diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox
index 7d38e016f0..3d89a0f0dd 100644
--- a/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox
+++ b/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox
@@ -1,32 +1,33 @@
/**
\page PluginListGeneralPage List of General Purpose Plugins
\li \subpage org_mitk_views_basicimageprocessing
\li \subpage org_mitk_views_datamanager
\li \subpage org_mitk_views_properties
\li \subpage org_mitk_editors_dicombrowser
\li \subpage org_mitk_views_dicominspector
\li \subpage org_mitk_views_imagecropper
\li \subpage org_mitk_views_imagenavigator
\li \subpage org_blueberry_views_logview
\li \subpage org_mitk_gui_qt_matchpoint_algorithm_batch
\li \subpage org_mitk_views_matchpoint_algorithm_browser
\li \subpage org_mitk_views_matchpoint_algorithm_control
\li \subpage org_mitk_views_matchpoint_evaluator
\li \subpage org_mitk_views_matchpoint_framereg
\li \subpage org_mitk_views_matchpoint_manipulator
\li \subpage org_mitk_views_matchpoint_mapper
\li \subpage org_mitk_views_matchpoint_visualizer
\li \subpage org_mitk_gui_qt_measurementtoolbox
\li \subpage org_mitk_views_moviemaker
\li \subpage org_mitk_views_multilabelsegmentation
\li \subpage org_mitk_views_pointsetinteraction
\li \subpage org_mitk_views_python
\li \subpage org_mitk_views_qt_remeshing
\li \subpage org_mitk_views_screenshotmaker
\li \subpage org_mitk_views_segmentation
+ \li \subpage org_mitk_views_deformableclippingplane
\li \subpage org_mitk_gui_qt_flow_segmentation
\li \subpage org_mitk_views_viewnavigatorview
\li \subpage org_mitk_views_volumevisualization
*/
diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox
index 2bcc3ca505..be3c4b4319 100644
--- a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox
+++ b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox
@@ -1,82 +1,83 @@
/**
\page PluginListPage MITK Plugin Manuals
The plugins and bundles provide much of the extended functionality of MITK. Each encapsulates a solution to a problem and associated features. This way one can easily assemble the necessary capabilites for a workflow without adding a lot of bloat, by combining plugins as needed.
\subpage PluginListGeneralPage
<ul>
<li> \ref org_mitk_views_basicimageprocessing </li>
<li> \ref org_mitk_views_datamanager </li>
<li> \ref org_mitk_editors_dicombrowser </li>
<li> \ref org_mitk_views_dicominspector </li>
<li> \ref org_mitk_views_imagecropper </li>
<li> \ref org_mitk_views_imagenavigator </li>
<li> \ref org_blueberry_views_logview </li>
<li> \ref org_mitk_views_matchpoint_algorithm_browser </li>
<li> \ref org_mitk_views_matchpoint_algorithm_control </li>
<li> \ref org_mitk_views_matchpoint_evaluator </li>
<li> \ref org_mitk_views_matchpoint_framereg </li>
<li> \ref org_mitk_views_matchpoint_manipulator </li>
<li> \ref org_mitk_views_matchpoint_mapper </li>
<li> \ref org_mitk_views_matchpoint_visualizer </li>
<li> \ref org_mitk_views_measurement </li>
<li> \ref org_mitk_views_imagestatistics </li>
<li> \ref org_mitk_views_moviemaker </li>
<li> \ref org_mitk_views_multilabelsegmentation </li>
<li> \ref org_mitk_views_pointsetinteraction </li>
<li> \ref org_mitk_views_python </li>
<li> \ref org_mitk_views_remeshing </li>
<li> \ref org_mitk_views_screenshotmaker </li>
<li> \ref org_mitk_views_segmentation </li>
+ <li> \ref org_mitk_views_deformableclippingplane </li>
<li> \ref org_mitk_views_viewnavigatorview </li>
<li> \ref org_mitk_views_volumevisualization </li>
<li> \ref org_mitk_views_properties </li>
</ul>
\subpage PluginListSpecificPage
<ul>
<li> \ref org_mitk_gui_qt_flowapplication </li>
<li> \ref org_mitk_views_flow_control </li>
<li> \ref org_mitk_gui_qt_aicpregistration </li>
<li> \ref org_mitk_gui_qt_cest </li>
<li> \ref org_mitk_gui_qt_classificationsegmentation </li>
<li> \ref org_mitk_views_cmdlinemodules </li>
<li> \ref org_mitk_views_pharmacokinetics_concentration_mri </li>
<li> \ref org_mitk_views_pharmacokinetics_mri </li>
<li> \ref org_mitk_views_pharmacokinetics_pet </li>
<li> \ref org_mitk_gui_qt_eventrecorder </li>
<li> \ref org_mitk_gui_qt_examples </li>
<li> \ref org_mitk_gui_qt_geometrytools </li>
<li> \ref org_mitk_gui_qt_igtexample </li>
<li> \ref org_mitk_gui_qt_igtlplugin </li>
<li> \ref org_mitk_gui_qt_igttracking </li>
<li> \ref org_mitk_views_igttrackingsemiautomaticmeasurement </li>
<li> \ref org_mitk_gui_qt_lasercontrol </li>
<li> \ref org_mitk_views_fit_demo </li>
<li> \ref org_mitk_views_fit_genericfitting </li>
<li> \ref org_mitk_views_fit_inspector </li>
<li> \ref org_mitkexamplesopencv </li>
<li> \ref org_mitk_gui_qt_overlaymanager </li>
<li> \ref org_mitk_gui_qt_mitkphenotyping </li>
<li> \ref org_mitk_gui_qt_photoacoustics_pausmotioncompensation </li>
<li> \ref org_mitk_example_gui_pcaexample </li>
<li> \ref org_mitk_gui_qt_preprocessing_resampling </li>
<li> \ref org_mitk_views_pharmacokinetics_curvedescriptor </li>
<li> \ref org_mitk_views_photoacoustics_imageprocessing </li>
<li> \ref org_mitk_gui_qt_pharmacokinetics_simulation </li>
<li> \ref org_mitk_gui_qt_pointsetinteractionmultispectrum </li>
<li> \ref org_mitk_gui_qt_renderwindowmanager </li>
<li> \ref org_mitk_gui_qt_photoacoustics_spectralunmixing </li>
<li> \ref org_mitk_gui_qt_spectrocamrecorder </li>
<li> \ref org_surfacematerialeditor </li>
<li> \ref org_toftutorial </li>
<li> \ref org_blueberry_ui_qt_objectinspector </li>
<li> \ref org_mitk_gui_qt_ultrasound </li>
<li> \ref org_mitk_gui_qt_igt_app_echotrack </li>
<li> \ref org_mitk_gui_qt_xnat </li>
</ul>
*/
diff --git a/Plugins/PluginList.cmake b/Plugins/PluginList.cmake
index a0899b3787..0d16bd73bc 100644
--- a/Plugins/PluginList.cmake
+++ b/Plugins/PluginList.cmake
@@ -1,96 +1,97 @@
# Plug-ins must be ordered according to their dependencies
set(MITK_PLUGINS
org.blueberry.core.runtime:ON
org.blueberry.core.expressions:OFF
org.blueberry.core.commands:OFF
org.blueberry.core.jobs:OFF
org.blueberry.ui.qt:OFF
org.blueberry.ui.qt.help:ON
org.blueberry.ui.qt.log:ON
org.blueberry.ui.qt.objectinspector:OFF
org.mitk.core.services:ON
org.mitk.gui.common:ON
org.mitk.planarfigure:ON
org.mitk.core.ext:OFF
org.mitk.core.jobs:OFF
org.mitk.gui.qt.application:ON
org.mitk.gui.qt.ext:OFF
org.mitk.gui.qt.extapplication:OFF
org.mitk.gui.qt.mitkworkbench.intro:OFF
org.mitk.gui.qt.common:ON
org.mitk.gui.qt.stdmultiwidgeteditor:ON
org.mitk.gui.qt.mxnmultiwidgeteditor:OFF
org.mitk.gui.qt.common.legacy:OFF
org.mitk.gui.qt.cmdlinemodules:OFF
org.mitk.gui.qt.chartExample:OFF
org.mitk.gui.qt.datamanager:ON
org.mitk.gui.qt.datamanagerlight:OFF
org.mitk.gui.qt.datastorageviewertest:OFF
org.mitk.gui.qt.properties:ON
org.mitk.gui.qt.basicimageprocessing:OFF
org.mitk.gui.qt.dicombrowser:OFF
org.mitk.gui.qt.dicominspector:OFF
org.mitk.gui.qt.dosevisualization:OFF
org.mitk.gui.qt.geometrytools:OFF
org.mitk.gui.qt.igtexamples:OFF
org.mitk.gui.qt.igttracking:OFF
org.mitk.gui.qt.lasercontrol:OFF
org.mitk.gui.qt.openigtlink:OFF
org.mitk.gui.qt.imagecropper:OFF
org.mitk.gui.qt.imagenavigator:ON
org.mitk.gui.qt.viewnavigator:OFF
org.mitk.gui.qt.materialeditor:OFF
org.mitk.gui.qt.measurementtoolbox:OFF
org.mitk.gui.qt.moviemaker:OFF
org.mitk.gui.qt.pointsetinteraction:OFF
org.mitk.gui.qt.pointsetinteractionmultispectrum:OFF
org.mitk.gui.qt.python:OFF
org.mitk.gui.qt.remeshing:OFF
org.mitk.gui.qt.segmentation:OFF
+ org.mitk.gui.qt.deformableclippingplane:OFF
org.mitk.gui.qt.aicpregistration:OFF
org.mitk.gui.qt.renderwindowmanager:OFF
org.mitk.gui.qt.semanticrelations:OFF
org.mitk.gui.qt.toftutorial:OFF
org.mitk.gui.qt.tofutil:OFF
org.mitk.gui.qt.tubegraph:OFF
org.mitk.gui.qt.ugvisualization:OFF
org.mitk.gui.qt.photoacoustics.pausviewer:OFF
org.mitk.gui.qt.photoacoustics.pausmotioncompensation:OFF
org.mitk.gui.qt.photoacoustics.imageprocessing:OFF
org.mitk.gui.qt.photoacoustics.simulation:OFF
org.mitk.gui.qt.photoacoustics.spectralunmixing:OFF
org.mitk.gui.qt.ultrasound:OFF
org.mitk.gui.qt.volumevisualization:OFF
org.mitk.gui.qt.eventrecorder:OFF
org.mitk.gui.qt.xnat:OFF
org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation:OFF
org.mitk.gui.qt.spectrocamrecorder:OFF
org.mitk.gui.qt.classificationsegmentation:OFF
org.mitk.gui.qt.overlaymanager:OFF
org.mitk.gui.qt.igt.app.hummelprotocolmeasurements:OFF
org.mitk.gui.qt.multilabelsegmentation:OFF
org.mitk.matchpoint.core.helper:OFF
org.mitk.gui.qt.matchpoint.algorithm.browser:OFF
org.mitk.gui.qt.matchpoint.algorithm.control:OFF
org.mitk.gui.qt.matchpoint.mapper:OFF
org.mitk.gui.qt.matchpoint.framereg:OFF
org.mitk.gui.qt.matchpoint.visualizer:OFF
org.mitk.gui.qt.matchpoint.evaluator:OFF
org.mitk.gui.qt.matchpoint.manipulator:OFF
org.mitk.gui.qt.preprocessing.resampling:OFF
org.mitk.gui.qt.radiomics:OFF
org.mitk.gui.qt.cest:OFF
org.mitk.gui.qt.fit.demo:OFF
org.mitk.gui.qt.fit.inspector:OFF
org.mitk.gui.qt.fit.genericfitting:OFF
org.mitk.gui.qt.pharmacokinetics.mri:OFF
org.mitk.gui.qt.pharmacokinetics.pet:OFF
org.mitk.gui.qt.pharmacokinetics.simulation:OFF
org.mitk.gui.qt.pharmacokinetics.curvedescriptor:OFF
org.mitk.gui.qt.pharmacokinetics.concentration.mri:OFF
org.mitk.gui.qt.flowapplication:OFF
org.mitk.gui.qt.flow.segmentation:OFF
)
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/CMakeLists.txt b/Plugins/org.mitk.gui.qt.deformableclippingplane/CMakeLists.txt
new file mode 100644
index 0000000000..8dd1c33292
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.deformableclippingplane/CMakeLists.txt
@@ -0,0 +1,6 @@
+project(org_mitk_gui_qt_deformableclippingplane)
+
+mitk_create_plugin(
+ EXPORT_DIRECTIVE DEFORMABLECLIPPINGPLANE_EXPORT
+ EXPORTED_INCLUDE_SUFFIXES src
+)
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkClippingPlane.dox b/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane.dox
similarity index 100%
rename from Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkClippingPlane.dox
rename to Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane.dox
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkClippingPlane_DataManager.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_DataManager.png
similarity index 100%
rename from Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkClippingPlane_DataManager.png
rename to Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_DataManager.png
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkClippingPlane_Icon.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Icon.png
similarity index 100%
rename from Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkClippingPlane_Icon.png
rename to Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Icon.png
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkClippingPlane_Interaction.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Interaction.png
similarity index 100%
rename from Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkClippingPlane_Interaction.png
rename to Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Interaction.png
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkClippingPlane_Overview.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Overview.png
similarity index 100%
rename from Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkClippingPlane_Overview.png
rename to Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Overview.png
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkClippingPlane_Overview2.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Overview2.png
similarity index 100%
rename from Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkClippingPlane_Overview2.png
rename to Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Overview2.png
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkClippingPlane_UpdateVolumina.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_UpdateVolumina.png
similarity index 100%
rename from Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkClippingPlane_UpdateVolumina.png
rename to Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_UpdateVolumina.png
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/files.cmake b/Plugins/org.mitk.gui.qt.deformableclippingplane/files.cmake
new file mode 100644
index 0000000000..d6fb308c8c
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.deformableclippingplane/files.cmake
@@ -0,0 +1,21 @@
+set(CPP_FILES
+ src/internal/QmitkDeformableClippingPlaneView.cpp
+ src/internal/mitkPluginActivator.cpp
+)
+
+set(MOC_H_FILES
+ src/internal/mitkPluginActivator.h
+ src/internal/QmitkDeformableClippingPlaneView.h
+)
+
+set(UI_FILES
+ src/internal/QmitkDeformableClippingPlaneViewControls.ui
+)
+
+set(CACHED_RESOURCE_FILES
+ resources/deformablePlane.png
+ resources/clipping_plane_translate_48x48.png
+ resources/clipping_plane_rotate48x48.png
+ resources/clipping_plane_deform48x48.png
+ plugin.xml
+)
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.deformableclippingplane/manifest_headers.cmake
new file mode 100644
index 0000000000..92f1980c68
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.deformableclippingplane/manifest_headers.cmake
@@ -0,0 +1,5 @@
+set(Plugin-Name "Clipping Plane")
+set(Plugin-Version "1.0.0")
+set(Plugin-Vendor "German Cancer Research Center (DKFZ)")
+set(Plugin-ContactAddress "http://www.mitk.org")
+set(Require-Plugin org.mitk.gui.qt.common org.mitk.gui.qt.datamanager)
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/plugin.xml b/Plugins/org.mitk.gui.qt.deformableclippingplane/plugin.xml
new file mode 100644
index 0000000000..7a6337fade
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.deformableclippingplane/plugin.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<plugin>
+ <extension point="org.blueberry.ui.views">
+ <view id="org.mitk.views.deformableclippingplane"
+ name="Clipping Plane"
+ category="Segmentation"
+ class="QmitkDeformableClippingPlaneView"
+ icon="resources/deformablePlane.png">
+ <description>Allow the clipping of a volume using a deformable plane.</description>
+ <keywordReference id="org.mitk.views.deformableclippingplane.ViewKeyword" />
+ </view>
+ </extension>
+ <extension point="org.blueberry.ui.keywords">
+ <keyword id="org.mitk.views.deformableclippingplane.ViewKeyword" label="Plane" />
+ <keyword id="org.mitk.views.deformableclippingplane.ViewKeyword" label="Volumne calculation" />
+ <keyword id="org.mitk.views.deformableclippingplane.ViewKeyword" label="Splitting" />
+ <keyword id="org.mitk.views.deformableclippingplane.ViewKeyword" label="Deformation" />
+ <keyword id="org.mitk.views.deformableclippingplane.ViewKeyword" label="Volume analysis" />
+ </extension>
+</plugin>
diff --git a/Plugins/org.mitk.gui.qt.segmentation/resources/clipping_plane_deform48x48.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_deform48x48.png
similarity index 100%
rename from Plugins/org.mitk.gui.qt.segmentation/resources/clipping_plane_deform48x48.png
rename to Plugins/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_deform48x48.png
diff --git a/Plugins/org.mitk.gui.qt.segmentation/resources/clipping_plane_rotate48x48.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_rotate48x48.png
similarity index 100%
rename from Plugins/org.mitk.gui.qt.segmentation/resources/clipping_plane_rotate48x48.png
rename to Plugins/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_rotate48x48.png
diff --git a/Plugins/org.mitk.gui.qt.segmentation/resources/clipping_plane_translate_48x48.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_translate_48x48.png
similarity index 100%
rename from Plugins/org.mitk.gui.qt.segmentation/resources/clipping_plane_translate_48x48.png
rename to Plugins/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_translate_48x48.png
diff --git a/Plugins/org.mitk.gui.qt.segmentation/resources/deformablePlane.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/resources/deformablePlane.png
similarity index 100%
rename from Plugins/org.mitk.gui.qt.segmentation/resources/deformablePlane.png
rename to Plugins/org.mitk.gui.qt.deformableclippingplane/resources/deformablePlane.png
diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkDeformableClippingPlaneView.cpp b/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneView.cpp
similarity index 100%
rename from Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkDeformableClippingPlaneView.cpp
rename to Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneView.cpp
diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkDeformableClippingPlaneView.h b/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneView.h
similarity index 100%
rename from Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkDeformableClippingPlaneView.h
rename to Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneView.h
diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkDeformableClippingPlaneViewControls.ui b/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneViewControls.ui
similarity index 94%
rename from Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkDeformableClippingPlaneViewControls.ui
rename to Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneViewControls.ui
index 0130bd6153..f19a2edcc3 100644
--- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkDeformableClippingPlaneViewControls.ui
+++ b/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneViewControls.ui
@@ -1,431 +1,429 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>QmitkDeformableClippingPlaneViewControls</class>
<widget class="QWidget" name="QmitkDeformableClippingPlaneViewControls">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>300</width>
<height>600</height>
</rect>
</property>
<property name="minimumSize">
<size>
<width>0</width>
<height>0</height>
</size>
</property>
<property name="windowTitle">
<string>Deformable surface</string>
</property>
<layout class="QVBoxLayout">
<item>
<layout class="QGridLayout" name="gridLayout">
<item row="0" column="0">
<widget class="QLabel" name="imageSelectionLabel">
<property name="text">
<string>Selected image</string>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QmitkSingleNodeSelectionWidget" name="imageSelectionWidget" native="true">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>0</width>
<height>40</height>
</size>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget class="QGroupBox" name="planeGroupBox">
<property name="checkable">
<bool>false</bool>
</property>
<property name="checked">
<bool>false</bool>
</property>
<layout class="QVBoxLayout" name="verticalLayout">
<item>
<layout class="QHBoxLayout" name="horizontalLayout_1">
<item>
<widget class="QPushButton" name="createNewPlanePushButton">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="text">
<string>Create new clipping plane</string>
</property>
</widget>
</item>
<item>
<widget class="QCheckBox" name="surfaceModelCheckBox">
<property name="layoutDirection">
<enum>Qt::RightToLeft</enum>
</property>
<property name="text">
<string>...with surface model</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
</layout>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_2">
<item>
<widget class="QLabel" name="clippingPlaneSelectorLabel">
<property name="sizePolicy">
<sizepolicy hsizetype="Maximum" vsizetype="Preferred">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>0</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>16777215</width>
<height>16777215</height>
</size>
</property>
<property name="text">
<string>Plane</string>
</property>
</widget>
</item>
<item>
<widget class="QmitkDataStorageComboBox" name="clippingPlaneSelector">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="sizeAdjustPolicy">
<enum>QComboBox::AdjustToMinimumContentsLength</enum>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget class="QGroupBox" name="interactionSelectionBox">
<property name="enabled">
<bool>true</bool>
</property>
<property name="font">
<font>
<weight>50</weight>
<bold>false</bold>
</font>
</property>
<layout class="QHBoxLayout" name="horizontalLayout_3">
<item>
<widget class="QPushButton" name="translationPushButton">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Preferred">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>20</width>
<height>50</height>
</size>
</property>
<property name="toolTip">
<string>Translation</string>
</property>
<property name="text">
<string/>
</property>
<property name="icon">
<iconset>
- <normaloff>:/org.mitk.gui.qt.segmentation/resources/clipping_plane_translate_48x48.png</normaloff>:/org.mitk.gui.qt.segmentation/resources/clipping_plane_translate_48x48.png</iconset>
+ <normaloff>:/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_translate_48x48.png</normaloff>:/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_translate_48x48.png</iconset>
</property>
<property name="iconSize">
<size>
<width>32</width>
<height>32</height>
</size>
</property>
<property name="checkable">
<bool>true</bool>
</property>
<property name="autoRepeat">
<bool>false</bool>
</property>
<property name="autoExclusive">
<bool>false</bool>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="rotationPushButton">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Preferred">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>20</width>
<height>50</height>
</size>
</property>
<property name="toolTip">
<string>Rotation</string>
</property>
<property name="text">
<string/>
</property>
<property name="icon">
<iconset>
- <normaloff>:/org.mitk.gui.qt.segmentation/resources/clipping_plane_rotate48x48.png</normaloff>:/org.mitk.gui.qt.segmentation/resources/clipping_plane_rotate48x48.png</iconset>
+ <normaloff>:/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_rotate48x48.png</normaloff>:/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_rotate48x48.png</iconset>
</property>
<property name="iconSize">
<size>
<width>32</width>
<height>32</height>
</size>
</property>
<property name="checkable">
<bool>true</bool>
</property>
<property name="autoExclusive">
<bool>false</bool>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="deformationPushButton">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Preferred">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>20</width>
<height>50</height>
</size>
</property>
<property name="toolTip">
<string>Deformation</string>
</property>
<property name="text">
<string/>
</property>
<property name="icon">
<iconset>
- <normaloff>:/org.mitk.gui.qt.segmentation/resources/clipping_plane_deform48x48.png</normaloff>:/org.mitk.gui.qt.segmentation/resources/clipping_plane_deform48x48.png</iconset>
+ <normaloff>:/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_deform48x48.png</normaloff>:/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_deform48x48.png</iconset>
</property>
<property name="iconSize">
<size>
<width>32</width>
<height>32</height>
</size>
</property>
<property name="checkable">
<bool>true</bool>
</property>
<property name="autoExclusive">
<bool>false</bool>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item>
<spacer name="verticalSpacer">
<property name="orientation">
<enum>Qt::Vertical</enum>
</property>
<property name="sizeType">
<enum>QSizePolicy::Preferred</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>20</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
</layout>
</widget>
</item>
<item>
<widget class="QLabel" name="planesWarningLabel">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Maximum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="text">
<string>Please select less or equal 6 clipping planes!</string>
</property>
</widget>
</item>
<item>
<widget class="QGroupBox" name="volumeGroupBox">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="title">
<string/>
</property>
<layout class="QVBoxLayout" name="verticalLayout_5">
<item>
<layout class="QHBoxLayout" name="horizontalLayout">
<item>
<layout class="QVBoxLayout" name="verticalLayout_2">
<item>
<widget class="QLabel" name="referenceImageLabel">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="text">
<string>Referenced image</string>
</property>
</widget>
</item>
<item>
<widget class="QLabel" name="clippingPlanesLabel">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Expanding">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="text">
<string>Clipping planes</string>
</property>
<property name="alignment">
<set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop</set>
</property>
</widget>
</item>
</layout>
</item>
<item>
<layout class="QVBoxLayout" name="verticalLayout_4">
<item>
<widget class="QLabel" name="selectedReferenceImageLabel">
<property name="enabled">
<bool>true</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
</widget>
</item>
<item>
<widget class="QLabel" name="selectedClippingPlanesLabel">
<property name="font">
<font>
<pointsize>8</pointsize>
</font>
</property>
<property name="alignment">
<set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop</set>
</property>
</widget>
</item>
</layout>
</item>
</layout>
</item>
<item>
<widget class="QPushButton" name="updateVolumePushButton">
<property name="text">
<string>Update Volumina</string>
</property>
</widget>
</item>
<item>
<spacer name="verticalSpacer_2">
<property name="orientation">
<enum>Qt::Vertical</enum>
</property>
<property name="sizeType">
<enum>QSizePolicy::Preferred</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>20</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
<item>
<widget class="QListWidget" name="volumeList">
<property name="enabled">
<bool>true</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
</widget>
</item>
</layout>
</widget>
</item>
</layout>
</widget>
<layoutdefault spacing="6" margin="11"/>
<customwidgets>
<customwidget>
<class>QmitkSingleNodeSelectionWidget</class>
<extends>QWidget</extends>
<header location="global">QmitkSingleNodeSelectionWidget.h</header>
</customwidget>
<customwidget>
<class>QmitkDataStorageComboBox</class>
<extends>QComboBox</extends>
<header location="global">QmitkDataStorageComboBox.h</header>
</customwidget>
</customwidgets>
- <resources>
- <include location="../../../../../../bin/mitk_debug/MITK-build/Plugins/org.mitk.gui.qt.segmentation/org_mitk_gui_qt_segmentation_cached.qrc"/>
- </resources>
+ <resources/>
<connections/>
</ui>
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/mitkPluginActivator.cpp
new file mode 100644
index 0000000000..6fdaaa8cdd
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/mitkPluginActivator.cpp
@@ -0,0 +1,23 @@
+/*============================================================================
+
+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 "mitkPluginActivator.h"
+#include "QmitkDeformableClippingPlaneView.h"
+
+void mitk::PluginActivator::start(ctkPluginContext *context)
+{
+ BERRY_REGISTER_EXTENSION_CLASS(QmitkDeformableClippingPlaneView, context)
+}
+
+void mitk::PluginActivator::stop(ctkPluginContext *)
+{
+}
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/mitkPluginActivator.h
new file mode 100644
index 0000000000..6a85b014de
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/mitkPluginActivator.h
@@ -0,0 +1,32 @@
+/*============================================================================
+
+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 PluginActivator_h
+#define PluginActivator_h
+
+#include <ctkPluginActivator.h>
+
+namespace mitk
+{
+ class PluginActivator : public QObject, public ctkPluginActivator
+ {
+ Q_OBJECT
+ Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_deformableclippingplane")
+ Q_INTERFACES(ctkPluginActivator)
+
+ public:
+ void start(ctkPluginContext *context) override;
+ void stop(ctkPluginContext *context) override;
+ };
+}
+
+#endif
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox
index 835a75a74b..771ab561da 100644
--- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox
+++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox
@@ -1,300 +1,299 @@
/**
\page org_mitk_views_segmentation The Segmentation View
\imageMacro{segmentation.svg,"Icon of the segmentation view",2.00}
<i>Some of the features described below are closed source additions to the open source toolkit MITK and are not available in every application.</i>
\tableofcontents
\section org_mitk_views_segmentationUserManualOverview Overview
-Segmentation is the act of partitioning an image into subsets by either manual or automated delineation to create i.e. a distinction between foreground and background.
+Segmentation is the act of partitioning an image into subsets by either manual or automated delineation to create i.e. a distinction between foreground and background.
The MITK <b>segmentation plugin</b> allows you to create segmentations of anatomical and pathological structures in medical images.
The plugin consists of a number of views:
<ul>
<li> <b>Segmentation View</b>: Manual and (semi-)automatic segmentation
<li> \subpage org_mitk_views_segmentationutilities : Segmentation post-processing
- <li> \subpage org_mitk_views_deformableclippingplane : Clipping of existing segmentations using a resection plane
</ul>
In this documentation, the features and usage of the segmentation view will be described.
For an introduction to the segmentation utilities and clipping plane views, please be referred to the respective documentation pages.
\imageMacro{QmitkSegmentationPlugin_Overview.png,"Segmentation plugin overview", 16.00}
\section org_mitk_views_segmentationPreferences Preferences
The segmentation plugin offers a number of preferences which can be set via the MITK Workbench application preferences:
\imageMacro{QmitkSegmentationPreferences.png,"Segmentation preferences", 10.00}
<ul>
<li> <b>Slim view:</b> Allows you to show or hide the tool button description of the segmentation view
<li> <b>2D display:</b> Specify whether the segmentation is drawn as outline or as a transparent overlay
<li> <b>3D display:</b> Activate 3D volume rendering for your segmentation
<li> <b>Data node selection mode:</b> If activated the segmentation image is automatically chosen from the data manager selection.
<li> <b>Smoothed surface creation:</b> Set certain smoothing parameters for surface creation
</ul>
\section org_mitk_views_segmentationUserManualTechnical Technical Issues
The segmentation plugin makes a number of assumptions:
<ul>
<li> Images must be 2D, 3D, or 3D+t.
<li> Images must be single-values, i.e. CT, MRI or "normal" ultrasound. Images from color doppler or photographic (RGB) images are only partially supported (please be aware that some tools might not be compatible with this image type).
<li> Segmentations are handled as binary images of the same extent as the original image.
</ul>
\section org_mitk_views_segmentationUserManualImageSelection Data Selection & Creating New Segmentations
-To select a reference image for the segmentation, click on the <i>Patient Image</i> selection widget and choose a suitable image from the selection available in the data manager.
+To select a reference image for the segmentation, click on the <i>Patient Image</i> selection widget and choose a suitable image from the selection available in the data manager.
By default the auto selection mode is enabled (see \ref org_mitk_views_segmentationPreferences).\n
Once a patient image is selected, a new segmentation can be created on this reference image by clicking the <i>New...</i> button to the right of the <i>Segmentation</i> selection widget.
An input field will appear which allows you to set the name and display color of the segmentation. Notice that the input field suggests names once you start typing and that it also suggests colors for known organ names.
Once generated the segmentation will be added with "binary mask" icon to the data manager as sub-node of the reference image. This item is automatically selected for you, allowing you to start editing the new segmentation right away.
\subsection org_mitk_views_segmentationUserManualManualKringeling2 Selecting Segmentations for Editing
Alternatively to creating a new segmentation, an existing one can be edited as well.
As you might have segmented multiple structures within a single image, the application needs to know which of them to use for editing.
-For that you click the segmentation selection widget and a selection field will open, containing all suitable segmentations for the parent dataset available in the data manager.
+For that you click the segmentation selection widget and a selection field will open, containing all suitable segmentations for the parent dataset available in the data manager.
\section org_mitk_views_segmentationUserManualToolOverview Segmentation Tool Overview
MITK offers a comprehensive set of slice-based 2D and (semi-)automated 3D segmentation tools.
The manual 2D tools require some user interaction and can only be applied to a single image slice whereas the 3D tools operate on the whole image. The 3D tools usually only
require a small amount of user interaction, i.e. placing seed points or setting/adjusting parameters.
You can switch between the different toolsets by selecting the 2D or 3D tab in the segmentation view.
\imageMacro{QmitkSegmentation_ToolOverview.png,"An overview of the existing 2D and 3D tools in MITK.",5.50}
\section org_mitk_views_segmentationUserManualManualKringeling 2D Segmentation Tools
With 2D manual contouring you define which voxels are part of the segmentation and which ones are not. This allows you to create segmentations of any structures of interest in an image.
You can also use manual contouring to correct segmentations that result from sub-optimal automatic methods.
The drawback of manual contouring is that you might need to define contours on many 2D slices. However, this is mitigated by the interpolation feature, which will make suggestions for a segmentation.
\subsection org_mitk_views_segmentationUserManualManualKringeling3 Selecting Editing Tools
To start using one of the editing tools, click its button from the displayed toolbox.
The selected editing tool will be active and its corresponding button will stay pressed until you click the button again.
Selecting a different tool also deactivates the previous one.\n
If you have to delineate a lot of images, shortcuts to switch between tools becomes convenient. For that, just hit the first letter of each tool to activate it (A for Add, S for Subtract, etc.).
\subsection org_mitk_views_segmentationUserManualManualKringeling4 Using Editing Tools
All of the editing tools work by the same principle: you use the mouse (left button) to click anywhere in a 2D window (any of the orientations axial, sagittal, or coronal),
move the mouse while holding the mouse button and release to finish the editing action.
Multi-step undo and redo is fully supported by all editing tools. Use the application-wide undo button in the toolbar to revert erroneous %actions.
<i>Remark</i>: If you are familiar with the MITK Workbench, you know that clicking and moving the mouse in any of the 2D render windows will move around the crosshair that defines what part of the image is displayed.
This behavior is disabled whilst any of the manual segmentation tools are active- otherwise you might have a hard time concentrating on the contour you are drawing.
\subsection org_mitk_views_segmentationUserManualAddSubtractTools Add and Subtract Tools
\imageMacro{QmitkSegmentation_IMGIconAddSubtract.png,"Add and Subtract Tools",7.70}
-Use the left mouse button to draw a closed contour. When releasing the mouse button, the contour will be added (Add tool) to or removed (Subtract tool) from the current segmentation.
+Use the left mouse button to draw a closed contour. When releasing the mouse button, the contour will be added (Add tool) to or removed (Subtract tool) from the current segmentation.
Adding and subtracting voxels can be iteratively repeated for the same segmentation. Holding CTRL / CMD while drawing will invert the current tool's behavior (i.e. instead of adding voxels, they will be subtracted).
\subsection org_mitk_views_segmentationUserManualPaintWipeTools Paint and Wipe Tools
\imageMacro{QmitkSegmentation_IMGIconPaintWipe.png,"Paint and Wipe Tools",7.68}
Use the <i>Size</i> slider to change the radius of the round paintbrush tool. Move the mouse in any 2D window and press the left button to draw or erase pixels.
Holding CTRL / CMD while drawing will invert the current tool's behavior (i.e. instead of painting voxels, they will be wiped).
\subsection org_mitk_views_segmentationUserManualRegionGrowingTool Region Growing Tool
\imageMacro{QmitkSegmentation_IMGIconRegionGrowing.png,"Region Growing Tool",3.81}
-Click at one point in a 2D slice widget to add an image region to the segmentation with the region growing tool.
+Click at one point in a 2D slice widget to add an image region to the segmentation with the region growing tool.
Region Growing selects all pixels around the mouse cursor that have a similar gray value as the pixel below the mouse cursor. This enables you to quickly create segmentations of structures that have a good contrast to surrounding tissue.
The tool operates based on the current level window, so changing the level window to optimize the contrast for the ROI is encouraged.
Moving the mouse up/down is different from left/right: Moving up the cursor while holding the left mouse button widens the range for the included grey values; moving it down narrows it. Moving the mouse left and right will shift the range.
The tool will select more or less pixels, corresponding to the changing gray value range.
\if THISISNOTIMPLEMENTEDATTHEMOMENT
A common issue with region growing is the so called "leakage" which happens when the structure of interest is connected to other pixels, of similar gray values, through a narrow "bridge" at the border of the structure.
The Region Growing tool comes with a "leakage detection/removal" feature. If leakage happens, you can left-click into the leakage region and the tool will try to automatically remove this region (see illustration below).
\imageMacro{QmitkSegmentation_IMGLeakage.png,"Leakage correction feature of the Region Growing tool",11.28}
\endif
\subsection org_mitk_views_segmentationUserManualCorrectionTool Correction Tool
<br>
\imageMacro{QmitkSegmentation_IMGIconCorrection.png,"Correction Tool",3.77}
You do not have to draw a closed contour to use the Correction tool and do not need to switch between the Add and Substract tool to perform
small corrective changes. The following figure shows the usage of this tool:
<ul>
<li> a) If the user draws a line which %starts and ends outside the segmenation a part of it is cut off.
<li> b) If the line is drawn fully inside the segmentation the marked region is added to the segmentation.
</ul>
\imageMacro{QmitkSegmentation_IMGCorrectionActions.png,"Usage of the Correction tool.",13.50}
<br>
\subsection org_mitk_views_segmentationUserManualFillTool Fill Tool
\imageMacro{QmitkSegmentation_IMGIconFill.png,"Fill Tool",3.81}
Left-click inside a segmentation with holes to completely fill all holes. Left-click inside a hole to fill only this specific hole.
\subsection org_mitk_views_segmentationUserManualEraseTool Erase Tool
\imageMacro{QmitkSegmentation_IMGIconErase.png,"Erase Tool",3.79}
This tool removes a connected part of pixels that form a segmentation. You may use it to remove single segmentations (left-click on specific segmentation) or to clear a whole slice at once (left-click outside a segmentation).
\subsection org_mitk_views_segmentationUserManualLiveWireTool Live Wire Tool
\imageMacro{QmitkSegmentation_IMGIconLiveWire.png,"Live Wire Tool",3.01}
The Live Wire Tool acts as a magnetic lasso with a contour snapping to edges of objects.
\imageMacro{QmitkSegmentation_IMGLiveWireUsage.PNG,"Steps for using the Live Wire Tool",16.00}
<ul>
<li>(1) To start the tool you have to double-click near the edge of the object you want to segment. The initial anchor point will snap to the edge within a 3x3 region.
<li>(2) Move the mouse. You don't have trace the edge of the object. The contour will automatically snap to it.
<li>(3) To fix a segment you can set anchor points by single left mouse button click.
<li>(4) Go on with moving the mouse and setting anchor points.
<li>(5) To close the contour double-click on the initial anchor point.
<li>(6) After closing, the contour can be edited by moving, inserting and deleting anchor points.
</ul>
The contour will be transferred to its binary image representation by deactivating the tool.
\subsection org_mitk_views_segmentationUserManual2DFastMarchingTool 2D Fast Marching Tool
\imageMacro{QmitkSegmentation_IMG2DFastMarchingUsage.png,"2D Fast Marching Tool",3.01}
Provides a fast marching based 2D interaction segmentation tool. You start with setting seed points in an image slice. Via several sliders you can adapt parameters and see the fast marching result instantly.
\subsection org_mitk_views_segmentationUserManualManualKringeling5 2D and 3D Interpolation
Creating segmentations using 2D manual contouring for large image volumes may be very time-consuming, because structures of interest may cover a large range of slices.
The segmentation view offers two helpful features to mitigate this drawback:
<ul>
<li> 2D Interpolation
<li> 3D Interpolation
</ul>
The <b>2D Interpolation</b> creates suggestions for a segmentation whenever you have a slice that
<ul>
<li> has got neighboring slices with segmentations (these do not need to be direct neighbors but could also be a couple of slices away) AND
<li> is completely clear of a manual segmentation, i.e. there will be no suggestion if there is even only a single pixel of segmentation in the current slice.
</ul>
\imageMacro{QmitkSegmentation_2DInterpolation.png,"2D Interpolation Usage",3.01}
Interpolated suggestions are displayed as outlines, until you confirm them as part of the segmentation.
To confirm single slices, click the <i>Confirm for single slice</i> button below the toolbox. You may also review the interpolations visually and then accept all of them at once by selecting <i>Confirm for all slices</i>.
The <b>3D interpolation</b> creates suggestions for 3D segmentations. That means if you start contouring, from the second contour onwards, the surface of the segmented area will be interpolated based on the given contour information.
-The interpolation works with all available manual tools. Please note that this is currently a pure mathematical interpolation, i.e. image intensity information is not taken into account.
-With each further contour the interpolation result will be improved, but the more contours you provide the longer the recalculation will take.
+The interpolation works with all available manual tools. Please note that this is currently a pure mathematical interpolation, i.e. image intensity information is not taken into account.
+With each further contour the interpolation result will be improved, but the more contours you provide the longer the recalculation will take.
To achieve an optimal interpolation result and in this way a most accurate segmentation you should try to describe the surface with sparse contours by segmenting in arbitrary
oriented planes. The 3D interpolation is not meant to be used for parallel slice-wise segmentation, but rather segmentations in i.e. the axial, coronal and sagittal plane.
\imageMacro{QmitkSegmentation_3DInterpolationWrongRight.png,"3D Interpolation Usage",16.00}
You can accept the interpolation result by clicking the <i>Confirm</i>-button below the tool buttons.
In this case the 3D interpolation will be deactivated automatically so that the result can be post-processed without any interpolation running in the background.
Additional to the surface, black contours are shown in the 3D render window, which mark all the drawn contours used for the interpolation.
-You can navigate between the drawn contours by clicking on the corresponding <i>position</i> nodes in the data manager which are stored as sub-nodes of the selected segmentation.
+You can navigate between the drawn contours by clicking on the corresponding <i>position</i> nodes in the data manager which are stored as sub-nodes of the selected segmentation.
If you do not want to see these nodes just uncheck the <i>Show Position Nodes</i> checkbox and these nodes will be hidden.
If you want to delete a drawn contour we recommend to use the Erase-Tool since Redo/Undo is not yet working for 3D interpolation.
-The current state of the 3D interpolation can be saved across application restart. For that, just click on save project during the interpolation is active.
+The current state of the 3D interpolation can be saved across application restart. For that, just click on save project during the interpolation is active.
After restarting the application and load your project you can click on "Reinit Interpolation" within the 3D interpolation GUI area.
\section org_mitk_views_segmentationUserManual3DSegmentationTools 3D Segmentation Tools
The 3D tools operate on the whole image and require usually a small amount of interaction like placing seed-points or specifying certain parameters. All 3D tools provide
an immediate segmentation feedback, which is displayed as a transparent green overlay. For accepting a preview you have to press the <i>Confirm</i> button of the selected tool.
The following 3D tools are available:
\subsection org_mitk_views_segmentationUserManual3DThresholdTool 3D Threshold Tool
The thresholding tool simply applies a 3D threshold to the patient image. All pixels with values equal or above the selected threshold are labeled as part of the segmentation.
You can change the threshold by either moving the slider of setting a certain value in the spinbox.
\imageMacro{QmitkSegmentation_3DThresholdTool.png,"3D Threshold tool",10.00}
\subsection org_mitk_views_segmentationUserManual3DULTool 3D Upper/Lower Threshold Tool
The Upper/Lower Thresholding tool works similar to the simple 3D threshold tool but allows you to define an upper and lower threshold. All pixels with
values within this threshold interval will be labeled as part of the segmentation.
\imageMacro{QmitkSegmentation_3DULThresholdTool.png,"3D Upper/Lower Threshold tool",10.00}
\subsection org_mitk_views_segmentationUserManual3DOtsuTool 3D Otsu Tool
The 3D Otsu tool provides a more sophisticated thresholding algorithm. It allows you to define a number of regions. Based on the image histogram the pixels will
then be divided into different regions. The more regions you define the longer the calculation will take. You can select afterwards which of these regions you want to confirm as segmentation.
\imageMacro{QmitkSegmentation_3DOtsuTool.png,"3D Otsu tool",10.00}
\subsection org_mitk_views_segmentationUserManual3DFMTool 3D Fast Marching Tool
The 3D Fast Marching tool works similar to the 2D pendant but on the whole image. Depending on your image size the calculation might take some time.
You can interactively set the parameters of the algorithm via the GUI. The resulting segmentation will be automatically updated.
\imageMacro{QmitkSegmentation_3DFMTool.png,"3D Fast Marching tool",10.00}
\subsection org_mitk_views_segmentationUserManual3DRGTool 3D Region Growing Tool
The 3D Region Growing tool works similar to the 2D pendant. At the beginning you have to place a seedpoint and define a threshold interval. If you press
<i>Run Segmentation</i> a preview is calculated. By moving the <i>Adapt region growing</i> slider you can interactively adapt the segmentation result.
\imageMacro{QmitkSegmentation_3DRGTool.png,"3D Region Growing tool",10.00}
\subsection org_mitk_views_segmentationUserManual3DWatershedTool 3D Watershed Tool
This tool provides a watershed based segmentation algorithm. For a detailed explanation of the parameters level and threshold, please be referred to https://itk.org/Doxygen/html/classitk_1_1WatershedImageFilter.html .
Remark: The tool is (due to its implementation) faster if you use lower levels. So in doubt you should start with high levels (supposed to undersegment) and then lower the levels until you are happy.
\imageMacro{QmitkSegmentation_3DWatershedTool.png,"3D Watershed tool",10.00}
\subsection org_mitk_views_segmentationUserManualPickingTool Picking Tool
The Picking tool allows you to select islands within your segmentation. This is especially useful if e.g. a thresholding provided you with several areas within
your image but you are just interested in one special region.
\imageMacro{QmitkSegmentation_PickingTool.png,"Picking tool",10.00}
\section org_mitk_views_segmentationUserManualPostprocessing Additional things you can do with segmentations
Segmentations are never an end in themselves. Consequently, the segmentation view adds a couple of "post-processing" actions, accessible through the context-menu of the data manager.
\imageMacro{QmitkSegmentation_IMGDataManagerContextMenu.png,"Context menu items for segmentations.",10.58}
<ul>
<li> <b>Create polygon %model</b> applies the marching cubes algorithm to the segmentation. This polygon %model can be used for visualization in 3D or other applications such as stereolithography (3D printing).
<li> <b>Create smoothed polygon %model</b> uses smoothing in addition to the marching cubes algorithm, which creates models that do not follow the exact outlines of the segmentation, but look smoother.
<li> <b>Autocrop</b> can save memory. Manual segmentations have the same extent as the patient image, even if the segmentation comprises only a small sub-volume. This invisible and meaningless margin is removed by autocropping.
</ul>
\section org_mitk_views_segmentationof3DTImages Segmentation of 3D+t images
For segmentation of 3D+t images, some tools give you the option to choose between creating dynamic and static masks.
<ul>
<li> Dynamic masks can be created on each time frame individually.
<li> Static masks will be defined on one time frame and will be the same for all other time frames.
</ul>
In general, segmentation is applied on the time frame that is selected when execution is performed. If you alter the time frame, the segmentation preview is adapted.
\section org_mitk_views_segmentationUserManualTechnicalDetail Technical Information for Developers
For technical specifications see \subpage QmitkSegmentationTechnicalPage and for information on the extensions of the tools system \subpage toolextensions .
*/
diff --git a/Plugins/org.mitk.gui.qt.segmentation/files.cmake b/Plugins/org.mitk.gui.qt.segmentation/files.cmake
index ae0e49a418..dd452ef63f 100644
--- a/Plugins/org.mitk.gui.qt.segmentation/files.cmake
+++ b/Plugins/org.mitk.gui.qt.segmentation/files.cmake
@@ -1,81 +1,74 @@
set(SRC_CPP_FILES
QmitkSegmentationPreferencePage.cpp
)
set(INTERNAL_CPP_FILES
mitkPluginActivator.cpp
QmitkSegmentationView.cpp
QmitkThresholdAction.cpp
QmitkCreatePolygonModelAction.cpp
#QmitkStatisticsAction.cpp
QmitkAutocropAction.cpp
QmitkAutocropLabelSetImageAction.cpp
- QmitkDeformableClippingPlaneView.cpp
Common/QmitkDataSelectionWidget.cpp
SegmentationUtilities/QmitkSegmentationUtilitiesView.cpp
SegmentationUtilities/QmitkSegmentationUtilityWidget.cpp
SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidget.cpp
SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.cpp
SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.cpp
SegmentationUtilities/MorphologicalOperations/QmitkMorphologicalOperationsWidget.cpp
SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidget.cpp
)
set(UI_FILES
src/internal/QmitkSegmentationControls.ui
- src/internal/QmitkDeformableClippingPlaneViewControls.ui
src/internal/Common/QmitkDataSelectionWidgetControls.ui
src/internal/SegmentationUtilities/QmitkSegmentationUtilitiesViewControls.ui
src/internal/SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidgetControls.ui
src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui
src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidgetControls.ui
src/internal/SegmentationUtilities/MorphologicalOperations/QmitkMorphologicalOperationsWidgetControls.ui
src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidgetControls.ui
)
set(MOC_H_FILES
src/QmitkSegmentationPreferencePage.h
src/internal/mitkPluginActivator.h
src/internal/QmitkSegmentationView.h
src/internal/QmitkThresholdAction.h
src/internal/QmitkCreatePolygonModelAction.h
#src/internal/QmitkStatisticsAction.h
src/internal/QmitkAutocropAction.h
src/internal/QmitkAutocropLabelSetImageAction.h
- src/internal/QmitkDeformableClippingPlaneView.h
src/internal/Common/QmitkDataSelectionWidget.h
src/internal/SegmentationUtilities/QmitkSegmentationUtilitiesView.h
src/internal/SegmentationUtilities/QmitkSegmentationUtilityWidget.h
src/internal/SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidget.h
src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.h
src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.h
src/internal/SegmentationUtilities/MorphologicalOperations/QmitkMorphologicalOperationsWidget.h
src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidget.h
)
set(CACHED_RESOURCE_FILES
resources/segmentation.svg
- resources/deformablePlane.png
- resources/clipping_plane_translate_48x48.png
- resources/clipping_plane_rotate48x48.png
- resources/clipping_plane_deform48x48.png
resources/segmentation_utilities.svg
plugin.xml
)
set(QRC_FILES
resources/segmentation.qrc
resources/SegmentationUtilities.qrc
resources/BooleanOperationsWidget.qrc
resources/MorphologicalOperationsWidget.qrc
)
set(CPP_FILES)
foreach(file ${SRC_CPP_FILES})
set(CPP_FILES ${CPP_FILES} src/${file})
endforeach(file ${SRC_CPP_FILES})
foreach(file ${INTERNAL_CPP_FILES})
set(CPP_FILES ${CPP_FILES} src/internal/${file})
endforeach(file ${INTERNAL_CPP_FILES})
diff --git a/Plugins/org.mitk.gui.qt.segmentation/plugin.xml b/Plugins/org.mitk.gui.qt.segmentation/plugin.xml
index 24f382cdeb..a72db4b004 100644
--- a/Plugins/org.mitk.gui.qt.segmentation/plugin.xml
+++ b/Plugins/org.mitk.gui.qt.segmentation/plugin.xml
@@ -1,94 +1,80 @@
<?xml version="1.0" encoding="UTF-8"?>
<?eclipse version="3.0"?>
<plugin>
<extension point="org.blueberry.ui.views">
<view id="org.mitk.views.segmentation"
name="Segmentation"
category="Segmentation"
icon="resources/segmentation.svg"
class="QmitkSegmentationView" >
<description>Allows the segmentation of images using different tools.</description>
<keywordReference id="org.mitk.views.segmentation.ViewKeyword"/>
- </view>
- <view id="org.mitk.views.deformableclippingplane"
- name="Clipping Plane"
- category="Segmentation"
- class="QmitkDeformableClippingPlaneView"
- icon="resources/deformablePlane.png" >
- <description>Allow the clipping of a volume using a deformable plane.</description>
- <keywordReference id="org.mitk.views.deformableclippingplane.ViewKeyword"/>
</view>
<view
id="org.mitk.views.segmentationutilities"
name="Segmentation Utilities"
category="Segmentation"
class="QmitkSegmentationUtilitiesView"
icon="resources/segmentation_utilities.svg" >
<description>Edit segmentations using standard operations. </description>
<keywordReference id="org.mitk.views.segmentationutilities.ViewKeyword"/>
</view>
</extension>
<extension point="org.blueberry.ui.preferencePages">
<page id="org.mitk.gui.qt.application.SegmentationPreferencePage" name="Segmentation" class="QmitkSegmentationPreferencePage">
<keywordreference id="org.mitk.gui.qt.application.SegmentationPreferencePageKeywords"></keywordreference>
</page>
</extension>
<extension point="org.blueberry.ui.keywords">
<keyword id="org.mitk.gui.qt.application.SegmentationPreferencePageKeywords" label="data manager"></keyword>
</extension>
<extension point="org.mitk.gui.qt.datamanager.contextMenuActions">
<contextMenuAction nodeDescriptorName="ImageMask" label="Create polygon model" icon="" smoothed="false" class="QmitkCreatePolygonModelAction" />
<contextMenuAction nodeDescriptorName="ImageMask" label="Create smoothed polygon model" icon="" smoothed = "true" class="QmitkCreatePolygonModelAction" />
<contextMenuAction nodeDescriptorName="ImageMask" label="Autocrop" icon="" class="QmitkAutocropAction" />
<contextMenuAction nodeDescriptorName="LabelSetImage" label="Create polygon model" icon="" smoothed="false" class="QmitkCreatePolygonModelAction" />
<contextMenuAction nodeDescriptorName="LabelSetImage" label="Create smoothed polygon model" icon="" smoothed = "true" class="QmitkCreatePolygonModelAction" />
<contextMenuAction nodeDescriptorName="LabelSetImage" label="Autocrop" icon="" class="QmitkAutocropLabelSetImageAction" />
</extension>
<extension point="org.blueberry.ui.keywords">
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Segmentation" />
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Otsu" />
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Correction" />
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Paint" />
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Wipe" />
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Region Growing" />
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Fill" />
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Erase" />
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Live Wire" />
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Fast Marching" />
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Threshold" />
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Watershed" />
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Picking" />
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Watershed" />
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Annotation annote" />
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Labeling" />
<keyword id="org.mitk.views.segmentation.ViewKeyword" label="Tools" />
- <keyword id="org.mitk.views.deformableclippingplane.ViewKeyword" label="Plane" />
- <keyword id="org.mitk.views.deformableclippingplane.ViewKeyword" label="Volumne calculation" />
- <keyword id="org.mitk.views.deformableclippingplane.ViewKeyword" label="Splitting" />
- <keyword id="org.mitk.views.deformableclippingplane.ViewKeyword" label="Deformation" />
- <keyword id="org.mitk.views.deformableclippingplane.ViewKeyword" label="Volume analysis" />
-
<keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Segmentation" />
<keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Difference" />
<keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Intersection" />
<keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Union" />
<keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Image Masking" />
<keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Surface Masking" />
<keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Dilatation" />
<keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Erosion" />
<keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Closing" />
<keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Opening" />
<keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Fill Holes" />
<keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Morphological Operations" />
<keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Boolean Operations" />
<keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Surface to Image" />
<keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Surface creation" />
<keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Surface operations" />
</extension>
</plugin>
diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/mitkPluginActivator.cpp
index 173eff2449..75912cd1a5 100644
--- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/mitkPluginActivator.cpp
+++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/mitkPluginActivator.cpp
@@ -1,65 +1,63 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkPluginActivator.h"
#include "QmitkSegmentationView.h"
#include "QmitkThresholdAction.h"
#include "QmitkCreatePolygonModelAction.h"
#include "QmitkAutocropAction.h"
#include "QmitkAutocropLabelSetImageAction.h"
#include "QmitkSegmentationPreferencePage.h"
-#include "QmitkDeformableClippingPlaneView.h"
#include "SegmentationUtilities/QmitkSegmentationUtilitiesView.h"
using namespace mitk;
ctkPluginContext* PluginActivator::m_context = nullptr;
PluginActivator* PluginActivator::m_Instance = nullptr;
PluginActivator::PluginActivator()
{
m_Instance = this;
}
PluginActivator::~PluginActivator()
{
m_Instance = nullptr;
}
void PluginActivator::start(ctkPluginContext *context)
{
BERRY_REGISTER_EXTENSION_CLASS(QmitkSegmentationView, context)
BERRY_REGISTER_EXTENSION_CLASS(QmitkThresholdAction, context)
BERRY_REGISTER_EXTENSION_CLASS(QmitkCreatePolygonModelAction, context)
BERRY_REGISTER_EXTENSION_CLASS(QmitkAutocropAction, context)
BERRY_REGISTER_EXTENSION_CLASS(QmitkAutocropLabelSetImageAction, context)
BERRY_REGISTER_EXTENSION_CLASS(QmitkSegmentationPreferencePage, context)
- BERRY_REGISTER_EXTENSION_CLASS(QmitkDeformableClippingPlaneView, context)
BERRY_REGISTER_EXTENSION_CLASS(QmitkSegmentationUtilitiesView, context)
this->m_context = context;
}
void PluginActivator::stop(ctkPluginContext *)
{
this->m_context = nullptr;
}
PluginActivator* PluginActivator::getDefault()
{
return m_Instance;
}
ctkPluginContext*PluginActivator::getContext()
{
return m_context;
}