name="text">
<string>0</string>
</property>
<property name="flags">
<set>ItemIsEnabled</set>
</property>
</item>
<item row="1" column="2">
<property name="text">
<string>0</string>
</property>
<property name="flags">
<set>ItemIsEnabled</set>
</property>
</item>
<item row="2" column="0">
<property name="text">
<string>0</string>
</property>
<property name="flags">
<set>ItemIsEnabled</set>
</property>
</item>
<item row="2" column="1">
<property name="text">
<string>0</string>
</property>
<property name="flags">
<set>ItemIsEnabled</set>
</property>
</item>
<item row="2" column="2">
<property name="text">
<string>0</string>
</property>
<property name="flags">
<set>ItemIsEnabled</set>
</property>
</item>
</widget>
</item>
<item>
<widget class="QLabel" name="label_26">
<property name="text">
- <string>FOV Reverence:</string>
+ <string>FOV Reference:</string>
</property>
</widget>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_7">
<property name="spacing">
<number>3</number>
</property>
<item>
<widget class="QmitkSingleNodeSelectionWidget" name="fovReferenceNodeSelector" native="true">
<property name="minimumSize">
<size>
<width>0</width>
<height>40</height>
</size>
</property>
</widget>
</item>
</layout>
</item>
<item>
<layout class="QGridLayout" name="gridLayout">
<item row="0" column="0">
<widget class="QCheckBox" name="m_checkUseRefSize">
<property name="text">
<string>size</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QCheckBox" name="m_checkUseRefOrigin">
<property name="text">
<string>origin</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QCheckBox" name="m_checkUseRefSpacing">
<property name="text">
<string>spacing</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="QCheckBox" name="m_checkUseRefOrientation">
<property name="text">
<string>orientation</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
</layout>
</item>
<item>
<spacer name="verticalSpacer_2">
<property name="orientation">
<enum>Qt::Vertical</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>20</width>
<height>40</height>
</size>
</property>
</spacer>
</item>
</layout>
</widget>
</widget>
</item>
</layout>
</widget>
</item>
<item>
<spacer name="verticalSpacer_5">
<property name="orientation">
<enum>Qt::Vertical</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>20</width>
<height>40</height>
</size>
</property>
</spacer>
</item>
</layout>
</widget>
<customwidgets>
<customwidget>
<class>QmitkSingleNodeSelectionWidget</class>
<extends>QWidget</extends>
<header location="global">QmitkSingleNodeSelectionWidget.h</header>
<container>1</container>
</customwidget>
<customwidget>
<class>ctkColorPickerButton</class>
<extends>QPushButton</extends>
<header>ctkColorPickerButton.h</header>
</customwidget>
</customwidgets>
<resources/>
<connections/>
<designerdata>
<property name="gridDeltaX">
<number>5</number>
</property>
<property name="gridDeltaY">
<number>5</number>
</property>
<property name="gridSnapX">
<bool>true</bool>
</property>
<property name="gridSnapY">
<bool>true</bool>
</property>
<property name="gridVisible">
<bool>true</bool>
</property>
</designerdata>
</ui>
diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics.dox b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics.dox
index 09555a1cce..f371747b7c 100644
--- a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics.dox
+++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics.dox
@@ -1,55 +1,63 @@
/**
\page org_mitk_views_imagestatistics The Image Statistics View
-\imageMacro{bar-chart.svg,"Icon of the Image Statistics View",2.00}
+\imageMacro{bar-chart2.svg,"Icon of the Image Statistics View",2.00}
\section QmitkImageStatisticsUserManualSummary Summary
This view provides an easy interface to quickly compute some features of a whole image or a region of interest.
This document will tell you how to use this view, but it is assumed that you already know how to use MITK in general.
Please see \ref QmitkImageStatisticsUserManualDetails for more detailed information on usage and supported filters.
-If you encounter problems using the view, please have a look at the \ref QmitkImageStatisticsUserManualTrouble page.
\section QmitkImageStatisticsUserManualDetails Details
Manual sections:
- \ref QmitkImageStatisticsUserManualOverview
- \ref QmitkImageStatisticsUserManualUsage
-- \ref QmitkImageStatisticsUserManualTrouble
\section QmitkImageStatisticsUserManualOverview Overview
This view provides an easy interface to quickly compute some features of a whole image or a region of interest.
\imageMacro{QmitkMeasurementToolbox_Interface.png,"The interface",9.10}
\section QmitkImageStatisticsUserManualUsage Usage
-After selection of an image or a binary mask of an image in the datamanager, the Image Statistics view shows some statistical information. If a mask is selected, the name of the mask and the name of the image, to which the mask is applied, are shown at the top. For time data the current time step is used for the selected mask and the selected image. If the total number of time steps on the selected mask is less than the current time step, the last time step of the mask is used. If a mask is selected, its used time step will be displayed next to its name like this: (t=0).
+
+To select the input data, either use the quick selection button (labeled "+"), or select the input data via the "Input Data" tab.
+
+\imageMacro{QmitkImageStatistics_InputData.png,"Select the input data via the \"Input data\" tab (marked red) or via the quick selection button (marked yellow)",10}
+
+\subsection QmitkImageStatisticStatistics Statistics
+After selection of an image or a binary mask as input data, the image statistics are calculated and displayed in the "Statistics" section. If masks (ROIs: segmentations, planarfigures, ...) are selected, the statistics for these masks are shown. For time data the statistics for each time step are calculated correspondingly.
+
+An example of parts of the calculated statistical features (Mean, Median, StandardDeviation, RMS, Max, MaxPosition, Min, MinPosition, Voxel, Volume [mm^3], Skewness, Kurtosis, Uniformity, Entropy, MPP, UPP and Variance) for different timesteps and different masks is pictured below.
+
+\imageMacro{QmitkImageStatistics_statistics.png, "Example of parts of the statistics for different masks and timestamps", 1.00}
Check "Ignore zero-valued voxels" to hide voxels with grayvalue zero.
-Below it is the statistics window which displays the calculated statistical features (such as mean, standard deviation...).
+\subsection QmitkImageStatisticHistogram Histogram
Beneath the statistics window is the histogram window, which shows the histogram of the current selection.
-Draw a rectangular window with pressed left button to zoom the histogram view in. With a double click in the view area you can zoom out to the default viewport.
-You can also just pan the view in horizontal or vertical direction by dragging with the left mousebutton in the respective direction.
+The histogram window is currently only available for a single image and no or one ROI: When selection multiple images and/or multiple masks, the histogram window is deactivated!
+
+Draw a rectangular window with a pressed left button to zoom in on the histogram. With a double click in the view area you can zoom out to the default viewport. You can also pan the view in horizontal or vertical direction by dragging with the left mouse button in the respective direction. Additionally, different options like "Custom Zoom", to set the maximum and minimum value, or by adjusting the number of bins, can be used to modify the view.
If the mask is not a closed planar figure or a segmentation an intensity profile is created instead of the histogram.
A tooltip is available by hovering over one of the bins.
-At the bottom of each view is one button. They copy their respective data in csv format to the clipboard.
-
-\section QmitkImageStatisticsUserManualTrouble Troubleshooting
+\subsection QmitkImageStatisticsUserManualCopytoClipboard Copy to Clipboard
-No known problems.
+At the bottom of each view is a "Copy to Clipboard" button, allowing to copy the respective data in csv format to the clipboard.
+Be aware of the following information regarding this functionality:
+\li The values are separated by tabulator.
+\li Numeric values will be converted using the system language (e.g. with German as system language the decimal separator will be ",", with English it will be '.').
+\li One can directly copy'n'paste into Excel (and alike) as long as Excel supports/is configured to the system language
-<B>All other problems.</B><BR>
-Please report to the MITK mailing list.
-See http://www.mitk.org/wiki/Mailinglist on how to do this.
*/
diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics_InputData.png b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics_InputData.png
new file mode 100644
index 0000000000..566a7bda72
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics_InputData.png differ
diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics_statistics.png b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics_statistics.png
new file mode 100644
index 0000000000..a070b24ad0
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics_statistics.png differ
diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox
index b71b4bc844..e1372508d9 100644
--- a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox
+++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox
@@ -1,90 +1,90 @@
/**
\page org_mitk_views_measurement The Measurement View
\imageMacro{measurement.svg,"Icon of the Measurement View",2.00}
<h1>Overview</h1>
-The Measurement view allows you to measure distances, angels, paths and several geometric figures on 2D images or image slices of 3D and 4D images. The measurement view is repeatedly useable with the same or different measurement figures, which are correlated to the chosen image and can be saved together with it for future use.
+The Measurement view allows you to measure distances, angles, paths and several geometric figures on 2D images or image slices of 3D and 4D images. The measurement view is repeatedly useable with the same or different measurement figures that are related to the chosen image and can be saved together with it for future use.
\imageMacro{QmitkMeasurementToolbox_BasicScreenEdited.jpg,"Image with measurements",16.00}
<h1>Usage</h1>
The first step to perform measurements is to select a reference image on top of the view. All resulting measurements will be assigned as child nodes of the image in the data manager. The standard working plane is 'Axial' but the other standard view planes ('Saggital' and 'Coronal') are also valid for measurements.
\imageMacro{QmitkMeasurementToolbox_MeasurementView.jpg,"Measurement View",7.60}
After selecting an image, you can click on any of the geometrical symbols. The respective measurement will appear as soon as you click on the image location you want to measure.
The view offers a variety of measurement options that are introduced in the following:
<ul>
<li> <b>Line:</b>
Draws a line between two set points and returns the distance between these points.
<li> <b>Path:</b>
-Draws a line between several set points (two and more) and calculates the overall length, which is all line's length summed up. Add the final point by double left-click.
+Draws a line between several set points (two and more) and calculates the overall length, which is all lines length summed up. Add the final point by double left-click.
<li> <b>Angle:</b>
Draws two lines from three set points connected in the second set point and return the inner angle at the second point.
<li> <b>Four Point / Double Angle:</b>
-Draws two lines that may but must not intersect from four set points. The returned angle is the one depicted in the icon.
+Draws two lines that may but do not have to intersect from four set points. The returned angle is the one depicted in the icon.
<li> <b>Circle:</b>
Draws a circle by setting two points, whereas the first set point is the center and the second the radius of the circle. The measured values are the radius and the included area.
<li> <b>Ellipse:</b>
Draws an ellipse that can be modified by three points. The middle point can be used to move the whole measurement. The lower point modifies the ellipse axes. The right point can be used to modify the radius of the ellipse. The measured values are the major and minor axes and the area.
<li> <b>Double Ellipse:</b>
Draws two ellipses by adjusting four points. The middle point can be used to move the whole measurement. The left point is used to adjust the distance between the two ellipses. The lower point modifies the ellipse axes. The right point can be used to modify the radius of the ellipse. Can be used for measuring e.g. the wall thickness of a vessel. The measured values are the major and minor axes and the thickness.
<li> <b>Rectangle:</b>
-Draws a rectangle by setting two points at the opposing edges of the rectangle starting with the upper left edge. The measured values are the circumference and the included area.
+Draws a rectangle by setting two points at the opposing edges of the rectangle starting with the upper left corner. The measured values are the circumference and the included area.
<li> <b>Polygon:</b>
Draws a closed polygon that can have an arbitrary number of points. New points are added by left mouse-click. To finish the drawing the user can double click on the last control point. The measured values are circumference and area.
<li> <b>Bezier curve:</b>
Draws a bezier curve by adding some control points with left mouse-click. To finish the drawing the user can double-click on the last control point. The measured value is the length of the bezier curve.
<li> <b>Subdivision Polygon:</b>
Draws a closed subdivision polygon by adding some control points with left mouse-click. To finish the drawing the user can double-click on the last control point. The measured value is the circumference of the polygon.
</ul>
<h2>Fixed sizes of measurement figures</h2>
-The measurement view offers a fixed size for circle and double ellipses to preset a radius and a thickness. This is useful e.g. for disagnostic studies where you want to derive gray value statistics from a well defined region.
+The measurement view offers a fixed size for circle and double ellipses to preset a radius and a thickness. This is useful e.g. for diagnostic studies where you want to derive gray value statistics from a well defined region.
<h2>Modify measurements</h2>
All measurements can be modified later on by moving the respective control points. Note that they can only be modified if the view is open.
<h2>Multiple measurement figures</h2>
When applying more than one measurement figure to the image the actual measurement figure is depicted in red and the displayed values belong to this measurement figure. All other measurement figures appear white. They can be selected by a left-mouse click on the respective node.
<h2>Save the measurement information</h2>
The entire scene containing the image and the measurement figures can be saved for future use. Scenes are saved with a '.mitk' extension by pressing 'Save Project' and contain all nodes and relevant information. Alternatively, you can just save the measurement solely (with file extension '.pf') by right-click on the node in the data manager.
The content of the measurement widget can be copied to the clipboard with the corresponding button for further use in a table calculation program (e.g. Open Office Calc etc.).
<h2>Remove measurement figures or image</h2>
-If the single measurement figures or the image is not needed any longer, it can be removed solely or as an entire group. The image can't be removed without simultaneously removing all the dependent measurement figures that belong to the image tree in the data manager. To remove just select the wanted items in the data manager list by left-clicking on the respective node or, if several items wanted to be removed, left-click on all wanted by simultaneously holding the ctrl-button pressed.
+If the single measurement figures or the image is not needed any longer, it can be removed solely or as an entire group. The image can't be removed without simultaneously removing all the dependent measurement figures that belong to the image tree in the data manager. To remove, just select the wanted items in the data manager list by right-clicking on the respective node or, if several items wanted to be removed, right-click on all wanted by simultaneously holding the ctrl-button pressed.
*/
\ No newline at end of file
diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolbox_Interface.png b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolbox_Interface.png
index 5950809ade..ce389086df 100644
Binary files a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolbox_Interface.png and b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolbox_Interface.png differ
diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/bar-chart2.svg b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/bar-chart2.svg
new file mode 100644
index 0000000000..6173a2c58d
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/bar-chart2.svg
@@ -0,0 +1,75 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:cc="http://creativecommons.org/ns#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:svg="http://www.w3.org/2000/svg"
+ xmlns="http://www.w3.org/2000/svg"
+ xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+ xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+ width="128"
+ height="128"
+ viewBox="0 0 2621440 2293760"
+ id="svg2"
+ version="1.1"
+ inkscape:version="0.92.3 (2405546, 2018-03-11)"
+ sodipodi:docname="bar-chart2.svg">
+ <metadata
+ id="metadata10">
+ <rdf:RDF>
+ <cc:Work
+ rdf:about="">
+ <dc:format>image/svg+xml</dc:format>
+ <dc:type
+ rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+ <dc:title></dc:title>
+ </cc:Work>
+ </rdf:RDF>
+ </metadata>
+ <defs
+ id="defs8" />
+ <sodipodi:namedview
+ pagecolor="#ffffff"
+ bordercolor="#666666"
+ borderopacity="1"
+ objecttolerance="10"
+ gridtolerance="10"
+ guidetolerance="10"
+ inkscape:pageopacity="0"
+ inkscape:pageshadow="2"
+ inkscape:window-width="1920"
+ inkscape:window-height="1137"
+ id="namedview6"
+ showgrid="false"
+ inkscape:zoom="4"
+ inkscape:cx="34.145726"
+ inkscape:cy="108.17143"
+ inkscape:window-x="-8"
+ inkscape:window-y="-8"
+ inkscape:window-maximized="1"
+ inkscape:current-layer="svg2"
+ units="px" />
+ <path
+ d="m 819200.07,1187840 v 655359.9 H 491520.05 V 1187840 Z m 481280.03,0 10240,655359.9 H 983040.12 l -10240,-655359.9 z m 1320960,819200 v 163840 H 0 V 204799.84 H 163840.02 V 2007040 Z M 1802240.2,860159.82 V 1843199.9 H 1474560.1 V 860159.82 Z m 491520,-491519.91 V 1843199.9 h -327680 V 368639.91 Z"
+ id="path4"
+ style="fill:#00ff00;fill-opacity:1;stroke:none;stroke-width:0.99999994"
+ inkscape:connector-curvature="0"
+ sodipodi:nodetypes="ccccccccccccccccccccccccccc" />
+ <path
+ sodipodi:type="star"
+ style="fill:#00ff00;stroke-width:24753.11132812"
+ id="path6589"
+ sodipodi:sides="5"
+ sodipodi:cx="889765.88"
+ sodipodi:cy="652603.44"
+ sodipodi:r1="601505.62"
+ sodipodi:r2="300752.81"
+ sodipodi:arg1="0.93141042"
+ sodipodi:arg2="1.559729"
+ inkscape:flatsided="false"
+ inkscape:rounded="0"
+ inkscape:randomized="0"
+ d="M 1248685.9,1135289 893094.34,953337.83 541616.98,1143114.8 604779.02,748701.03 315677.95,473070.5 710305.85,411260.62 883108.92,51134.65 l 180731.38,356213.13 395899.3,53060.44 -282929.8,281961.7 z"
+ inkscape:transform-center-x="2057.1205"
+ inkscape:transform-center-y="-55478.7" />
+</svg>
diff --git a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox
index 0d7bcb3f5f..2cbc42acca 100644
--- a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox
+++ b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox
@@ -1,64 +1,64 @@
/**
\page org_mitk_views_moviemaker The Movie Maker
-\imageMacro{video-camera.svg,"Icon of the Movie Maker Plugin.",2.00}
+\imageMacro{moviemakericon_black.svg,"Icon of the Movie Maker Plugin.",2.00}
\tableofcontents
\section org_mitk_views_moviemakerOverview Overview
The Movie Maker View allows you to create basic animations of your scene and to record them to video files.
Individual animations are arranged in a timeline and can be played back sequential or in parallel.
The Movie Maker View uses the external FFmpeg command line utility to write compressed video files.
<b>You have to manually install FFmpeg and set the corresponding path in "External Programs" in the MITK Workbench Preferences (Ctrl+P) in order to record your movies to video files.</b>
\imageMacro{QmitkMovieMaker_Preferences.png,"The External Programs preferences page.",12.00}
\section org_mitk_views_moviemakerUsage Usage
\imageMacro{QmitkMovieMaker_MovieMakerView.png,"The Movie Maker View.",16.00}
To create a movie you have to add an animation to the timeline by clicking the "Add animation" button.
You can choose between the available types of animations, e.g., Orbit or Slice.
The timeline surrounding bottons allow you to arrange, remove, or add further animations to your movie.
Each animation can be set to either begin with the previous animation, i.e., run in parallel, or to start after the previous animation, i.e., run sequential.
In combination with delays, rather complex animation arrangements are possible.
To set animation specific parameters, select the corresponding animation in the timeline first.
You can play back, pause and stop your movie with the according controls at the bottom of the Movie Maker View.
Click the "Record" button to finally record your movie to a video file with the specified number of frames per second.
You have to choose the render window which you want to record.
\subsection org_mitk_views_moviemakerOrbitUsage Orbit Animation
The Orbit animation rotates the camera in the 3D window around the scene.
Align the camera directly in the 3D window and enter the number of degrees for the orbitting.
If you are planning to have a specific view in the middle of your movie you can play the movie and pause it at the specific frame of interest.
Adjust the camera in the 3D window and restart the animation.
\imageMacro{QmitkMovieMaker_Orbit.png,"The Orbit animation.",12.00}
\subsection org_mitk_views_moviemakerSliceUsage Slice Animation
The Slice animation slices through an image.
You can choose the image plane (axial, sagittal, or coronal), as well as the start and end points of the slicing.
Use the image navigator in the bottom left of the Workbench to get an idea of the desired values.
Check "Reverse" in order to slice from the higher slice number to the lower slice number.
\imageMacro{QmitkMovieMaker_Slice.png,"The Slice animation.",12.00}
\subsection org_mitk_views_moviemakerTimeUsage Time Animation
The Time animation steps through the individual time steps of the current scene.
You can specify the range of the animated time steps.
Use the image navigator in the bottom left of the Workbench to get an idea of the desired values.
Check "Reverse" in order to step from later time steps to previous time steps.
\imageMacro{QmitkMovieMaker_Time.gif,"The Time animation.",12.00}
*/
diff --git a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker_Icon.png b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker_Icon.png
deleted file mode 100644
index e7751d99a6..0000000000
Binary files a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker_Icon.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/video-camera.svg b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/moviemakericon_black.svg
similarity index 100%
rename from Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/video-camera.svg
rename to Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/moviemakericon_black.svg
diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_multilabelsegmentation.dox b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_multilabelsegmentation.dox
index 5259fa5e35..6b11a85216 100644
--- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_multilabelsegmentation.dox
+++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_multilabelsegmentation.dox
@@ -1,114 +1,101 @@
/**
\page org_mitk_views_multilabelsegmentation The Multilabel Segmentation
\imageMacro{"multilabelsegmentation.svg", "Icon of the MultiLabelSegmentation Plugin", 12}
-Please reference \ref org_mitk_views_segmentation for the description of the general segmentation tools.
+The difference between a binary and a multi-label segmentation is that a multi-label segmentation can not only contain more than one label but also more than one layer. This allows you to create different labels for different regions of interest encapsulated in one single image. The difference between labels and layers is that labels on one layer cannot overlap but labels on different layers can.
+
+Hereinafter, a description is given on how multi-label segmentations can be created and modified. Please refer to \ref org_mitk_views_segmentation for a description of the general segmentation tools.
\tableofcontents
-\section org_mitk_views_multilabelsegmentationUserManualCreateOpenSaveImportAdd Start Segmenting
+\section org_mitk_views_multilabelsegmentationUserManualCreateOpenSaveImportAdd Data Selection
-To start using the <b>Segmentation Perspective</b> you will have to either create a new segmentation session or
-load an existing one from disk. The <b>Segmentation toolbar</b> collects buttons for the these actions:
+In the 'MultiLabel Segmentation' view you can first select an image. Thereafter, you can either create a new segmentation session by pressing the symbol right to the selection widget or select an existing one.
-\imageMacro{"org_mitk_views_multilabelsegmentationIMGtoolbar.png", "Segmentation toolbar", 12}
+\imageMacro{"org_mitk_views_multilabelsegmentationIMGtoolbar.png", "Data selection",12}
-<ul>
- <li>Create segmentation session</li> a new segmentation session is created.
- <li>Load segmentation session</li> a segmentation session can be loaded from disk (.lset file extensions).
- <li>Save segmentation session</li> the current segmentation session can be saved to disk.
- <li>Import segmentation session</li> a segmentation session can be incorporated into the current one. All new labels will be appended
- at the end of the table.
- <li>Add label</li> a new label is appended to the current segmentation session, at the end of the table.
-</ul>
-\section org_mitk_views_multilabelsegmentationUserManualLabelTable The Label Table
+\section org_mitk_views_multilabelsegmentationUserManualLayerTable Segmentation Layers
+Once you started a segmentation session you can add or delete different layers. You can use the layers independently and switch layers by the left and right arrows.
+
+
+\imageMacro{"org_mitk_views_multilabelsegmentationIMGlayerManager.png", "Layer selection",12}
+
+\subsection org_mitk_views_multilabelsegmentationUserManualLayerCreation Creating a New Layer
+
+A layer is a set of labels that occupy a non-overlapping anatomical space. The best way to describe them is by a real use case. Imagine you are working on a radiotherapy planning application. In the first layer of your segmentation
+session, you would like to trace the contours of the liver and neighboring organs. You can accommodate all these segmentations in separate labels because they all occupy different anatomical regions and do not overlap. Now say you would like to segment the arteries and veins inside the liver. If you don't trace them in a different layer, you will overwrite the previous ones. You may also need a third layer for segmenting the different irrigation territories in the liver and a fourth layer to contain the lesion you would like to treat.
+
+\section org_mitk_views_multilabelsegmentationUserManualLabelTable Segmentation Labels
-The following label properties are readily available to modify:
+For each layer, you can add one or more labels. Pressing the double arrow on the right, all created labels are shown in the 'Lable Table'. The following label properties are available:
<ul>
- <li>Name</li> the name of the label. Can be a predefined one or any other.
- <li>Color</li> the color of the label.
- <li>Visible</li> whether the label is currently visible or hiden.
- <li>Locked</li> whether the label is locked or editable. A locked label cannot be overwritten by another.
+ <li><b>Name:</b></li> the name of the label. Can be a predefined one or any other.
+ <li><b>Locked:</b></li> whether the label is locked or editable. A locked label cannot be overwritten by another.
+ <li><b>Color:</b></li> the color of the label.
+ <li><b>Visible:</b></li> whether the label is currently visible or hidden.
</ul>
-The Label Table is shown below:
-\imageMacro{"org_mitk_views_multilabelsegmentationIMGlabeltable.png", "The <b>Label Table</b> showing all the labels in the current segmentation session", 12}
+\imageMacro{"org_mitk_views_multilabelsegmentationIMGlabeltable.png", "The 'Label Table' shows all labels in the current segmentation session", 12}
-\section org_mitk_views_multilabelsegmentationUserManualLabelCreation Creating a New Label
+\subsection org_mitk_views_multilabelsegmentationUserManualLabelCreation Creating a New Label
-Click the "New Label" button to add a new label. A dialog will show-up to enter the name and color. Preset organ names and
-corresponding colors are offered while you type in, but you can set any name. The new name if not known will be automatically
-remembered and made available the next time you create a new label. In the current implementation of the plugin,
-the maximum number of labels is restricted to 255. If you need more, you will have to create a new segmentation session.
+Click the 'New Label' button to add a new label. A dialog will show up to enter the name and color. Preset organ names and
+corresponding colors are offered while you type in, but you can set any name. The new name - if not known - will be automatically remembered and made available the next time you create a new label. In the current implementation of the plugin, the maximum number of labels is restricted to 255. If you need more, you will have to create a new segmentation session.
-\section org_mitk_views_multilabelsegmentationUserManualLayerCreation Creating a New Layer
-A layer is a set of labels that occupy a non-overlapping anatomical space. The best way to describe them is by a real use
-case. Imagine you are working on a radiotherpay planning application. In the first <b> layer </b> of your segmentation
-session you would like to trace the contours of the liver and neighboring organs. You can accomodate all these segmentations
-in separate labels because they all occupy different anamical regions and do not overlap. Now say you would like to segment
-the arteries and veins inside the liver. If you don´t trace them in a different layer, you will overwrite the previous ones.
-You may also need a third layer for segmenting the different irrigation territories in the liver and a fourth layer to contain
-the lession you would like to treat.
+\subsection org_mitk_views_multilabelsegmentationUserManualLabelSearch Searching a Label
-The next figure illustrates the <b> Layer Manager </b>. The buttons in it contained serve for adding a new layer, selecting the
-previous and the next one. The active layer is shown together with the buttons.
+It may happen that many labels (e.g. > 200) are present in a segmentation session and therefore manual searching can be time-consuming.
+The 'Label Search' edit box allows for quickly finding the label you want. Just start writing its name and you will get assistance for completing its name. If the label you were searching is found, press 'enter' and it will become the active one.
-\imageMacro{"org_mitk_views_multilabelsegmentationIMGlayerManager.png", "Correction Tool",12}
-\section org_mitk_views_multilabelsegmentationUserManualLabelSearch Searching a Label
+\subsection org_mitk_views_multilabelsegmentationUserManualLabelEditing Label Editing
-It may happen that many labels (e.g. > 200) are present in a segmentation session and therefore manual searching is time consuming.
-The <b> Label Search </b> edit box allows for quickly finding the label you want. Just start writing its name and and you will get
-assitance for completing its name. If the label you were searching is found, press enter and it will became the active one.
+Here the actual segmentation takes place. First of all, you have to select the active label by clicking on the corresponding row in the 'Label Table'. Note that only one label can be active at the time. Then you can select segmentation tool in the toolbox.
-\imageMacro{"org_mitk_views_multilabelsegmentationIMGsearchlabel.png", "Label search", 12}
+\imageMacro{"org_mitk_views_multilabelsegmentationIMGSegmentationToolbox.png", "Segmentation toolbox", 12}
-\section org_mitk_views_multilabelsegmentationUserManualLabelEditing Label Editing
-First of all, you have to select the active label by clicking on the corresponding row in the <b>Label Table</b>. Only one label
-can be active at the time. Then you can select an editing tool in the toolbox.
+\note Not all segmentation tools can be found here. This is because some of the semi-automatic tools can not be applied in case of multiple labels.
-\section org_mitk_views_multilabelsegmentationUserManualOperationsOnLabels Operations on Labels
+\subsection org_mitk_views_multilabelsegmentationUserManualOperationsOnLabels Operations on Labels
-Depending on your selection in the <b> Label Table </b>, several actions are offered:
+Depending on your selection in the 'Label Table', several actions are offered:
-\subsection org_mitk_views_multilabelsegmentationUserManualOperationsOnSingleSelection Single Label Selection
+\subsubsection org_mitk_views_multilabelsegmentationUserManualOperationsOnSingleSelection Single Label Selection
-If you right click on any label in the table, a menu will pop-up offering the following actions to be performed on the selected label:
+If you right click on any label in the table, a pop-up menu offers the following actions to be performed on the selected label:
<ul>
- <li><b>Rename...</b></li> : change the name and/or color of the selected label.
- <li><b>Remove label </b></li> : delete the selected label.
- <li><b>Erase label </b></li> : only clear the contents of the selected label.
- <li><b>Random color </b></li> : generate a surface mesh out of the selected label.
- <li><b>View only </b></li> : generate a mask out of the selected label. A mask is a binary image with "1" inside and "0" outside.
- <li><b>View/Hide all </b></li> : generate a mask out of the selected label. A mask is a binary image with "1" inside and "0" outside.
- <li><b>Lock/Unlock all </b></li> : generate a mask out of the selected label. A mask is a binary image with "1" inside and "0" outside.
- <li><b>Create surface </b></li> : generate a surface out of the selected label.
+<li><b>Rename...</b></li> : change the name and/or color of the selected label.
+<li><b>Remove...</b></li> : delete the selected label.
+<li><b>Erase...</b></li> : only clear the contents of the selected label.
+<li><b>Merge...</b></li> : merge two labels by selecting a second label.
+<li><b>Random color </b></li> : assign a random color to the label.
+<li><b>View only </b></li> : make all labels except the current selected label invisible.
+<li><b>View/Hide all </b></li> : make all labels visible / invisible
+<li><b>Lock/Unlock all </b></li> : lock or unlock all labels.
+<li><b>Create surface </b></li> : generate a surface out of the selected label.
<li><b>Create mask </b></li> : generate a mask out of the selected label. A mask is a binary image with "1" inside and "0" outside.
+ <li><b>Create cropped mask </b></li> : generate a binary mask out of the selected label. Crop changes the extent of the resulting image to the extent of the label.
</ul>
\imageMacro{"org_mitk_views_multilabelsegmentationIMGLabelTableSingleSelectionContextMenu.png", "Context menu for single label selection", 12}
-\subsection org_mitk_views_multilabelsegmentationUserManualOperationsOnMultipleSelection Multiple Label Selection
+\subsubsection org_mitk_views_multilabelsegmentationUserManualOperationsOnMultipleSelection Multiple Label Selection
-If more than one label is selected, a different menu will show up:
+You can select more than one label by shift-click on other labels. If more than one label is selected, different options will appear in the menu:
\imageMacro{"org_mitk_views_multilabelsegmentationIMGLabelTableMultipleSelectionContextMenu.png", "Context menu for multiple label selection", 12}
<ul>
- <li><b>Merge selection on current label</b></li> : transfer the contents of the selected labels in the <b>Label Table</b> into the current one.
+ <li><b>Merge selection on current label</b></li> : transfer the contents of the selected labels in the 'Label Table' into the current one.
<li><b>Remove selected labels</b></li> : delete the selected labels.
<li><b>Erase selected labels</b></li> : only clear the contents of the selected labels.
- <li><b>Create a surface for each selected label</b></li> : generate a surface mesh out of each selected label.
- <li><b>Combine and create a surface</b></li> : generate a surface out of the combination of the selected labels.
- <li><b>Create a mask for each selected label</b></li> : generate a mask out of each selected label. A mask is a binary image with "1" inside and "0" outside.
- <li><b>Combine and create a mask</b></li> : generate a mask out of the combination of the selected labels.
</ul>
*/
diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGLabelTableMultipleSelectionContextMenu.png b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGLabelTableMultipleSelectionContextMenu.png
index 536652b87b..465c1b8b2f 100644
Binary files a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGLabelTableMultipleSelectionContextMenu.png and b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGLabelTableMultipleSelectionContextMenu.png differ
diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGLabelTableSingleSelectionContextMenu.png b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGLabelTableSingleSelectionContextMenu.png
index 9af8f3d450..aa39547388 100644
Binary files a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGLabelTableSingleSelectionContextMenu.png and b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGLabelTableSingleSelectionContextMenu.png differ
diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGSegmentationToolbox.png b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGSegmentationToolbox.png
new file mode 100644
index 0000000000..eeb06e60d2
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGSegmentationToolbox.png differ
diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGlabeltable.png b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGlabeltable.png
index 95ce38ccda..a5987203f8 100644
Binary files a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGlabeltable.png and b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGlabeltable.png differ
diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGlayerManager.png b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGlayerManager.png
index fa7ef60d7b..5ad4c638a9 100644
Binary files a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGlayerManager.png and b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGlayerManager.png differ
diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGtoolbar.png b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGtoolbar.png
index 82b39fbbd7..a46e147708 100644
Binary files a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGtoolbar.png and b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_views_multilabelsegmentationIMGtoolbar.png differ
diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/Manual.dox
index 79c3c04ad5..7c16b548b7 100644
--- a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/Manual.dox
+++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/Manual.dox
@@ -1,16 +1,35 @@
/**
-\page org_mitk_gui_qt_pharmacokinetics_concentration_mri The Concentration Curve Converter View
+\page org_mitk_views_pharmacokinetics_concentration_mri The DCE Concentration Curve Converter View
-\imageMacro{pharmacokinetics_concentration_doc.svg,"Icon of the Concentration Curve Converter View",3.0}
+\imageMacro{pharmacokinetics_concentration_doc.svg,"Icon of the DCE Concentration Curve Converter View",3.0}
\tableofcontents
-\section org_mitk_gui_qt_pharmacokinetics_concentration_mri_overview Overview
-Stand-alone conversion of image signal intensities to contrast agent concentration units can be performed with a dedicated plugin. The plugin distinguishes between T1 weighted and T2 weighted sequences. T1 conversion can be performed in terms of absolute and relative signal enhancement as well as turbo flash sequences for both 3D images (baseline images S0 without contrast enhancement (pre-contrast) input required) and 4D sequences (baseline selected as first frame of time series).
+\section org_mitk_views_pharmacokinetics_concentration_mri_overview Overview
+This view offers a dedicated tool for the conversion of DCE MR image signal intensities to contrast agent (CA) concentration.
+It contains a subset of the conversion tools for T1-weighted signal intensities, which are a part of the DCE MR Perfusion Datafit View (see \ref FIT_DCE_Settings_concentration).
+Additionally, it allows for the conversion between T2-weighted MR signal intensities and contrast agent concentration.
-\section org_mitk_gui_qt_pharmacokinetics_concentration_mri_Contact Contact information
-This plug-in is being developed by Charlotte Debus and the SIDT group (Software development for Integrated Diagnostics
-and Therapy) at the German Cancer Research Center (DKFZ).
+\section org_mitk_views_pharmacokinetics_concentration_mri_Contact Contact information
If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org.
+\section org_mitk_views_pharmacokinetics_concentration_mri_T1_conversion Conversion of T1-weighted MRI data
+
+\imageMacro{concentration_curve_converter_T1_weighted4D.png,"Example screenshot of the conversion of T1-weighted MR images",3.0}
+The view offers the choice between a <i>3D Image</i> and a <i>4D image</i>. If a 4D image is selected, the <i>Selected Time Series</i> needs to be specified.
+In this case, the baseline image is automatically extracted as the first time point image of the time series.
+In case of a 3D image to be converted, additionally to the selected 3D image a <i>Baseline Image (without CA)</i> has to be specified.\n\n
+
+In the configuration section, the following types of conversion can be chosen:
+- <i>Absolute Signal Enhancement</i>: The contrast agent concentration <i>c</i> is calculated according to the formula: <i>c = k*(S(t)-S(0))</i>, where <i>S(t)</i> is the dynamic T1-weighted signal intensity, <i>S(0)</i> the baseline signal and <i>k</i> a user-defined conversion factor.
+- <i>Relative Signal Enhancement</i>: The contrast agent concentration <i>c</i> is calculated according to the formula: <i>c = k*(S(t)-S(0))/S(0)</i>, where <i>S(t)</i> is the dynamic T1-weighted signal intensity, <i>S(0)</i> the baseline signal and <i>k</i> a user-defined conversion factor.
+- <i>Turbo FLASH Sequence</i>: The conversion from signal <i>S(t)</i> to contrast agent concentration <i>c</i> is calculated according to the turboFLASH (ultrafast gradient echo) sequence specific formula.
+
+
+\section org_mitk_views_pharmacokinetics_concentration_mri_T2_conversion Conversion of T2-weighted MRI data
+\imageMacro{concentration_curve_converter_T2_weighted.png,"Example screenshot of the conversion of T2-weighted MR images",3.0}
+
+The contrast agent concentration <i>c</i> is calculated according to the formula: <i>c = -k/TE*ln(S(t)/S(0))</i>, where <i>S(t)</i> is the dynamic T2-weighted signal intensity, <i>S(0)</i> the baseline signal, <i>k</i> a user-defined conversion factor and <i>TE</i> the echo time of the employed sequence.
+In practice, the factor <i>k</i> is often set to unity.
+
*/
diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T1_weighted4D.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T1_weighted4D.png
new file mode 100644
index 0000000000..ef521cc592
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T1_weighted4D.png differ
diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T2_weighted.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T2_weighted.png
new file mode 100644
index 0000000000..cd4158f49d
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T2_weighted.png differ
diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/plugin.xml b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/plugin.xml
index ca8c8a0fe5..0e19a70b02 100644
--- a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/plugin.xml
+++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/plugin.xml
@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<plugin>
<extension point="org.blueberry.ui.views">
- <view id="org.mitk.gui.qt.pharmacokinetics.concentration.mri"
+ <view id="org.mitk.views.pharmacokinetics.concentration.mri"
name="Concentration Curve Converter View"
category="Perfusion"
class="ConcentrationCurveConverterView"
icon="resources/icon.svg" />
</extension>
</plugin>
diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/Manual.dox
index d5ece877b8..1814f00b35 100644
--- a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/Manual.dox
+++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/Manual.dox
@@ -1,26 +1,27 @@
/**
-\page org_mitk_gui_qt_pharmacokinetics_curvedescriptor The Perfusion Curve Description Parameters View
+\page org_mitk_views_pharmacokinetics_curvedescriptor The Perfusion Curve Description Parameters View
\imageMacro{pharmacokinetics_curve_desc_doc.svg,"Icon of the Perfusion Curve Description Parameters View",3.0}
\tableofcontents
-\section org_mitk_gui_qt_pharmacokinetics_curvedescriptor_overview Overview
-In cases where data quality is not sufficient for dedicated pharmacokinetic analysis, or if global scouting of the overall image should be performed to identify regions of interest, it is often advisable to use semi-quantitative measures that describe the general shape and type of the curve. The Perfusion Curve Description Parameters plugin can be used to voxelwise calculate these parameters.
-Currently the following parameters are offered by the tool:
-- area-under-the-curve (AUC)
-- area-under the first moment curve (AUMC),
-- mean-residence-time (MRT; AUMC/AUC)
-- time to peak and maximum signal
-
-These parameters are calculated directly from the sampled data.
-AUC and AUMC are calculated by step-wise integration with linear interpolation between sampling points. Maximum and time to peak are derived from the highest intensity value (overall maximum) of all data points.
-Note: If semi-quantitative parameters should be calculated from concentration time curves rather than raw data signal intensities, use the concentration n curve converter view (See 5)
-Parameters of interest can be selected from the list. Selecting a 4D image in the Data manager enables the Calculate Parameters button. Resulting parameter maps will afterwards be added to the data manager as subnodes to the analyzed 4D image.
-
-\section org_mitk_gui_qt_pharmacokinetics_curvedescriptor_Contact Contact information
-This plug-in is being developed by Charlotte Debus and the SIDT group (Software development for Integrated Diagnostics
-and Therapy) at the German Cancer Research Center (DKFZ).
-If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org.
+\section org_mitk_views_pharmacokinetics_curvedescriptor_overview Overview
+In cases where data quality is not sufficient for dedicated pharmacokinetic analysis, or if global scouting of the overall image is performed to identify regions of interest, it is often advisable to use semi-quantitative measures that describe the general shape and type of the curve.
+The Perfusion Curve Description Parameters View can be used to voxelwise calculate these parameters.
+
+Currently the following parameters are offered by the tool (visualized in figure 1):
+\imageMacro{pharmacokinetics_curve_desc_parameter_description.png,"Figure 1: Calculation of currently available descriptive parameters",3.0}
+
+- <i>area-under-the-curve (AUC)</i>: The area under the signal time curve is calculated by step-wise integration with linear interpolation between sampling points.
+- <i>area-under the first moment curve (AUMC)</i>: The area under the first moment signal time curve is calculated by step-wise integration with linear interpolation between sampling points.
+- <i>mean-residence-time (MRT)</i>: The mean residence time is calculated as MRT = AUMC/AUC.
+- <i>time-to-peak</i>: The duration between the onset time and the time of the maximum signal of the curve.
+- <i>maximum signal</i>: The overall maximum of all data points of the curve.
+
+These parameters are usually calculated directly from the raw data signal intensities of the acquired MR image.
+Alternatively, if semi-quantitative parameters should be calculated from concentration time curves, use the \ref org_mitk_views_pharmacokinetics_concentration_mri prior to the parameter calculation.
+Parameters of interest can be selected from the list. Selecting a 4D image enables the <i>Calculate Parameters</i> button.
+Resulting parameter maps will afterwards be added to the data manager as subnodes to the analyzed 4D image.
+
*/
diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/pharmacokinetics_curve_desc_parameter_description.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/pharmacokinetics_curve_desc_parameter_description.png
new file mode 100644
index 0000000000..61f2919454
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/pharmacokinetics_curve_desc_parameter_description.png differ
diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/plugin.xml b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/plugin.xml
index 3239639a5f..6a25813a56 100644
--- a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/plugin.xml
+++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/plugin.xml
@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<plugin>
<extension point="org.blueberry.ui.views">
- <view id="org.mitk.gui.qt.pharmacokinetics.curvedescriptor"
+ <view id="org.mitk.views.pharmacokinetics.curvedescriptor"
name="Perfusion Curve Description Parameters View"
category="Perfusion"
class="PerfusionCurveDescriptionParameterView"
icon="resources/icon.svg" />
</extension>
</plugin>
diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionView.cpp b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionView.cpp
index b225533dc8..9ee2b5e3f5 100644
--- a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionView.cpp
+++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionView.cpp
@@ -1,1487 +1,1485 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "MRPerfusionView.h"
#include "boost/tokenizer.hpp"
#include "boost/math/constants/constants.hpp"
#include <iostream>
#include "mitkWorkbenchUtil.h"
#include "mitkAterialInputFunctionGenerator.h"
#include "mitkConcentrationCurveGenerator.h"
#include <mitkDescriptivePharmacokineticBrixModelFactory.h>
#include <mitkDescriptivePharmacokineticBrixModelParameterizer.h>
#include <mitkDescriptivePharmacokineticBrixModelValueBasedParameterizer.h>
#include "mitkThreeStepLinearModelFactory.h"
#include "mitkThreeStepLinearModelParameterizer.h"
#include "mitkTwoStepLinearModelFactory.h"
#include "mitkTwoStepLinearModelParameterizer.h"
#include <mitkExtendedToftsModelFactory.h>
#include <mitkExtendedToftsModelParameterizer.h>
#include <mitkStandardToftsModelFactory.h>
#include <mitkStandardToftsModelParameterizer.h>
#include "mitkTwoCompartmentExchangeModelFactory.h"
#include "mitkTwoCompartmentExchangeModelParameterizer.h"
#include "mitkNumericTwoCompartmentExchangeModelFactory.h"
#include "mitkNumericTwoCompartmentExchangeModelParameterizer.h"
#include <mitkInitialParameterizationDelegateBase.h>
#include <mitkNodePredicateAnd.h>
#include <mitkNodePredicateOr.h>
#include <mitkNodePredicateNot.h>
#include <mitkNodePredicateProperty.h>
#include <mitkNodePredicateDataType.h>
#include <mitkNodePredicateDimension.h>
#include "mitkNodePredicateFunction.h"
#include <mitkPixelBasedParameterFitImageGenerator.h>
#include <mitkROIBasedParameterFitImageGenerator.h>
#include <mitkLevenbergMarquardtModelFitFunctor.h>
#include <mitkSumOfSquaredDifferencesFitCostFunction.h>
#include <mitkNormalizedSumOfSquaredDifferencesFitCostFunction.h>
#include <mitkSimpleBarrierConstraintChecker.h>
#include <mitkModelFitResultHelper.h>
#include <mitkImageTimeSelector.h>
#include <mitkMaskedDynamicImageStatisticsGenerator.h>
#include <mitkExtractTimeGrid.h>
+#include <mitkModelFitResultRelationRule.h>
#include <QMessageBox>
#include <QThreadPool>
#include <QFileDialog>
// Includes for image casting between ITK and MITK
#include <mitkImage.h>
#include "mitkImageCast.h"
#include "mitkITKImageImport.h"
#include <itkImage.h>
#include <itkImageRegionIterator.h>
const std::string MRPerfusionView::VIEW_ID = "org.mitk.gui.qt.pharmacokinetics.mri";
inline double convertToDouble(const std::string& data)
{
std::istringstream stepStream(data);
stepStream.imbue(std::locale("C"));
double value = 0.0;
if (!(stepStream >> value) || !(stepStream.eof()))
{
mitkThrow() << "Cannot convert string to double. String: " << data;
}
return value;
}
void MRPerfusionView::SetFocus()
{
m_Controls.btnModelling->setFocus();
}
void MRPerfusionView::CreateQtPartControl(QWidget* parent)
{
m_Controls.setupUi(parent);
m_Controls.btnModelling->setEnabled(false);
this->InitModelComboBox();
m_Controls.timeSeriesNodeSelector->SetNodePredicate(this->m_isValidTimeSeriesImagePredicate);
m_Controls.timeSeriesNodeSelector->SetDataStorage(this->GetDataStorage());
m_Controls.timeSeriesNodeSelector->SetSelectionIsOptional(false);
m_Controls.timeSeriesNodeSelector->SetInvalidInfo("Please select time series.");
m_Controls.timeSeriesNodeSelector->SetAutoSelectNewNodes(true);
m_Controls.maskNodeSelector->SetNodePredicate(this->m_IsMaskPredicate);
m_Controls.maskNodeSelector->SetDataStorage(this->GetDataStorage());
m_Controls.maskNodeSelector->SetSelectionIsOptional(true);
m_Controls.maskNodeSelector->SetEmptyInfo("Please select (optional) mask.");
connect(m_Controls.btnModelling, SIGNAL(clicked()), this, SLOT(OnModellingButtonClicked()));
connect(m_Controls.comboModel, SIGNAL(currentIndexChanged(int)), this, SLOT(OnModellSet(int)));
connect(m_Controls.radioPixelBased, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.timeSeriesNodeSelector,
&QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged,
this,
&MRPerfusionView::OnNodeSelectionChanged);
connect(m_Controls.maskNodeSelector,
&QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged,
this,
&MRPerfusionView::OnNodeSelectionChanged);
connect(m_Controls.AIFMaskNodeSelector,
&QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged,
this,
&MRPerfusionView::UpdateGUIControls);
connect(m_Controls.AIFImageNodeSelector,
&QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged,
this,
&MRPerfusionView::UpdateGUIControls);
//AIF setting
m_Controls.groupAIF->hide();
m_Controls.btnAIFFile->setEnabled(false);
m_Controls.btnAIFFile->setEnabled(false);
m_Controls.radioAIFImage->setChecked(true);
m_Controls.AIFMaskNodeSelector->SetDataStorage(this->GetDataStorage());
m_Controls.AIFMaskNodeSelector->SetNodePredicate(m_IsMaskPredicate);
m_Controls.AIFMaskNodeSelector->setVisible(true);
m_Controls.AIFMaskNodeSelector->setEnabled(true);
m_Controls.AIFMaskNodeSelector->SetAutoSelectNewNodes(true);
m_Controls.AIFImageNodeSelector->SetDataStorage(this->GetDataStorage());
m_Controls.AIFImageNodeSelector->SetNodePredicate(this->m_isValidTimeSeriesImagePredicate);
m_Controls.AIFImageNodeSelector->setEnabled(false);
m_Controls.checkDedicatedAIFImage->setEnabled(true);
m_Controls.HCLSpinBox->setValue(mitk::AterialInputFunctionGenerator::DEFAULT_HEMATOCRIT_LEVEL);
m_Controls.spinBox_baselineEndTimeStep->setMinimum(0);
m_Controls.spinBox_baselineStartTimeStep->setMinimum(0);
connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.AIFMaskNodeSelector, SLOT(setVisible(bool)));
connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.labelAIFMask, SLOT(setVisible(bool)));
connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.checkDedicatedAIFImage, SLOT(setVisible(bool)));
connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.AIFMaskNodeSelector, SLOT(setEnabled(bool)));
connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.checkDedicatedAIFImage, SLOT(setEnabled(bool)));
connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.checkDedicatedAIFImage, SLOT(setVisible(bool)));
connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.AIFImageNodeSelector, SLOT(setVisible(bool)));
connect(m_Controls.checkDedicatedAIFImage, SIGNAL(toggled(bool)), m_Controls.AIFImageNodeSelector, SLOT(setEnabled(bool)));
connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.radioAIFFile, SIGNAL(toggled(bool)), m_Controls.btnAIFFile, SLOT(setEnabled(bool)));
connect(m_Controls.radioAIFFile, SIGNAL(toggled(bool)), m_Controls.aifFilePath, SLOT(setEnabled(bool)));
connect(m_Controls.radioAIFFile, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.btnAIFFile, SIGNAL(clicked()), this, SLOT(LoadAIFfromFile()));
//Brix setting
m_Controls.groupDescBrix->hide();
connect(m_Controls.injectiontime, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls()));
//Num2CX setting
m_Controls.groupNum2CXM->hide();
connect(m_Controls.odeStepSize, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls()));
//Model fit configuration
m_Controls.groupBox_FitConfiguration->hide();
m_Controls.checkBox_Constraints->setEnabled(false);
m_Controls.constraintManager->setEnabled(false);
m_Controls.initialValuesManager->setEnabled(false);
m_Controls.initialValuesManager->setDataStorage(this->GetDataStorage());
connect(m_Controls.radioButton_StartParameters, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.checkBox_Constraints, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.initialValuesManager, SIGNAL(initialValuesChanged(void)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.radioButton_StartParameters, SIGNAL(toggled(bool)), m_Controls.initialValuesManager, SLOT(setEnabled(bool)));
connect(m_Controls.checkBox_Constraints, SIGNAL(toggled(bool)), m_Controls.constraintManager, SLOT(setEnabled(bool)));
connect(m_Controls.checkBox_Constraints, SIGNAL(toggled(bool)), m_Controls.constraintManager, SLOT(setVisible(bool)));
//Concentration
m_Controls.groupConcentration->hide();
m_Controls.groupBoxEnhancement->hide();
m_Controls.groupBoxTurboFlash->hide();
m_Controls.radioButtonNoConversion->setChecked(true);
m_Controls.groupBox_T1MapviaVFA->hide();
m_Controls.spinBox_baselineStartTimeStep->setValue(0);
m_Controls.spinBox_baselineEndTimeStep->setValue(0);
connect(m_Controls.radioButtonTurboFlash, SIGNAL(toggled(bool)), m_Controls.groupBoxTurboFlash, SLOT(setVisible(bool)));
connect(m_Controls.radioButtonTurboFlash, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.relaxationtime, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.recoverytime, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.relaxivity, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.radioButton_absoluteEnhancement, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.radioButton_relativeEnchancement, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.radioButton_absoluteEnhancement, SIGNAL(toggled(bool)), m_Controls.groupBoxEnhancement, SLOT(setVisible(bool)));
connect(m_Controls.radioButton_relativeEnchancement, SIGNAL(toggled(bool)), m_Controls.groupBoxEnhancement, SLOT(setVisible(bool)));
connect(m_Controls.factorSpinBox, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.spinBox_baselineStartTimeStep, SIGNAL(valueChanged(int)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.spinBox_baselineEndTimeStep, SIGNAL(valueChanged(int)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.radioButtonUsingT1viaVFA, SIGNAL(toggled(bool)), m_Controls.groupBox_T1MapviaVFA, SLOT(setVisible(bool)));
connect(m_Controls.radioButtonUsingT1viaVFA, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.FlipangleSpinBox, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.RelaxivitySpinBox, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls()));
connect(m_Controls.TRSpinBox, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls()));
m_Controls.PDWImageNodeSelector->SetNodePredicate(m_isValidPDWImagePredicate);
m_Controls.PDWImageNodeSelector->SetDataStorage(this->GetDataStorage());
m_Controls.PDWImageNodeSelector->SetInvalidInfo("Please select PDW Image.");
m_Controls.PDWImageNodeSelector->setEnabled(false);
connect(m_Controls.radioButtonUsingT1viaVFA, SIGNAL(toggled(bool)), m_Controls.PDWImageNodeSelector, SLOT(setEnabled(bool)));
UpdateGUIControls();
}
bool MRPerfusionView::IsTurboFlashSequenceFlag() const
{
return this->m_Controls.radioButtonTurboFlash->isChecked();
};
void MRPerfusionView::UpdateGUIControls()
{
m_Controls.lineFitName->setPlaceholderText(QString::fromStdString(this->GetDefaultFitName()));
m_Controls.lineFitName->setEnabled(!m_FittingInProgress);
m_Controls.checkBox_Constraints->setEnabled(m_modelConstraints.IsNotNull());
bool isDescBrixFactory = dynamic_cast<mitk::DescriptivePharmacokineticBrixModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
bool isToftsFactory = dynamic_cast<mitk::StandardToftsModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr ||
dynamic_cast<mitk::ExtendedToftsModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
bool is2CXMFactory = dynamic_cast<mitk::TwoCompartmentExchangeModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr ||
dynamic_cast<mitk::NumericTwoCompartmentExchangeModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
bool isNum2CXMFactory = dynamic_cast<mitk::NumericTwoCompartmentExchangeModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
bool isSLFactory = dynamic_cast<mitk::ThreeStepLinearModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr ||
dynamic_cast<mitk::TwoStepLinearModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
m_Controls.groupAIF->setVisible(isToftsFactory || is2CXMFactory);
m_Controls.groupDescBrix->setVisible(isDescBrixFactory);
m_Controls.groupNum2CXM->setVisible(isNum2CXMFactory);
m_Controls.groupConcentration->setVisible(isToftsFactory || is2CXMFactory || isSLFactory);
m_Controls.groupBox_FitConfiguration->setVisible(m_selectedModelFactory);
m_Controls.groupBox->setEnabled(!m_FittingInProgress);
m_Controls.comboModel->setEnabled(!m_FittingInProgress);
m_Controls.groupAIF->setEnabled(!m_FittingInProgress);
m_Controls.groupDescBrix->setEnabled(!m_FittingInProgress);
m_Controls.groupNum2CXM->setEnabled(!m_FittingInProgress);
m_Controls.groupConcentration->setEnabled(!m_FittingInProgress);
m_Controls.groupBox_FitConfiguration->setEnabled(!m_FittingInProgress);
m_Controls.radioROIbased->setEnabled(m_selectedMask.IsNotNull());
m_Controls.btnModelling->setEnabled(m_selectedImage.IsNotNull()
&& m_selectedModelFactory.IsNotNull() && !m_FittingInProgress && CheckModelSettings());
m_Controls.spinBox_baselineStartTimeStep->setEnabled(m_Controls.radioButtonTurboFlash->isChecked() || m_Controls.radioButton_absoluteEnhancement->isChecked() || m_Controls.radioButton_relativeEnchancement->isChecked() || m_Controls.radioButtonUsingT1viaVFA->isChecked());
m_Controls.spinBox_baselineEndTimeStep->setEnabled(m_Controls.radioButton_absoluteEnhancement->isChecked() || m_Controls.radioButton_relativeEnchancement->isChecked() || m_Controls.radioButtonUsingT1viaVFA->isChecked() || m_Controls.radioButtonTurboFlash->isChecked());
}
void MRPerfusionView::OnModellSet(int index)
{
m_selectedModelFactory = nullptr;
if (index > 0)
{
if (static_cast<ModelFactoryStackType::size_type>(index) <= m_FactoryStack.size() )
{
m_selectedModelFactory = m_FactoryStack[index - 1];
}
else
{
MITK_WARN << "Invalid model index. Index outside of the factory stack. Factory stack size: "<< m_FactoryStack.size() << "; invalid index: "<< index;
}
}
if (m_selectedModelFactory)
{
this->m_modelConstraints = dynamic_cast<mitk::SimpleBarrierConstraintChecker*>
(m_selectedModelFactory->CreateDefaultConstraints().GetPointer());
m_Controls.initialValuesManager->setInitialValues(m_selectedModelFactory->GetParameterNames(),
m_selectedModelFactory->GetDefaultInitialParameterization());
if (this->m_modelConstraints.IsNull())
{
this->m_modelConstraints = mitk::SimpleBarrierConstraintChecker::New();
}
m_Controls.constraintManager->setChecker(this->m_modelConstraints,
this->m_selectedModelFactory->GetParameterNames());
}
UpdateGUIControls();
}
std::string MRPerfusionView::GetFitName() const
{
std::string fitName = m_Controls.lineFitName->text().toStdString();
if (fitName.empty())
{
fitName = m_Controls.lineFitName->placeholderText().toStdString();
}
return fitName;
}
std::string MRPerfusionView::GetDefaultFitName() const
{
std::string defaultName = "undefined model";
if (this->m_selectedModelFactory.IsNotNull())
{
defaultName = this->m_selectedModelFactory->GetClassID();
}
if (this->m_Controls.radioPixelBased->isChecked())
{
defaultName += "_pixel";
}
else
{
defaultName += "_roi";
}
return defaultName;
}
void MRPerfusionView::OnModellingButtonClicked()
{
//check if all static parameters set
if (m_selectedModelFactory.IsNotNull() && CheckModelSettings())
{
m_HasGeneratedNewInput = false;
m_HasGeneratedNewInputAIF = false;
mitk::ParameterFitImageGeneratorBase::Pointer generator = nullptr;
mitk::modelFit::ModelFitInfo::Pointer fitSession = nullptr;
bool isDescBrixFactory = dynamic_cast<mitk::DescriptivePharmacokineticBrixModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
bool is3LinearFactory = dynamic_cast<mitk::ThreeStepLinearModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
bool is2LinearFactory = dynamic_cast<mitk::TwoStepLinearModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
bool isExtToftsFactory = dynamic_cast<mitk::ExtendedToftsModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
bool isStanToftsFactory = dynamic_cast<mitk::StandardToftsModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
bool is2CXMFactory = dynamic_cast<mitk::TwoCompartmentExchangeModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
bool isNum2CXMFactory = dynamic_cast<mitk::NumericTwoCompartmentExchangeModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
if (isDescBrixFactory)
{
if (this->m_Controls.radioPixelBased->isChecked())
{
GenerateDescriptiveBrixModel_PixelBased(fitSession, generator);
}
else
{
GenerateDescriptiveBrixModel_ROIBased(fitSession, generator);
}
}
else if (is2LinearFactory)
{
if (this->m_Controls.radioPixelBased->isChecked())
{
GenerateLinearModelFit_PixelBased<mitk::TwoStepLinearModelParameterizer>(fitSession, generator);
}
else
{
GenerateLinearModelFit_ROIBased<mitk::TwoStepLinearModelParameterizer>(fitSession, generator);
}
}
else if (is3LinearFactory)
{
if (this->m_Controls.radioPixelBased->isChecked())
{
GenerateLinearModelFit_PixelBased<mitk::ThreeStepLinearModelParameterizer>(fitSession, generator);
}
else
{
GenerateLinearModelFit_ROIBased<mitk::ThreeStepLinearModelParameterizer>(fitSession, generator);
}
}
else if (isStanToftsFactory)
{
if (this->m_Controls.radioPixelBased->isChecked())
{
GenerateAIFbasedModelFit_PixelBased<mitk::StandardToftsModelParameterizer>(fitSession, generator);
}
else
{
GenerateAIFbasedModelFit_ROIBased<mitk::StandardToftsModelParameterizer>(fitSession, generator);
}
}
else if (isExtToftsFactory)
{
if (this->m_Controls.radioPixelBased->isChecked())
{
GenerateAIFbasedModelFit_PixelBased<mitk::ExtendedToftsModelParameterizer>(fitSession, generator);
}
else
{
GenerateAIFbasedModelFit_ROIBased<mitk::ExtendedToftsModelParameterizer>(fitSession, generator);
}
}
else if (is2CXMFactory)
{
if (this->m_Controls.radioPixelBased->isChecked())
{
GenerateAIFbasedModelFit_PixelBased<mitk::TwoCompartmentExchangeModelParameterizer>(fitSession, generator);
}
else
{
GenerateAIFbasedModelFit_ROIBased<mitk::TwoCompartmentExchangeModelParameterizer>(fitSession, generator);
}
}
else if (isNum2CXMFactory)
{
if (this->m_Controls.radioPixelBased->isChecked())
{
GenerateAIFbasedModelFit_PixelBased<mitk::NumericTwoCompartmentExchangeModelParameterizer>(fitSession,
generator);
}
else
{
GenerateAIFbasedModelFit_ROIBased<mitk::NumericTwoCompartmentExchangeModelParameterizer>(fitSession,
generator);
}
}
//add other models with else if
if (generator.IsNotNull() && fitSession.IsNotNull())
{
m_FittingInProgress = true;
UpdateGUIControls();
DoFit(fitSession, generator);
}
else
{
QMessageBox box;
box.setText("Fitting error!");
box.setInformativeText("Could not establish fitting job. Error when setting ab generator, model parameterizer or session info.");
box.setStandardButtons(QMessageBox::Ok);
box.setDefaultButton(QMessageBox::Ok);
box.setIcon(QMessageBox::Warning);
box.exec();
}
}
else
{
QMessageBox box;
box.setText("Static parameters for model are not set!");
box.setInformativeText("Some static parameters, that are needed for calculation are not set and equal to zero. Modeling not possible");
box.setStandardButtons(QMessageBox::Ok);
box.setDefaultButton(QMessageBox::Ok);
box.setIcon(QMessageBox::Warning);
box.exec();
}
}
void MRPerfusionView::OnNodeSelectionChanged(QList<mitk::DataNode::Pointer>/*nodes*/)
{
m_selectedMaskNode = nullptr;
m_selectedMask = nullptr;
if (m_Controls.timeSeriesNodeSelector->GetSelectedNode().IsNotNull())
{
this->m_selectedNode = m_Controls.timeSeriesNodeSelector->GetSelectedNode();
m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData());
if (m_selectedImage)
{
this->m_Controls.initialValuesManager->setReferenceImageGeometry(m_selectedImage->GetGeometry());
}
else
{
this->m_Controls.initialValuesManager->setReferenceImageGeometry(nullptr);
}
}
else
{
this->m_selectedNode = nullptr;
this->m_selectedImage = nullptr;
this->m_Controls.initialValuesManager->setReferenceImageGeometry(nullptr);
}
if (m_Controls.maskNodeSelector->GetSelectedNode().IsNotNull())
{
this->m_selectedMaskNode = m_Controls.maskNodeSelector->GetSelectedNode();
this->m_selectedMask = dynamic_cast<mitk::Image*>(m_selectedMaskNode->GetData());
if (this->m_selectedMask.IsNotNull() && this->m_selectedMask->GetTimeSteps() > 1)
{
MITK_INFO <<
"Selected mask has multiple timesteps. Only use first timestep to mask model fit. Mask name: " <<
m_Controls.maskNodeSelector->GetSelectedNode()->GetName();
mitk::ImageTimeSelector::Pointer maskedImageTimeSelector = mitk::ImageTimeSelector::New();
maskedImageTimeSelector->SetInput(this->m_selectedMask);
maskedImageTimeSelector->SetTimeNr(0);
maskedImageTimeSelector->UpdateLargestPossibleRegion();
this->m_selectedMask = maskedImageTimeSelector->GetOutput();
}
}
if (m_selectedMask.IsNull())
{
this->m_Controls.radioPixelBased->setChecked(true);
}
if (this->m_selectedImage.IsNotNull())
{
m_Controls.spinBox_baselineStartTimeStep->setMaximum((this->m_selectedImage->GetDimension(3))-1);
m_Controls.spinBox_baselineEndTimeStep->setMaximum((this->m_selectedImage->GetDimension(3)) - 1);
}
UpdateGUIControls();
}
bool MRPerfusionView::CheckModelSettings() const
{
bool ok = true;
//check wether any model is set at all. Otherwise exit with false
if (m_selectedModelFactory.IsNotNull())
{
bool isDescBrixFactory = dynamic_cast<mitk::DescriptivePharmacokineticBrixModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
bool is3LinearFactory = dynamic_cast<mitk::ThreeStepLinearModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
bool is2LinearFactory = dynamic_cast<mitk::TwoStepLinearModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
bool isToftsFactory = dynamic_cast<mitk::StandardToftsModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr||
dynamic_cast<mitk::ExtendedToftsModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
bool is2CXMFactory = dynamic_cast<mitk::TwoCompartmentExchangeModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
bool isNum2CXMFactory = dynamic_cast<mitk::NumericTwoCompartmentExchangeModelFactory*>
(m_selectedModelFactory.GetPointer()) != nullptr;
if (isDescBrixFactory)
{
//if all static parameters for this model are set, exit with true, Otherwise exit with false
ok = m_Controls.injectiontime->value() > 0;
}
else if (is3LinearFactory || is2LinearFactory)
{
if (this->m_Controls.radioButtonTurboFlash->isChecked() )
{
ok = ok && (m_Controls.recoverytime->value() > 0);
ok = ok && (m_Controls.relaxationtime->value() > 0);
ok = ok && (m_Controls.relaxivity->value() > 0);
ok = ok && (m_Controls.AifRecoverytime->value() > 0);
ok = ok && CheckBaselineSelectionSettings();
}
else if (this->m_Controls.radioButton_absoluteEnhancement->isChecked()
|| this->m_Controls.radioButton_relativeEnchancement->isChecked() )
{
ok = ok && (m_Controls.factorSpinBox->value() > 0);
ok = ok && CheckBaselineSelectionSettings();
}
else if (this->m_Controls.radioButtonUsingT1viaVFA->isChecked() )
{
ok = ok && (m_Controls.FlipangleSpinBox->value() > 0);
ok = ok && (m_Controls.TRSpinBox->value() > 0);
ok = ok && (m_Controls.RelaxivitySpinBox->value() > 0);
ok = ok && (m_Controls.PDWImageNodeSelector->GetSelectedNode().IsNotNull());
ok = ok && CheckBaselineSelectionSettings();
}
else if (this->m_Controls.radioButtonNoConversion->isChecked())
{
ok = true;
}
else
{
ok = false;
}
}
else if (isToftsFactory || is2CXMFactory || isNum2CXMFactory)
{
if (this->m_Controls.radioAIFImage->isChecked())
{
ok = ok && m_Controls.AIFMaskNodeSelector->GetSelectedNode().IsNotNull();
if (this->m_Controls.checkDedicatedAIFImage->isChecked())
{
ok = ok && m_Controls.AIFImageNodeSelector->GetSelectedNode().IsNotNull();
}
}
else if (this->m_Controls.radioAIFFile->isChecked())
{
ok = ok && (this->AIFinputGrid.size() != 0) && (this->AIFinputFunction.size() != 0);
}
else
{
ok = false;
}
if (this->m_Controls.radioButtonTurboFlash->isChecked() )
{
ok = ok && (m_Controls.recoverytime->value() > 0);
ok = ok && (m_Controls.relaxationtime->value() > 0);
ok = ok && (m_Controls.relaxivity->value() > 0);
ok = ok && (m_Controls.AifRecoverytime->value() > 0);
ok = ok && CheckBaselineSelectionSettings();
}
else if (this->m_Controls.radioButton_absoluteEnhancement->isChecked()
|| this->m_Controls.radioButton_relativeEnchancement->isChecked() )
{
ok = ok && (m_Controls.factorSpinBox->value() > 0);
ok = ok && CheckBaselineSelectionSettings();
}
else if (this->m_Controls.radioButtonUsingT1viaVFA->isChecked() )
{
ok = ok && (m_Controls.FlipangleSpinBox->value() > 0);
ok = ok && (m_Controls.TRSpinBox->value() > 0);
ok = ok && (m_Controls.RelaxivitySpinBox->value() > 0);
ok = ok && (m_Controls.PDWImageNodeSelector->GetSelectedNode().IsNotNull());
ok = ok && CheckBaselineSelectionSettings();
}
else if (this->m_Controls.radioButtonNoConversion->isChecked())
{
ok = ok && true;
}
else
{
ok = false;
}
if (isNum2CXMFactory)
{
ok = ok && (this->m_Controls.odeStepSize->value() > 0);
}
}
//add other models as else if and check wether all needed static parameters are set
else
{
ok = false;
}
if (this->m_Controls.radioButton_StartParameters->isChecked() && !this->m_Controls.initialValuesManager->hasValidInitialValues())
{
std::string warning = "Warning. Invalid start parameters. At least one parameter as an invalid image setting as source.";
MITK_ERROR << warning;
m_Controls.infoBox->append(QString("<font color='red'><b>") + QString::fromStdString(warning) + QString("</b></font>"));
ok = false;
};
}
else
{
ok = false;
}
return ok;
}
bool MRPerfusionView::CheckBaselineSelectionSettings() const
{
return m_Controls.spinBox_baselineStartTimeStep->value() <= m_Controls.spinBox_baselineEndTimeStep->value();
}
void MRPerfusionView::ConfigureInitialParametersOfParameterizer(mitk::ModelParameterizerBase*
parameterizer) const
{
if (m_Controls.radioButton_StartParameters->isChecked())
{
//use user defined initial parameters
mitk::InitialParameterizationDelegateBase::Pointer paramDelegate = m_Controls.initialValuesManager->getInitialParametrizationDelegate();
parameterizer->SetInitialParameterizationDelegate(paramDelegate);
}
}
void MRPerfusionView::GenerateDescriptiveBrixModel_PixelBased(mitk::modelFit::ModelFitInfo::Pointer&
modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator)
{
mitk::PixelBasedParameterFitImageGenerator::Pointer fitGenerator =
mitk::PixelBasedParameterFitImageGenerator::New();
mitk::DescriptivePharmacokineticBrixModelParameterizer::Pointer modelParameterizer =
mitk::DescriptivePharmacokineticBrixModelParameterizer::New();
//Model configuration (static parameters) can be done now
modelParameterizer->SetTau(m_Controls.injectiontime->value());
mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New();
imageTimeSelector->SetInput(this->m_selectedImage);
imageTimeSelector->SetTimeNr(0);
imageTimeSelector->UpdateLargestPossibleRegion();
mitk::DescriptivePharmacokineticBrixModelParameterizer::BaseImageType::Pointer baseImage;
mitk::CastToItkImage(imageTimeSelector->GetOutput(), baseImage);
modelParameterizer->SetBaseImage(baseImage);
this->ConfigureInitialParametersOfParameterizer(modelParameterizer);
//Specify fitting strategy and criterion parameters
mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer);
//Parametrize fit generator
fitGenerator->SetModelParameterizer(modelParameterizer);
std::string roiUID = "";
if (m_selectedMask.IsNotNull())
{
fitGenerator->SetMask(m_selectedMask);
roiUID = m_selectedMask->GetUID();
}
fitGenerator->SetDynamicImage(m_selectedImage);
fitGenerator->SetFitFunctor(fitFunctor);
generator = fitGenerator.GetPointer();
//Create model info
modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer,
m_selectedNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), this->GetFitName(), roiUID);
}
void MRPerfusionView::GenerateDescriptiveBrixModel_ROIBased(mitk::modelFit::ModelFitInfo::Pointer&
modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator)
{
if (m_selectedMask.IsNull())
{
return;
}
mitk::ROIBasedParameterFitImageGenerator::Pointer fitGenerator =
mitk::ROIBasedParameterFitImageGenerator::New();
mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::Pointer modelParameterizer =
mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::New();
//Compute ROI signal
mitk::MaskedDynamicImageStatisticsGenerator::Pointer signalGenerator =
mitk::MaskedDynamicImageStatisticsGenerator::New();
signalGenerator->SetMask(m_selectedMask);
signalGenerator->SetDynamicImage(m_selectedImage);
signalGenerator->Generate();
mitk::MaskedDynamicImageStatisticsGenerator::ResultType roiSignal = signalGenerator->GetMean();
//Model configuration (static parameters) can be done now
modelParameterizer->SetTau(m_Controls.injectiontime->value());
modelParameterizer->SetBaseValue(roiSignal[0]);
this->ConfigureInitialParametersOfParameterizer(modelParameterizer);
//Specify fitting strategy and criterion parameters
mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer);
//Parametrize fit generator
fitGenerator->SetModelParameterizer(modelParameterizer);
fitGenerator->SetMask(m_selectedMask);
fitGenerator->SetFitFunctor(fitFunctor);
fitGenerator->SetSignal(roiSignal);
fitGenerator->SetTimeGrid(mitk::ExtractTimeGrid(m_selectedImage));
generator = fitGenerator.GetPointer();
std::string roiUID = this->m_selectedMask->GetUID();
//Create model info
modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer,
m_selectedNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), this->GetFitName(), roiUID);
mitk::ScalarListLookupTable::ValueType infoSignal;
for (mitk::MaskedDynamicImageStatisticsGenerator::ResultType::const_iterator pos =
roiSignal.begin(); pos != roiSignal.end(); ++pos)
{
infoSignal.push_back(*pos);
}
modelFitInfo->inputData.SetTableValue("ROI", infoSignal);
}
template <typename TParameterizer>
void MRPerfusionView::GenerateLinearModelFit_PixelBased(mitk::modelFit::ModelFitInfo::Pointer&
modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator)
{
mitk::PixelBasedParameterFitImageGenerator::Pointer fitGenerator =
mitk::PixelBasedParameterFitImageGenerator::New();
typename TParameterizer::Pointer modelParameterizer = TParameterizer::New();
this->ConfigureInitialParametersOfParameterizer(modelParameterizer);
//Specify fitting strategy and criterion parameters
mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer);
//Parametrize fit generator
fitGenerator->SetModelParameterizer(modelParameterizer);
std::string roiUID = "";
if (m_selectedMask.IsNotNull())
{
fitGenerator->SetMask(m_selectedMask);
roiUID = this->m_selectedMask->GetUID();
}
fitGenerator->SetDynamicImage(m_selectedImage);
fitGenerator->SetFitFunctor(fitFunctor);
generator = fitGenerator.GetPointer();
//Create model info
modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer,
m_selectedNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), this->GetFitName(), roiUID);
}
template <typename TParameterizer>
void MRPerfusionView::GenerateLinearModelFit_ROIBased(mitk::modelFit::ModelFitInfo::Pointer&
modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator)
{
if (m_selectedMask.IsNull())
{
return;
}
mitk::ROIBasedParameterFitImageGenerator::Pointer fitGenerator =
mitk::ROIBasedParameterFitImageGenerator::New();
typename TParameterizer::Pointer modelParameterizer = TParameterizer::New();
//Compute ROI signal
mitk::MaskedDynamicImageStatisticsGenerator::Pointer signalGenerator =
mitk::MaskedDynamicImageStatisticsGenerator::New();
signalGenerator->SetMask(m_selectedMask);
signalGenerator->SetDynamicImage(m_selectedImage);
signalGenerator->Generate();
mitk::MaskedDynamicImageStatisticsGenerator::ResultType roiSignal = signalGenerator->GetMean();
//Model configuration (static parameters) can be done now
this->ConfigureInitialParametersOfParameterizer(modelParameterizer);
//Specify fitting strategy and criterion parameters
mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer);
//Parametrize fit generator
fitGenerator->SetModelParameterizer(modelParameterizer);
fitGenerator->SetMask(m_selectedMask);
fitGenerator->SetFitFunctor(fitFunctor);
fitGenerator->SetSignal(roiSignal);
fitGenerator->SetTimeGrid(mitk::ExtractTimeGrid(m_selectedImage));
generator = fitGenerator.GetPointer();
std::string roiUID = this->m_selectedMask->GetUID();
//Create model info
modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer,
m_selectedNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), this->GetFitName(), roiUID);
mitk::ScalarListLookupTable::ValueType infoSignal;
for (mitk::MaskedDynamicImageStatisticsGenerator::ResultType::const_iterator pos =
roiSignal.begin(); pos != roiSignal.end(); ++pos)
{
infoSignal.push_back(*pos);
}
modelFitInfo->inputData.SetTableValue("ROI", infoSignal);
}
template <typename TParameterizer>
void MRPerfusionView::GenerateAIFbasedModelFit_PixelBased(mitk::modelFit::ModelFitInfo::Pointer&
modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator)
{
mitk::PixelBasedParameterFitImageGenerator::Pointer fitGenerator =
mitk::PixelBasedParameterFitImageGenerator::New();
typename TParameterizer::Pointer modelParameterizer =
TParameterizer::New();
PrepareConcentrationImage();
mitk::AIFBasedModelBase::AterialInputFunctionType aif;
mitk::AIFBasedModelBase::AterialInputFunctionType aifTimeGrid;
GetAIF(aif, aifTimeGrid);
modelParameterizer->SetAIF(aif);
modelParameterizer->SetAIFTimeGrid(aifTimeGrid);
this->ConfigureInitialParametersOfParameterizer(modelParameterizer);
mitk::NumericTwoCompartmentExchangeModelParameterizer* numTCXParametrizer =
dynamic_cast<mitk::NumericTwoCompartmentExchangeModelParameterizer*>
(modelParameterizer.GetPointer());
if (numTCXParametrizer)
{
numTCXParametrizer->SetODEINTStepSize(this->m_Controls.odeStepSize->value());
}
//Specify fitting strategy and criterion parameters
mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer);
//Parametrize fit generator
fitGenerator->SetModelParameterizer(modelParameterizer);
std::string roiUID = "";
if (m_selectedMask.IsNotNull())
{
fitGenerator->SetMask(m_selectedMask);
roiUID = this->m_selectedMask->GetUID();
}
fitGenerator->SetDynamicImage(this->m_inputImage);
fitGenerator->SetFitFunctor(fitFunctor);
generator = fitGenerator.GetPointer();
//Create model info
modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer,
this->m_inputImage, mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), this->GetFitName(),
roiUID);
mitk::ScalarListLookupTable::ValueType infoSignal;
for (mitk::AIFBasedModelBase::AterialInputFunctionType::const_iterator pos =
aif.begin(); pos != aif.end(); ++pos)
{
infoSignal.push_back(*pos);
}
modelFitInfo->inputData.SetTableValue("AIF", infoSignal);
}
template <typename TParameterizer>
void MRPerfusionView::GenerateAIFbasedModelFit_ROIBased(
mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo,
mitk::ParameterFitImageGeneratorBase::Pointer& generator)
{
if (m_selectedMask.IsNull())
{
return;
}
mitk::ROIBasedParameterFitImageGenerator::Pointer fitGenerator =
mitk::ROIBasedParameterFitImageGenerator::New();
typename TParameterizer::Pointer modelParameterizer =
TParameterizer::New();
PrepareConcentrationImage();
mitk::AIFBasedModelBase::AterialInputFunctionType aif;
mitk::AIFBasedModelBase::AterialInputFunctionType aifTimeGrid;
GetAIF(aif, aifTimeGrid);
modelParameterizer->SetAIF(aif);
modelParameterizer->SetAIFTimeGrid(aifTimeGrid);
this->ConfigureInitialParametersOfParameterizer(modelParameterizer);
mitk::NumericTwoCompartmentExchangeModelParameterizer* numTCXParametrizer =
dynamic_cast<mitk::NumericTwoCompartmentExchangeModelParameterizer*>
(modelParameterizer.GetPointer());
if (numTCXParametrizer)
{
numTCXParametrizer->SetODEINTStepSize(this->m_Controls.odeStepSize->value());
}
//Compute ROI signal
mitk::MaskedDynamicImageStatisticsGenerator::Pointer signalGenerator =
mitk::MaskedDynamicImageStatisticsGenerator::New();
signalGenerator->SetMask(m_selectedMask);
signalGenerator->SetDynamicImage(this->m_inputImage);
signalGenerator->Generate();
mitk::MaskedDynamicImageStatisticsGenerator::ResultType roiSignal = signalGenerator->GetMean();
//Specify fitting strategy and criterion parameters
mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer);
//Parametrize fit generator
fitGenerator->SetModelParameterizer(modelParameterizer);
fitGenerator->SetMask(m_selectedMask);
fitGenerator->SetFitFunctor(fitFunctor);
fitGenerator->SetSignal(roiSignal);
fitGenerator->SetTimeGrid(mitk::ExtractTimeGrid(this->m_inputImage));
generator = fitGenerator.GetPointer();
std::string roiUID = this->m_selectedMask->GetUID();
//Create model info
modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer,
this->m_inputImage, mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), this->GetFitName(),
roiUID);
mitk::ScalarListLookupTable::ValueType infoSignal;
for (mitk::MaskedDynamicImageStatisticsGenerator::ResultType::const_iterator pos =
roiSignal.begin(); pos != roiSignal.end(); ++pos)
{
infoSignal.push_back(*pos);
}
modelFitInfo->inputData.SetTableValue("ROI", infoSignal);
infoSignal.clear();
for (mitk::AIFBasedModelBase::AterialInputFunctionType::const_iterator pos =
aif.begin(); pos != aif.end(); ++pos)
{
infoSignal.push_back(*pos);
}
modelFitInfo->inputData.SetTableValue("AIF", infoSignal);
}
void MRPerfusionView::DoFit(const mitk::modelFit::ModelFitInfo* fitSession,
mitk::ParameterFitImageGeneratorBase* generator)
{
this->m_Controls.infoBox->append(QString("<font color='green'>" + QString("Fitting Data Set . . .") + QString ("</font>")));
/////////////////////////
//create job and put it into the thread pool
mitk::modelFit::ModelFitResultNodeVectorType additionalNodes;
if (m_HasGeneratedNewInput)
{
additionalNodes.push_back(m_inputNode);
}
if (m_HasGeneratedNewInputAIF)
{
additionalNodes.push_back(m_inputAIFNode);
}
ParameterFitBackgroundJob* pJob = new ParameterFitBackgroundJob(generator, fitSession,
this->m_selectedNode, additionalNodes);
pJob->setAutoDelete(true);
connect(pJob, SIGNAL(Error(QString)), this, SLOT(OnJobError(QString)));
connect(pJob, SIGNAL(Finished()), this, SLOT(OnJobFinished()));
connect(pJob, SIGNAL(ResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType,
const ParameterFitBackgroundJob*)), this,
SLOT(OnJobResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType,
const ParameterFitBackgroundJob*)), Qt::BlockingQueuedConnection);
connect(pJob, SIGNAL(JobProgress(double)), this, SLOT(OnJobProgress(double)));
connect(pJob, SIGNAL(JobStatusChanged(QString)), this, SLOT(OnJobStatusChanged(QString)));
QThreadPool* threadPool = QThreadPool::globalInstance();
threadPool->start(pJob);
}
MRPerfusionView::MRPerfusionView() : m_FittingInProgress(false), m_HasGeneratedNewInput(false), m_HasGeneratedNewInputAIF(false)
{
m_selectedImage = nullptr;
m_selectedMask = nullptr;
mitk::ModelFactoryBase::Pointer factory =
mitk::DescriptivePharmacokineticBrixModelFactory::New().GetPointer();
m_FactoryStack.push_back(factory);
factory = mitk::TwoStepLinearModelFactory::New().GetPointer();
m_FactoryStack.push_back(factory);
factory = mitk::ThreeStepLinearModelFactory::New().GetPointer();
m_FactoryStack.push_back(factory);
factory = mitk::StandardToftsModelFactory::New().GetPointer();
m_FactoryStack.push_back(factory);
factory = mitk::ExtendedToftsModelFactory::New().GetPointer();
m_FactoryStack.push_back(factory);
factory = mitk::TwoCompartmentExchangeModelFactory::New().GetPointer();
m_FactoryStack.push_back(factory);
factory = mitk::NumericTwoCompartmentExchangeModelFactory::New().GetPointer();
m_FactoryStack.push_back(factory);
mitk::NodePredicateDataType::Pointer isLabelSet = mitk::NodePredicateDataType::New("LabelSetImage");
mitk::NodePredicateDataType::Pointer isImage = mitk::NodePredicateDataType::New("Image");
mitk::NodePredicateProperty::Pointer isBinary = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true));
mitk::NodePredicateAnd::Pointer isLegacyMask = mitk::NodePredicateAnd::New(isImage, isBinary);
mitk::NodePredicateDimension::Pointer is3D = mitk::NodePredicateDimension::New(3);
mitk::NodePredicateOr::Pointer isMask = mitk::NodePredicateOr::New(isLegacyMask, isLabelSet);
mitk::NodePredicateAnd::Pointer isNoMask = mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isMask));
mitk::NodePredicateAnd::Pointer is3DImage = mitk::NodePredicateAnd::New(isImage, is3D, isNoMask);
this->m_IsMaskPredicate = mitk::NodePredicateAnd::New(isMask, mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))).GetPointer();
this->m_IsNoMaskImagePredicate = mitk::NodePredicateAnd::New(isNoMask, mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))).GetPointer();
auto isDynamicData = mitk::NodePredicateFunction::New([](const mitk::DataNode* node)
{
return (node && node->GetData() && node->GetData()->GetTimeSteps() > 1);
});
- auto isNoModelFitNodePredicate = mitk::NodePredicateFunction::New([](const mitk::DataNode* node) {
- bool isNoModelFitNode = node->GetData()->GetProperty(mitk::ModelFitConstants::FIT_UID_PROPERTY_NAME().c_str()).IsNull();
- return isNoModelFitNode;
- });
-
+ auto modelFitResultRelationRule = mitk::ModelFitResultRelationRule::New();
+ auto isNoModelFitNodePredicate = mitk::NodePredicateNot::New(modelFitResultRelationRule->GetConnectedSourcesDetector());
this->m_isValidPDWImagePredicate = mitk::NodePredicateAnd::New(is3DImage, isNoModelFitNodePredicate);
this->m_isValidTimeSeriesImagePredicate = mitk::NodePredicateAnd::New(isDynamicData, isImage, isNoMask);
}
void MRPerfusionView::OnJobFinished()
{
this->m_Controls.infoBox->append(QString("Fitting finished."));
this->m_FittingInProgress = false;
this->UpdateGUIControls();
};
void MRPerfusionView::OnJobError(QString err)
{
MITK_ERROR << err.toStdString().c_str();
m_Controls.infoBox->append(QString("<font color='red'><b>") + err + QString("</b></font>"));
};
void MRPerfusionView::OnJobResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType results,
const ParameterFitBackgroundJob* pJob)
{
//Store the resulting parameter fit image via convenience helper function in data storage
//(handles the correct generation of the nodes and their properties)
mitk::modelFit::StoreResultsInDataStorage(this->GetDataStorage(), results, pJob->GetParentNode());
//this stores the concentration image and AIF concentration image, if generated for this fit in the storage.
//if not generated for this fit, relevant nodes are empty.
mitk::modelFit::StoreResultsInDataStorage(this->GetDataStorage(), pJob->GetAdditionalRelevantNodes(), pJob->GetParentNode());
};
void MRPerfusionView::OnJobProgress(double progress)
{
QString report = QString("Progress. ") + QString::number(progress);
this->m_Controls.infoBox->append(report);
};
void MRPerfusionView::OnJobStatusChanged(QString info)
{
this->m_Controls.infoBox->append(info);
}
void MRPerfusionView::InitModelComboBox() const
{
this->m_Controls.comboModel->clear();
this->m_Controls.comboModel->addItem(tr("No model selected"));
for (ModelFactoryStackType::const_iterator pos = m_FactoryStack.begin();
pos != m_FactoryStack.end(); ++pos)
{
this->m_Controls.comboModel->addItem(QString::fromStdString((*pos)->GetClassID()));
}
this->m_Controls.comboModel->setCurrentIndex(0);
};
mitk::DataNode::Pointer MRPerfusionView::GenerateConcentrationNode(mitk::Image* image,
const std::string& nodeName) const
{
if (!image)
{
mitkThrow() << "Cannot generate concentration node. Passed image is null. parameter name: ";
}
mitk::DataNode::Pointer result = mitk::DataNode::New();
result->SetData(image);
result->SetName(nodeName);
result->SetVisibility(true);
return result;
};
mitk::Image::Pointer MRPerfusionView::ConvertConcentrationImage(bool AIFMode)
{
//Compute Concentration image
mitk::ConcentrationCurveGenerator::Pointer concentrationGen =
mitk::ConcentrationCurveGenerator::New();
if (m_Controls.checkDedicatedAIFImage->isChecked() && AIFMode)
{
concentrationGen->SetDynamicImage(this->m_selectedAIFImage);
}
else
{
concentrationGen->SetDynamicImage(this->m_selectedImage);
}
concentrationGen->SetisTurboFlashSequence(IsTurboFlashSequenceFlag());
concentrationGen->SetAbsoluteSignalEnhancement(m_Controls.radioButton_absoluteEnhancement->isChecked());
concentrationGen->SetRelativeSignalEnhancement(m_Controls.radioButton_relativeEnchancement->isChecked());
concentrationGen->SetUsingT1Map(m_Controls.radioButtonUsingT1viaVFA->isChecked());
if (IsTurboFlashSequenceFlag())
{
if (AIFMode)
{
concentrationGen->SetRecoveryTime(m_Controls.AifRecoverytime->value());
}
else
{
concentrationGen->SetRecoveryTime(m_Controls.recoverytime->value());
}
concentrationGen->SetRelaxationTime(m_Controls.relaxationtime->value());
concentrationGen->SetRelaxivity(m_Controls.relaxivity->value());
concentrationGen->SetBaselineStartTimeStep(m_Controls.spinBox_baselineStartTimeStep->value());
concentrationGen->SetBaselineEndTimeStep(m_Controls.spinBox_baselineEndTimeStep->value());
}
else if (this->m_Controls.radioButtonUsingT1viaVFA->isChecked())
{
concentrationGen->SetRecoveryTime(m_Controls.TRSpinBox->value());
concentrationGen->SetRelaxivity(m_Controls.RelaxivitySpinBox->value());
concentrationGen->SetT10Image(dynamic_cast<mitk::Image*>(m_Controls.PDWImageNodeSelector->GetSelectedNode()->GetData()));
concentrationGen->SetBaselineStartTimeStep(m_Controls.spinBox_baselineStartTimeStep->value());
concentrationGen->SetBaselineEndTimeStep(m_Controls.spinBox_baselineEndTimeStep->value());
//Convert Flipangle from degree to radiant
double alpha = m_Controls.FlipangleSpinBox->value()/360*2* boost::math::constants::pi<double>();
concentrationGen->SetFlipAngle(alpha);
}
else
{
concentrationGen->SetFactor(m_Controls.factorSpinBox->value());
concentrationGen->SetBaselineStartTimeStep(m_Controls.spinBox_baselineStartTimeStep->value());
concentrationGen->SetBaselineEndTimeStep(m_Controls.spinBox_baselineEndTimeStep->value());
}
mitk::Image::Pointer concentrationImage = concentrationGen->GetConvertedImage();
return concentrationImage;
}
void MRPerfusionView::GetAIF(mitk::AIFBasedModelBase::AterialInputFunctionType& aif,
mitk::AIFBasedModelBase::AterialInputFunctionType& aifTimeGrid)
{
if (this->m_Controls.radioAIFFile->isChecked())
{
aif.clear();
aifTimeGrid.clear();
aif.SetSize(AIFinputFunction.size());
aifTimeGrid.SetSize(AIFinputGrid.size());
aif.fill(0.0);
aifTimeGrid.fill(0.0);
itk::Array<double>::iterator aifPos = aif.begin();
for (std::vector<double>::const_iterator pos = AIFinputFunction.begin();
pos != AIFinputFunction.end(); ++pos, ++aifPos)
{
*aifPos = *pos;
}
itk::Array<double>::iterator gridPos = aifTimeGrid.begin();
for (std::vector<double>::const_iterator pos = AIFinputGrid.begin(); pos != AIFinputGrid.end();
++pos, ++gridPos)
{
*gridPos = *pos;
}
}
else if (this->m_Controls.radioAIFImage->isChecked())
{
aif.clear();
aifTimeGrid.clear();
mitk::AterialInputFunctionGenerator::Pointer aifGenerator =
mitk::AterialInputFunctionGenerator::New();
//Hematocrit level
aifGenerator->SetHCL(this->m_Controls.HCLSpinBox->value());
//mask settings
this->m_selectedAIFMaskNode = m_Controls.AIFMaskNodeSelector->GetSelectedNode();
this->m_selectedAIFMask = dynamic_cast<mitk::Image*>(this->m_selectedAIFMaskNode->GetData());
if (this->m_selectedAIFMask->GetTimeSteps() > 1)
{
MITK_INFO <<
"Selected AIF mask has multiple timesteps. Only use first timestep to mask model fit. AIF Mask name: "
<<
m_selectedAIFMaskNode->GetName() ;
mitk::ImageTimeSelector::Pointer maskedImageTimeSelector = mitk::ImageTimeSelector::New();
maskedImageTimeSelector->SetInput(this->m_selectedAIFMask);
maskedImageTimeSelector->SetTimeNr(0);
maskedImageTimeSelector->UpdateLargestPossibleRegion();
this->m_selectedAIFMask = maskedImageTimeSelector->GetOutput();
}
if (this->m_selectedAIFMask.IsNotNull())
{
aifGenerator->SetMask(this->m_selectedAIFMask);
}
//image settings
if (this->m_Controls.checkDedicatedAIFImage->isChecked())
{
this->m_selectedAIFImageNode = m_Controls.AIFImageNodeSelector->GetSelectedNode();
this->m_selectedAIFImage = dynamic_cast<mitk::Image*>(this->m_selectedAIFImageNode->GetData());
}
else
{
this->m_selectedAIFImageNode = m_selectedNode;
this->m_selectedAIFImage = m_selectedImage;
}
this->PrepareAIFConcentrationImage();
aifGenerator->SetDynamicImage(this->m_inputAIFImage);
aif = aifGenerator->GetAterialInputFunction();
aifTimeGrid = aifGenerator->GetAterialInputFunctionTimeGrid();
}
else
{
mitkThrow() << "Cannot generate AIF. View is in a invalide state. No AIF mode selected.";
}
}
void MRPerfusionView::LoadAIFfromFile()
{
QFileDialog dialog;
dialog.setNameFilter(tr("Images (*.csv"));
QString fileName = dialog.getOpenFileName();
m_Controls.aifFilePath->setText(fileName);
std::string m_aifFilePath = fileName.toStdString();
//Read Input
typedef boost::tokenizer< boost::escaped_list_separator<char> > Tokenizer;
/////////////////////////////////////////////////////////////////////////////////////////////////
//AIF Data
std::ifstream in1(m_aifFilePath.c_str());
if (!in1.is_open())
{
this->m_Controls.infoBox->append(QString("Could not open AIF File!"));
}
std::vector< std::string > vec1;
std::string line1;
while (getline(in1, line1))
{
Tokenizer tok(line1);
vec1.assign(tok.begin(), tok.end());
this->AIFinputGrid.push_back(convertToDouble(vec1[0]));
this->AIFinputFunction.push_back(convertToDouble(vec1[1]));
}
}
void MRPerfusionView::PrepareConcentrationImage()
{
mitk::Image::Pointer concentrationImage = this->m_selectedImage;
mitk::DataNode::Pointer concentrationNode = this->m_selectedNode;
m_HasGeneratedNewInput = false;
if (!this->m_Controls.radioButtonNoConversion->isChecked())
{
concentrationImage = this->ConvertConcentrationImage(false);
concentrationNode = GenerateConcentrationNode(concentrationImage, "Concentration");
m_HasGeneratedNewInput = true;
}
m_inputImage = concentrationImage;
m_inputNode = concentrationNode;
}
void MRPerfusionView::PrepareAIFConcentrationImage()
{
mitk::Image::Pointer concentrationImage = this->m_selectedImage;
mitk::DataNode::Pointer concentrationNode = this->m_selectedNode;
m_HasGeneratedNewInputAIF = false;
if (this->m_Controls.checkDedicatedAIFImage->isChecked())
{
concentrationImage = this->m_selectedAIFImage;
concentrationNode = this->m_selectedAIFImageNode;
}
if (!this->m_Controls.radioButtonNoConversion->isChecked())
{
if (!IsTurboFlashSequenceFlag() && !this->m_Controls.checkDedicatedAIFImage->isChecked())
{
if (m_inputImage.IsNull())
{
mitkThrow() <<
"Cannot get AIF concentration image. Invalid view state. Input image is not defined yet, but should be.";
}
//we can directly use the concentration input image/node (generated by GetConcentrationImage) also for the AIF
concentrationImage = this->m_inputImage;
concentrationNode = this->m_inputNode;
}
else
{
concentrationImage = this->ConvertConcentrationImage(true);
concentrationNode = GenerateConcentrationNode(concentrationImage, "AIF Concentration");
m_HasGeneratedNewInputAIF = true;
}
}
m_inputAIFImage = concentrationImage;
m_inputAIFNode = concentrationNode;
}
mitk::ModelFitFunctorBase::Pointer MRPerfusionView::CreateDefaultFitFunctor(
const mitk::ModelParameterizerBase* parameterizer) const
{
mitk::LevenbergMarquardtModelFitFunctor::Pointer fitFunctor =
mitk::LevenbergMarquardtModelFitFunctor::New();
mitk::NormalizedSumOfSquaredDifferencesFitCostFunction::Pointer chi2 =
mitk::NormalizedSumOfSquaredDifferencesFitCostFunction::New();
fitFunctor->RegisterEvaluationParameter("Chi^2", chi2);
if (m_Controls.checkBox_Constraints->isChecked())
{
fitFunctor->SetConstraintChecker(m_modelConstraints);
}
mitk::ModelBase::Pointer refModel = parameterizer->GenerateParameterizedModel();
::itk::LevenbergMarquardtOptimizer::ScalesType scales;
scales.SetSize(refModel->GetNumberOfParameters());
scales.Fill(1.0);
fitFunctor->SetScales(scales);
fitFunctor->SetDebugParameterMaps(m_Controls.checkDebug->isChecked());
return fitFunctor.GetPointer();
}
diff --git a/Plugins/org.mitk.gui.qt.properties/documentation/UserManual/PropertiesView.dox b/Plugins/org.mitk.gui.qt.properties/documentation/UserManual/PropertiesView.dox
index e22620785d..2b4644144a 100644
--- a/Plugins/org.mitk.gui.qt.properties/documentation/UserManual/PropertiesView.dox
+++ b/Plugins/org.mitk.gui.qt.properties/documentation/UserManual/PropertiesView.dox
@@ -1,57 +1,57 @@
/**
\page org_mitk_views_properties The Properties
\imageMacro{icon.svg,"Icon of the Properties View.",2.00}
\tableofcontents
\section org_mitk_views_propertiesOverview Overview
The Properties View allows you to inspect and change properties of a selected data node and its attached data.
This View is only for advanced users and developers, as it is easy to alter the program state in unexpected ways.
It can be considered as a complete exposure of parts of the backend that are usually supposed to be accessed only through dedicated frontend components like the color or opacity widgets in the context menu of a data node in the Data Manager View.
\section org_mitk_views_propertiesUsage Usage
\imageMacro{view.png,"The Properties View.",12.00}
\subsection org_mitk_views_propertiesUsagePropertyListTypes Property list types
After you selected a data node, the Property View allows you to switch between several property lists that are attached to the selected data node and its actual data.
By default, you see the common data node property list.
There are two types of property lists: data node property lists and data property lists.
Data node property lists consist of properties that the application attaches mainly for rendering settings.
They are not intrinsically part of the actual data and are only persisted when saving the MITK scene as a whole.
A typical example of such a property is "visible", which decides if the data should be rendered or hidden.
The common data node property list is applied to all render windows but there are also render window specific data node property lists.
Any property that is found in both the common list and a render window specific list is overriden by the latter one.
For example, if you want to hide an image only in the 3d render window but show it in all other render windows, you check "visible" in the common list, add the same property to the 3d render window specific list, and uncheck it there.
There is only a single data property list.
It represents the true metadata of the selected data like DICOM tags of a DICOM image.
When saving specific data, most data properties are written to the data file, as long as the selected file format supports metadata.
A popular example is the NRRD image format that allows to save custom key value pairs in text format in the file header.
Not all data properties are meant for persistence, though.
-To check if a certain data property will be written to a metadata-enabled file format, click on in the properties tree view and check if there is a save icon at the bottom in the additional property info box.
+To check if a certain data property will be written to a metadata-enabled file format, click on it in the properties tree view and check if there is a save icon at the bottom in the additional property info box.
\subsection org_mitk_views_propertiesUsageFilter Filter
Property lists can be quite large and complex, shown as a tree structure in the Properties View.
To quickly find properties of interest you can use the filter text box, which will filter the properties while you type.
\subsection org_mitk_views_propertiesUsageEditProperties Edit properties
Most property value types like numbers, strings, boolean values, or colors can be edited by either clicking or double-clicking in the Value column.
For example, to edit color properties, double-click on the colored Value cell.
You can either enter a color by name like "yellow", in hex notation like "#ffff00" (or abbreviated "#ff0"), or click on the "..." button to open a color picker dialog.
\subsection org_mitk_views_propertiesUsagePropertyInfos Additional property information
Some properties have additional information attached like a description, aliases, or a persistence flag.
This information is shown at the bottom of the Properties View.
When no additional information is available, the additional property info box is hidden.
*/
diff --git a/Plugins/org.mitk.gui.qt.radiomics/documentation/UserManual/QmitkPhenotypingPortalPage.dox b/Plugins/org.mitk.gui.qt.radiomics/documentation/UserManual/QmitkPhenotypingPortalPage.dox
index 69c9dce5b6..aebb075d1b 100644
--- a/Plugins/org.mitk.gui.qt.radiomics/documentation/UserManual/QmitkPhenotypingPortalPage.dox
+++ b/Plugins/org.mitk.gui.qt.radiomics/documentation/UserManual/QmitkPhenotypingPortalPage.dox
@@ -1,41 +1,41 @@
/**
\page org_mitk_gui_qt_mitkphenotyping The Phenotyping
\tableofcontents
MITK Phenotyping is a selection of algorithms that can be used to extract image-based phenotypes, for example using a radiomics approach. The software is part of the research of the <a href="https://www.dkfz.de/en/mic/index.php">Division of Medical Image Computing</a> of the German Cancer Research Center (DKFZ). MITK Phenotyping is not intended to be a single application, it is rather a collection of the necessary plugins within the offical MITK releases.
The functionality of MITK Phenotyping can be accessed in different ways: Using the graphical interface using the Plugins listed below, using command line applications, or using one of the programming interfaces.
\section org_mitk_gui_qt_mitkphenotyping_Tutorials Tutorials
\li \subpage org_mitk_views_radiomicstutorial_gui_portal A tutorial on how to use the grapical interface of MITK Phenotying
\section org_mitk_gui_qt_mitkphenotyping_Views Views
\subsection sub2 Specific Views:
Views that were developed with the main focus on Radiomics. They still might be used in other use-cases as well:
\li \subpage org_mitk_views_radiomicstransformationview : Image transformations like Resampling, Laplacian of Gaussian, and Wavelet Transformations
\li \subpage org_mitk_views_radiomicsmaskprocessingview : Processing and Cleaning of Masks
\li \subpage org_mitk_views_radiomicsarithmetricview : Processing images using mathematical operations
\li \subpage org_mitk_views_radiomicsstatisticview : Calculate Radiomics Features
\subsection sub1 Non-Specific Views:
This section contains views that are included within MITK Phenotyping, but were developed with a broader application in mind.
-\li \subpage org_mitk_views_basicimageprocessing : Deprecated plugin for performing different image-related tasks like subtraction, mutliplaction, filtering etc.
-\li \subpage org_mitk_views_matchpoint_algorithm_browser : Selection of MatchPoint (Registration) Algorithm
-\li \subpage org_mitk_views_matchpoint_algorithm_control : Configuring and Controlling MatchPoint (Registration) Algorithm
-\li \subpage org_mitk_views_matchpoint_evaluator : Evaluate the Registration performance using MatchPoint
-\li \subpage org_mitk_views_matchpoint_manipulator : Adapt a registration calculated using MatchPoint
-\li \subpage org_mitk_views_matchpoint_mapper : Apply a MatchPoint Registration to a specific image
-\li \subpage org_mitk_views_matchpoint_visualizer : Visualize a Registration obtained with MatchPoint
-\li \subpage org_mitk_views_matchpoint_algorithm_batch : Running MatchPoint over multiple images (BatchMode)
-\li \subpage org_mitk_views_multilabelsegmentation : Create and editing of Multilabel-Segmentations.
-\li \subpage org_mitk_views_segmentation : Create simple segmentations
-\li \subpage org_mitk_views_segmentationutilities : Utilities for the processing of simple segmentations.
+\li \ref org_mitk_views_basicimageprocessing : Deprecated plugin for performing different image-related tasks like subtraction, mutliplaction, filtering etc.
+\li \ref org_mitk_views_matchpoint_algorithm_browser : Selection of MatchPoint (Registration) Algorithm
+\li \ref org_mitk_views_matchpoint_algorithm_control : Configuring and Controlling MatchPoint (Registration) Algorithm
+\li \ref org_mitk_views_matchpoint_evaluator : Evaluate the Registration performance using MatchPoint
+\li \ref org_mitk_views_matchpoint_manipulator : Adapt a registration calculated using MatchPoint
+\li \ref org_mitk_views_matchpoint_mapper : Apply a MatchPoint Registration to a specific image
+\li \ref org_mitk_views_matchpoint_visualizer : Visualize a Registration obtained with MatchPoint
+\li \ref org_mitk_views_matchpoint_algorithm_batch : Running MatchPoint over multiple images (BatchMode)
+\li \ref org_mitk_views_multilabelsegmentation : Create and editing of Multilabel-Segmentations.
+\li \ref org_mitk_views_segmentation : Create simple segmentations
+\li \ref org_mitk_views_segmentationutilities : Utilities for the processing of simple segmentations.
\section radiomics_miniapps MiniApps (Command line Tools)
\li \subpage MiniAppExplainPage Explanation of the Command Line App concept in MITK
\li \subpage mitkBasicImageProcessingMiniAppsPortalPage : List of common preprocessing MiniApps
\li \subpage mitkClassificationMiniAppsPortalPage : (Incomplete) list of MITK Classification MiniApps
*/
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox
index 8465c4c126..835a75a74b 100644
--- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox
+++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox
@@ -1,317 +1,300 @@
/**
-\page org_mitk_views_segmentation The Segmentation
+\page org_mitk_views_segmentation The Segmentation View
-\imageMacro{segmentation.svg,"Icon of the Segmentation Plugin",2.00}
+\imageMacro{segmentation.svg,"Icon of the segmentation view",2.00}
<i>Some of the features described below are closed source additions to the open source toolkit MITK and are not available in every application.</i>
\tableofcontents
-\section org_mitk_gui_qt_segmentationUserManualOverview Overview
+\section org_mitk_views_segmentationUserManualOverview Overview
-The <b>Segmentation plugin</b> allows you to create segmentations of anatomical and pathological structures in medical images of the human body.
-The plugin consists of a number of view which can be used for:
+Segmentation is the act of partitioning an image into subsets by either manual or automated delineation to create i.e. a distinction between foreground and background.
+The MITK <b>segmentation plugin</b> allows you to create segmentations of anatomical and pathological structures in medical images.
+The plugin consists of a number of views:
<ul>
- <li> manual and (semi-)automatic segmentation of organs on CT or MR image volumes via the <b>Segmentation View</b>
- <li> segmentation postprocessing via the \subpage org_mitk_views_segmentationutilities
- <li> clipping of existing segmentations using a resection plane via the \subpage org_mitk_views_deformableclippingplane
+ <li> <b>Segmentation View</b>: Manual and (semi-)automatic segmentation
+ <li> \subpage org_mitk_views_segmentationutilities : Segmentation post-processing
+ <li> \subpage org_mitk_views_deformableclippingplane : Clipping of existing segmentations using a resection plane
</ul>
+In this documentation, the features and usage of the segmentation view will be described.
+For an introduction to the segmentation utilities and clipping plane views, please be referred to the respective documentation pages.
-\imageMacro{QmitkSegmentation_IMGApplication.png,"Segmentation Plugin consisting of the Segmentation View the Segmentation Utilities View and the Clipping Plane View", 16.00}
+\imageMacro{QmitkSegmentationPlugin_Overview.png,"Segmentation plugin overview", 16.00}
-The segmentation plugin offers a number of preferences which can be set via the MITK Workbench application preference dialog:
+\section org_mitk_views_segmentationPreferences Preferences
+The segmentation plugin offers a number of preferences which can be set via the MITK Workbench application preferences:
-\imageMacro{QmitkSegmentation_IMGPreferences.png,"Segmentation Plugin consisting of the Segmentation View the Segmentation Utilities View and the Clipping Plane View", 10.00}
+\imageMacro{QmitkSegmentationPreferences.png,"Segmentation preferences", 10.00}
-The following preferences can be set:
<ul>
- <li> <b>Slim view:</b> Allows you to show or hide the tool button description of the Segmentation View
+ <li> <b>Slim view:</b> Allows you to show or hide the tool button description of the segmentation view
<li> <b>2D display:</b> Specify whether the segmentation is drawn as outline or as a transparent overlay
<li> <b>3D display:</b> Activate 3D volume rendering for your segmentation
- <li> <b>Data node selection mode:</b> If activated the segmentation image combo box is always sychronized with the data manager selection.
+ <li> <b>Data node selection mode:</b> If activated the segmentation image is automatically chosen from the data manager selection.
<li> <b>Smoothed surface creation:</b> Set certain smoothing parameters for surface creation
</ul>
-If you wonder what segmentations are good for, we shortly revisit the concept of a segmentation here.
-A CT or MR image is made up of volume of physical measurements (volume elements are called voxels).
-In CT images, for example, the gray value of each voxel corresponds to the mass absorbtion coefficient for X-rays in this voxel, which is similar in many %parts of the human body.
-The gray value does not contain any further information, so the computer does not know whether a given voxel is part of the body or the background, nor can it tell a brain from a liver.
-However, the distinction between a foreground and a background structure is required when:
-<ul>
-<li>you want to know the volume of a given organ (the computer needs to know which %parts of the image belong to this organ)
-<li>you want to create 3D polygon visualizations (the computer needs to know the surfaces of structures that should be drawn)
-<li>as a necessary pre-processing step for therapy planning, therapy support, and therapy monitoring
-</ul>
-Creating this distinction between foreground and background is called <i>segmentation</i>.
-The Segmentation perspective of the MITK Workbench uses a voxel based approach to segmentation, i.e. each voxel of an image must be completely assigned to either foreground or background.
-This is in contrast to some other applications which might use an approach based on contours, where the border of a structure might cut a voxel into two %parts.
-
-The remainder of this document will summarize the features of the Segmentation perspective and how they are used.
-\section org_mitk_gui_qt_segmentationUserManualTechnical Technical Issues
+\section org_mitk_views_segmentationUserManualTechnical Technical Issues
-The Segmentation perspective makes a number of assumptions. To know what this view can be used for, it will help you to know that:
+The segmentation plugin makes a number of assumptions:
<ul>
- <li> Images must be 2D, 3D, or 3D+t
- <li> Images must be single-values, i.e. CT, MRI or "normal" ultrasound. Images from color doppler or photographic (RGB) images are not supported
- <li> Segmentations are handled as binary images of the same extent as the original image
+ <li> Images must be 2D, 3D, or 3D+t.
+ <li> Images must be single-values, i.e. CT, MRI or "normal" ultrasound. Images from color doppler or photographic (RGB) images are only partially supported (please be aware that some tools might not be compatible with this image type).
+ <li> Segmentations are handled as binary images of the same extent as the original image.
</ul>
-\section org_mitk_gui_qt_segmentationUserManualImageSelection Image Selection
-
-The Segmentation perspective makes use of the Data Manager view to give you an overview of all images and segmentations.
-
-\imageMacro{QmitkSegmentation_IMGSelection.png,"Data Manager is used for selecting the current segmentation. The reference image is selected in the drop down box of the control area.",5.50}
-
-To select the reference image (e.g. the original CT/MR image) use the patient image drop down box in the control area of the Segmentation view. The segmentation image selected in the Data Manager is displayed below in the segmentation drop down box.
-By default the auto selection mode is enabled, which always keeps the selection of the segmentation drop down box in synch with the selection in the data manager.
-If you disable the auto selection mode the selection of the right segmentation image has to be done via the drop down box.
-If no segmentation image exists or none is selected create a new segmentation image by using the "New segmentation" button on the right of the Segmentation drop down box.
-Some items of the graphical user interface might be disabled when no image is selected or the selected image does not fit to the patient image's geoemtry.
-In any case, the application will give you hints if a selection is needed.
-
-\section org_mitk_gui_qt_segmentationUserManualToolOverview Tool overview
-
-MITK comes with a comprehensive set of segmentation tools. These tools can be differenciated between manual slice-based 2D segmentation tools and (semi-)automated 3D tools.
-The manual 2D tools require a big amount of user interaction and can only be applied to a single image slice whereas the 3D tools operate on the hole image. The 3D tools usually
-require a small amount of interaction like placin seedpoints of setting some parameters.
-You can switch between the different toolsets by switching the 2D/3D tab in the segmentation view.
-
-\imageMacro{QmitkSegmentation_ToolOverview.png,"An overview of the existing tools in MITK. There are interactive 2D tools as well as (semi-)automated 3D tools",5.50}
+\section org_mitk_views_segmentationUserManualImageSelection Data Selection & Creating New Segmentations
-\section org_mitk_gui_qt_segmentationUserManualManualKringeling Manual Contouring
+To select a reference image for the segmentation, click on the <i>Patient Image</i> selection widget and choose a suitable image from the selection available in the data manager.
+By default the auto selection mode is enabled (see \ref org_mitk_views_segmentationPreferences).\n
+Once a patient image is selected, a new segmentation can be created on this reference image by clicking the <i>New...</i> button to the right of the <i>Segmentation</i> selection widget.
+An input field will appear which allows you to set the name and display color of the segmentation. Notice that the input field suggests names once you start typing and that it also suggests colors for known organ names.
+Once generated the segmentation will be added with "binary mask" icon to the data manager as sub-node of the reference image. This item is automatically selected for you, allowing you to start editing the new segmentation right away.
-With manual contouring you define which voxels are part of the segmentation and which are not.
-This allows you to create segmentations of any structeres that you may find in an image, even if they are not part of the human body.
-You might also use manual contouring to correct segmentations that result from sub-optimal automatic methods.
-The drawback of manual contouring is that you might need to define contours on many 2D slices.
-However, this is moderated by the interpolation feature, which will make suggestions for a segmentation.
-\subsection org_mitk_gui_qt_segmentationUserManualManualKringeling1 Creating New Segmentations
+\subsection org_mitk_views_segmentationUserManualManualKringeling2 Selecting Segmentations for Editing
+Alternatively to creating a new segmentation, an existing one can be edited as well.
+As you might have segmented multiple structures within a single image, the application needs to know which of them to use for editing.
+For that you click the segmentation selection widget and a selection field will open, containing all suitable segmentations for the parent dataset available in the data manager.
-Unless you want to edit existing segmentations, you have to create a new, empty segmentation before you can edit it.
-To do so, click the "New manual segmentation" button.
-Input fields will appear where you can choose a name for the new segmentation and a color for its display.
-Click the checkmark button to confirm or the X button to cancel the new segmentation.
-Notice that the input field suggests names once you %start typing and that it also suggests colors for known organ names.
-If you use names that are not yet known to the application, it will automatically remember these names and consider them the next time you create a new segmentation.
-Once you created a new segmentation, you can notice a new item with the "binary mask" icon in the Data Manager tree view.
-This item is automatically selected for you, allowing you to %start editing the new segmentation right away.
+\section org_mitk_views_segmentationUserManualToolOverview Segmentation Tool Overview
-\subsection org_mitk_gui_qt_segmentationUserManualManualKringeling2 Selecting Segmentations for Editing
+MITK offers a comprehensive set of slice-based 2D and (semi-)automated 3D segmentation tools.
+The manual 2D tools require some user interaction and can only be applied to a single image slice whereas the 3D tools operate on the whole image. The 3D tools usually only
+require a small amount of user interaction, i.e. placing seed points or setting/adjusting parameters.
+You can switch between the different toolsets by selecting the 2D or 3D tab in the segmentation view.
-As you might want to have segmentations of multiple structures in a single patient image, the application needs to know which of them to use for editing.
-You select a segmenation by clicking it in the tree view of Data Manager. Note that segmentations are usually displayed as sub-items of "their" patient image.
-In the rare case, where you need to edit a segmentation that is not displayed as a a sub-item, you can click both the original image AND the segmentation while holding down CTRL or for macOS the CMD on the keyboard.
+\imageMacro{QmitkSegmentation_ToolOverview.png,"An overview of the existing 2D and 3D tools in MITK.",5.50}
-When a selection is made, the Segmentation View will hide all but the selected segmentation and the corresponding original image.
-When there are multiple segmentations, the unselected ones will remain in the Data Manager, you can make them visible at any time by selecting them.
+\section org_mitk_views_segmentationUserManualManualKringeling 2D Segmentation Tools
-\subsection org_mitk_gui_qt_segmentationUserManualManualKringeling3 Selecting Editing Tools
+With 2D manual contouring you define which voxels are part of the segmentation and which ones are not. This allows you to create segmentations of any structures of interest in an image.
+You can also use manual contouring to correct segmentations that result from sub-optimal automatic methods.
+The drawback of manual contouring is that you might need to define contours on many 2D slices. However, this is mitigated by the interpolation feature, which will make suggestions for a segmentation.
-If you are familiar with the MITK Workbench, you know that clicking and moving the mouse in any of the 2D render windows will move around the crosshair that defines what part of the image is displayed.
-This behavior is disabled while any of the manual segmentation tools are active -- otherwise you might have a hard time concentrating on the contour you are drawing.
+\subsection org_mitk_views_segmentationUserManualManualKringeling3 Selecting Editing Tools
-To %start using one of the editing tools, click its button the the displayed toolbox.
+To start using one of the editing tools, click its button from the displayed toolbox.
The selected editing tool will be active and its corresponding button will stay pressed until you click the button again.
-Selecting a different tool also deactivates the previous one.
+Selecting a different tool also deactivates the previous one.\n
+If you have to delineate a lot of images, shortcuts to switch between tools becomes convenient. For that, just hit the first letter of each tool to activate it (A for Add, S for Subtract, etc.).
-If you have to delineate a lot of images, you should try using shortcuts to switch tools. Just hit the first letter of each tool to activate it (A for Add, S for Subtract, etc.).
+\subsection org_mitk_views_segmentationUserManualManualKringeling4 Using Editing Tools
-\subsection org_mitk_gui_qt_segmentationUserManualManualKringeling4 Using Editing Tools
+All of the editing tools work by the same principle: you use the mouse (left button) to click anywhere in a 2D window (any of the orientations axial, sagittal, or coronal),
+move the mouse while holding the mouse button and release to finish the editing action.
+Multi-step undo and redo is fully supported by all editing tools. Use the application-wide undo button in the toolbar to revert erroneous %actions.
-All of the editing tools work by the same principle: you use the mouse (left button) to click anywhere in a 2D window (any of the orientations axial, sagittal, or frontal), move the mouse while holding the mouse button and release to finish the editing action.
+<i>Remark</i>: If you are familiar with the MITK Workbench, you know that clicking and moving the mouse in any of the 2D render windows will move around the crosshair that defines what part of the image is displayed.
+This behavior is disabled whilst any of the manual segmentation tools are active- otherwise you might have a hard time concentrating on the contour you are drawing.
-Multi-step undo and redo is fully supported by all editing tools. Use the application-wide undo button in the toolbar to revert erroneous %actions.
+\subsection org_mitk_views_segmentationUserManualAddSubtractTools Add and Subtract Tools
\imageMacro{QmitkSegmentation_IMGIconAddSubtract.png,"Add and Subtract Tools",7.70}
-Use the left mouse button to draw a closed contour. When releasing the mouse button, the contour will be added (Add tool) to or removed from (Subtract tool) the current segmentation.
-Hold down the CTRL / CMD key to invert the operation (this will switch tools temporarily to allow for quick corrections).
+Use the left mouse button to draw a closed contour. When releasing the mouse button, the contour will be added (Add tool) to or removed (Subtract tool) from the current segmentation.
+Adding and subtracting voxels can be iteratively repeated for the same segmentation. Holding CTRL / CMD while drawing will invert the current tool's behavior (i.e. instead of adding voxels, they will be subtracted).
+\subsection org_mitk_views_segmentationUserManualPaintWipeTools Paint and Wipe Tools
\imageMacro{QmitkSegmentation_IMGIconPaintWipe.png,"Paint and Wipe Tools",7.68}
-Use the slider below the toolbox to change the radius of these round paintbrush tools. Move the mouse in any 2D window and press the left button to draw or erase pixels.
-As the Add/Subtract tools, holding CTRL / CMD while drawing will invert the current tool's behavior.
+Use the <i>Size</i> slider to change the radius of the round paintbrush tool. Move the mouse in any 2D window and press the left button to draw or erase pixels.
+Holding CTRL / CMD while drawing will invert the current tool's behavior (i.e. instead of painting voxels, they will be wiped).
+\subsection org_mitk_views_segmentationUserManualRegionGrowingTool Region Growing Tool
\imageMacro{QmitkSegmentation_IMGIconRegionGrowing.png,"Region Growing Tool",3.81}
-Click at one point in a 2D slice widget to add an image region to the segmentation with the region growing tool. Moving up the cursor while holding the left mouse button widens the range for the included grey values; moving it down narrows it. Moving the mouse left and right will shift the range.
+Click at one point in a 2D slice widget to add an image region to the segmentation with the region growing tool.
+Region Growing selects all pixels around the mouse cursor that have a similar gray value as the pixel below the mouse cursor. This enables you to quickly create segmentations of structures that have a good contrast to surrounding tissue.
+The tool operates based on the current level window, so changing the level window to optimize the contrast for the ROI is encouraged.
+Moving the mouse up/down is different from left/right: Moving up the cursor while holding the left mouse button widens the range for the included grey values; moving it down narrows it. Moving the mouse left and right will shift the range.
+The tool will select more or less pixels, corresponding to the changing gray value range.
+
+
-Region Growing selects all pixels around the mouse cursor that have a similar gray value as the pixel below the mouse cursor.
-This enables you to quickly create segmentations of structures that have a good contrast to surrounding tissue, e.g. the lungs.
-The tool will select more or less pixels (corresponding to a changing gray value interval width) when you move the mouse up or down while holding down the left mouse button.
\if THISISNOTIMPLEMENTEDATTHEMOMENT
A common issue with region growing is the so called "leakage" which happens when the structure of interest is connected to other pixels, of similar gray values, through a narrow "bridge" at the border of the structure.
The Region Growing tool comes with a "leakage detection/removal" feature. If leakage happens, you can left-click into the leakage region and the tool will try to automatically remove this region (see illustration below).
\imageMacro{QmitkSegmentation_IMGLeakage.png,"Leakage correction feature of the Region Growing tool",11.28}
\endif
+
+\subsection org_mitk_views_segmentationUserManualCorrectionTool Correction Tool
<br>
\imageMacro{QmitkSegmentation_IMGIconCorrection.png,"Correction Tool",3.77}
You do not have to draw a closed contour to use the Correction tool and do not need to switch between the Add and Substract tool to perform
small corrective changes. The following figure shows the usage of this tool:
<ul>
-<li> if the user draws a line which %starts and ends outside the segmenation AND it intersects no other segmentation the endpoints of the line are connected and the resulting contour is filled
-<li> if the user draws a line which %starts and ends outside the segmenation a part of it is cut off (left image)
-<li> if the line is drawn fully inside the segmentation the marked region is added to the segmentation (right image)
+<li> a) If the user draws a line which %starts and ends outside the segmenation a part of it is cut off.
+<li> b) If the line is drawn fully inside the segmentation the marked region is added to the segmentation.
</ul>
-\imageMacro{QmitkSegmentation_IMGCorrectionActions.png,"%Actions of the Correction tool illustrated.",13.50}
+\imageMacro{QmitkSegmentation_IMGCorrectionActions.png,"Usage of the Correction tool.",13.50}
<br>
+
+\subsection org_mitk_views_segmentationUserManualFillTool Fill Tool
\imageMacro{QmitkSegmentation_IMGIconFill.png,"Fill Tool",3.81}
-Left-click inside a segmentation with holes to completely fill all holes (left-click outside a segmentation).
+Left-click inside a segmentation with holes to completely fill all holes. Left-click inside a hole to fill only this specific hole.
+
+\subsection org_mitk_views_segmentationUserManualEraseTool Erase Tool
\imageMacro{QmitkSegmentation_IMGIconErase.png,"Erase Tool",3.79}
-This tool removes a connected part of pixels that form a segmentation. You may use it to remove so called islands (see picture) or to clear a whole slice at once (left-click outside a segmentation).
+This tool removes a connected part of pixels that form a segmentation. You may use it to remove single segmentations (left-click on specific segmentation) or to clear a whole slice at once (left-click outside a segmentation).
-\imageMacro{QmitkSegmentation_IMGIconLiveWire.png,"LiveWire Tool",3.01}
+\subsection org_mitk_views_segmentationUserManualLiveWireTool Live Wire Tool
-The LiveWire Tool acts as a magnetic lasso with a contour snapping to edges of objects.
+\imageMacro{QmitkSegmentation_IMGIconLiveWire.png,"Live Wire Tool",3.01}
-\imageMacro{QmitkSegmentation_IMGLiveWireUsage.PNG,"Steps for using LiveWire Tool",16.00}
+The Live Wire Tool acts as a magnetic lasso with a contour snapping to edges of objects.
+
+\imageMacro{QmitkSegmentation_IMGLiveWireUsage.PNG,"Steps for using the Live Wire Tool",16.00}
<ul>
-<li>(1) To start the Tool you have to double click near the edge of the object you want to segment. The initial anchor point will snap to the edge within a 3x3 region.
+<li>(1) To start the tool you have to double-click near the edge of the object you want to segment. The initial anchor point will snap to the edge within a 3x3 region.
<li>(2) Move the mouse. You don't have trace the edge of the object. The contour will automatically snap to it.
<li>(3) To fix a segment you can set anchor points by single left mouse button click.
<li>(4) Go on with moving the mouse and setting anchor points.
-<li>(5) To close the contour double click on the initial anchor point.
-<li>(6) After closing the contour can be edited by moving, inserting and deleting anchor points.
+<li>(5) To close the contour double-click on the initial anchor point.
+<li>(6) After closing, the contour can be edited by moving, inserting and deleting anchor points.
</ul>
-The contour will be transfered to its binary image representation by deactivating the tool.
+The contour will be transferred to its binary image representation by deactivating the tool.
-\imageMacro{QmitkSegmentation_IMG2DFastMarchingUsage.png,"2D Fast Marching Tool",3.01}
+\subsection org_mitk_views_segmentationUserManual2DFastMarchingTool 2D Fast Marching Tool
-Provides a fast marching based 2D interaction segmentation tool. You start with setting seedpoints in an image slice. Via several sliders you can
-adapt parameters and see the fast marching result instantly.
+\imageMacro{QmitkSegmentation_IMG2DFastMarchingUsage.png,"2D Fast Marching Tool",3.01}
-\subsection org_mitk_gui_qt_segmentationUserManualManualKringeling5 Interpolation
+Provides a fast marching based 2D interaction segmentation tool. You start with setting seed points in an image slice. Via several sliders you can adapt parameters and see the fast marching result instantly.
-Creating segmentations for modern CT volumes is very time-consuming, because structures of interest can easily cover a range of 50 or more slices.
-The Manual Segmentation View offers two helpful features for these cases:
+\subsection org_mitk_views_segmentationUserManualManualKringeling5 2D and 3D Interpolation
+Creating segmentations using 2D manual contouring for large image volumes may be very time-consuming, because structures of interest may cover a large range of slices.
+The segmentation view offers two helpful features to mitigate this drawback:
<ul>
-<li> <b>3D Interpolation</b>
-<li> <b>2D Interpolation</b>
+<li> 2D Interpolation
+<li> 3D Interpolation
</ul>
-<br>
-<b>The 3D interpolation</b> is activated by default when using the manual segmentation tools. That means if you start contouring, from the second contour onwards, the surface of the segmented area will be interpolated based on the given contour information.
-The interpolation works with all available manual tools. Please note that this is currently a pure mathematical interpolation, i.e. image intensity information is not taken into account. With each further contour the interpolation result will be improved,
-but the more contours you provide the longer the recalculation will take. To achieve an optimal interpolation result and in this way a most accurate segmentation you should try to describe the surface with sparse contours by segmenting in arbitrary
-oriented planes. The 3D interpolation is not meant to be used for parallel slice-wise segmentation.
-
-\imageMacro{QmitkSegmentation_3DInterpolationWrongRight.png,"3D Interpolation HowTo",16.00}
-
-You can accept the interpolation result by clicking the "Accept" - button below the tool buttons.
-In this case the 3D interpolation will be deactivated automatically so that the result can be postprocessed without any interpolation running in background. During recalculation the interpolated surface is blinking yellow/white. When the interpolation
-has finished the surface is shown yellow with a small opacity. Additional to the surface, black contours are shown in the 3D render window. They mark the positions of all the drawn contours which were used for the interpolation.
-You can navigate between the drawn contours by clicking on the „Position“ - Nodes in the datamanager which are located below the selected segmentation. If you don't want to see these nodes just unckeck the „Show Position Nodes“ Checkbox and these nodes will be hidden.
-If you want to delete a drawn contour we recommend to use the Erase-Tool since Redo/Undo is not yet working for 3D interpolation.
-The current state of the 3D interpolation can be saved accross application restart. Therefor just click on save project during the interpolation is active. After restarting the application and load your project you can click on "Reinit Interpolation" within the 3D interpolation GUI area.
-<br>
-<b>The 2D Interpolation</b> creates suggestions for a segmentation whenever you have a slice that
+The <b>2D Interpolation</b> creates suggestions for a segmentation whenever you have a slice that
<ul>
<li> has got neighboring slices with segmentations (these do not need to be direct neighbors but could also be a couple of slices away) AND
-<li> is completely clear of a manual segmentation -- i.e. there will be no suggestion if there is even only a single pixel of segmentation in the current slice.
+<li> is completely clear of a manual segmentation, i.e. there will be no suggestion if there is even only a single pixel of segmentation in the current slice.
</ul>
-Interpolated suggestions are displayed in a different way than manual segmentations are, until you "accept" them as part of the segmentation.
-To accept single slices, click the "Accept" button below the toolbox.
-If you have segmented a whole organ in every-x-slice, you may also review the interpolations and then accept all of them at once by clicking "... all slices".
+\imageMacro{QmitkSegmentation_2DInterpolation.png,"2D Interpolation Usage",3.01}
+
+Interpolated suggestions are displayed as outlines, until you confirm them as part of the segmentation.
+To confirm single slices, click the <i>Confirm for single slice</i> button below the toolbox. You may also review the interpolations visually and then accept all of them at once by selecting <i>Confirm for all slices</i>.
-\section org_mitk_gui_qt_segmentationUserManual3DSegmentationTools 3D Segmenation tools
+The <b>3D interpolation</b> creates suggestions for 3D segmentations. That means if you start contouring, from the second contour onwards, the surface of the segmented area will be interpolated based on the given contour information.
+The interpolation works with all available manual tools. Please note that this is currently a pure mathematical interpolation, i.e. image intensity information is not taken into account.
+With each further contour the interpolation result will be improved, but the more contours you provide the longer the recalculation will take.
+To achieve an optimal interpolation result and in this way a most accurate segmentation you should try to describe the surface with sparse contours by segmenting in arbitrary
+oriented planes. The 3D interpolation is not meant to be used for parallel slice-wise segmentation, but rather segmentations in i.e. the axial, coronal and sagittal plane.
-The 3D tools operate on the hole image and require usually a small amount of interaction like placing seed-points or specifying certain parameters. All 3D tools provide
-an immediate segmentation feedback, which is displayed as a transparent green overlay. For accepting a preview you have to press the "Comfirm" button of the selected tool.
-The following 3D tools are at your disposal:
+\imageMacro{QmitkSegmentation_3DInterpolationWrongRight.png,"3D Interpolation Usage",16.00}
-\subsection org_mitk_gui_qt_segmentationUserManual3DThresholdTool 3D Threshold tool
+You can accept the interpolation result by clicking the <i>Confirm</i>-button below the tool buttons.
+In this case the 3D interpolation will be deactivated automatically so that the result can be post-processed without any interpolation running in the background.
-The Thresholding tool simply applies a 3D threshold to the patient image. All pixels with values equal or above the selected threshold are labeled.
+Additional to the surface, black contours are shown in the 3D render window, which mark all the drawn contours used for the interpolation.
+You can navigate between the drawn contours by clicking on the corresponding <i>position</i> nodes in the data manager which are stored as sub-nodes of the selected segmentation.
+If you do not want to see these nodes just uncheck the <i>Show Position Nodes</i> checkbox and these nodes will be hidden.
+
+If you want to delete a drawn contour we recommend to use the Erase-Tool since Redo/Undo is not yet working for 3D interpolation.
+The current state of the 3D interpolation can be saved across application restart. For that, just click on save project during the interpolation is active.
+After restarting the application and load your project you can click on "Reinit Interpolation" within the 3D interpolation GUI area.
+
+
+\section org_mitk_views_segmentationUserManual3DSegmentationTools 3D Segmentation Tools
+
+The 3D tools operate on the whole image and require usually a small amount of interaction like placing seed-points or specifying certain parameters. All 3D tools provide
+an immediate segmentation feedback, which is displayed as a transparent green overlay. For accepting a preview you have to press the <i>Confirm</i> button of the selected tool.
+The following 3D tools are available:
+
+\subsection org_mitk_views_segmentationUserManual3DThresholdTool 3D Threshold Tool
+
+The thresholding tool simply applies a 3D threshold to the patient image. All pixels with values equal or above the selected threshold are labeled as part of the segmentation.
You can change the threshold by either moving the slider of setting a certain value in the spinbox.
\imageMacro{QmitkSegmentation_3DThresholdTool.png,"3D Threshold tool",10.00}
-\subsection org_mitk_gui_qt_segmentationUserManual3DULTool 3D Upper/Lower Threshold tool
+\subsection org_mitk_views_segmentationUserManual3DULTool 3D Upper/Lower Threshold Tool
The Upper/Lower Thresholding tool works similar to the simple 3D threshold tool but allows you to define an upper and lower threshold. All pixels with
-values within this threshold intervall will be labeled
+values within this threshold interval will be labeled as part of the segmentation.
\imageMacro{QmitkSegmentation_3DULThresholdTool.png,"3D Upper/Lower Threshold tool",10.00}
-\subsection org_mitk_gui_qt_segmentationUserManual3DOtsuTool 3D Otsu tool
+\subsection org_mitk_views_segmentationUserManual3DOtsuTool 3D Otsu Tool
The 3D Otsu tool provides a more sophisticated thresholding algorithm. It allows you to define a number of regions. Based on the image histogram the pixels will
-then divided into different regions. There more regions you define the longer will the calculation take.
+then be divided into different regions. The more regions you define the longer the calculation will take. You can select afterwards which of these regions you want to confirm as segmentation.
\imageMacro{QmitkSegmentation_3DOtsuTool.png,"3D Otsu tool",10.00}
-\subsection org_mitk_gui_qt_segmentationUserManual3DFMTool 3D Fast Marching tool
+\subsection org_mitk_views_segmentationUserManual3DFMTool 3D Fast Marching Tool
-The 3D Fast Marching tools works similar to the 2D pendant but on the hole image. Depending on you image's size the calculation will take some time.
-You can interactive set the parameters of the algorithm via the tool GUI.
+The 3D Fast Marching tool works similar to the 2D pendant but on the whole image. Depending on your image size the calculation might take some time.
+You can interactively set the parameters of the algorithm via the GUI. The resulting segmentation will be automatically updated.
\imageMacro{QmitkSegmentation_3DFMTool.png,"3D Fast Marching tool",10.00}
-\subsection org_mitk_gui_qt_segmentationUserManual3DRGTool 3D Region Growing tool
+\subsection org_mitk_views_segmentationUserManual3DRGTool 3D Region Growing Tool
-The 3D Region Growing tool works similar to the 2D pendant. At the beginning you have to place a seedpoint and define a threshold intervall. If you press
-"Run segmentation" a preview is calculated, if the "3D preview" box is checked you will also see the result in 3D. By moving the "Adapt region growing slider"
-you can interactively adapt the result to you image.
+The 3D Region Growing tool works similar to the 2D pendant. At the beginning you have to place a seedpoint and define a threshold interval. If you press
+<i>Run Segmentation</i> a preview is calculated. By moving the <i>Adapt region growing</i> slider you can interactively adapt the segmentation result.
\imageMacro{QmitkSegmentation_3DRGTool.png,"3D Region Growing tool",10.00}
-+\subsection org_mitk_gui_qt_segmentationUserManual3DWatershedTool 3D Watershed tool
+\subsection org_mitk_views_segmentationUserManual3DWatershedTool 3D Watershed Tool
-This tool provides a watershed based segmentation algorithm.
+This tool provides a watershed based segmentation algorithm. For a detailed explanation of the parameters level and threshold, please be referred to https://itk.org/Doxygen/html/classitk_1_1WatershedImageFilter.html .
+Remark: The tool is (due to its implementation) faster if you use lower levels. So in doubt you should start with high levels (supposed to undersegment) and then lower the levels until you are happy.
\imageMacro{QmitkSegmentation_3DWatershedTool.png,"3D Watershed tool",10.00}
-\subsection org_mitk_gui_qt_segmentationUserManualPickingTool Picking tool
+\subsection org_mitk_views_segmentationUserManualPickingTool Picking Tool
-The Picking tool allows you to select islands within your segmentation. This is especially usefull if e.g. a thresholding delivered your several areas within
+The Picking tool allows you to select islands within your segmentation. This is especially useful if e.g. a thresholding provided you with several areas within
your image but you are just interested in one special region.
\imageMacro{QmitkSegmentation_PickingTool.png,"Picking tool",10.00}
-\section org_mitk_gui_qt_segmentationUserManualPostprocessing Things you can do with segmentations
+\section org_mitk_views_segmentationUserManualPostprocessing Additional things you can do with segmentations
-As mentioned in the introduction, segmentations are never an end in themselves.
-Consequently, the Segmentation view adds a couple of "post-processing" %actions to the Data Manager.
-These %actions are accessible through the context-menu of segmentations in Data Manager's list view
+Segmentations are never an end in themselves. Consequently, the segmentation view adds a couple of "post-processing" actions, accessible through the context-menu of the data manager.
\imageMacro{QmitkSegmentation_IMGDataManagerContextMenu.png,"Context menu items for segmentations.",10.58}
<ul>
-<li> <b>Create polygon %model</b> applies the marching cubes algorithms to the segmentation. This polygon %model can be used for visualization in 3D or other things such as stereolithography (3D printing).
-<li> <b>Create smoothed polygon %model</b> uses smoothing in addition to the marching cubes algorithms, which creates models that do not follow the exact outlines of the segmentation, but look smoother.
+<li> <b>Create polygon %model</b> applies the marching cubes algorithm to the segmentation. This polygon %model can be used for visualization in 3D or other applications such as stereolithography (3D printing).
+<li> <b>Create smoothed polygon %model</b> uses smoothing in addition to the marching cubes algorithm, which creates models that do not follow the exact outlines of the segmentation, but look smoother.
<li> <b>Autocrop</b> can save memory. Manual segmentations have the same extent as the patient image, even if the segmentation comprises only a small sub-volume. This invisible and meaningless margin is removed by autocropping.
</ul>
-\section QmitkSegmentation_UserManualSurfaceMasking Surface Masking
-
-You can use the surface masking tool to create binary images from a surface which
-is used used as a mask on an image. This task is demonstrated below:
-\imageMacro{QmitkSegmentation_FromSurfaceBefore.png,"Load an image and a surface.",16.00}
+\section org_mitk_views_segmentationof3DTImages Segmentation of 3D+t images
-Select the image and the surface in the corresponding drop-down boxes (both are selected automatically if there is just one image and one surface)
+For segmentation of 3D+t images, some tools give you the option to choose between creating dynamic and static masks.
+<ul>
+<li> Dynamic masks can be created on each time frame individually.
+<li> Static masks will be defined on one time frame and will be the same for all other time frames.
+</ul>
+In general, segmentation is applied on the time frame that is selected when execution is performed. If you alter the time frame, the segmentation preview is adapted.
-\imageMacro{QmitkSegmentation_FromSurfaceAfter.png,"Create segmentation from surface",16.00}
-After clicking "Create segmentation from surface" the newly created binary image is inserted in the DataManager and can be used for further processing
-\section org_mitk_gui_qt_segmentationUserManualTechnicalDetail Technical Information for Developers
+\section org_mitk_views_segmentationUserManualTechnicalDetail Technical Information for Developers
For technical specifications see \subpage QmitkSegmentationTechnicalPage and for information on the extensions of the tools system \subpage toolextensions .
*/
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationPlugin_Overview.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationPlugin_Overview.png
new file mode 100644
index 0000000000..b4c6f19548
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationPlugin_Overview.png differ
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationPreferences.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationPreferences.png
new file mode 100644
index 0000000000..f86a955ee4
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationPreferences.png differ
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_2DInterpolation.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_2DInterpolation.png
new file mode 100644
index 0000000000..aace28a35b
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_2DInterpolation.png differ
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DFMTool.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DFMTool.png
index d46344f413..0058ece1c4 100644
Binary files a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DFMTool.png and b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DFMTool.png differ
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DOtsuTool.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DOtsuTool.png
index 6948b817a2..97fbb89cb3 100644
Binary files a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DOtsuTool.png and b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DOtsuTool.png differ
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DRGTool.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DRGTool.png
index 9ff28155c9..e3f0257cf1 100644
Binary files a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DRGTool.png and b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DRGTool.png differ
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DThresholdTool.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DThresholdTool.png
index 08402efa92..eddaa1654c 100644
Binary files a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DThresholdTool.png and b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DThresholdTool.png differ
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DULThresholdTool.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DULThresholdTool.png
index e461f1298b..a4ecd5aba4 100644
Binary files a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DULThresholdTool.png and b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_3DULThresholdTool.png differ
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGCorrectionActions.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGCorrectionActions.png
index 648dc52668..52a07f399a 100644
Binary files a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGCorrectionActions.png and b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGCorrectionActions.png differ
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGCorrectionActions.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGCorrectionActionsx.png
similarity index 100%
copy from Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGCorrectionActions.png
copy to Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGCorrectionActionsx.png
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGDataManagerContextMenu.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGDataManagerContextMenu.png
index b80ada6333..1076624c71 100644
Binary files a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGDataManagerContextMenu.png and b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGDataManagerContextMenu.png differ
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGSelection.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGSelection.png
deleted file mode 100644
index 081eb6b4a9..0000000000
Binary files a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGSelection.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_PickingTool.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_PickingTool.png
index 9d9bad348f..78ccccd56f 100644
Binary files a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_PickingTool.png and b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_PickingTool.png differ
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_ToolOverview.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_ToolOverview.png
index a0be9911e0..69d020b069 100644
Binary files a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_ToolOverview.png and b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_ToolOverview.png differ
diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp
index 299883d318..d608a7078f 100644
--- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp
+++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp
@@ -1,903 +1,907 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include <QObject>
#include "mitkProperties.h"
#include "mitkSegTool2D.h"
#include "mitkStatusBar.h"
#include "QmitkNewSegmentationDialog.h"
#include <QmitkSegmentationOrganNamesHandling.cpp>
#include <QMessageBox>
#include <berryIWorkbenchPage.h>
#include "QmitkSegmentationView.h"
#include <mitkSurfaceToImageFilter.h>
#include "mitkVtkResliceInterpolationProperty.h"
#include "mitkApplicationCursor.h"
#include "mitkSegmentationObjectFactory.h"
#include "mitkPluginActivator.h"
#include "mitkCameraController.h"
#include "mitkLabelSetImage.h"
#include "mitkImageTimeSelector.h"
#include "mitkNodePredicateSubGeometry.h"
#include <QmitkRenderWindow.h>
#include "usModuleResource.h"
#include "usModuleResourceStream.h"
//micro service to get the ToolManager instance
#include "mitkToolManagerProvider.h"
#include <mitkWorkbenchUtil.h>
#include <regex>
const std::string QmitkSegmentationView::VIEW_ID = "org.mitk.views.segmentation";
QmitkSegmentationView::QmitkSegmentationView()
: m_Parent(nullptr)
, m_Controls(nullptr)
, m_RenderWindowPart(nullptr)
, m_MouseCursorSet(false)
, m_DataSelectionChanged(false)
{
mitk::TNodePredicateDataType<mitk::Image>::Pointer isImage = mitk::TNodePredicateDataType<mitk::Image>::New();
mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage");
mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage");
mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("OdfImage");
auto isSegment = mitk::NodePredicateDataType::New("Segment");
mitk::NodePredicateOr::Pointer validImages = mitk::NodePredicateOr::New();
validImages->AddPredicate(mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isSegment)));
validImages->AddPredicate(isDwi);
validImages->AddPredicate(isDti);
validImages->AddPredicate(isOdf);
m_IsNotAHelperObject = mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object", mitk::BoolProperty::New(true)));
m_IsOfTypeImagePredicate = mitk::NodePredicateAnd::New(validImages, m_IsNotAHelperObject);
mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true));
mitk::NodePredicateNot::Pointer isNotBinaryPredicate = mitk::NodePredicateNot::New(isBinaryPredicate);
mitk::NodePredicateAnd::Pointer isABinaryImagePredicate = mitk::NodePredicateAnd::New(m_IsOfTypeImagePredicate, isBinaryPredicate);
mitk::NodePredicateAnd::Pointer isNotABinaryImagePredicate = mitk::NodePredicateAnd::New(m_IsOfTypeImagePredicate, isNotBinaryPredicate);
- m_IsASegmentationImagePredicate = mitk::NodePredicateOr::New(isABinaryImagePredicate, mitk::TNodePredicateDataType<mitk::LabelSetImage>::New());
- m_IsAPatientImagePredicate = mitk::NodePredicateAnd::New(isNotABinaryImagePredicate, mitk::NodePredicateNot::New(mitk::TNodePredicateDataType<mitk::LabelSetImage>::New()));
+ auto isMLImageType = mitk::TNodePredicateDataType<mitk::LabelSetImage>::New();
+ mitk::NodePredicateAnd::Pointer isAMLImagePredicate = mitk::NodePredicateAnd::New(isMLImageType, m_IsNotAHelperObject);
+ mitk::NodePredicateAnd::Pointer isNotAMLImagePredicate = mitk::NodePredicateAnd::New(mitk::NodePredicateNot::New(isMLImageType), m_IsNotAHelperObject);
+
+ m_IsASegmentationImagePredicate = mitk::NodePredicateOr::New(isABinaryImagePredicate, isAMLImagePredicate);
+ m_IsAPatientImagePredicate = mitk::NodePredicateAnd::New(isNotABinaryImagePredicate, isNotAMLImagePredicate);
}
QmitkSegmentationView::~QmitkSegmentationView()
{
if (m_Controls)
{
SetToolSelectionBoxesEnabled(false);
// deactivate all tools
mitk::ToolManagerProvider::GetInstance()->GetToolManager()->ActivateTool(-1);
// removing all observers
for (NodeTagMapType::iterator dataIter = m_WorkingDataObserverTags.begin(); dataIter != m_WorkingDataObserverTags.end(); ++dataIter)
{
(*dataIter).first->GetProperty("visible")->RemoveObserver((*dataIter).second);
}
m_WorkingDataObserverTags.clear();
mitk::RenderingManager::GetInstance()->RemoveObserver(m_RenderingManagerObserverTag);
ctkPluginContext* context = mitk::PluginActivator::getContext();
ctkServiceReference ppmRef = context->getServiceReference<mitk::PlanePositionManagerService>();
mitk::PlanePositionManagerService* service = context->getService<mitk::PlanePositionManagerService>(ppmRef);
service->RemoveAllPlanePositions();
context->ungetService(ppmRef);
SetToolManagerSelection(nullptr, nullptr);
}
delete m_Controls;
}
void QmitkSegmentationView::NewNodeObjectsGenerated(mitk::ToolManager::DataVectorType* nodes)
{
if (!nodes) return;
mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager();
if (!toolManager) return;
for (mitk::ToolManager::DataVectorType::iterator iter = nodes->begin(); iter != nodes->end(); ++iter)
{
this->FireNodeSelected( *iter );
// only last iteration meaningful, multiple generated objects are not taken into account here
}
}
void QmitkSegmentationView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart)
{
if (m_RenderWindowPart != renderWindowPart)
{
m_RenderWindowPart = renderWindowPart;
}
if (m_Parent)
{
m_Parent->setEnabled(true);
}
// tell the interpolation about tool manager, data storage and render window part
if (m_Controls)
{
mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager();
m_Controls->m_SlicesInterpolator->SetDataStorage(this->GetDataStorage());
QList<mitk::SliceNavigationController*> controllers;
controllers.push_back(renderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController());
controllers.push_back(renderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController());
controllers.push_back(renderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController());
m_Controls->m_SlicesInterpolator->Initialize(toolManager, controllers);
}
}
void QmitkSegmentationView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* /*renderWindowPart*/)
{
m_RenderWindowPart = nullptr;
if (m_Parent)
{
m_Parent->setEnabled(false);
}
}
void QmitkSegmentationView::OnPreferencesChanged(const berry::IBerryPreferences* prefs)
{
if (m_Controls != nullptr)
{
bool slimView = prefs->GetBool("slim view", false);
m_Controls->m_ManualToolSelectionBox2D->SetShowNames(!slimView);
m_Controls->m_ManualToolSelectionBox3D->SetShowNames(!slimView);
m_Controls->btnNewSegmentation->setToolButtonStyle(slimView
? Qt::ToolButtonIconOnly
: Qt::ToolButtonTextOnly);
}
auto autoSelectionEnabled = prefs->GetBool("auto selection", true);
m_Controls->patImageSelector->SetAutoSelectNewNodes(autoSelectionEnabled);
m_Controls->segImageSelector->SetAutoSelectNewNodes(autoSelectionEnabled);
this->ForceDisplayPreferencesUponAllImages();
}
void QmitkSegmentationView::CreateNewSegmentation()
{
mitk::DataNode::Pointer node = mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetReferenceData(0);
if (node.IsNotNull())
{
mitk::Image::ConstPointer referenceImage = dynamic_cast<mitk::Image*>(node->GetData());
if (referenceImage.IsNotNull())
{
if (referenceImage->GetDimension() > 1)
{
// ask about the name and organ type of the new segmentation
QmitkNewSegmentationDialog* dialog = new QmitkNewSegmentationDialog(m_Parent); // needs a QWidget as parent, "this" is not QWidget
QStringList organColors = mitk::OrganNamesHandling::GetDefaultOrganColorString();;
dialog->SetSuggestionList(organColors);
int dialogReturnValue = dialog->exec();
if (dialogReturnValue == QDialog::Rejected)
{
// user clicked cancel or pressed Esc or something similar
return;
}
const auto currentTimePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint();
unsigned int imageTimeStep = 0;
if (referenceImage->GetTimeGeometry()->IsValidTimePoint(currentTimePoint))
{
imageTimeStep = referenceImage->GetTimeGeometry()->TimePointToTimeStep(currentTimePoint);
}
auto segTemplateImage = referenceImage;
if (referenceImage->GetDimension() > 3)
{
auto result = QMessageBox::question(m_Parent, tr("Generate a static mask?"),tr("The selected image has multiple time steps. You can either generate a simple/static masks resembling the geometry of the first timestep of the image. Or you can generate a dynamic mask that equals the selected image in geometry and number of timesteps; thus a dynamic mask can change over time (e.g. according to the image)."), tr("Yes, generate a static mask"), tr("No, generate a dynamic mask"), QString(), 0,0);
if (result == 0)
{
auto selector = mitk::ImageTimeSelector::New();
selector->SetInput(referenceImage);
selector->SetTimeNr(0);
selector->Update();
const auto refTimeGeometry = referenceImage->GetTimeGeometry();
auto newTimeGeometry = mitk::ProportionalTimeGeometry::New();
newTimeGeometry->SetFirstTimePoint(refTimeGeometry->GetMinimumTimePoint());
newTimeGeometry->SetStepDuration(refTimeGeometry->GetMaximumTimePoint() - refTimeGeometry->GetMinimumTimePoint());
mitk::Image::Pointer newImage = selector->GetOutput();
newTimeGeometry->SetTimeStepGeometry(referenceImage->GetGeometry(imageTimeStep), 0);
newImage->SetTimeGeometry(newTimeGeometry);
segTemplateImage = newImage;
}
}
// ask the user about an organ type and name, add this information to the image's (!) propertylist
// create a new image of the same dimensions and smallest possible pixel type
mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager();
mitk::Tool* firstTool = toolManager->GetToolById(0);
if (firstTool)
{
try
{
std::string newNodeName = dialog->GetSegmentationName().toStdString();
if (newNodeName.empty())
{
newNodeName = "no_name";
}
mitk::DataNode::Pointer emptySegmentation = firstTool->CreateEmptySegmentationNode(segTemplateImage, newNodeName, dialog->GetColor());
// initialize showVolume to false to prevent recalculating the volume while working on the segmentation
emptySegmentation->SetProperty("showVolume", mitk::BoolProperty::New(false));
if (!emptySegmentation)
{
return; // could be aborted by user
}
mitk::OrganNamesHandling::UpdateOrganList(organColors, dialog->GetSegmentationName(), dialog->GetColor());
// escape ';' here (replace by '\;'), see longer comment above
QString stringForStorage = organColors.replaceInStrings(";", "\\;").join(";");
MITK_DEBUG << "Will store: " << stringForStorage;
this->GetPreferences()->Put("Organ-Color-List", stringForStorage);
this->GetPreferences()->Flush();
if (mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetWorkingData(0))
{
mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetWorkingData(0)->SetSelected(false);
}
emptySegmentation->SetSelected(true);
this->GetDataStorage()->Add(emptySegmentation, node); // add as a child, because the segmentation "derives" from the original
m_Controls->segImageSelector->SetCurrentSelectedNode(emptySegmentation);
mitk::RenderingManager::GetInstance()->InitializeViews(referenceImage->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true);
mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetTime()->SetPos(imageTimeStep);
}
catch (const std::bad_alloc&)
{
QMessageBox::warning(nullptr, tr("Create new segmentation"), tr("Could not allocate memory for new segmentation"));
}
}
}
else
{
QMessageBox::information(nullptr, tr("Segmentation"), tr("Segmentation is currently not supported for 2D images"));
}
}
}
else
{
MITK_ERROR << "'Create new segmentation' button should never be clickable unless a patient image is selected...";
}
}
void QmitkSegmentationView::OnVisiblePropertyChanged()
{
this->CheckRenderingState();
}
void QmitkSegmentationView::NodeAdded(const mitk::DataNode *node)
{
if (!m_IsASegmentationImagePredicate->CheckNode(node))
{
return;
}
itk::SimpleMemberCommand<QmitkSegmentationView>::Pointer command = itk::SimpleMemberCommand<QmitkSegmentationView>::New();
command->SetCallbackFunction(this, &QmitkSegmentationView::OnVisiblePropertyChanged);
m_WorkingDataObserverTags.insert(std::pair<mitk::DataNode*, unsigned long>(const_cast<mitk::DataNode*>(node), node->GetProperty("visible")->AddObserver(itk::ModifiedEvent(), command)));
ApplyDisplayOptions(const_cast<mitk::DataNode*>(node));
}
void QmitkSegmentationView::NodeRemoved(const mitk::DataNode* node)
{
if (m_IsASegmentationImagePredicate->CheckNode(node))
{
//First of all remove all possible contour markers of the segmentation
mitk::DataStorage::SetOfObjects::ConstPointer allContourMarkers = this->GetDataStorage()->GetDerivations(node, mitk::NodePredicateProperty::New("isContourMarker", mitk::BoolProperty::New(true)));
ctkPluginContext* context = mitk::PluginActivator::getContext();
ctkServiceReference ppmRef = context->getServiceReference<mitk::PlanePositionManagerService>();
mitk::PlanePositionManagerService* service = context->getService<mitk::PlanePositionManagerService>(ppmRef);
for (mitk::DataStorage::SetOfObjects::ConstIterator it = allContourMarkers->Begin(); it != allContourMarkers->End(); ++it)
{
std::string nodeName = node->GetName();
unsigned int t = nodeName.find_last_of(" ");
unsigned int id = atof(nodeName.substr(t + 1).c_str()) - 1;
service->RemovePlanePosition(id);
this->GetDataStorage()->Remove(it->Value());
}
context->ungetService(ppmRef);
service = nullptr;
if ((mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetWorkingData(0) == node) && m_Controls->patImageSelector->GetSelectedNode().IsNotNull())
{
this->SetToolManagerSelection(mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetReferenceData(0), nullptr);
this->UpdateWarningLabel(tr("Select or create a segmentation"));
}
mitk::Image* image = dynamic_cast<mitk::Image*>(node->GetData());
mitk::SurfaceInterpolationController::GetInstance()->RemoveInterpolationSession(image);
}
mitk::DataNode* tempNode = const_cast<mitk::DataNode*>(node);
//Remove observer if one was registered
auto finding = m_WorkingDataObserverTags.find(tempNode);
if (finding != m_WorkingDataObserverTags.end())
{
node->GetProperty("visible")->RemoveObserver(m_WorkingDataObserverTags[tempNode]);
m_WorkingDataObserverTags.erase(tempNode);
}
}
void QmitkSegmentationView::OnPatientSelectionChanged(QList<mitk::DataNode::Pointer> nodes)
{
if(! nodes.empty())
{
this->UpdateWarningLabel("");
auto node = nodes.first();
auto segPredicate = mitk::NodePredicateAnd::New(m_IsASegmentationImagePredicate.GetPointer(), mitk::NodePredicateSubGeometry::New(node->GetData()->GetGeometry()));
m_Controls->segImageSelector->SetNodePredicate(segPredicate);
mitk::DataNode* segNode = m_Controls->segImageSelector->GetSelectedNode();
this->SetToolManagerSelection(node, segNode);
if (segNode)
{
//Doing this we can assure that the segmentation is always visible if the segmentation and the patient image are
//loaded separately
int layer(10);
node->GetIntProperty("layer", layer);
layer++;
segNode->SetProperty("layer", mitk::IntProperty::New(layer));
this->CheckRenderingState();
}
else
{
this->SetToolSelectionBoxesEnabled( false );
this->UpdateWarningLabel(tr("Select or create a segmentation"));
}
}
else
{
m_Controls->segImageSelector->SetNodePredicate(m_IsASegmentationImagePredicate);
this->UpdateWarningLabel(tr("Please select an image!"));
this->SetToolSelectionBoxesEnabled( false );
}
}
void QmitkSegmentationView::OnSegmentationSelectionChanged(QList<mitk::DataNode::Pointer> nodes)
{
if (nodes.empty())
{
this->UpdateWarningLabel(tr("Select or create a segmentation"));
this->SetToolSelectionBoxesEnabled( false );
return;
}
auto refNode = m_Controls->patImageSelector->GetSelectedNode();
auto segNode = nodes.front();
if (!refNode)
{
this->UpdateWarningLabel(tr("Please select the matching patient image!"));
this->SetToolSelectionBoxesEnabled(false);
this->SetToolManagerSelection(nullptr, segNode);
return;
}
this->CheckRenderingState();
if ( m_Controls->lblSegmentationWarnings->isVisible()) // "this->CheckRenderingState()" caused a warning. we do not need to go any further
return;
this->SetToolManagerSelection(refNode, segNode);
if (segNode)
{
//Doing this we can assure that the segmenation is always visible if the segmentation and the patient image are
//loaded separately
int layer(10);
refNode->GetIntProperty("layer", layer);
layer++;
segNode->SetProperty("layer", mitk::IntProperty::New(layer));
}
else
{
this->SetToolSelectionBoxesEnabled(false);
this->UpdateWarningLabel(tr("Select or create a segmentation"));
}
mitk::IRenderWindowPart* renderWindowPart = this->GetRenderWindowPart();
if (!renderWindowPart || !segNode->IsVisible(renderWindowPart->GetQmitkRenderWindow("axial")->GetRenderer()))
{
this->UpdateWarningLabel(tr("The selected segmentation is currently not visible!"));
this->SetToolSelectionBoxesEnabled( false );
}
}
void QmitkSegmentationView::OnShowMarkerNodes (bool state)
{
mitk::SegTool2D::Pointer manualSegmentationTool;
unsigned int numberOfExistingTools = mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetTools().size();
for(unsigned int i = 0; i < numberOfExistingTools; i++)
{
manualSegmentationTool = dynamic_cast<mitk::SegTool2D*>(mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetToolById(i));
if (manualSegmentationTool)
{
if(state == true)
{
manualSegmentationTool->SetShowMarkerNodes( true );
}
else
{
manualSegmentationTool->SetShowMarkerNodes( false );
}
}
}
}
void QmitkSegmentationView::OnContourMarkerSelected(const mitk::DataNode *node)
{
QmitkRenderWindow* selectedRenderWindow = nullptr;
QmitkRenderWindow* axialRenderWindow = GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindow("axial");
QmitkRenderWindow* sagittalRenderWindow = GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindow("sagittal");
QmitkRenderWindow* coronalRenderWindow = GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindow("coronal");
QmitkRenderWindow* _3DRenderWindow = GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindow("3d");
bool PlanarFigureInitializedWindow = false;
// find initialized renderwindow
if (node->GetBoolProperty("PlanarFigureInitializedWindow",
PlanarFigureInitializedWindow, axialRenderWindow->GetRenderer()))
{
selectedRenderWindow = axialRenderWindow;
}
if (!selectedRenderWindow && node->GetBoolProperty(
"PlanarFigureInitializedWindow", PlanarFigureInitializedWindow,
sagittalRenderWindow->GetRenderer()))
{
selectedRenderWindow = sagittalRenderWindow;
}
if (!selectedRenderWindow && node->GetBoolProperty(
"PlanarFigureInitializedWindow", PlanarFigureInitializedWindow,
coronalRenderWindow->GetRenderer()))
{
selectedRenderWindow = coronalRenderWindow;
}
if (!selectedRenderWindow && node->GetBoolProperty(
"PlanarFigureInitializedWindow", PlanarFigureInitializedWindow,
_3DRenderWindow->GetRenderer()))
{
selectedRenderWindow = _3DRenderWindow;
}
// make node visible
if (selectedRenderWindow)
{
std::string nodeName = node->GetName();
unsigned int t = nodeName.find_last_of(" ");
unsigned int id = atof(nodeName.substr(t+1).c_str())-1;
{
ctkPluginContext* context = mitk::PluginActivator::getContext();
ctkServiceReference ppmRef = context->getServiceReference<mitk::PlanePositionManagerService>();
mitk::PlanePositionManagerService* service = context->getService<mitk::PlanePositionManagerService>(ppmRef);
selectedRenderWindow->GetSliceNavigationController()->ExecuteOperation(service->GetPlanePosition(id));
context->ungetService(ppmRef);
}
selectedRenderWindow->GetRenderer()->GetCameraController()->Fit();
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
}
void QmitkSegmentationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList<mitk::DataNode::Pointer> &nodes)
{
if (nodes.size() != 0)
{
std::string markerName = "Position";
unsigned int numberOfNodes = nodes.size();
std::string nodeName = nodes.at(0)->GetName();
if ((numberOfNodes == 1) && (nodeName.find(markerName) == 0))
{
this->OnContourMarkerSelected(nodes.at(0));
return;
}
}
}
void QmitkSegmentationView::OnTabWidgetChanged(int id)
{
//always disable tools on tab changed
mitk::ToolManagerProvider::GetInstance()->GetToolManager()->ActivateTool(-1);
//2D Tab ID = 0
//3D Tab ID = 1
if (id == 0)
{
//Hide 3D selection box, show 2D selection box
m_Controls->m_ManualToolSelectionBox3D->hide();
m_Controls->m_ManualToolSelectionBox2D->show();
//Deactivate possible active tool
//TODO Remove possible visible interpolations -> Maybe changes in SlicesInterpolator
}
else
{
//Hide 3D selection box, show 2D selection box
m_Controls->m_ManualToolSelectionBox2D->hide();
m_Controls->m_ManualToolSelectionBox3D->show();
//Deactivate possible active tool
}
}
void QmitkSegmentationView::SetToolManagerSelection(mitk::DataNode* referenceData, mitk::DataNode* workingData)
{
// called as a result of new BlueBerry selections
// tells the ToolManager for manual segmentation about new selections
// updates GUI information about what the user should select
mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager();
toolManager->SetReferenceData(const_cast<mitk::DataNode*>(referenceData));
toolManager->SetWorkingData(const_cast<mitk::DataNode*>(workingData));
m_Controls->btnNewSegmentation->setEnabled(referenceData != nullptr);
}
void QmitkSegmentationView::ForceDisplayPreferencesUponAllImages()
{
if (!m_Parent)
{
return;
}
// check all images and segmentations in DataStorage:
// (items in brackets are implicitly done by previous steps)
// 1.
// if a reference image is selected,
// show the reference image
// and hide all other images (orignal and segmentation),
// (and hide all segmentations of the other original images)
// and show all the reference's segmentations
// if no reference image is selected, do do nothing
//
// 2.
// if a segmentation is selected,
// show it
// (and hide all all its siblings (childs of the same parent, incl, nullptr parent))
// if no segmentation is selected, do nothing
if (!m_Controls)
{
return; // might happen on initialization (preferences loaded)
}
mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager();
mitk::DataNode::Pointer referenceData = toolManager->GetReferenceData(0);
mitk::DataNode::Pointer workingData = toolManager->GetWorkingData(0);
// 1.
if (referenceData.IsNotNull())
{
// iterate all images
mitk::DataStorage::SetOfObjects::ConstPointer allImages = this->GetDataStorage()->GetSubset(m_IsASegmentationImagePredicate);
for ( mitk::DataStorage::SetOfObjects::const_iterator iter = allImages->begin(); iter != allImages->end(); ++iter)
{
mitk::DataNode* node = *iter;
// apply display preferences
ApplyDisplayOptions(node);
// set visibility
node->SetVisibility(node == referenceData);
}
}
// 2.
if (workingData.IsNotNull())
workingData->SetVisibility(true);
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void QmitkSegmentationView::ApplyDisplayOptions(mitk::DataNode* node)
{
if (!node)
{
return;
}
mitk::BoolProperty::Pointer drawOutline = mitk::BoolProperty::New(GetPreferences()->GetBool("draw outline", true));
mitk::BoolProperty::Pointer volumeRendering = mitk::BoolProperty::New(GetPreferences()->GetBool("volume rendering", false));
mitk::LabelSetImage* labelSetImage = dynamic_cast<mitk::LabelSetImage*>(node->GetData());
if (nullptr != labelSetImage)
{
// node is actually a multi label segmentation,
// but its outline property can be set in the 'single label' segmentation preference page as well
node->SetProperty("labelset.contour.active", drawOutline);
//node->SetProperty("opacity", mitk::FloatProperty::New(drawOutline->GetValue() ? 1.0f : 0.3f));
node->SetProperty("volumerendering", volumeRendering);
// force render window update to show outline
node->GetData()->Modified();
}
else
{
// node is a 'single label' segmentation
bool isBinary = false;
node->GetBoolProperty("binary", isBinary);
if (isBinary)
{
node->SetProperty("outline binary", drawOutline);
node->SetProperty("outline width", mitk::FloatProperty::New(2.0));
//node->SetProperty("opacity", mitk::FloatProperty::New(drawOutline->GetValue() ? 1.0f : 0.3f));
node->SetProperty("volumerendering", volumeRendering);
// force render window update to show outline
node->GetData()->Modified();
}
}
}
void QmitkSegmentationView::CheckRenderingState()
{
mitk::IRenderWindowPart* renderWindowPart = this->GetRenderWindowPart();
mitk::DataNode* workingNode = m_Controls->segImageSelector->GetSelectedNode();
if (!workingNode)
{
this->SetToolSelectionBoxesEnabled(false);
this->UpdateWarningLabel(tr("Select or create a segmentation"));
return;
}
bool selectedNodeIsVisible = renderWindowPart && workingNode->IsVisible(renderWindowPart->GetQmitkRenderWindow("axial")->GetRenderer());
if (!selectedNodeIsVisible)
{
this->SetToolSelectionBoxesEnabled(false);
this->UpdateWarningLabel(tr("The selected segmentation is currently not visible!"));
return;
}
/*
* Here we check whether the geometry of the selected segmentation image if aligned with the worldgeometry
* At the moment it is not supported to use a geometry different from the selected image for reslicing.
* For further information see Bug 16063
*/
const mitk::BaseGeometry* worldGeo = this->GetRenderWindowPart()->GetQmitkRenderWindow("3d")->GetSliceNavigationController()->GetCurrentGeometry3D();
if (workingNode && worldGeo)
{
const mitk::BaseGeometry* workingNodeGeo = workingNode->GetData()->GetGeometry();
const mitk::BaseGeometry* worldGeo = this->GetRenderWindowPart()->GetQmitkRenderWindow("3d")->GetSliceNavigationController()->GetCurrentGeometry3D();
if (mitk::Equal(*workingNodeGeo->GetBoundingBox(), *worldGeo->GetBoundingBox(), mitk::eps, true))
{
this->SetToolManagerSelection(m_Controls->patImageSelector->GetSelectedNode(), workingNode);
this->SetToolSelectionBoxesEnabled(true);
this->UpdateWarningLabel("");
return;
}
}
this->SetToolManagerSelection(m_Controls->patImageSelector->GetSelectedNode(), nullptr);
this->SetToolSelectionBoxesEnabled(false);
this->UpdateWarningLabel(tr("Please perform a reinit on the segmentation image!"));
}
void QmitkSegmentationView::UpdateWarningLabel(QString text)
{
if (text.size() == 0)
m_Controls->lblSegmentationWarnings->hide();
else
m_Controls->lblSegmentationWarnings->show();
m_Controls->lblSegmentationWarnings->setText("<font color=\"red\">" + text + "</font>");
}
void QmitkSegmentationView::CreateQtPartControl(QWidget* parent)
{
// setup the basic GUI of this view
m_Parent = parent;
m_Controls = new Ui::QmitkSegmentationControls;
m_Controls->setupUi(parent);
m_Controls->patImageSelector->SetDataStorage(GetDataStorage());
m_Controls->patImageSelector->SetNodePredicate(m_IsAPatientImagePredicate);
m_Controls->patImageSelector->SetSelectionIsOptional(false);
m_Controls->patImageSelector->SetInvalidInfo("Select an image.");
m_Controls->patImageSelector->SetPopUpTitel("Select an image.");
m_Controls->patImageSelector->SetPopUpHint("Select an image that should be used to define the geometry and bounds of the segmentation.");
UpdateWarningLabel(tr("Please select an image"));
if (m_Controls->patImageSelector->GetSelectedNode().IsNotNull())
{
UpdateWarningLabel(tr("Select or create a new segmentation"));
}
m_Controls->segImageSelector->SetDataStorage(GetDataStorage());
m_Controls->segImageSelector->SetNodePredicate(m_IsASegmentationImagePredicate);
m_Controls->segImageSelector->SetSelectionIsOptional(false);
m_Controls->segImageSelector->SetInvalidInfo("Select a segmentation.");
m_Controls->segImageSelector->SetPopUpTitel("Select a segmentation.");
m_Controls->segImageSelector->SetPopUpHint("Select a segmentation that should be modified. Only segmentation with the same geometry and within the bounds of the reference image are selected.");
if (m_Controls->segImageSelector->GetSelectedNode().IsNotNull())
{
UpdateWarningLabel("");
}
mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager();
assert(toolManager);
toolManager->SetDataStorage(*(GetDataStorage()));
toolManager->InitializeTools();
QString segTools2D = tr("Add Subtract Correction Paint Wipe 'Region Growing' Fill Erase 'Live Wire' '2D Fast Marching'");
QString segTools3D = tr("Threshold 'UL Threshold' Otsu 'Fast Marching 3D' 'Region Growing 3D' Watershed Picking");
std::regex extSegTool2DRegEx("SegTool2D$");
std::regex extSegTool3DRegEx("SegTool3D$");
auto tools = toolManager->GetTools();
for (const auto &tool : tools)
{
if (std::regex_search(tool->GetNameOfClass(), extSegTool2DRegEx))
{
segTools2D.append(QString(" '%1'").arg(tool->GetName()));
}
else if (std::regex_search(tool->GetNameOfClass(), extSegTool3DRegEx))
{
segTools3D.append(QString(" '%1'").arg(tool->GetName()));
}
}
// all part of open source MITK
m_Controls->m_ManualToolSelectionBox2D->setEnabled(true);
m_Controls->m_ManualToolSelectionBox2D->SetGenerateAccelerators(true);
m_Controls->m_ManualToolSelectionBox2D->SetToolGUIArea(m_Controls->m_ManualToolGUIContainer2D);
m_Controls->m_ManualToolSelectionBox2D->SetDisplayedToolGroups(segTools2D.toStdString());
m_Controls->m_ManualToolSelectionBox2D->SetLayoutColumns(3);
m_Controls->m_ManualToolSelectionBox2D->SetEnabledMode(QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible);
connect(m_Controls->m_ManualToolSelectionBox2D, &QmitkToolSelectionBox::ToolSelected, this, &QmitkSegmentationView::OnManualTool2DSelected);
//setup 3D Tools
m_Controls->m_ManualToolSelectionBox3D->setEnabled(true);
m_Controls->m_ManualToolSelectionBox3D->SetGenerateAccelerators(true);
m_Controls->m_ManualToolSelectionBox3D->SetToolGUIArea(m_Controls->m_ManualToolGUIContainer3D);
//specify tools to be added to 3D Tool area
m_Controls->m_ManualToolSelectionBox3D->SetDisplayedToolGroups(segTools3D.toStdString());
m_Controls->m_ManualToolSelectionBox3D->SetLayoutColumns(3);
m_Controls->m_ManualToolSelectionBox3D->SetEnabledMode(QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible);
//Hide 3D selection box, show 2D selection box
m_Controls->m_ManualToolSelectionBox3D->hide();
m_Controls->m_ManualToolSelectionBox2D->show();
// update the list of segmentations
toolManager->NewNodeObjectsGenerated += mitk::MessageDelegate1<QmitkSegmentationView, mitk::ToolManager::DataVectorType*>(this, &QmitkSegmentationView::NewNodeObjectsGenerated);
// create signal/slot connections
connect(m_Controls->patImageSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkSegmentationView::OnPatientSelectionChanged);
connect(m_Controls->segImageSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkSegmentationView::OnSegmentationSelectionChanged);
connect(m_Controls->btnNewSegmentation, &QToolButton::clicked, this, &QmitkSegmentationView::CreateNewSegmentation);
connect(m_Controls->tabWidgetSegmentationTools, &QTabWidget::currentChanged, this, &QmitkSegmentationView::OnTabWidgetChanged);
connect(m_Controls->m_SlicesInterpolator, &QmitkSlicesInterpolator::SignalShowMarkerNodes, this, &QmitkSegmentationView::OnShowMarkerNodes);
// set callback function for already existing nodes (images & segmentations)
mitk::DataStorage::SetOfObjects::ConstPointer allImages = GetDataStorage()->GetSubset(m_IsOfTypeImagePredicate);
for (mitk::DataStorage::SetOfObjects::const_iterator iter = allImages->begin(); iter != allImages->end(); ++iter)
{
mitk::DataNode* node = *iter;
itk::SimpleMemberCommand<QmitkSegmentationView>::Pointer command = itk::SimpleMemberCommand<QmitkSegmentationView>::New();
command->SetCallbackFunction(this, &QmitkSegmentationView::OnVisiblePropertyChanged);
m_WorkingDataObserverTags.insert(std::pair<mitk::DataNode*, unsigned long>(node, node->GetProperty("visible")->AddObserver(itk::ModifiedEvent(), command)));
}
itk::SimpleMemberCommand<QmitkSegmentationView>::Pointer command = itk::SimpleMemberCommand<QmitkSegmentationView>::New();
command->SetCallbackFunction(this, &QmitkSegmentationView::CheckRenderingState);
m_RenderingManagerObserverTag = mitk::RenderingManager::GetInstance()->AddObserver(mitk::RenderingManagerViewsInitializedEvent(), command);
SetToolManagerSelection(m_Controls->patImageSelector->GetSelectedNode(), m_Controls->segImageSelector->GetSelectedNode());
m_RenderWindowPart = GetRenderWindowPart();
if (m_RenderWindowPart)
{
RenderWindowPartActivated(m_RenderWindowPart);
}
//Should be done last, if everything else is configured because it triggers the autoselection of data.
m_Controls->patImageSelector->SetAutoSelectNewNodes(true);
m_Controls->segImageSelector->SetAutoSelectNewNodes(true);
}
void QmitkSegmentationView::SetFocus()
{
m_Controls->btnNewSegmentation->setFocus();
}
void QmitkSegmentationView::OnManualTool2DSelected(int id)
{
if (id >= 0)
{
std::string text = "Active Tool: \"";
mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager();
text += toolManager->GetToolById(id)->GetName();
text += "\"";
mitk::StatusBar::GetInstance()->DisplayText(text.c_str());
us::ModuleResource resource = toolManager->GetToolById(id)->GetCursorIconResource();
this->SetMouseCursor(resource, 0, 0);
}
else
{
this->ResetMouseCursor();
mitk::StatusBar::GetInstance()->DisplayText("");
}
}
void QmitkSegmentationView::ResetMouseCursor()
{
if ( m_MouseCursorSet )
{
mitk::ApplicationCursor::GetInstance()->PopCursor();
m_MouseCursorSet = false;
}
}
void QmitkSegmentationView::SetMouseCursor( const us::ModuleResource& resource, int hotspotX, int hotspotY )
{
// Remove previously set mouse cursor
if (m_MouseCursorSet)
this->ResetMouseCursor();
if (resource)
{
us::ModuleResourceStream cursor(resource, std::ios::binary);
mitk::ApplicationCursor::GetInstance()->PushCursor(cursor, hotspotX, hotspotY);
m_MouseCursorSet = true;
}
}
void QmitkSegmentationView::SetToolSelectionBoxesEnabled(bool status)
{
if (status)
{
m_Controls->m_ManualToolSelectionBox2D->RecreateButtons();
m_Controls->m_ManualToolSelectionBox3D->RecreateButtons();
}
m_Controls->m_ManualToolSelectionBox2D->setEnabled(status);
m_Controls->m_ManualToolSelectionBox3D->setEnabled(status);
m_Controls->m_SlicesInterpolator->setEnabled(status);
}
diff --git a/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/CMakeLists.txt b/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/CMakeLists.txt
index 2976e1079d..d8535984e4 100755
--- a/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/CMakeLists.txt
@@ -1,8 +1,7 @@
project(org_mitk_gui_qt_stdmultiwidgeteditor)
mitk_create_plugin(
EXPORT_DIRECTIVE ORG_MITK_GUI_QT_STDMULTIWIDGETEDITOR
EXPORTED_INCLUDE_SUFFIXES src
MODULE_DEPENDS MitkQtWidgets
- SUBPROJECTS MITK-CoreUI
)
diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox
index 49360ff183..c1c47212a6 100644
--- a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox
+++ b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox
@@ -1,154 +1,140 @@
/**
\page org_mitk_views_volumevisualization The Volume Visualization Plugin
\imageMacro{volume_visualization.svg,"Icon of the Volume Visualization Plugin",2.00}
\tableofcontents
\section QVV_Overview Overview
-The <b> Volume Visualization Plugin </b> is a basic tool for visualizing three dimensional medical images.
-MITK provides generic transfer function presets for medical CT data.
-These functions, that map the gray-value to color and opacity, can be interactively edited.
-Additionally, there are controls to quickly generate common used transfer function shapes
-like the threshold and bell curve to help identify a range of grey-values.
+The <b> Volume Visualization Plugin </b> is a basic tool for volume rendering of three dimensional medical images.
+MITK provides generic transfer function presets for medical CT and MRT data.
+These functions that map the gray-value to color and opacity can be interactively edited.
+Additionally, there are controls to quickly generate commonly used transfer function shapes like the threshold and bell curve to help identify a range of grey-values.
\imageMacro{QmitkVolumeVisualization_Overview.png,"",16.00}
-\section QVV_EnableVRPage Enable Volume Rendering
+\section QVV_EnableVRPage Volume Rendering
-\subsection QVV_LoadingImage Loading an image into the application
+\subsection QVV_LoadingImage Select an image and enable volume rendering
-Load an image into the application by
+\imageMacro{QmitkVolumeVisualization_Checkboxen.png,"",8.21}
-<ul>
-<li> dragging a file into the application window.
-<li> selecting file / load from the menu.
-</ul>
+Select an image on top of the view and click on the checkbox left of 'Volumerendering'. Please be patient, while the image is prepared for rendering, which can take up to a half minute.
+\note
Volume Visualization imposes following restrictions on images:
-
<ul>
-<li> It has to be a 3D-Image Scalar image, that means a normal CT or MRT.
-<li> 3D+T are supported for rendering, but the histograms are not computed.
-<li> Also be aware that volume visualization requires a huge amount of memory.
- Very large images may not work, unless you use the 64bit version.
+<li> It has to be a 3D scalar image, that means e.g. a CT or MRT image.
+<li> 3D+t images are supported for rendering, but the histograms are not computed.
+<li> Also be aware that volume visualization requires a huge amount of memory. Very large images may not work unless you use the 64bit version.
</ul>
-\subsection QVV_EnableVR Enable Volumerendering
-
-\imageMacro{QmitkVolumeVisualization_Checkboxen.png,"",8.21}
-
-Select an image in datamanager and click on the checkbox left of "Volumerendering".
-Please be patient, while the image is prepared for rendering, which can take up to a half minute.
\subsection QVV_LODGPU Dropdown menus for the rendering and blend modes
-Two dropdown menus allow selection of rendering mode (Default, RayCast, GPU) and the blend mode (Composite, Max, Min, Avg, Add).
+Two dropdown menus are located right next to the 'Volumerendering' checkbox. They allow you to select a rendering mode (Default, RayCast, GPU) and the blend mode (Composite, Max, Min, Avg, Add).
-Any Volume Rendering mode requires a lot of computing resources including processor, memory and often also graphics card.
-The Default selection usually finds the best rendering mode for the available hardware.
-Alternatively, it is possible to manually specify the selections RayCast and GPU.
-The RayCast selection is based on CPU computation and therefore typically slow, but allows to render without hardware acceleration.
-The GPU selection uses computing resources on the graphics card to accelerate volume rendering.
-It requires a powerful graphics card and OpenGL hardware support for shaders, but achieves much higher frame rates than software-rendering.
+Any rendering mode requires a lot of computing resources including processor, memory and often also graphics card.
+The 'Default' selection usually finds the best 'rendering' mode for the available hardware.
+Alternatively, it is possible to manually specify the selections 'RayCast' and 'GPU'.
+The 'RayCast' selection is based on CPU computation and therefore typically slow, but allows to render without hardware acceleration.
+The 'GPU' selection uses computing resources on the graphics card to accelerate volume rendering.
+It requires a powerful graphics card and OpenGL hardware support for shaders but achieves much higher frame rates than software-rendering.
-Blend modes define how the volume voxels intersected by the rendering rays are pooled. The composite mode specifies standard volume rendering,
-for which each voxel contributes equally with opacity and color. Other blend modes simply visualize the voxel of maximum /
-minimum intensity and average / add the intentities along the rendering ray.
+Blend modes define how the volume voxels, intersected by the rendering rays, are pooled. The 'Composite' mode specifies standard volume rendering,
+for which each voxel contributes equally with opacity and color. Other 'blend' modes simply visualize the voxel of the maximum /
+minimum intensity and average / add the intensities along the rendering ray.
\section QVV_PresetPage Applying premade presets
\subsection QVV_Preset Internal presets
-There are some internal presets given, that can be used with normal CT data (given in Houndsfield units).
-A large set of medical data has been tested with that presets, but it may not suit on some special cases.
+There are some internal presets given that can be used with normal CT data (given in Houndsfield units).
+A large set of medical data has been tested with those presets, but they may not suit some special cases.
-Click on the "Preset" tab for using internal or custom presets.
+Click on the 'Preset' tab for using internal or custom presets.
\imageMacro{QmitkVolumeVisualization_InternalPresets.png,"",8.30}
<ul>
-<li> "CT Generic" is the default transferfunction that is first applied.
-<li> "CT Black&White" does not use any colors, as it may be distracting on some data.
-<li> "CT Cardiac" tries to increase detail on CTs from the heart.
-<li> "CT Bone" emphasizes bones and shows other areas more transparent.
-<li> "CT Bone (Gradient)" is like "CT Bone", but shows from other organs only the surface by using the gradient.
-<li> "MR Generic" is the default transferfunction that we use on MRT data (which is not normalized like CT data).
-<li> "CT Thorax small" tries to increase detail.
-<li> "CT Thorax large" tries to increase detail.
+<li> 'CT Generic' is the default transfer function that is first applied.
+<li> 'CT Black&White' does not use any colors for the volume visualization as it may be distracting on some data.
+<li> 'CT Cardiac' is well-suited for CT images containing the heart.
+<li> 'CT Bone' emphasizes bones and shows other areas more transparent.
+<li> 'CT Bone (Gradient)' is like 'CT Bone' but shows only the surface from other organs by using the gradient.
+<li> 'MR Generic' is the default transfer function that can be used on MRT data (which is not normalized like CT data).
+<li> 'CT Thorax small' is useful if only a proportion of the thorax is selected to emphasize details.
+<li> 'CT Thorax large' is useful if a large proportion or the entire thorax is selected to emphasize details.
</ul>
\subsection QVV_CustomPreset Saving and loading custom presets
-After creating or editing a transferfunction (see \ref QVV_Editing or \ref QVV_ThresholdBell),
-the custom transferfunction can be stored and later retrieved on the filesystem.
-Click "Save" (respectively "Load") button to save (load) the threshold-, color- and gradient function combined in a single .xml file.
-
-\section QVV_ThresholdBell Interactively create transferfunctions
+After creating or editing a transfer function (see \ref QVV_Editing or \ref QVV_ThresholdBell),
+the custom transfer function can be stored and later retrieved on the filesystem.
+Click 'Save' (respectively 'Load') button below the preset selection to save (load) the threshold-, color- and gradient function combined in a single .xml file.
-Beside the possibility to directly edit the transferfunctions (\ref QVV_Editing),
-a one-click generation of two commonly known shapes is given.
+\section QVV_ThresholdBell Interactively create transfer functions
-Both generators have two parameters, that can be modified by first clicking on the cross and then moving the mouse up/down and left/right.
+Besides the possibility to directly edit the transfer functions (\ref QVV_Editing), the plugin provides two commonly known shapes to quickly generate transfer functions with a few clicks. Both generators have two parameters that can be modified by first clicking on the cross and then moving the mouse up/down and left/right.
-The first parameter "center" (controlled by horizontal movement of the mouse) specifies the gravalue where the center of the shape will be located.
+The first parameter 'center' (controlled by horizontal movement of the mouse) specifies the gray value where the center of the shape will be located.
-The second parameter "width" (controlled by vertical movement of the mouse) specifies the width (or steepness) of the shape.
+The second parameter 'width' (controlled by vertical movement of the mouse) specifies the width (or steepness) of the shape.
\subsection Threshold
-Click on the "Threshold" tab to active the threshold function generator.
+Click on the 'Threshold' tab to activate the threshold function generator.
\imageMacro{QmitkVolumeVisualization_Threshold.png,"",8.21}
-A threshold shape begins with zero and raises to one across the "center" parameter. Lower widths results in steeper threshold functions.
+A threshold shape begins with zero and raises to one across the 'center' parameter. Lower widths result in steeper threshold functions.
\subsection Bell
-Click on the "Bell" tab to active the threshold function generator.
+Click on the 'Bell' tab to activate the bell-shaped threshold function generator.
\imageMacro{QmitkVolumeVisualization_Bell.png,"",8.23}
-A threshold shape begins with zero and raises to one at the "center" parameter and the lowers agains to zero. The "width" parameter correspondens to the width of the bell.
+A threshold shape begins with zero and raises to one at the 'center' parameter and then lowers again to zero. The 'width' parameter corresponds to the width of the bell.
-\section QVV_Editing Customize transferfunctions in detail
+\section QVV_Editing Customize transfer functions in detail
-\subsection QVV_Navigate Choosing grayvalue interval to edit
+\subsection QVV_Navigate Choosing gray value interval to edit
\imageMacro{QmitkVolumeVisualization_Slider.png,"",8.23}
-To navigate across the grayvalue range or to zoom in some ranges use the "range"-slider.
+To navigate across the gray value range or to zoom in some ranges use the 'range'-slider.
All three function editors have in common following:
<ul>
<li> By left-clicking a new point is added.
<li> By right-clicking a point is deleted.
<li> By left-clicking and holding, an exisiting point can be dragged.
<li> By pressing arrow keys, the currently selected point is moved.
-<li> By pressing the "DELETE" key, the currently selected point is deleted.
+<li> By pressing the 'DELETE' key, the currently selected point is deleted.
<li> Between points the transferfunctions are linear interpolated.
</ul>
-There are three transferfunctions to customize:
+There are three transfer functions to customize:
\subsection QVV_GO Grayvalue -> Opacity
-\imageMacro{QmitkVolumeVisualization_Opacity.png,"grayvalues will be mapped to opacity.",8.04}
+\imageMacro{QmitkVolumeVisualization_Opacity.png,"Gray values will be mapped to opacity.",8.04}
+
+An opacity of 0 means total transparent, an opacity of 1 means total opaque. The opacity editor allows changing the opacity for all gray values independently. You can alter the position of control points using your mouse. You can add control points by left-clicking on the graph. To remove a control point again you can right-click on the respective point.
-An opacity of 0 means total transparent, an opacity of 1 means total opaque.
\subsection QVV_GC Grayvalue -> Color
-\imageMacro{QmitkVolumeVisualization_Color.png,"grayvalues will be mapped to color.",8.81}
+\imageMacro{QmitkVolumeVisualization_Color.png,"Gray values will be mapped to color.",8.81}
-The color transferfunction editor also allows by double-clicking a point to change its color.
+The color transfer function editor also allows you to change its color by double-clicking a point. You can add color control points by left-clicking on the color bar. To remove a control point again right-click on the respective point.
\subsection QVV_GGO Grayvalue and Gradient -> Opacity
\imageMacro{QmitkVolumeVisualization_Gradient.png,"",8.85}
-Here the influence of the gradient is controllable at specific grayvalues.
-
+The gradient editor allows you to change the gradient influence for all gray values independently. You can move the existing control points using your mouse. Additionally, you can add control points by left-clicking on the graph. To remove a control point again, right-click on the respective point.
*/
diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Bell.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Bell.png
index 7cf0b2eed9..a4df90bd88 100644
Binary files a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Bell.png and b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Bell.png differ
diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Checkboxen.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Checkboxen.png
index f395d4cb7d..dac50d7795 100644
Binary files a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Checkboxen.png and b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Checkboxen.png differ
diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Color.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Color.png
index befafba215..4b346432fe 100644
Binary files a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Color.png and b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Color.png differ
diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Gradient.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Gradient.png
index c9bf5ef70f..d4ba5b74f9 100644
Binary files a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Gradient.png and b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Gradient.png differ
diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_InternalPresets.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_InternalPresets.png
index a769755e2a..78bd1e14c1 100644
Binary files a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_InternalPresets.png and b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_InternalPresets.png differ
diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Opacity.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Opacity.png
index c31fbc8aca..79f549f869 100644
Binary files a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Opacity.png and b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Opacity.png differ
diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Overview.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Overview.png
index 2c190a8ce2..555de51a10 100644
Binary files a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Overview.png and b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Overview.png differ
diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Slider.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Slider.png
index f65e9d6da5..c1237a7f12 100644
Binary files a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Slider.png and b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Slider.png differ
diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Threshold.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Threshold.png
index fe6fc3b653..a12fcf586f 100644
Binary files a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Threshold.png and b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization_Threshold.png differ
diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/src/internal/QmitkVolumeVisualizationView.cpp b/Plugins/org.mitk.gui.qt.volumevisualization/src/internal/QmitkVolumeVisualizationView.cpp
index 51d291a500..7ab3ab1e54 100755
--- a/Plugins/org.mitk.gui.qt.volumevisualization/src/internal/QmitkVolumeVisualizationView.cpp
+++ b/Plugins/org.mitk.gui.qt.volumevisualization/src/internal/QmitkVolumeVisualizationView.cpp
@@ -1,291 +1,292 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "QmitkVolumeVisualizationView.h"
#include <vtkSmartVolumeMapper.h>
#include <mitkImage.h>
#include <mitkTransferFunction.h>
#include <mitkTransferFunctionInitializer.h>
#include <mitkTransferFunctionProperty.h>
#include <mitkNodePredicateDataType.h>
#include <mitkNodePredicateDimension.h>
#include <mitkNodePredicateAnd.h>
#include <mitkNodePredicateNot.h>
#include <mitkNodePredicateOr.h>
#include <mitkNodePredicateProperty.h>
#include <mitkProperties.h>
const std::string QmitkVolumeVisualizationView::VIEW_ID = "org.mitk.views.volumevisualization";
enum
{
DEFAULT_RENDERMODE = 0,
RAYCAST_RENDERMODE = 1,
GPU_RENDERMODE = 2
};
QmitkVolumeVisualizationView::QmitkVolumeVisualizationView()
: QmitkAbstractView()
, m_Controls(nullptr)
{
}
void QmitkVolumeVisualizationView::SetFocus()
{
}
void QmitkVolumeVisualizationView::CreateQtPartControl(QWidget* parent)
{
m_Controls = new Ui::QmitkVolumeVisualizationViewControls;
m_Controls->setupUi(parent);
m_Controls->volumeSelectionWidget->SetDataStorage(GetDataStorage());
m_Controls->volumeSelectionWidget->SetNodePredicate(mitk::NodePredicateAnd::New(
mitk::TNodePredicateDataType<mitk::Image>::New(),
mitk::NodePredicateOr::New(mitk::NodePredicateDimension::New(3), mitk::NodePredicateDimension::New(4)),
mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))));
-
m_Controls->volumeSelectionWidget->SetSelectionIsOptional(true);
m_Controls->volumeSelectionWidget->SetEmptyInfo(QString("Please select a 3D / 4D image volume"));
m_Controls->volumeSelectionWidget->SetPopUpTitel(QString("Select image volume"));
// Fill the transfer function presets in the generator widget
std::vector<std::string> names;
mitk::TransferFunctionInitializer::GetPresetNames(names);
for (const auto& name : names)
{
m_Controls->transferFunctionGeneratorWidget->AddPreset(QString::fromStdString(name));
}
// see enum in vtkSmartVolumeMapper
m_Controls->renderMode->addItem("Default");
m_Controls->renderMode->addItem("RayCast");
m_Controls->renderMode->addItem("GPU");
// see vtkVolumeMapper::BlendModes
m_Controls->blendMode->addItem("Comp");
m_Controls->blendMode->addItem("Max");
m_Controls->blendMode->addItem("Min");
m_Controls->blendMode->addItem("Avg");
m_Controls->blendMode->addItem("Add");
connect(m_Controls->volumeSelectionWidget, &QmitkSingleNodeSelectionWidget::CurrentSelectionChanged,
this, &QmitkVolumeVisualizationView::OnCurrentSelectionChanged);
connect(m_Controls->enableRenderingCB, SIGNAL(toggled(bool)), this, SLOT(OnEnableRendering(bool)));
connect(m_Controls->renderMode, SIGNAL(activated(int)), this, SLOT(OnRenderMode(int)));
connect(m_Controls->blendMode, SIGNAL(activated(int)), this, SLOT(OnBlendMode(int)));
connect(m_Controls->transferFunctionGeneratorWidget, SIGNAL(SignalUpdateCanvas()),
m_Controls->transferFunctionWidget, SLOT(OnUpdateCanvas()));
connect(m_Controls->transferFunctionGeneratorWidget, SIGNAL(SignalTransferFunctionModeChanged(int)),
SLOT(OnMitkInternalPreset(int)));
m_Controls->enableRenderingCB->setEnabled(false);
m_Controls->blendMode->setEnabled(false);
m_Controls->renderMode->setEnabled(false);
m_Controls->transferFunctionWidget->setEnabled(false);
m_Controls->transferFunctionGeneratorWidget->setEnabled(false);
+
+ m_Controls->volumeSelectionWidget->SetAutoSelectNewNodes(true);
}
void QmitkVolumeVisualizationView::OnMitkInternalPreset(int mode)
{
if (m_SelectedNode.IsExpired())
{
return;
}
auto node = m_SelectedNode.Lock();
mitk::TransferFunctionProperty::Pointer transferFuncProp;
if (node->GetProperty(transferFuncProp, "TransferFunction"))
{
// first item is only information
if (--mode == -1)
return;
// -- Creat new TransferFunction
mitk::TransferFunctionInitializer::Pointer tfInit = mitk::TransferFunctionInitializer::New(transferFuncProp->GetValue());
tfInit->SetTransferFunctionMode(mode);
RequestRenderWindowUpdate();
m_Controls->transferFunctionWidget->OnUpdateCanvas();
}
}
void QmitkVolumeVisualizationView::OnCurrentSelectionChanged(QList<mitk::DataNode::Pointer> nodes)
{
m_SelectedNode = nullptr;
if (nodes.empty() || nodes.front().IsNull())
{
UpdateInterface();
return;
}
auto selectedNode = nodes.front();
auto image = dynamic_cast<mitk::Image*>(selectedNode->GetData());
if (nullptr != image)
{
m_SelectedNode = selectedNode;
}
UpdateInterface();
}
void QmitkVolumeVisualizationView::OnEnableRendering(bool state)
{
if (m_SelectedNode.IsExpired())
{
return;
}
m_SelectedNode.Lock()->SetProperty("volumerendering", mitk::BoolProperty::New(state));
UpdateInterface();
RequestRenderWindowUpdate();
}
void QmitkVolumeVisualizationView::OnRenderMode(int mode)
{
if (m_SelectedNode.IsExpired())
{
return;
}
auto selectedNode = m_SelectedNode.Lock();
bool usegpu = false;
bool useray = false;
if (DEFAULT_RENDERMODE == mode)
{
useray = true;
usegpu = true;
}
else if (GPU_RENDERMODE == mode)
{
usegpu = true;
}
else if (RAYCAST_RENDERMODE == mode)
{
useray = true;
}
selectedNode->SetProperty("volumerendering.usegpu", mitk::BoolProperty::New(usegpu));
selectedNode->SetProperty("volumerendering.useray", mitk::BoolProperty::New(useray));
RequestRenderWindowUpdate();
}
void QmitkVolumeVisualizationView::OnBlendMode(int mode)
{
if (m_SelectedNode.IsExpired())
{
return;
}
auto selectedNode = m_SelectedNode.Lock();
bool usemip = false;
if (vtkVolumeMapper::MAXIMUM_INTENSITY_BLEND == mode)
{
usemip = true;
}
selectedNode->SetProperty("volumerendering.usemip", mitk::BoolProperty::New(usemip));
selectedNode->SetProperty("volumerendering.blendmode", mitk::IntProperty::New(mode));
RequestRenderWindowUpdate();
}
void QmitkVolumeVisualizationView::UpdateInterface()
{
if (m_SelectedNode.IsExpired())
{
// turnoff all
m_Controls->enableRenderingCB->setChecked(false);
m_Controls->enableRenderingCB->setEnabled(false);
m_Controls->blendMode->setCurrentIndex(0);
m_Controls->blendMode->setEnabled(false);
m_Controls->renderMode->setCurrentIndex(0);
m_Controls->renderMode->setEnabled(false);
m_Controls->transferFunctionWidget->SetDataNode(nullptr);
m_Controls->transferFunctionWidget->setEnabled(false);
m_Controls->transferFunctionGeneratorWidget->SetDataNode(nullptr);
m_Controls->transferFunctionGeneratorWidget->setEnabled(false);
return;
}
bool enabled = false;
auto selectedNode = m_SelectedNode.Lock();
selectedNode->GetBoolProperty("volumerendering", enabled);
m_Controls->enableRenderingCB->setEnabled(true);
m_Controls->enableRenderingCB->setChecked(enabled);
if (!enabled)
{
// turnoff all except volumerendering checkbox
m_Controls->blendMode->setCurrentIndex(0);
m_Controls->blendMode->setEnabled(false);
m_Controls->renderMode->setCurrentIndex(0);
m_Controls->renderMode->setEnabled(false);
m_Controls->transferFunctionWidget->SetDataNode(nullptr);
m_Controls->transferFunctionWidget->setEnabled(false);
m_Controls->transferFunctionGeneratorWidget->SetDataNode(nullptr);
m_Controls->transferFunctionGeneratorWidget->setEnabled(false);
return;
}
// otherwise we can activate em all
m_Controls->blendMode->setEnabled(true);
m_Controls->renderMode->setEnabled(true);
// Determine Combo Box mode
{
bool usegpu = false;
bool useray = false;
bool usemip = false;
selectedNode->GetBoolProperty("volumerendering.usegpu", usegpu);
selectedNode->GetBoolProperty("volumerendering.useray", useray);
selectedNode->GetBoolProperty("volumerendering.usemip", usemip);
int blendMode;
if (selectedNode->GetIntProperty("volumerendering.blendmode", blendMode))
m_Controls->blendMode->setCurrentIndex(blendMode);
if (usemip)
m_Controls->blendMode->setCurrentIndex(vtkVolumeMapper::MAXIMUM_INTENSITY_BLEND);
int mode = DEFAULT_RENDERMODE;
if (useray)
mode = RAYCAST_RENDERMODE;
else if (usegpu)
mode = GPU_RENDERMODE;
m_Controls->renderMode->setCurrentIndex(mode);
}
m_Controls->transferFunctionWidget->SetDataNode(selectedNode);
m_Controls->transferFunctionWidget->setEnabled(true);
m_Controls->transferFunctionGeneratorWidget->SetDataNode(selectedNode);
m_Controls->transferFunctionGeneratorWidget->setEnabled(true);
}
diff --git a/SuperBuild.cmake b/SuperBuild.cmake
index cfe9d86ca3..683b5634cf 100644
--- a/SuperBuild.cmake
+++ b/SuperBuild.cmake
@@ -1,505 +1,510 @@
#-----------------------------------------------------------------------------
# Convenient macro allowing to download a file
#-----------------------------------------------------------------------------
if(NOT MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL)
set(MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL http://mitk.org/download/thirdparty)
endif()
macro(downloadFile url dest)
file(DOWNLOAD ${url} ${dest} STATUS status)
list(GET status 0 error_code)
list(GET status 1 error_msg)
if(error_code)
message(FATAL_ERROR "error: Failed to download ${url} - ${error_msg}")
endif()
endmacro()
#-----------------------------------------------------------------------------
# MITK Prerequisites
#-----------------------------------------------------------------------------
if(UNIX AND NOT APPLE)
include(mitkFunctionCheckPackageHeader)
# Check for libxt-dev
mitkFunctionCheckPackageHeader(StringDefs.h libxt-dev /usr/include/X11/)
# Check for libtiff4-dev
mitkFunctionCheckPackageHeader(tiff.h libtiff4-dev)
endif()
# We need a proper patch program. On Linux and MacOS, we assume
# that "patch" is available. On Windows, we download patch.exe
# if not patch program is found.
find_program(PATCH_COMMAND patch)
if((NOT PATCH_COMMAND OR NOT EXISTS ${PATCH_COMMAND}) AND WIN32)
downloadFile(${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/patch.exe
${CMAKE_CURRENT_BINARY_DIR}/patch.exe)
find_program(PATCH_COMMAND patch ${CMAKE_CURRENT_BINARY_DIR})
endif()
if(NOT PATCH_COMMAND)
message(FATAL_ERROR "No patch program found.")
endif()
#-----------------------------------------------------------------------------
# ExternalProjects
#-----------------------------------------------------------------------------
get_property(external_projects GLOBAL PROPERTY MITK_EXTERNAL_PROJECTS)
if(MITK_CTEST_SCRIPT_MODE)
# Write a file containing the list of enabled external project targets.
# This file can be read by a ctest script to separately build projects.
set(SUPERBUILD_TARGETS )
foreach(proj ${external_projects})
if(MITK_USE_${proj})
list(APPEND SUPERBUILD_TARGETS ${proj})
endif()
endforeach()
file(WRITE "${CMAKE_BINARY_DIR}/SuperBuildTargets.cmake" "set(SUPERBUILD_TARGETS ${SUPERBUILD_TARGETS})")
endif()
# A list of "nice" external projects, playing well together with CMake
set(nice_external_projects ${external_projects})
list(REMOVE_ITEM nice_external_projects Boost)
foreach(proj ${nice_external_projects})
if(MITK_USE_${proj})
set(EXTERNAL_${proj}_DIR "${${proj}_DIR}" CACHE PATH "Path to ${proj} build directory")
mark_as_advanced(EXTERNAL_${proj}_DIR)
if(EXTERNAL_${proj}_DIR)
set(${proj}_DIR ${EXTERNAL_${proj}_DIR})
endif()
endif()
endforeach()
set(EXTERNAL_BOOST_ROOT "${BOOST_ROOT}" CACHE PATH "Path to Boost directory")
mark_as_advanced(EXTERNAL_BOOST_ROOT)
if(EXTERNAL_BOOST_ROOT)
set(BOOST_ROOT ${EXTERNAL_BOOST_ROOT})
endif()
-# Setup file for setting custom ctest vars
-configure_file(
- CMake/SuperbuildCTestCustom.cmake.in
- ${MITK_BINARY_DIR}/CTestCustom.cmake
- @ONLY
-)
-
if(BUILD_TESTING)
set(EXTERNAL_MITK_DATA_DIR "${MITK_DATA_DIR}" CACHE PATH "Path to the MITK data directory")
mark_as_advanced(EXTERNAL_MITK_DATA_DIR)
if(EXTERNAL_MITK_DATA_DIR)
set(MITK_DATA_DIR ${EXTERNAL_MITK_DATA_DIR})
endif()
endif()
#-----------------------------------------------------------------------------
# External project settings
#-----------------------------------------------------------------------------
include(ExternalProject)
include(mitkMacroQueryCustomEPVars)
include(mitkFunctionInstallExternalCMakeProject)
include(mitkFunctionCleanExternalProject)
option(MITK_AUTOCLEAN_EXTERNAL_PROJECTS "Experimental: Clean external project builds if updated" OFF)
mark_as_advanced(MITK_AUTOCLEAN_EXTERNAL_PROJECTS)
set(ep_prefix "${CMAKE_BINARY_DIR}/ep")
set_property(DIRECTORY PROPERTY EP_PREFIX ${ep_prefix})
# Compute -G arg for configuring external projects with the same CMake generator:
if(CMAKE_EXTRA_GENERATOR)
set(gen "${CMAKE_EXTRA_GENERATOR} - ${CMAKE_GENERATOR}")
else()
set(gen "${CMAKE_GENERATOR}")
endif()
set(gen_platform ${CMAKE_GENERATOR_PLATFORM})
# Use this value where semi-colons are needed in ep_add args:
set(sep "^^")
##
if(MSVC_VERSION)
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} /bigobj /MP")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /bigobj /MP")
endif()
if(MITK_USE_Boost_LIBRARIES)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DBOOST_ALL_DYN_LINK")
endif()
# This is a workaround for passing linker flags
# actually down to the linker invocation
set(_cmake_required_flags_orig ${CMAKE_REQUIRED_FLAGS})
set(CMAKE_REQUIRED_FLAGS "-Wl,-rpath")
mitkFunctionCheckCompilerFlags(${CMAKE_REQUIRED_FLAGS} _has_rpath_flag)
set(CMAKE_REQUIRED_FLAGS ${_cmake_required_flags_orig})
set(_install_rpath_linkflag )
if(_has_rpath_flag)
if(APPLE)
set(_install_rpath_linkflag "-Wl,-rpath,@loader_path/../lib")
else()
set(_install_rpath_linkflag "-Wl,-rpath='$ORIGIN/../lib'")
endif()
endif()
set(_install_rpath)
if(APPLE)
set(_install_rpath "@loader_path/../lib")
elseif(UNIX)
# this work for libraries as well as executables
set(_install_rpath "\$ORIGIN/../lib")
endif()
set(ep_common_args
-DCMAKE_CXX_EXTENSIONS:STRING=${CMAKE_CXX_EXTENSIONS}
-DCMAKE_CXX_STANDARD:STRING=${CMAKE_CXX_STANDARD}
-DCMAKE_CXX_STANDARD_REQUIRED:BOOL=${CMAKE_CXX_STANDARD_REQUIRED}
-DCMAKE_MACOSX_RPATH:BOOL=TRUE
"-DCMAKE_INSTALL_RPATH:STRING=${_install_rpath}"
-DBUILD_TESTING:BOOL=OFF
-DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR>
-DBUILD_SHARED_LIBS:BOOL=ON
-DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
-DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER}
-DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS}
"-DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS} ${MITK_CXX14_FLAG}"
#debug flags
-DCMAKE_CXX_FLAGS_DEBUG:STRING=${CMAKE_CXX_FLAGS_DEBUG}
-DCMAKE_C_FLAGS_DEBUG:STRING=${CMAKE_C_FLAGS_DEBUG}
#release flags
-DCMAKE_CXX_FLAGS_RELEASE:STRING=${CMAKE_CXX_FLAGS_RELEASE}
-DCMAKE_C_FLAGS_RELEASE:STRING=${CMAKE_C_FLAGS_RELEASE}
#relwithdebinfo
-DCMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_CXX_FLAGS_RELWITHDEBINFO}
-DCMAKE_C_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_C_FLAGS_RELWITHDEBINFO}
#link flags
-DCMAKE_EXE_LINKER_FLAGS:STRING=${CMAKE_EXE_LINKER_FLAGS}
-DCMAKE_SHARED_LINKER_FLAGS:STRING=${CMAKE_SHARED_LINKER_FLAGS}
-DCMAKE_MODULE_LINKER_FLAGS:STRING=${CMAKE_MODULE_LINKER_FLAGS}
)
if(MSVC_VERSION)
list(APPEND ep_common_args
-DCMAKE_DEBUG_POSTFIX:STRING=d
)
set(DCMTK_CMAKE_DEBUG_POSTFIX d)
endif()
set(ep_common_cache_args
)
set(ep_common_cache_default_args
"-DCMAKE_PREFIX_PATH:PATH=<INSTALL_DIR>;${CMAKE_PREFIX_PATH}"
"-DCMAKE_INCLUDE_PATH:PATH=${CMAKE_INCLUDE_PATH}"
"-DCMAKE_LIBRARY_PATH:PATH=${CMAKE_LIBRARY_PATH}"
)
# Pass the CMAKE_OSX variables to external projects
if(APPLE)
set(MAC_OSX_ARCHITECTURE_ARGS
-DCMAKE_OSX_ARCHITECTURES:PATH=${CMAKE_OSX_ARCHITECTURES}
-DCMAKE_OSX_DEPLOYMENT_TARGET:PATH=${CMAKE_OSX_DEPLOYMENT_TARGET}
-DCMAKE_OSX_SYSROOT:PATH=${CMAKE_OSX_SYSROOT}
)
set(ep_common_args
${MAC_OSX_ARCHITECTURE_ARGS}
${ep_common_args}
)
endif()
set(mitk_superbuild_ep_args)
set(mitk_depends )
# Include external projects
include(CMakeExternals/MITKData.cmake)
foreach(p ${external_projects})
set(p_hash "")
set(p_file "${CMAKE_SOURCE_DIR}/CMakeExternals/${p}.cmake")
if(EXISTS ${p_file})
file(MD5 ${p_file} p_hash)
else()
foreach(MITK_EXTENSION_DIR ${MITK_EXTENSION_DIRS})
get_filename_component(MITK_EXTENSION_DIR ${MITK_EXTENSION_DIR} ABSOLUTE)
set(MITK_CMAKE_EXTERNALS_EXTENSION_DIR ${MITK_EXTENSION_DIR}/CMakeExternals)
set(p_file "${MITK_CMAKE_EXTERNALS_EXTENSION_DIR}/${p}.cmake")
if(EXISTS ${p_file})
file(MD5 ${p_file} p_hash)
break()
endif()
endforeach()
endif()
if(p_hash)
set(p_hash_file "${ep_prefix}/tmp/${p}-hash.txt")
if(MITK_AUTOCLEAN_EXTERNAL_PROJECTS)
if(EXISTS ${p_hash_file})
file(READ ${p_hash_file} p_prev_hash)
if(NOT p_hash STREQUAL p_prev_hash)
mitkCleanExternalProject(${p})
endif()
endif()
endif()
file(WRITE ${p_hash_file} ${p_hash})
endif()
include(${p_file} OPTIONAL)
list(APPEND mitk_superbuild_ep_args
-DMITK_USE_${p}:BOOL=${MITK_USE_${p}}
)
get_property(_package GLOBAL PROPERTY MITK_${p}_PACKAGE)
if(_package)
list(APPEND mitk_superbuild_ep_args -D${p}_DIR:PATH=${${p}_DIR})
endif()
list(APPEND mitk_depends ${${p}_DEPENDS})
endforeach()
if (SWIG_EXECUTABLE)
list(APPEND mitk_superbuild_ep_args -DSWIG_EXECUTABLE=${SWIG_EXECUTABLE})
endif()
#-----------------------------------------------------------------------------
# Set superbuild boolean args
#-----------------------------------------------------------------------------
set(mitk_cmake_boolean_args
BUILD_SHARED_LIBS
WITH_COVERAGE
BUILD_TESTING
MITK_BUILD_ALL_PLUGINS
MITK_BUILD_ALL_APPS
MITK_BUILD_EXAMPLES
MITK_USE_Qt5
MITK_USE_SYSTEM_Boost
MITK_USE_BLUEBERRY
MITK_USE_OpenCL
MITK_USE_OpenMP
MITK_ENABLE_PIC_READER
)
#-----------------------------------------------------------------------------
# Create the final variable containing superbuild boolean args
#-----------------------------------------------------------------------------
set(mitk_superbuild_boolean_args)
foreach(mitk_cmake_arg ${mitk_cmake_boolean_args})
list(APPEND mitk_superbuild_boolean_args -D${mitk_cmake_arg}:BOOL=${${mitk_cmake_arg}})
endforeach()
if(MITK_BUILD_ALL_PLUGINS)
list(APPEND mitk_superbuild_boolean_args -DBLUEBERRY_BUILD_ALL_PLUGINS:BOOL=ON)
endif()
#-----------------------------------------------------------------------------
# MITK Utilities
#-----------------------------------------------------------------------------
set(proj MITK-Utilities)
ExternalProject_Add(${proj}
DOWNLOAD_COMMAND ""
CONFIGURE_COMMAND ""
BUILD_COMMAND ""
INSTALL_COMMAND ""
DEPENDS
${mitk_depends}
)
#-----------------------------------------------------------------------------
# Additional MITK CXX/C Flags
#-----------------------------------------------------------------------------
set(MITK_ADDITIONAL_C_FLAGS "" CACHE STRING "Additional C Flags for MITK")
set(MITK_ADDITIONAL_C_FLAGS_RELEASE "" CACHE STRING "Additional Release C Flags for MITK")
set(MITK_ADDITIONAL_C_FLAGS_DEBUG "" CACHE STRING "Additional Debug C Flags for MITK")
mark_as_advanced(MITK_ADDITIONAL_C_FLAGS MITK_ADDITIONAL_C_FLAGS_DEBUG MITK_ADDITIONAL_C_FLAGS_RELEASE)
set(MITK_ADDITIONAL_CXX_FLAGS "" CACHE STRING "Additional CXX Flags for MITK")
set(MITK_ADDITIONAL_CXX_FLAGS_RELEASE "" CACHE STRING "Additional Release CXX Flags for MITK")
set(MITK_ADDITIONAL_CXX_FLAGS_DEBUG "" CACHE STRING "Additional Debug CXX Flags for MITK")
mark_as_advanced(MITK_ADDITIONAL_CXX_FLAGS MITK_ADDITIONAL_CXX_FLAGS_DEBUG MITK_ADDITIONAL_CXX_FLAGS_RELEASE)
set(MITK_ADDITIONAL_EXE_LINKER_FLAGS "" CACHE STRING "Additional exe linker flags for MITK")
set(MITK_ADDITIONAL_SHARED_LINKER_FLAGS "" CACHE STRING "Additional shared linker flags for MITK")
set(MITK_ADDITIONAL_MODULE_LINKER_FLAGS "" CACHE STRING "Additional module linker flags for MITK")
mark_as_advanced(MITK_ADDITIONAL_EXE_LINKER_FLAGS MITK_ADDITIONAL_SHARED_LINKER_FLAGS MITK_ADDITIONAL_MODULE_LINKER_FLAGS)
#-----------------------------------------------------------------------------
# MITK Configure
#-----------------------------------------------------------------------------
if(MITK_INITIAL_CACHE_FILE)
set(mitk_initial_cache_arg -C "${MITK_INITIAL_CACHE_FILE}")
endif()
set(mitk_optional_cache_args )
foreach(type RUNTIME ARCHIVE LIBRARY)
if(DEFINED CTK_PLUGIN_${type}_OUTPUT_DIRECTORY)
list(APPEND mitk_optional_cache_args -DCTK_PLUGIN_${type}_OUTPUT_DIRECTORY:PATH=${CTK_PLUGIN_${type}_OUTPUT_DIRECTORY})
endif()
endforeach()
# Optional python variables
if(MITK_USE_Python3)
list(APPEND mitk_optional_cache_args
-DMITK_USE_Python3:BOOL=${MITK_USE_Python3}
"-DPython3_EXECUTABLE:FILEPATH=${Python3_EXECUTABLE}"
"-DPython3_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIRS}"
"-DPython3_LIBRARY:FILEPATH=${Python3_LIBRARY}"
"-DPython3_STDLIB:FILEPATH=${Python3_STDLIB}"
"-DPython3_SITELIB:FILEPATH=${Python3_SITELIB}"
)
endif()
if(OPENSSL_ROOT_DIR)
list(APPEND mitk_optional_cache_args
"-DOPENSSL_ROOT_DIR:PATH=${OPENSSL_ROOT_DIR}"
)
endif()
if(CMAKE_FRAMEWORK_PATH)
list(APPEND mitk_optional_cache_args
"-DCMAKE_FRAMEWORK_PATH:PATH=${CMAKE_FRAMEWORK_PATH}"
)
endif()
if(Eigen_INCLUDE_DIR)
list(APPEND mitk_optional_cache_args
-DEigen_INCLUDE_DIR:PATH=${Eigen_INCLUDE_DIR}
)
endif()
# Optional pass through of Doxygen
if(DOXYGEN_EXECUTABLE)
list(APPEND mitk_optional_cache_args
-DDOXYGEN_EXECUTABLE:FILEPATH=${DOXYGEN_EXECUTABLE}
)
endif()
+if(MITK_DOXYGEN_BUILD_ALWAYS)
+ list(APPEND mitk_optional_cache_args
+ -DMITK_DOXYGEN_BUILD_ALWAYS:BOOL=${MITK_DOXYGEN_BUILD_ALWAYS}
+ )
+endif()
+
+if(BLUEBERRY_DOC_TOOLS_DIR)
+ list(APPEND mitk_optional_cache_args
+ "-DBLUEBERRY_DOC_TOOLS_DIR:PATH=${BLUEBERRY_DOC_TOOLS_DIR}"
+ )
+endif()
+
set(proj MITK-Configure)
ExternalProject_Add(${proj}
LIST_SEPARATOR ${sep}
DOWNLOAD_COMMAND ""
CMAKE_GENERATOR ${gen}
CMAKE_GENERATOR_PLATFORM ${gen_platform}
CMAKE_CACHE_ARGS
# --------------- Build options ----------------
-DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX}
-DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
"-DCMAKE_PREFIX_PATH:PATH=${ep_prefix};${CMAKE_PREFIX_PATH}"
"-DCMAKE_LIBRARY_PATH:PATH=${CMAKE_LIBRARY_PATH}"
"-DCMAKE_INCLUDE_PATH:PATH=${CMAKE_INCLUDE_PATH}"
# --------------- Compile options ----------------
-DCMAKE_CXX_EXTENSIONS:STRING=${CMAKE_CXX_EXTENSIONS}
-DCMAKE_CXX_STANDARD:STRING=${CMAKE_CXX_STANDARD}
-DCMAKE_CXX_STANDARD_REQUIRED:BOOL=${CMAKE_CXX_STANDARD_REQUIRED}
-DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER}
"-DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS} ${MITK_ADDITIONAL_C_FLAGS}"
"-DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS} ${MITK_ADDITIONAL_CXX_FLAGS}"
# debug flags
"-DCMAKE_CXX_FLAGS_DEBUG:STRING=${CMAKE_CXX_FLAGS_DEBUG} ${MITK_ADDITIONAL_CXX_FLAGS_DEBUG}"
"-DCMAKE_C_FLAGS_DEBUG:STRING=${CMAKE_C_FLAGS_DEBUG} ${MITK_ADDITIONAL_C_FLAGS_DEBUG}"
# release flags
"-DCMAKE_CXX_FLAGS_RELEASE:STRING=${CMAKE_CXX_FLAGS_RELEASE} ${MITK_ADDITIONAL_CXX_FLAGS_RELEASE}"
"-DCMAKE_C_FLAGS_RELEASE:STRING=${CMAKE_C_FLAGS_RELEASE} ${MITK_ADDITIONAL_C_FLAGS_RELEASE}"
# relwithdebinfo
-DCMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_CXX_FLAGS_RELWITHDEBINFO}
-DCMAKE_C_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_C_FLAGS_RELWITHDEBINFO}
# link flags
"-DCMAKE_EXE_LINKER_FLAGS:STRING=${CMAKE_EXE_LINKER_FLAGS} ${MITK_ADDITIONAL_EXE_LINKER_FLAGS}"
"-DCMAKE_SHARED_LINKER_FLAGS:STRING=${CMAKE_SHARED_LINKER_FLAGS} ${MITK_ADDITIONAL_SHARED_LINKER_FLAGS}"
"-DCMAKE_MODULE_LINKER_FLAGS:STRING=${CMAKE_MODULE_LINKER_FLAGS} ${MITK_ADDITIONAL_MODULE_LINKER_FLAGS}"
# Output directories
-DMITK_CMAKE_LIBRARY_OUTPUT_DIRECTORY:PATH=${MITK_CMAKE_LIBRARY_OUTPUT_DIRECTORY}
-DMITK_CMAKE_RUNTIME_OUTPUT_DIRECTORY:PATH=${MITK_CMAKE_RUNTIME_OUTPUT_DIRECTORY}
-DMITK_CMAKE_ARCHIVE_OUTPUT_DIRECTORY:PATH=${MITK_CMAKE_ARCHIVE_OUTPUT_DIRECTORY}
# ------------- Boolean build options --------------
${mitk_superbuild_boolean_args}
${mitk_optional_cache_args}
-DMITK_USE_SUPERBUILD:BOOL=OFF
-DMITK_BUILD_CONFIGURATION:STRING=${MITK_BUILD_CONFIGURATION}
-DMITK_FAST_TESTING:BOOL=${MITK_FAST_TESTING}
-DMITK_XVFB_TESTING:BOOL=${MITK_XVFB_TESTING}
-DMITK_XVFB_TESTING_COMMAND:STRING=${MITK_XVFB_TESTING_COMMAND}
-DCTEST_USE_LAUNCHERS:BOOL=${CTEST_USE_LAUNCHERS}
# ----------------- Miscellaneous ---------------
-DCMAKE_LIBRARY_PATH:PATH=${CMAKE_LIBRARY_PATH}
-DCMAKE_INCLUDE_PATH:PATH=${CMAKE_INCLUDE_PATH}
-DMITK_CTEST_SCRIPT_MODE:STRING=${MITK_CTEST_SCRIPT_MODE}
-DMITK_SUPERBUILD_BINARY_DIR:PATH=${MITK_BINARY_DIR}
-DMITK_MODULES_TO_BUILD:INTERNAL=${MITK_MODULES_TO_BUILD}
-DMITK_WHITELIST:STRING=${MITK_WHITELIST}
-DMITK_WHITELISTS_EXTERNAL_PATH:STRING=${MITK_WHITELISTS_EXTERNAL_PATH}
-DMITK_WHITELISTS_INTERNAL_PATH:STRING=${MITK_WHITELISTS_INTERNAL_PATH}
-DMITK_EXTENSION_DIRS:STRING=${MITK_EXTENSION_DIRS}
-DMITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES:STRING=${MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES}
-DMITK_ACCESSBYITK_FLOATING_PIXEL_TYPES:STRING=${MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES}
-DMITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES:STRING=${MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES}
-DMITK_ACCESSBYITK_VECTOR_PIXEL_TYPES:STRING=${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES}
-DMITK_ACCESSBYITK_DIMENSIONS:STRING=${MITK_ACCESSBYITK_DIMENSIONS}
-DMITK_CUSTOM_REVISION_DESC:STRING=${MITK_CUSTOM_REVISION_DESC}
# --------------- External project options ---------------
-DMITK_DATA_DIR:PATH=${MITK_DATA_DIR}
-DMITK_EXTERNAL_PROJECT_PREFIX:PATH=${ep_prefix}
-DCppMicroServices_DIR:PATH=${CppMicroServices_DIR}
-DDCMTK_CMAKE_DEBUG_POSTFIX:STRING=${DCMTK_CMAKE_DEBUG_POSTFIX}
-DBOOST_ROOT:PATH=${BOOST_ROOT}
-DBOOST_LIBRARYDIR:PATH=${BOOST_LIBRARYDIR}
-DMITK_USE_Boost_LIBRARIES:STRING=${MITK_USE_Boost_LIBRARIES}
-DQt5_DIR:PATH=${Qt5_DIR}
CMAKE_ARGS
${mitk_initial_cache_arg}
${MAC_OSX_ARCHITECTURE_ARGS}
${mitk_superbuild_ep_args}
SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}
BINARY_DIR ${CMAKE_BINARY_DIR}/MITK-build
BUILD_COMMAND ""
INSTALL_COMMAND ""
DEPENDS
MITK-Utilities
)
mitkFunctionInstallExternalCMakeProject(${proj})
#-----------------------------------------------------------------------------
# MITK
#-----------------------------------------------------------------------------
if(CMAKE_GENERATOR MATCHES ".*Makefiles.*")
set(mitk_build_cmd "$(MAKE)")
else()
set(mitk_build_cmd ${CMAKE_COMMAND} --build ${CMAKE_CURRENT_BINARY_DIR}/MITK-build --config ${CMAKE_CFG_INTDIR})
endif()
if(NOT DEFINED SUPERBUILD_EXCLUDE_MITKBUILD_TARGET OR NOT SUPERBUILD_EXCLUDE_MITKBUILD_TARGET)
set(MITKBUILD_TARGET_ALL_OPTION "ALL")
else()
set(MITKBUILD_TARGET_ALL_OPTION "")
endif()
add_custom_target(MITK-build ${MITKBUILD_TARGET_ALL_OPTION}
COMMAND ${mitk_build_cmd}
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/MITK-build
DEPENDS MITK-Configure
)
#-----------------------------------------------------------------------------
# Custom target allowing to drive the build of the MITK project itself
#-----------------------------------------------------------------------------
add_custom_target(MITK
COMMAND ${mitk_build_cmd}
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/MITK-build
)