diff --git a/Modules/DiffusionImaging/DiffusionCore/cmdapps/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCore/cmdapps/CMakeLists.txt index 83a538fd92..df36d8afdc 100644 --- a/Modules/DiffusionImaging/DiffusionCore/cmdapps/CMakeLists.txt +++ b/Modules/DiffusionImaging/DiffusionCore/cmdapps/CMakeLists.txt @@ -1,45 +1,44 @@ option(BUILD_DiffusionCoreCmdApps "Build commandline tools for diffusion" OFF) if(BUILD_DiffusionCoreCmdApps OR MITK_BUILD_ALL_APPS) # needed include directories include_directories( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR} ) # list of diffusion cmdapps # if an app requires additional dependencies # they are added after a "^^" and separated by "_" set( diffusioncorecmdapps - DwiDenoising^^ ImageResampler^^ ExportShImage^^ CopyGeometry^^ Registration^^ DiffusionDICOMLoader^^ ResampleGradients^^ ) foreach(diffusioncorecmdapp ${diffusioncorecmdapps}) # extract cmd app name and dependencies string(REPLACE "^^" "\\;" cmdapp_info ${diffusioncorecmdapp}) set(cmdapp_info_list ${cmdapp_info}) list(GET cmdapp_info_list 0 appname) list(GET cmdapp_info_list 1 raw_dependencies) string(REPLACE "_" "\\;" dependencies "${raw_dependencies}") set(dependencies_list ${dependencies}) mitkFunctionCreateCommandLineApp( NAME ${appname} DEPENDS MitkCore MitkDiffusionCore ${dependencies_list} PACKAGE_DEPENDS ITK ) endforeach() - + endif() mitkFunctionCreateCommandLineApp( NAME Dicom2Nrrd DEPENDS MitkCore ${dependencies_list} ) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/CMakeLists.txt index 490c2f7ba4..83ef9b42fc 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/CMakeLists.txt @@ -1,9 +1,9 @@ # The project name must correspond to the directory name of your plug-in # and must not contain periods. project(org_mitk_gui_qt_diffusionimaging_preprocessing) mitk_create_plugin( EXPORT_DIRECTIVE DIFFUSIONIMAGING_PREPROCESSING_EXPORT EXPORTED_INCLUDE_SUFFIXES src - MODULE_DEPENDS MitkDiffusionCore + MODULE_DEPENDS MitkDiffusionCore MitkPython MitkQtPython ) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/files.cmake index 0009a93c61..61c991d6e5 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/files.cmake +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/files.cmake @@ -1,42 +1,45 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES mitkPluginActivator.cpp QmitkPreprocessingView.cpp + QmitkBrainExtractionView.cpp ) set(UI_FILES src/internal/QmitkPreprocessingViewControls.ui + src/internal/QmitkBrainExtractionViewControls.ui ) set(MOC_H_FILES src/internal/mitkPluginActivator.h src/internal/QmitkPreprocessingView.h + src/internal/QmitkBrainExtractionView.h ) set(CACHED_RESOURCE_FILES plugin.xml resources/preprocessing.png resources/dwi2.png ) 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.diffusionimaging.preprocessing/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/plugin.xml index f19813d57d..c441b6d060 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/plugin.xml +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/plugin.xml @@ -1,17 +1,25 @@ - + + + + + - + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkBrainExtractionView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkBrainExtractionView.cpp new file mode 100644 index 0000000000..d9d4475c43 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkBrainExtractionView.cpp @@ -0,0 +1,149 @@ +/*=================================================================== + +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. + +===================================================================*/ + +//misc +#define _USE_MATH_DEFINES +#include + +// Blueberry +#include +#include + +// Qmitk +#include "QmitkBrainExtractionView.h" + +// MITK +#include + +// Qt +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#define _USE_MATH_DEFINES +#include + +const std::string QmitkBrainExtractionView::VIEW_ID = "org.mitk.views.brainextraction"; + +QmitkBrainExtractionView::QmitkBrainExtractionView() + : QmitkAbstractView() + , m_Controls( 0 ) + , m_DiffusionImage( nullptr ) +{ + +} + +// Destructor +QmitkBrainExtractionView::~QmitkBrainExtractionView() +{ +} + +void QmitkBrainExtractionView::CreateQtPartControl( QWidget *parent ) +{ + // build up qt view, unless already done + if ( !m_Controls ) + { + // create GUI widgets from the Qt Designer's .ui file + m_Controls = new Ui::QmitkBrainExtractionViewControls; + m_Controls->setupUi( parent ); + connect( m_Controls->m_ImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGUI()) ); + connect( m_Controls->m_StartButton, SIGNAL(clicked()), this, SLOT(StartBrainExtraction()) ); + this->m_Parent = parent; + + m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage()); + mitk::NodePredicateDimension::Pointer dimPred = mitk::NodePredicateDimension::New(3); + mitk::TNodePredicateDataType::Pointer isImagePredicate = mitk::TNodePredicateDataType::New(); + m_Controls->m_ImageBox->SetPredicate(mitk::NodePredicateAnd::New(isImagePredicate,dimPred)); + + UpdateGUI(); + + std::string module_library_full_path = us::GetModuleContext()->GetModule()->GetLocation(); + std::string library_file; + itksys::SystemTools::SplitProgramPath(module_library_full_path, m_ModulePath, library_file); + } +} + +void QmitkBrainExtractionView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList& ) +{ +} + +void QmitkBrainExtractionView::UpdateGUI() +{ + if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull()) + m_Controls->m_StartButton->setEnabled(true); + else + m_Controls->m_StartButton->setEnabled(false); +} + +void QmitkBrainExtractionView::SetFocus() +{ + UpdateGUI(); + m_Controls->m_StartButton->setFocus(); +} + +void QmitkBrainExtractionView::StartBrainExtraction() +{ + mitk::DataNode::Pointer node = m_Controls->m_ImageBox->GetSelectedNode(); + mitk::Image::Pointer mitk_image = dynamic_cast(node->GetData()); + + us::ModuleContext* context = us::GetModuleContext(); + us::ServiceReference m_PythonServiceRef = context->GetServiceReference(); + mitk::IPythonService* m_PythonService = dynamic_cast ( context->GetService(m_PythonServiceRef) ); + mitk::IPythonService::ForceLoadModule(); + + m_PythonService->Execute("import SimpleITK as sitk"); + m_PythonService->Execute("import SimpleITK._SimpleITK as _SimpleITK"); + m_PythonService->Execute("import numpy"); + m_PythonService->CopyToPythonAsSimpleItkImage( mitk_image, "in_image"); + m_PythonService->Execute("model=\""+m_ModulePath+"/brain_extraction_model.model\""); + m_PythonService->ExecuteScript(m_ModulePath + "/brain_extraction_script.py"); + + { + mitk::Image::Pointer image = m_PythonService->CopySimpleItkImageFromPython("brain_mask"); + mitk::DataNode::Pointer corrected_node = mitk::DataNode::New(); + corrected_node->SetData( image ); + QString name(node->GetName().c_str()); + name += "_BrainMask"; + corrected_node->SetName(name.toStdString()); + GetDataStorage()->Add(corrected_node, node); + } + + { + mitk::Image::Pointer image = m_PythonService->CopySimpleItkImageFromPython("brain_extracted"); + mitk::DataNode::Pointer corrected_node = mitk::DataNode::New(); + corrected_node->SetData( image ); + QString name(node->GetName().c_str()); + name += "_SkullStripped"; + corrected_node->SetName(name.toStdString()); + GetDataStorage()->Add(corrected_node, node); + } +} diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkBrainExtractionView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkBrainExtractionView.h new file mode 100644 index 0000000000..2f8193f297 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkBrainExtractionView.h @@ -0,0 +1,72 @@ +/*=================================================================== + +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 +#include + +#include +#include "ui_QmitkBrainExtractionViewControls.h" +#include +#include +#include + +/*! +\brief View for diffusion image registration / head motion correction +*/ +class QmitkBrainExtractionView : 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; + + QmitkBrainExtractionView(); + virtual ~QmitkBrainExtractionView(); + + virtual void CreateQtPartControl(QWidget *parent) override; + void SetFocus() override; + +protected slots: + + void StartBrainExtraction(); + void UpdateGUI(); ///< update button activity etc. dpending on current datamanager selection + + +protected: + + /// \brief called by QmitkAbstractView when DataManager's selection has changed + virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList& nodes) override; + + Ui::QmitkBrainExtractionViewControls* m_Controls; + + mitk::Image::Pointer m_DiffusionImage; + std::vector< mitk::DataNode::Pointer > m_SelectedDiffusionNodes; + +private: + + void UpdateRegistrationStatus(); ///< update textual status display of the Registration process + + // the Qt parent of our GUI (NOT of this object) + QWidget* m_Parent; + std::string m_ModulePath; + +}; diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkBrainExtractionViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkBrainExtractionViewControls.ui new file mode 100644 index 0000000000..22a52561f5 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkBrainExtractionViewControls.ui @@ -0,0 +1,88 @@ + + + QmitkBrainExtractionViewControls + + + + 0 + 0 + 435 + 744 + + + + Form + + + + + + false + + + + + + Start Brain Extraction + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + 0 + + + 0 + + + 0 + + + + + + + + Input Image: + + + + + + + + + + + QmitkDataStorageComboBox + QComboBox +
QmitkDataStorageComboBox.h
+ + + + + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/mitkPluginActivator.cpp index cdf7135bad..aafe6330b1 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/mitkPluginActivator.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/mitkPluginActivator.cpp @@ -1,38 +1,44 @@ /*=================================================================== 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 "mitkPluginActivator.h" #include "src/internal/QmitkPreprocessingView.h" +#include "src/internal/QmitkBrainExtractionView.h" +#include + ctkPluginContext* mitk::PluginActivator::m_Context = nullptr; +US_INITIALIZE_MODULE + ctkPluginContext* mitk::PluginActivator::GetContext() { return m_Context; } void mitk::PluginActivator::start(ctkPluginContext* context) { BERRY_REGISTER_EXTENSION_CLASS(QmitkPreprocessingView, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkBrainExtractionView, context) m_Context = context; } void mitk::PluginActivator::stop(ctkPluginContext* context) { Q_UNUSED(context) m_Context = nullptr; }