diff --git a/Applications/FlowBench/CMakeLists.txt b/Applications/FlowBench/CMakeLists.txt
index d3f14cafcd..2e3b433260 100644
--- a/Applications/FlowBench/CMakeLists.txt
+++ b/Applications/FlowBench/CMakeLists.txt
@@ -1,50 +1,50 @@
-project(Workbench)
+project(FlowBench)
# Create a cache entry for the provisioning file which is used to export
# the file name in the MITKConfig.cmake file. This will keep external projects
# which rely on this file happy.
set(MITK_FLOWBENCH_PROVISIONING_FILE "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/MitkFlowBench.provisioning" CACHE INTERNAL "MitkFlowBench provisioning file" FORCE)
# Plug-ins listed below will not be
# - added as a build-time dependency to the executable
# - listed in the provisioning file for the executable
# - installed if they are external plug-ins
set(_exclude_plugins
org.blueberry.test
org.blueberry.uitest
org.mitk.gui.qt.coreapplication
org.mitk.gui.qt.diffusionimagingapp
org.mitk.example.gui.customviewer
org.mitk.example.gui.customviewer.views
org.mitk.example.gui.selectionservicemitk
org.mitk.example.gui.selectionservicemitk.views
org.mitk.example.gui.selectionserviceqt
org.mitk.example.gui.extensionpointcontribution
org.mitk.example.gui.extensionpointdefinition
org.mitk.example.gui.minimalapplication
org.mitk.example.gui.multipleperspectives
)
mitkFunctionCreateBlueBerryApplication(
NAME MitkFlowBench
DESCRIPTION "MITK FlowBench"
EXCLUDE_PLUGINS ${_exclude_plugins}
)
# Add meta dependencies (e.g. on auto-load modules from depending modules)
if(TARGET ${CMAKE_PROJECT_NAME}-autoload)
add_dependencies(MitkFlowBench ${CMAKE_PROJECT_NAME}-autoload)
endif()
#Setting application icon for macOS systems
set_target_properties(MitkFlowBench PROPERTIES MACOSX_BUNDLE_ICON_FILE "icon.icns")
if(APPLE)
install(FILES "icons/icon.icns" DESTINATION "MitkFlowBench.app/Contents/Resources")
endif(APPLE)
# Add a build time dependency to legacy BlueBerry bundles.
if(MITK_MODULES_ENABLED_PLUGINS)
add_dependencies(MitkFlowBench ${MITK_MODULES_ENABLED_PLUGINS})
endif()
diff --git a/Applications/FlowBench/icons/mitkWorkbench.rc b/Applications/FlowBench/icons/mitkFlowBench.rc
similarity index 100%
rename from Applications/FlowBench/icons/mitkWorkbench.rc
rename to Applications/FlowBench/icons/mitkFlowBench.rc
diff --git a/CMake/Whitelists/FlowBenchSegmentation.cmake b/CMake/Whitelists/FlowBenchSegmentation.cmake
index da16f6fad7..36bf724a76 100644
--- a/CMake/Whitelists/FlowBenchSegmentation.cmake
+++ b/CMake/Whitelists/FlowBenchSegmentation.cmake
@@ -1,55 +1,56 @@
set(enabled_modules
Core
CppMicroServices
DICOM
DICOMPM
DataTypesExt
AlgorithmsExt
DICOMQI
Multilabel
SceneSerializationBase
DICOMPMIO
DICOMImageIO
ContourModel
DICOMSegIO
LegacyGL
MapperExt
SceneSerialization
LegacyIO
IOExt
MultilabelIO
AppUtil
QtWidgets
QtWidgetsExt
Segmentation
SegmentationUI
PlanarFigure
Annotation
SurfaceInterpolation
GraphAlgorithms
ImageExtraction
ImageStatistics
)
set(enabled_plugins
org.blueberry.core.commands
org.blueberry.core.expressions
org.blueberry.core.runtime
org.blueberry.ui.qt
org.blueberry.ui.qt.help
org.blueberry.ui.qt.log
org.mitk.core.ext
org.mitk.core.services
org.mitk.gui.common
org.mitk.gui.qt.application
org.mitk.gui.qt.common
org.mitk.gui.qt.datamanager
+org.mitk.gui.qt.ext
org.mitk.gui.qt.flow.segmentation
org.mitk.gui.qt.flowapplication
org.mitk.gui.qt.imagenavigator
org.mitk.gui.qt.multilabelsegmentation
org.mitk.gui.qt.properties
org.mitk.gui.qt.segmentation
org.mitk.gui.qt.stdmultiwidgeteditor
org.mitk.planarfigure
)
diff --git a/Documentation/Doxygen/3-DeveloperManual/Concepts/Concepts.dox b/Documentation/Doxygen/3-DeveloperManual/Concepts/Concepts.dox
index bfddaa5cf1..9c9306d6b5 100644
--- a/Documentation/Doxygen/3-DeveloperManual/Concepts/Concepts.dox
+++ b/Documentation/Doxygen/3-DeveloperManual/Concepts/Concepts.dox
@@ -1,31 +1,32 @@
/**
\page Concepts MITK Concepts
The following items describe some issues about MITK on a more abstract level.
-# \subpage CodingPage "Coding Concepts"
-# \ref CodingPageGeneral
-# \ref CodingPageStyle
-# \ref CodingPageMITKMacros
-# \subpage MicroServices_Overview
-# Data Concepts
-# \subpage BasicDataTypesPage
-# \subpage DataManagementPage
-# \subpage ReaderWriterPage
-# \subpage MitkImagePage
+ -# \subpage MITKSegmentationTaskListsPage
-# \subpage PropertiesPage
-# \subpage GeometryOverviewPage
-# \subpage PipelineingConceptPage
-# \subpage AnnotationPage
-# \subpage PersistenceConceptPage
-# \subpage SelectionConceptPage
-# \subpage QVTKRendering
-# Interaction
-# \subpage DataInteractionPage
-# \subpage InteractionPage
-# \subpage LoggingPage
-# \subpage ExceptionPage
-# \subpage ModularizationPage "Modularization Concept"
-# \ref ModularizationPageOverview
-# \ref ModularizationPageHowTo
*/
diff --git a/Documentation/Doxygen/3-DeveloperManual/Concepts/MITKSegmentationTaskLists.md b/Documentation/Doxygen/3-DeveloperManual/Concepts/MITKSegmentationTaskLists.md
new file mode 100644
index 0000000000..ddbb5b926b
--- /dev/null
+++ b/Documentation/Doxygen/3-DeveloperManual/Concepts/MITKSegmentationTaskLists.md
@@ -0,0 +1,145 @@
+# MITK Segmentation Task Lists {#MITKSegmentationTaskListsPage}
+
+[TOC]
+
+## Overview
+
+MITK Segmentation Task Lists are a JSON-based file format defining a list of segmentation tasks.
+Segmentation tasks consist at least of a path to a reference image and a unique result path.
+The result path specifies where the final segmentation of the task is expected to be located once it is done.
+
+Optional properties of a segmentation task include a task name and description as well as various degrees of start conditions for the segmentation like a label name, a list of suggested names and colors for new labels, a label set preset, or even a pre-segmentation to begin with.
+The complete set of properties is specified further below in the file format specification.
+
+MITK Segmentation Task Lists must be considered experimental at the moment and are prone to change without any prior warning.
+They are currently supported only in the MITK FlowBench application where a dedicated widget for task navigation and management appears if an MITK Segmentation Task List has been opened.
+
+## File format
+
+MITK Segmentation Task Lists are JSON files containing a JSON object as root, which must contain the two mandatory properties `FileFormat` and `Version`:
+
+~~~{.json}
+{
+ "FileFormat": "MITK Segmentation Task List",
+ "Version": 1
+}
+~~~
+
+We also recommend to specify an optional `Name` that is used in the application if present instead of the plain filename of the JSON file:
+
+~~~{.json}
+{
+ "FileFormat": "MITK Segmentation Task List",
+ "Version": 1,
+ "Name": "My First Task List"
+}
+~~~
+
+### Tasks
+
+The root object must also contain a mandatory `Tasks` array containing JSON objects that specify the individual tasks of the task list.
+A minimum task object must consist of `Image` and `Result` file paths.
+`Image` is a path to the reference image for the task and `Result` is a path where the final segmentation is expected to be stored once it is done.
+Paths can be absolute or relative to the MITK Segmentation Task List file.
+
+~~~{.json}
+{
+ "FileFormat": "MITK Segmentation Task List",
+ "Version": 1,
+ "Tasks": [
+ {
+ "Image": "images/input.nrrd",
+ "Result": "results/output.nrrd"
+ }
+ ]
+}
+~~~
+
+In addition, tasks can define various optional properties that mainly specify the start conditions for a segmentation:
+
+- `Name` (*string*): A name for the task.
+- `Description` (*string*): A short description/definition of the task.
+- `LabelName` (*string*): The name of the first label in a new segmentation that is created for the task on the fly.
+- `LabelNameSuggestions` (*file path*): A Label Suggestions JSON file specifying names and optional colors that are suggested to the user for new labels in the segmentation.
+- `Preset` (*file path*): A Label Set Preset XML file in MITK's .lsetp file format. The preset is applied to a new segmentation that is created for the task on the fly. We recommend to use the Segmentation plugin to create such label set preset files as described in its [user guide](@ref org_mitk_views_segmentationlabelpresets).
+- `Segmentation` (*file path*): A pre-segmentation that a user can start with or should refine.
+- `Dynamic` (*boolean*): In case `Image` refers to a dynamic (3d+t) image, specifies whether the segmentation should be static (*false*), i.e. equal for all time steps, or dynamic (*true*), i.e. individual for each time step.
+
+### Task defaults / common properties
+
+If a task list contains multiple tasks with common properties, they do not have to be specified for each and every task again and again.
+Instead, the root object may contain an optional `Defaults` object that is identical in format to the tasks specified above.
+There is one exception, though: A `Defaults` object must not contain a `Result` file path, since result files of tasks must be distinct by definition.
+As the name indicates, default properties can still be overridden by individual tasks if they are specified explicitly.
+
+### Example
+
+The following example is a complete showcase of the properties and features listed above.
+It defines four tasks, three of which refer to the same reference image so it is specified as default.
+
+Remember that the only task property required to be distinct is `Result` so you are pretty free in your task design.
+For simplicity, we chose to define tasks around organs for this example and named the tasks accordingly:
+
+~~~{.json}
+{
+ "FileFormat": "MITK Segmentation Task List",
+ "Version": 1,
+ "Name": "Example Segmentation Task List",
+ "Defaults": {
+ "Image": "images/Pic3D.nrrd"
+ },
+ "Tasks": [
+ {
+ "Name": "Liver",
+ "LabelName": "Liver",
+ "LabelNameSuggestions": "suggestions/label_suggestions.json",
+ "Description": "This task provides an image and label name suggestions for new labels. The segmentation will start with an empty label named Liver.",
+ "Result": "results/liver.nrrd"
+ },
+ {
+ "Name": "Kidneys",
+ "Description": "This task provides an image and a label set preset that is applied to the new segmentation.",
+ "Preset": "presets/kidneys.lsetp",
+ "Result": "results/kidneys.nrrd"
+ },
+ {
+ "Name": "Spleen",
+ "Description": "This task provides an image and an initial (pre-)segmentation.",
+ "Segmentation": "segmentations/spleen.nrrd",
+ "Result": "results/spleen.nrrd"
+ },
+ {
+ "Name": "Surprise",
+ "Description": "And now for something completely different. This task overrides the default Image and starts with an empty static segmentation for a dynamic image.",
+ "Image": "images/US4DCyl.nrrd",
+ "Result": "results/US4DCyl.nrrd",
+ "Dynamic": false
+ }
+ ]
+}
+~~~
+
+## Label name suggestions
+
+The `LabelNameSuggestions` property of segmentation tasks is supposed to reference a JSON file that consists of an array of objects with a mandatory `name` property and an optional `color` property.
+For example:
+
+~~~{.json}
+[
+ {
+ "name": "Abdomen",
+ "color": "red"
+ },
+ {
+ "name": "Lung",
+ "color": "#00ff00"
+ },
+ {
+ "name": "Heart"
+ },
+ {
+ "name": "Aortic Valve",
+ "color": "CornflowerBlue"
+ }
+]
+~~~
diff --git a/Documentation/doxygen.conf.in b/Documentation/doxygen.conf.in
index 3ff5b9c956..d1f45ed1f2 100644
--- a/Documentation/doxygen.conf.in
+++ b/Documentation/doxygen.conf.in
@@ -1,2432 +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\" "
# 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 = 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_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 \
*.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 = "@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@/Modules/CppMicroServices/third_party" \
"@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@/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_SOURCE_DIR@/Modules/CppMicroServices/" \
"@MITK_SOURCE_DIR@/Modules/OpenCL/Documentation/doxygen/snippets/" \
"@MITK_SOURCE_DIR@/Modules/IGT/Tutorial/" \
"@MITK_SOURCE_DIR@/Plugins/org.mitk.gui.common/src/" \
"@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@" \
@MITK_DOXYGEN_ADDITIONAL_IMAGE_PATHS@
# 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 = 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 = 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" \
+ "mitkSegmentationTaskValueMacro(type, name)=bool Has##name() const; type Get##name() const; void Set##name(const type& value);" \
+ "mitkSegmentationTaskListValueMacro(type, name)=bool Has##name(size_t index) const; type Get##name(size_t index) const; void SetDefault##name(const type& value);" \
@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,
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# dependency relations are determined by the #include relations between the
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#
# 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.
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diff --git a/Modules/Core/include/mitkAbstractFileReader.h b/Modules/Core/include/mitkAbstractFileReader.h
index ee51b225f8..7b61ca5b32 100644
--- a/Modules/Core/include/mitkAbstractFileReader.h
+++ b/Modules/Core/include/mitkAbstractFileReader.h
@@ -1,239 +1,243 @@
/*============================================================================
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 AbstractFileReader_H_HEADER_INCLUDED_C1E7E521
#define AbstractFileReader_H_HEADER_INCLUDED_C1E7E521
// Macro
#include <MitkCoreExports.h>
// MITK
#include <mitkBaseData.h>
#include <mitkIFileReader.h>
#include <mitkMimeType.h>
// Microservices
#include <usGetModuleContext.h>
#include <usServiceProperties.h>
#include <usServiceRegistration.h>
namespace us
{
struct PrototypeServiceFactory;
}
namespace mitk
{
class CustomMimeType;
/**
* @brief Base class for creating mitk::BaseData objects from files or streams.
* @ingroup IO
*/
class MITKCORE_EXPORT AbstractFileReader : public mitk::IFileReader
{
public:
void SetInput(const std::string &location) override;
void SetInput(const std::string &location, std::istream *is) override;
std::string GetInputLocation() const override;
std::istream *GetInputStream() const override;
MimeType GetRegisteredMimeType() const;
/**
* @brief Reads a path or stream and creates a list of BaseData objects.
*
* The default implementation of this method (1) calls DoRead()
* (Implement the specific reader operation there) and (2) it addes general
* meta information about the loading process.
*/
std::vector<itk::SmartPointer<BaseData>> Read() override;
DataStorage::SetOfObjects::Pointer Read(mitk::DataStorage &ds) override;
ConfidenceLevel GetConfidenceLevel() const override;
Options GetOptions() const override;
us::Any GetOption(const std::string &name) const override;
void SetOptions(const Options &options) override;
void SetOption(const std::string &name, const us::Any &value) override;
void AddProgressCallback(const ProgressCallback &callback) override;
void RemoveProgressCallback(const ProgressCallback &callback) override;
/**
* Associate this reader with the MIME type returned by the current IMimeTypeProvider
* service for the provided extension if the MIME type exists, otherwise registers
* a new MIME type when RegisterService() is called.
*
* If no MIME type for \c extension is already registered, a call to RegisterService()
* will register a new MIME type and associate this reader instance with it. The MIME
* type id can be set via SetMimeType() or it will be auto-generated using \c extension,
* having the form "application/vnd.mitk.<extension>".
*
* @param context
*/
us::ServiceRegistration<IFileReader> RegisterService(us::ModuleContext *context = us::GetModuleContext());
void UnregisterService();
/**
* @return A list of files that were loaded during the last call of Read. Has to be filled by the actual reader class.
*/
std::vector< std::string > GetReadFiles() override;
+ void SetProperties(const PropertyList* properties) override;
+
protected:
/**
* @brief An input stream wrapper.
*
* If a reader can only work with input streams, use an instance
* of this class to either wrap the specified input stream or
* create a new input stream based on the input location in the
* file system.
*/
class MITKCORE_EXPORT InputStream : public std::istream
{
public:
InputStream(IFileReader *writer, std::ios_base::openmode mode = std::ios_base::in);
~InputStream() override;
private:
std::istream *m_Stream;
};
AbstractFileReader();
~AbstractFileReader() override;
AbstractFileReader(const AbstractFileReader &other);
/**
* Associate this reader instance with the given MIME type.
*
* If \c mimeType does not provide an extension list, an already
* registered mime-type object is used. Otherwise, the first entry in
* the extensions list is used to construct a mime-type name and
* register it as a new CustomMimeType service object in the default
* implementation of RegisterMimeType().
*
* @param mimeType The mime type this reader can read.
* @param description A human readable description of this reader.
*
* @throws std::invalid_argument if \c mimeType is empty.
*
* @see RegisterService
*/
explicit AbstractFileReader(const CustomMimeType &mimeType, const std::string &description);
/** Method that should be implemented by derived classes and does the real loading.
* This method is called by Read().
* This method must be implemented for each specific reader. Call
* GetInputStream() first and check for a non-null stream to read from.
* If the input stream is \c nullptr, use GetInputLocation() to read from a local
* file-system path.
*
* If the reader cannot use streams directly, use GetLocalFileName() instead.
*
* @return The created BaseData objects.
* @throws mitk::Exception
*
* @see GetLocalFileName()
* @see IFileReader::Read()
*/
virtual std::vector<itk::SmartPointer<BaseData>> DoRead() = 0;
virtual us::ServiceProperties GetServiceProperties() const;
/**
* Registers a new CustomMimeType service object.
*
* This method is called from RegisterService and the default implementation
* registers a new mime-type service object if all of the following conditions
* are true:
*
* - TODO
*
* @param context
* @return
* @throws std::invalid_argument if \c context is nullptr.
*/
virtual us::ServiceRegistration<CustomMimeType> RegisterMimeType(us::ModuleContext *context);
void SetMimeType(const CustomMimeType &mimeType);
/**
* @return The mime-type this reader can handle.
*/
const CustomMimeType *GetMimeType() const;
void SetMimeTypePrefix(const std::string &prefix);
std::string GetMimeTypePrefix() const;
void SetDescription(const std::string &description);
std::string GetDescription() const;
void SetDefaultOptions(const Options &defaultOptions);
Options GetDefaultOptions() const;
/**
* \brief Set the service ranking for this file reader.
*
* Default is zero and should only be chosen differently for a reason.
* The ranking is used to determine which reader to use if several
* equivalent readers have been found.
* It may be used to replace a default reader from MITK in your own project.
* E.g. if you want to use your own reader for nrrd files instead of the default,
* implement it and give it a higher ranking than zero.
*/
void SetRanking(int ranking);
int GetRanking() const;
/**
* @brief Get a local file name for reading.
*
* This is a convenience method for readers which cannot work natively
* with input streams. If no input stream has been been set,
* this method just returns the result of GetLocation(). However, if
* SetLocation(std::string, std::istream*) has been called with a non-null
* input stream, this method writes the contents of the stream to a temporary
* file and returns the name of the temporary file.
*
* The temporary file is deleted when either SetLocation(std::string, std::istream*)
* is called again with a different input stream or the destructor of this
* class is called.
*
* This method does not validate file names set via SetInput(std::string).
*
* @return A file path in the local file-system for reading.
*/
std::string GetLocalFileName() const;
virtual void SetDefaultDataNodeProperties(DataNode *node, const std::string &filePath);
+ const PropertyList* GetProperties() const override;
+
std::vector< std::string > m_ReadFiles;
private:
AbstractFileReader &operator=(const AbstractFileReader &other);
virtual mitk::IFileReader *Clone() const = 0;
class Impl;
std::unique_ptr<Impl> d;
};
} // namespace mitk
#endif /* AbstractFileReader_H_HEADER_INCLUDED_C1E7E521 */
diff --git a/Modules/Core/include/mitkDataNode.h b/Modules/Core/include/mitkDataNode.h
index 74dedd5ae5..b90c2e03e8 100644
--- a/Modules/Core/include/mitkDataNode.h
+++ b/Modules/Core/include/mitkDataNode.h
@@ -1,598 +1,618 @@
/*============================================================================
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 DATATREENODE_H_HEADER_INCLUDED_C1E14338
#define DATATREENODE_H_HEADER_INCLUDED_C1E14338
#include "mitkBaseData.h"
//#include "mitkMapper.h"
#include "mitkDataInteractor.h"
#include "mitkIdentifiable.h"
#include "mitkIPropertyOwner.h"
#include <fstream>
#include <iostream>
#include "mitkColorProperty.h"
#include "mitkPropertyList.h"
#include "mitkStringProperty.h"
//#include "mitkMapper.h"
#include "mitkGeometry3D.h"
#include "mitkLevelWindow.h"
#include <map>
#include <set>
class vtkLinearTransform;
namespace mitk
{
class BaseRenderer;
class Mapper;
/**
* \brief Definition of an itk::Event that is invoked when
* a DataInteractor is set on this DataNode.
*/
itkEventMacroDeclaration(InteractorChangedEvent, itk::AnyEvent);
/**
* \brief Class for nodes of the DataTree
*
* Contains the data (instance of BaseData), a list of mappers, which can
* draw the data, a transform (vtkTransform) and a list of properties
* (PropertyList).
* \ingroup DataManagement
*
* \todo clean up all the GetProperty methods. There are too many different flavours... Can most probably be reduced
* to
* <tt>bool GetProperty<type>(type&)</tt>
*
* \warning Change in semantics of SetProperty() since Aug 25th 2006. Check your usage of this method if you do
* more with properties than just call <tt>SetProperty( "key", new SomeProperty("value") )</tt>.
*/
class MITKCORE_EXPORT DataNode : public itk::DataObject, public IPropertyOwner
{
public:
typedef mitk::Geometry3D::Pointer Geometry3DPointer;
typedef std::vector<itk::SmartPointer<Mapper>> MapperVector;
typedef std::map<std::string, mitk::PropertyList::Pointer> MapOfPropertyLists;
typedef std::vector<MapOfPropertyLists::key_type> PropertyListKeyNames;
typedef std::set<std::string> GroupTagList;
mitkClassMacroItkParent(DataNode, itk::DataObject);
itkFactorylessNewMacro(Self);
// IPropertyProvider
BaseProperty::ConstPointer GetConstProperty(const std::string &propertyKey, const std::string &contextName = "", bool fallBackOnDefaultContext = true) const override;
std::vector<std::string> GetPropertyKeys(const std::string &contextName = "", bool includeDefaultContext = false) const override;
std::vector<std::string> GetPropertyContextNames() const override;
// IPropertyOwner
BaseProperty * GetNonConstProperty(const std::string &propertyKey, const std::string &contextName = "", bool fallBackOnDefaultContext = true) override;
void SetProperty(const std::string &propertyKey, BaseProperty *property, const std::string &contextName = "", bool fallBackOnDefaultContext = false) override;
void RemoveProperty(const std::string &propertyKey, const std::string &contextName = "", bool fallBackOnDefaultContext = false) override;
mitk::Mapper *GetMapper(MapperSlotId id) const;
/**
* \brief Get the data object (instance of BaseData, e.g., an Image)
* managed by this DataNode
*/
BaseData *GetData() const;
/**
* \brief Get the transformation applied prior to displaying the data as
* a vtkTransform
* \deprecated use GetData()->GetGeometry()->GetVtkTransform() instead
*/
vtkLinearTransform *GetVtkTransform(int t = 0) const;
/**
* \brief Set the data object (instance of BaseData, e.g., an Image)
* managed by this DataNode
*
* Prior set properties are kept if previous data of the node already exists and has the same
* type as the new data to be set. Otherwise, the default properties are used.
* In case that previous data already exists, the property list of the data node is cleared
* before setting new default properties.
*
* \warning the actor-mode of the vtkInteractor does not work any more, if the transform of the
* data-tree-node is connected to the transform of the basedata via vtkTransform->SetInput.
*/
virtual void SetData(mitk::BaseData *baseData);
/**
* \brief Set the Interactor.
*/
virtual void SetDataInteractor(const DataInteractor::Pointer interactor);
virtual DataInteractor::Pointer GetDataInteractor() const;
mitk::DataNode &operator=(const DataNode &right);
mitk::DataNode &operator=(BaseData *right);
virtual void SetMapper(MapperSlotId id, mitk::Mapper *mapper);
void UpdateOutputInformation() override;
void SetRequestedRegionToLargestPossibleRegion() override;
bool RequestedRegionIsOutsideOfTheBufferedRegion() override;
bool VerifyRequestedRegion() override;
void SetRequestedRegion(const itk::DataObject *data) override;
void CopyInformation(const itk::DataObject *data) override;
/**
* \brief The "names" used for (renderer-specific) PropertyLists in GetPropertyList(string).
*
* All possible values for the "renderer" parameters of
* the diverse GetProperty/List() methods.
*/
PropertyListKeyNames GetPropertyListNames() const;
/**
* \brief Set the property (instance of BaseProperty) with key \a propertyKey in the PropertyList
* of the \a renderer (if nullptr, use BaseRenderer-independent PropertyList). This is set-by-value.
*
* \warning Change in semantics since Aug 25th 2006. Check your usage of this method if you do
* more with properties than just call <tt>SetProperty( "key", new SomeProperty("value") )</tt>.
*
* \sa GetProperty
* \sa m_PropertyList
* \sa m_MapOfPropertyLists
*/
void SetProperty(const char *propertyKey, BaseProperty *property, const mitk::BaseRenderer *renderer = nullptr);
/**
* \brief Replace the property (instance of BaseProperty) with key \a propertyKey in the PropertyList
* of the \a renderer (if nullptr, use BaseRenderer-independent PropertyList). This is set-by-reference.
*
* If \a renderer is \a nullptr the property is set in the BaseRenderer-independent
* PropertyList of this DataNode.
* \sa GetProperty
* \sa m_PropertyList
* \sa m_MapOfPropertyLists
*/
void ReplaceProperty(const char *propertyKey, BaseProperty *property, const mitk::BaseRenderer *renderer = nullptr);
/**
* \brief Add the property (instance of BaseProperty) if it does
* not exist (or always if\a overwrite is\a true)
* with key \a propertyKey in the PropertyList
* of the \a renderer (if nullptr, use BaseRenderer-independent
* PropertyList). This is set-by-value.
*
* For\a overwrite ==\a false the property is\em not changed
* if it already exists. For\a overwrite ==\a true the method
* is identical to SetProperty.
*
* \sa SetProperty
* \sa GetProperty
* \sa m_PropertyList
* \sa m_MapOfPropertyLists
*/
void AddProperty(const char *propertyKey,
BaseProperty *property,
const mitk::BaseRenderer *renderer = nullptr,
bool overwrite = false);
/**
* \brief Get the PropertyList of the \a renderer. If \a renderer is \a
* nullptr, the BaseRenderer-independent PropertyList of this DataNode
* is returned.
* \sa GetProperty
* \sa m_PropertyList
* \sa m_MapOfPropertyLists
*/
mitk::PropertyList *GetPropertyList(const mitk::BaseRenderer *renderer = nullptr) const;
mitk::PropertyList *GetPropertyList(const std::string &rendererName) const;
/**
* \brief Add values from another PropertyList.
*
* Overwrites values in m_PropertyList only when possible (i.e. when types are compatible).
* If you want to allow for object type changes (replacing a "visible":BoolProperty with "visible":IntProperty,
* set \c replace .
*
* \param replace true: if \param pList contains a property "visible" of type ColorProperty and our m_PropertyList
* also has a "visible" property of a different type (e.g. BoolProperty), change the type, i.e. replace the objects
* behind the pointer.
*
* \sa SetProperty
* \sa ReplaceProperty
* \sa m_PropertyList
*/
void ConcatenatePropertyList(PropertyList *pList, bool replace = false);
/**
* \brief Get the property (instance of BaseProperty) with key \a propertyKey from the PropertyList
* of the \a renderer, if available there, otherwise use the BaseRenderer-independent PropertyList.
*
* If \a renderer is \a nullptr or the \a propertyKey cannot be found
* in the PropertyList specific to \a renderer or is disabled there, the BaseRenderer-independent
* PropertyList of this DataNode is queried.
*
* If \a fallBackOnDataProperties is true, the data property list is queried as a last resort.
*
* \sa GetPropertyList
* \sa m_PropertyList
* \sa m_MapOfPropertyLists
*/
mitk::BaseProperty *GetProperty(const char *propertyKey, const mitk::BaseRenderer *renderer = nullptr, bool fallBackOnDataProperties = true) const;
/**
* \brief Get the property of type T with key \a propertyKey from the PropertyList
* of the \a renderer, if available there, otherwise use the BaseRenderer-independent PropertyList.
*
* If \a renderer is \a nullptr or the \a propertyKey cannot be found
* in the PropertyList specific to \a renderer or is disabled there, the BaseRenderer-independent
* PropertyList of this DataNode is queried.
* \sa GetPropertyList
* \sa m_PropertyList
* \sa m_MapOfPropertyLists
*/
template <typename T>
bool GetProperty(itk::SmartPointer<T> &property,
const char *propertyKey,
const mitk::BaseRenderer *renderer = nullptr) const
{
property = dynamic_cast<T *>(GetProperty(propertyKey, renderer));
return property.IsNotNull();
}
/**
* \brief Get the property of type T with key \a propertyKey from the PropertyList
* of the \a renderer, if available there, otherwise use the BaseRenderer-independent PropertyList.
*
* If \a renderer is \a nullptr or the \a propertyKey cannot be found
* in the PropertyList specific to \a renderer or is disabled there, the BaseRenderer-independent
* PropertyList of this DataNode is queried.
* \sa GetPropertyList
* \sa m_PropertyList
* \sa m_MapOfPropertyLists
*/
template <typename T>
bool GetProperty(T *&property, const char *propertyKey, const mitk::BaseRenderer *renderer = nullptr) const
{
property = dynamic_cast<T *>(GetProperty(propertyKey, renderer));
return property != nullptr;
}
/**
* \brief Convenience access method for GenericProperty<T> properties
* (T being the type of the second parameter)
* \return \a true property was found
*/
template <typename T>
bool GetPropertyValue(const char *propertyKey, T &value, const mitk::BaseRenderer *renderer = nullptr) const
{
GenericProperty<T> *gp = dynamic_cast<GenericProperty<T> *>(GetProperty(propertyKey, renderer));
if (gp != nullptr)
{
value = gp->GetValue();
return true;
}
return false;
}
/// \brief Get a set of all group tags from this node's property list
GroupTagList GetGroupTags() const;
/**
* \brief Convenience access method for bool properties (instances of
* BoolProperty)
* \return \a true property was found
*/
bool GetBoolProperty(const char *propertyKey, bool &boolValue, const mitk::BaseRenderer *renderer = nullptr) const;
/**
* \brief Convenience access method for int properties (instances of
* IntProperty)
* \return \a true property was found
*/
bool GetIntProperty(const char *propertyKey, int &intValue, const mitk::BaseRenderer *renderer = nullptr) const;
/**
* \brief Convenience access method for float properties (instances of
* FloatProperty)
* \return \a true property was found
*/
bool GetFloatProperty(const char *propertyKey,
float &floatValue,
const mitk::BaseRenderer *renderer = nullptr) const;
/**
* \brief Convenience access method for double properties (instances of
* DoubleProperty)
*
* If there is no DoubleProperty for the given\c propertyKey argument, the method
* looks for a corresponding FloatProperty instance.
*
* \return \a true property was found
*/
bool GetDoubleProperty(const char *propertyKey,
double &doubleValue,
const mitk::BaseRenderer *renderer = nullptr) const;
/**
* \brief Convenience access method for string properties (instances of
* StringProperty)
* \return \a true property was found
*/
bool GetStringProperty(const char *propertyKey,
std::string &string,
const mitk::BaseRenderer *renderer = nullptr) const;
/**
* \brief Convenience access method for color properties (instances of
* ColorProperty)
* \return \a true property was found
*/
bool GetColor(float rgb[3], const mitk::BaseRenderer *renderer = nullptr, const char *propertyKey = "color") const;
/**
* \brief Convenience access method for level-window properties (instances of
* LevelWindowProperty)
* \return \a true property was found
*/
bool GetLevelWindow(mitk::LevelWindow &levelWindow,
const mitk::BaseRenderer *renderer = nullptr,
const char *propertyKey = "levelwindow") const;
/**
* \brief set the node as selected
*/
void SetSelected(bool selected, const mitk::BaseRenderer *renderer = nullptr);
/**
* \brief set the node as selected
* \return \a true node is selected
*/
bool IsSelected(const mitk::BaseRenderer *renderer = nullptr);
/**
* \brief Convenience access method for accessing the name of an object (instance of
* StringProperty with property-key "name")
* \return \a true property was found
*/
bool GetName(std::string &nodeName,
const mitk::BaseRenderer *renderer = nullptr,
const char *propertyKey = "name") const
{
return GetStringProperty(propertyKey, nodeName, renderer);
}
/**
* \brief Extra convenience access method for accessing the name of an object (instance of
* StringProperty with property-key "name").
*
* This method does not take the renderer specific
* propertylists into account, because the name of an object should never be renderer specific.
* \returns a std::string with the name of the object (content of "name" Property).
* If there is no "name" Property, an empty string will be returned.
*/
virtual std::string GetName() const
{
mitk::StringProperty *sp = dynamic_cast<mitk::StringProperty *>(this->GetProperty("name"));
if (sp == nullptr)
return "";
return sp->GetValue();
}
/** Value constant that is used indicate that node names are not set so far.*/
static std::string NO_NAME_VALUE()
{
return "No Name!";
}
/**
* \brief Extra convenience access method to set the name of an object.
*
- * The name will be stored in the non-renderer-specific PropertyList in a StringProperty named "name".
+ * If the data has already a "name" property, the name will be stored in it. Otherwise, the name will be stored in
+ * the non-renderer-specific PropertyList in a StringProperty named "name".
*/
virtual void SetName(const char *name)
{
if (name == nullptr)
return;
- this->SetProperty("name", StringProperty::New(name));
+
+ auto* data = this->GetData();
+
+ if (nullptr != data)
+ {
+ auto property = data->GetProperty("name");
+
+ if (property.IsNotNull())
+ {
+ auto* stringProperty = dynamic_cast<StringProperty*>(property.GetPointer());
+
+ if (nullptr != stringProperty)
+ {
+ stringProperty->SetValue(name);
+ return;
+ }
+ }
+ }
+
+ this->SetStringProperty("name", name);
}
/**
* \brief Extra convenience access method to set the name of an object.
*
- * The name will be stored in the non-renderer-specific PropertyList in a StringProperty named "name".
+ * \sa SetName(const char*)
*/
- virtual void SetName(const std::string name) { this->SetName(name.c_str()); }
+ virtual void SetName(const std::string& name) { this->SetName(name.c_str()); }
/**
* \brief Convenience access method for visibility properties (instances
* of BoolProperty with property-key "visible")
* \return \a true property was found
* \sa IsVisible
*/
bool GetVisibility(bool &visible, const mitk::BaseRenderer *renderer, const char *propertyKey = "visible") const
{
return GetBoolProperty(propertyKey, visible, renderer);
}
/**
* \brief Convenience access method for opacity properties (instances of
* FloatProperty)
* \return \a true property was found
*/
bool GetOpacity(float &opacity, const mitk::BaseRenderer *renderer, const char *propertyKey = "opacity") const;
/**
* \brief Convenience access method for boolean properties (instances
* of BoolProperty). Return value is the value of the property. If the property is
* not found, the value of \a defaultIsOn is returned.
*
* Thus, the return value has a different meaning than in the
* GetBoolProperty method!
* \sa GetBoolProperty
*/
bool IsOn(const char *propertyKey, const mitk::BaseRenderer *renderer, bool defaultIsOn = true) const
{
if (propertyKey == nullptr)
return defaultIsOn;
GetBoolProperty(propertyKey, defaultIsOn, renderer);
return defaultIsOn;
}
/**
* \brief Convenience access method for visibility properties (instances
* of BoolProperty). Return value is the visibility. Default is
* visible==true, i.e., true is returned even if the property (\a
* propertyKey) is not found.
*
* Thus, the return value has a different meaning than in the
* GetVisibility method!
* \sa GetVisibility
* \sa IsOn
*/
bool IsVisible(const mitk::BaseRenderer *renderer,
const char *propertyKey = "visible",
bool defaultIsOn = true) const
{
return IsOn(propertyKey, renderer, defaultIsOn);
}
/**
* \brief Convenience method for setting color properties (instances of
* ColorProperty)
*/
void SetColor(const mitk::Color &color,
const mitk::BaseRenderer *renderer = nullptr,
const char *propertyKey = "color");
/**
* \brief Convenience method for setting color properties (instances of
* ColorProperty)
*/
void SetColor(float red,
float green,
float blue,
const mitk::BaseRenderer *renderer = nullptr,
const char *propertyKey = "color");
/**
* \brief Convenience method for setting color properties (instances of
* ColorProperty)
*/
void SetColor(const float rgb[3], const mitk::BaseRenderer *renderer = nullptr, const char *propertyKey = "color");
/**
* \brief Convenience method for setting visibility properties (instances
* of BoolProperty)
* \param visible If set to true, the data will be rendered. If false, the render will skip this data.
* \param renderer Specify a renderer if the visibility shall be specific to a renderer
* \param propertyKey Can be used to specify a user defined name of the visibility propery.
*/
void SetVisibility(bool visible, const mitk::BaseRenderer *renderer = nullptr, const char *propertyKey = "visible");
/**
* \brief Convenience method for setting opacity properties (instances of
* FloatProperty)
*/
void SetOpacity(float opacity, const mitk::BaseRenderer *renderer = nullptr, const char *propertyKey = "opacity");
/**
* \brief Convenience method for setting level-window properties
* (instances of LevelWindowProperty)
*/
void SetLevelWindow(mitk::LevelWindow levelWindow,
const mitk::BaseRenderer *renderer = nullptr,
const char *propertyKey = "levelwindow");
/**
* \brief Convenience method for setting int properties (instances of
* IntProperty)
*/
void SetIntProperty(const char *propertyKey, int intValue, const mitk::BaseRenderer *renderer = nullptr);
/**
* \brief Convenience method for setting boolean properties (instances of
* BoolProperty)
*/
void SetBoolProperty(const char *propertyKey, bool boolValue, const mitk::BaseRenderer *renderer = nullptr);
/**
* \brief Convenience method for setting float properties (instances of
* FloatProperty)
*/
void SetFloatProperty(const char *propertyKey, float floatValue, const mitk::BaseRenderer *renderer = nullptr);
/**
* \brief Convenience method for setting double properties (instances of
* DoubleProperty)
*/
void SetDoubleProperty(const char *propertyKey, double doubleValue, const mitk::BaseRenderer *renderer = nullptr);
/**
* \brief Convenience method for setting string properties (instances of
* StringProperty)
*/
void SetStringProperty(const char *propertyKey, const char *string, const mitk::BaseRenderer *renderer = nullptr);
/**
* \brief Get the timestamp of the last change of the contents of this node or
* the referenced BaseData.
*/
itk::ModifiedTimeType GetMTime() const override;
/**
* \brief Get the timestamp of the last change of the reference to the
* BaseData.
*/
unsigned long GetDataReferenceChangedTime() const { return m_DataReferenceChangedTime.GetMTime(); }
protected:
DataNode();
~DataNode() override;
/// Invoked when the property list was modified. Calls Modified() of the DataNode
virtual void PropertyListModified(const itk::Object *caller, const itk::EventObject &event);
/// \brief Mapper-slots
mutable MapperVector m_Mappers;
/**
* \brief The data object (instance of BaseData, e.g., an Image) managed
* by this DataNode
*/
BaseData::Pointer m_Data;
/**
* \brief BaseRenderer-independent PropertyList
*
* Properties herein can be overwritten specifically for each BaseRenderer
* by the BaseRenderer-specific properties defined in m_MapOfPropertyLists.
*/
PropertyList::Pointer m_PropertyList;
/// \brief Map associating each BaseRenderer with its own PropertyList
mutable MapOfPropertyLists m_MapOfPropertyLists;
DataInteractor::Pointer m_DataInteractor;
/// \brief Timestamp of the last change of m_Data
itk::TimeStamp m_DataReferenceChangedTime;
unsigned long m_PropertyListModifiedObserverTag;
};
MITKCORE_EXPORT std::istream &operator>>(std::istream &i, DataNode::Pointer &dtn);
MITKCORE_EXPORT std::ostream &operator<<(std::ostream &o, DataNode::Pointer &dtn);
} // namespace mitk
#endif /* DATATREENODE_H_HEADER_INCLUDED_C1E14338 */
diff --git a/Modules/Core/include/mitkIFileReader.h b/Modules/Core/include/mitkIFileReader.h
index c67c925778..615cb27f80 100644
--- a/Modules/Core/include/mitkIFileReader.h
+++ b/Modules/Core/include/mitkIFileReader.h
@@ -1,131 +1,156 @@
/*============================================================================
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 IFileReader_H_HEADER_INCLUDED_C1E7E521
#define IFileReader_H_HEADER_INCLUDED_C1E7E521
#include <mitkDataStorage.h>
#include <mitkIFileIO.h>
#include <mitkServiceInterface.h>
namespace mitk
{
class BaseData;
+ class PropertyList;
}
namespace itk
{
template <class T>
class SmartPointer;
}
namespace mitk
{
/**
* \ingroup IO
* \ingroup MicroServices_Interfaces
*
* \brief The common interface for all MITK file readers.
*
* Implementations of this interface must be registered as a service
* to make themselve available via the service registry. If the
* implementation is state-full, the service should be registered using
* a PrototypeServiceFactory.
*
* The file reader implementation is associated with a mime-type, specified
* in the service property PROP_MIMETYPE(). The specified mime-type should
* have a corresponding CustomMimeType service object, registered by the reader
* or some other party.
*
* It is recommended to derive new implementations from AbstractFileReader or
* from AbstractFileIO (if both reader and writer is implemented),
* which provide correct service registration semantics.
*
* \sa AbstractFileReader
* \sa AbstractFileIO
* \sa CustomMimeType
* \sa FileReaderRegistry
* \sa IFileWriter
*/
struct MITKCORE_EXPORT IFileReader : public IFileIO
{
~IFileReader() override;
/**
* \brief Set the input location.
* \param location The file name to read from.
*/
virtual void SetInput(const std::string &location) = 0;
/**
* @brief Set an input stream to read from.
* @param location A custom label for the input stream.
* @param is The input stream.
*
* If \c is is \c nullptr, this clears the current input stream and \c location
* is interpreted as a file-system path. Otherwise, \c location is a custom
* label describing the input stream \c is.
*/
virtual void SetInput(const std::string &location, std::istream *is) = 0;
/**
* @brief Get the current input location.
* @return The input location.
*/
virtual std::string GetInputLocation() const = 0;
/**
* @brief Get the input stream.
* @return The currently set input stream.
*/
virtual std::istream *GetInputStream() const = 0;
/**
* \brief Reads the specified file or input stream and returns its contents.
*
* \return A list of created BaseData objects.
*
* If GetInputStream() returns a non-null value, this method must use
* the returned stream object to read the data from. If no input stream
* was set, the data must be read from the path returned by GetInputLocation().
*
* \throws mitk::Exception
*/
virtual std::vector<itk::SmartPointer<BaseData>> Read() = 0;
/**
* \brief Reads the specified file or input stream, loading its
* contents into the provided DataStorage.
*
* \param ds The DataStorage to which the data is added.
* \return The set of added DataNodes to \c ds.
*
* This method may be overridden by implementations to create or
* reconstructed a hierarchy of mitk::DataNode instances in the
* provided mitk::DataStorage.
*
* \throws mitk::Exception
*/
virtual DataStorage::SetOfObjects::Pointer Read(mitk::DataStorage &ds) = 0;
/**
* @return A list of files that were loaded during the last call of Read.
*/
virtual std::vector< std::string > GetReadFiles() = 0;
+
+ /**
+ * \brief Optionally provide base data properties as a source of meta data.
+ *
+ * The purpose of this method is not to preset the base data property list
+ * of the read data but to provide access to meta data of previous read
+ * operations that may be beneficial for the new read operation.
+ *
+ * A typical usecase may occur when reading files from an MITK scene file
+ * in which case base data properties are already provided in addition to
+ * the actual data file. If such a data file references other files
+ * relative to its original location on the filesystem, the original
+ * location can be retrieved from the base data properties. In this
+ * scenario, GetInputLocation() would return a path within a temporary
+ * directory in which the scene file has been extracted. This is not the
+ * intended base path for searching referenced external data files.
+ */
+ virtual void SetProperties(const PropertyList* properties) = 0;
+
+ protected:
+
+ /** \sa SetProperties().
+ */
+ virtual const PropertyList* GetProperties() const = 0;
};
} // namespace mitk
MITK_DECLARE_SERVICE_INTERFACE(mitk::IFileReader, "org.mitk.IFileReader")
#endif /* IFileReader_H_HEADER_INCLUDED_C1E7E521 */
diff --git a/Modules/Core/include/mitkIOUtil.h b/Modules/Core/include/mitkIOUtil.h
index 24f878efa2..036258e4f6 100644
--- a/Modules/Core/include/mitkIOUtil.h
+++ b/Modules/Core/include/mitkIOUtil.h
@@ -1,434 +1,440 @@
/*============================================================================
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 MITKIOUTIL_H
#define MITKIOUTIL_H
#include <MitkCoreExports.h>
#include <mitkDataStorage.h>
#include <mitkImage.h>
#include <mitkPointSet.h>
#include <mitkSurface.h>
#include <mitkFileReaderSelector.h>
#include <mitkFileWriterSelector.h>
#include <mitkIFileReader.h>
#include <mitkIFileWriter.h>
#include <fstream>
namespace us
{
class ModuleResource;
}
namespace mitk
{
+ class PropertyList;
+
/**
* \ingroup IO
*
* \brief A utility class to load and save data from/to the local file system.
*
* \see QmitkIOUtil
*/
class MITKCORE_EXPORT IOUtil
{
public:
/**Struct that containes information regarding the current loading process. (e.g. Path that should be loaded,
all found readers for the load path,...). It is set be IOUtil and used to pass information via the option callback
in load operations.
*/
struct MITKCORE_EXPORT LoadInfo
{
LoadInfo(const std::string &path);
std::string m_Path;
std::vector<BaseData::Pointer> m_Output;
FileReaderSelector m_ReaderSelector;
bool m_Cancel;
+
+ const PropertyList* m_Properties;
};
/**Struct that is the base class for option callbacks used in load operations. The callback is used by IOUtil, if
more than one suitable reader was found or the a reader containes options that can be set. The callback allows to
change option settings and select the reader that should be used (via loadInfo).
*/
struct MITKCORE_EXPORT ReaderOptionsFunctorBase
{
virtual bool operator()(LoadInfo &loadInfo) const = 0;
};
struct MITKCORE_EXPORT SaveInfo
{
SaveInfo(const BaseData *baseData, const MimeType &mimeType, const std::string &path);
bool operator<(const SaveInfo &other) const;
/// The BaseData object to save.
const BaseData *m_BaseData;
/// Contains a set of IFileWriter objects.
FileWriterSelector m_WriterSelector;
/// The selected mime-type, used to restrict results from FileWriterSelector.
MimeType m_MimeType;
/// The path to write the BaseData object to.
std::string m_Path;
/// Flag indicating if sub-sequent save operations are to be canceled.
bool m_Cancel;
};
/**Struct that is the base class for option callbacks used in save operations. The callback is used by IOUtil, if
more than one suitable writer was found or the a writer containes options that can be set. The callback allows to
change option settings and select the writer that should be used (via saveInfo).
*/
struct MITKCORE_EXPORT WriterOptionsFunctorBase
{
virtual bool operator()(SaveInfo &saveInfo) const = 0;
};
/**
* Get the file system path where the running executable is located.
*
* @return The location of the currently running executable, without the filename.
*/
static std::string GetProgramPath();
/**
* Get the default temporary path.
*
* @return The default path for temporary data.
*/
static std::string GetTempPath();
/**
* Returns the Directory Seperator for the current OS.
*
* @return the Directory Seperator for the current OS, i.e. "\\" for Windows and "/" otherwise.
*/
static char GetDirectorySeparator();
/**
* Create and open a temporary file.
*
* This method generates a unique temporary filename from \c templateName, creates
* and opens the file using the output stream \c tmpStream and returns the name of
* the newly create file.
*
* The \c templateName argument must contain six consective 'X' characters ("XXXXXX")
* and these are replaced with a string that makes the filename unique.
*
* The file is created with read and write permissions for owner only.
*
* @param tmpStream The output stream for writing to the temporary file.
* @param templateName An optional template for the filename.
* @param path An optional path where the temporary file should be created. Defaults
* to the default temp path as returned by GetTempPath().
* @return The filename of the created temporary file.
*
* @throw mitk::Exception if the temporary file could not be created.
*/
static std::string CreateTemporaryFile(std::ofstream &tmpStream,
const std::string &templateName = "XXXXXX",
std::string path = std::string());
/**
* Create and open a temporary file.
*
* This method generates a unique temporary filename from \c templateName, creates
* and opens the file using the output stream \c tmpStream and the specified open
* mode \c mode and returns the name of the newly create file. The open mode is always
* OR'd with <code>std::ios_base::out | std::ios_base::trunc</code>.
*
* The \c templateName argument must contain six consective 'X' characters ("XXXXXX")
* and these are replaced with a string that makes the filename unique.
*
* The file is created with read and write permissions for owner only.
*
* @param tmpStream The output stream for writing to the temporary file.
* @param mode The open mode for the temporary file stream.
* @param templateName An optional template for the filename.
* @param path An optional path where the temporary file should be created. Defaults
* to the default temp path as returned by GetTempPath().
* @return The filename of the created temporary file.
*
* @throw mitk::Exception if the temporary file could not be created.
*/
static std::string CreateTemporaryFile(std::ofstream &tmpStream,
std::ios_base::openmode mode,
const std::string &templateName = "XXXXXX",
std::string path = std::string());
/**
* Creates an empty temporary file.
*
* This method generates a unique temporary filename from \c templateName and creates
* this file.
*
* The file is created with read and write permissions for owner only.
*
* ---
* This version is potentially unsafe because the created temporary file is not kept open
* and could be used by another process between calling this method and opening the returned
* file path for reading or writing.
* ---
*
* @return The filename of the created temporary file.
* @param templateName An optional template for the filename.
* @param path An optional path where the temporary file should be created. Defaults
* to the default temp path as returned by GetTempPath().
* @throw mitk::Exception if the temporary file could not be created.
*/
static std::string CreateTemporaryFile(const std::string &templateName = "XXXXXX",
std::string path = std::string());
/**
* Create a temporary directory.
*
* This method generates a uniquely named temporary directory from \c templateName.
* The last set of six consecutive 'X' characters in \c templateName is replaced
* with a string that makes the directory name unique.
*
* The directory is created with read, write and executable permissions for owner only.
*
* @param templateName An optional template for the directory name.
* @param path An optional path where the temporary directory should be created. Defaults
* to the default temp path as returned by GetTempPath().
* @return The filename of the created temporary file.
*
* @throw mitk::Exception if the temporary directory could not be created.
*/
static std::string CreateTemporaryDirectory(const std::string &templateName = "XXXXXX",
std::string path = std::string());
/**
* @brief Load a file into the given DataStorage.
*
* This method calls Load(const std::vector<std::string>&, DataStorage&) with a
* one-element vector.
*
* @param path The absolute file name including the file extension.
* @param storage A DataStorage object to which the loaded data will be added.
* @param optionsCallback Pointer to a callback instance. The callback is used by
* the load operation if more the suitable reader was found or the reader has options
* that can be set.
* @return The set of added DataNode objects.
* @throws mitk::Exception if \c path could not be loaded.
*
* @sa Load(const std::vector<std::string>&, DataStorage&)
*/
static DataStorage::SetOfObjects::Pointer Load(const std::string &path, DataStorage &storage,
const ReaderOptionsFunctorBase *optionsCallback = nullptr);
/**
* @brief Load a file into the given DataStorage given user defined IFileReader::Options.
*
* This method calls Load(const std::vector<std::string>&, DataStorage&) with a
* one-element vector.
*
* @param path The absolute file name including the file extension.
* @param options IFileReader option instance that should be used if selected reader
* has options.
* @param storage A DataStorage object to which the loaded data will be added.
* @return The set of added DataNode objects.
* @throws mitk::Exception if \c path could not be loaded.
*
* @sa Load(const std::vector<std::string>&, DataStorage&)
*/
static DataStorage::SetOfObjects::Pointer Load(const std::string &path,
const IFileReader::Options &options,
DataStorage &storage);
/**
* @brief Load a file and return the loaded data.
*
* This method calls Load(const std::vector<std::string>&) with a
* one-element vector.
*
* @param path The absolute file name including the file extension.
* @param optionsCallback Pointer to a callback instance. The callback is used by
* the load operation if more the suitable reader was found or the reader has options
* that can be set.
* @return The set of added DataNode objects.
* @throws mitk::Exception if \c path could not be loaded.
*
* @sa Load(const std::vector<std::string>&, DataStorage&)
*/
static std::vector<BaseData::Pointer> Load(const std::string &path,
const ReaderOptionsFunctorBase *optionsCallback = nullptr);
template <typename T>
static typename T::Pointer Load(const std::string& path, const ReaderOptionsFunctorBase *optionsCallback = nullptr)
{
return dynamic_cast<T*>(Load(path, optionsCallback).at(0).GetPointer());
}
/**
* @brief Load a file and return the loaded data.
*
* This method calls Load(const std::vector<std::string>&) with a
* one-element vector.
*
* @param path The absolute file name including the file extension.
* @param options IFileReader option instance that should be used if selected reader
* has options.
* @return The set of added DataNode objects.
* @throws mitk::Exception if \c path could not be loaded.
*
* @sa Load(const std::vector<std::string>&, DataStorage&)
*/
static std::vector<BaseData::Pointer> Load(const std::string &path, const IFileReader::Options &options);
template <typename T>
static typename T::Pointer Load(const std::string& path, const IFileReader::Options &options)
{
return dynamic_cast<T*>(Load(path, options).at(0).GetPointer());
}
/**
* @brief Loads a list of file paths into the given DataStorage.
*
* If an entry in \c paths cannot be loaded, this method will continue to load
* the remaining entries into \c storage and throw an exception afterwards.
*
* @param paths A list of absolute file names including the file extension.
* @param storage A DataStorage object to which the loaded data will be added.
* @param optionsCallback Pointer to a callback instance. The callback is used by
* the load operation if more the suitable reader was found or the reader has options
* that can be set.
* @return The set of added DataNode objects.
* @throws mitk::Exception if an entry in \c paths could not be loaded.
*/
static DataStorage::SetOfObjects::Pointer Load(const std::vector<std::string> &paths, DataStorage &storage,
const ReaderOptionsFunctorBase *optionsCallback = nullptr);
static std::vector<BaseData::Pointer> Load(const std::vector<std::string> &paths,
const ReaderOptionsFunctorBase *optionsCallback = nullptr);
/**
* @brief Loads the contents of a us::ModuleResource and returns the corresponding mitk::BaseData
* @param usResource a ModuleResource, representing a BaseData object
* @param mode Optional parameter to set the openmode of the stream
* @return The set of loaded BaseData objects. \c Should contain either one or zero elements, since a resource
* stream
* respresents one object.
* @throws mitk::Exception if no reader was found for the stream.
*/
static std::vector<BaseData::Pointer> Load(const us::ModuleResource &usResource,
std::ios_base::openmode mode = std::ios_base::in);
template <typename T>
static typename T::Pointer Load(const us::ModuleResource &usResource, std::ios_base::openmode mode = std::ios_base::in)
{
return dynamic_cast<T*>(Load(usResource, mode).at(0).GetPointer());
}
+ static BaseData::Pointer Load(const std::string& path, const PropertyList* properties);
+
/**
* @brief Save a mitk::BaseData instance.
* @param data The data to save.
* @param path The path to the image including file name and and optional file extension.
* If no extension is set, the default extension and mime-type for the
* BaseData type of \c data is used.
* @param setPathProperty
* @throws mitk::Exception if no writer for \c data is available or the writer
* is not able to write the image.
*/
static void Save(const mitk::BaseData *data, const std::string &path, bool setPathProperty = false);
/**
* @brief Save a mitk::BaseData instance.
* @param data The data to save.
* @param path The path to the image including file name and an optional file extension.
* If no extension is set, the default extension and mime-type for the
* BaseData type of \c data is used.
* @param options The IFileWriter options to use for the selected writer.
* @param setPathProperty
* @throws mitk::Exception if no writer for \c data is available or the writer
* is not able to write the image.
*/
static void Save(const mitk::BaseData *data, const std::string &path, const IFileWriter::Options &options, bool setPathProperty = false);
/**
* @brief Save a mitk::BaseData instance.
* @param data The data to save.
* @param mimeType The mime-type to use for writing \c data.
* @param path The path to the image including file name and an optional file extension.
* @param addExtension If \c true, an extension according to the given \c mimeType
* is added to \c path if it does not contain one. If \c path already contains
* a file name extension, it is not checked for compatibility with \c mimeType.
* @param setPathProperty
*
* @throws mitk::Exception if no writer for the combination of \c data and \c mimeType is
* available or the writer is not able to write the image.
*/
static void Save(const mitk::BaseData *data,
const std::string &mimeType,
const std::string &path,
bool addExtension = true,
bool setPathProperty = false);
/**
* @brief Save a mitk::BaseData instance.
* @param data The data to save.
* @param mimeType The mime-type to use for writing \c data.
* @param path The path to the image including file name and an optional file extension.
* @param options Configuration data for the used IFileWriter instance.
* @param addExtension If \c true, an extension according to the given \c mimeType
* is added to \c path if it does not contain one. If \c path already contains
* a file name extension, it is not checked for compatibility with \c mimeType.
* @param setPathProperty
*
* @throws mitk::Exception if no writer for the combination of \c data and \c mimeType is
* available or the writer is not able to write the image.
*/
static void Save(const mitk::BaseData *data,
const std::string &mimeType,
const std::string &path,
const mitk::IFileWriter::Options &options,
bool addExtension = true,
bool setPathProperty = false);
/**
* @brief Use SaveInfo objects to save BaseData instances.
*
* This is a low-level method for directly working with SaveInfo objects. Usually,
* the Save() methods taking a BaseData object as an argument are more appropriate.
*
* @param saveInfos A list of SaveInfo objects for saving contained BaseData objects.
* @param setPathProperty
*
* @see Save(const mitk::BaseData*, const std::string&)
*/
static void Save(std::vector<SaveInfo> &saveInfos, bool setPathProperty = false);
protected:
static std::string Load(std::vector<LoadInfo> &loadInfos,
DataStorage::SetOfObjects *nodeResult,
DataStorage *ds,
const ReaderOptionsFunctorBase *optionsCallback);
static std::string Save(const BaseData *data,
const std::string &mimeType,
const std::string &path,
WriterOptionsFunctorBase *optionsCallback,
bool addExtension,
bool setPathProperty);
static std::string Save(std::vector<SaveInfo> &saveInfos,
WriterOptionsFunctorBase *optionsCallback,
bool setPathProperty);
private:
struct Impl;
};
}
#endif // MITKIOUTIL_H
diff --git a/Modules/Core/src/IO/mitkAbstractFileReader.cpp b/Modules/Core/src/IO/mitkAbstractFileReader.cpp
index 3085cb6efd..afadf96376 100644
--- a/Modules/Core/src/IO/mitkAbstractFileReader.cpp
+++ b/Modules/Core/src/IO/mitkAbstractFileReader.cpp
@@ -1,334 +1,340 @@
/*============================================================================
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 <mitkAbstractFileReader.h>
#include <mitkCustomMimeType.h>
#include <mitkIOUtil.h>
#include <mitkUtf8Util.h>
#include <mitkFileReaderWriterBase.h>
#include <mitkVersion.h>
#include <mitkIOMetaInformationPropertyConstants.h>
#include <usGetModuleContext.h>
#include <usModuleContext.h>
#include <usPrototypeServiceFactory.h>
#include <itksys/SystemTools.hxx>
#include <fstream>
namespace mitk
{
AbstractFileReader::InputStream::InputStream(IFileReader *reader, std::ios_base::openmode mode)
: std::istream(nullptr), m_Stream(nullptr)
{
std::istream *stream = reader->GetInputStream();
if (stream)
{
this->init(stream->rdbuf());
}
else
{
m_Stream = new std::ifstream(reader->GetInputLocation().c_str(), mode);
this->init(m_Stream->rdbuf());
}
}
AbstractFileReader::InputStream::~InputStream() { delete m_Stream; }
class AbstractFileReader::Impl : public FileReaderWriterBase
{
public:
Impl() : FileReaderWriterBase(), m_Stream(nullptr), m_PrototypeFactory(nullptr) {}
Impl(const Impl &other) : FileReaderWriterBase(other), m_Stream(nullptr), m_PrototypeFactory(nullptr) {}
std::string m_Location;
std::string m_TmpFile;
std::istream *m_Stream;
us::PrototypeServiceFactory *m_PrototypeFactory;
us::ServiceRegistration<IFileReader> m_Reg;
+
+ const PropertyList* m_Properties;
};
AbstractFileReader::AbstractFileReader() : d(new Impl) {}
AbstractFileReader::~AbstractFileReader()
{
UnregisterService();
delete d->m_PrototypeFactory;
if (!d->m_TmpFile.empty())
{
std::remove(d->m_TmpFile.c_str());
}
}
AbstractFileReader::AbstractFileReader(const AbstractFileReader &other) : IFileReader(), d(new Impl(*other.d.get()))
{
}
AbstractFileReader::AbstractFileReader(const CustomMimeType &mimeType, const std::string &description) : d(new Impl)
{
d->SetMimeType(mimeType);
d->SetDescription(description);
}
////////////////////// Reading /////////////////////////
std::vector<BaseData::Pointer> AbstractFileReader::Read()
{
std::vector<BaseData::Pointer> result = this->DoRead();
const auto options = this->GetOptions();
for (auto& data : result)
{
data->SetProperty(PropertyKeyPathToPropertyName(IOMetaInformationPropertyConstants::READER_DESCRIPTION()), StringProperty::New(d->GetDescription()));
data->SetProperty(PropertyKeyPathToPropertyName(IOMetaInformationPropertyConstants::READER_VERSION()), StringProperty::New(MITK_VERSION_STRING));
data->SetProperty(PropertyKeyPathToPropertyName(IOMetaInformationPropertyConstants::READER_MIME_NAME()), StringProperty::New(d->GetMimeType()->GetName()));
data->SetProperty(PropertyKeyPathToPropertyName(IOMetaInformationPropertyConstants::READER_MIME_CATEGORY()), StringProperty::New(d->GetMimeType()->GetCategory()));
if (this->GetInputStream() == nullptr)
{
data->SetProperty(PropertyKeyPathToPropertyName(IOMetaInformationPropertyConstants::READER_INPUTLOCATION()), StringProperty::New(Utf8Util::Local8BitToUtf8(this->GetInputLocation())));
}
for (const auto& option : options)
{
auto optionpath = IOMetaInformationPropertyConstants::READER_OPTION_ROOT().AddElement(option.first);
data->SetProperty(PropertyKeyPathToPropertyName(optionpath), StringProperty::New(option.second.ToString()));
}
}
return result;
}
DataStorage::SetOfObjects::Pointer AbstractFileReader::Read(DataStorage &ds)
{
DataStorage::SetOfObjects::Pointer result = DataStorage::SetOfObjects::New();
std::vector<BaseData::Pointer> data = this->Read();
for (auto iter = data.begin(); iter != data.end(); ++iter)
{
mitk::DataNode::Pointer node = mitk::DataNode::New();
node->SetData(*iter);
this->SetDefaultDataNodeProperties(node, this->GetInputLocation());
ds.Add(node);
result->InsertElement(result->Size(), node);
}
return result;
}
IFileReader::ConfidenceLevel AbstractFileReader::GetConfidenceLevel() const
{
if (d->m_Stream)
{
if (*d->m_Stream)
return Supported;
}
else
{
if (itksys::SystemTools::FileExists(Utf8Util::Local8BitToUtf8(this->GetInputLocation()).c_str(), true))
{
return Supported;
}
}
return Unsupported;
}
//////////// µS Registration & Properties //////////////
us::ServiceRegistration<IFileReader> AbstractFileReader::RegisterService(us::ModuleContext *context)
{
if (d->m_PrototypeFactory)
return us::ServiceRegistration<IFileReader>();
if (context == nullptr)
{
context = us::GetModuleContext();
}
d->RegisterMimeType(context);
if (this->GetMimeType()->GetName().empty())
{
MITK_WARN << "Not registering reader due to empty MIME type.";
return us::ServiceRegistration<IFileReader>();
}
struct PrototypeFactory : public us::PrototypeServiceFactory
{
AbstractFileReader *const m_Prototype;
PrototypeFactory(AbstractFileReader *prototype) : m_Prototype(prototype) {}
us::InterfaceMap GetService(us::Module * /*module*/,
const us::ServiceRegistrationBase & /*registration*/) override
{
return us::MakeInterfaceMap<IFileReader>(m_Prototype->Clone());
}
void UngetService(us::Module * /*module*/,
const us::ServiceRegistrationBase & /*registration*/,
const us::InterfaceMap &service) override
{
delete us::ExtractInterface<IFileReader>(service);
}
};
d->m_PrototypeFactory = new PrototypeFactory(this);
us::ServiceProperties props = this->GetServiceProperties();
d->m_Reg = context->RegisterService<IFileReader>(d->m_PrototypeFactory, props);
return d->m_Reg;
}
void AbstractFileReader::UnregisterService()
{
try
{
d->m_Reg.Unregister();
}
catch (const std::exception &)
{
}
}
us::ServiceProperties AbstractFileReader::GetServiceProperties() const
{
us::ServiceProperties result;
result[IFileReader::PROP_DESCRIPTION()] = this->GetDescription();
result[IFileReader::PROP_MIMETYPE()] = this->GetMimeType()->GetName();
result[us::ServiceConstants::SERVICE_RANKING()] = this->GetRanking();
return result;
}
us::ServiceRegistration<CustomMimeType> AbstractFileReader::RegisterMimeType(us::ModuleContext *context)
{
return d->RegisterMimeType(context);
}
std::vector< std::string > AbstractFileReader::GetReadFiles(){ return m_ReadFiles; }
void AbstractFileReader::SetMimeType(const CustomMimeType &mimeType) { d->SetMimeType(mimeType); }
void AbstractFileReader::SetDescription(const std::string &description) { d->SetDescription(description); }
void AbstractFileReader::SetRanking(int ranking) { d->SetRanking(ranking); }
int AbstractFileReader::GetRanking() const { return d->GetRanking(); }
std::string AbstractFileReader::GetLocalFileName() const
{
std::string localFileName;
if (d->m_Stream)
{
if (d->m_TmpFile.empty())
{
// write the stream contents to temporary file
std::string ext = Utf8Util::Utf8ToLocal8Bit(itksys::SystemTools::GetFilenameExtension(Utf8Util::Local8BitToUtf8(this->GetInputLocation())));
std::ofstream tmpStream;
localFileName = mitk::IOUtil::CreateTemporaryFile(
tmpStream, std::ios_base::out | std::ios_base::trunc | std::ios_base::binary, "XXXXXX" + ext);
tmpStream << d->m_Stream->rdbuf();
d->m_TmpFile = localFileName;
}
else
{
localFileName = d->m_TmpFile;
}
}
else
{
localFileName = d->m_Location;
}
return localFileName;
}
//////////////////////// Options ///////////////////////
void AbstractFileReader::SetDefaultOptions(const IFileReader::Options &defaultOptions)
{
d->SetDefaultOptions(defaultOptions);
}
IFileReader::Options AbstractFileReader::GetDefaultOptions() const { return d->GetDefaultOptions(); }
void AbstractFileReader::SetInput(const std::string &location)
{
d->m_Location = location;
d->m_Stream = nullptr;
}
void AbstractFileReader::SetInput(const std::string &location, std::istream *is)
{
if (d->m_Stream != is && !d->m_TmpFile.empty())
{
std::remove(d->m_TmpFile.c_str());
d->m_TmpFile.clear();
}
d->m_Location = location;
d->m_Stream = is;
}
std::string AbstractFileReader::GetInputLocation() const { return d->m_Location; }
std::istream *AbstractFileReader::GetInputStream() const { return d->m_Stream; }
MimeType AbstractFileReader::GetRegisteredMimeType() const { return d->GetRegisteredMimeType(); }
IFileReader::Options AbstractFileReader::GetOptions() const { return d->GetOptions(); }
us::Any AbstractFileReader::GetOption(const std::string &name) const { return d->GetOption(name); }
void AbstractFileReader::SetOptions(const Options &options) { d->SetOptions(options); }
void AbstractFileReader::SetOption(const std::string &name, const us::Any &value) { d->SetOption(name, value); }
////////////////// MISC //////////////////
void AbstractFileReader::AddProgressCallback(const ProgressCallback &callback) { d->AddProgressCallback(callback); }
void AbstractFileReader::RemoveProgressCallback(const ProgressCallback &callback)
{
d->RemoveProgressCallback(callback);
}
+ void AbstractFileReader::SetProperties(const PropertyList* properties)
+ {
+ d->m_Properties = properties;
+ }
+
+ const PropertyList* AbstractFileReader::GetProperties() const
+ {
+ return d->m_Properties;
+ }
+
////////////////// µS related Getters //////////////////
const CustomMimeType *AbstractFileReader::GetMimeType() const { return d->GetMimeType(); }
void AbstractFileReader::SetMimeTypePrefix(const std::string &prefix) { d->SetMimeTypePrefix(prefix); }
std::string AbstractFileReader::GetMimeTypePrefix() const { return d->GetMimeTypePrefix(); }
std::string AbstractFileReader::GetDescription() const { return d->GetDescription(); }
void AbstractFileReader::SetDefaultDataNodeProperties(DataNode *node, const std::string &filePath)
{
// path
if (!filePath.empty())
{
auto path = itksys::SystemTools::GetFilenamePath(Utf8Util::Local8BitToUtf8(filePath));
node->SetProperty(StringProperty::PATH, mitk::StringProperty::New(path));
}
// name already defined?
- mitk::StringProperty::Pointer nameProp = dynamic_cast<mitk::StringProperty *>(node->GetProperty("name"));
+ mitk::StringProperty::Pointer nameProp = dynamic_cast<mitk::StringProperty *>(node->GetProperty("name", nullptr, false));
if (nameProp.IsNull() || nameProp->GetValue() == DataNode::NO_NAME_VALUE())
{
// name already defined in BaseData
mitk::StringProperty::Pointer baseDataNameProp =
dynamic_cast<mitk::StringProperty *>(node->GetData()->GetProperty("name").GetPointer());
if (baseDataNameProp.IsNull() || baseDataNameProp->GetValue() == DataNode::NO_NAME_VALUE())
{
// name neither defined in node, nor in BaseData -> name = filebasename;
auto name = this->GetRegisteredMimeType().GetFilenameWithoutExtension(filePath);
name = Utf8Util::Local8BitToUtf8(name);
nameProp = mitk::StringProperty::New(name);
node->SetProperty("name", nameProp);
}
- else
- {
- // name defined in BaseData!
- nameProp = mitk::StringProperty::New(baseDataNameProp->GetValue());
- node->SetProperty("name", nameProp);
- }
}
// visibility
if (!node->GetProperty("visible"))
{
node->SetVisibility(true);
}
}
}
diff --git a/Modules/Core/src/IO/mitkIOUtil.cpp b/Modules/Core/src/IO/mitkIOUtil.cpp
index 5cf1ecba84..edef3c2d4a 100644
--- a/Modules/Core/src/IO/mitkIOUtil.cpp
+++ b/Modules/Core/src/IO/mitkIOUtil.cpp
@@ -1,991 +1,1015 @@
/*============================================================================
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 "mitkIOUtil.h"
#include <mitkCoreObjectFactory.h>
#include <mitkCoreServices.h>
#include <mitkExceptionMacro.h>
#include <mitkFileReaderRegistry.h>
#include <mitkFileWriterRegistry.h>
#include <mitkIMimeTypeProvider.h>
#include <mitkProgressBar.h>
#include <mitkStandaloneDataStorage.h>
#include <usGetModuleContext.h>
#include <usLDAPProp.h>
#include <usModuleContext.h>
#include <usModuleResource.h>
#include <usModuleResourceStream.h>
#include <mitkAbstractFileReader.h>
#include <mitkUtf8Util.h>
// ITK
#include <itksys/SystemTools.hxx>
// VTK
#include <vtkPolyData.h>
#include <vtkSmartPointer.h>
#include <vtkTriangleFilter.h>
#include <cerrno>
#include <cstdlib>
static std::string GetLastErrorStr()
{
#ifdef US_PLATFORM_POSIX
return std::string(strerror(errno));
#else
// Retrieve the system error message for the last-error code
LPVOID lpMsgBuf;
DWORD dw = GetLastError();
FormatMessage(FORMAT_MESSAGE_ALLOCATE_BUFFER | FORMAT_MESSAGE_FROM_SYSTEM | FORMAT_MESSAGE_IGNORE_INSERTS,
nullptr,
dw,
MAKELANGID(LANG_NEUTRAL, SUBLANG_DEFAULT),
(LPTSTR)&lpMsgBuf,
0,
nullptr);
std::string errMsg((LPCTSTR)lpMsgBuf);
LocalFree(lpMsgBuf);
return errMsg;
#endif
}
#ifdef US_PLATFORM_WINDOWS
#include <direct.h>
#include <io.h>
// make the posix flags point to the obsolte bsd types on windows
#define S_IRUSR S_IREAD
#define S_IWUSR S_IWRITE
#else
#include <sys/time.h>
#include <sys/types.h>
#include <unistd.h>
#endif
#include <fcntl.h>
#include <sys/stat.h>
static const char validLetters[] = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789";
// A cross-platform version of the mkstemps function
static int mkstemps_compat(char *tmpl, int suffixlen)
{
static unsigned long long value = 0;
int savedErrno = errno;
// Lower bound on the number of temporary files to attempt to generate.
#define ATTEMPTS_MIN (62 * 62 * 62)
/* The number of times to attempt to generate a temporary file. To
conform to POSIX, this must be no smaller than TMP_MAX. */
#if ATTEMPTS_MIN < TMP_MAX
const unsigned int attempts = TMP_MAX;
#else
const unsigned int attempts = ATTEMPTS_MIN;
#endif
const int len = strlen(tmpl);
if ((len - suffixlen) < 6 || strncmp(&tmpl[len - 6 - suffixlen], "XXXXXX", 6))
{
errno = EINVAL;
return -1;
}
/* This is where the Xs start. */
char *XXXXXX = &tmpl[len - 6 - suffixlen];
/* Get some more or less random data. */
#ifdef US_PLATFORM_WINDOWS
{
SYSTEMTIME stNow;
FILETIME ftNow;
// get system time
GetSystemTime(&stNow);
stNow.wMilliseconds = 500;
if (!SystemTimeToFileTime(&stNow, &ftNow))
{
errno = -1;
return -1;
}
unsigned long long randomTimeBits = ((static_cast<unsigned long long>(ftNow.dwHighDateTime) << 32) |
static_cast<unsigned long long>(ftNow.dwLowDateTime));
value = randomTimeBits ^ static_cast<unsigned long long>(GetCurrentThreadId());
}
#else
{
struct timeval tv;
gettimeofday(&tv, nullptr);
unsigned long long randomTimeBits =
((static_cast<unsigned long long>(tv.tv_usec) << 32) | static_cast<unsigned long long>(tv.tv_sec));
value = randomTimeBits ^ static_cast<unsigned long long>(getpid());
}
#endif
for (unsigned int count = 0; count < attempts; value += 7777, ++count)
{
unsigned long long v = value;
/* Fill in the random bits. */
XXXXXX[0] = validLetters[v % 62];
v /= 62;
XXXXXX[1] = validLetters[v % 62];
v /= 62;
XXXXXX[2] = validLetters[v % 62];
v /= 62;
XXXXXX[3] = validLetters[v % 62];
v /= 62;
XXXXXX[4] = validLetters[v % 62];
v /= 62;
XXXXXX[5] = validLetters[v % 62];
int fd = open(tmpl, O_RDWR | O_CREAT | O_EXCL, S_IRUSR | S_IWUSR);
if (fd >= 0)
{
errno = savedErrno;
return fd;
}
else if (errno != EEXIST)
{
return -1;
}
}
/* We got out of the loop because we ran out of combinations to try. */
errno = EEXIST;
return -1;
}
// A cross-platform version of the POSIX mkdtemp function
static char *mkdtemps_compat(char *tmpl, int suffixlen)
{
static unsigned long long value = 0;
int savedErrno = errno;
// Lower bound on the number of temporary dirs to attempt to generate.
#define ATTEMPTS_MIN (62 * 62 * 62)
/* The number of times to attempt to generate a temporary dir. To
conform to POSIX, this must be no smaller than TMP_MAX. */
#if ATTEMPTS_MIN < TMP_MAX
const unsigned int attempts = TMP_MAX;
#else
const unsigned int attempts = ATTEMPTS_MIN;
#endif
const int len = strlen(tmpl);
if ((len - suffixlen) < 6 || strncmp(&tmpl[len - 6 - suffixlen], "XXXXXX", 6))
{
errno = EINVAL;
return nullptr;
}
/* This is where the Xs start. */
char *XXXXXX = &tmpl[len - 6 - suffixlen];
/* Get some more or less random data. */
#ifdef US_PLATFORM_WINDOWS
{
SYSTEMTIME stNow;
FILETIME ftNow;
// get system time
GetSystemTime(&stNow);
stNow.wMilliseconds = 500;
if (!SystemTimeToFileTime(&stNow, &ftNow))
{
errno = -1;
return nullptr;
}
unsigned long long randomTimeBits = ((static_cast<unsigned long long>(ftNow.dwHighDateTime) << 32) |
static_cast<unsigned long long>(ftNow.dwLowDateTime));
value = randomTimeBits ^ static_cast<unsigned long long>(GetCurrentThreadId());
}
#else
{
struct timeval tv;
gettimeofday(&tv, nullptr);
unsigned long long randomTimeBits =
((static_cast<unsigned long long>(tv.tv_usec) << 32) | static_cast<unsigned long long>(tv.tv_sec));
value = randomTimeBits ^ static_cast<unsigned long long>(getpid());
}
#endif
unsigned int count = 0;
for (; count < attempts; value += 7777, ++count)
{
unsigned long long v = value;
/* Fill in the random bits. */
XXXXXX[0] = validLetters[v % 62];
v /= 62;
XXXXXX[1] = validLetters[v % 62];
v /= 62;
XXXXXX[2] = validLetters[v % 62];
v /= 62;
XXXXXX[3] = validLetters[v % 62];
v /= 62;
XXXXXX[4] = validLetters[v % 62];
v /= 62;
XXXXXX[5] = validLetters[v % 62];
#ifdef US_PLATFORM_WINDOWS
int fd = _mkdir(tmpl); //, _S_IREAD | _S_IWRITE | _S_IEXEC);
#else
int fd = mkdir(tmpl, S_IRUSR | S_IWUSR | S_IXUSR);
#endif
if (fd >= 0)
{
errno = savedErrno;
return tmpl;
}
else if (errno != EEXIST)
{
return nullptr;
}
}
/* We got out of the loop because we ran out of combinations to try. */
errno = EEXIST;
return nullptr;
}
//#endif
//**************************************************************
// mitk::IOUtil method definitions
namespace mitk
{
struct IOUtil::Impl
{
struct FixedReaderOptionsFunctor : public ReaderOptionsFunctorBase
{
FixedReaderOptionsFunctor(const IFileReader::Options &options) : m_Options(options) {}
bool operator()(LoadInfo &loadInfo) const override
{
IFileReader *reader = loadInfo.m_ReaderSelector.GetSelected().GetReader();
if (reader)
{
reader->SetOptions(m_Options);
}
return false;
}
private:
const IFileReader::Options &m_Options;
};
struct FixedWriterOptionsFunctor : public WriterOptionsFunctorBase
{
FixedWriterOptionsFunctor(const IFileReader::Options &options) : m_Options(options) {}
bool operator()(SaveInfo &saveInfo) const override
{
IFileWriter *writer = saveInfo.m_WriterSelector.GetSelected().GetWriter();
if (writer)
{
writer->SetOptions(m_Options);
}
return false;
}
private:
const IFileWriter::Options &m_Options;
};
static BaseData::Pointer LoadBaseDataFromFile(const std::string &path, const ReaderOptionsFunctorBase* optionsCallback = nullptr);
};
BaseData::Pointer IOUtil::Impl::LoadBaseDataFromFile(const std::string &path,
const ReaderOptionsFunctorBase *optionsCallback)
{
std::vector<BaseData::Pointer> baseDataList = Load(path, optionsCallback);
// The Load(path) call above should throw an exception if nothing could be loaded
assert(!baseDataList.empty());
return baseDataList.front();
}
#ifdef US_PLATFORM_WINDOWS
std::string IOUtil::GetProgramPath()
{
char path[512];
std::size_t index = std::string(path, GetModuleFileName(nullptr, path, 512)).find_last_of('\\');
return std::string(path, index);
}
#elif defined(US_PLATFORM_APPLE)
#include <mach-o/dyld.h>
std::string IOUtil::GetProgramPath()
{
char path[512];
uint32_t size = sizeof(path);
if (_NSGetExecutablePath(path, &size) == 0)
{
std::size_t index = std::string(path).find_last_of('/');
std::string strPath = std::string(path, index);
// const char* execPath = strPath.c_str();
// mitk::StandardFileLocations::GetInstance()->AddDirectoryForSearch(execPath,false);
return strPath;
}
return std::string();
}
#else
#include <sstream>
#include <sys/types.h>
#include <unistd.h>
std::string IOUtil::GetProgramPath()
{
std::stringstream ss;
ss << "/proc/" << getpid() << "/exe";
char proc[512] = {0};
ssize_t ch = readlink(ss.str().c_str(), proc, 512);
if (ch == -1)
return std::string();
std::size_t index = std::string(proc).find_last_of('/');
return std::string(proc, index);
}
#endif
char IOUtil::GetDirectorySeparator()
{
#ifdef US_PLATFORM_WINDOWS
return '\\';
#else
return '/';
#endif
}
std::string IOUtil::GetTempPath()
{
static std::string result;
if (result.empty())
{
#ifdef US_PLATFORM_WINDOWS
char tempPathTestBuffer[1];
DWORD bufferLength = ::GetTempPath(1, tempPathTestBuffer);
if (bufferLength == 0)
{
mitkThrow() << GetLastErrorStr();
}
std::vector<char> tempPath(bufferLength);
bufferLength = ::GetTempPath(bufferLength, &tempPath[0]);
if (bufferLength == 0)
{
mitkThrow() << GetLastErrorStr();
}
result.assign(tempPath.begin(), tempPath.begin() + static_cast<std::size_t>(bufferLength));
#else
result = "/tmp/";
#endif
}
return result;
}
std::string IOUtil::CreateTemporaryFile(const std::string &templateName, std::string path)
{
std::ofstream tmpOutputStream;
std::string returnValue = CreateTemporaryFile(tmpOutputStream, templateName, path);
tmpOutputStream.close();
return returnValue;
}
std::string IOUtil::CreateTemporaryFile(std::ofstream &f, const std::string &templateName, std::string path)
{
return CreateTemporaryFile(f, std::ios_base::out | std::ios_base::trunc, templateName, path);
}
std::string IOUtil::CreateTemporaryFile(std::ofstream &f,
std::ios_base::openmode mode,
const std::string &templateName,
std::string path)
{
if (path.empty())
{
path = GetTempPath();
}
path += templateName;
std::vector<char> dst_path(path.begin(), path.end());
dst_path.push_back('\0');
std::size_t lastX = path.find_last_of('X');
std::size_t firstX = path.find_last_not_of('X', lastX);
int firstNonX = firstX == std::string::npos ? -1 : firstX - 1;
while (lastX != std::string::npos && (lastX - firstNonX) < 6)
{
lastX = path.find_last_of('X', firstX);
firstX = path.find_last_not_of('X', lastX);
firstNonX = firstX == std::string::npos ? -1 : firstX - 1;
}
std::size_t suffixlen = lastX == std::string::npos ? path.size() : path.size() - lastX - 1;
int fd = mkstemps_compat(&dst_path[0], suffixlen);
if (fd != -1)
{
path.assign(dst_path.begin(), dst_path.end() - 1);
f.open(path.c_str(), mode | std::ios_base::out | std::ios_base::trunc);
close(fd);
}
else
{
mitkThrow() << "Creating temporary file " << &dst_path[0] << " failed: " << GetLastErrorStr();
}
return path;
}
std::string IOUtil::CreateTemporaryDirectory(const std::string &templateName, std::string path)
{
if (path.empty())
{
path = GetTempPath();
}
path += GetDirectorySeparator() + templateName;
std::vector<char> dst_path(path.begin(), path.end());
dst_path.push_back('\0');
std::size_t lastX = path.find_last_of('X');
std::size_t firstX = path.find_last_not_of('X', lastX);
int firstNonX = firstX == std::string::npos ? -1 : firstX - 1;
while (lastX != std::string::npos && (lastX - firstNonX) < 6)
{
lastX = path.find_last_of('X', firstX);
firstX = path.find_last_not_of('X', lastX);
firstNonX = firstX == std::string::npos ? -1 : firstX - 1;
}
std::size_t suffixlen = lastX == std::string::npos ? path.size() : path.size() - lastX - 1;
if (mkdtemps_compat(&dst_path[0], suffixlen) == nullptr)
{
mitkThrow() << "Creating temporary directory " << &dst_path[0] << " failed: " << GetLastErrorStr();
}
path.assign(dst_path.begin(), dst_path.end() - 1);
return path;
}
DataStorage::SetOfObjects::Pointer IOUtil::Load(const std::string &path, DataStorage &storage, const ReaderOptionsFunctorBase *optionsCallback)
{
std::vector<std::string> paths;
paths.push_back(path);
return Load(paths, storage, optionsCallback);
}
DataStorage::SetOfObjects::Pointer IOUtil::Load(const std::string &path,
const IFileReader::Options &options,
DataStorage &storage)
{
std::vector<LoadInfo> loadInfos;
loadInfos.push_back(LoadInfo(path));
DataStorage::SetOfObjects::Pointer nodeResult = DataStorage::SetOfObjects::New();
Impl::FixedReaderOptionsFunctor optionsCallback(options);
std::string errMsg = Load(loadInfos, nodeResult, &storage, &optionsCallback);
if (!errMsg.empty())
{
mitkThrow() << errMsg;
}
return nodeResult;
}
std::vector<BaseData::Pointer> IOUtil::Load(const std::string &path, const ReaderOptionsFunctorBase *optionsCallback)
{
std::vector<std::string> paths;
paths.push_back(path);
return Load(paths, optionsCallback);
}
std::vector<BaseData::Pointer> IOUtil::Load(const std::string &path, const IFileReader::Options &options)
{
std::vector<LoadInfo> loadInfos;
loadInfos.push_back(LoadInfo(path));
Impl::FixedReaderOptionsFunctor optionsCallback(options);
std::string errMsg = Load(loadInfos, nullptr, nullptr, &optionsCallback);
if (!errMsg.empty())
{
mitkThrow() << errMsg;
}
return loadInfos.front().m_Output;
}
DataStorage::SetOfObjects::Pointer IOUtil::Load(const std::vector<std::string> &paths, DataStorage &storage, const ReaderOptionsFunctorBase *optionsCallback)
{
DataStorage::SetOfObjects::Pointer nodeResult = DataStorage::SetOfObjects::New();
std::vector<LoadInfo> loadInfos;
for (const auto &loadInfo : paths)
{
loadInfos.emplace_back(loadInfo);
}
std::string errMsg = Load(loadInfos, nodeResult, &storage, optionsCallback);
if (!errMsg.empty())
{
mitkThrow() << errMsg;
}
return nodeResult;
}
std::vector<BaseData::Pointer> IOUtil::Load(const std::vector<std::string> &paths, const ReaderOptionsFunctorBase *optionsCallback)
{
std::vector<BaseData::Pointer> result;
std::vector<LoadInfo> loadInfos;
for (const auto &loadInfo : paths)
{
loadInfos.emplace_back(loadInfo);
}
std::string errMsg = Load(loadInfos, nullptr, nullptr, optionsCallback);
if (!errMsg.empty())
{
mitkThrow() << errMsg;
}
for (std::vector<LoadInfo>::const_iterator iter = loadInfos.begin(), iterEnd = loadInfos.end(); iter != iterEnd;
++iter)
{
result.insert(result.end(), iter->m_Output.begin(), iter->m_Output.end());
}
return result;
}
std::string IOUtil::Load(std::vector<LoadInfo> &loadInfos,
DataStorage::SetOfObjects *nodeResult,
DataStorage *ds,
const ReaderOptionsFunctorBase *optionsCallback)
{
if (loadInfos.empty())
{
return "No input files given";
}
int filesToRead = loadInfos.size();
mitk::ProgressBar::GetInstance()->AddStepsToDo(2 * filesToRead);
std::string errMsg;
std::map<std::string, FileReaderSelector::Item> usedReaderItems;
std::vector< std::string > read_files;
for (auto &loadInfo : loadInfos)
{
if(std::find(read_files.begin(), read_files.end(), loadInfo.m_Path) != read_files.end())
continue;
std::vector<FileReaderSelector::Item> readers = loadInfo.m_ReaderSelector.Get();
if (readers.empty())
{
if (!itksys::SystemTools::FileExists(Utf8Util::Local8BitToUtf8(loadInfo.m_Path).c_str()))
{
errMsg += "File '" + loadInfo.m_Path + "' does not exist\n";
}
else
{
errMsg += "No reader available for '" + loadInfo.m_Path + "'\n";
}
continue;
}
bool callOptionsCallback = readers.size() > 1 || !readers.front().GetReader()->GetOptions().empty();
// check if we already used a reader which should be re-used
std::vector<MimeType> currMimeTypes = loadInfo.m_ReaderSelector.GetMimeTypes();
std::string selectedMimeType;
for (std::vector<MimeType>::const_iterator mimeTypeIter = currMimeTypes.begin(),
mimeTypeIterEnd = currMimeTypes.end();
mimeTypeIter != mimeTypeIterEnd;
++mimeTypeIter)
{
std::map<std::string, FileReaderSelector::Item>::const_iterator oldSelectedItemIter =
usedReaderItems.find(mimeTypeIter->GetName());
if (oldSelectedItemIter != usedReaderItems.end())
{
// we found an already used item for a mime-type which is contained
// in the current reader set, check all current readers if there service
// id equals the old reader
for (std::vector<FileReaderSelector::Item>::const_iterator currReaderItem = readers.begin(),
currReaderItemEnd = readers.end();
currReaderItem != currReaderItemEnd;
++currReaderItem)
{
if (currReaderItem->GetMimeType().GetName() == mimeTypeIter->GetName() &&
currReaderItem->GetServiceId() == oldSelectedItemIter->second.GetServiceId() &&
currReaderItem->GetConfidenceLevel() >= oldSelectedItemIter->second.GetConfidenceLevel())
{
// okay, we used the same reader already, re-use its options
selectedMimeType = mimeTypeIter->GetName();
callOptionsCallback = false;
loadInfo.m_ReaderSelector.Select(oldSelectedItemIter->second.GetServiceId());
loadInfo.m_ReaderSelector.GetSelected().GetReader()->SetOptions(
oldSelectedItemIter->second.GetReader()->GetOptions());
break;
}
}
if (!selectedMimeType.empty())
break;
}
}
if (callOptionsCallback && optionsCallback)
{
callOptionsCallback = (*optionsCallback)(loadInfo);
if (!callOptionsCallback && !loadInfo.m_Cancel)
{
usedReaderItems.erase(selectedMimeType);
FileReaderSelector::Item selectedItem = loadInfo.m_ReaderSelector.GetSelected();
usedReaderItems.insert(std::make_pair(selectedItem.GetMimeType().GetName(), selectedItem));
}
}
if (loadInfo.m_Cancel)
{
errMsg += "Reading operation(s) cancelled.";
break;
}
IFileReader *reader = loadInfo.m_ReaderSelector.GetSelected().GetReader();
if (reader == nullptr)
{
errMsg += "Unexpected nullptr reader.";
break;
}
+ reader->SetProperties(loadInfo.m_Properties);
+
// Do the actual reading
try
{
DataStorage::SetOfObjects::Pointer nodes;
if (ds != nullptr)
{
nodes = reader->Read(*ds);
std::vector< std::string > new_files = reader->GetReadFiles();
read_files.insert( read_files.end(), new_files.begin(), new_files.end() );
}
else
{
nodes = DataStorage::SetOfObjects::New();
std::vector<mitk::BaseData::Pointer> baseData = reader->Read();
for (auto iter = baseData.begin(); iter != baseData.end(); ++iter)
{
if (iter->IsNotNull())
{
mitk::DataNode::Pointer node = mitk::DataNode::New();
node->SetData(*iter);
nodes->InsertElement(nodes->Size(), node);
}
}
std::vector< std::string > new_files = reader->GetReadFiles();
read_files.insert( read_files.end(), new_files.begin(), new_files.end() );
}
for (DataStorage::SetOfObjects::ConstIterator nodeIter = nodes->Begin(), nodeIterEnd = nodes->End();
nodeIter != nodeIterEnd;
++nodeIter)
{
const mitk::DataNode::Pointer &node = nodeIter->Value();
mitk::BaseData::Pointer data = node->GetData();
if (data.IsNull())
{
continue;
}
data->SetProperty("path", mitk::StringProperty::New(Utf8Util::Local8BitToUtf8(loadInfo.m_Path)));
loadInfo.m_Output.push_back(data);
if (nodeResult)
{
nodeResult->push_back(nodeIter->Value());
}
}
if (loadInfo.m_Output.empty() || (nodeResult && nodeResult->Size() == 0))
{
errMsg += "Unknown read error occurred reading " + loadInfo.m_Path;
}
}
catch (const std::exception &e)
{
errMsg += "Exception occured when reading file " + loadInfo.m_Path + ":\n" + e.what() + "\n\n";
}
mitk::ProgressBar::GetInstance()->Progress(2);
--filesToRead;
}
if (!errMsg.empty())
{
MITK_ERROR << errMsg;
}
mitk::ProgressBar::GetInstance()->Progress(2 * filesToRead);
return errMsg;
}
std::vector<BaseData::Pointer> IOUtil::Load(const us::ModuleResource &usResource, std::ios_base::openmode mode)
{
us::ModuleResourceStream resStream(usResource, mode);
mitk::CoreServicePointer<mitk::IMimeTypeProvider> mimeTypeProvider(mitk::CoreServices::GetMimeTypeProvider());
std::vector<MimeType> mimetypes = mimeTypeProvider->GetMimeTypesForFile(usResource.GetResourcePath());
std::vector<mitk::BaseData::Pointer> data;
if (mimetypes.empty())
{
mitkThrow() << "No mimetype for resource stream: " << usResource.GetResourcePath();
return data;
}
mitk::FileReaderRegistry fileReaderRegistry;
std::vector<us::ServiceReference<IFileReader>> refs = fileReaderRegistry.GetReferences(mimetypes[0]);
if (refs.empty())
{
mitkThrow() << "No reader available for resource stream: " << usResource.GetResourcePath();
return data;
}
mitk::IFileReader *reader = fileReaderRegistry.GetReader(refs[0]);
reader->SetInput(usResource.GetResourcePath(), &resStream);
data = reader->Read();
return data;
}
+ BaseData::Pointer IOUtil::Load(const std::string& path, const PropertyList* properties)
+ {
+ LoadInfo loadInfo(path);
+ loadInfo.m_Properties = properties;
+
+ std::vector<LoadInfo> loadInfos;
+ loadInfos.push_back(loadInfo);
+
+ auto errMsg = Load(loadInfos, nullptr, nullptr, nullptr);
+
+ if (!errMsg.empty())
+ mitkThrow() << errMsg;
+
+ return loadInfos.front().m_Output.front();
+ }
+
void IOUtil::Save(const BaseData *data, const std::string &path, bool setPathProperty) { Save(data, path, IFileWriter::Options(), setPathProperty); }
void IOUtil::Save(const BaseData *data, const std::string &path, const IFileWriter::Options &options, bool setPathProperty)
{
Save(data, std::string(), path, options, setPathProperty);
}
void IOUtil::Save(const BaseData *data, const std::string &mimeType, const std::string &path, bool addExtension, bool setPathProperty)
{
Save(data, mimeType, path, IFileWriter::Options(), addExtension, setPathProperty);
}
void IOUtil::Save(const BaseData *data,
const std::string &mimeType,
const std::string &path,
const IFileWriter::Options &options,
bool addExtension,
bool setPathProperty)
{
if ((data == nullptr) || (data->IsEmpty()))
mitkThrow() << "BaseData cannotbe null or empty for save methods in IOUtil.h.";
std::string errMsg;
if (options.empty())
{
errMsg = Save(data, mimeType, path, nullptr, addExtension, setPathProperty);
}
else
{
Impl::FixedWriterOptionsFunctor optionsCallback(options);
errMsg = Save(data, mimeType, path, &optionsCallback, addExtension, setPathProperty);
}
if (!errMsg.empty())
{
mitkThrow() << errMsg;
}
}
void IOUtil::Save(std::vector<IOUtil::SaveInfo> &saveInfos, bool setPathProperty)
{
std::string errMsg = Save(saveInfos, nullptr, setPathProperty);
if (!errMsg.empty())
{
mitkThrow() << errMsg;
}
}
std::string IOUtil::Save(const BaseData *data,
const std::string &mimeTypeName,
const std::string &path,
WriterOptionsFunctorBase *optionsCallback,
bool addExtension,
bool setPathProperty)
{
if (path.empty())
{
return "No output filename given";
}
mitk::CoreServicePointer<mitk::IMimeTypeProvider> mimeTypeProvider(mitk::CoreServices::GetMimeTypeProvider());
MimeType mimeType = mimeTypeProvider->GetMimeTypeForName(mimeTypeName);
SaveInfo saveInfo(data, mimeType, path);
std::string ext = Utf8Util::Utf8ToLocal8Bit(itksys::SystemTools::GetFilenameExtension(Utf8Util::Local8BitToUtf8(path)));
if (saveInfo.m_WriterSelector.IsEmpty())
{
return std::string("No suitable writer found for the current data of type ") + data->GetNameOfClass() +
(mimeType.IsValid() ? (std::string(" and mime-type ") + mimeType.GetName()) : std::string()) +
(ext.empty() ? std::string() : (std::string(" with extension ") + ext));
}
// Add an extension if not already specified
if (ext.empty() && addExtension)
{
ext = saveInfo.m_MimeType.GetExtensions().empty() ? std::string() : "." + saveInfo.m_MimeType.GetExtensions().front();
saveInfo.m_Path += ext;
}
std::vector<SaveInfo> infos;
infos.push_back(saveInfo);
return Save(infos, optionsCallback, setPathProperty);
}
std::string IOUtil::Save(std::vector<SaveInfo> &saveInfos, WriterOptionsFunctorBase *optionsCallback, bool setPathProperty)
{
if (saveInfos.empty())
{
return "No data for saving available";
}
int filesToWrite = saveInfos.size();
mitk::ProgressBar::GetInstance()->AddStepsToDo(2 * filesToWrite);
std::string errMsg;
std::set<SaveInfo> usedSaveInfos;
for (auto &saveInfo : saveInfos)
{
const std::string baseDataType = saveInfo.m_BaseData->GetNameOfClass();
std::vector<FileWriterSelector::Item> writers = saveInfo.m_WriterSelector.Get();
// Error out if no compatible Writer was found
if (writers.empty())
{
errMsg += std::string("No writer available for ") + baseDataType + " data.\n";
continue;
}
bool callOptionsCallback = writers.size() > 1 || !writers[0].GetWriter()->GetOptions().empty();
// check if we already used a writer for this base data type
// which should be re-used
auto oldSaveInfoIter = usedSaveInfos.find(saveInfo);
if (oldSaveInfoIter != usedSaveInfos.end())
{
// we previously saved a base data object of the same data with the same mime-type,
// check if the same writer is contained in the current writer set and if the
// confidence level matches
FileWriterSelector::Item oldSelectedItem =
oldSaveInfoIter->m_WriterSelector.Get(oldSaveInfoIter->m_WriterSelector.GetSelectedId());
for (std::vector<FileWriterSelector::Item>::const_iterator currWriterItem = writers.begin(),
currWriterItemEnd = writers.end();
currWriterItem != currWriterItemEnd;
++currWriterItem)
{
if (currWriterItem->GetServiceId() == oldSelectedItem.GetServiceId() &&
currWriterItem->GetConfidenceLevel() >= oldSelectedItem.GetConfidenceLevel())
{
// okay, we used the same writer already, re-use its options
callOptionsCallback = false;
saveInfo.m_WriterSelector.Select(oldSaveInfoIter->m_WriterSelector.GetSelectedId());
saveInfo.m_WriterSelector.GetSelected().GetWriter()->SetOptions(oldSelectedItem.GetWriter()->GetOptions());
break;
}
}
}
if (callOptionsCallback && optionsCallback)
{
callOptionsCallback = (*optionsCallback)(saveInfo);
if (!callOptionsCallback && !saveInfo.m_Cancel)
{
usedSaveInfos.erase(saveInfo);
usedSaveInfos.insert(saveInfo);
}
}
if (saveInfo.m_Cancel)
{
errMsg += "Writing operation(s) cancelled.";
break;
}
IFileWriter *writer = saveInfo.m_WriterSelector.GetSelected().GetWriter();
if (writer == nullptr)
{
errMsg += "Unexpected nullptr writer.";
break;
}
// Do the actual writing
try
{
writer->SetOutputLocation(saveInfo.m_Path);
writer->Write();
}
catch (const std::exception &e)
{
errMsg += std::string("Exception occurred when writing to ") + saveInfo.m_Path + ":\n" + e.what() + "\n";
}
if (setPathProperty)
saveInfo.m_BaseData->GetPropertyList()->SetStringProperty("path", Utf8Util::Local8BitToUtf8(saveInfo.m_Path).c_str());
mitk::ProgressBar::GetInstance()->Progress(2);
--filesToWrite;
}
if (!errMsg.empty())
{
MITK_ERROR << errMsg;
}
mitk::ProgressBar::GetInstance()->Progress(2 * filesToWrite);
return errMsg;
}
IOUtil::SaveInfo::SaveInfo(const BaseData *baseData, const MimeType &mimeType, const std::string &path)
: m_BaseData(baseData),
m_WriterSelector(baseData, mimeType.GetName(), path),
m_MimeType(mimeType.IsValid() ? mimeType // use the original mime-type
:
(m_WriterSelector.IsEmpty() ?
mimeType // no writer found, use the original invalid mime-type
:
m_WriterSelector.GetDefault().GetMimeType() // use the found default mime-type
)),
m_Path(path),
m_Cancel(false)
{
}
bool IOUtil::SaveInfo::operator<(const IOUtil::SaveInfo &other) const
{
int r = strcmp(m_BaseData->GetNameOfClass(), other.m_BaseData->GetNameOfClass());
if (r == 0)
{
return m_WriterSelector.GetSelected().GetMimeType() < other.m_WriterSelector.GetSelected().GetMimeType();
}
return r < 0;
}
- IOUtil::LoadInfo::LoadInfo(const std::string &path) : m_Path(path), m_ReaderSelector(path), m_Cancel(false) {}
+ IOUtil::LoadInfo::LoadInfo(const std::string &path)
+ : m_Path(path),
+ m_ReaderSelector(path),
+ m_Cancel(false),
+ m_Properties(nullptr)
+ {
+ }
}
diff --git a/Modules/DICOM/include/mitkDICOMIOHelper.h b/Modules/DICOM/include/mitkDICOMIOHelper.h
index 33506e22e7..1f2374a89c 100644
--- a/Modules/DICOM/include/mitkDICOMIOHelper.h
+++ b/Modules/DICOM/include/mitkDICOMIOHelper.h
@@ -1,36 +1,38 @@
/*============================================================================
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 MITKDICOMIOHelper_H
-#define MITKDICOMIOHelper_H
+#ifndef mitkDICOMIOHelper_h
+#define mitkDICOMIOHelper_h
-#include "mitkDICOMDatasetAccessingImageFrameInfo.h"
-#include "mitkIDICOMTagsOfInterest.h"
+#include <mitkDICOMDatasetAccessingImageFrameInfo.h>
+#include <mitkIDICOMTagsOfInterest.h>
#include <MitkDICOMExports.h>
namespace mitk
{
class BaseData;
- typedef std::vector<mitk::DICOMDatasetAccess::FindingsListType> FindingsListVectorType;
- typedef BaseData *BaseDataPointer;
+ namespace DICOMIOHelper
+ {
+ using FindingsListVectorType = std::vector<DICOMDatasetAccess::FindingsListType>;
- MITKDICOM_EXPORT mitk::IDICOMTagsOfInterest *GetDicomTagsOfInterestService();
+ MITKDICOM_EXPORT IDICOMTagsOfInterest* GetTagsOfInterestService();
- MITKDICOM_EXPORT FindingsListVectorType ExtractPathsOfInterest(const DICOMTagPathList &pathsOfInterest,
- const DICOMDatasetAccessingImageFrameList &frames);
+ MITKDICOM_EXPORT FindingsListVectorType ExtractPathsOfInterest(const DICOMTagPathList& pathsOfInterest,
+ const DICOMDatasetAccessingImageFrameList& frames);
- MITKDICOM_EXPORT void SetProperties(BaseDataPointer image, const FindingsListVectorType &findings);
+ MITKDICOM_EXPORT void SetProperties(BaseData* image, const FindingsListVectorType& findings);
+ }
}
#endif
diff --git a/Modules/DICOM/src/mitkDICOMIOHelper.cpp b/Modules/DICOM/src/mitkDICOMIOHelper.cpp
index 648d18a6c6..11f92bd917 100644
--- a/Modules/DICOM/src/mitkDICOMIOHelper.cpp
+++ b/Modules/DICOM/src/mitkDICOMIOHelper.cpp
@@ -1,71 +1,70 @@
/*============================================================================
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 "mitkDICOMIOHelper.h"
+#include <mitkDICOMIOHelper.h>
#include <mitkImage.h>
#include <mitkTemporoSpatialStringProperty.h>
#include <usGetModuleContext.h>
#include <usModuleContext.h>
-namespace mitk
+namespace mitk::DICOMIOHelper
{
- mitk::IDICOMTagsOfInterest *GetDicomTagsOfInterestService()
+ IDICOMTagsOfInterest* GetTagsOfInterestService()
{
- mitk::IDICOMTagsOfInterest *result = nullptr;
+ auto* context = us::GetModuleContext();
- us::ModuleContext *context = us::GetModuleContext();
if (context == nullptr)
{
MITK_WARN << "No MitkDICOM module context found.";
- return result;
+ return nullptr;
}
- std::vector<us::ServiceReference<mitk::IDICOMTagsOfInterest>> toiRegisters =
- context->GetServiceReferences<mitk::IDICOMTagsOfInterest>();
+
+ auto toiRegisters = context->GetServiceReferences<mitk::IDICOMTagsOfInterest>();
+
if (!toiRegisters.empty())
{
if (toiRegisters.size() > 1)
- {
MITK_WARN << "Multiple DICOM tags of interest services found. Using just one.";
- }
- result = us::GetModuleContext()->GetService<mitk::IDICOMTagsOfInterest>(toiRegisters.front());
+
+ return us::GetModuleContext()->GetService<mitk::IDICOMTagsOfInterest>(toiRegisters.front());
}
- return result;
+ return nullptr;
}
- FindingsListVectorType ExtractPathsOfInterest(const DICOMTagPathList &pathsOfInterest,
- const DICOMDatasetAccessingImageFrameList &frames)
+ FindingsListVectorType ExtractPathsOfInterest(const DICOMTagPathList& pathsOfInterest,
+ const DICOMDatasetAccessingImageFrameList& frames)
{
- std::vector<mitk::DICOMDatasetAccess::FindingsListType> findings;
- for (const auto &entry : pathsOfInterest)
- {
+ std::vector<DICOMDatasetAccess::FindingsListType> findings;
+
+ for (const auto& entry : pathsOfInterest)
findings.push_back(frames.front()->GetTagValueAsString(entry));
- }
+
return findings;
}
- void SetProperties(BaseDataPointer image, const FindingsListVectorType &findings)
+ void SetProperties(BaseData* image, const FindingsListVectorType& findings)
{
- for (const auto &finding : findings)
+ for (const auto& finding : findings)
{
- for (const auto &entry : finding)
+ for (const auto& entry : finding)
{
- const std::string propertyName = mitk::DICOMTagPathToPropertyName(entry.path);
- auto property = mitk::TemporoSpatialStringProperty::New();
+ auto property = TemporoSpatialStringProperty::New();
property->SetValue(entry.value);
- image->SetProperty(propertyName.c_str(), property);
+
+ image->SetProperty(DICOMTagPathToPropertyName(entry.path), property);
}
}
}
}
diff --git a/Modules/Multilabel/autoload/DICOMSegIO/mitkDICOMSegmentationIO.cpp b/Modules/Multilabel/autoload/DICOMSegIO/mitkDICOMSegmentationIO.cpp
index ec08b5baf2..914afc9cfa 100644
--- a/Modules/Multilabel/autoload/DICOMSegIO/mitkDICOMSegmentationIO.cpp
+++ b/Modules/Multilabel/autoload/DICOMSegIO/mitkDICOMSegmentationIO.cpp
@@ -1,704 +1,704 @@
/*============================================================================
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 __mitkDICOMSegmentationIO__cpp
#define __mitkDICOMSegmentationIO__cpp
#include "mitkDICOMSegmentationIO.h"
#include "mitkDICOMSegIOMimeTypes.h"
#include "mitkDICOMSegmentationConstants.h"
#include <mitkDICOMDCMTKTagScanner.h>
#include <mitkDICOMIOHelper.h>
#include <mitkDICOMProperty.h>
#include <mitkIDICOMTagsOfInterest.h>
#include <mitkImageAccessByItk.h>
#include <mitkImageCast.h>
#include <mitkLocaleSwitch.h>
#include <mitkPropertyNameHelper.h>
// itk
#include <itkThresholdImageFilter.h>
// dcmqi
#include <dcmqi/ImageSEGConverter.h>
// us
#include <usGetModuleContext.h>
#include <usModuleContext.h>
namespace mitk
{
DICOMSegmentationIO::DICOMSegmentationIO()
: AbstractFileIO(LabelSetImage::GetStaticNameOfClass(),
mitk::MitkDICOMSEGIOMimeTypes::DICOMSEG_MIMETYPE_NAME(),
"DICOM Segmentation")
{
AbstractFileWriter::SetRanking(10);
AbstractFileReader::SetRanking(10);
this->RegisterService();
}
std::vector<mitk::DICOMTagPath> DICOMSegmentationIO::GetDICOMTagsOfInterest()
{
std::vector<mitk::DICOMTagPath> result;
result.emplace_back(DICOMSegmentationConstants::SEGMENT_SEQUENCE_PATH());
result.emplace_back(DICOMSegmentationConstants::SEGMENT_NUMBER_PATH());
result.emplace_back(DICOMSegmentationConstants::SEGMENT_LABEL_PATH());
result.emplace_back(DICOMSegmentationConstants::SEGMENT_ALGORITHM_TYPE_PATH());
result.emplace_back(DICOMSegmentationConstants::ANATOMIC_REGION_SEQUENCE_PATH());
result.emplace_back(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_VALUE_PATH());
result.emplace_back(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_SCHEME_PATH());
result.emplace_back(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_MEANING_PATH());
result.emplace_back(DICOMSegmentationConstants::SEGMENTED_PROPERTY_CATEGORY_SEQUENCE_PATH());
result.emplace_back(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_VALUE_PATH());
result.emplace_back(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_SCHEME_PATH());
result.emplace_back(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_MEANING_PATH());
result.emplace_back(DICOMSegmentationConstants::SEGMENTED_PROPERTY_TYPE_SEQUENCE_PATH());
result.emplace_back(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_VALUE_PATH());
result.emplace_back(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_SCHEME_PATH());
result.emplace_back(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_MEANING_PATH());
result.emplace_back(DICOMSegmentationConstants::SEGMENTED_PROPERTY_MODIFIER_SEQUENCE_PATH());
result.emplace_back(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_VALUE_PATH());
result.emplace_back(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_SCHEME_PATH());
result.emplace_back(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_MEANING_PATH());
return result;
}
IFileIO::ConfidenceLevel DICOMSegmentationIO::GetWriterConfidenceLevel() const
{
if (AbstractFileIO::GetWriterConfidenceLevel() == Unsupported)
return Unsupported;
// Check if the input file is a segmentation
const LabelSetImage *input = static_cast<const LabelSetImage *>(this->GetInput());
if (input)
{
if ((input->GetDimension() != 3))
{
MITK_INFO << "DICOM segmentation writer is tested only with 3D images, sorry.";
return Unsupported;
}
// Check if input file has dicom information for the referenced image (original DICOM image, e.g. CT) Still necessary, see write()
mitk::StringLookupTableProperty::Pointer dicomFilesProp =
dynamic_cast<mitk::StringLookupTableProperty *>(input->GetProperty("referenceFiles").GetPointer());
if (dicomFilesProp.IsNotNull())
return Supported;
}
return Unsupported;
}
void DICOMSegmentationIO::Write()
{
ValidateOutputLocation();
mitk::LocaleSwitch localeSwitch("C");
LocalFile localFile(this);
const std::string path = localFile.GetFileName();
auto input = dynamic_cast<const LabelSetImage *>(this->GetInput());
if (input == nullptr)
mitkThrow() << "Cannot write non-image data";
// Get DICOM information from referenced image
vector<std::unique_ptr<DcmDataset>> dcmDatasetsSourceImage;
std::unique_ptr<DcmFileFormat> readFileFormat(new DcmFileFormat());
try
{
// TODO: Generate dcmdataset witk DICOM tags from property list; ATM the source are the filepaths from the
// property list
mitk::StringLookupTableProperty::Pointer filesProp =
dynamic_cast<mitk::StringLookupTableProperty *>(input->GetProperty("referenceFiles").GetPointer());
if (filesProp.IsNull())
{
mitkThrow() << "No property with dicom file path.";
return;
}
StringLookupTable filesLut = filesProp->GetValue();
const StringLookupTable::LookupTableType &lookUpTableMap = filesLut.GetLookupTable();
for (const auto &it : lookUpTableMap)
{
const char *fileName = (it.second).c_str();
if (readFileFormat->loadFile(fileName, EXS_Unknown).good())
{
std::unique_ptr<DcmDataset> readDCMDataset(readFileFormat->getAndRemoveDataset());
dcmDatasetsSourceImage.push_back(std::move(readDCMDataset));
}
}
}
catch (const std::exception &e)
{
MITK_ERROR << "An error occurred while getting the dicom informations: " << e.what() << endl;
return;
}
// Iterate over all layers. For each a dcm file will be generated
for (unsigned int layer = 0; layer < input->GetNumberOfLayers(); ++layer)
{
vector<itkInternalImageType::Pointer> segmentations;
try
{
// Hack: Remove the const attribute to switch between the layer images. Normally you could get the different
// layer images by input->GetLayerImage(layer)
mitk::LabelSetImage *mitkLayerImage = const_cast<mitk::LabelSetImage *>(input);
mitkLayerImage->SetActiveLayer(layer);
// Cast mitk layer image to itk
ImageToItk<itkInputImageType>::Pointer imageToItkFilter = ImageToItk<itkInputImageType>::New();
imageToItkFilter->SetInput(mitkLayerImage);
// Cast from original itk type to dcmqi input itk image type
typedef itk::CastImageFilter<itkInputImageType, itkInternalImageType> castItkImageFilterType;
castItkImageFilterType::Pointer castFilter = castItkImageFilterType::New();
castFilter->SetInput(imageToItkFilter->GetOutput());
castFilter->Update();
itkInternalImageType::Pointer itkLabelImage = castFilter->GetOutput();
itkLabelImage->DisconnectPipeline();
// Iterate over all labels. For each label a segmentation image will be created
const LabelSet *labelSet = input->GetLabelSet(layer);
auto labelIter = labelSet->IteratorConstBegin();
// Ignore background label
++labelIter;
for (; labelIter != labelSet->IteratorConstEnd(); ++labelIter)
{
// Thresold over the image with the given label value
itk::ThresholdImageFilter<itkInternalImageType>::Pointer thresholdFilter =
itk::ThresholdImageFilter<itkInternalImageType>::New();
thresholdFilter->SetInput(itkLabelImage);
thresholdFilter->ThresholdOutside(labelIter->first, labelIter->first);
thresholdFilter->SetOutsideValue(0);
thresholdFilter->Update();
itkInternalImageType::Pointer segmentImage = thresholdFilter->GetOutput();
segmentImage->DisconnectPipeline();
segmentations.push_back(segmentImage);
}
}
catch (const itk::ExceptionObject &e)
{
MITK_ERROR << e.GetDescription() << endl;
return;
}
// Create segmentation meta information
const std::string tmpMetaInfoFile = this->CreateMetaDataJsonFile(layer);
MITK_INFO << "Writing image: " << path << std::endl;
try
{
//TODO is there a better way? Interface expects a vector of raw pointer.
vector<DcmDataset*> rawVecDataset;
for (const auto& dcmDataSet : dcmDatasetsSourceImage)
rawVecDataset.push_back(dcmDataSet.get());
// Convert itk segmentation images to dicom image
std::unique_ptr<dcmqi::ImageSEGConverter> converter = std::make_unique<dcmqi::ImageSEGConverter>();
std::unique_ptr<DcmDataset> result(converter->itkimage2dcmSegmentation(rawVecDataset, segmentations, tmpMetaInfoFile, false));
// Write dicom file
DcmFileFormat dcmFileFormat(result.get());
std::string filePath = path.substr(0, path.find_last_of("."));
// If there is more than one layer, we have to write more than 1 dicom file
if (input->GetNumberOfLayers() != 1)
filePath = filePath + std::to_string(layer) + ".dcm";
else
filePath = filePath + ".dcm";
dcmFileFormat.saveFile(filePath.c_str(), EXS_LittleEndianExplicit);
}
catch (const std::exception &e)
{
MITK_ERROR << "An error occurred during writing the DICOM Seg: " << e.what() << endl;
return;
}
} // Write a dcm file for the next layer
}
IFileIO::ConfidenceLevel DICOMSegmentationIO::GetReaderConfidenceLevel() const
{
if (AbstractFileIO::GetReaderConfidenceLevel() == Unsupported)
return Unsupported;
const std::string fileName = this->GetLocalFileName();
DcmFileFormat dcmFileFormat;
OFCondition status = dcmFileFormat.loadFile(fileName.c_str());
if (status.bad())
return Unsupported;
OFString modality;
if (dcmFileFormat.getDataset()->findAndGetOFString(DCM_Modality, modality).good())
{
if (modality.compare("SEG") == 0)
return Supported;
else
return Unsupported;
}
return Unsupported;
}
std::vector<BaseData::Pointer> DICOMSegmentationIO::DoRead()
{
mitk::LocaleSwitch localeSwitch("C");
LabelSetImage::Pointer labelSetImage;
std::vector<BaseData::Pointer> result;
const std::string path = this->GetLocalFileName();
MITK_INFO << "loading " << path << std::endl;
if (path.empty())
mitkThrow() << "Empty filename in mitk::ItkImageIO ";
try
{
// Get the dcm data set from file path
DcmFileFormat dcmFileFormat;
OFCondition status = dcmFileFormat.loadFile(path.c_str());
if (status.bad())
mitkThrow() << "Can't read the input file!";
DcmDataset *dataSet = dcmFileFormat.getDataset();
if (dataSet == nullptr)
mitkThrow() << "Can't read data from input file!";
//=============================== dcmqi part ====================================
// Read the DICOM SEG images (segItkImages) and DICOM tags (metaInfo)
std::unique_ptr<dcmqi::ImageSEGConverter> converter = std::make_unique<dcmqi::ImageSEGConverter>();
pair<map<unsigned, itkInternalImageType::Pointer>, string> dcmqiOutput =
converter->dcmSegmentation2itkimage(dataSet);
map<unsigned, itkInternalImageType::Pointer> segItkImages = dcmqiOutput.first;
dcmqi::JSONSegmentationMetaInformationHandler metaInfo(dcmqiOutput.second.c_str());
metaInfo.read();
MITK_INFO << "Input " << metaInfo.getJSONOutputAsString();
//===============================================================================
// Get the label information from segment attributes for each itk image
vector<map<unsigned, dcmqi::SegmentAttributes *>>::const_iterator segmentIter =
metaInfo.segmentsAttributesMappingList.begin();
// For each itk image add a layer to the LabelSetImage output
for (auto &element : segItkImages)
{
// Get the labeled image and cast it to mitkImage
typedef itk::CastImageFilter<itkInternalImageType, itkInputImageType> castItkImageFilterType;
castItkImageFilterType::Pointer castFilter = castItkImageFilterType::New();
castFilter->SetInput(element.second);
castFilter->Update();
Image::Pointer layerImage;
CastToMitkImage(castFilter->GetOutput(), layerImage);
// Get pixel value of the label
itkInternalImageType::ValueType segValue = 1;
typedef itk::ImageRegionIterator<const itkInternalImageType> IteratorType;
// Iterate over the image to find the pixel value of the label
IteratorType iter(element.second, element.second->GetLargestPossibleRegion());
iter.GoToBegin();
while (!iter.IsAtEnd())
{
itkInputImageType::PixelType value = iter.Get();
if (value != 0)
{
segValue = value;
break;
}
++iter;
}
// Get Segment information map
map<unsigned, dcmqi::SegmentAttributes *> segmentMap = (*segmentIter);
map<unsigned, dcmqi::SegmentAttributes *>::const_iterator segmentMapIter = (*segmentIter).begin();
dcmqi::SegmentAttributes *segmentAttribute = (*segmentMapIter).second;
OFString labelName;
if (segmentAttribute->getSegmentedPropertyTypeCodeSequence() != nullptr)
{
segmentAttribute->getSegmentedPropertyTypeCodeSequence()->getCodeMeaning(labelName);
if (segmentAttribute->getSegmentedPropertyTypeModifierCodeSequence() != nullptr)
{
OFString modifier;
segmentAttribute->getSegmentedPropertyTypeModifierCodeSequence()->getCodeMeaning(modifier);
labelName.append(" (").append(modifier).append(")");
}
}
else
{
labelName = std::to_string(segmentAttribute->getLabelID()).c_str();
if (labelName.empty())
labelName = "Unnamed";
}
float tmp[3] = { 0.0, 0.0, 0.0 };
if (segmentAttribute->getRecommendedDisplayRGBValue() != nullptr)
{
tmp[0] = segmentAttribute->getRecommendedDisplayRGBValue()[0] / 255.0;
tmp[1] = segmentAttribute->getRecommendedDisplayRGBValue()[1] / 255.0;
tmp[2] = segmentAttribute->getRecommendedDisplayRGBValue()[2] / 255.0;
}
Label *newLabel = nullptr;
// If labelSetImage do not exists (first image)
if (labelSetImage.IsNull())
{
// Initialize the labelSetImage with the read image
labelSetImage = LabelSetImage::New();
labelSetImage->InitializeByLabeledImage(layerImage);
// Already a label was generated, so set the information to this
newLabel = labelSetImage->GetActiveLabel(labelSetImage->GetActiveLayer());
newLabel->SetName(labelName.c_str());
newLabel->SetColor(Color(tmp));
newLabel->SetValue(segValue);
}
else
{
// Add a new layer to the labelSetImage. Background label is set automatically
labelSetImage->AddLayer(layerImage);
// Add new label
newLabel = new Label;
newLabel->SetName(labelName.c_str());
newLabel->SetColor(Color(tmp));
newLabel->SetValue(segValue);
labelSetImage->GetLabelSet(labelSetImage->GetActiveLayer())->AddLabel(newLabel);
}
// Add some more label properties
this->SetLabelProperties(newLabel, segmentAttribute);
++segmentIter;
}
labelSetImage->GetLabelSet()->SetAllLabelsVisible(true);
// Add some general DICOM Segmentation properties
- mitk::IDICOMTagsOfInterest *toiSrv = GetDicomTagsOfInterestService();
+ mitk::IDICOMTagsOfInterest *toiSrv = DICOMIOHelper::GetTagsOfInterestService();
auto tagsOfInterest = toiSrv->GetTagsOfInterest();
DICOMTagPathList tagsOfInterestList;
for (const auto &tag : tagsOfInterest)
{
tagsOfInterestList.push_back(tag.first);
}
mitk::DICOMDCMTKTagScanner::Pointer scanner = mitk::DICOMDCMTKTagScanner::New();
scanner->SetInputFiles({ GetInputLocation() });
scanner->AddTagPaths(tagsOfInterestList);
scanner->Scan();
mitk::DICOMDatasetAccessingImageFrameList frames = scanner->GetFrameInfoList();
if (frames.empty())
{
MITK_ERROR << "Error reading the DICOM Seg file" << std::endl;
return result;
}
- auto findings = ExtractPathsOfInterest(tagsOfInterestList, frames);
- SetProperties(labelSetImage, findings);
+ auto findings = DICOMIOHelper::ExtractPathsOfInterest(tagsOfInterestList, frames);
+ DICOMIOHelper::SetProperties(labelSetImage, findings);
// Set active layer to the first layer of the labelset image
if (labelSetImage->GetNumberOfLayers() > 1 && labelSetImage->GetActiveLayer() != 0)
labelSetImage->SetActiveLayer(0);
}
catch (const std::exception &e)
{
MITK_ERROR << "An error occurred while reading the DICOM Seg file: " << e.what();
return result;
}
catch (...)
{
MITK_ERROR << "An error occurred in dcmqi while reading the DICOM Seg file";
return result;
}
result.push_back(labelSetImage.GetPointer());
return result;
}
const std::string mitk::DICOMSegmentationIO::CreateMetaDataJsonFile(int layer)
{
const mitk::LabelSetImage *image = dynamic_cast<const mitk::LabelSetImage *>(this->GetInput());
const std::string output;
dcmqi::JSONSegmentationMetaInformationHandler handler;
// 1. Metadata attributes that will be listed in the resulting DICOM SEG object
std::string contentCreatorName;
if (!image->GetPropertyList()->GetStringProperty(GeneratePropertyNameForDICOMTag(0x0070, 0x0084).c_str(),
contentCreatorName))
contentCreatorName = "MITK";
handler.setContentCreatorName(contentCreatorName);
std::string clinicalTrailSeriesId;
if (!image->GetPropertyList()->GetStringProperty(GeneratePropertyNameForDICOMTag(0x0012, 0x0071).c_str(),
clinicalTrailSeriesId))
clinicalTrailSeriesId = "Session 1";
handler.setClinicalTrialSeriesID(clinicalTrailSeriesId);
std::string clinicalTrialTimePointID;
if (!image->GetPropertyList()->GetStringProperty(GeneratePropertyNameForDICOMTag(0x0012, 0x0050).c_str(),
clinicalTrialTimePointID))
clinicalTrialTimePointID = "0";
handler.setClinicalTrialTimePointID(clinicalTrialTimePointID);
std::string clinicalTrialCoordinatingCenterName = "";
if (!image->GetPropertyList()->GetStringProperty(GeneratePropertyNameForDICOMTag(0x0012, 0x0060).c_str(),
clinicalTrialCoordinatingCenterName))
clinicalTrialCoordinatingCenterName = "Unknown";
handler.setClinicalTrialCoordinatingCenterName(clinicalTrialCoordinatingCenterName);
std::string seriesDescription;
if (!image->GetPropertyList()->GetStringProperty("name", seriesDescription))
seriesDescription = "MITK Segmentation";
handler.setSeriesDescription(seriesDescription);
handler.setSeriesNumber("0" + std::to_string(layer));
handler.setInstanceNumber("1");
handler.setBodyPartExamined("");
const LabelSet *labelSet = image->GetLabelSet(layer);
auto labelIter = labelSet->IteratorConstBegin();
// Ignore background label
++labelIter;
for (; labelIter != labelSet->IteratorConstEnd(); ++labelIter)
{
const Label *label = labelIter->second;
if (label != nullptr)
{
TemporoSpatialStringProperty *segmentNumberProp = dynamic_cast<mitk::TemporoSpatialStringProperty *>(label->GetProperty(
mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_NUMBER_PATH()).c_str()));
TemporoSpatialStringProperty *segmentLabelProp = dynamic_cast<mitk::TemporoSpatialStringProperty *>(label->GetProperty(
mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_LABEL_PATH()).c_str()));
TemporoSpatialStringProperty *algorithmTypeProp = dynamic_cast<mitk::TemporoSpatialStringProperty *>(label->GetProperty(
mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_ALGORITHM_TYPE_PATH()).c_str()));
TemporoSpatialStringProperty *segmentCategoryCodeValueProp = dynamic_cast<mitk::TemporoSpatialStringProperty *>(label->GetProperty(
mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_VALUE_PATH()).c_str()));
TemporoSpatialStringProperty *segmentCategoryCodeSchemeProp = dynamic_cast<mitk::TemporoSpatialStringProperty *>(label->GetProperty(
mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_SCHEME_PATH()).c_str()));
TemporoSpatialStringProperty *segmentCategoryCodeMeaningProp = dynamic_cast<mitk::TemporoSpatialStringProperty *>(label->GetProperty(
mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_MEANING_PATH()).c_str()));
TemporoSpatialStringProperty *segmentTypeCodeValueProp = dynamic_cast<mitk::TemporoSpatialStringProperty *>(label->GetProperty(
mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_VALUE_PATH()).c_str()));
TemporoSpatialStringProperty *segmentTypeCodeSchemeProp = dynamic_cast<mitk::TemporoSpatialStringProperty *>(label->GetProperty(
mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_SCHEME_PATH()).c_str()));
TemporoSpatialStringProperty *segmentTypeCodeMeaningProp = dynamic_cast<mitk::TemporoSpatialStringProperty *>(label->GetProperty(
mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_MEANING_PATH()).c_str()));
TemporoSpatialStringProperty *segmentModifierCodeValueProp = dynamic_cast<mitk::TemporoSpatialStringProperty *>(label->GetProperty(
mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_VALUE_PATH()).c_str()));
TemporoSpatialStringProperty *segmentModifierCodeSchemeProp = dynamic_cast<mitk::TemporoSpatialStringProperty *>(label->GetProperty(
mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_SCHEME_PATH()).c_str()));
TemporoSpatialStringProperty *segmentModifierCodeMeaningProp = dynamic_cast<mitk::TemporoSpatialStringProperty *>(label->GetProperty(
mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_MEANING_PATH()).c_str()));
dcmqi::SegmentAttributes *segmentAttribute = nullptr;
if (segmentNumberProp->GetValue() == "")
{
MITK_ERROR << "Something went wrong with the label ID.";
}
else
{
int labelId = std::stoi(segmentNumberProp->GetValue());
segmentAttribute = handler.createAndGetNewSegment(labelId);
}
if (segmentAttribute != nullptr)
{
segmentAttribute->setSegmentDescription(segmentLabelProp->GetValueAsString());
segmentAttribute->setSegmentAlgorithmType(algorithmTypeProp->GetValueAsString());
segmentAttribute->setSegmentAlgorithmName("MITK Segmentation");
if (segmentCategoryCodeValueProp != nullptr && segmentCategoryCodeSchemeProp != nullptr &&
segmentCategoryCodeMeaningProp != nullptr)
segmentAttribute->setSegmentedPropertyCategoryCodeSequence(
segmentCategoryCodeValueProp->GetValueAsString(),
segmentCategoryCodeSchemeProp->GetValueAsString(),
segmentCategoryCodeMeaningProp->GetValueAsString());
else
// some default values
segmentAttribute->setSegmentedPropertyCategoryCodeSequence(
"M-01000", "SRT", "Morphologically Altered Structure");
if (segmentTypeCodeValueProp != nullptr && segmentTypeCodeSchemeProp != nullptr &&
segmentTypeCodeMeaningProp != nullptr)
{
segmentAttribute->setSegmentedPropertyTypeCodeSequence(segmentTypeCodeValueProp->GetValueAsString(),
segmentTypeCodeSchemeProp->GetValueAsString(),
segmentTypeCodeMeaningProp->GetValueAsString());
handler.setBodyPartExamined(segmentTypeCodeMeaningProp->GetValueAsString());
}
else
{
// some default values
segmentAttribute->setSegmentedPropertyTypeCodeSequence("M-03000", "SRT", "Mass");
handler.setBodyPartExamined("Mass");
}
if (segmentModifierCodeValueProp != nullptr && segmentModifierCodeSchemeProp != nullptr &&
segmentModifierCodeMeaningProp != nullptr)
segmentAttribute->setSegmentedPropertyTypeModifierCodeSequence(
segmentModifierCodeValueProp->GetValueAsString(),
segmentModifierCodeSchemeProp->GetValueAsString(),
segmentModifierCodeMeaningProp->GetValueAsString());
Color color = label->GetColor();
segmentAttribute->setRecommendedDisplayRGBValue(color[0] * 255, color[1] * 255, color[2] * 255);
}
}
}
return handler.getJSONOutputAsString();
}
void mitk::DICOMSegmentationIO::SetLabelProperties(mitk::Label *label, dcmqi::SegmentAttributes *segmentAttribute)
{
// Segment Number:Identification number of the segment.The value of Segment Number(0062, 0004) shall be unique
// within the Segmentation instance in which it is created
label->SetProperty(DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_NUMBER_PATH()).c_str(),
TemporoSpatialStringProperty::New(std::to_string(label->GetValue())));
// Segment Label: User-defined label identifying this segment.
label->SetProperty(DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_LABEL_PATH()).c_str(),
TemporoSpatialStringProperty::New(label->GetName()));
// Segment Algorithm Type: Type of algorithm used to generate the segment.
if (!segmentAttribute->getSegmentAlgorithmType().empty())
label->SetProperty(DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_ALGORITHM_TYPE_PATH()).c_str(),
TemporoSpatialStringProperty::New(segmentAttribute->getSegmentAlgorithmType()));
// Add Segmented Property Category Code Sequence tags
auto categoryCodeSequence = segmentAttribute->getSegmentedPropertyCategoryCodeSequence();
if (categoryCodeSequence != nullptr)
{
OFString codeValue; // (0008,0100) Code Value
categoryCodeSequence->getCodeValue(codeValue);
label->SetProperty(
DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_VALUE_PATH()).c_str(),
TemporoSpatialStringProperty::New(codeValue.c_str()));
OFString codeScheme; // (0008,0102) Coding Scheme Designator
categoryCodeSequence->getCodingSchemeDesignator(codeScheme);
label->SetProperty(
DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_SCHEME_PATH()).c_str(),
TemporoSpatialStringProperty::New(codeScheme.c_str()));
OFString codeMeaning; // (0008,0104) Code Meaning
categoryCodeSequence->getCodeMeaning(codeMeaning);
label->SetProperty(
DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_MEANING_PATH()).c_str(),
TemporoSpatialStringProperty::New(codeMeaning.c_str()));
}
// Add Segmented Property Type Code Sequence tags
auto typeCodeSequence = segmentAttribute->getSegmentedPropertyTypeCodeSequence();
if (typeCodeSequence != nullptr)
{
OFString codeValue; // (0008,0100) Code Value
typeCodeSequence->getCodeValue(codeValue);
label->SetProperty(DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_VALUE_PATH()).c_str(),
TemporoSpatialStringProperty::New(codeValue.c_str()));
OFString codeScheme; // (0008,0102) Coding Scheme Designator
typeCodeSequence->getCodingSchemeDesignator(codeScheme);
label->SetProperty(
DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_SCHEME_PATH()).c_str(),
TemporoSpatialStringProperty::New(codeScheme.c_str()));
OFString codeMeaning; // (0008,0104) Code Meaning
typeCodeSequence->getCodeMeaning(codeMeaning);
label->SetProperty(
DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_MEANING_PATH()).c_str(),
TemporoSpatialStringProperty::New(codeMeaning.c_str()));
}
// Add Segmented Property Type Modifier Code Sequence tags
auto modifierCodeSequence = segmentAttribute->getSegmentedPropertyTypeModifierCodeSequence();
if (modifierCodeSequence != nullptr)
{
OFString codeValue; // (0008,0100) Code Value
modifierCodeSequence->getCodeValue(codeValue);
label->SetProperty(
DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_VALUE_PATH()).c_str(),
TemporoSpatialStringProperty::New(codeValue.c_str()));
OFString codeScheme; // (0008,0102) Coding Scheme Designator
modifierCodeSequence->getCodingSchemeDesignator(codeScheme);
label->SetProperty(
DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_SCHEME_PATH()).c_str(),
TemporoSpatialStringProperty::New(codeScheme.c_str()));
OFString codeMeaning; // (0008,0104) Code Meaning
modifierCodeSequence->getCodeMeaning(codeMeaning);
label->SetProperty(
DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_MEANING_PATH()).c_str(),
TemporoSpatialStringProperty::New(codeMeaning.c_str()));
}
// Add Atomic RegionSequence tags
auto atomicRegionSequence = segmentAttribute->getAnatomicRegionSequence();
if (atomicRegionSequence != nullptr)
{
OFString codeValue; // (0008,0100) Code Value
atomicRegionSequence->getCodeValue(codeValue);
label->SetProperty(
DICOMTagPathToPropertyName(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_VALUE_PATH()).c_str(),
TemporoSpatialStringProperty::New(codeValue.c_str()));
OFString codeScheme; // (0008,0102) Coding Scheme Designator
atomicRegionSequence->getCodingSchemeDesignator(codeScheme);
label->SetProperty(
DICOMTagPathToPropertyName(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_SCHEME_PATH()).c_str(),
TemporoSpatialStringProperty::New(codeScheme.c_str()));
OFString codeMeaning; // (0008,0104) Code Meaning
atomicRegionSequence->getCodeMeaning(codeMeaning);
label->SetProperty(
DICOMTagPathToPropertyName(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_MEANING_PATH()).c_str(),
TemporoSpatialStringProperty::New(codeMeaning.c_str()));
}
}
DICOMSegmentationIO *DICOMSegmentationIO::IOClone() const { return new DICOMSegmentationIO(*this); }
} // namespace
#endif //__mitkDICOMSegmentationIO__cpp
diff --git a/Modules/Multilabel/autoload/IO/CMakeLists.txt b/Modules/Multilabel/autoload/IO/CMakeLists.txt
index a61aebf0db..ae9c56dfe8 100644
--- a/Modules/Multilabel/autoload/IO/CMakeLists.txt
+++ b/Modules/Multilabel/autoload/IO/CMakeLists.txt
@@ -1,5 +1,5 @@
mitk_create_module(MultilabelIO
DEPENDS PUBLIC MitkMultilabel MitkSceneSerialization
- PACKAGE_DEPENDS PRIVATE ITK|IONRRD
+ PACKAGE_DEPENDS PRIVATE ITK|IONRRD nlohmann_json
AUTOLOAD_WITH MitkCore
)
diff --git a/Modules/Multilabel/autoload/IO/files.cmake b/Modules/Multilabel/autoload/IO/files.cmake
index a5079ce423..71bd04bf86 100644
--- a/Modules/Multilabel/autoload/IO/files.cmake
+++ b/Modules/Multilabel/autoload/IO/files.cmake
@@ -1,8 +1,13 @@
set(CPP_FILES
mitkLabelSetImageIO.cpp
mitkLabelSetImageIO.h
mitkLabelSetImageSerializer.cpp
mitkLabelSetImageSerializer.h
mitkMultilabelActivator.cpp
+ mitkMultilabelIOMimeTypes.cpp
+ mitkMultilabelIOMimeTypes.h
+ mitkSegmentationTaskListIO.cpp
+ mitkSegmentationTaskListIO.h
+ mitkSegmentationTaskListSerializer.cpp
+ mitkSegmentationTaskListSerializer.h
)
-
diff --git a/Modules/Multilabel/autoload/IO/mitkMultilabelActivator.cpp b/Modules/Multilabel/autoload/IO/mitkMultilabelActivator.cpp
index f70ac539e2..58201f45c4 100644
--- a/Modules/Multilabel/autoload/IO/mitkMultilabelActivator.cpp
+++ b/Modules/Multilabel/autoload/IO/mitkMultilabelActivator.cpp
@@ -1,44 +1,55 @@
/*============================================================================
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 <usGetModuleContext.h>
#include <usModule.h>
#include <usModuleActivator.h>
#include <usModuleContext.h>
#include "mitkLabelSetImageIO.h"
+#include "mitkMultilabelIOMimeTypes.h"
+#include "mitkSegmentationTaskListIO.h"
namespace mitk
{
/**
\brief Registers services for multilabel module.
*/
class MultilabelIOModuleActivator : public us::ModuleActivator
{
std::vector<AbstractFileIO *> m_FileIOs;
public:
- void Load(us::ModuleContext * /*context*/) override
+ void Load(us::ModuleContext *context) override
{
+ auto mimeTypes = MitkMultilabelIOMimeTypes::Get();
+
+ us::ServiceProperties props;
+ props[us::ServiceConstants::SERVICE_RANKING()] = 10;
+
+ for (const auto &mimeType : mimeTypes)
+ context->RegisterService(mimeType, props);
+
m_FileIOs.push_back(new LabelSetImageIO());
+ m_FileIOs.push_back(new SegmentationTaskListIO);
}
void Unload(us::ModuleContext *) override
{
for (auto &elem : m_FileIOs)
{
delete elem;
}
}
};
}
US_EXPORT_MODULE_ACTIVATOR(mitk::MultilabelIOModuleActivator)
diff --git a/Modules/Multilabel/autoload/IO/mitkMultilabelIOMimeTypes.cpp b/Modules/Multilabel/autoload/IO/mitkMultilabelIOMimeTypes.cpp
new file mode 100644
index 0000000000..231f8d4aed
--- /dev/null
+++ b/Modules/Multilabel/autoload/IO/mitkMultilabelIOMimeTypes.cpp
@@ -0,0 +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.
+
+============================================================================*/
+
+#include "mitkMultilabelIOMimeTypes.h"
+#include <mitkIOMimeTypes.h>
+
+#include <filesystem>
+#include <fstream>
+
+#include <nlohmann/json.hpp>
+
+mitk::MitkMultilabelIOMimeTypes::MitkSegmentationTaskListMimeType::MitkSegmentationTaskListMimeType()
+ : CustomMimeType(SEGMENTATIONTASKLIST_MIMETYPE_NAME())
+{
+ this->AddExtension("json");
+ this->SetCategory("MITK Segmentation Task List");
+ this->SetComment("MITK Segmentation Task List");
+}
+
+bool mitk::MitkMultilabelIOMimeTypes::MitkSegmentationTaskListMimeType::AppliesTo(const std::string& path) const
+{
+ bool result = CustomMimeType::AppliesTo(path);
+
+ if (!std::filesystem::exists(path)) // T18572
+ return result;
+
+ std::ifstream file(path);
+
+ if (!file.is_open())
+ return false;
+
+ auto json = nlohmann::json::parse(file, nullptr, false);
+
+ if (json.is_discarded() || !json.is_object())
+ return false;
+
+ if ("MITK Segmentation Task List" != json.value("FileFormat", ""))
+ return false;
+
+ if (1 != json.value<int>("Version", 0))
+ return false;
+
+ return true;
+}
+
+mitk::MitkMultilabelIOMimeTypes::MitkSegmentationTaskListMimeType* mitk::MitkMultilabelIOMimeTypes::MitkSegmentationTaskListMimeType::Clone() const
+{
+ return new MitkSegmentationTaskListMimeType(*this);
+}
+
+mitk::MitkMultilabelIOMimeTypes::MitkSegmentationTaskListMimeType mitk::MitkMultilabelIOMimeTypes::SEGMENTATIONTASKLIST_MIMETYPE()
+{
+ return MitkSegmentationTaskListMimeType();
+}
+
+std::string mitk::MitkMultilabelIOMimeTypes::SEGMENTATIONTASKLIST_MIMETYPE_NAME()
+{
+ return IOMimeTypes::DEFAULT_BASE_NAME() + ".segmentationtasklist";
+}
+
+std::vector<mitk::CustomMimeType*> mitk::MitkMultilabelIOMimeTypes::Get()
+{
+ std::vector<CustomMimeType*> mimeTypes;
+ mimeTypes.push_back(SEGMENTATIONTASKLIST_MIMETYPE().Clone());
+ return mimeTypes;
+}
diff --git a/Modules/Multilabel/autoload/IO/mitkMultilabelIOMimeTypes.h b/Modules/Multilabel/autoload/IO/mitkMultilabelIOMimeTypes.h
new file mode 100644
index 0000000000..7343895f13
--- /dev/null
+++ b/Modules/Multilabel/autoload/IO/mitkMultilabelIOMimeTypes.h
@@ -0,0 +1,39 @@
+/*============================================================================
+
+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 mitkMultilabelIOMimeTypes_h
+#define mitkMultilabelIOMimeTypes_h
+
+#include <mitkCustomMimeType.h>
+#include <MitkMultilabelIOExports.h>
+
+namespace mitk
+{
+ namespace MitkMultilabelIOMimeTypes
+ {
+ class MITKMULTILABELIO_EXPORT MitkSegmentationTaskListMimeType : public CustomMimeType
+ {
+ public:
+ MitkSegmentationTaskListMimeType();
+
+ bool AppliesTo(const std::string& path) const override;
+ MitkSegmentationTaskListMimeType* Clone() const override;
+ };
+
+ MITKMULTILABELIO_EXPORT MitkSegmentationTaskListMimeType SEGMENTATIONTASKLIST_MIMETYPE();
+ MITKMULTILABELIO_EXPORT std::string SEGMENTATIONTASKLIST_MIMETYPE_NAME();
+
+ MITKMULTILABELIO_EXPORT std::vector<CustomMimeType*> Get();
+ }
+}
+
+#endif
diff --git a/Modules/Multilabel/autoload/IO/mitkSegmentationTaskListIO.cpp b/Modules/Multilabel/autoload/IO/mitkSegmentationTaskListIO.cpp
new file mode 100644
index 0000000000..6afa7c5a81
--- /dev/null
+++ b/Modules/Multilabel/autoload/IO/mitkSegmentationTaskListIO.cpp
@@ -0,0 +1,267 @@
+/*============================================================================
+
+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 "mitkSegmentationTaskListIO.h"
+#include "mitkMultilabelIOMimeTypes.h"
+
+#include <mitkSegmentationTaskList.h>
+
+#include <nlohmann/json.hpp>
+
+#include <filesystem>
+#include <fstream>
+
+namespace mitk
+{
+ void to_json(nlohmann::json& json, const SegmentationTaskList::Task& task)
+ {
+ if (task.HasName())
+ json["Name"] = task.GetName();
+
+ if (task.HasDescription())
+ json["Description"] = task.GetDescription();
+
+ if (task.HasImage())
+ json["Image"] = task.GetImage().string();
+
+ if (task.HasSegmentation())
+ json["Segmentation"] = task.GetSegmentation().string();
+
+ if (task.HasLabelName())
+ json["LabelName"] = task.GetLabelName();
+
+ if (task.HasLabelNameSuggestions())
+ json["LabelNameSuggestions"] = task.GetLabelNameSuggestions().string();
+
+ if (task.HasPreset())
+ json["Preset"] = task.GetPreset().string();
+
+ if (task.HasResult())
+ json["Result"] = task.GetResult().string();
+
+ if (task.HasDynamic())
+ json["Dynamic"] = task.GetDynamic();
+ }
+
+ void from_json(const nlohmann::json& json, SegmentationTaskList::Task& task)
+ {
+ auto iter = json.find("Name");
+
+ if (iter != json.end())
+ task.SetName(json["Name"].get<std::string>());
+
+ iter = json.find("Description");
+
+ if (iter != json.end())
+ task.SetDescription(json["Description"].get<std::string>());
+
+ iter = json.find("Image");
+
+ if (iter != json.end())
+ task.SetImage(json["Image"].get<std::string>());
+
+ iter = json.find("Segmentation");
+
+ if (iter != json.end())
+ task.SetSegmentation(json["Segmentation"].get<std::string>());
+
+ iter = json.find("LabelName");
+
+ if (iter != json.end())
+ task.SetLabelName(json["LabelName"].get<std::string>());
+
+ iter = json.find("LabelNameSuggestions");
+
+ if (iter != json.end())
+ task.SetLabelNameSuggestions(json["LabelNameSuggestions"].get<std::string>());
+
+ iter = json.find("Preset");
+
+ if (iter != json.end())
+ task.SetPreset(json["Preset"].get<std::string>());
+
+ iter = json.find("Result");
+
+ if (iter != json.end())
+ task.SetResult(json["Result"].get<std::string>());
+
+ iter = json.find("Dynamic");
+
+ if (iter != json.end())
+ task.SetDynamic(json["Dynamic"].get<bool>());
+ }
+}
+
+mitk::SegmentationTaskListIO::SegmentationTaskListIO()
+ : AbstractFileIO(SegmentationTaskList::GetStaticNameOfClass(), MitkMultilabelIOMimeTypes::SEGMENTATIONTASKLIST_MIMETYPE(), "MITK Segmentation Task List")
+{
+ this->RegisterService();
+}
+
+std::vector<mitk::BaseData::Pointer> mitk::SegmentationTaskListIO::DoRead()
+{
+ auto* stream = this->GetInputStream();
+ std::ifstream fileStream;
+
+ if (nullptr == stream)
+ {
+ auto filename = this->GetInputLocation();
+
+ if (filename.empty() || !std::filesystem::exists(filename))
+ mitkThrow() << "Invalid or nonexistent filename: \"" << filename << "\"!";
+
+ fileStream.open(filename);
+
+ if (!fileStream.is_open())
+ mitkThrow() << "Could not open file \"" << filename << "\" for reading!";
+
+ stream = &fileStream;
+ }
+
+ nlohmann::json json;
+
+ try
+ {
+ json = nlohmann::json::parse(*stream);
+ }
+ catch (const nlohmann::json::exception& e)
+ {
+ mitkThrow() << e.what();
+ }
+
+ if (!json.is_object())
+ mitkThrow() << "Unknown file format (expected JSON object as root)!";
+
+ if ("MITK Segmentation Task List" != json.value("FileFormat", ""))
+ mitkThrow() << "Unknown file format (expected \"MITK Segmentation Task List\")!";
+
+ if (1 != json.value<int>("Version", 0))
+ mitkThrow() << "Unknown file format version (expected \"1\")!";
+
+ if (!json.contains("Tasks") || !json["Tasks"].is_array())
+ mitkThrow() << "Tasks array not found!";
+
+ auto segmentationTaskList = SegmentationTaskList::New();
+
+ if (json.contains("Name"))
+ segmentationTaskList->SetProperty("name", StringProperty::New(json["Name"].get<std::string>()));
+
+ try
+ {
+ if (json.contains("Defaults"))
+ {
+ segmentationTaskList->SetDefaults(json["Defaults"].get<SegmentationTaskList::Task>());
+
+ if (segmentationTaskList->GetDefaults().HasResult())
+ mitkThrow() << "Defaults must not contain \"Result\"!";
+ }
+
+ for (const auto& task : json["Tasks"])
+ {
+ auto i = segmentationTaskList->AddTask(task.get<SegmentationTaskList::Task>());
+
+ if (!segmentationTaskList->HasImage(i))
+ mitkThrow() << "Task " << i << " must contain \"Image\"!";
+
+ std::filesystem::path imagePath(segmentationTaskList->GetImage(i));
+
+ if (imagePath.is_relative())
+ {
+ auto inputLocation = this->GetInputLocation();
+
+ /* If we have access to properties, we are reading from an MITK scene
+ * file. In this case, paths are still relative to the original input
+ * location, which is preserved in the properties.
+ */
+
+ const auto* properties = this->GetProperties();
+
+ if (properties != nullptr)
+ properties->GetStringProperty("MITK.IO.reader.inputlocation", inputLocation);
+
+ imagePath = std::filesystem::path(inputLocation).remove_filename() / imagePath;
+ }
+
+ if (!std::filesystem::exists(imagePath))
+ mitkThrow() << "Referenced image \"" << imagePath << "\" in task " << i << " does not exist!";
+
+ if (!segmentationTaskList->HasResult(i))
+ mitkThrow() << "Task " << i << " must contain \"Result\"!";
+ }
+ }
+ catch (const nlohmann::json::type_error& e)
+ {
+ mitkThrow() << e.what();
+ }
+
+ std::vector<BaseData::Pointer> result;
+ result.push_back(segmentationTaskList.GetPointer());
+
+ return result;
+}
+
+void mitk::SegmentationTaskListIO::Write()
+{
+ auto segmentationTaskList = dynamic_cast<const SegmentationTaskList*>(this->GetInput());
+
+ if (nullptr == segmentationTaskList)
+ mitkThrow() << "Invalid input for writing!";
+
+ if (segmentationTaskList->GetNumberOfTasks() == 0)
+ mitkThrow() << "No tasks found!";
+
+ auto* stream = this->GetOutputStream();
+ std::ofstream fileStream;
+
+ if (nullptr == stream)
+ {
+ auto filename = this->GetOutputLocation();
+
+ if (filename.empty())
+ mitkThrow() << "Neither an output stream nor an output filename was specified!";
+
+ fileStream.open(filename);
+
+ if (!fileStream.is_open())
+ mitkThrow() << "Could not open file \"" << filename << "\" for writing!";
+
+ stream = &fileStream;
+ }
+
+ if (!stream->good())
+ mitkThrow() << "Stream for writing is not good!";
+
+ nlohmann::ordered_json json = {
+ { "FileFormat", "MITK Segmentation Task List" },
+ { "Version", 1 },
+ { "Name", segmentationTaskList->GetProperty("name")->GetValueAsString() }
+ };
+
+ nlohmann::json defaults = segmentationTaskList->GetDefaults();
+
+ if (!defaults.is_null())
+ json["Defaults"] = defaults;
+
+ nlohmann::json tasks;
+
+ for (const auto& task : *segmentationTaskList)
+ tasks.push_back(task);
+
+ json["Tasks"] = tasks;
+
+ *stream << std::setw(2) << json << std::endl;
+}
+
+mitk::SegmentationTaskListIO* mitk::SegmentationTaskListIO::IOClone() const
+{
+ return new SegmentationTaskListIO(*this);
+}
diff --git a/Modules/Multilabel/autoload/IO/mitkSegmentationTaskListIO.h b/Modules/Multilabel/autoload/IO/mitkSegmentationTaskListIO.h
new file mode 100644
index 0000000000..71aed1550d
--- /dev/null
+++ b/Modules/Multilabel/autoload/IO/mitkSegmentationTaskListIO.h
@@ -0,0 +1,36 @@
+/*============================================================================
+
+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 mitkSegmentationTaskListIO_h
+#define mitkSegmentationTaskListIO_h
+
+#include <mitkAbstractFileIO.h>
+
+namespace mitk
+{
+ class SegmentationTaskListIO : public AbstractFileIO
+ {
+ public:
+ SegmentationTaskListIO();
+
+ using AbstractFileReader::Read;
+ void Write() override;
+
+ protected:
+ std::vector<BaseData::Pointer> DoRead() override;
+
+ private:
+ SegmentationTaskListIO* IOClone() const override;
+ };
+}
+
+#endif
diff --git a/Modules/Multilabel/autoload/IO/mitkSegmentationTaskListSerializer.cpp b/Modules/Multilabel/autoload/IO/mitkSegmentationTaskListSerializer.cpp
new file mode 100644
index 0000000000..279826d5f7
--- /dev/null
+++ b/Modules/Multilabel/autoload/IO/mitkSegmentationTaskListSerializer.cpp
@@ -0,0 +1,55 @@
+/*============================================================================
+
+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 "mitkSegmentationTaskListSerializer.h"
+#include "mitkSegmentationTaskList.h"
+
+#include <mitkIOUtil.h>
+
+MITK_REGISTER_SERIALIZER(SegmentationTaskListSerializer)
+
+mitk::SegmentationTaskListSerializer::SegmentationTaskListSerializer()
+{
+}
+
+mitk::SegmentationTaskListSerializer::~SegmentationTaskListSerializer()
+{
+}
+
+std::string mitk::SegmentationTaskListSerializer::Serialize()
+{
+ auto segmentationTaskList = dynamic_cast<const SegmentationTaskList*>(m_Data.GetPointer());
+
+ if (nullptr == segmentationTaskList)
+ {
+ MITK_ERROR << "Object at " << (const void*)this->m_Data << " is not an mitk::SegmentationTaskList. Cannot serialize as MITK Segmentation Task List.";
+ return "";
+ }
+
+ auto filename = this->GetUniqueFilenameInWorkingDirectory();
+ filename += "_" + m_FilenameHint + ".json";
+
+ std::string path = m_WorkingDirectory;
+ path += IOUtil::GetDirectorySeparator() + filename;
+
+ try
+ {
+ IOUtil::Save(segmentationTaskList, path);
+ }
+ catch (std::exception& e)
+ {
+ MITK_ERROR << "Error serializing object at " << (const void*)this->m_Data << " to " << path << ": " << e.what();
+ return "";
+ }
+
+ return filename;
+}
diff --git a/Modules/Multilabel/autoload/IO/mitkSegmentationTaskListSerializer.h b/Modules/Multilabel/autoload/IO/mitkSegmentationTaskListSerializer.h
new file mode 100644
index 0000000000..a8e2579fd4
--- /dev/null
+++ b/Modules/Multilabel/autoload/IO/mitkSegmentationTaskListSerializer.h
@@ -0,0 +1,34 @@
+/*============================================================================
+
+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 mitkSegmentationTaskListSerializer_h
+#define mitkSegmentationTaskListSerializer_h
+
+#include <mitkBaseDataSerializer.h>
+
+namespace mitk
+{
+ class SegmentationTaskListSerializer : public BaseDataSerializer
+ {
+ public:
+ mitkClassMacro(SegmentationTaskListSerializer, BaseDataSerializer)
+ itkFactorylessNewMacro(Self)
+
+ std::string Serialize() override;
+
+ protected:
+ SegmentationTaskListSerializer();
+ ~SegmentationTaskListSerializer() override;
+ };
+}
+
+#endif
diff --git a/Modules/Multilabel/files.cmake b/Modules/Multilabel/files.cmake
index 6f267f401b..0524d4f98c 100644
--- a/Modules/Multilabel/files.cmake
+++ b/Modules/Multilabel/files.cmake
@@ -1,20 +1,21 @@
set(CPP_FILES
mitkLabel.cpp
mitkLabelSet.cpp
mitkLabelSetImage.cpp
mitkLabelSetImageConverter.cpp
mitkLabelSetImageSource.cpp
mitkLabelSetImageHelper.cpp
mitkLabelSetImageSurfaceStampFilter.cpp
mitkLabelSetImageToSurfaceFilter.cpp
mitkLabelSetImageToSurfaceThreadedFilter.cpp
mitkLabelSetImageVtkMapper2D.cpp
mitkMultilabelObjectFactory.cpp
mitkLabelSetIOHelper.cpp
mitkDICOMSegmentationPropertyHelper.cpp
mitkDICOMSegmentationConstants.cpp
+ mitkSegmentationTaskList.cpp
)
set(RESOURCE_FILES
)
diff --git a/Modules/Multilabel/mitkSegmentationTaskList.cpp b/Modules/Multilabel/mitkSegmentationTaskList.cpp
new file mode 100644
index 0000000000..a1a844bc8a
--- /dev/null
+++ b/Modules/Multilabel/mitkSegmentationTaskList.cpp
@@ -0,0 +1,174 @@
+/*============================================================================
+
+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 "mitkSegmentationTaskList.h"
+
+#include <mitkIOUtil.h>
+#include <mitkProperties.h>
+
+mitk::SegmentationTaskList::Task::Task()
+ : m_Defaults(nullptr)
+{
+}
+
+mitk::SegmentationTaskList::Task::~Task()
+{
+}
+
+void mitk::SegmentationTaskList::Task::SetDefaults(const Task* defaults)
+{
+ m_Defaults = defaults;
+}
+
+mitk::SegmentationTaskList::SegmentationTaskList()
+{
+ // A base data cannot be serialized if empty. To be not considered empty its
+ // geometry must consist of at least one time step. However, a segmentation
+ // task would then appear as invisible spacial object in a scene. This can
+ // be prevented by excluding it from the scene's bounding box calculations.
+ this->GetTimeGeometry()->Expand(1);
+ this->SetProperty("includeInBoundingBox", BoolProperty::New(false));
+}
+
+mitk::SegmentationTaskList::SegmentationTaskList(const Self& other)
+ : BaseData(other)
+{
+}
+
+mitk::SegmentationTaskList::~SegmentationTaskList()
+{
+}
+
+size_t mitk::SegmentationTaskList::GetNumberOfTasks() const
+{
+ return m_Tasks.size();
+}
+
+size_t mitk::SegmentationTaskList::AddTask(const Task& subtask)
+{
+ m_Tasks.push_back(subtask);
+ m_Tasks.back().SetDefaults(&m_Defaults);
+ return m_Tasks.size() - 1;
+}
+
+const mitk::SegmentationTaskList::Task* mitk::SegmentationTaskList::GetTask(size_t index) const
+{
+ return &m_Tasks.at(index);
+}
+
+mitk::SegmentationTaskList::Task* mitk::SegmentationTaskList::GetTask(size_t index)
+{
+ return &m_Tasks.at(index);
+}
+
+const mitk::SegmentationTaskList::Task& mitk::SegmentationTaskList::GetDefaults() const
+{
+ return m_Defaults;
+}
+
+void mitk::SegmentationTaskList::SetDefaults(const Task& defaults)
+{
+ m_Defaults = defaults;
+
+ for (auto& subtask : m_Tasks)
+ subtask.SetDefaults(&m_Defaults);
+}
+
+bool mitk::SegmentationTaskList::IsDone() const
+{
+ for (size_t i = 0; i < m_Tasks.size(); ++i)
+ {
+ if (!this->IsDone(i))
+ return false;
+ }
+
+ return true;
+}
+
+bool mitk::SegmentationTaskList::IsDone(size_t index) const
+{
+ return std::filesystem::exists(this->GetAbsolutePath(m_Tasks.at(index).GetResult()));
+}
+
+std::filesystem::path mitk::SegmentationTaskList::GetInputLocation() const
+{
+ std::string inputLocation;
+ this->GetPropertyList()->GetStringProperty("MITK.IO.reader.inputlocation", inputLocation);
+
+ return !inputLocation.empty()
+ ? std::filesystem::path(inputLocation).lexically_normal()
+ : std::filesystem::path();
+}
+
+std::filesystem::path mitk::SegmentationTaskList::GetBasePath() const
+{
+ return this->GetInputLocation().remove_filename();
+}
+
+std::filesystem::path mitk::SegmentationTaskList::GetAbsolutePath(const std::filesystem::path& path) const
+{
+ if (path.empty())
+ return path;
+
+ auto normalizedPath = path.lexically_normal();
+
+ return !normalizedPath.is_absolute()
+ ? this->GetBasePath() / normalizedPath
+ : normalizedPath;
+}
+
+void mitk::SegmentationTaskList::SaveTask(size_t index, const BaseData* segmentation)
+{
+ if (segmentation == nullptr)
+ return;
+
+ auto path = this->GetAbsolutePath(this->GetResult(index));
+ IOUtil::Save(segmentation, path.string());
+}
+
+std::vector<mitk::SegmentationTaskList::Task>::const_iterator mitk::SegmentationTaskList::begin() const
+{
+ return m_Tasks.begin();
+}
+
+std::vector<mitk::SegmentationTaskList::Task>::const_iterator mitk::SegmentationTaskList::end() const
+{
+ return m_Tasks.end();
+}
+
+std::vector<mitk::SegmentationTaskList::Task>::iterator mitk::SegmentationTaskList::begin()
+{
+ return m_Tasks.begin();
+}
+
+std::vector<mitk::SegmentationTaskList::Task>::iterator mitk::SegmentationTaskList::end()
+{
+ return m_Tasks.end();
+}
+
+void mitk::SegmentationTaskList::SetRequestedRegionToLargestPossibleRegion()
+{
+}
+
+bool mitk::SegmentationTaskList::RequestedRegionIsOutsideOfTheBufferedRegion()
+{
+ return false;
+}
+
+bool mitk::SegmentationTaskList::VerifyRequestedRegion()
+{
+ return true;
+}
+
+void mitk::SegmentationTaskList::SetRequestedRegion(const itk::DataObject*)
+{
+}
diff --git a/Modules/Multilabel/mitkSegmentationTaskList.h b/Modules/Multilabel/mitkSegmentationTaskList.h
new file mode 100644
index 0000000000..dae82b718e
--- /dev/null
+++ b/Modules/Multilabel/mitkSegmentationTaskList.h
@@ -0,0 +1,110 @@
+/*============================================================================
+
+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 mitkSegmentationTaskList_h
+#define mitkSegmentationTaskList_h
+
+#include <mitkBaseData.h>
+#include <mitkSegmentationTaskListMacros.h>
+
+#include <MitkMultilabelExports.h>
+
+#include <filesystem>
+#include <optional>
+
+namespace mitk
+{
+ /** \brief A list of segmentation tasks.
+ *
+ * See \ref MITKSegmentationTaskListsPage for more information.
+ */
+ class MITKMULTILABEL_EXPORT SegmentationTaskList : public BaseData
+ {
+ public:
+ class MITKMULTILABEL_EXPORT Task
+ {
+ public:
+ Task();
+ ~Task();
+
+ void SetDefaults(const Task* defaults);
+
+ mitkSegmentationTaskValueMacro(std::string, Name)
+ mitkSegmentationTaskValueMacro(std::string, Description)
+ mitkSegmentationTaskValueMacro(std::filesystem::path, Image)
+ mitkSegmentationTaskValueMacro(std::filesystem::path, Segmentation)
+ mitkSegmentationTaskValueMacro(std::string, LabelName)
+ mitkSegmentationTaskValueMacro(std::filesystem::path, LabelNameSuggestions)
+ mitkSegmentationTaskValueMacro(std::filesystem::path, Preset)
+ mitkSegmentationTaskValueMacro(std::filesystem::path, Result)
+ mitkSegmentationTaskValueMacro(bool, Dynamic)
+
+ private:
+ const Task* m_Defaults;
+ };
+
+ mitkClassMacro(SegmentationTaskList, BaseData)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
+
+ mitkSegmentationTaskListValueMacro(std::string, Name)
+ mitkSegmentationTaskListValueMacro(std::string, Description)
+ mitkSegmentationTaskListValueMacro(std::filesystem::path, Image)
+ mitkSegmentationTaskListValueMacro(std::filesystem::path, Segmentation)
+ mitkSegmentationTaskListValueMacro(std::string, LabelName)
+ mitkSegmentationTaskListValueMacro(std::filesystem::path, LabelNameSuggestions)
+ mitkSegmentationTaskListValueMacro(std::filesystem::path, Preset)
+ mitkSegmentationTaskListValueMacro(std::filesystem::path, Result)
+ mitkSegmentationTaskListValueMacro(bool, Dynamic)
+
+ size_t GetNumberOfTasks() const;
+ size_t AddTask(const Task& subtask);
+ const Task* GetTask(size_t index) const;
+ Task* GetTask(size_t index);
+
+ const Task& GetDefaults() const;
+ void SetDefaults(const Task& defaults);
+
+ bool IsDone() const;
+ bool IsDone(size_t index) const;
+
+ std::filesystem::path GetInputLocation() const;
+ std::filesystem::path GetBasePath() const;
+ std::filesystem::path GetAbsolutePath(const std::filesystem::path& path) const;
+
+ void SaveTask(size_t index, const BaseData* segmentation);
+
+ std::vector<Task>::const_iterator begin() const;
+ std::vector<Task>::const_iterator end() const;
+
+ std::vector<Task>::iterator begin();
+ std::vector<Task>::iterator end();
+
+ void SetRequestedRegionToLargestPossibleRegion() override;
+ bool RequestedRegionIsOutsideOfTheBufferedRegion() override;
+ bool VerifyRequestedRegion() override;
+ void SetRequestedRegion(const itk::DataObject*) override;
+
+ protected:
+ mitkCloneMacro(Self)
+
+ SegmentationTaskList();
+ SegmentationTaskList(const Self& other);
+ ~SegmentationTaskList() override;
+
+ private:
+ Task m_Defaults;
+ std::vector<Task> m_Tasks;
+ };
+}
+
+#endif
diff --git a/Modules/Multilabel/mitkSegmentationTaskListMacros.h b/Modules/Multilabel/mitkSegmentationTaskListMacros.h
new file mode 100644
index 0000000000..0d16a63d3a
--- /dev/null
+++ b/Modules/Multilabel/mitkSegmentationTaskListMacros.h
@@ -0,0 +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 mitkSegmentationTaskListMacros_h
+#define mitkSegmentationTaskListMacros_h
+
+#define mitkSegmentationTaskHasValueMacro(name) \
+ bool Has##name() const { \
+ return m_##name.has_value(); \
+ }
+
+#define mitkSegmentationTaskGetValueMacro(type, name) \
+ type Get##name() const { \
+ if (m_##name.has_value()) return m_##name.value(); \
+ if (m_Defaults != nullptr && m_Defaults->m_##name.has_value()) return m_Defaults->m_##name.value(); \
+ return type(); \
+ }
+
+#define mitkSegmentationTaskSetValueMacro(type, name) \
+ void Set##name(const type& value) { \
+ m_##name = value; \
+ }
+
+#define mitkSegmentationTaskValueMacro(type, name) \
+ public: \
+ mitkSegmentationTaskHasValueMacro(name) \
+ mitkSegmentationTaskGetValueMacro(type, name) \
+ mitkSegmentationTaskSetValueMacro(type, name) \
+ private: \
+ std::optional<type> m_##name;
+
+#define mitkSegmentationTaskListGetValueMacro(type, name) \
+ type Get##name(size_t index) const { \
+ return index < m_Tasks.size() ? m_Tasks[index].Get##name() : type(); \
+ }
+
+#define mitkSegmentationTaskListHasValueMacro(name) \
+ bool Has##name(size_t index) const { \
+ return index < m_Tasks.size() && (m_Tasks[index].Has##name() || m_Defaults.Has##name()); \
+ }
+
+#define mitkSegmentationTaskListSetDefaultMacro(type, name) \
+ void SetDefault##name(const type& value) { \
+ m_Defaults.Set##name(value); \
+ }
+
+#define mitkSegmentationTaskListValueMacro(type, name) \
+ mitkSegmentationTaskListHasValueMacro(name) \
+ mitkSegmentationTaskListGetValueMacro(type, name) \
+ mitkSegmentationTaskListSetDefaultMacro(type, name)
+
+#endif
diff --git a/Modules/QtWidgets/include/QmitkStyleManager.h b/Modules/QtWidgets/include/QmitkStyleManager.h
index c2acc0d6e6..ea81d89dab 100644
--- a/Modules/QtWidgets/include/QmitkStyleManager.h
+++ b/Modules/QtWidgets/include/QmitkStyleManager.h
@@ -1,32 +1,35 @@
/*============================================================================
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 QmitkStyleManager_h
#define QmitkStyleManager_h
#include <MitkQtWidgetsExports.h>
#include <QByteArray>
#include <QIcon>
#include <QString>
class MITKQTWIDGETS_EXPORT QmitkStyleManager
{
public:
static QIcon ThemeIcon(const QByteArray &originalSVG);
static QIcon ThemeIcon(const QString &resourcePath);
+ static QString GetIconColor();
+ static QString GetIconAccentColor();
+
QmitkStyleManager() = delete;
~QmitkStyleManager() = delete;
};
#endif
diff --git a/Modules/QtWidgets/src/QmitkDataStorageTableModel.cpp b/Modules/QtWidgets/src/QmitkDataStorageTableModel.cpp
index a877e2f8ee..bdb8eaa359 100644
--- a/Modules/QtWidgets/src/QmitkDataStorageTableModel.cpp
+++ b/Modules/QtWidgets/src/QmitkDataStorageTableModel.cpp
@@ -1,509 +1,509 @@
/*============================================================================
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 "QmitkDataStorageTableModel.h"
//# Own includes
#include "QmitkCustomVariants.h"
#include "QmitkEnums.h"
#include "mitkNodePredicateBase.h"
#include "mitkProperties.h"
#include "mitkRenderingManager.h"
#include <QmitkNodeDescriptorManager.h>
//# Toolkit includes
#include <QFile>
#include <QIcon>
#include <itkCommand.h>
//#CTORS/DTOR
QmitkDataStorageTableModel::QmitkDataStorageTableModel(mitk::DataStorage::Pointer _DataStorage,
mitk::NodePredicateBase *_Predicate,
QObject *parent)
: QAbstractTableModel(parent),
m_DataStorage(nullptr),
m_Predicate(nullptr),
m_BlockEvents(false),
m_SortDescending(false)
{
this->SetPredicate(_Predicate);
this->SetDataStorage(_DataStorage);
}
QmitkDataStorageTableModel::~QmitkDataStorageTableModel()
{
// set data storage 0 to remove event listeners
this->SetDataStorage(nullptr);
}
//# Public GETTER
const mitk::DataStorage::Pointer QmitkDataStorageTableModel::GetDataStorage() const
{
return m_DataStorage.Lock();
}
mitk::NodePredicateBase::Pointer QmitkDataStorageTableModel::GetPredicate() const
{
return m_Predicate;
}
mitk::DataNode::Pointer QmitkDataStorageTableModel::GetNode(const QModelIndex &index) const
{
mitk::DataNode::Pointer node;
if (index.isValid())
{
node = m_NodeSet.at(index.row());
}
return node;
}
QVariant QmitkDataStorageTableModel::headerData(int section, Qt::Orientation orientation, int role) const
{
QVariant headerData;
// show only horizontal header
if (role == Qt::DisplayRole)
{
if (orientation == Qt::Horizontal)
{
// first column: "Name"
if (section == 0)
headerData = "Name";
else if (section == 1)
headerData = "Data Type";
else if (section == 2)
headerData = "Visibility";
}
else if (orientation == Qt::Vertical)
{
// show numbers for rows
headerData = section + 1;
}
}
return headerData;
}
Qt::ItemFlags QmitkDataStorageTableModel::flags(const QModelIndex &index) const
{
Qt::ItemFlags flags = QAbstractItemModel::flags(index);
// name & visibility is editable
if (index.column() == 0)
{
flags |= Qt::ItemIsEditable;
}
else if (index.column() == 2)
{
flags |= Qt::ItemIsUserCheckable;
}
return flags;
}
int QmitkDataStorageTableModel::rowCount(const QModelIndex &) const
{
return m_NodeSet.size();
}
int QmitkDataStorageTableModel::columnCount(const QModelIndex &) const
{
// show name, type and visible columnn
int columns = 3;
return columns;
}
QVariant QmitkDataStorageTableModel::data(const QModelIndex &index, int role) const
{
QVariant data;
if (index.isValid() && !m_NodeSet.empty())
{
mitk::DataNode::Pointer node = m_NodeSet.at(index.row());
std::string nodeName = node->GetName();
if (nodeName.empty())
nodeName = "unnamed";
// get name
if (index.column() == 0)
{
// get name of node (may also be edited)
if (role == Qt::DisplayRole || role == Qt::EditRole)
{
data = QString::fromStdString(nodeName);
}
else if (role == QmitkDataNodeRole)
{
data = QVariant::fromValue(node);
}
}
else if (index.column() == 1)
{
QmitkNodeDescriptor *nodeDescriptor = QmitkNodeDescriptorManager::GetInstance()->GetDescriptor(node);
// get type property of mitk::BaseData
if (role == Qt::DisplayRole)
{
data = nodeDescriptor->GetNameOfClass();
}
// show some nice icons for datatype
else if (role == Qt::DecorationRole)
{
data = nodeDescriptor->GetIcon(node);
}
}
else if (index.column() == 2)
{
// get visible property of mitk::BaseData
bool visibility = false;
if (node->GetVisibility(visibility, nullptr) && role == Qt::CheckStateRole)
{
data = (visibility ? Qt::Checked : Qt::Unchecked);
} // node->GetVisibility(visibility, 0) && role == Qt::CheckStateRole
} // index.column() == 2
} // index.isValid() && !m_NodeSet.empty()
return data;
}
//# Public SETTERS
void QmitkDataStorageTableModel::SetPredicate(mitk::NodePredicateBase *_Predicate)
{
// ensure that a new predicate is set in order to avoid unnecessary changed events
if (m_Predicate != _Predicate)
{
m_Predicate = _Predicate;
this->Reset();
}
}
void QmitkDataStorageTableModel::SetDataStorage(mitk::DataStorage::Pointer _DataStorage)
{
// only proceed if we have a new datastorage
if (m_DataStorage != _DataStorage)
{
auto dataStorage = m_DataStorage.Lock();
// if a data storage was set before remove old event listeners
if (dataStorage.IsNotNull())
{
dataStorage->AddNodeEvent.RemoveListener(
mitk::MessageDelegate1<QmitkDataStorageTableModel, const mitk::DataNode *>(
this, &QmitkDataStorageTableModel::AddNode));
dataStorage->RemoveNodeEvent.RemoveListener(
mitk::MessageDelegate1<QmitkDataStorageTableModel, const mitk::DataNode *>(
this, &QmitkDataStorageTableModel::RemoveNode));
}
// set new data storage
m_DataStorage = _DataStorage;
dataStorage = m_DataStorage.Lock();
// if new storage is not 0 subscribe for events
if (dataStorage.IsNotNull())
{
// subscribe for node added/removed events
dataStorage->AddNodeEvent.AddListener(
mitk::MessageDelegate1<QmitkDataStorageTableModel, const mitk::DataNode *>(
this, &QmitkDataStorageTableModel::AddNode));
dataStorage->RemoveNodeEvent.AddListener(
mitk::MessageDelegate1<QmitkDataStorageTableModel, const mitk::DataNode *>(
this, &QmitkDataStorageTableModel::RemoveNode));
}
// Reset model (even if datastorage is 0->will be checked in Reset())
this->Reset();
}
}
void QmitkDataStorageTableModel::AddNode(const mitk::DataNode *node)
{
// garantuee no recursions when a new node event is thrown
if (!m_BlockEvents)
{
// if we have a predicate, check node against predicate first
if (m_Predicate.IsNotNull() && !m_Predicate->CheckNode(node))
return;
// dont add nodes without data (formerly known as helper objects)
if (node->GetData() == nullptr)
return;
// create listener commands to listen to changes in the name or the visibility of the node
itk::MemberCommand<QmitkDataStorageTableModel>::Pointer propertyModifiedCommand =
itk::MemberCommand<QmitkDataStorageTableModel>::New();
propertyModifiedCommand->SetCallbackFunction(this, &QmitkDataStorageTableModel::PropertyModified);
mitk::BaseProperty *tempProperty = nullptr;
// add listener for properties
tempProperty = node->GetProperty("visible");
if (tempProperty)
m_VisiblePropertyModifiedObserverTags[tempProperty] =
tempProperty->AddObserver(itk::ModifiedEvent(), propertyModifiedCommand);
tempProperty = node->GetProperty("name");
if (tempProperty)
m_NamePropertyModifiedObserverTags[tempProperty] =
tempProperty->AddObserver(itk::ModifiedEvent(), propertyModifiedCommand);
// emit beginInsertRows event
beginInsertRows(QModelIndex(), m_NodeSet.size(), m_NodeSet.size());
// add node
m_NodeSet.push_back(const_cast<mitk::DataNode *>(node));
// emit endInsertRows event
endInsertRows();
}
}
void QmitkDataStorageTableModel::RemoveNode(const mitk::DataNode *node)
{
// garantuee no recursions when a new node event is thrown
if (!m_BlockEvents)
{
// find corresponding node
auto nodeIt = std::find(m_NodeSet.begin(), m_NodeSet.end(), node);
if (nodeIt != m_NodeSet.end())
{
// now: remove listeners for name property ...
mitk::BaseProperty *tempProperty = nullptr;
tempProperty = (*nodeIt)->GetProperty("visible");
if (tempProperty)
tempProperty->RemoveObserver(m_VisiblePropertyModifiedObserverTags[tempProperty]);
m_VisiblePropertyModifiedObserverTags.erase(tempProperty);
// ... and visibility property
tempProperty = (*nodeIt)->GetProperty("name");
if (tempProperty)
tempProperty->RemoveObserver(m_NamePropertyModifiedObserverTags[tempProperty]);
m_NamePropertyModifiedObserverTags.erase(tempProperty);
// get an index from iterator
int row = std::distance(m_NodeSet.begin(), nodeIt);
// emit beginRemoveRows event (QModelIndex is empty because we dont have a tree model)
this->beginRemoveRows(QModelIndex(), row, row);
// remove node
m_NodeSet.erase(nodeIt);
// emit endRemoveRows event
endRemoveRows();
}
}
}
void QmitkDataStorageTableModel::PropertyModified(const itk::Object *caller, const itk::EventObject &)
{
if (!m_BlockEvents)
{
// get modified property
const mitk::BaseProperty *modifiedProperty = dynamic_cast<const mitk::BaseProperty *>(caller);
if (modifiedProperty)
{
// find node that holds the modified property
int row = -1;
int column = -1;
std::vector<mitk::DataNode *>::iterator it;
mitk::BaseProperty *visibilityProperty = nullptr;
mitk::BaseProperty *nameProperty = nullptr;
// search for property that changed and emit datachanged on the corresponding ModelIndex
for (it = m_NodeSet.begin(); it != m_NodeSet.end(); it++)
{
// check for the visible property or the name property
visibilityProperty = (*it)->GetProperty("visible");
if (modifiedProperty == visibilityProperty)
{
column = 2;
break;
}
nameProperty = (*it)->GetProperty("name");
if (modifiedProperty == nameProperty)
{
column = 0;
break;
}
}
// if we have the property we have a valid iterator
if (it != m_NodeSet.end())
row = std::distance(m_NodeSet.begin(), it);
// now emit the dataChanged signal
QModelIndex indexOfChangedProperty = index(row, column);
emit dataChanged(indexOfChangedProperty, indexOfChangedProperty);
}
}
}
bool QmitkDataStorageTableModel::setData(const QModelIndex &index, const QVariant &value, int role)
{
bool noErr = false;
if (index.isValid() && (role == Qt::EditRole || role == Qt::CheckStateRole))
{
// any change events produced here should not be caught in this class
// --> set m_BlockEvents to true
m_BlockEvents = true;
mitk::DataNode::Pointer node = m_NodeSet.at(index.row());
if (index.column() == 0)
{
- node->SetStringProperty("name", value.toString().toStdString().c_str());
+ node->SetName(value.toString().toStdString());
}
else if (index.column() == 2)
{
node->SetBoolProperty("visible", (value.toInt() == Qt::Checked ? true : false));
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
// inform listeners about changes
emit dataChanged(index, index);
m_BlockEvents = false;
noErr = true;
}
return noErr;
}
//#Protected SETTER
void QmitkDataStorageTableModel::Reset()
{
mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet;
// remove all nodes now (dont use iterators because removing elements
// would invalidate the iterator)
// start at the last element: first in, last out
unsigned int i = m_NodeSet.size();
while (!m_NodeSet.empty())
{
--i;
this->RemoveNode(m_NodeSet.at(i));
}
// normally now everything should be empty->just to be sure
// erase all arrays again
m_NamePropertyModifiedObserverTags.clear();
m_VisiblePropertyModifiedObserverTags.clear();
m_NodeSet.clear();
auto dataStorage = m_DataStorage.Lock();
// the whole reset depends on the fact if a data storage is set or not
if (dataStorage.IsNotNull())
{
_NodeSet = m_Predicate.IsNotNull()
? dataStorage->GetSubset(m_Predicate)
: dataStorage->GetAll();
// finally add all nodes to the model
for (auto it = _NodeSet->begin(); it != _NodeSet->end(); it++)
{
// save node
this->AddNode(*it);
}
}
}
void QmitkDataStorageTableModel::sort(int column, Qt::SortOrder order /*= Qt::AscendingOrder */)
{
bool sortDescending = (order == Qt::DescendingOrder) ? true : false;
// do not sort twice !!! (dont know why, but qt calls this func twice. STUPID!)
/*
if(sortDescending != m_SortDescending)
{*/
// m_SortDescending = sortDescending;
DataNodeCompareFunction::CompareCriteria _CompareCriteria = DataNodeCompareFunction::CompareByName;
DataNodeCompareFunction::CompareOperator _CompareOperator =
sortDescending ? DataNodeCompareFunction::Greater : DataNodeCompareFunction::Less;
if (column == 1)
_CompareCriteria = DataNodeCompareFunction::CompareByClassName;
else if (column == 2)
_CompareCriteria = DataNodeCompareFunction::CompareByVisibility;
DataNodeCompareFunction compareFunc(_CompareCriteria, _CompareOperator);
std::sort(m_NodeSet.begin(), m_NodeSet.end(), compareFunc);
QAbstractTableModel::beginResetModel();
QAbstractTableModel::endResetModel();
//}
}
std::vector<mitk::DataNode *> QmitkDataStorageTableModel::GetNodeSet() const
{
return m_NodeSet;
}
QmitkDataStorageTableModel::DataNodeCompareFunction::DataNodeCompareFunction(CompareCriteria _CompareCriteria,
CompareOperator _CompareOperator)
: m_CompareCriteria(_CompareCriteria), m_CompareOperator(_CompareOperator)
{
}
bool QmitkDataStorageTableModel::DataNodeCompareFunction::operator()(const mitk::DataNode::Pointer &_Left,
const mitk::DataNode::Pointer &_Right) const
{
switch (m_CompareCriteria)
{
case CompareByClassName:
if (m_CompareOperator == Less)
return (_Left->GetData()->GetNameOfClass() < _Right->GetData()->GetNameOfClass());
else
return (_Left->GetData()->GetNameOfClass() > _Right->GetData()->GetNameOfClass());
break;
case CompareByVisibility:
{
bool _LeftVisibility = false;
bool _RightVisibility = false;
_Left->GetVisibility(_LeftVisibility, nullptr);
_Right->GetVisibility(_RightVisibility, nullptr);
if (m_CompareOperator == Less)
return (_LeftVisibility < _RightVisibility);
else
return (_LeftVisibility > _RightVisibility);
}
break;
// CompareByName:
default:
if (m_CompareOperator == Less)
return (_Left->GetName() < _Right->GetName());
else
return (_Left->GetName() > _Right->GetName());
break;
}
}
diff --git a/Modules/QtWidgets/src/QmitkDataStorageTreeModel.cpp b/Modules/QtWidgets/src/QmitkDataStorageTreeModel.cpp
index c9e6644716..a5a56029c5 100644
--- a/Modules/QtWidgets/src/QmitkDataStorageTreeModel.cpp
+++ b/Modules/QtWidgets/src/QmitkDataStorageTreeModel.cpp
@@ -1,884 +1,884 @@
/*============================================================================
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 <mitkNodePredicateAnd.h>
#include <mitkNodePredicateData.h>
#include <mitkNodePredicateFirstLevel.h>
#include <mitkNodePredicateNot.h>
#include <mitkNodePredicateOr.h>
#include <mitkNodePredicateProperty.h>
#include <mitkPlanarFigure.h>
#include <mitkProperties.h>
#include <mitkRenderingManager.h>
#include <mitkStringProperty.h>
#include <mitkPropertyNameHelper.h>
#include "QmitkDataStorageTreeModel.h"
#include "QmitkDataStorageTreeModelInternalItem.h"
#include "QmitkNodeDescriptorManager.h"
#include <QmitkCustomVariants.h>
#include <QmitkEnums.h>
#include <QmitkMimeTypes.h>
#include <QFile>
#include <QIcon>
#include <QMimeData>
#include <QTextStream>
#include <map>
#include <mitkCoreServices.h>
QmitkDataStorageTreeModel::QmitkDataStorageTreeModel(mitk::DataStorage *_DataStorage,
bool _PlaceNewNodesOnTop,
QObject *parent)
: QAbstractItemModel(parent),
m_DataStorage(nullptr),
m_PlaceNewNodesOnTop(_PlaceNewNodesOnTop),
m_Root(nullptr),
m_BlockDataStorageEvents(false),
m_AllowHierarchyChange(false)
{
this->SetDataStorage(_DataStorage);
}
QmitkDataStorageTreeModel::~QmitkDataStorageTreeModel()
{
// set data storage to 0 = remove all listeners
this->SetDataStorage(nullptr);
m_Root->Delete();
m_Root = nullptr;
}
mitk::DataNode::Pointer QmitkDataStorageTreeModel::GetNode(const QModelIndex &index) const
{
return this->TreeItemFromIndex(index)->GetDataNode();
}
const mitk::DataStorage::Pointer QmitkDataStorageTreeModel::GetDataStorage() const
{
return m_DataStorage.Lock();
}
QModelIndex QmitkDataStorageTreeModel::index(int row, int column, const QModelIndex &parent) const
{
TreeItem *parentItem;
if (!parent.isValid())
parentItem = m_Root;
else
parentItem = static_cast<TreeItem *>(parent.internalPointer());
TreeItem *childItem = parentItem->GetChild(row);
if (childItem)
return createIndex(row, column, childItem);
else
return QModelIndex();
}
int QmitkDataStorageTreeModel::rowCount(const QModelIndex &parent) const
{
TreeItem *parentTreeItem = this->TreeItemFromIndex(parent);
return parentTreeItem->GetChildCount();
}
Qt::ItemFlags QmitkDataStorageTreeModel::flags(const QModelIndex &index) const
{
if (index.isValid())
{
return Qt::ItemIsUserCheckable | Qt::ItemIsEnabled | Qt::ItemIsSelectable | Qt::ItemIsEditable |
Qt::ItemIsDragEnabled | Qt::ItemIsDropEnabled;
}
else
{
return Qt::ItemIsDropEnabled;
}
}
int QmitkDataStorageTreeModel::columnCount(const QModelIndex & /* parent = QModelIndex() */) const
{
return 1;
}
QModelIndex QmitkDataStorageTreeModel::parent(const QModelIndex &index) const
{
if (!index.isValid())
return QModelIndex();
TreeItem *childItem = this->TreeItemFromIndex(index);
TreeItem *parentItem = childItem->GetParent();
if (parentItem == m_Root)
return QModelIndex();
return this->createIndex(parentItem->GetIndex(), 0, parentItem);
}
QmitkDataStorageTreeModel::TreeItem *QmitkDataStorageTreeModel::TreeItemFromIndex(const QModelIndex &index) const
{
if (index.isValid())
return static_cast<TreeItem *>(index.internalPointer());
else
return m_Root;
}
Qt::DropActions QmitkDataStorageTreeModel::supportedDropActions() const
{
return Qt::CopyAction | Qt::MoveAction;
}
Qt::DropActions QmitkDataStorageTreeModel::supportedDragActions() const
{
return Qt::CopyAction | Qt::MoveAction;
}
bool QmitkDataStorageTreeModel::dropMimeData(
const QMimeData *data, Qt::DropAction action, int row, int /*column*/, const QModelIndex &parent)
{
// Early exit, returning true, but not actually doing anything (ignoring data).
if (action == Qt::IgnoreAction)
{
return true;
}
// Note, we are returning true if we handled it, and false otherwise
bool returnValue = false;
if (data->hasFormat("application/x-qabstractitemmodeldatalist"))
{
returnValue = true;
// First we extract a Qlist of TreeItem* pointers.
QList<TreeItem *> listOfItemsToDrop = ToTreeItemPtrList(data);
if (listOfItemsToDrop.empty())
{
return false;
}
// Retrieve the TreeItem* where we are dropping stuff, and its parent.
TreeItem *dropItem = this->TreeItemFromIndex(parent);
TreeItem *parentItem = dropItem->GetParent();
// If item was dropped onto empty space, we select the root node
if (dropItem == m_Root)
{
parentItem = m_Root;
}
// Dragging and Dropping is only allowed within the same parent, so use the first item in list to validate.
// (otherwise, you could have a derived image such as a segmentation, and assign it to another image).
// NOTE: We are assuming the input list is valid... i.e. when it was dragged, all the items had the same parent.
// Determine whether or not the drag and drop operation is a valid one.
// Examples of invalid operations include:
// - dragging nodes with different parents
// - dragging nodes from one parent to another parent, if m_AllowHierarchyChange is false
// - dragging a node on one of its child nodes (only relevant if m_AllowHierarchyChange is true)
bool isValidDragAndDropOperation(true);
// different parents
{
TreeItem *firstParent = listOfItemsToDrop[0]->GetParent();
QList<TreeItem *>::iterator diIter;
for (diIter = listOfItemsToDrop.begin() + 1; diIter != listOfItemsToDrop.end(); diIter++)
{
if (firstParent != (*diIter)->GetParent())
{
isValidDragAndDropOperation = false;
break;
}
}
}
// dragging from one parent to another
if ((!m_AllowHierarchyChange) && isValidDragAndDropOperation)
{
if (row == -1) // drag onto a node
{
isValidDragAndDropOperation = listOfItemsToDrop[0]->GetParent() == parentItem;
}
else // drag between nodes
{
isValidDragAndDropOperation = listOfItemsToDrop[0]->GetParent() == dropItem;
}
}
// dragging on a child node of one the dragged nodes
{
QList<TreeItem *>::iterator diIter;
for (diIter = listOfItemsToDrop.begin(); diIter != listOfItemsToDrop.end(); diIter++)
{
TreeItem *tempItem = dropItem;
while (tempItem != m_Root)
{
tempItem = tempItem->GetParent();
if (tempItem == *diIter)
{
isValidDragAndDropOperation = false;
}
}
}
}
if (!isValidDragAndDropOperation)
return isValidDragAndDropOperation;
if (listOfItemsToDrop[0] != dropItem && isValidDragAndDropOperation)
{
// Retrieve the index of where we are dropping stuff.
QModelIndex parentModelIndex = this->IndexFromTreeItem(parentItem);
int dragIndex = 0;
// Iterate through the list of TreeItem (which may be at non-consecutive indexes).
QList<TreeItem *>::iterator diIter;
for (diIter = listOfItemsToDrop.begin(); diIter != listOfItemsToDrop.end(); diIter++)
{
TreeItem *itemToDrop = *diIter;
// if the item is dragged down we have to compensate its final position for the
// fact it is deleted lateron, this only applies if it is dragged within the same level
if ((itemToDrop->GetIndex() < row) && (itemToDrop->GetParent() == dropItem))
{
dragIndex = 1;
}
// Here we assume that as you remove items, one at a time, that GetIndex() will be valid.
this->beginRemoveRows(
this->IndexFromTreeItem(itemToDrop->GetParent()), itemToDrop->GetIndex(), itemToDrop->GetIndex());
itemToDrop->GetParent()->RemoveChild(itemToDrop);
this->endRemoveRows();
}
// row = -1 dropped on an item, row != -1 dropped in between two items
// Select the target index position, or put it at the end of the list.
int dropIndex = 0;
if (row != -1)
{
if (dragIndex == 0)
dropIndex = std::min(row, parentItem->GetChildCount() - 1);
else
dropIndex = std::min(row - 1, parentItem->GetChildCount() - 1);
}
else
{
dropIndex = dropItem->GetIndex();
}
QModelIndex dropItemModelIndex = this->IndexFromTreeItem(dropItem);
if ((row == -1 && dropItemModelIndex.row() == -1) || dropItemModelIndex.row() > parentItem->GetChildCount())
dropIndex = parentItem->GetChildCount() - 1;
// Now insert items again at the drop item position
if (m_AllowHierarchyChange)
{
this->beginInsertRows(dropItemModelIndex, dropIndex, dropIndex + listOfItemsToDrop.size() - 1);
}
else
{
this->beginInsertRows(parentModelIndex, dropIndex, dropIndex + listOfItemsToDrop.size() - 1);
}
for (diIter = listOfItemsToDrop.begin(); diIter != listOfItemsToDrop.end(); diIter++)
{
// dropped on node, behaviour depends on preference setting
if (m_AllowHierarchyChange)
{
auto dataStorage = m_DataStorage.Lock();
m_BlockDataStorageEvents = true;
mitk::DataNode::Pointer droppedNode = (*diIter)->GetDataNode();
mitk::DataNode *dropOntoNode = dropItem->GetDataNode();
dataStorage->Remove(droppedNode);
dataStorage->Add(droppedNode, dropOntoNode);
m_BlockDataStorageEvents = false;
dropItem->InsertChild((*diIter), dropIndex);
}
else
{
if (row == -1) // drag onto a node
{
parentItem->InsertChild((*diIter), dropIndex);
}
else // drag between nodes
{
dropItem->InsertChild((*diIter), dropIndex);
}
}
dropIndex++;
}
this->endInsertRows();
// Change Layers to match.
this->AdjustLayerProperty();
}
}
else if (data->hasFormat("application/x-mitk-datanodes"))
{
returnValue = true;
int numberOfNodesDropped = 0;
QList<mitk::DataNode *> dataNodeList = QmitkMimeTypes::ToDataNodePtrList(data);
mitk::DataNode *node = nullptr;
foreach (node, dataNodeList)
{
auto datastorage = m_DataStorage.Lock();
if (node && datastorage.IsNotNull() && !datastorage->Exists(node))
{
m_DataStorage.Lock()->Add(node);
mitk::BaseData::Pointer basedata = node->GetData();
if (basedata.IsNotNull())
{
mitk::RenderingManager::GetInstance()->InitializeViews(basedata->GetTimeGeometry());
numberOfNodesDropped++;
}
}
}
// Only do a rendering update, if we actually dropped anything.
if (numberOfNodesDropped > 0)
{
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
}
return returnValue;
}
QStringList QmitkDataStorageTreeModel::mimeTypes() const
{
QStringList types = QAbstractItemModel::mimeTypes();
types << "application/x-qabstractitemmodeldatalist";
types << "application/x-mitk-datanodes";
return types;
}
QMimeData *QmitkDataStorageTreeModel::mimeData(const QModelIndexList &indexes) const
{
return mimeDataFromModelIndexList(indexes);
}
QMimeData *QmitkDataStorageTreeModel::mimeDataFromModelIndexList(const QModelIndexList &indexes)
{
QMimeData *ret = new QMimeData;
QString treeItemAddresses("");
QString dataNodeAddresses("");
QByteArray baTreeItemPtrs;
QByteArray baDataNodePtrs;
QDataStream dsTreeItemPtrs(&baTreeItemPtrs, QIODevice::WriteOnly);
QDataStream dsDataNodePtrs(&baDataNodePtrs, QIODevice::WriteOnly);
for (int i = 0; i < indexes.size(); i++)
{
TreeItem *treeItem = static_cast<TreeItem *>(indexes.at(i).internalPointer());
dsTreeItemPtrs << reinterpret_cast<quintptr>(treeItem);
dsDataNodePtrs << reinterpret_cast<quintptr>(treeItem->GetDataNode().GetPointer());
// --------------- deprecated -----------------
unsigned long long treeItemAddress = reinterpret_cast<unsigned long long>(treeItem);
unsigned long long dataNodeAddress = reinterpret_cast<unsigned long long>(treeItem->GetDataNode().GetPointer());
QTextStream(&treeItemAddresses) << treeItemAddress;
QTextStream(&dataNodeAddresses) << dataNodeAddress;
if (i != indexes.size() - 1)
{
QTextStream(&treeItemAddresses) << ",";
QTextStream(&dataNodeAddresses) << ",";
}
// -------------- end deprecated -------------
}
// ------------------ deprecated -----------------
ret->setData("application/x-qabstractitemmodeldatalist", QByteArray(treeItemAddresses.toLatin1()));
ret->setData("application/x-mitk-datanodes", QByteArray(dataNodeAddresses.toLatin1()));
// --------------- end deprecated -----------------
ret->setData(QmitkMimeTypes::DataStorageTreeItemPtrs, baTreeItemPtrs);
ret->setData(QmitkMimeTypes::DataNodePtrs, baDataNodePtrs);
return ret;
}
QVariant QmitkDataStorageTreeModel::data(const QModelIndex &index, int role) const
{
mitk::DataNode *dataNode = this->TreeItemFromIndex(index)->GetDataNode();
// get name of treeItem (may also be edited)
QString nodeName = QString::fromStdString(dataNode->GetName());
if (nodeName.isEmpty())
{
nodeName = "unnamed";
}
if (role == Qt::DisplayRole)
return nodeName;
else if (role == Qt::ToolTipRole)
return nodeName;
else if (role == Qt::DecorationRole)
{
QmitkNodeDescriptor *nodeDescriptor = QmitkNodeDescriptorManager::GetInstance()->GetDescriptor(dataNode);
return nodeDescriptor->GetIcon(dataNode);
}
else if (role == Qt::CheckStateRole)
{
return dataNode->IsVisible(nullptr);
}
else if (role == QmitkDataNodeRole)
{
return QVariant::fromValue<mitk::DataNode::Pointer>(mitk::DataNode::Pointer(dataNode));
}
else if (role == QmitkDataNodeRawPointerRole)
{
return QVariant::fromValue<mitk::DataNode *>(dataNode);
}
return QVariant();
}
bool QmitkDataStorageTreeModel::DicomPropertiesExists(const mitk::DataNode &node) const
{
bool propertiesExists = false;
mitk::BaseProperty *seriesDescription_deprecated = (node.GetProperty("dicom.series.SeriesDescription"));
mitk::BaseProperty *studyDescription_deprecated = (node.GetProperty("dicom.study.StudyDescription"));
mitk::BaseProperty *patientsName_deprecated = (node.GetProperty("dicom.patient.PatientsName"));
mitk::BaseProperty *seriesDescription =
(node.GetProperty(mitk::GeneratePropertyNameForDICOMTag(0x0008, 0x103e).c_str()));
mitk::BaseProperty *studyDescription =
(node.GetProperty(mitk::GeneratePropertyNameForDICOMTag(0x0008, 0x1030).c_str()));
mitk::BaseProperty *patientsName = (node.GetProperty(mitk::GeneratePropertyNameForDICOMTag(0x0010, 0x0010).c_str()));
if (patientsName != nullptr && studyDescription != nullptr && seriesDescription != nullptr)
{
if ((!patientsName->GetValueAsString().empty()) && (!studyDescription->GetValueAsString().empty()) &&
(!seriesDescription->GetValueAsString().empty()))
{
propertiesExists = true;
}
}
/** Code coveres the deprecated property naming for backwards compatibility */
if (patientsName_deprecated != nullptr && studyDescription_deprecated != nullptr && seriesDescription_deprecated != nullptr)
{
if ((!patientsName_deprecated->GetValueAsString().empty()) &&
(!studyDescription_deprecated->GetValueAsString().empty()) &&
(!seriesDescription_deprecated->GetValueAsString().empty()))
{
propertiesExists = true;
}
}
return propertiesExists;
}
QVariant QmitkDataStorageTreeModel::headerData(int /*section*/, Qt::Orientation orientation, int role) const
{
if (orientation == Qt::Horizontal && role == Qt::DisplayRole && m_Root)
return QString::fromStdString(m_Root->GetDataNode()->GetName());
return QVariant();
}
void QmitkDataStorageTreeModel::SetDataStorage(mitk::DataStorage *_DataStorage)
{
if (m_DataStorage != _DataStorage) // dont take the same again
{
auto dataStorage = m_DataStorage.Lock();
if (dataStorage.IsNotNull())
{
// remove Listener for the data storage itself
dataStorage->RemoveObserver(m_DataStorageDeletedTag);
// remove listeners for the nodes
dataStorage->AddNodeEvent.RemoveListener(
mitk::MessageDelegate1<QmitkDataStorageTreeModel, const mitk::DataNode *>(this,
&QmitkDataStorageTreeModel::AddNode));
dataStorage->ChangedNodeEvent.RemoveListener(
mitk::MessageDelegate1<QmitkDataStorageTreeModel, const mitk::DataNode *>(
this, &QmitkDataStorageTreeModel::SetNodeModified));
dataStorage->RemoveNodeEvent.RemoveListener(
mitk::MessageDelegate1<QmitkDataStorageTreeModel, const mitk::DataNode *>(
this, &QmitkDataStorageTreeModel::RemoveNode));
}
this->beginResetModel();
// take over the new data storage
m_DataStorage = _DataStorage;
// delete the old root (if necessary, create new)
if (m_Root)
m_Root->Delete();
mitk::DataNode::Pointer rootDataNode = mitk::DataNode::New();
rootDataNode->SetName("Data Manager");
m_Root = new TreeItem(rootDataNode, nullptr);
dataStorage = m_DataStorage.Lock();
if (dataStorage.IsNotNull())
{
// add Listener for the data storage itself
auto command = itk::SimpleMemberCommand<QmitkDataStorageTreeModel>::New();
command->SetCallbackFunction(this, &QmitkDataStorageTreeModel::SetDataStorageDeleted);
m_DataStorageDeletedTag = dataStorage->AddObserver(itk::DeleteEvent(), command);
// add listeners for the nodes
dataStorage->AddNodeEvent.AddListener(mitk::MessageDelegate1<QmitkDataStorageTreeModel, const mitk::DataNode *>(
this, &QmitkDataStorageTreeModel::AddNode));
dataStorage->ChangedNodeEvent.AddListener(
mitk::MessageDelegate1<QmitkDataStorageTreeModel, const mitk::DataNode *>(
this, &QmitkDataStorageTreeModel::SetNodeModified));
dataStorage->RemoveNodeEvent.AddListener(
mitk::MessageDelegate1<QmitkDataStorageTreeModel, const mitk::DataNode *>(
this, &QmitkDataStorageTreeModel::RemoveNode));
// finally add all nodes to the model
this->Update();
}
this->endResetModel();
}
}
void QmitkDataStorageTreeModel::SetDataStorageDeleted()
{
this->SetDataStorage(nullptr);
}
void QmitkDataStorageTreeModel::AddNodeInternal(const mitk::DataNode *node)
{
auto dataStorage = m_DataStorage.Lock();
if (node == nullptr || dataStorage.IsNull() || !dataStorage->Exists(node) || m_Root->Find(node) != nullptr)
return;
// find out if we have a root node
TreeItem *parentTreeItem = m_Root;
QModelIndex index;
mitk::DataNode *parentDataNode = this->GetParentNode(node);
if (parentDataNode) // no top level data node
{
parentTreeItem = m_Root->Find(parentDataNode); // find the corresponding tree item
if (!parentTreeItem)
{
this->AddNode(parentDataNode);
parentTreeItem = m_Root->Find(parentDataNode);
if (!parentTreeItem)
return;
}
// get the index of this parent with the help of the grand parent
index = this->createIndex(parentTreeItem->GetIndex(), 0, parentTreeItem);
}
// add node
if (m_PlaceNewNodesOnTop)
{
// emit beginInsertRows event
beginInsertRows(index, 0, 0);
parentTreeItem->InsertChild(new TreeItem(const_cast<mitk::DataNode *>(node)), 0);
}
else
{
int firstRowWithASiblingBelow = 0;
int nodeLayer = -1;
node->GetIntProperty("layer", nodeLayer);
for (TreeItem* siblingTreeItem: parentTreeItem->GetChildren())
{
int siblingLayer = -1;
if (mitk::DataNode* siblingNode = siblingTreeItem->GetDataNode())
{
siblingNode->GetIntProperty("layer", siblingLayer);
}
if (nodeLayer > siblingLayer)
{
break;
}
++firstRowWithASiblingBelow;
}
beginInsertRows(index, firstRowWithASiblingBelow, firstRowWithASiblingBelow);
parentTreeItem->InsertChild(new TreeItem(const_cast<mitk::DataNode*>(node)), firstRowWithASiblingBelow);
}
// emit endInsertRows event
endInsertRows();
if(m_PlaceNewNodesOnTop)
{
this->AdjustLayerProperty();
}
}
void QmitkDataStorageTreeModel::AddNode(const mitk::DataNode *node)
{
auto dataStorage = m_DataStorage.Lock();
if (node == nullptr || m_BlockDataStorageEvents || dataStorage.IsNull() || !dataStorage->Exists(node) ||
m_Root->Find(node) != nullptr)
return;
this->AddNodeInternal(node);
}
void QmitkDataStorageTreeModel::SetPlaceNewNodesOnTop(bool _PlaceNewNodesOnTop)
{
m_PlaceNewNodesOnTop = _PlaceNewNodesOnTop;
}
void QmitkDataStorageTreeModel::RemoveNodeInternal(const mitk::DataNode *node)
{
if (!m_Root)
return;
TreeItem *treeItem = m_Root->Find(node);
if (!treeItem)
return; // return because there is no treeitem containing this node
TreeItem *parentTreeItem = treeItem->GetParent();
QModelIndex parentIndex = this->IndexFromTreeItem(parentTreeItem);
// emit beginRemoveRows event (QModelIndex is empty because we dont have a tree model)
this->beginRemoveRows(parentIndex, treeItem->GetIndex(), treeItem->GetIndex());
// remove node
std::vector<TreeItem*> children = treeItem->GetChildren();
delete treeItem;
// emit endRemoveRows event
endRemoveRows();
// move all children of deleted node into its parent
for (std::vector<TreeItem*>::iterator it = children.begin(); it != children.end(); it++)
{
// emit beginInsertRows event
beginInsertRows(parentIndex, parentTreeItem->GetChildCount(), parentTreeItem->GetChildCount());
// add nodes again
parentTreeItem->AddChild(*it);
// emit endInsertRows event
endInsertRows();
}
this->AdjustLayerProperty();
}
void QmitkDataStorageTreeModel::RemoveNode(const mitk::DataNode *node)
{
if (node == nullptr || m_BlockDataStorageEvents)
return;
this->RemoveNodeInternal(node);
}
void QmitkDataStorageTreeModel::SetNodeModified(const mitk::DataNode *node)
{
TreeItem *treeItem = m_Root->Find(node);
if (treeItem)
{
TreeItem *parentTreeItem = treeItem->GetParent();
// as the root node should not be removed one should always have a parent item
if (!parentTreeItem)
return;
QModelIndex index = this->createIndex(treeItem->GetIndex(), 0, treeItem);
// now emit the dataChanged signal
emit dataChanged(index, index);
}
}
mitk::DataNode *QmitkDataStorageTreeModel::GetParentNode(const mitk::DataNode *node) const
{
mitk::DataNode *dataNode = nullptr;
mitk::DataStorage::SetOfObjects::ConstPointer _Sources = m_DataStorage.Lock()->GetSources(node);
if (_Sources->Size() > 0)
dataNode = _Sources->front();
return dataNode;
}
bool QmitkDataStorageTreeModel::setData(const QModelIndex &index, const QVariant &value, int role)
{
mitk::DataNode *dataNode = this->TreeItemFromIndex(index)->GetDataNode();
if (!dataNode)
return false;
if (role == Qt::EditRole && !value.toString().isEmpty())
{
- dataNode->SetStringProperty("name", value.toString().toStdString().c_str());
+ dataNode->SetName(value.toString().toStdString());
mitk::PlanarFigure *planarFigure = dynamic_cast<mitk::PlanarFigure *>(dataNode->GetData());
if (planarFigure != nullptr)
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
else if (role == Qt::CheckStateRole)
{
// Please note: value.toInt() returns 2, independentely from the actual checkstate of the index element.
// Therefore the checkstate is being estimated again here.
QVariant qcheckstate = index.data(Qt::CheckStateRole);
int checkstate = qcheckstate.toInt();
bool isVisible = bool(checkstate);
dataNode->SetVisibility(!isVisible);
emit nodeVisibilityChanged();
}
// inform listeners about changes
emit dataChanged(index, index);
return true;
}
bool QmitkDataStorageTreeModel::setHeaderData(int /*section*/,
Qt::Orientation /*orientation*/,
const QVariant & /* value */,
int /*role = Qt::EditRole*/)
{
return false;
}
void QmitkDataStorageTreeModel::AdjustLayerProperty()
{
/// transform the tree into an array and set the layer property descending
std::vector<TreeItem *> vec;
this->TreeToVector(m_Root, vec);
int i = vec.size() - 1;
for (std::vector<TreeItem *>::const_iterator it = vec.begin(); it != vec.end(); ++it)
{
mitk::DataNode::Pointer dataNode = (*it)->GetDataNode();
bool fixedLayer = false;
if (!(dataNode->GetBoolProperty("fixedLayer", fixedLayer) && fixedLayer))
dataNode->SetIntProperty("layer", i);
--i;
}
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void QmitkDataStorageTreeModel::TreeToVector(TreeItem *parent, std::vector<TreeItem *> &vec) const
{
TreeItem *current;
for (int i = 0; i < parent->GetChildCount(); ++i)
{
current = parent->GetChild(i);
this->TreeToVector(current, vec);
vec.push_back(current);
}
}
QModelIndex QmitkDataStorageTreeModel::IndexFromTreeItem(TreeItem *item) const
{
if (item == m_Root)
return QModelIndex();
else
return this->createIndex(item->GetIndex(), 0, item);
}
QList<mitk::DataNode::Pointer> QmitkDataStorageTreeModel::GetNodeSet() const
{
QList<mitk::DataNode::Pointer> res;
if (m_Root)
this->TreeToNodeSet(m_Root, res);
return res;
}
void QmitkDataStorageTreeModel::TreeToNodeSet(TreeItem *parent, QList<mitk::DataNode::Pointer> &vec) const
{
TreeItem *current;
for (int i = 0; i < parent->GetChildCount(); ++i)
{
current = parent->GetChild(i);
vec.push_back(current->GetDataNode());
this->TreeToNodeSet(current, vec);
}
}
QModelIndex QmitkDataStorageTreeModel::GetIndex(const mitk::DataNode *node) const
{
if (m_Root)
{
TreeItem *item = m_Root->Find(node);
if (item)
return this->IndexFromTreeItem(item);
}
return QModelIndex();
}
QList<QmitkDataStorageTreeModel::TreeItem *> QmitkDataStorageTreeModel::ToTreeItemPtrList(const QMimeData *mimeData)
{
if (mimeData == nullptr || !mimeData->hasFormat(QmitkMimeTypes::DataStorageTreeItemPtrs))
{
return QList<TreeItem *>();
}
return ToTreeItemPtrList(mimeData->data(QmitkMimeTypes::DataStorageTreeItemPtrs));
}
QList<QmitkDataStorageTreeModel::TreeItem *> QmitkDataStorageTreeModel::ToTreeItemPtrList(const QByteArray &ba)
{
QList<TreeItem *> result;
QDataStream ds(ba);
while (!ds.atEnd())
{
quintptr treeItemPtr;
ds >> treeItemPtr;
result.push_back(reinterpret_cast<TreeItem *>(treeItemPtr));
}
return result;
}
void QmitkDataStorageTreeModel::Update()
{
auto datastorage = m_DataStorage.Lock();
if (datastorage.IsNotNull())
{
mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = datastorage->GetAll();
/// Regardless the value of this preference, the new nodes must not be inserted
/// at the top now, but at the position according to their layer.
bool newNodesWereToBePlacedOnTop = m_PlaceNewNodesOnTop;
m_PlaceNewNodesOnTop = false;
for (const auto& node : *_NodeSet)
{
this->AddNodeInternal(node);
}
m_PlaceNewNodesOnTop = newNodesWereToBePlacedOnTop;
/// Adjust the layers to ensure that derived nodes are above their sources.
this->AdjustLayerProperty();
}
}
void QmitkDataStorageTreeModel::SetAllowHierarchyChange(bool allowHierarchyChange)
{
m_AllowHierarchyChange = allowHierarchyChange;
}
diff --git a/Modules/QtWidgets/src/QmitkStyleManager.cpp b/Modules/QtWidgets/src/QmitkStyleManager.cpp
index 3f1270a8ed..cdb10e0262 100644
--- a/Modules/QtWidgets/src/QmitkStyleManager.cpp
+++ b/Modules/QtWidgets/src/QmitkStyleManager.cpp
@@ -1,69 +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.
============================================================================*/
#include <QmitkStyleManager.h>
#include <mitkLogMacros.h>
#include <QApplication>
#include <QFile>
#include <QImage>
#include <QPixmap>
#include <QRegularExpression>
namespace
{
- QString ParseColor(const QString &subject, const QString &pattern, const QString &fallback)
+ QString ParseColor(const QString &subject, const QString &colorName, const QString &fallback)
{
+ const QString pattern = QString("%1\\s*[=:]\\s*(#[0-9a-f]{6})").arg(colorName);
+
QRegularExpression re(pattern, QRegularExpression::CaseInsensitiveOption);
auto match = re.match(subject);
return match.hasMatch()
? match.captured(1)
: fallback;
}
}
QIcon QmitkStyleManager::ThemeIcon(const QByteArray &originalSVG)
{
auto styleSheet = qApp->styleSheet();
if (styleSheet.isEmpty())
return QPixmap::fromImage(QImage::fromData(originalSVG));
- auto iconColor = ParseColor(styleSheet,
- QStringLiteral("iconColor\\s*[=:]\\s*(#[0-9a-f]{6})"),
- QStringLiteral("#000000"));
-
- auto iconAccentColor = ParseColor(styleSheet,
- QStringLiteral("iconAccentColor\\s*[=:]\\s*(#[0-9a-f]{6})"),
- QStringLiteral("#ffffff"));
+ auto iconColor = GetIconColor();
+ auto iconAccentColor = GetIconAccentColor();
auto themedSVG = QString(originalSVG).replace(QStringLiteral("#00ff00"), iconColor, Qt::CaseInsensitive);
themedSVG = themedSVG.replace(QStringLiteral("#ff00ff"), iconAccentColor, Qt::CaseInsensitive);
return QPixmap::fromImage(QImage::fromData(themedSVG.toLatin1()));
}
QIcon QmitkStyleManager::ThemeIcon(const QString &resourcePath)
{
QFile resourceFile(resourcePath);
if (resourceFile.open(QIODevice::ReadOnly))
{
auto originalSVG = resourceFile.readAll();
return ThemeIcon(originalSVG);
}
MITK_WARN << "Could not read " << resourcePath.toStdString();
return QIcon();
}
+
+QString QmitkStyleManager::GetIconColor()
+{
+ const auto styleSheet = qApp->styleSheet();
+ const auto fallback = QStringLiteral("#000000");
+
+ return !styleSheet.isEmpty()
+ ? ParseColor(styleSheet, QStringLiteral("iconColor"), fallback)
+ : fallback;
+}
+
+QString QmitkStyleManager::GetIconAccentColor()
+{
+ const auto styleSheet = qApp->styleSheet();
+ const auto fallback = QStringLiteral("#ffffff");
+
+ return !styleSheet.isEmpty()
+ ? ParseColor(styleSheet, QStringLiteral("iconAccentColor"), fallback)
+ : fallback;
+}
diff --git a/Modules/RT/autoload/DICOMRTIO/mitkRTDoseReaderService.cpp b/Modules/RT/autoload/DICOMRTIO/mitkRTDoseReaderService.cpp
index 50f4a52ad0..906eb0599f 100644
--- a/Modules/RT/autoload/DICOMRTIO/mitkRTDoseReaderService.cpp
+++ b/Modules/RT/autoload/DICOMRTIO/mitkRTDoseReaderService.cpp
@@ -1,171 +1,171 @@
/*============================================================================
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 <mitkRTDoseReaderService.h>
#include <mitkLexicalCast.h>
#include <mitkImageAccessByItk.h>
#include <mitkImageCast.h>
#include <mitkDICOMFileReaderSelector.h>
#include <mitkDICOMFileReader.h>
#include <mitkRTConstants.h>
#include <mitkImageStatisticsHolder.h>
#include <mitkDICOMTagPath.h>
#include <mitkDICOMDCMTKTagScanner.h>
#include <mitkDICOMRTMimeTypes.h>
#include <mitkDICOMIOHelper.h>
#include <mitkProperties.h>
#include <mitkDICOMProperty.h>
#include <dcmtk/dcmrt/drtdose.h>
#include <itkShiftScaleImageFilter.h>
#include <itkCastImageFilter.h>
namespace mitk
{
RTDoseReaderService::RTDoseReaderService() : AbstractFileReader(CustomMimeType(mitk::DICOMRTMimeTypes::DICOMRT_DOSE_MIMETYPE_NAME()), mitk::DICOMRTMimeTypes::DICOMRT_DOSE_MIMETYPE_DESCRIPTION()) {
m_FileReaderServiceReg = RegisterService();
}
RTDoseReaderService::RTDoseReaderService(const RTDoseReaderService& other) : mitk::AbstractFileReader(other)
{
}
RTDoseReaderService::~RTDoseReaderService() {}
template<typename TPixel, unsigned int VImageDimension>
void RTDoseReaderService::MultiplyGridScaling(itk::Image<TPixel, VImageDimension>* image, float gridscale)
{
typedef itk::Image<Float32, VImageDimension> OutputImageType;
typedef itk::Image<TPixel, VImageDimension> InputImageType;
typedef itk::CastImageFilter<InputImageType, OutputImageType> CastFilterType;
typedef itk::ShiftScaleImageFilter<OutputImageType, OutputImageType> ScaleFilterType;
typename CastFilterType::Pointer castFilter = CastFilterType::New();
typename ScaleFilterType::Pointer scaleFilter = ScaleFilterType::New();
castFilter->SetInput(image);
scaleFilter->SetInput(castFilter->GetOutput());
scaleFilter->SetScale(gridscale);
scaleFilter->Update();
typename OutputImageType::Pointer scaledOutput = scaleFilter->GetOutput();
this->scaledDoseImage = mitk::Image::New();
mitk::CastToMitkImage(scaledOutput, this->scaledDoseImage);
}
std::vector<itk::SmartPointer<BaseData> > RTDoseReaderService::DoRead()
{
std::vector<itk::SmartPointer<mitk::BaseData> > result;
- mitk::IDICOMTagsOfInterest* toiSrv = GetDicomTagsOfInterestService();
+ mitk::IDICOMTagsOfInterest* toiSrv = DICOMIOHelper::GetTagsOfInterestService();
auto tagsOfInterest = toiSrv->GetTagsOfInterest();
DICOMTagPathList tagsOfInterestList;
for (const auto& tag : tagsOfInterest) {
tagsOfInterestList.push_back(tag.first);
}
std::string location = GetInputLocation();
mitk::DICOMFileReaderSelector::Pointer selector = mitk::DICOMFileReaderSelector::New();
selector->LoadBuiltIn3DConfigs();
selector->SetInputFiles({ location });
mitk::DICOMFileReader::Pointer reader = selector->GetFirstReaderWithMinimumNumberOfOutputImages();
reader->SetAdditionalTagsOfInterest(toiSrv->GetTagsOfInterest());
reader->SetTagLookupTableToPropertyFunctor(mitk::GetDICOMPropertyForDICOMValuesFunctor);
reader->SetInputFiles({ location });
reader->AnalyzeInputFiles();
reader->LoadImages();
if (reader->GetNumberOfOutputs() == 0) {
MITK_ERROR << "Could not determine a DICOM reader for this file" << std::endl;
return result;
}
mitk::DICOMDCMTKTagScanner::Pointer scanner = mitk::DICOMDCMTKTagScanner::New();
scanner->SetInputFiles({ location });
scanner->AddTagPaths(tagsOfInterestList);
scanner->Scan();
mitk::DICOMDatasetAccessingImageFrameList frames = scanner->GetFrameInfoList();
if (frames.empty()) {
MITK_ERROR << "Error reading the RTDOSE file" << std::endl;
return result;
}
const mitk::DICOMImageBlockDescriptor& desc = reader->GetOutput(0);
mitk::Image::Pointer originalImage = desc.GetMitkImage();
if (originalImage.IsNull())
{
MITK_ERROR << "Error reading the RTDOSE file in mitk::DicomFileReader" << std::endl;
return result;
}
DcmFileFormat fileformat;
OFCondition outp = fileformat.loadFile(location.c_str(), EXS_Unknown);
if (outp.bad())
{
MITK_ERROR << "Error reading the RTDOSE file in DCMTK" << std::endl;
return result;
}
DcmDataset *dataset = fileformat.getDataset();
DRTDoseIOD doseObject;
OFCondition DCMTKresult = doseObject.read(*dataset);
if (DCMTKresult.bad())
{
MITK_ERROR << "Error reading the RTDOSE file in DCMTK" << std::endl;
return result;
}
auto findingsGridScaling = frames.front()->GetTagValueAsString(DICOMTagPath(0x3004, 0x000e)); //(0x3004, 0x000e) is grid scaling
double gridScaling;
if (findingsGridScaling.empty()) {
MITK_ERROR << "Could not find DoseGridScaling tag" << std::endl;
return result;
}
else {
gridScaling = boost::lexical_cast<double>(findingsGridScaling.front().value);
}
AccessByItk_1(originalImage, MultiplyGridScaling, gridScaling);
auto statistics = this->scaledDoseImage->GetStatistics();
double maxDose = statistics->GetScalarValueMax();
this->scaledDoseImage->SetPropertyList(originalImage->GetPropertyList());
this->scaledDoseImage->SetProperty(mitk::RTConstants::PRESCRIBED_DOSE_PROPERTY_NAME.c_str(), mitk::DoubleProperty::New(0.8*maxDose));
- auto findings = ExtractPathsOfInterest(tagsOfInterestList, frames);
- SetProperties(this->scaledDoseImage, findings);
+ auto findings = DICOMIOHelper::ExtractPathsOfInterest(tagsOfInterestList, frames);
+ DICOMIOHelper::SetProperties(this->scaledDoseImage, findings);
result.push_back(this->scaledDoseImage.GetPointer());
return result;
}
RTDoseReaderService* RTDoseReaderService::Clone() const
{
return new RTDoseReaderService(*this);
}
}
diff --git a/Modules/RT/autoload/DICOMRTIO/mitkRTPlanReaderService.cpp b/Modules/RT/autoload/DICOMRTIO/mitkRTPlanReaderService.cpp
index 9952d979b7..13b77a0607 100644
--- a/Modules/RT/autoload/DICOMRTIO/mitkRTPlanReaderService.cpp
+++ b/Modules/RT/autoload/DICOMRTIO/mitkRTPlanReaderService.cpp
@@ -1,82 +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.
============================================================================*/
#include <mitkRTPlanReaderService.h>
#include <mitkImage.h>
#include <mitkDICOMDCMTKTagScanner.h>
#include <mitkIOMimeTypes.h>
#include <mitkDICOMIOHelper.h>
#include <mitkDICOMTagPath.h>
#include <mitkIDICOMTagsOfInterest.h>
#include <mitkDICOMDatasetAccessingImageFrameInfo.h>
#include <mitkDICOMRTMimeTypes.h>
namespace mitk
{
RTPlanReaderService::RTPlanReaderService() : AbstractFileReader(CustomMimeType(mitk::DICOMRTMimeTypes::DICOMRT_PLAN_MIMETYPE_NAME()), mitk::DICOMRTMimeTypes::DICOMRT_PLAN_MIMETYPE_DESCRIPTION()) {
m_FileReaderServiceReg = RegisterService();
}
RTPlanReaderService::RTPlanReaderService(const RTPlanReaderService& other) : mitk::AbstractFileReader(other)
{
}
RTPlanReaderService::~RTPlanReaderService() {}
std::vector<itk::SmartPointer<BaseData> > RTPlanReaderService::DoRead()
{
std::vector<itk::SmartPointer<mitk::BaseData> > result;
- auto DICOMTagsOfInterestService = GetDicomTagsOfInterestService();
+ auto DICOMTagsOfInterestService = DICOMIOHelper::GetTagsOfInterestService();
auto tagsOfInterest = DICOMTagsOfInterestService->GetTagsOfInterest();
DICOMTagPathList tagsOfInterestList;
for (const auto& tag : tagsOfInterest) {
tagsOfInterestList.push_back(tag.first);
}
std::string location = GetInputLocation();
mitk::StringList files = { location };
mitk::DICOMDCMTKTagScanner::Pointer scanner = mitk::DICOMDCMTKTagScanner::New();
scanner->SetInputFiles(files);
scanner->AddTagPaths(tagsOfInterestList);
scanner->Scan();
mitk::DICOMDatasetAccessingImageFrameList frames = scanner->GetFrameInfoList();
if (frames.empty()) {
MITK_ERROR << "Error reading the RTPLAN file" << std::endl;
return result;
}
- auto findings = ExtractPathsOfInterest(tagsOfInterestList, frames);
+ auto findings = DICOMIOHelper::ExtractPathsOfInterest(tagsOfInterestList, frames);
//just create empty image. No image information available in RTPLAN. But properties will be attached.
Image::Pointer dummyImage = Image::New();
mitk::PixelType pt = mitk::MakeScalarPixelType<int>();
unsigned int dim[] = { 1,1};
dummyImage->Initialize(pt, 2, dim);
- SetProperties(dummyImage, findings);
+ DICOMIOHelper::SetProperties(dummyImage, findings);
result.push_back(dummyImage.GetPointer());
return result;
}
RTPlanReaderService* RTPlanReaderService::Clone() const
{
return new RTPlanReaderService(*this);
}
}
diff --git a/Modules/RT/autoload/DICOMRTIO/mitkRTStructureSetReaderService.cpp b/Modules/RT/autoload/DICOMRTIO/mitkRTStructureSetReaderService.cpp
index 5455f4112e..0bc75d83b4 100644
--- a/Modules/RT/autoload/DICOMRTIO/mitkRTStructureSetReaderService.cpp
+++ b/Modules/RT/autoload/DICOMRTIO/mitkRTStructureSetReaderService.cpp
@@ -1,288 +1,288 @@
/*============================================================================
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 "mitkRTStructureSetReaderService.h"
#include <mitkDICOMRTMimeTypes.h>
#include <mitkDICOMIOHelper.h>
#include <mitkDICOMTagPath.h>
#include <mitkDICOMDCMTKTagScanner.h>
#include "dcmtk/dcmrt/drtstrct.h"
namespace mitk
{
RTStructureSetReaderService::RTStructureSetReaderService() : AbstractFileReader(CustomMimeType(mitk::DICOMRTMimeTypes::DICOMRT_STRUCT_MIMETYPE_NAME()), mitk::DICOMRTMimeTypes::DICOMRT_STRUCT_MIMETYPE_DESCRIPTION()) {
m_FileReaderServiceReg = RegisterService();
}
RTStructureSetReaderService::RTStructureSetReaderService(const RTStructureSetReaderService& other) : mitk::AbstractFileReader(other)
{
}
RTStructureSetReaderService::~RTStructureSetReaderService() {}
RTStructureSetReaderService::RoiEntry::RoiEntry()
{
Number = 0;
DisplayColor[0] = 1.0;
DisplayColor[1] = 0.0;
DisplayColor[2] = 0.0;
ContourModelSet = mitk::ContourModelSet::New();
}
RTStructureSetReaderService::RoiEntry::RoiEntry(const RoiEntry& src)
{
Number = src.Number;
Name = src.Name;
Description = src.Description;
DisplayColor[0] = src.DisplayColor[0];
DisplayColor[1] = src.DisplayColor[1];
DisplayColor[2] = src.DisplayColor[2];
ContourModelSet = mitk::ContourModelSet::New();
SetPolyData(src.ContourModelSet);
}
RTStructureSetReaderService::RoiEntry::~RoiEntry() {}
RTStructureSetReaderService::RoiEntry& RTStructureSetReaderService::
RoiEntry::operator =(const RoiEntry& src)
{
Number = src.Number;
Name = src.Name;
Description = src.Description;
DisplayColor[0] = src.DisplayColor[0];
DisplayColor[1] = src.DisplayColor[1];
DisplayColor[2] = src.DisplayColor[2];
SetPolyData(src.ContourModelSet);
return (*this);
}
void RTStructureSetReaderService::RoiEntry::
SetPolyData(mitk::ContourModelSet::Pointer roiPolyData)
{
if (roiPolyData == this->ContourModelSet)
{
return;
}
this->ContourModelSet = roiPolyData;
}
size_t RTStructureSetReaderService::GetNumberOfROIs() const
{
return this->ROISequenceVector.size();
}
RTStructureSetReaderService::RoiEntry* RTStructureSetReaderService::
FindRoiByNumber(unsigned int roiNum)
{
for (unsigned int i = 0; i < this->ROISequenceVector.size(); ++i)
{
if (this->ROISequenceVector[i].Number == roiNum)
{
return &this->ROISequenceVector[i];
}
}
return nullptr;
}
std::vector<itk::SmartPointer<BaseData> > RTStructureSetReaderService::DoRead()
{
std::vector<itk::SmartPointer<mitk::BaseData> > result;
std::string location = GetInputLocation();
- auto DICOMTagsOfInterestService = GetDicomTagsOfInterestService();
+ auto DICOMTagsOfInterestService = DICOMIOHelper::GetTagsOfInterestService();
auto tagsOfInterest = DICOMTagsOfInterestService->GetTagsOfInterest();
DICOMTagPathList tagsOfInterestList;
for (const auto& tag : tagsOfInterest) {
tagsOfInterestList.push_back(tag.first);
}
mitk::DICOMDCMTKTagScanner::Pointer scanner = mitk::DICOMDCMTKTagScanner::New();
scanner->SetInputFiles({ location });
scanner->AddTagPaths(tagsOfInterestList);
scanner->Scan();
mitk::DICOMDatasetAccessingImageFrameList frames = scanner->GetFrameInfoList();
if (frames.empty()) {
MITK_ERROR << "Error reading the RTSTRUCT file" << std::endl;
return result;
}
- auto findings = ExtractPathsOfInterest(tagsOfInterestList, frames);
+ auto findings = DICOMIOHelper::ExtractPathsOfInterest(tagsOfInterestList, frames);
DcmFileFormat file;
OFCondition output = file.loadFile(location.c_str(), EXS_Unknown);
if (output.bad())
{
MITK_ERROR << "Can't read the file" << std::endl;
return result;
}
DcmDataset* dataset = file.getDataset();
DRTStructureSetIOD structureSetObject;
OFCondition outp = structureSetObject.read(*dataset);
if (!outp.good())
{
MITK_ERROR << "Error reading the file" << std::endl;
return result;
}
DRTStructureSetROISequence& roiSequence =
structureSetObject.getStructureSetROISequence();
if (!roiSequence.gotoFirstItem().good())
{
MITK_ERROR << "Error reading the structure sequence" << std::endl;
return result;
}
do
{
DRTStructureSetROISequence::Item& currentSequence =
roiSequence.getCurrentItem();
if (!currentSequence.isValid())
{
continue;
}
OFString roiName;
OFString roiDescription;
Sint32 roiNumber;
RoiEntry roi;
currentSequence.getROIName(roiName);
currentSequence.getROIDescription(roiDescription);
currentSequence.getROINumber(roiNumber);
roi.Name = roiName.c_str();
roi.Description = roiDescription.c_str();
roi.Number = roiNumber;
this->ROISequenceVector.push_back(roi);
} while (roiSequence.gotoNextItem().good());
Sint32 refRoiNumber;
DRTROIContourSequence& roiContourSeqObject =
structureSetObject.getROIContourSequence();
if (!roiContourSeqObject.gotoFirstItem().good())
{
MITK_ERROR << "Error reading the contour sequence" << std::endl;
return result;
}
do
{
mitk::ContourModelSet::Pointer contourSet = mitk::ContourModelSet::New();
DRTROIContourSequence::Item& currentRoiObject =
roiContourSeqObject.getCurrentItem();
if (!currentRoiObject.isValid())
{
continue;
}
currentRoiObject.getReferencedROINumber(refRoiNumber);
DRTContourSequence& contourSeqObject =
currentRoiObject.getContourSequence();
if (contourSeqObject.getNumberOfItems() > 0 && contourSeqObject.gotoFirstItem().good())
{
do
{
DRTContourSequence::Item& contourItem =
contourSeqObject.getCurrentItem();
if (!contourItem.isValid())
{
continue;
}
OFString contourNumber;
OFString numberOfPoints;
OFVector<Float64> contourData_LPS;
mitk::ContourModel::Pointer contourSequence =
mitk::ContourModel::New();
contourItem.getContourNumber(contourNumber);
contourItem.getNumberOfContourPoints(numberOfPoints);
contourItem.getContourData(contourData_LPS);
for (unsigned int i = 0; i < contourData_LPS.size() / 3; i++)
{
mitk::Point3D point;
point[0] = contourData_LPS.at(3 * i);
point[1] = contourData_LPS.at(3 * i + 1);
point[2] = contourData_LPS.at(3 * i + 2);
contourSequence->AddVertex(point);
}
contourSequence->Close();
contourSet->AddContourModel(contourSequence);
} while (contourSeqObject.gotoNextItem().good());
}
else
{
MITK_WARN << "contourSeqObject has no items in sequence. Object is neglected and not read. Struct name: " << this->FindRoiByNumber(refRoiNumber)->Name << std::endl;
}
RoiEntry* refROI = this->FindRoiByNumber(refRoiNumber);
if (refROI == nullptr)
{
MITK_ERROR << "Can not find references ROI" << std::endl;
continue;
}
Sint32 roiColor;
for (unsigned int j = 0; j < 3; j++)
{
currentRoiObject.getROIDisplayColor(roiColor, j);
refROI->DisplayColor[j] = roiColor / 255.0;
}
refROI->ContourModelSet = contourSet;
contourSet->SetProperty("name", mitk::StringProperty::New(refROI->Name));
contourSet->SetProperty("contour.color", mitk::ColorProperty::New(
refROI->DisplayColor[0],
refROI->DisplayColor[1],
refROI->DisplayColor[2]));
} while (roiContourSeqObject.gotoNextItem().good());
for (auto const& aROI : ROISequenceVector)
{
result.push_back(aROI.ContourModelSet.GetPointer());
result.at(result.size() - 1)->SetProperty("name", aROI.ContourModelSet->GetProperty("name"));
result.at(result.size() - 1)->SetProperty("color", aROI.ContourModelSet->GetProperty("contour.color"));
result.at(result.size() - 1)->SetProperty("contour.color", aROI.ContourModelSet->GetProperty("contour.color"));
- SetProperties(result.at(result.size() - 1).GetPointer(), findings);
+ DICOMIOHelper::SetProperties(result.at(result.size() - 1).GetPointer(), findings);
}
return result;
}
RTStructureSetReaderService* RTStructureSetReaderService::Clone() const
{
return new RTStructureSetReaderService(*this);
}
}
diff --git a/Modules/SceneSerialization/src/mitkSceneReaderV1.cpp b/Modules/SceneSerialization/src/mitkSceneReaderV1.cpp
index 46060c5661..c28b3e54ce 100644
--- a/Modules/SceneSerialization/src/mitkSceneReaderV1.cpp
+++ b/Modules/SceneSerialization/src/mitkSceneReaderV1.cpp
@@ -1,462 +1,463 @@
/*============================================================================
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 "mitkSceneReaderV1.h"
#include "Poco/Path.h"
#include "mitkBaseRenderer.h"
#include "mitkIOUtil.h"
#include "mitkProgressBar.h"
#include "mitkPropertyListDeserializer.h"
#include "mitkSerializerMacros.h"
#include <mitkUIDManipulator.h>
#include <mitkRenderingModeProperty.h>
#include <tinyxml2.h>
+#include <filesystem>
+#include <map>
+
MITK_REGISTER_SERIALIZER(SceneReaderV1)
namespace
{
typedef std::pair<mitk::DataNode::Pointer, std::list<std::string>> NodesAndParentsPair;
bool NodeSortByLayerIsLessThan(const NodesAndParentsPair &left, const NodesAndParentsPair &right)
{
if (left.first.IsNotNull() && right.first.IsNotNull())
{
int leftLayer;
int rightLayer;
if (left.first->GetIntProperty("layer", leftLayer) && right.first->GetIntProperty("layer", rightLayer))
{
return leftLayer < rightLayer;
}
else
{
// fall back to name sort
return left.first->GetName() < right.first->GetName();
}
}
// in all other cases, fall back to stupid pointer comparison
// this is not reasonable but at least answers the sorting
// question clearly
return left.first.GetPointer() < right.first.GetPointer();
}
// This is a workaround until we are able to save time-related information in an
// actual file format of surfaces.
void ApplyProportionalTimeGeometryProperties(mitk::BaseData* data)
{
- if (nullptr == data)
- return;
-
- auto properties = data->GetPropertyList();
-
- if (properties.IsNull())
- return;
-
auto* geometry = dynamic_cast<mitk::ProportionalTimeGeometry*>(data->GetTimeGeometry());
if (nullptr == geometry)
return;
+ auto properties = data->GetPropertyList();
float value = 0.0f;
if (properties->GetFloatProperty("ProportionalTimeGeometry.FirstTimePoint", value))
{
if (value == -std::numeric_limits<float>::infinity())
value = std::numeric_limits<float>::lowest();
geometry->SetFirstTimePoint(value);
}
if (properties->GetFloatProperty("ProportionalTimeGeometry.StepDuration", value))
geometry->SetStepDuration(value);
}
+
+ mitk::PropertyList::Pointer DeserializeProperties(const tinyxml2::XMLElement *propertiesElement, const std::filesystem::path& basePath)
+ {
+ if (propertiesElement == nullptr)
+ return nullptr;
+
+ std::filesystem::path path(propertiesElement->Attribute("file"));
+
+ if (path.empty())
+ return nullptr;
+
+ if (!basePath.empty())
+ path = basePath / path;
+
+ auto deserializer = mitk::PropertyListDeserializer::New();
+ deserializer->SetFilename(path.string());
+ deserializer->Deserialize();
+
+ return deserializer->GetOutput();
+ }
}
bool mitk::SceneReaderV1::LoadScene(tinyxml2::XMLDocument &document, const std::string &workingDirectory, DataStorage *storage)
{
assert(storage);
bool error(false);
// TODO prepare to detect errors (such as cycles) from wrongly written or edited xml files
// Get number of elements to initialze progress bar
// 1. if there is a <data type="..." file="..."> element,
// - construct a name for the appropriate serializer
// - try to instantiate this serializer via itk object factory
// - if serializer could be created, use it to read the file into a BaseData object
// - if successful, call the new node's SetData(..)
// create a node for the tag "data" and test if node was created
typedef std::vector<mitk::DataNode::Pointer> DataNodeVector;
DataNodeVector DataNodes;
unsigned int listSize = 0;
for (auto *element = document.FirstChildElement("node"); element != nullptr;
element = element->NextSiblingElement("node"))
{
++listSize;
}
ProgressBar::GetInstance()->AddStepsToDo(listSize * 2);
+ // Deserialize base data properties before reading the actual data to be
+ // able to provide them as read-only meta data to the data reader.
+ std::map<std::string, PropertyList::Pointer> baseDataPropertyLists;
+
+ for (auto *nodeElement = document.FirstChildElement("node"); nodeElement != nullptr;
+ nodeElement = nodeElement->NextSiblingElement("node"))
+ {
+ const auto *uid = nodeElement->Attribute("UID");
+
+ if (uid == nullptr)
+ continue;
+
+ auto *dataElement = nodeElement->FirstChildElement("data");
+
+ if (dataElement != nullptr)
+ {
+ auto properties = DeserializeProperties(dataElement->FirstChildElement("properties"), workingDirectory);
+
+ if (properties.IsNotNull())
+ baseDataPropertyLists[uid] = properties;
+ }
+ }
+
for (auto *element = document.FirstChildElement("node"); element != nullptr;
element = element->NextSiblingElement("node"))
{
- DataNodes.push_back(LoadBaseDataFromDataTag(element->FirstChildElement("data"), workingDirectory, error));
+ mitk::PropertyList* properties = nullptr;
+ const auto *uid = element->Attribute("UID");
+
+ if (uid != nullptr)
+ {
+ auto iter = baseDataPropertyLists.find(uid);
+
+ if (iter != baseDataPropertyLists.end())
+ properties = iter->second;
+ }
+
+ const auto *dataElement = element->FirstChildElement("data");
+ auto dataNode = this->LoadBaseDataFromDataTag(dataElement, properties, workingDirectory, error);
+
+ if (dataNode.IsNull())
+ continue;
+
+ auto* baseData = dataNode->GetData();
+
+ if (baseData != nullptr && properties != nullptr)
+ {
+ baseData->SetPropertyList(properties);
+ ApplyProportionalTimeGeometryProperties(baseData);
+ }
+
+ DataNodes.push_back(dataNode);
+
ProgressBar::GetInstance()->Progress();
}
// iterate all nodes
// first level nodes should be <node> elements
auto nit = DataNodes.begin();
for (auto *element = document.FirstChildElement("node"); element != nullptr || nit != DataNodes.end();
element = element->NextSiblingElement("node"), ++nit)
{
mitk::DataNode::Pointer node = *nit;
- // in case dataXmlElement is valid test whether it containts the "properties" child tag
- // and process further if and only if yes
- auto *dataXmlElement = element->FirstChildElement("data");
- if (dataXmlElement && dataXmlElement->FirstChildElement("properties"))
- {
- auto *baseDataElement = dataXmlElement->FirstChildElement("properties");
- if (node->GetData())
- {
- DecorateBaseDataWithProperties(node->GetData(), baseDataElement, workingDirectory);
- ApplyProportionalTimeGeometryProperties(node->GetData());
- }
- else
- {
- MITK_WARN << "BaseData properties stored in scene file, but BaseData could not be read" << std::endl;
- }
- }
- // 2. check child nodes
+ // 1. check child nodes
const char *uida = element->Attribute("UID");
std::string uid("");
if (uida)
{
uid = uida;
m_NodeForID[uid] = node.GetPointer();
m_IDForNode[node.GetPointer()] = uid;
}
else
{
MITK_ERROR << "No UID found for current node. Node will have no parents.";
error = true;
}
- // 3. if there are <properties> nodes,
+ // 2. if there are <properties> nodes,
// - instantiate the appropriate PropertyListDeSerializer
// - use them to construct PropertyList objects
// - add these properties to the node (if necessary, use renderwindow name)
bool success = DecorateNodeWithProperties(node, element, workingDirectory);
if (!success)
{
MITK_ERROR << "Could not load properties for node.";
error = true;
}
// remember node for later adding to DataStorage
m_OrderedNodePairs.push_back(std::make_pair(node, std::list<std::string>()));
- // 4. if there are <source> elements, remember parent objects
+ // 3. if there are <source> elements, remember parent objects
for (auto *source = element->FirstChildElement("source"); source != nullptr;
source = source->NextSiblingElement("source"))
{
const char *sourceUID = source->Attribute("UID");
if (sourceUID)
{
m_OrderedNodePairs.back().second.push_back(std::string(sourceUID));
}
}
ProgressBar::GetInstance()->Progress();
} // end for all <node>
// sort our nodes by their "layer" property
// (to be inserted in that order)
m_OrderedNodePairs.sort(&NodeSortByLayerIsLessThan);
// remove all unknown parent UIDs
for (auto nodesIter = m_OrderedNodePairs.begin(); nodesIter != m_OrderedNodePairs.end();
++nodesIter)
{
for (auto parentsIter = nodesIter->second.begin();
parentsIter != nodesIter->second.end();)
{
if (m_NodeForID.find(*parentsIter) == m_NodeForID.end())
{
parentsIter = nodesIter->second.erase(parentsIter);
MITK_WARN << "Found a DataNode with unknown parents. Will add it to DataStorage without any parent objects.";
error = true;
}
else
{
++parentsIter;
}
}
}
// repeat the following loop ...
// ... for all created nodes
unsigned int lastMapSize(0);
while (lastMapSize !=
m_OrderedNodePairs
.size()) // this is to prevent infinite loops; each iteration must at least add one node to DataStorage
{
lastMapSize = m_OrderedNodePairs.size();
// iterate (layer) ordered nodes backwards
// we insert the highest layers first
for (auto nodesIter = m_OrderedNodePairs.begin(); nodesIter != m_OrderedNodePairs.end();
++nodesIter)
{
bool addThisNode(true);
// if any parent node is not yet in DataStorage, skip node for now and check later
for (auto parentsIter = nodesIter->second.begin();
parentsIter != nodesIter->second.end();
++parentsIter)
{
if (!storage->Exists(m_NodeForID[*parentsIter]))
{
addThisNode = false;
break;
}
}
if (addThisNode)
{
DataStorage::SetOfObjects::Pointer parents = DataStorage::SetOfObjects::New();
for (auto parentsIter = nodesIter->second.begin();
parentsIter != nodesIter->second.end();
++parentsIter)
{
parents->push_back(m_NodeForID[*parentsIter]);
}
// if all parents are found in datastorage (or are unknown), add node to DataStorage
storage->Add(nodesIter->first, parents);
// remove this node from m_OrderedNodePairs
m_OrderedNodePairs.erase(nodesIter);
// break this for loop because iterators are probably invalid
break;
}
}
}
// All nodes that are still in m_OrderedNodePairs at this point are not part of a proper directed graph structure.
// We'll add such nodes without any parent information.
for (auto nodesIter = m_OrderedNodePairs.begin(); nodesIter != m_OrderedNodePairs.end();
++nodesIter)
{
storage->Add(nodesIter->first);
MITK_WARN << "Encountered node that is not part of a directed graph structure. Will be added to DataStorage "
"without parents.";
error = true;
}
return !error;
}
mitk::DataNode::Pointer mitk::SceneReaderV1::LoadBaseDataFromDataTag(const tinyxml2::XMLElement *dataElement,
+ const PropertyList *properties,
const std::string &workingDirectory,
bool &error)
{
DataNode::Pointer node;
if (dataElement)
{
const char *filename = dataElement->Attribute("file");
if (filename && strlen(filename) != 0)
{
try
{
- std::vector<BaseData::Pointer> baseData = IOUtil::Load(workingDirectory + Poco::Path::separator() + filename);
- if (baseData.size() > 1)
- {
- MITK_WARN << "Discarding multiple base data results from " << filename << " except the first one.";
- }
+ auto baseData = IOUtil::Load(workingDirectory + Poco::Path::separator() + filename, properties);
+
node = DataNode::New();
- node->SetData(baseData.front());
+ node->SetData(baseData);
}
catch (std::exception &e)
{
MITK_ERROR << "Error during attempt to read '" << filename << "'. Exception says: " << e.what();
error = true;
}
if (node.IsNull())
{
MITK_ERROR << "Error during attempt to read '" << filename << "'. Factory returned nullptr object.";
error = true;
}
}
const char* dataUID = dataElement->Attribute("UID");
if (!error && dataUID != nullptr)
{
UIDManipulator manip(node->GetData());
manip.SetUID(dataUID);
}
}
// in case there was no <data> element we create a new empty node (for appending a propertylist later)
if (node.IsNull())
{
node = DataNode::New();
}
return node;
}
void mitk::SceneReaderV1::ClearNodePropertyListWithExceptions(DataNode &node, PropertyList &propertyList)
{
// Basically call propertyList.Clear(), but implement exceptions (see bug 19354)
BaseData *data = node.GetData();
PropertyList::Pointer propertiesToKeep = PropertyList::New();
if (dynamic_cast<Image *>(data))
{
/*
Older scene files (before changes of bug 17547) could contain
a RenderingMode property with value "LevelWindow_Color".
Since bug 17547 this value has been removed and replaced by
the default value LookupTable_LevelWindow_Color.
This new default value does only result in "black-to-white"
CT images (or others) if there is a corresponding lookup
table. Such a lookup table is provided as a default value
by the Image mapper. Since that value was never present in
older scene files, we do well in not removing the new
default value here. Otherwise the mapper would fall back
to another default which is all the colors of the rainbow :-(
*/
BaseProperty::Pointer lutProperty = propertyList.GetProperty("LookupTable");
propertiesToKeep->SetProperty("LookupTable", lutProperty);
/*
Older scene files (before changes of T14807) may contain
multi-component images without the "Image.Displayed Component"
property.
As the treatment as multi-component image and the corresponding
visualization options hinges on that property we should not delete
it, if it was added by the mapper.
This is a fix for the issue reported in T19919.
*/
BaseProperty::Pointer compProperty = propertyList.GetProperty("Image.Displayed Component");
if (compProperty.IsNotNull())
{
propertiesToKeep->SetProperty("Image.Displayed Component", compProperty);
}
}
propertyList.Clear();
propertyList.ConcatenatePropertyList(propertiesToKeep);
}
bool mitk::SceneReaderV1::DecorateNodeWithProperties(DataNode *node,
const tinyxml2::XMLElement *nodeElement,
const std::string &workingDirectory)
{
assert(node);
assert(nodeElement);
bool error(false);
for (auto *properties = nodeElement->FirstChildElement("properties"); properties != nullptr;
properties = properties->NextSiblingElement("properties"))
{
const char *propertiesfilea(properties->Attribute("file"));
std::string propertiesfile(propertiesfilea ? propertiesfilea : "");
const char *renderwindowa(properties->Attribute("renderwindow"));
std::string renderwindow(renderwindowa ? renderwindowa : "");
PropertyList::Pointer propertyList =
node->GetPropertyList(renderwindow); // DataNode implementation always returns a propertylist
ClearNodePropertyListWithExceptions(*node, *propertyList);
// use deserializer to construct new properties
PropertyListDeserializer::Pointer deserializer = PropertyListDeserializer::New();
deserializer->SetFilename(workingDirectory + Poco::Path::separator() + propertiesfile);
bool success = deserializer->Deserialize();
error |= !success;
PropertyList::Pointer readProperties = deserializer->GetOutput();
if (readProperties.IsNotNull())
{
propertyList->ConcatenatePropertyList(readProperties, true); // true = replace
}
else
{
MITK_ERROR << "Property list reader did not return a property list. This is an implementation error. Please tell "
"your developer.";
error = true;
}
}
return !error;
}
-
-bool mitk::SceneReaderV1::DecorateBaseDataWithProperties(BaseData::Pointer data,
- const tinyxml2::XMLElement *baseDataNodeElem,
- const std::string &workingDir)
-{
- // check given variables, initialize error variable
- assert(baseDataNodeElem);
- bool error(false);
-
- // get the file name stored in the <properties ...> tag
- const char *baseDataPropertyFile(baseDataNodeElem->Attribute("file"));
- // check if the filename was found
- if (baseDataPropertyFile)
- {
- // PropertyList::Pointer dataPropList = data->GetPropertyList();
-
- PropertyListDeserializer::Pointer propertyDeserializer = PropertyListDeserializer::New();
-
- // initialize the property reader
- propertyDeserializer->SetFilename(workingDir + Poco::Path::separator() + baseDataPropertyFile);
- bool ioSuccess = propertyDeserializer->Deserialize();
- error = !ioSuccess;
-
- // get the output
- PropertyList::Pointer inProperties = propertyDeserializer->GetOutput();
-
- // store the read-in properties to the given node or throw error otherwise
- if (inProperties.IsNotNull())
- {
- data->SetPropertyList(inProperties);
- }
- else
- {
- MITK_ERROR << "The property deserializer did not return a (valid) property list.";
- error = true;
- }
- }
- else
- {
- MITK_ERROR << "Function DecorateBaseDataWithProperties(...) called with false XML element. \n \t ->Given element "
- "does not contain a 'file' attribute. \n";
- error = true;
- }
-
- return !error;
-}
diff --git a/Modules/SceneSerialization/src/mitkSceneReaderV1.h b/Modules/SceneSerialization/src/mitkSceneReaderV1.h
index 548fbe428a..8d0aacedff 100644
--- a/Modules/SceneSerialization/src/mitkSceneReaderV1.h
+++ b/Modules/SceneSerialization/src/mitkSceneReaderV1.h
@@ -1,79 +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.
============================================================================*/
#include "mitkSceneReader.h"
namespace tinyxml2
{
class XMLElement;
}
namespace mitk
{
class SceneReaderV1 : public SceneReader
{
public:
mitkClassMacro(SceneReaderV1, SceneReader);
itkFactorylessNewMacro(Self);
itkCloneMacro(Self);
bool LoadScene(tinyxml2::XMLDocument &document,
const std::string &workingDirectory,
DataStorage *storage) override;
protected:
/**
\brief tries to create one DataNode from a given XML \<node\> element
*/
DataNode::Pointer LoadBaseDataFromDataTag(const tinyxml2::XMLElement *dataElement,
+ const PropertyList *properties,
const std::string &workingDirectory,
bool &error);
/**
\brief reads all the properties from the XML document and recreates them in node
*/
bool DecorateNodeWithProperties(DataNode *node, const tinyxml2::XMLElement *nodeElement, const std::string &workingDirectory);
/**
\brief Clear a default property list and handle some exceptions.
Called after assigning a BaseData object to a fresh DataNode via SetData().
This call to SetData() would create default properties that have not been
there when saving the scene. Since they can produce problems, we clear the
list and use only those properties that we read from the scene file.
This method also handles some exceptions for backwards compatibility.
Those exceptions are documented directly in the code of the method.
*/
void ClearNodePropertyListWithExceptions(DataNode &node, PropertyList &propertyList);
- /**
- \brief reads all properties assigned to a base data element and assigns the list to the base data object
-
- The baseDataNodeElem is supposed to be the \c \<properties file="..."\> element.
- */
- bool DecorateBaseDataWithProperties(BaseData::Pointer data,
- const tinyxml2::XMLElement *baseDataNodeElem,
- const std::string &workingDir);
-
typedef std::pair<DataNode::Pointer, std::list<std::string>> NodesAndParentsPair;
typedef std::list<NodesAndParentsPair> OrderedNodesList;
typedef std::map<std::string, DataNode *> IDToNodeMappingType;
typedef std::map<DataNode *, std::string> NodeToIDMappingType;
OrderedNodesList m_OrderedNodePairs;
IDToNodeMappingType m_NodeForID;
NodeToIDMappingType m_IDForNode;
UIDGenerator m_UIDGen;
};
}
diff --git a/Modules/Segmentation/Algorithms/mitkSegmentationHelper.cpp b/Modules/Segmentation/Algorithms/mitkSegmentationHelper.cpp
new file mode 100644
index 0000000000..c65ac2c200
--- /dev/null
+++ b/Modules/Segmentation/Algorithms/mitkSegmentationHelper.cpp
@@ -0,0 +1,45 @@
+/*============================================================================
+
+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 "mitkSegmentationHelper.h"
+
+#include <mitkImageTimeSelector.h>
+#include <mitkRenderingManager.h>
+#include <mitkSliceNavigationController.h>
+
+mitk::Image::Pointer mitk::SegmentationHelper::GetStaticSegmentationTemplate(const Image* referenceImage)
+{
+ if (referenceImage == nullptr)
+ return nullptr;
+
+ const auto* referenceGeometry = referenceImage->GetTimeGeometry();
+
+ const auto timePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint();
+ const auto timeStep = referenceGeometry->IsValidTimePoint(timePoint)
+ ? referenceGeometry->TimePointToTimeStep(timePoint)
+ : 0;
+
+ auto geometry = ProportionalTimeGeometry::New();
+ geometry->SetFirstTimePoint(referenceGeometry->GetMinimumTimePoint());
+ geometry->SetStepDuration(referenceGeometry->GetMaximumTimePoint() - referenceGeometry->GetMinimumTimePoint());
+ geometry->SetTimeStepGeometry(referenceImage->GetGeometry(timeStep), 0);
+
+ auto selector = mitk::ImageTimeSelector::New();
+ selector->SetInput(referenceImage);
+ selector->SetTimeNr(timeStep);
+ selector->Update();
+
+ Image::Pointer templateImage = selector->GetOutput();
+ templateImage->SetTimeGeometry(geometry);
+
+ return templateImage;
+}
diff --git a/Modules/QtWidgets/include/QmitkStyleManager.h b/Modules/Segmentation/Algorithms/mitkSegmentationHelper.h
similarity index 50%
copy from Modules/QtWidgets/include/QmitkStyleManager.h
copy to Modules/Segmentation/Algorithms/mitkSegmentationHelper.h
index c2acc0d6e6..7da2fa57ae 100644
--- a/Modules/QtWidgets/include/QmitkStyleManager.h
+++ b/Modules/Segmentation/Algorithms/mitkSegmentationHelper.h
@@ -1,32 +1,26 @@
/*============================================================================
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 QmitkStyleManager_h
-#define QmitkStyleManager_h
+#ifndef mitkSegmentationHelper_h
+#define mitkSegmentationHelper_h
-#include <MitkQtWidgetsExports.h>
+#include <mitkImage.h>
+#include <MitkSegmentationExports.h>
-#include <QByteArray>
-#include <QIcon>
-#include <QString>
-
-class MITKQTWIDGETS_EXPORT QmitkStyleManager
+namespace mitk::SegmentationHelper
{
-public:
- static QIcon ThemeIcon(const QByteArray &originalSVG);
- static QIcon ThemeIcon(const QString &resourcePath);
-
- QmitkStyleManager() = delete;
- ~QmitkStyleManager() = delete;
-};
+ /** \brief Get a template image for a static segmentation of a dynamic (3d+t) reference image.
+ */
+ MITKSEGMENTATION_EXPORT Image::Pointer GetStaticSegmentationTemplate(const Image* referenceImage);
+}
#endif
diff --git a/Modules/Segmentation/files.cmake b/Modules/Segmentation/files.cmake
index d931118bc0..c35539f7fe 100644
--- a/Modules/Segmentation/files.cmake
+++ b/Modules/Segmentation/files.cmake
@@ -1,107 +1,108 @@
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/mitkSegmentationHelper.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/mitkAddContourTool.cpp
Interactions/mitkAutoCropTool.cpp
Interactions/mitkSegWithPreviewTool.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/mitkCreateSurfaceTool.cpp
Interactions/mitkDrawPaintbrushTool.cpp
Interactions/mitkErasePaintbrushTool.cpp
Interactions/mitkEraseRegionTool.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/mitkPickingTool.cpp
Interactions/mitknnUnetTool.cpp
Interactions/mitkSegmentationInteractor.cpp #SO
Interactions/mitkProcessExecutor.cpp
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
AI_48x48.png
AI_Cursor_32x32.png
Erase_48x48.png
Erase_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
Wipe_48x48.png
Wipe_Cursor_32x32.png
Interactions/dummy.xml
Interactions/LiveWireTool.xml
Interactions/PickingTool.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/QmitkStaticDynamicSegmentationDialog.cpp b/Modules/SegmentationUI/Qmitk/QmitkStaticDynamicSegmentationDialog.cpp
index 280a3b5107..01cd216935 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkStaticDynamicSegmentationDialog.cpp
+++ b/Modules/SegmentationUI/Qmitk/QmitkStaticDynamicSegmentationDialog.cpp
@@ -1,75 +1,52 @@
/*============================================================================
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 "QmitkStaticDynamicSegmentationDialog.h"
-#include <mitkImageTimeSelector.h>
-#include <mitkRenderingManager.h>
-#include <mitkSliceNavigationController.h>
+#include <mitkSegmentationHelper.h>
#include <QPushButton>
QmitkStaticDynamicSegmentationDialog::QmitkStaticDynamicSegmentationDialog(QWidget *parent)
: QMessageBox(parent)
{
this->setWindowModality(Qt::WindowModality::NonModal);
this->setIcon(QMessageBox::Question);
this->setWindowTitle(tr("Create a static or dynamic segmentation?"));
this->setText(tr("The selected image has multiple time steps."));
this->setInformativeText(tr("Do you want to create a static "
"segmentation that is identical for all time steps or do you want to create a "
"dynamic segmentation to segment individual time steps?"));
QAbstractButton* staticButton = this->addButton(tr("Create static segmentation"), QMessageBox::AcceptRole);
this->addButton(tr("Create dynamic segmentation"), QMessageBox::AcceptRole);
// only the static button needs to be connected to take care of the special case, where
// the time steps of the 4D image are combined into a single time step of the 3D segmentation.
connect(staticButton, &QAbstractButton::clicked, this, &QmitkStaticDynamicSegmentationDialog::OnStaticButtonClicked);
}
void QmitkStaticDynamicSegmentationDialog::SetReferenceImage(const mitk::Image* referenceImage)
{
m_ReferenceImage = referenceImage;
m_SegmentationTemplate = referenceImage;
-
- const auto currentTimePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint();
- m_ImageTimeStep = 0;
- if (m_ReferenceImage->GetTimeGeometry()->IsValidTimePoint(currentTimePoint))
- {
- m_ImageTimeStep = m_ReferenceImage->GetTimeGeometry()->TimePointToTimeStep(currentTimePoint);
- }
}
mitk::Image::ConstPointer QmitkStaticDynamicSegmentationDialog::GetSegmentationTemplate() const
{
return m_SegmentationTemplate;
}
void QmitkStaticDynamicSegmentationDialog::OnStaticButtonClicked(bool /*checked*/)
{
- auto selector = mitk::ImageTimeSelector::New();
- selector->SetInput(m_ReferenceImage);
- selector->SetTimeNr(m_ImageTimeStep);
- selector->Update();
- mitk::Image::Pointer newImage = selector->GetOutput();
-
- const auto referenceTimeGeometry = m_ReferenceImage->GetTimeGeometry();
- auto timeGeometry = mitk::ProportionalTimeGeometry::New();
- timeGeometry->SetFirstTimePoint(referenceTimeGeometry->GetMinimumTimePoint());
- timeGeometry->SetStepDuration(referenceTimeGeometry->GetMaximumTimePoint() - referenceTimeGeometry->GetMinimumTimePoint());
- timeGeometry->SetTimeStepGeometry(m_ReferenceImage->GetGeometry(m_ImageTimeStep), 0);
-
- newImage->SetTimeGeometry(timeGeometry);
-
- m_SegmentationTemplate = newImage;
+ m_SegmentationTemplate = mitk::SegmentationHelper::GetStaticSegmentationTemplate(m_ReferenceImage);
}
diff --git a/Modules/SegmentationUI/Qmitk/QmitkStaticDynamicSegmentationDialog.h b/Modules/SegmentationUI/Qmitk/QmitkStaticDynamicSegmentationDialog.h
index 28b933cf59..8633f26ff3 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkStaticDynamicSegmentationDialog.h
+++ b/Modules/SegmentationUI/Qmitk/QmitkStaticDynamicSegmentationDialog.h
@@ -1,53 +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 QMITKSTATICDYNAMICSEGMENTATIONDIALOG_H
#define QMITKSTATICDYNAMICSEGMENTATIONDIALOG_H
#include <MitkSegmentationUIExports.h>
#include <QMessageBox>
#include <mitkImage.h>
/**
* \brief Dialog for static / dynamic segmentation node creation.
*
* This dialog is used to ask a user about the dimensionality of a newly created segmentation.
* If the user wants to create a static / 3D segmentation image from a given 4D reference image,
* the time steps of the reference image are combined into a single time step, with a step duration
* that is as long as the step duration of all 4D time steps combined.
*/
class MITKSEGMENTATIONUI_EXPORT QmitkStaticDynamicSegmentationDialog : public QMessageBox
{
Q_OBJECT
public:
QmitkStaticDynamicSegmentationDialog(QWidget* parent = nullptr);
void SetReferenceImage(const mitk::Image* referenceImage);
mitk::Image::ConstPointer GetSegmentationTemplate() const;
private Q_SLOTS:
void OnStaticButtonClicked(bool checked = false);
private:
mitk::Image::ConstPointer m_SegmentationTemplate;
const mitk::Image* m_ReferenceImage;
- unsigned int m_ImageTimeStep = 0;
-
};
#endif // QMITKSTATICDYNAMICSEGMENTATIONDIALOG_H
diff --git a/Plugins/org.mitk.gui.qt.ext/src/internal/QmitkCommonExtPlugin.cpp b/Plugins/org.mitk.gui.qt.ext/src/internal/QmitkCommonExtPlugin.cpp
index d4307e29a1..5c2a1f3381 100644
--- a/Plugins/org.mitk.gui.qt.ext/src/internal/QmitkCommonExtPlugin.cpp
+++ b/Plugins/org.mitk.gui.qt.ext/src/internal/QmitkCommonExtPlugin.cpp
@@ -1,223 +1,233 @@
/*============================================================================
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 "QmitkCommonExtPlugin.h"
#include <QtWidgetsExtRegisterClasses.h>
#include "QmitkAboutHandler.h"
#include "QmitkAppInstancesPreferencePage.h"
#include "QmitkExternalProgramsPreferencePage.h"
#include "QmitkInputDevicesPrefPage.h"
#include "QmitkModuleView.h"
#include <mitkIDataStorageService.h>
#include <mitkSceneIO.h>
#include <mitkProgressBar.h>
#include <mitkRenderingManager.h>
#include <mitkIOUtil.h>
#include <mitkBaseApplication.h>
#include <berryPlatformUI.h>
#include <berryIPreferencesService.h>
#include <berryPlatform.h>
#include <Poco/Util/OptionProcessor.h>
#include <QProcess>
#include <QMainWindow>
ctkPluginContext* QmitkCommonExtPlugin::_context = nullptr;
void QmitkCommonExtPlugin::start(ctkPluginContext* context)
{
this->_context = context;
QtWidgetsExtRegisterClasses();
BERRY_REGISTER_EXTENSION_CLASS(QmitkAboutHandler, context)
BERRY_REGISTER_EXTENSION_CLASS(QmitkAppInstancesPreferencePage, context)
BERRY_REGISTER_EXTENSION_CLASS(QmitkExternalProgramsPreferencePage, context)
BERRY_REGISTER_EXTENSION_CLASS(QmitkInputDevicesPrefPage, context)
BERRY_REGISTER_EXTENSION_CLASS(QmitkModuleView, context)
if (qApp->metaObject()->indexOfSignal("messageReceived(QByteArray)") > -1)
{
connect(qApp, SIGNAL(messageReceived(QByteArray)), this, SLOT(handleIPCMessage(QByteArray)));
}
// This is a potentially long running operation.
loadDataFromDisk(berry::Platform::GetApplicationArgs(), true);
}
void QmitkCommonExtPlugin::stop(ctkPluginContext* context)
{
Q_UNUSED(context)
this->_context = nullptr;
}
ctkPluginContext* QmitkCommonExtPlugin::getContext()
{
return _context;
}
void QmitkCommonExtPlugin::loadDataFromDisk(const QStringList &arguments, bool globalReinit)
{
if (!arguments.empty())
{
ctkServiceReference serviceRef = _context->getServiceReference<mitk::IDataStorageService>();
if (serviceRef)
{
mitk::IDataStorageService* dataStorageService = _context->getService<mitk::IDataStorageService>(serviceRef);
mitk::DataStorage::Pointer dataStorage = dataStorageService->GetDefaultDataStorage()->GetDataStorage();
int argumentsAdded = 0;
for (int i = 0; i < arguments.size(); ++i)
{
if (arguments[i].right(5) == ".mitk")
{
mitk::SceneIO::Pointer sceneIO = mitk::SceneIO::New();
bool clearDataStorageFirst(false);
mitk::ProgressBar::GetInstance()->AddStepsToDo(2);
dataStorage = sceneIO->LoadScene( arguments[i].toLocal8Bit().constData(), dataStorage, clearDataStorageFirst );
mitk::ProgressBar::GetInstance()->Progress(2);
argumentsAdded++;
}
+ else if (arguments[i].right(15) == ".mitksceneindex")
+ {
+ mitk::SceneIO::Pointer sceneIO = mitk::SceneIO::New();
+
+ bool clearDataStorageFirst(false);
+ mitk::ProgressBar::GetInstance()->AddStepsToDo(2);
+ dataStorage = sceneIO->LoadSceneUnzipped(arguments[i].toLocal8Bit().constData(), dataStorage, clearDataStorageFirst);
+ mitk::ProgressBar::GetInstance()->Progress(2);
+ argumentsAdded++;
+ }
else
{
try
{
const std::string path(arguments[i].toStdString());
auto addedNodes = mitk::IOUtil::Load(path, *dataStorage);
for (const auto& node : *addedNodes )
{
node->SetIntProperty("layer", argumentsAdded);
}
argumentsAdded++;
}
catch(...)
{
MITK_WARN << "Failed to load command line argument: " << arguments[i].toStdString();
}
}
} // end for each command line argument
if (argumentsAdded > 0 && globalReinit)
{
// calculate bounding geometry
mitk::RenderingManager::GetInstance()->InitializeViews(dataStorage->ComputeBoundingGeometry3D());
}
}
else
{
MITK_ERROR << "A service reference for mitk::IDataStorageService does not exist";
}
}
}
void QmitkCommonExtPlugin::startNewInstance(const QStringList &args, const QStringList& files)
{
QStringList newArgs(args);
#ifdef Q_OS_UNIX
newArgs << QString("--") + mitk::BaseApplication::ARG_NEWINSTANCE;
#else
newArgs << QString("/") + mitk::BaseApplication::ARG_NEWINSTANCE;
#endif
newArgs << files;
QProcess::startDetached(qApp->applicationFilePath(), newArgs);
}
void QmitkCommonExtPlugin::handleIPCMessage(const QByteArray& msg)
{
QDataStream ds(msg);
QString msgType;
ds >> msgType;
// we only handle messages containing command line arguments
if (msgType != "$cmdLineArgs") return;
// activate the current workbench window
berry::IWorkbenchWindow::Pointer window =
berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow();
QMainWindow* mainWindow =
static_cast<QMainWindow*> (window->GetShell()->GetControl());
mainWindow->setWindowState(mainWindow->windowState() & ~Qt::WindowMinimized);
mainWindow->raise();
mainWindow->activateWindow();
// Get the preferences for the instantiation behavior
berry::IPreferencesService* prefService = berry::Platform::GetPreferencesService();
berry::IPreferences::Pointer prefs = prefService->GetSystemPreferences()->Node("/General");
bool newInstanceAlways = prefs->GetBool("newInstance.always", false);
bool newInstanceScene = prefs->GetBool("newInstance.scene", true);
QStringList args;
ds >> args;
QStringList fileArgs;
QStringList sceneArgs;
foreach (QString arg, args)
{
if (arg.endsWith(".mitk"))
{
sceneArgs << arg;
}
else
{
fileArgs << arg;
}
}
if (newInstanceAlways)
{
if (newInstanceScene)
{
startNewInstance(args, fileArgs);
foreach(QString sceneFile, sceneArgs)
{
startNewInstance(args, QStringList(sceneFile));
}
}
else
{
fileArgs.append(sceneArgs);
startNewInstance(args, fileArgs);
}
}
else
{
loadDataFromDisk(fileArgs, false);
if (newInstanceScene)
{
foreach(QString sceneFile, sceneArgs)
{
startNewInstance(args, QStringList(sceneFile));
}
}
else
{
loadDataFromDisk(sceneArgs, false);
}
}
}
diff --git a/Plugins/org.mitk.gui.qt.flow.segmentation/files.cmake b/Plugins/org.mitk.gui.qt.flow.segmentation/files.cmake
index 2d5b0a93a5..965a81bd30 100644
--- a/Plugins/org.mitk.gui.qt.flow.segmentation/files.cmake
+++ b/Plugins/org.mitk.gui.qt.flow.segmentation/files.cmake
@@ -1,46 +1,49 @@
set(SRC_CPP_FILES
)
set(INTERNAL_CPP_FILES
org_mitk_gui_qt_flow_segmentation_Activator.cpp
QmitkSegmentationFlowControlView.cpp
+ QmitkSegmentationTaskListWidget.cpp
perspectives/QmitkFlowSegmentationPerspective.cpp
)
set(UI_FILES
src/internal/QmitkSegmentationFlowControlView.ui
+ src/internal/QmitkSegmentationTaskListWidget.ui
)
set(MOC_H_FILES
src/internal/org_mitk_gui_qt_flow_segmentation_Activator.h
src/internal/QmitkSegmentationFlowControlView.h
+ src/internal/QmitkSegmentationTaskListWidget.h
src/internal/perspectives/QmitkFlowSegmentationPerspective.h
)
# list of resource files which can be used by the plug-in
# system without loading the plug-ins shared library,
# for example the icon used in the menu and tabs for the
# plug-in views in the workbench
set(CACHED_RESOURCE_FILES
resources/icon.svg
plugin.xml
resources/perspectives/segmentation_icon.svg
)
# list of Qt .qrc files which contain additional resources
# specific to this plugin
set(QRC_FILES
-
+ resources/SegmentationTaskList.qrc
)
set(CPP_FILES )
foreach(file ${SRC_CPP_FILES})
set(CPP_FILES ${CPP_FILES} src/${file})
endforeach(file ${SRC_CPP_FILES})
foreach(file ${INTERNAL_CPP_FILES})
set(CPP_FILES ${CPP_FILES} src/internal/${file})
endforeach(file ${INTERNAL_CPP_FILES})
diff --git a/Plugins/org.mitk.gui.qt.flow.segmentation/resources/SegmentationTaskList.qrc b/Plugins/org.mitk.gui.qt.flow.segmentation/resources/SegmentationTaskList.qrc
new file mode 100644
index 0000000000..327fbe97d1
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.flow.segmentation/resources/SegmentationTaskList.qrc
@@ -0,0 +1,5 @@
+<RCC>
+ <qresource prefix="/SegmentationTaskList">
+ <file alias="Icon.svg">SegmentationTaskListIcon.svg</file>
+ </qresource>
+</RCC>
diff --git a/Plugins/org.mitk.gui.qt.flow.segmentation/resources/SegmentationTaskListIcon.svg b/Plugins/org.mitk.gui.qt.flow.segmentation/resources/SegmentationTaskListIcon.svg
new file mode 100644
index 0000000000..1beb5d6b9e
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.flow.segmentation/resources/SegmentationTaskListIcon.svg
@@ -0,0 +1,170 @@
+<?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"
+ sodipodi:docname="SegmentationTaskIcon.svg"
+ inkscape:version="1.0 (4035a4fb49, 2020-05-01)"
+ id="svg8"
+ version="1.1"
+ viewBox="0 0 8.4666665 8.4666669"
+ height="32"
+ width="32">
+ <defs
+ id="defs2" />
+ <sodipodi:namedview
+ inkscape:window-maximized="1"
+ inkscape:window-y="-8"
+ inkscape:window-x="-8"
+ inkscape:window-height="1377"
+ inkscape:window-width="2560"
+ inkscape:showpageshadow="false"
+ borderlayer="false"
+ showborder="true"
+ inkscape:pagecheckerboard="true"
+ units="px"
+ showgrid="true"
+ inkscape:document-rotation="0"
+ inkscape:current-layer="g920"
+ inkscape:document-units="mm"
+ inkscape:cy="21.616923"
+ inkscape:cx="12.070777"
+ inkscape:zoom="20"
+ inkscape:pageshadow="2"
+ inkscape:pageopacity="1"
+ borderopacity="1.0"
+ bordercolor="#666666"
+ pagecolor="#676767"
+ id="base" />
+ <metadata
+ id="metadata5">
+ <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>
+ <g
+ id="layer1"
+ inkscape:groupmode="layer"
+ inkscape:label="Layer 1">
+ <rect
+ ry="0.26458332"
+ rx="0.26458332"
+ y="0.92604148"
+ x="1.1906248"
+ height="7.1437502"
+ width="6.0854168"
+ id="rect835"
+ style="fill:none;fill-opacity:1;stroke:#00ff00;stroke-width:0.264583;stroke-linecap:round;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1" />
+ <g
+ transform="translate(-3.3333334e-8,0.13229177)"
+ id="g920">
+ <path
+ style="fill:none;stroke:#00ff00;stroke-width:0.330729;stroke-linecap:round;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ d="M 3.9626056,3.036013 H 6.4629181"
+ id="path857" />
+ <path
+ style="fill:none;stroke:#ff00ff;stroke-width:0.396875;stroke-linecap:round;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ d="M 1.852084,3.10621 2.4500425,3.7041689 3.3469803,2.2092717"
+ id="path859" />
+ </g>
+ <g
+ id="g970">
+ <circle
+ style="fill:#00ff00;fill-opacity:1;stroke:none;stroke-width:0.264583;stroke-linecap:round;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ id="path943"
+ cx="2.3812499"
+ cy="1.6497022"
+ r="0.39687496" />
+ <path
+ style="fill:none;stroke:#00ff00;stroke-width:0.330728;stroke-linecap:round;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ d="M 2.38125,1.5875 V 0.52916667"
+ id="path857-1" />
+ </g>
+ <g
+ id="g970-7"
+ transform="translate(1.2347223)">
+ <circle
+ r="0.39687496"
+ cy="1.6497022"
+ cx="2.3812499"
+ id="path943-9"
+ style="fill:#00ff00;fill-opacity:1;stroke:none;stroke-width:0.264583;stroke-linecap:round;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1" />
+ <path
+ id="path857-1-8"
+ d="M 2.38125,1.5875 V 0.52916667"
+ style="fill:none;stroke:#00ff00;stroke-width:0.330728;stroke-linecap:round;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1" />
+ </g>
+ <g
+ transform="translate(2.4694441)"
+ id="g970-4">
+ <circle
+ style="fill:#00ff00;fill-opacity:1;stroke:none;stroke-width:0.264583;stroke-linecap:round;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ id="path943-1"
+ cx="2.3812499"
+ cy="1.6497022"
+ r="0.39687496" />
+ <path
+ style="fill:none;stroke:#00ff00;stroke-width:0.330728;stroke-linecap:round;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ d="M 2.38125,1.5875 V 0.52916667"
+ id="path857-1-5" />
+ </g>
+ <g
+ transform="translate(3.7041667)"
+ id="g970-9">
+ <circle
+ style="fill:#00ff00;fill-opacity:1;stroke:none;stroke-width:0.264583;stroke-linecap:round;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ id="path943-6"
+ cx="2.3812499"
+ cy="1.6497022"
+ r="0.39687496" />
+ <path
+ style="fill:none;stroke:#00ff00;stroke-width:0.330728;stroke-linecap:round;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ d="M 2.38125,1.5875 V 0.52916667"
+ id="path857-1-9" />
+ </g>
+ <g
+ transform="translate(-6.6666669e-8,-0.26458327)"
+ id="g1080">
+ <path
+ style="fill:none;stroke:#00ff00;stroke-width:0.330729;stroke-linecap:round;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ d="M 3.9626056,5.2849714 H 6.4629181"
+ id="path857-0" />
+ <rect
+ style="fill:none;fill-opacity:1;stroke:#00ff00;stroke-width:0.330999;stroke-linecap:round;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ id="rect1060"
+ width="1.256501"
+ height="1.256501"
+ x="1.8519536"
+ y="4.6634164"
+ rx="0.26458332"
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+ </g>
+ <g
+ transform="translate(-3.3333334e-8,1.5875)"
+ id="g1080-1">
+ <path
+ id="path857-0-3"
+ d="M 3.9626056,5.2849714 H 6.4629181"
+ style="fill:none;stroke:#00ff00;stroke-width:0.330729;stroke-linecap:round;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1" />
+ <rect
+ ry="0.26458332"
+ rx="0.26458332"
+ y="4.6634164"
+ x="1.8519536"
+ height="1.256501"
+ width="1.256501"
+ id="rect1060-3"
+ style="fill:none;fill-opacity:1;stroke:#00ff00;stroke-width:0.330999;stroke-linecap:round;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1" />
+ </g>
+ </g>
+</svg>
diff --git a/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationFlowControlView.cpp b/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationFlowControlView.cpp
index bc674b04d4..e089c1d057 100644
--- a/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationFlowControlView.cpp
+++ b/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationFlowControlView.cpp
@@ -1,104 +1,180 @@
/*============================================================================
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_flow_segmentation_Activator.h"
// Blueberry
#include <berryISelectionService.h>
#include <berryIWorkbenchWindow.h>
#include <itksys/SystemTools.hxx>
//MITK
#include <mitkBaseApplication.h>
#include <mitkLabelSetImage.h>
#include <mitkNodePredicateAnd.h>
#include <mitkNodePredicateNot.h>
#include <mitkNodePredicateProperty.h>
#include <mitkNodePredicateDataType.h>
#include <mitkIOUtil.h>
// Qmitk
#include "QmitkSegmentationFlowControlView.h"
+#include <ui_QmitkSegmentationFlowControlView.h>
+
// Qt
#include <QMessageBox>
#include <QDir>
+#include <filesystem>
+
const std::string QmitkSegmentationFlowControlView::VIEW_ID = "org.mitk.views.flow.control";
QmitkSegmentationFlowControlView::QmitkSegmentationFlowControlView()
- : m_Parent(nullptr)
+ : m_Controls(new Ui::SegmentationFlowControlView),
+ m_Parent(nullptr)
{
- auto nodePredicate = mitk::NodePredicateAnd::New();
- nodePredicate->AddPredicate(mitk::TNodePredicateDataType<mitk::LabelSetImage>::New());
- nodePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object")));
- m_SegmentationPredicate = nodePredicate;
+ auto notHelperObject = mitk::NodePredicateNot::New(
+ mitk::NodePredicateProperty::New("helper object"));
+
+ m_SegmentationPredicate = mitk::NodePredicateAnd::New(
+ mitk::TNodePredicateDataType<mitk::LabelSetImage>::New(),
+ notHelperObject);
+
+ m_SegmentationTaskListPredicate = mitk::NodePredicateAnd::New(
+ mitk::TNodePredicateDataType<mitk::SegmentationTaskList>::New(),
+ notHelperObject);
}
void QmitkSegmentationFlowControlView::SetFocus()
{
- m_Controls.btnStoreAndAccept->setFocus();
+ m_Controls->btnStoreAndAccept->setFocus();
}
void QmitkSegmentationFlowControlView::CreateQtPartControl(QWidget* parent)
{
// create GUI widgets from the Qt Designer's .ui file
- m_Controls.setupUi(parent);
+ m_Controls->setupUi(parent);
m_Parent = parent;
- connect(m_Controls.btnStoreAndAccept, SIGNAL(clicked()), this, SLOT(OnAcceptButtonPushed()));
+ using Self = QmitkSegmentationFlowControlView;
- m_Controls.labelStored->setVisible(false);
+ connect(m_Controls->btnStoreAndAccept, &QPushButton::clicked, this, &Self::OnAcceptButtonPushed);
+ connect(m_Controls->segmentationTaskListWidget, &QmitkSegmentationTaskListWidget::ActiveTaskChanged, this, &Self::OnActiveTaskChanged);
+ connect(m_Controls->segmentationTaskListWidget, &QmitkSegmentationTaskListWidget::CurrentTaskChanged, this, &Self::OnCurrentTaskChanged);
+
+ m_Controls->segmentationTaskListWidget->setVisible(false);
+ m_Controls->labelStored->setVisible(false);
UpdateControls();
m_OutputDir = QString::fromStdString(mitk::BaseApplication::instance().config().getString("flow.outputdir", itksys::SystemTools::GetCurrentWorkingDirectory()));
m_OutputDir = QDir::fromNativeSeparators(m_OutputDir);
m_FileExtension = QString::fromStdString(mitk::BaseApplication::instance().config().getString("flow.outputextension", "nrrd"));
}
void QmitkSegmentationFlowControlView::OnAcceptButtonPushed()
{
- auto nodes = this->GetDataStorage()->GetSubset(m_SegmentationPredicate);
-
- for (auto node : *nodes)
+ if (m_Controls->segmentationTaskListWidget->isVisible())
+ {
+ auto* taskList = m_Controls->segmentationTaskListWidget->GetTaskList();
+
+ if (taskList != nullptr)
+ {
+ auto activeTaskIndex = m_Controls->segmentationTaskListWidget->GetActiveTaskIndex();
+
+ if (activeTaskIndex.has_value())
+ {
+ auto segmentationNode = m_Controls->segmentationTaskListWidget->GetSegmentationDataNode(activeTaskIndex.value());
+
+ if (segmentationNode != nullptr)
+ {
+ QApplication::setOverrideCursor(Qt::BusyCursor);
+
+ try
+ {
+ taskList->SaveTask(activeTaskIndex.value(), segmentationNode->GetData());
+ m_Controls->segmentationTaskListWidget->OnUnsavedChangesSaved();
+ }
+ catch (const mitk::Exception& e)
+ {
+ MITK_ERROR << e;
+ }
+
+ QApplication::restoreOverrideCursor();
+ }
+ }
+ }
+ }
+ else
{
- QString outputpath = m_OutputDir + "/" + QString::fromStdString(node->GetName()) + "." + m_FileExtension;
- outputpath = QDir::toNativeSeparators(QDir::cleanPath(outputpath));
- mitk::IOUtil::Save(node->GetData(), outputpath.toStdString());
+ auto nodes = this->GetDataStorage()->GetSubset(m_SegmentationPredicate);
+
+ for (auto node : *nodes)
+ {
+ QString outputpath = m_OutputDir + "/" + QString::fromStdString(node->GetName()) + "." + m_FileExtension;
+ outputpath = QDir::toNativeSeparators(QDir::cleanPath(outputpath));
+ mitk::IOUtil::Save(node->GetData(), outputpath.toStdString());
+ }
+
+ m_Controls->labelStored->setVisible(true);
}
+}
+
+void QmitkSegmentationFlowControlView::OnActiveTaskChanged(const std::optional<size_t>&)
+{
+ this->UpdateControls();
+}
- m_Controls.labelStored->setVisible(true);
+void QmitkSegmentationFlowControlView::OnCurrentTaskChanged(const std::optional<size_t>&)
+{
+ this->UpdateControls();
}
void QmitkSegmentationFlowControlView::UpdateControls()
{
- auto nodes = this->GetDataStorage()->GetSubset(m_SegmentationPredicate);
- m_Controls.btnStoreAndAccept->setEnabled(!nodes->empty());
-};
+ auto dataStorage = this->GetDataStorage();
+
+ auto hasTaskList = !dataStorage->GetSubset(m_SegmentationTaskListPredicate)->empty();
+ m_Controls->segmentationTaskListWidget->setVisible(hasTaskList);
+
+ if (hasTaskList)
+ {
+ auto activeTaskIsShown = m_Controls->segmentationTaskListWidget->ActiveTaskIsShown();
+ m_Controls->btnStoreAndAccept->setEnabled(activeTaskIsShown);
+ }
+ else
+ {
+ auto hasSegmentation = !dataStorage->GetSubset(m_SegmentationPredicate)->empty();
+ m_Controls->btnStoreAndAccept->setEnabled(hasSegmentation);
+ }
+}
-void QmitkSegmentationFlowControlView::NodeAdded(const mitk::DataNode* /*node*/)
+void QmitkSegmentationFlowControlView::NodeAdded(const mitk::DataNode* node)
{
- UpdateControls();
-};
+ if (dynamic_cast<const mitk::LabelSetImage*>(node->GetData()) != nullptr)
+ this->UpdateControls();
+}
-void QmitkSegmentationFlowControlView::NodeChanged(const mitk::DataNode* /*node*/)
+void QmitkSegmentationFlowControlView::NodeChanged(const mitk::DataNode* node)
{
- UpdateControls();
-};
+ if (dynamic_cast<const mitk::LabelSetImage*>(node->GetData()) != nullptr)
+ this->UpdateControls();
+}
-void QmitkSegmentationFlowControlView::NodeRemoved(const mitk::DataNode* /*node*/)
+void QmitkSegmentationFlowControlView::NodeRemoved(const mitk::DataNode* node)
{
- UpdateControls();
-};
+ if (dynamic_cast<const mitk::LabelSetImage*>(node->GetData()) != nullptr)
+ this->UpdateControls();
+}
diff --git a/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationFlowControlView.h b/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationFlowControlView.h
index 1d8cc9f646..49335b6def 100644
--- a/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationFlowControlView.h
+++ b/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationFlowControlView.h
@@ -1,74 +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 __Q_MITK_MATCHPOINT_MAPPER_H
#define __Q_MITK_MATCHPOINT_MAPPER_H
#include <berryISelectionListener.h>
#include <QmitkAbstractView.h>
#include "mitkNodePredicateBase.h"
-#include "ui_QmitkSegmentationFlowControlView.h"
+#include <optional>
+
+namespace Ui
+{
+ class SegmentationFlowControlView;
+}
/*!
\brief QmitkSegmentationFlowControlView
Class that "controls" the segmentation view. It offers the possibility to accept a segmentation.
Accepting the segmentation stores the segmentation to the given working directory.
The working directory is specified by command line arguments. If no commandline flag is set the current working directory will be used.
*/
class QmitkSegmentationFlowControlView : public QmitkAbstractView
{
// this is needed for all Qt objects that should have a Qt meta-object
// (everything that derives from QObject and wants to have signal/slots)
Q_OBJECT
public:
static const std::string VIEW_ID;
/**
* Creates smartpointer typedefs
*/
berryObjectMacro(QmitkSegmentationFlowControlView)
QmitkSegmentationFlowControlView();
void CreateQtPartControl(QWidget *parent) override;
protected slots:
void OnAcceptButtonPushed();
+ void OnActiveTaskChanged(const std::optional<size_t>& index);
+ void OnCurrentTaskChanged(const std::optional<size_t>& index);
protected:
void SetFocus() override;
void NodeAdded(const mitk::DataNode* node) override;
void NodeChanged(const mitk::DataNode* node) override;
void NodeRemoved(const mitk::DataNode* node) override;
void UpdateControls();
- Ui::SegmentationFlowControlView m_Controls;
+ Ui::SegmentationFlowControlView* m_Controls;
private:
QWidget *m_Parent;
mitk::NodePredicateBase::Pointer m_SegmentationPredicate;
+ mitk::NodePredicateBase::Pointer m_SegmentationTaskListPredicate;
QString m_OutputDir;
QString m_FileExtension;
};
#endif // MatchPoint_h
diff --git a/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationFlowControlView.ui b/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationFlowControlView.ui
index 05d90c45ef..e404561a09 100644
--- a/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationFlowControlView.ui
+++ b/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationFlowControlView.ui
@@ -1,99 +1,110 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>SegmentationFlowControlView</class>
<widget class="QWidget" name="SegmentationFlowControlView">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>392</width>
<height>324</height>
</rect>
</property>
<layout class="QVBoxLayout" name="verticalLayout">
<property name="spacing">
<number>20</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>
<spacer name="verticalSpacer">
<property name="orientation">
<enum>Qt::Vertical</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>20</width>
<height>40</height>
</size>
</property>
</spacer>
</item>
+ <item>
+ <widget class="QmitkSegmentationTaskListWidget" name="segmentationTaskListWidget" native="true"/>
+ </item>
<item>
<widget class="QPushButton" name="btnStoreAndAccept">
<property name="minimumSize">
<size>
<width>0</width>
<height>50</height>
</size>
</property>
<property name="text">
<string>Accept segmentation</string>
</property>
</widget>
</item>
<item>
<widget class="QLabel" name="labelStored">
<property name="text">
<string><html><head/><body><p><span style=" font-size:12pt;">Segmentation stored! Flow on...</span></p></body></html></string>
</property>
<property name="alignment">
<set>Qt::AlignCenter</set>
</property>
</widget>
</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>
+ <customwidgets>
+ <customwidget>
+ <class>QmitkSegmentationTaskListWidget</class>
+ <extends>QWidget</extends>
+ <header location="global">internal/QmitkSegmentationTaskListWidget.h</header>
+ <container>1</container>
+ </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.flow.segmentation/src/internal/QmitkSegmentationTaskListWidget.cpp b/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationTaskListWidget.cpp
new file mode 100644
index 0000000000..00a1ec5af0
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationTaskListWidget.cpp
@@ -0,0 +1,769 @@
+/*============================================================================
+
+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 "QmitkSegmentationTaskListWidget.h"
+#include "org_mitk_gui_qt_flow_segmentation_Activator.h"
+
+#include <berryIPreferences.h>
+#include <berryIPreferencesService.h>
+#include <berryPlatform.h>
+
+#include <mitkIDataStorageService.h>
+#include <mitkIOUtil.h>
+#include <mitkLabelSetIOHelper.h>
+#include <mitkLabelSetImageHelper.h>
+#include <mitkNodePredicateDataType.h>
+#include <mitkNodePredicateFunction.h>
+#include <mitkRenderingManager.h>
+#include <mitkSegmentationHelper.h>
+
+#include <QmitkStaticDynamicSegmentationDialog.h>
+#include <QmitkStyleManager.h>
+
+#include <ui_QmitkSegmentationTaskListWidget.h>
+
+#include <QFileSystemWatcher>
+#include <QMessageBox>
+
+#include <filesystem>
+
+namespace
+{
+ berry::IPreferences::Pointer GetSegmentationPreferences()
+ {
+ return berry::Platform::GetPreferencesService()->GetSystemPreferences()->Node("/org.mitk.views.segmentation");
+ }
+
+ mitk::DataStorage* GetDataStorage()
+ {
+ auto* pluginContext = org_mitk_gui_qt_flow_segmentation_Activator::GetContext();
+ auto dataStorageServiceReference = pluginContext->getServiceReference<mitk::IDataStorageService>();
+
+ if (dataStorageServiceReference)
+ {
+ auto* dataStorageService = pluginContext->getService<mitk::IDataStorageService>(dataStorageServiceReference);
+
+ if (dataStorageService != nullptr)
+ {
+ auto dataStorageReference = dataStorageService->GetDataStorage();
+ pluginContext->ungetService(dataStorageServiceReference);
+
+ return dataStorageReference->GetDataStorage();
+ }
+ }
+
+ return nullptr;
+ }
+
+ std::filesystem::path GetInputLocation(const mitk::BaseData* data)
+ {
+ std::string result;
+
+ if (data != nullptr)
+ data->GetPropertyList()->GetStringProperty("MITK.IO.reader.inputlocation", result);
+
+ return result;
+ }
+
+ QString ColorString(const QString& string, const QColor& color, const QColor& backgroundColor = QColor::Invalid)
+ {
+ if (!color.isValid() && !backgroundColor.isValid())
+ return string;
+
+ auto result = QStringLiteral("<span style=\"");
+ QStringList strings;
+
+ if (color.isValid())
+ strings << QString("color: %1;").arg(color.name());
+
+ if (backgroundColor.isValid())
+ strings << QString("background-color: %1;").arg(backgroundColor.name());
+
+ result += strings.join(' ') + QString("\">%1</span>").arg(string);
+
+ return result;
+ }
+}
+
+/* This constructor has three objectives:
+ * 1. Do widget initialization that cannot be done in the .ui file
+ * 2. Connect signals and slots
+ * 3. Explicitly trigger a reset to a valid initial widget state
+ */
+QmitkSegmentationTaskListWidget::QmitkSegmentationTaskListWidget(QWidget* parent)
+ : QWidget(parent),
+ m_Ui(new Ui::QmitkSegmentationTaskListWidget),
+ m_FileSystemWatcher(new QFileSystemWatcher(this)),
+ m_UnsavedChanges(false)
+{
+ m_Ui->setupUi(this);
+
+ m_Ui->selectionWidget->SetDataStorage(GetDataStorage());
+ m_Ui->selectionWidget->SetSelectionIsOptional(true);
+ m_Ui->selectionWidget->SetEmptyInfo(QStringLiteral("Select a segmentation task list"));
+ m_Ui->selectionWidget->SetAutoSelectNewNodes(true);
+ m_Ui->selectionWidget->SetNodePredicate(mitk::TNodePredicateDataType<mitk::SegmentationTaskList>::New());
+
+ m_Ui->progressBar->setStyleSheet(QString("QProgressBar::chunk { background-color: %1; }").arg(QmitkStyleManager::GetIconAccentColor()));
+
+ using Self = QmitkSegmentationTaskListWidget;
+
+ connect(m_Ui->selectionWidget, &QmitkSingleNodeSelectionWidget::CurrentSelectionChanged, this, &Self::OnSelectionChanged);
+ connect(m_Ui->previousButton, &QToolButton::clicked, this, &Self::OnPreviousButtonClicked);
+ connect(m_Ui->nextButton, &QToolButton::clicked, this, &Self::OnNextButtonClicked);
+ connect(m_Ui->loadButton, &QPushButton::clicked, this, &Self::OnLoadButtonClicked);
+
+ connect(m_FileSystemWatcher, &QFileSystemWatcher::directoryChanged, this, &Self::OnResultDirectoryChanged);
+
+ this->OnSelectionChanged(m_Ui->selectionWidget->GetSelectedNodes());
+}
+
+QmitkSegmentationTaskListWidget::~QmitkSegmentationTaskListWidget()
+{
+}
+
+mitk::SegmentationTaskList* QmitkSegmentationTaskListWidget::GetTaskList() const
+{
+ return m_TaskList;
+}
+
+std::optional<size_t> QmitkSegmentationTaskListWidget::GetActiveTaskIndex() const
+{
+ return m_ActiveTaskIndex;
+}
+
+std::optional<size_t> QmitkSegmentationTaskListWidget::GetCurrentTaskIndex() const
+{
+ return m_CurrentTaskIndex;
+}
+
+void QmitkSegmentationTaskListWidget::OnUnsavedChangesSaved()
+{
+ if (m_UnsavedChanges)
+ {
+ m_UnsavedChanges = false;
+
+ if (this->ActiveTaskIsShown())
+ this->UpdateDetailsLabel();
+ }
+}
+
+/* Make sure that the widget transitions into a valid state whenever the
+ * selection changes.
+ */
+void QmitkSegmentationTaskListWidget::OnSelectionChanged(const QmitkSingleNodeSelectionWidget::NodeList& nodes)
+{
+ this->UnloadTasks();
+ this->ResetControls();
+
+ if (!nodes.empty())
+ {
+ m_TaskListNode = nodes.front();
+ auto taskList = dynamic_cast<mitk::SegmentationTaskList*>(m_TaskListNode->GetData());
+
+ if (taskList != nullptr)
+ {
+ this->OnTaskListChanged(taskList);
+ return;
+ }
+ }
+
+ this->SetTaskList(nullptr);
+ m_TaskListNode = nullptr;
+}
+
+/* Reset all controls to a default state as a common basis for further
+ * adjustments.
+ */
+void QmitkSegmentationTaskListWidget::ResetControls()
+{
+ m_Ui->progressBar->setEnabled(false);
+ m_Ui->progressBar->setFormat("");
+ m_Ui->progressBar->setValue(0);
+ m_Ui->progressBar->setMaximum(1);
+
+ m_Ui->previousButton->setEnabled(false);
+ m_Ui->nextButton->setEnabled(false);
+
+ this->UpdateLoadButton();
+ this->UpdateDetailsLabel();
+}
+
+/* If the segmentation task changed, reset all member variables to expected
+ * default values and reset the file system watcher.
+ */
+void QmitkSegmentationTaskListWidget::SetTaskList(mitk::SegmentationTaskList* taskList)
+{
+ if (m_TaskList != taskList)
+ {
+ m_TaskList = taskList;
+
+ if (taskList != nullptr)
+ {
+ this->SetCurrentTaskIndex(0);
+ }
+ else
+ {
+ this->SetCurrentTaskIndex(std::nullopt);
+ }
+
+ this->ResetFileSystemWatcher();
+ }
+}
+
+void QmitkSegmentationTaskListWidget::ResetFileSystemWatcher()
+{
+ auto paths = m_FileSystemWatcher->directories();
+
+ if (!paths.empty())
+ m_FileSystemWatcher->removePaths(paths);
+
+ if (m_TaskList.IsNotNull())
+ {
+ for (const auto& task : *m_TaskList)
+ {
+ auto resultPath = m_TaskList->GetAbsolutePath(task.GetResult()).remove_filename();
+
+ if (!std::filesystem::exists(resultPath))
+ {
+ try
+ {
+ std::filesystem::create_directories(resultPath);
+ }
+ catch (const std::filesystem::filesystem_error& e)
+ {
+ MITK_ERROR << e.what();
+ }
+ }
+
+ if (std::filesystem::exists(resultPath))
+ m_FileSystemWatcher->addPath(QString::fromStdString(resultPath.string()));
+ }
+ }
+}
+
+void QmitkSegmentationTaskListWidget::OnResultDirectoryChanged(const QString&)
+{
+ // TODO: If a segmentation was modified ("Unsaved changes"), saved ("Done"), and then the file is deleted, the status should be "Unsaved changes" instead of "Not done".
+ this->UpdateProgressBar();
+ this->UpdateDetailsLabel();
+}
+
+void QmitkSegmentationTaskListWidget::UpdateProgressBar()
+{
+ int progress = 0;
+
+ for (size_t i = 0; i < m_TaskList->GetNumberOfTasks(); ++i)
+ {
+ if (m_TaskList->IsDone(i))
+ ++progress;
+ }
+
+ m_Ui->progressBar->setValue(progress);
+}
+
+/* Provided that a valid segmentation task list is currently selected and the
+ * widget is in its default state, update all controls accordingly.
+ */
+void QmitkSegmentationTaskListWidget::OnTaskListChanged(mitk::SegmentationTaskList* taskList)
+{
+ this->SetTaskList(taskList);
+
+ const auto numTasks = taskList->GetNumberOfTasks();
+
+ m_Ui->progressBar->setMaximum(numTasks);
+ m_Ui->progressBar->setFormat(QStringLiteral("%v/%m Task(s) done"));
+ m_Ui->progressBar->setEnabled(true);
+
+ this->UpdateProgressBar();
+
+ m_Ui->loadButton->setEnabled(true);
+
+ if (numTasks > 1)
+ m_Ui->nextButton->setEnabled(true);
+}
+
+/* If possible, change the currently displayed task to the previous task.
+ * Enable/disable navigation buttons according to the task's position.
+ */
+void QmitkSegmentationTaskListWidget::OnPreviousButtonClicked()
+{
+ const auto maxIndex = m_TaskList->GetNumberOfTasks() - 1;
+ auto current = m_CurrentTaskIndex.value();
+
+ if (current != 0)
+ this->SetCurrentTaskIndex(current - 1);
+
+ current = m_CurrentTaskIndex.value();
+
+ if (current == 0)
+ m_Ui->previousButton->setEnabled(false);
+
+ if (current < maxIndex)
+ m_Ui->nextButton->setEnabled(true);
+}
+
+/* If possible, change the currently displayed task to the next task.
+ * Enable/disable navigation buttons according to the task's position.
+ */
+void QmitkSegmentationTaskListWidget::OnNextButtonClicked()
+{
+ const auto maxIndex = m_TaskList->GetNumberOfTasks() - 1;
+ auto current = m_CurrentTaskIndex.value();
+
+ if (current < maxIndex)
+ this->SetCurrentTaskIndex(current + 1);
+
+ current = m_CurrentTaskIndex.value();
+
+ if (current != 0)
+ m_Ui->previousButton->setEnabled(true);
+
+ if (current >= maxIndex)
+ m_Ui->nextButton->setEnabled(false);
+}
+
+/* Update affected controls when the currently displayed task changed.
+ */
+void QmitkSegmentationTaskListWidget::OnCurrentTaskChanged()
+{
+ this->UpdateLoadButton();
+ this->UpdateDetailsLabel();
+}
+
+/* Update the load button according to the currently displayed task.
+ */
+void QmitkSegmentationTaskListWidget::UpdateLoadButton()
+{
+ auto text = !this->ActiveTaskIsShown()
+ ? QStringLiteral("Load task")
+ : QStringLiteral("Task");
+
+ if (m_CurrentTaskIndex.has_value())
+ {
+ const auto current = m_CurrentTaskIndex.value();
+
+ if (m_TaskList.IsNotNull())
+ {
+ text += QString(" %1/%2").arg(current + 1).arg(m_TaskList->GetNumberOfTasks());
+
+ if (m_TaskList->HasName(current))
+ text += QStringLiteral(":\n") + QString::fromStdString(m_TaskList->GetName(current));
+ }
+
+ m_Ui->loadButton->setDisabled(this->ActiveTaskIsShown());
+ }
+ else
+ {
+ m_Ui->loadButton->setEnabled(false);
+ }
+
+ m_Ui->loadButton->setText(text);
+}
+
+/* Update the details label according to the currently display task.
+ * The text is composed of the status of the task and a variable number
+ * of text blocks according to the optional values provided by the task.
+ */
+void QmitkSegmentationTaskListWidget::UpdateDetailsLabel()
+{
+ if (!m_CurrentTaskIndex.has_value())
+ {
+ m_Ui->detailsLabel->clear();
+ return;
+ }
+
+ const auto current = m_CurrentTaskIndex.value();
+ bool isDone = m_TaskList->IsDone(current);
+
+ auto details = QString("<p><b>Status: %1</b> / <b>").arg(this->ActiveTaskIsShown()
+ ? ColorString("Active", Qt::white, QColor(Qt::green).darker())
+ : ColorString("Inactive", Qt::white, QColor(Qt::red).darker()));
+
+ if (m_UnsavedChanges && this->ActiveTaskIsShown())
+ {
+ details += QString("%1</b></p>").arg(ColorString("Unsaved changes", Qt::white, QColor(Qt::red).darker()));
+ }
+ else
+ {
+ details += QString("%1</b></p>").arg(isDone
+ ? ColorString("Done", Qt::white, QColor(Qt::green).darker())
+ : ColorString("Not done", Qt::white, QColor(Qt::red).darker()));
+ }
+
+ if (m_TaskList->HasDescription(current))
+ details += QString("<p><b>Description:</b> %1</p>").arg(QString::fromStdString(m_TaskList->GetDescription(current)));
+
+ QStringList stringList;
+
+ if (m_TaskList->HasImage(current))
+ stringList << QString::fromStdString("<b>Image:</b> " + m_TaskList->GetImage(current).string());
+
+ if (m_TaskList->HasSegmentation(current))
+ stringList << QString::fromStdString("<b>Segmentation:</b> " + m_TaskList->GetSegmentation(current).string());
+
+ if (m_TaskList->HasLabelName(current))
+ stringList << QString::fromStdString("<b>Label name:</b> " + m_TaskList->GetLabelName(current));
+
+ if (m_TaskList->HasLabelNameSuggestions(current))
+ stringList << QString::fromStdString("<b>Label name suggestions:</b> " + m_TaskList->GetLabelNameSuggestions(current).string());
+
+ if (m_TaskList->HasPreset(current))
+ stringList << QString::fromStdString("<b>Label set preset:</b> " + m_TaskList->GetPreset(current).string());
+
+ if (m_TaskList->HasDynamic(current))
+ stringList << QString("<b>Segmentation type:</b> %1").arg(m_TaskList->GetDynamic(current) ? "Dynamic" : "Static");
+
+ if (!stringList.empty())
+ details += QString("<p>%1</p>").arg(stringList.join(QStringLiteral("<br>")));
+
+ m_Ui->detailsLabel->setText(details);
+}
+
+/* Load/activate the currently displayed task. Unload all data nodes from
+ * previously active tasks first, but spare and reuse the image if possible.
+ */
+void QmitkSegmentationTaskListWidget::OnLoadButtonClicked()
+{
+ if (!this->HandleUnsavedChanges() || m_UnsavedChanges)
+ return;
+
+ m_Ui->loadButton->setEnabled(false);
+
+ QApplication::setOverrideCursor(Qt::BusyCursor);
+ this->LoadTask(this->GetImageDataNode(m_CurrentTaskIndex.value()));
+ QApplication::restoreOverrideCursor();
+}
+
+/* If present, return the image data node for the task with the specified
+ * index. Otherwise, return nullptr.
+ */
+mitk::DataNode* QmitkSegmentationTaskListWidget::GetImageDataNode(size_t index) const
+{
+ const auto imagePath = m_TaskList->GetAbsolutePath(m_TaskList->GetImage(index));
+
+ auto imageNodes = GetDataStorage()->GetDerivations(m_TaskListNode, mitk::NodePredicateFunction::New([imagePath](const mitk::DataNode* node) {
+ return imagePath == GetInputLocation(node->GetData());
+ }));
+
+ return !imageNodes->empty()
+ ? imageNodes->front()
+ : nullptr;
+}
+
+/* If present, return the segmentation data node for the task with the
+ * specified index. Otherwise, return nullptr.
+ */
+mitk::DataNode* QmitkSegmentationTaskListWidget::GetSegmentationDataNode(size_t index) const
+{
+ const auto* imageNode = this->GetImageDataNode(index);
+
+ if (imageNode != nullptr)
+ {
+ auto segmentations = GetDataStorage()->GetDerivations(imageNode, mitk::TNodePredicateDataType<mitk::LabelSetImage>::New());
+
+ if (!segmentations->empty())
+ return segmentations->front();
+ }
+
+ return nullptr;
+}
+
+/* Unload all task data nodes but spare the passed image data node.
+ */
+void QmitkSegmentationTaskListWidget::UnloadTasks(const mitk::DataNode* skip)
+{
+ this->UnsubscribeFromActiveSegmentation();
+
+ if (m_TaskListNode.IsNotNull())
+ {
+ mitk::DataStorage::Pointer dataStorage = GetDataStorage();
+
+ auto imageNodes = dataStorage->GetDerivations(m_TaskListNode, mitk::TNodePredicateDataType<mitk::Image>::New());
+
+ for (auto imageNode : *imageNodes)
+ {
+ dataStorage->Remove(dataStorage->GetDerivations(imageNode, nullptr, false));
+
+ if (imageNode != skip)
+ dataStorage->Remove(imageNode);
+ }
+ }
+
+ this->SetActiveTaskIndex(std::nullopt);
+}
+
+/* Load/activate the currently displayed task. The task must specify
+ * an image. The segmentation is either created from scratch with an optional
+ * name for the first label, possibly based on a label set preset specified by
+ * the task, or loaded as specified by the task. If a result file does
+ * exist, it is chosen as segmentation instead.
+ */
+void QmitkSegmentationTaskListWidget::LoadTask(mitk::DataNode::Pointer imageNode)
+{
+ this->UnloadTasks(imageNode);
+
+ const auto current = m_CurrentTaskIndex.value();
+
+ mitk::Image::Pointer image;
+ mitk::LabelSetImage::Pointer segmentation;
+
+ try
+ {
+ if (imageNode.IsNull())
+ {
+ const auto path = m_TaskList->GetAbsolutePath(m_TaskList->GetImage(current));
+ image = mitk::IOUtil::Load<mitk::Image>(path.string());
+ }
+
+ const auto path = m_TaskList->GetAbsolutePath(m_TaskList->GetResult(current));
+
+ if (std::filesystem::exists(path))
+ {
+ segmentation = mitk::IOUtil::Load<mitk::LabelSetImage>(path.string());
+ }
+ else if (m_TaskList->HasSegmentation(current))
+ {
+ const auto path = m_TaskList->GetAbsolutePath(m_TaskList->GetSegmentation(current));
+ segmentation = mitk::IOUtil::Load<mitk::LabelSetImage>(path.string());
+ }
+ }
+ catch (const mitk::Exception&)
+ {
+ return;
+ }
+
+ auto dataStorage = GetDataStorage();
+
+ if (imageNode.IsNull())
+ {
+ imageNode = mitk::DataNode::New();
+ imageNode->SetData(image);
+
+ dataStorage->Add(imageNode, m_TaskListNode);
+
+ mitk::RenderingManager::GetInstance()->InitializeViews(image->GetTimeGeometry());
+ }
+ else
+ {
+ image = static_cast<mitk::Image*>(imageNode->GetData());
+ }
+
+ auto name = "Task " + std::to_string(current + 1);
+ imageNode->SetName(name);
+
+ if (segmentation.IsNull())
+ {
+ mitk::Image::ConstPointer templateImage = image;
+
+ if (templateImage->GetDimension() > 3)
+ {
+ if (m_TaskList->HasDynamic(current))
+ {
+ if (!m_TaskList->GetDynamic(current))
+ templateImage = mitk::SegmentationHelper::GetStaticSegmentationTemplate(image);
+ }
+ else
+ {
+ QmitkStaticDynamicSegmentationDialog dialog(this);
+ dialog.SetReferenceImage(templateImage);
+ dialog.exec();
+
+ templateImage = dialog.GetSegmentationTemplate();
+ }
+ }
+
+ auto segmentationNode = mitk::LabelSetImageHelper::CreateNewSegmentationNode(imageNode, templateImage, name);
+ segmentation = static_cast<mitk::LabelSetImage*>(segmentationNode->GetData());
+
+ if (m_TaskList->HasPreset(current))
+ {
+ const auto path = m_TaskList->GetAbsolutePath(m_TaskList->GetPreset(current));
+ mitk::LabelSetIOHelper::LoadLabelSetImagePreset(path.string(), segmentation);
+ }
+ else
+ {
+ auto label = mitk::LabelSetImageHelper::CreateNewLabel(segmentation);
+
+ if (m_TaskList->HasLabelName(current))
+ label->SetName(m_TaskList->GetLabelName(current));
+
+ segmentation->GetActiveLabelSet()->AddLabel(label);
+ }
+
+ dataStorage->Add(segmentationNode, imageNode);
+ }
+ else
+ {
+ auto segmentationNode = mitk::DataNode::New();
+ segmentationNode->SetName(name);
+ segmentationNode->SetData(segmentation);
+
+ dataStorage->Add(segmentationNode, imageNode);
+ }
+
+ auto prefs = GetSegmentationPreferences();
+
+ if (prefs.IsNotNull())
+ {
+ if (m_TaskList->HasLabelNameSuggestions(current))
+ {
+ auto path = m_TaskList->GetAbsolutePath(m_TaskList->GetLabelNameSuggestions(current));
+
+ prefs->PutBool("default label naming", false);
+ prefs->Put("label suggestions", QString::fromStdString(path.string()));
+ prefs->PutBool("replace standard suggestions", true);
+ prefs->PutBool("suggest once", true);
+ }
+ else
+ {
+ prefs->PutBool("default label naming", true);
+ prefs->Put("label suggestions", "");
+ }
+ }
+
+ m_UnsavedChanges = false;
+
+ this->SetActiveTaskIndex(current);
+ this->SubscribeToActiveSegmentation();
+
+ this->OnCurrentTaskChanged();
+}
+
+void QmitkSegmentationTaskListWidget::SubscribeToActiveSegmentation()
+{
+ if (m_ActiveTaskIndex.has_value())
+ {
+ auto segmentationNode = this->GetSegmentationDataNode(m_ActiveTaskIndex.value());
+
+ if (segmentationNode != nullptr)
+ {
+ auto segmentation = static_cast<mitk::LabelSetImage*>(segmentationNode->GetData());
+
+ auto command = itk::SimpleMemberCommand<QmitkSegmentationTaskListWidget>::New();
+ command->SetCallbackFunction(this, &QmitkSegmentationTaskListWidget::OnSegmentationModified);
+
+ m_SegmentationModifiedObserverTag = segmentation->AddObserver(itk::ModifiedEvent(), command);
+ }
+ }
+}
+
+void QmitkSegmentationTaskListWidget::UnsubscribeFromActiveSegmentation()
+{
+ if (m_ActiveTaskIndex.has_value() && m_SegmentationModifiedObserverTag.has_value())
+ {
+ auto segmentationNode = this->GetSegmentationDataNode(m_ActiveTaskIndex.value());
+
+ if (segmentationNode != nullptr)
+ {
+ auto segmentation = static_cast<mitk::LabelSetImage*>(segmentationNode->GetData());
+ segmentation->RemoveObserver(m_SegmentationModifiedObserverTag.value());
+ }
+
+ m_SegmentationModifiedObserverTag.reset();
+ }
+}
+
+void QmitkSegmentationTaskListWidget::OnSegmentationModified()
+{
+ if (!m_UnsavedChanges)
+ {
+ m_UnsavedChanges = true;
+
+ if (m_ActiveTaskIndex.value() == m_CurrentTaskIndex)
+ this->UpdateDetailsLabel();
+ }
+}
+
+void QmitkSegmentationTaskListWidget::SetActiveTaskIndex(const std::optional<size_t>& index)
+{
+ if (m_ActiveTaskIndex != index)
+ {
+ m_ActiveTaskIndex = index;
+ emit ActiveTaskChanged(m_ActiveTaskIndex);
+ }
+}
+
+void QmitkSegmentationTaskListWidget::SetCurrentTaskIndex(const std::optional<size_t>& index)
+{
+ if (m_CurrentTaskIndex != index)
+ {
+ m_CurrentTaskIndex = index;
+ this->OnCurrentTaskChanged();
+ emit CurrentTaskChanged(m_CurrentTaskIndex);
+ }
+}
+
+bool QmitkSegmentationTaskListWidget::ActiveTaskIsShown() const
+{
+ return m_ActiveTaskIndex.has_value() && m_CurrentTaskIndex.has_value() && m_ActiveTaskIndex == m_CurrentTaskIndex;
+}
+
+bool QmitkSegmentationTaskListWidget::HandleUnsavedChanges()
+{
+ if (m_UnsavedChanges)
+ {
+ const auto active = m_ActiveTaskIndex.value();
+ const auto current = m_CurrentTaskIndex.value();
+
+ auto title = QString("Load task %1").arg(current + 1);
+
+ if (m_TaskList->HasName(current))
+ title += ": " + QString::fromStdString(m_TaskList->GetName(current));
+
+ auto text = QString("The currently active task %1 ").arg(active + 1);
+
+ if (m_TaskList->HasName(active))
+ text += "(" + QString::fromStdString(m_TaskList->GetName(active)) + ") ";
+
+ text += "has unsaved changes.";
+
+ auto reply = QMessageBox::question(this, title, text, QMessageBox::Save | QMessageBox::Discard | QMessageBox::Cancel, QMessageBox::Cancel);
+
+ switch (reply)
+ {
+ case QMessageBox::Save:
+ this->SaveActiveTask();
+ break;
+
+ case QMessageBox::Discard:
+ m_UnsavedChanges = false;
+ break;
+
+ default:
+ return false;
+ }
+ }
+
+ return true;
+}
+
+void QmitkSegmentationTaskListWidget::SaveActiveTask()
+{
+ if (!m_ActiveTaskIndex.has_value())
+ return;
+
+ QApplication::setOverrideCursor(Qt::BusyCursor);
+
+ try
+ {
+ const auto active = m_ActiveTaskIndex.value();
+ m_TaskList->SaveTask(active, this->GetSegmentationDataNode(active)->GetData());
+ this->OnUnsavedChangesSaved();
+ }
+ catch (const mitk::Exception& e)
+ {
+ MITK_ERROR << e;
+ }
+
+ QApplication::restoreOverrideCursor();
+}
diff --git a/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationTaskListWidget.h b/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationTaskListWidget.h
new file mode 100644
index 0000000000..f1cf781021
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationTaskListWidget.h
@@ -0,0 +1,87 @@
+/*============================================================================
+
+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 QmitkSegmentationTaskListWidget_h
+#define QmitkSegmentationTaskListWidget_h
+
+#include <mitkSegmentationTaskList.h>
+
+#include <MitkSegmentationUIExports.h>
+
+#include <QmitkSingleNodeSelectionWidget.h>
+
+#include <QWidget>
+
+#include <optional>
+
+class QFileSystemWatcher;
+
+namespace Ui
+{
+ class QmitkSegmentationTaskListWidget;
+}
+
+class QmitkSegmentationTaskListWidget : public QWidget
+{
+ Q_OBJECT
+
+public:
+ explicit QmitkSegmentationTaskListWidget(QWidget* parent = nullptr);
+ ~QmitkSegmentationTaskListWidget() override;
+
+ mitk::SegmentationTaskList* GetTaskList() const;
+ std::optional<size_t> GetActiveTaskIndex() const;
+ std::optional<size_t> GetCurrentTaskIndex() const;
+ mitk::DataNode* GetSegmentationDataNode(size_t index) const;
+ void OnUnsavedChangesSaved();
+ bool ActiveTaskIsShown() const;
+
+signals:
+ void ActiveTaskChanged(const std::optional<size_t>& index);
+ void CurrentTaskChanged(const std::optional<size_t>& index);
+
+private:
+ void OnSelectionChanged(const QmitkSingleNodeSelectionWidget::NodeList& nodes);
+ void ResetControls();
+ void SetTaskList(mitk::SegmentationTaskList* task);
+ void ResetFileSystemWatcher();
+ void OnResultDirectoryChanged(const QString&);
+ void UpdateProgressBar();
+ void OnTaskListChanged(mitk::SegmentationTaskList* task);
+ void OnPreviousButtonClicked();
+ void OnNextButtonClicked();
+ void OnCurrentTaskChanged();
+ void UpdateLoadButton();
+ void UpdateDetailsLabel();
+ void OnLoadButtonClicked();
+ mitk::DataNode* GetImageDataNode(size_t index) const;
+ void UnloadTasks(const mitk::DataNode* skip = nullptr);
+ void LoadTask(mitk::DataNode::Pointer imageNode = nullptr);
+ void SubscribeToActiveSegmentation();
+ void UnsubscribeFromActiveSegmentation();
+ void OnSegmentationModified();
+ void SetActiveTaskIndex(const std::optional<size_t>& index);
+ void SetCurrentTaskIndex(const std::optional<size_t>& index);
+ bool HandleUnsavedChanges();
+ void SaveActiveTask();
+
+ Ui::QmitkSegmentationTaskListWidget* m_Ui;
+ QFileSystemWatcher* m_FileSystemWatcher;
+ mitk::SegmentationTaskList::Pointer m_TaskList;
+ mitk::DataNode::Pointer m_TaskListNode;
+ std::optional<size_t> m_CurrentTaskIndex;
+ std::optional<size_t> m_ActiveTaskIndex;
+ std::optional<unsigned long> m_SegmentationModifiedObserverTag;
+ bool m_UnsavedChanges;
+};
+
+#endif
diff --git a/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationTaskListWidget.ui b/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationTaskListWidget.ui
new file mode 100644
index 0000000000..db3f206306
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationTaskListWidget.ui
@@ -0,0 +1,150 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>QmitkSegmentationTaskListWidget</class>
+ <widget class="QWidget" name="QmitkSegmentationTaskListWidget">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>299</width>
+ <height>329</height>
+ </rect>
+ </property>
+ <property name="title" stdset="0">
+ <string>Segmentation Task List</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout_2">
+ <property name="leftMargin">
+ <number>0</number>
+ </property>
+ <property name="topMargin">
+ <number>0</number>
+ </property>
+ <property name="rightMargin">
+ <number>0</number>
+ </property>
+ <property name="bottomMargin">
+ <number>0</number>
+ </property>
+ <item>
+ <widget class="QGroupBox" name="groupBox">
+ <property name="title">
+ <string>Segmentation Task List</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout">
+ <item>
+ <widget class="QmitkSingleNodeSelectionWidget" name="selectionWidget" native="true">
+ <property name="minimumSize">
+ <size>
+ <width>0</width>
+ <height>40</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QProgressBar" name="progressBar">
+ <property name="minimumSize">
+ <size>
+ <width>0</width>
+ <height>40</height>
+ </size>
+ </property>
+ <property name="value">
+ <number>0</number>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignCenter</set>
+ </property>
+ <property name="format">
+ <string/>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout">
+ <item>
+ <widget class="QToolButton" name="previousButton">
+ <property name="minimumSize">
+ <size>
+ <width>40</width>
+ <height>40</height>
+ </size>
+ </property>
+ <property name="toolTip">
+ <string>Previous subtask</string>
+ </property>
+ <property name="arrowType">
+ <enum>Qt::LeftArrow</enum>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="loadButton">
+ <property name="minimumSize">
+ <size>
+ <width>0</width>
+ <height>40</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Load subtask</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QToolButton" name="nextButton">
+ <property name="minimumSize">
+ <size>
+ <width>40</width>
+ <height>40</height>
+ </size>
+ </property>
+ <property name="toolTip">
+ <string>Next subtask</string>
+ </property>
+ <property name="arrowType">
+ <enum>Qt::RightArrow</enum>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <widget class="QLabel" name="detailsLabel">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="MinimumExpanding">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="text">
+ <string/>
+ </property>
+ <property name="textFormat">
+ <enum>Qt::RichText</enum>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop</set>
+ </property>
+ <property name="wordWrap">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ <customwidgets>
+ <customwidget>
+ <class>QmitkSingleNodeSelectionWidget</class>
+ <extends>QWidget</extends>
+ <header location="global">QmitkSingleNodeSelectionWidget.h</header>
+ <container>1</container>
+ </customwidget>
+ </customwidgets>
+ <resources/>
+ <connections/>
+</ui>
diff --git a/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/org_mitk_gui_qt_flow_segmentation_Activator.cpp b/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/org_mitk_gui_qt_flow_segmentation_Activator.cpp
index 692c89b6b7..963fa8b0ee 100644
--- a/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/org_mitk_gui_qt_flow_segmentation_Activator.cpp
+++ b/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/org_mitk_gui_qt_flow_segmentation_Activator.cpp
@@ -1,38 +1,55 @@
/*============================================================================
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_flow_segmentation_Activator.h"
#include "QmitkSegmentationFlowControlView.h"
#include "perspectives/QmitkFlowSegmentationPerspective.h"
+#include <mitkNodePredicateDataType.h>
+#include <mitkSegmentationTaskList.h>
+
+#include <QmitkNodeDescriptorManager.h>
+#include <QmitkStyleManager.h>
+
ctkPluginContext* org_mitk_gui_qt_flow_segmentation_Activator::m_Context = nullptr;
void org_mitk_gui_qt_flow_segmentation_Activator::start(ctkPluginContext* context)
{
BERRY_REGISTER_EXTENSION_CLASS(QmitkSegmentationFlowControlView, context)
BERRY_REGISTER_EXTENSION_CLASS(QmitkFlowSegmentationPerspective, context);
+ auto* descriptorManager = QmitkNodeDescriptorManager::GetInstance();
+
+ if (descriptorManager != nullptr)
+ {
+ auto icon = QmitkStyleManager::ThemeIcon(QStringLiteral(":/SegmentationTaskList/Icon.svg"));
+ auto predicate = mitk::TNodePredicateDataType<mitk::SegmentationTaskList>::New();
+ auto* descriptor = new QmitkNodeDescriptor("SegmentationTaskList", icon, predicate, descriptorManager);
+
+ descriptorManager->AddDescriptor(descriptor);
+ }
+
m_Context = context;
}
void org_mitk_gui_qt_flow_segmentation_Activator::stop(ctkPluginContext* context)
{
Q_UNUSED(context)
m_Context = nullptr;
}
ctkPluginContext* org_mitk_gui_qt_flow_segmentation_Activator::GetContext()
{
return m_Context;
}
diff --git a/Plugins/org.mitk.gui.qt.flowapplication/src/internal/QmitkFlowApplicationPlugin.cpp b/Plugins/org.mitk.gui.qt.flowapplication/src/internal/QmitkFlowApplicationPlugin.cpp
index cd487ca748..e045321fa6 100644
--- a/Plugins/org.mitk.gui.qt.flowapplication/src/internal/QmitkFlowApplicationPlugin.cpp
+++ b/Plugins/org.mitk.gui.qt.flowapplication/src/internal/QmitkFlowApplicationPlugin.cpp
@@ -1,199 +1,81 @@
/*============================================================================
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 "QmitkFlowApplicationPlugin.h"
#include "QmitkFlowApplication.h"
-#include <service/cm/ctkConfigurationAdmin.h>
-#include <service/cm/ctkConfiguration.h>
-
-#include <berryPlatform.h>
-#include <berryPlatformUI.h>
-#include <berryIPreferencesService.h>
-#include <berryIPreferences.h>
-
-#include <mitkVersion.h>
-#include <mitkLogMacros.h>
-
-#include <mitkIDataStorageService.h>
-#include <mitkSceneIO.h>
-#include <mitkProgressBar.h>
-#include <mitkRenderingManager.h>
-#include <mitkIOUtil.h>
+#include <berryMacros.h>
#include <QtWidgetsExtRegisterClasses.h>
-#include <QProcess>
-#include <QMainWindow>
-#include <QCoreApplication>
-
+#include <service/cm/ctkConfigurationAdmin.h>
QmitkFlowApplicationPlugin* QmitkFlowApplicationPlugin::inst = nullptr;
QmitkFlowApplicationPlugin::QmitkFlowApplicationPlugin()
+ : _context(nullptr)
{
inst = this;
}
QmitkFlowApplicationPlugin::~QmitkFlowApplicationPlugin()
{
}
QmitkFlowApplicationPlugin* QmitkFlowApplicationPlugin::GetDefault()
{
return inst;
}
void QmitkFlowApplicationPlugin::start(ctkPluginContext* context)
{
berry::AbstractUICTKPlugin::start(context);
this->_context = context;
QtWidgetsExtRegisterClasses();
BERRY_REGISTER_EXTENSION_CLASS(QmitkFlowApplication, context);
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
if (configAdmin)
{
ctkConfigurationPtr conf = configAdmin->getConfiguration("org.blueberry.services.help", QString());
ctkDictionary helpProps;
helpProps.insert("homePage", "qthelp://org.mitk.gui.qt.flowapplication/bundle/index.html");
conf->update(helpProps);
context->ungetService(cmRef);
}
else
{
MITK_WARN << "Configuration Admin service unavailable, cannot set home page url.";
}
-
- if (qApp->metaObject()->indexOfSignal("messageReceived(QByteArray)") > -1)
- {
- connect(qApp, SIGNAL(messageReceived(QByteArray)), this, SLOT(handleIPCMessage(QByteArray)));
- }
-
- // This is a potentially long running operation.
- loadDataFromDisk(berry::Platform::GetApplicationArgs(), true);
}
void QmitkFlowApplicationPlugin::stop(ctkPluginContext* context)
{
Q_UNUSED(context)
this->_context = nullptr;
}
ctkPluginContext* QmitkFlowApplicationPlugin::GetPluginContext() const
{
return _context;
}
-
-void QmitkFlowApplicationPlugin::loadDataFromDisk(const QStringList &arguments, bool globalReinit)
-{
- if (!arguments.empty())
- {
- ctkServiceReference serviceRef = _context->getServiceReference<mitk::IDataStorageService>();
- if (serviceRef)
- {
- mitk::IDataStorageService* dataStorageService = _context->getService<mitk::IDataStorageService>(serviceRef);
- mitk::DataStorage::Pointer dataStorage = dataStorageService->GetDefaultDataStorage()->GetDataStorage();
-
- int argumentsAdded = 0;
- for (int i = 0; i < arguments.size(); ++i)
- {
- if (arguments[i].right(5) == ".mitk")
- {
- mitk::SceneIO::Pointer sceneIO = mitk::SceneIO::New();
-
- bool clearDataStorageFirst(false);
- mitk::ProgressBar::GetInstance()->AddStepsToDo(2);
- dataStorage = sceneIO->LoadScene(arguments[i].toLocal8Bit().constData(), dataStorage, clearDataStorageFirst);
- mitk::ProgressBar::GetInstance()->Progress(2);
- argumentsAdded++;
- }
- else if (arguments[i].right(15) == ".mitksceneindex")
- {
- mitk::SceneIO::Pointer sceneIO = mitk::SceneIO::New();
-
- bool clearDataStorageFirst(false);
- mitk::ProgressBar::GetInstance()->AddStepsToDo(2);
- dataStorage = sceneIO->LoadSceneUnzipped(arguments[i].toLocal8Bit().constData(), dataStorage, clearDataStorageFirst);
- mitk::ProgressBar::GetInstance()->Progress(2);
- argumentsAdded++;
- }
- else
- {
- try
- {
- const std::string path(arguments[i].toStdString());
- auto addedNodes = mitk::IOUtil::Load(path, *dataStorage);
-
- for (const auto& node : *addedNodes)
- {
- node->SetIntProperty("layer", argumentsAdded);
- }
-
- argumentsAdded++;
- }
- catch (...)
- {
- MITK_WARN << "Failed to load command line argument: " << arguments[i].toStdString();
- }
- }
- } // end for each command line argument
-
- if (argumentsAdded > 0 && globalReinit)
- {
- // calculate bounding geometry
- mitk::RenderingManager::GetInstance()->InitializeViews(dataStorage->ComputeBoundingGeometry3D());
- }
- }
- else
- {
- MITK_ERROR << "A service reference for mitk::IDataStorageService does not exist";
- }
- }
-}
-
-void QmitkFlowApplicationPlugin::handleIPCMessage(const QByteArray& msg)
-{
- QDataStream ds(msg);
- QString msgType;
- ds >> msgType;
-
- // we only handle messages containing command line arguments
- if (msgType != "$cmdLineArgs") return;
-
- // activate the current workbench window
- berry::IWorkbenchWindow::Pointer window =
- berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow();
-
- QMainWindow* mainWindow =
- static_cast<QMainWindow*> (window->GetShell()->GetControl());
-
- mainWindow->setWindowState(mainWindow->windowState() & ~Qt::WindowMinimized);
- mainWindow->raise();
- mainWindow->activateWindow();
-
- QStringList args;
- ds >> args;
-
- loadDataFromDisk(args, false);
-}
diff --git a/Plugins/org.mitk.gui.qt.flowapplication/src/internal/QmitkFlowApplicationPlugin.h b/Plugins/org.mitk.gui.qt.flowapplication/src/internal/QmitkFlowApplicationPlugin.h
index b2cb08a37c..f8016f359a 100644
--- a/Plugins/org.mitk.gui.qt.flowapplication/src/internal/QmitkFlowApplicationPlugin.h
+++ b/Plugins/org.mitk.gui.qt.flowapplication/src/internal/QmitkFlowApplicationPlugin.h
@@ -1,57 +1,46 @@
/*============================================================================
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 QMITKFLOWAPPLICATIONLICATIONPLUGIN_H_
#define QMITKFLOWAPPLICATIONLICATIONPLUGIN_H_
#include <berryAbstractUICTKPlugin.h>
#include <QString>
class QmitkFlowApplicationPlugin : public berry::AbstractUICTKPlugin
{
Q_OBJECT
Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_flowapplication")
Q_INTERFACES(ctkPluginActivator)
public:
QmitkFlowApplicationPlugin();
~QmitkFlowApplicationPlugin() override;
static QmitkFlowApplicationPlugin* GetDefault();
ctkPluginContext* GetPluginContext() const;
void start(ctkPluginContext*) override;
void stop(ctkPluginContext* context) override;
- QString GetQtHelpCollectionFile() const;
-
-private:
-
- void loadDataFromDisk(const QStringList& args, bool globalReinit);
- void startNewInstance(const QStringList& args, const QStringList &files);
-
-private Q_SLOTS:
-
- void handleIPCMessage(const QByteArray &msg);
-
private:
static QmitkFlowApplicationPlugin* inst;
ctkPluginContext* _context;
};
#endif /* QMITKFLOWAPPLICATIONLICATIONPLUGIN_H_ */
diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.cpp
index 02ed890382..845bc60741 100644
--- a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.cpp
+++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.cpp
@@ -1,317 +1,311 @@
/*============================================================================
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 "QmitkNewSegmentationDialog.h"
#include <ui_QmitkNewSegmentationDialog.h>
#include <mitkAnatomicalStructureColorPresets.h>
#include <mitkBaseApplication.h>
#include <mitkLabelSetImage.h>
#include <berryIPreferences.h>
#include <berryIPreferencesService.h>
#include <berryPlatform.h>
#include <algorithm>
#include <iterator>
#include <vtkNew.h>
#include <QColorDialog>
-#include <QCompleter>
#include <QPushButton>
-#include <QStringListModel>
#include <nlohmann/json.hpp>
namespace
{
// Get standard label name and color suggestions from embedded XML preset file for anatomical structures.
QmitkNewSegmentationDialog::SuggestionsType GetStandardSuggestions()
{
QmitkNewSegmentationDialog::SuggestionsType standardSuggestions;
vtkNew<mitk::AnatomicalStructureColorPresets> presets;
presets->LoadPreset();
for (const auto& preset : presets->GetColorPresets())
{
auto name = QString::fromStdString(preset.first);
auto color = QColor::fromRgbF(preset.second.GetRed(), preset.second.GetGreen(), preset.second.GetBlue());
standardSuggestions.emplace(name, color);
}
return standardSuggestions;
}
// Parse label name and color suggestions from a JSON file. An array of objects is expected, each consisting
// of a "name" string and an optional "color" string. If present, the "color" string must follow the conventions
// of QColor::setNamedColor(), i.e., #rrggbb or any SVG color keyword name like CornflowerBlue. Everything else
// in the JSON file is simply ignored. In case of any error, an empty map is returned.
QmitkNewSegmentationDialog::SuggestionsType ParseSuggestions(const std::string& filename)
{
std::ifstream file(filename);
if (!file.is_open())
{
MITK_ERROR << "Could not open \"" << filename << "\"!";
return {};
}
auto json = nlohmann::json::parse(file, nullptr, false);
if (json.is_discarded() || !json.is_array())
{
MITK_ERROR << "Could not parse \"" << filename << "\" as JSON array!";
return {};
}
QmitkNewSegmentationDialog::SuggestionsType parsedSuggestions;
for (const auto& obj : json)
{
if (!obj.is_object() || !obj.contains("name"))
continue;
auto name = QString::fromStdString(obj["name"]);
QColor color(QColor::Invalid);
if (obj.contains("color"))
color.setNamedColor(QString::fromStdString(obj["color"]));
parsedSuggestions.emplace(name, color);
}
if (parsedSuggestions.empty())
MITK_WARN << "Could not parse any suggestions from \"" << filename << "\"!";
return parsedSuggestions;
}
struct Preferences
{
QString labelSuggestions;
bool replaceStandardSuggestions;
bool suggestOnce;
};
// Get all relevant preferences and consider command-line arguments overrides.
Preferences GetPreferences()
{
auto nodePrefs = berry::Platform::GetPreferencesService()->GetSystemPreferences()->Node("/org.mitk.views.segmentation");
Preferences prefs;
prefs.labelSuggestions = QString::fromStdString(mitk::BaseApplication::instance().config().getString(mitk::BaseApplication::ARG_SEGMENTATION_LABEL_SUGGESTIONS.toStdString(), ""));
if (prefs.labelSuggestions.isEmpty())
prefs.labelSuggestions = nodePrefs->Get("label suggestions", "");
prefs.replaceStandardSuggestions = nodePrefs->GetBool("replace standard suggestions", true);
prefs.suggestOnce = nodePrefs->GetBool("suggest once", true);
return prefs;
}
// Get names of all labels in all layers of a LabelSetImage.
QStringList GetExistingLabelNames(mitk::LabelSetImage* labelSetImage)
{
QStringList existingLabelNames;
existingLabelNames.reserve(labelSetImage->GetTotalNumberOfLabels());
const auto numLayers = labelSetImage->GetNumberOfLayers();
for (std::remove_const_t<decltype(numLayers)> layerIndex = 0; layerIndex < numLayers; ++layerIndex)
{
const auto* labelSet = labelSetImage->GetLabelSet(layerIndex);
for (auto labelIter = labelSet->IteratorConstBegin(); labelIter != labelSet->IteratorConstEnd(); ++labelIter)
{
if (0 == labelIter->first)
continue; // Ignore background label
auto name = QString::fromStdString(labelIter->second->GetName());
if (!name.isEmpty()) // Potential duplicates do not matter for our purpose
existingLabelNames.push_back(name);
}
}
return existingLabelNames;
}
// Remove blacklisted suggestions.
QmitkNewSegmentationDialog::SuggestionsType FilterSuggestions(const QmitkNewSegmentationDialog::SuggestionsType& suggestions, const QStringList& blacklist)
{
QmitkNewSegmentationDialog::SuggestionsType filteredSuggestions;
std::remove_copy_if(suggestions.begin(), suggestions.end(), std::inserter(filteredSuggestions, filteredSuggestions.end()), [&blacklist](const auto& suggestion) {
return blacklist.contains(suggestion.first);
});
return filteredSuggestions;
}
}
QmitkNewSegmentationDialog::QmitkNewSegmentationDialog(QWidget *parent, mitk::LabelSetImage* labelSetImage, Mode mode)
: QDialog(parent),
m_Ui(new Ui::QmitkNewSegmentationDialog),
m_SuggestOnce(true),
m_Color(Qt::red)
{
m_Ui->setupUi(this);
if (RenameLabel == mode)
{
this->setWindowTitle("Rename Label");
m_Ui->label->setText("New name and color of the label");
m_Ui->buttonBox->button(QDialogButtonBox::Ok)->setText("Rename label");
}
else
{
m_Ui->buttonBox->button(QDialogButtonBox::Ok)->setText("Create label");
}
- auto* completer = new QCompleter(QStringList());
- completer->setCaseSensitivity(Qt::CaseInsensitive);
+ m_Ui->nameComboBox->setFocus();
- m_Ui->nameLineEdit->setCompleter(completer);
- m_Ui->nameLineEdit->setFocus();
-
- connect(completer, qOverload<const QString&>(&QCompleter::activated), this, qOverload<const QString&>(&QmitkNewSegmentationDialog::OnSuggestionSelected));
connect(m_Ui->colorButton, &QToolButton::clicked, this, &QmitkNewSegmentationDialog::OnColorButtonClicked);
+ connect(m_Ui->nameComboBox, &QComboBox::currentTextChanged, this, &QmitkNewSegmentationDialog::OnSuggestionSelected);
connect(m_Ui->buttonBox, &QDialogButtonBox::accepted, this, &QmitkNewSegmentationDialog::OnAccept);
this->UpdateColorButtonBackground();
auto prefs = GetPreferences();
if (!prefs.labelSuggestions.isEmpty())
{
auto suggestions = ParseSuggestions(prefs.labelSuggestions.toStdString());
this->SetSuggestions(suggestions, prefs.replaceStandardSuggestions && !suggestions.empty());
}
else
{
this->SetSuggestions(GetStandardSuggestions(), true);
}
if (nullptr != labelSetImage && prefs.suggestOnce)
{
auto existingLabelNames = GetExistingLabelNames(labelSetImage);
m_Suggestions = FilterSuggestions(m_Suggestions, existingLabelNames);
this->UpdateCompleterModel();
}
}
QmitkNewSegmentationDialog::~QmitkNewSegmentationDialog()
{
}
void QmitkNewSegmentationDialog::UpdateColorButtonBackground()
{
m_Ui->colorButton->setStyleSheet("background-color:" + m_Color.name());
}
QString QmitkNewSegmentationDialog::GetName() const
{
return m_Name;
}
mitk::Color QmitkNewSegmentationDialog::GetColor() const
{
mitk::Color color;
if (m_Color.isValid())
{
color.SetRed(m_Color.redF());
color.SetGreen(m_Color.greenF());
color.SetBlue(m_Color.blueF());
}
else
{
color.Set(1.0f, 0.0f, 0.0f);
}
return color;
}
void QmitkNewSegmentationDialog::SetName(const QString& name)
{
- m_Ui->nameLineEdit->setText(name);
+ m_Ui->nameComboBox->setEditText(name);
}
void QmitkNewSegmentationDialog::SetColor(const mitk::Color& color)
{
m_Color.setRgbF(color.GetRed(), color.GetGreen(), color.GetBlue());
this->UpdateColorButtonBackground();
}
void QmitkNewSegmentationDialog::SetSuggestions(const SuggestionsType& suggestions, bool replaceStandardSuggestions)
{
if (replaceStandardSuggestions)
{
m_Suggestions = suggestions;
}
else
{
m_Suggestions = GetStandardSuggestions();
for (const auto& [name, color] : suggestions)
{
if (m_Suggestions.end() == m_Suggestions.find(name))
m_Suggestions[name] = color;
}
}
this->UpdateCompleterModel();
}
void QmitkNewSegmentationDialog::UpdateCompleterModel()
{
QStringList names;
for (const auto& suggestion : m_Suggestions)
names << suggestion.first;
- auto* completerModel = static_cast<QStringListModel*>(m_Ui->nameLineEdit->completer()->model());
- completerModel->setStringList(names);
+ m_Ui->nameComboBox->clear();
+ m_Ui->nameComboBox->addItems(names);
}
void QmitkNewSegmentationDialog::OnAccept()
{
- m_Name = m_Ui->nameLineEdit->text();
+ m_Name = m_Ui->nameComboBox->currentText();
this->accept();
}
void QmitkNewSegmentationDialog::OnColorButtonClicked()
{
auto color = QColorDialog::getColor(m_Color);
if (color.isValid())
{
m_Color = color;
this->UpdateColorButtonBackground();
}
}
void QmitkNewSegmentationDialog::OnSuggestionSelected(const QString &name)
{
auto color = m_Suggestions[name];
if (color.isValid())
{
m_Color = color;
this->UpdateColorButtonBackground();
}
}
diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.ui b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.ui
index ae71e75c55..d75e20262c 100644
--- a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.ui
+++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.ui
@@ -1,98 +1,105 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>QmitkNewSegmentationDialog</class>
<widget class="QDialog" name="QmitkNewSegmentationDialog">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>250</width>
<height>105</height>
</rect>
</property>
<property name="windowTitle">
<string>Create Label</string>
</property>
<layout class="QVBoxLayout" name="verticalLayout">
<item>
<layout class="QGridLayout" name="gridLayout">
<item row="0" column="0" colspan="2">
<widget class="QLabel" name="label">
<property name="text">
<string>Name and color of the label</string>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QToolButton" name="colorButton">
<property name="text">
<string/>
</property>
</widget>
</item>
<item row="1" column="1">
- <widget class="QLineEdit" name="nameLineEdit"/>
+ <widget class="QComboBox" name="nameComboBox">
+ <property name="editable">
+ <bool>true</bool>
+ </property>
+ <property name="insertPolicy">
+ <enum>QComboBox::NoInsert</enum>
+ </property>
+ </widget>
</item>
</layout>
</item>
<item>
<spacer name="verticalSpacer">
<property name="orientation">
<enum>Qt::Vertical</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>20</width>
<height>40</height>
</size>
</property>
</spacer>
</item>
<item>
<widget class="QDialogButtonBox" name="buttonBox">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="standardButtons">
<set>QDialogButtonBox::Cancel|QDialogButtonBox::Ok</set>
</property>
</widget>
</item>
</layout>
</widget>
<resources/>
<connections>
<connection>
<sender>buttonBox</sender>
<signal>accepted()</signal>
<receiver>QmitkNewSegmentationDialog</receiver>
<slot>accept()</slot>
<hints>
<hint type="sourcelabel">
<x>248</x>
<y>254</y>
</hint>
<hint type="destinationlabel">
<x>157</x>
<y>274</y>
</hint>
</hints>
</connection>
<connection>
<sender>buttonBox</sender>
<signal>rejected()</signal>
<receiver>QmitkNewSegmentationDialog</receiver>
<slot>reject()</slot>
<hints>
<hint type="sourcelabel">
<x>316</x>
<y>260</y>
</hint>
<hint type="destinationlabel">
<x>286</x>
<y>274</y>
</hint>
</hints>
</connection>
</connections>
</ui>