diff --git a/Plugins/PluginList.cmake b/Plugins/PluginList.cmake
index e4fab2431d..fea3835632 100644
--- a/Plugins/PluginList.cmake
+++ b/Plugins/PluginList.cmake
@@ -1,114 +1,115 @@
# 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.blueberry.test:ON
#org.blueberry.uitest:ON
#Testing/org.blueberry.core.runtime.tests:ON
#Testing/org.blueberry.osgi.tests:ON
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.coreapplication:OFF
org.mitk.gui.qt.ext:OFF
org.mitk.gui.qt.extapplication:OFF
org.mitk.gui.qt.common:ON
org.mitk.gui.qt.stdmultiwidgeteditor:ON
org.mitk.gui.qt.common.legacy:OFF
org.mitk.gui.qt.cmdlinemodules:OFF
org.mitk.gui.qt.diffusionimagingapp: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.bonesegmentation:ON
org.mitk.gui.qt.dicom:OFF
org.mitk.gui.qt.dicominspector:OFF
org.mitk.gui.qt.diffusionimaging:OFF
org.mitk.gui.qt.diffusionimaging.connectomics:OFF
org.mitk.gui.qt.diffusionimaging.denoising:OFF
org.mitk.gui.qt.diffusionimaging.fiberfox:OFF
org.mitk.gui.qt.diffusionimaging.fiberprocessing:OFF
org.mitk.gui.qt.diffusionimaging.ivim:OFF
org.mitk.gui.qt.diffusionimaging.odfpeaks:OFF
org.mitk.gui.qt.diffusionimaging.partialvolume:OFF
org.mitk.gui.qt.diffusionimaging.preprocessing:OFF
org.mitk.gui.qt.diffusionimaging.reconstruction:OFF
org.mitk.gui.qt.diffusionimaging.registration:OFF
org.mitk.gui.qt.diffusionimaging.tbss:OFF
org.mitk.gui.qt.diffusionimaging.tractography:OFF
org.mitk.gui.qt.diffusionimaging.python: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.aicpregistration:OFF
org.mitk.gui.qt.renderwindowmanager: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.echotrack: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.algorithm.batch: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
)
diff --git a/Plugins/org.mitk.gui.qt.bonesegmentation/CMakeLists.txt b/Plugins/org.mitk.gui.qt.bonesegmentation/CMakeLists.txt
new file mode 100644
index 0000000000..537a83c7a2
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.bonesegmentation/CMakeLists.txt
@@ -0,0 +1,7 @@
+project(org_mitk_gui_qt_bonesegmentation)
+
+mitk_create_plugin(
+ EXPORT_DIRECTIVE BONESEGMENTATION_EXPORT
+ EXPORTED_INCLUDE_SUFFIXES src
+ MODULE_DEPENDS MitkQtWidgetsExt
+)
diff --git a/Plugins/org.mitk.gui.qt.bonesegmentation/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.bonesegmentation/documentation/UserManual/Manual.dox
new file mode 100644
index 0000000000..d556a8b7b1
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.bonesegmentation/documentation/UserManual/Manual.dox
@@ -0,0 +1,17 @@
+/**
+\page org_mitk_gui_qt_bonesegmentation The Bonesegmentation
+
+\imageMacro{icon.png,"Icon of Bonesegmentation",2.00}
+
+\tableofcontents
+
+\section org_mitk_gui_qt_bonesegmentationOverview Overview
+Describe the features of your awesome plugin here
+
+- Increases productivity
+
- Creates beautiful images
+
- Generates PhD thesis
+
- Brings world peace
+
+
+*/
diff --git a/Plugins/org.mitk.gui.qt.bonesegmentation/documentation/UserManual/icon.xpm b/Plugins/org.mitk.gui.qt.bonesegmentation/documentation/UserManual/icon.xpm
new file mode 100644
index 0000000000..9057c20bc6
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.bonesegmentation/documentation/UserManual/icon.xpm
@@ -0,0 +1,21 @@
+/* XPM */
+static const char * icon_xpm[] = {
+"16 16 2 1",
+" c #FF0000",
+". c #000000",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" "};
diff --git a/Plugins/org.mitk.gui.qt.bonesegmentation/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.bonesegmentation/documentation/doxygen/modules.dox
new file mode 100644
index 0000000000..6d9975611f
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.bonesegmentation/documentation/doxygen/modules.dox
@@ -0,0 +1,16 @@
+/**
+ \defgroup org_mitk_gui_qt_bonesegmentation org.mitk.gui.qt.bonesegmentation
+ \ingroup MITKPlugins
+
+ \brief Describe your plugin here.
+
+*/
+
+/**
+ \defgroup org_mitk_gui_qt_bonesegmentation_internal Internal
+ \ingroup org_mitk_gui_qt_bonesegmentation
+
+ \brief This subcategory includes the internal classes of the org.mitk.gui.qt.bonesegmentation plugin. Other
+ plugins must not rely on these classes. They contain implementation details and their interface
+ may change at any time. We mean it.
+*/
diff --git a/Plugins/org.mitk.gui.qt.bonesegmentation/files.cmake b/Plugins/org.mitk.gui.qt.bonesegmentation/files.cmake
new file mode 100644
index 0000000000..49d48068ad
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.bonesegmentation/files.cmake
@@ -0,0 +1,42 @@
+set(SRC_CPP_FILES
+
+)
+
+set(INTERNAL_CPP_FILES
+ org_mitk_gui_qt_bonesegmentation_Activator.cpp
+ QmitkBoneSegmentation.cpp
+)
+
+set(UI_FILES
+ src/internal/QmitkBoneSegmentationControls.ui
+)
+
+set(MOC_H_FILES
+ src/internal/org_mitk_gui_qt_bonesegmentation_Activator.h
+ src/internal/QmitkBoneSegmentation.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.xpm
+ plugin.xml
+)
+
+# list of Qt .qrc files which contain additional resources
+# specific to this plugin
+set(QRC_FILES
+
+)
+
+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.bonesegmentation/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.bonesegmentation/manifest_headers.cmake
new file mode 100644
index 0000000000..d85840cc19
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.bonesegmentation/manifest_headers.cmake
@@ -0,0 +1,5 @@
+set(Plugin-Name "Bonesegmentation")
+set(Plugin-Version "0.1")
+set(Plugin-Vendor "DKFZ")
+set(Plugin-ContactAddress "")
+set(Require-Plugin org.mitk.gui.qt.common)
diff --git a/Plugins/org.mitk.gui.qt.bonesegmentation/plugin.xml b/Plugins/org.mitk.gui.qt.bonesegmentation/plugin.xml
new file mode 100644
index 0000000000..ed64c14a41
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.bonesegmentation/plugin.xml
@@ -0,0 +1,11 @@
+
+
+
+
+
+
+
+
diff --git a/Plugins/org.mitk.gui.qt.bonesegmentation/resources/icon.xpm b/Plugins/org.mitk.gui.qt.bonesegmentation/resources/icon.xpm
new file mode 100644
index 0000000000..9057c20bc6
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.bonesegmentation/resources/icon.xpm
@@ -0,0 +1,21 @@
+/* XPM */
+static const char * icon_xpm[] = {
+"16 16 2 1",
+" c #FF0000",
+". c #000000",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" ",
+" "};
diff --git a/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/QmitkBoneSegmentation.cpp b/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/QmitkBoneSegmentation.cpp
new file mode 100644
index 0000000000..4ede16b008
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/QmitkBoneSegmentation.cpp
@@ -0,0 +1,143 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+
+
+// Blueberry
+#include
+#include
+
+// Qmitk
+#include "QmitkBoneSegmentation.h"
+
+// Qt
+#include
+
+// mitk image
+#include
+#include
+// #include "BetData.h"
+
+const std::string QmitkBoneSegmentation::VIEW_ID = "org.mitk.views.bonesegmentation";
+
+void QmitkBoneSegmentation::SetFocus()
+{
+ m_Controls.buttonPerformImageProcessing->setFocus();
+}
+
+void QmitkBoneSegmentation::CreateQtPartControl(QWidget *parent)
+{
+ // create GUI widgets from the Qt Designer's .ui file
+ m_Controls.setupUi(parent);
+ connect(m_Controls.buttonPerformImageProcessing, &QPushButton::clicked, this, &QmitkBoneSegmentation::StartPythonProcess);
+
+ m_process = new QProcess();
+ connect(m_process, SIGNAL(finished(int, QProcess::ExitStatus )),this, SLOT(doSomethingWhenItsDone()));
+ m_Controls.buttonPerformImageProcessing->setText("Start Bone Segmentation");
+}
+
+void QmitkBoneSegmentation::doSomethingWhenItsDone()
+{
+ MITK_INFO << "Ended calculation thread.";
+ //m_Controls.m_StartButton->setText("Start Bone Segmentation");
+ //m_Controls.m_StartButton->setEnabled(true);
+
+ mitk::IOUtil::Load("/media/kleina/Data/Data/bone_seg_ijcars/nrrd/temp_CT_output.nrrd", *GetDataStorage());
+
+ if( remove( "/media/kleina/Data/Data/bone_seg_ijcars/nrrd/temp_CT_1.nrrd" ) != 0 )
+ MITK_WARN << "Error deleting file" ;
+ else
+ MITK_INFO << "File successfully deleted" ;
+
+ if( remove( "/media/kleina/Data/Data/bone_seg_ijcars/nrrd/temp_CT_output.nrrd" ) != 0 )
+ MITK_WARN << "Error deleting file" ;
+ else
+ MITK_INFO << "File successfully deleted" ;
+}
+
+void QmitkBoneSegmentation::StartPythonProcess()
+{
+ MITK_INFO << "[START] StartPythonProcess()";
+ //m_Controls.m_StartButton->setText("Segmentation running... This can take a few minutes.");
+ //m_Controls.m_StartButton->setEnabled(false);
+
+ QList nodes = this->GetDataManagerSelection();
+ if (nodes.empty())
+ return;
+
+
+ mitk::DataNode::Pointer node = nodes.front(); //TODO = m_Controls.m_ImageBox->GetSelectedNode();
+ mitk::Image::Pointer mitk_image = dynamic_cast(node->GetData());
+
+ mitk::IOUtil::Save(mitk_image, "/media/kleina/Data/Data/bone_seg_ijcars/nrrd/temp_CT_1.nrrd");
+
+ QString programCall("python"); // + QString::fromStdString(GetPythonFile("segment.py")) + " /media/kleina/Data/Data/bone_seg_ijcars/nrrd/temp_CT_1.nrrd");
+ QStringList arguments = QStringList() << QString::fromStdString(GetPythonFile("segment.py"))
+ << "/media/kleina/Data/Data/bone_seg_ijcars/nrrd/temp_CT_1.nrrd";
+ //QStringList arguments; // = {QString::fromStdString(GetPythonFile("segment.py")), "/media/kleina/Data/Data/bone_seg_ijcars/nrrd/temp_CT_1.nrrd"};
+
+ MITK_INFO << programCall;
+
+ m_process->start(programCall, arguments);
+ MITK_INFO << "[END] StartPythonProcess()";
+}
+
+void QmitkBoneSegmentation::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/,
+ const QList &nodes)
+{
+ // iterate all selected objects, adjust warning visibility
+ foreach (mitk::DataNode::Pointer node, nodes)
+ {
+ if (node.IsNotNull() && dynamic_cast(node->GetData()))
+ {
+ m_Controls.labelWarning->setVisible(false);
+ m_Controls.buttonPerformImageProcessing->setEnabled(true);
+ return;
+ }
+ }
+
+ m_Controls.labelWarning->setVisible(true);
+ m_Controls.buttonPerformImageProcessing->setEnabled(false);
+}
+
+std::string QmitkBoneSegmentation::GetPythonFile(std::string filename)
+{
+ std::string out = filename; //"";
+ //std::string exec_dir = QCoreApplication::applicationDirPath().toStdString();
+ //for (auto dir : mitk::bet::relative_search_dirs)
+ //{
+ // if ( ist::FileExists( ist::GetCurrentWorkingDirectory() + dir + filename) )
+ // {
+ // out = ist::GetCurrentWorkingDirectory() + dir + filename;
+ // return out;
+ // }
+ // if ( ist::FileExists( exec_dir + dir + filename) )
+ // {
+ // out = exec_dir + dir + filename;
+ // return out;
+ // }
+ //}
+ //for (auto dir : mitk::bet::absolute_search_dirs)
+ //{
+ // if ( ist::FileExists( dir + filename) )
+ // {
+ // out = dir + filename;
+ // return out;
+ // }
+ //}
+
+ MITK_WARN << out;
+ return out;
+}
diff --git a/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/QmitkBoneSegmentation.cpp.autosave b/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/QmitkBoneSegmentation.cpp.autosave
new file mode 100644
index 0000000000..c746cba0f6
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/QmitkBoneSegmentation.cpp.autosave
@@ -0,0 +1,142 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+
+
+// Blueberry
+#include
+#include
+
+// Qmitk
+#include "QmitkBoneSegmentation.h"
+
+// Qt
+#include
+
+// mitk image
+#include
+#include
+// #include "BetData.h"
+
+const std::string QmitkBoneSegmentation::VIEW_ID = "org.mitk.views.bonesegmentation";
+
+void QmitkBoneSegmentation::SetFocus()
+{
+ m_Controls.buttonPerformImageProcessing->setFocus();
+}
+
+void QmitkBoneSegmentation::CreateQtPartControl(QWidget *parent)
+{
+ // create GUI widgets from the Qt Designer's .ui file
+ m_Controls.setupUi(parent);
+ connect(m_Controls.buttonPerformImageProcessing, &QPushButton::clicked, this, &QmitkBoneSegmentation::StartPythonProcess);
+
+ m_process = new QProcess();
+ connect(m_process, SIGNAL(finished(int, QProcess::ExitStatus )),this, SLOT(doSomethingWhenItsDone()));
+ m_Controls.buttonPerformImageProcessing->setText("Start Bone Segmentation");
+}
+
+void QmitkBoneSegmentation::doSomethingWhenItsDone()
+{
+ MITK_INFO << "Ended calculation thread.";
+ //m_Controls.m_StartButton->setText("Start Bone Segmentation");
+ //m_Controls.m_StartButton->setEnabled(true);
+
+ mitk::IOUtil::Load("/media/kleina/Data/Data/bone_seg_ijcars/nrrd/temp_CT_output.nrrd", *GetDataStorage());
+
+ if( remove( "/media/kleina/Data/Data/bone_seg_ijcars/nrrd/temp_CT_1.nrrd" ) != 0 )
+ MITK_WARN << "Error deleting file" ;
+ else
+ MITK_INFO << "File successfully deleted" ;
+
+ if( remove( "/media/kleina/Data/Data/bone_seg_ijcars/nrrd/temp_CT_output.nrrd" ) != 0 )
+ MITK_WARN << "Error deleting file" ;
+ else
+ MITK_INFO << "File successfully deleted" ;
+}
+
+void QmitkBoneSegmentation::StartPythonProcess()
+{
+ MITK_INFO << "[START] StartPythonProcess()";
+ //m_Controls.m_StartButton->setText("Segmentation running... This can take a few minutes.");
+ //m_Controls.m_StartButton->setEnabled(false);
+
+ QList nodes = this->GetDataManagerSelection();
+ if (nodes.empty())
+ return;
+
+ mitk::DataNode::Pointer node = nodes.front(); //TODO = m_Controls.m_ImageBox->GetSelectedNode();
+ mitk::Image::Pointer mitk_image = dynamic_cast(node->GetData());
+
+ mitk::IOUtil::Save(mitk_image, "/media/kleina/Data/Data/bone_seg_ijcars/nrrd/temp_CT_1.nrrd");
+
+ QString programCall("python"); // + QString::fromStdString(GetPythonFile("segment.py")) + " /media/kleina/Data/Data/bone_seg_ijcars/nrrd/temp_CT_1.nrrd");
+ QStringList arguments = QStringList() << QString::fromStdString(GetPythonFile("segment.py"))
+ << "/media/kleina/Data/Data/bone_seg_ijcars/nrrd/temp_CT_1.nrrd";
+ //QStringList arguments; // = {QString::fromStdString(GetPythonFile("segment.py")), "/media/kleina/Data/Data/bone_seg_ijcars/nrrd/temp_CT_1.nrrd"};
+
+ MITK_INFO << programCall;
+
+ m_process->start(programCall, arguments);
+ MITK_INFO << "[END] StartPythonProcess()";
+}
+
+void QmitkBoneSegmentation::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/,
+ const QList &nodes)
+{
+ // iterate all selected objects, adjust warning visibility
+ foreach (mitk::DataNode::Pointer node, nodes)
+ {
+ if (node.IsNotNull() && dynamic_cast(node->GetData()))
+ {
+ m_Controls.labelWarning->setVisible(false);
+ m_Controls.buttonPerformImageProcessing->setEnabled(true);
+ return;
+ }
+ }
+
+ m_Controls.labelWarning->setVisible(true);
+ m_Controls.buttonPerformImageProcessing->setEnabled(false);
+}
+
+std::string QmitkBoneSegmentation::GetPythonFile(std::string filename)
+{
+ std::string out = filename; //"";
+ //std::string exec_dir = QCoreApplication::applicationDirPath().toStdString();
+ //for (auto dir : mitk::bet::relative_search_dirs)
+ //{
+ // if ( ist::FileExists( ist::GetCurrentWorkingDirectory() + dir + filename) )
+ // {
+ // out = ist::GetCurrentWorkingDirectory() + dir + filename;
+ // return out;
+ // }
+ // if ( ist::FileExists( exec_dir + dir + filename) )
+ // {
+ // out = exec_dir + dir + filename;
+ // return out;
+ // }
+ //}
+ //for (auto dir : mitk::bet::absolute_search_dirs)
+ //{
+ // if ( ist::FileExists( dir + filename) )
+ // {
+ // out = dir + filename;
+ // return out;
+ // }
+ //}
+
+ MITK_WARN << out;
+ return out;
+}
diff --git a/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/QmitkBoneSegmentation.h b/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/QmitkBoneSegmentation.h
new file mode 100644
index 0000000000..77400c269d
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/QmitkBoneSegmentation.h
@@ -0,0 +1,64 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+
+
+#ifndef QmitkBoneSegmentation_h
+#define QmitkBoneSegmentation_h
+
+#include
+
+#include
+
+#include "ui_QmitkBoneSegmentationControls.h"
+
+#include
+#include
+/**
+ \brief QmitkBoneSegmentation
+
+ \warning This class is not yet documented. Use "git blame" and ask the author to provide basic documentation.
+
+ \sa QmitkAbstractView
+ \ingroup ${plugin_target}_internal
+*/
+class QmitkBoneSegmentation : 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;
+ std::string GetPythonFile(std::string filename);
+
+protected slots:
+ void StartPythonProcess();
+ void doSomethingWhenItsDone();
+
+protected:
+ virtual void CreateQtPartControl(QWidget *parent) override;
+
+ virtual void SetFocus() override;
+
+ /// \brief called by QmitkFunctionality when DataManager's selection has changed
+ virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer source,
+ const QList &nodes) override;
+
+ QProcess* m_process;
+ Ui::QmitkBoneSegmentationControls m_Controls;
+};
+
+#endif // QmitkBoneSegmentation_h
diff --git a/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/QmitkBoneSegmentationControls.ui b/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/QmitkBoneSegmentationControls.ui
new file mode 100644
index 0000000000..c65b6542d6
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/QmitkBoneSegmentationControls.ui
@@ -0,0 +1,64 @@
+
+
+ QmitkBoneSegmentationControls
+
+
+
+ 0
+ 0
+ 222
+ 161
+
+
+
+
+ 0
+ 0
+
+
+
+ QmitkTemplate
+
+
+ -
+
+
+ QLabel { color: rgb(255, 0, 0) }
+
+
+ Please select an image!
+
+
+
+ -
+
+
+ Do image processing
+
+
+ Do Something
+
+
+
+ -
+
+
+ Qt::Vertical
+
+
+ QSizePolicy::Expanding
+
+
+
+ 20
+ 220
+
+
+
+
+
+
+
+
+
+
diff --git a/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/org_mitk_gui_qt_bonesegmentation_Activator.cpp b/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/org_mitk_gui_qt_bonesegmentation_Activator.cpp
new file mode 100644
index 0000000000..7432c1ad7b
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/org_mitk_gui_qt_bonesegmentation_Activator.cpp
@@ -0,0 +1,29 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+
+
+#include "org_mitk_gui_qt_bonesegmentation_Activator.h"
+#include "QmitkBoneSegmentation.h"
+
+namespace mitk
+{
+ void org_mitk_gui_qt_bonesegmentation_Activator::start(ctkPluginContext *context)
+ {
+ BERRY_REGISTER_EXTENSION_CLASS(QmitkBoneSegmentation, context)
+ }
+
+ void org_mitk_gui_qt_bonesegmentation_Activator::stop(ctkPluginContext *context) { Q_UNUSED(context) }
+}
diff --git a/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/org_mitk_gui_qt_bonesegmentation_Activator.h b/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/org_mitk_gui_qt_bonesegmentation_Activator.h
new file mode 100644
index 0000000000..1003010ac9
--- /dev/null
+++ b/Plugins/org.mitk.gui.qt.bonesegmentation/src/internal/org_mitk_gui_qt_bonesegmentation_Activator.h
@@ -0,0 +1,38 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+
+
+#ifndef org_mitk_gui_qt_bonesegmentation_Activator_h
+#define org_mitk_gui_qt_bonesegmentation_Activator_h
+
+#include
+
+namespace mitk
+{
+ class org_mitk_gui_qt_bonesegmentation_Activator : public QObject, public ctkPluginActivator
+ {
+ Q_OBJECT
+ Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_bonesegmentation")
+ Q_INTERFACES(ctkPluginActivator)
+
+ public:
+ void start(ctkPluginContext *context);
+ void stop(ctkPluginContext *context);
+
+ }; // org_mitk_gui_qt_bonesegmentation_Activator
+}
+
+#endif // org_mitk_gui_qt_bonesegmentation_Activator_h