diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionImageNrrdReaderService.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionImageNrrdReaderService.cpp index c7c9931f52..f20e032301 100644 --- a/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionImageNrrdReaderService.cpp +++ b/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionImageNrrdReaderService.cpp @@ -1,269 +1,268 @@ /*=================================================================== 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 __mitkDiffusionImageNrrdReaderService_cpp #define __mitkDiffusionImageNrrdReaderService_cpp #include "mitkDiffusionImageNrrdReaderService.h" #include #include // Diffusion properties #include #include #include #include // ITK includes #include #include #include "itksys/SystemTools.hxx" #include "itkImageFileReader.h" #include "itkMetaDataObject.h" #include "itkNrrdImageIO.h" #include "mitkCustomMimeType.h" #include "mitkDiffusionIOMimeTypes.h" #include -#include #include #include #include "mitkIOUtil.h" namespace mitk { DiffusionImageNrrdReaderService:: DiffusionImageNrrdReaderService(const DiffusionImageNrrdReaderService & other) : AbstractFileReader(other) { } DiffusionImageNrrdReaderService* DiffusionImageNrrdReaderService::Clone() const { return new DiffusionImageNrrdReaderService(*this); } DiffusionImageNrrdReaderService:: ~DiffusionImageNrrdReaderService() {} DiffusionImageNrrdReaderService:: DiffusionImageNrrdReaderService() : mitk::AbstractFileReader( CustomMimeType( mitk::DiffusionIOMimeTypes::DWI_NRRD_MIMETYPE() ), mitk::DiffusionIOMimeTypes::DWI_NRRD_MIMETYPE_DESCRIPTION() ) { m_ServiceReg = this->RegisterService(); } std::vector > DiffusionImageNrrdReaderService:: Read() { std::vector > result; // Since everything is completely read in GenerateOutputInformation() it is stored // in a cache variable. A timestamp is associated. // If the timestamp of the cache variable is newer than the MTime, we only need to // assign the cache variable to the DataObject. // Otherwise, the tree must be read again from the file and OuputInformation must // be updated! if(m_OutputCache.IsNull()) InternalRead(); result.push_back(m_OutputCache.GetPointer()); return result; } void DiffusionImageNrrdReaderService::InternalRead() { OutputType::Pointer outputForCache = OutputType::New(); if ( this->GetInputLocation() == "") { throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename to be read is empty!"); } else { try { const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, NULL ); if ( locale.compare(currLocale)!=0 ) { try { setlocale(LC_ALL, locale.c_str()); } catch(...) { MITK_INFO << "Could not set locale " << locale; } } MITK_INFO << "DiffusionImageNrrdReaderService: reading image information"; VectorImageType::Pointer itkVectorImage; std::string ext = this->GetMimeType()->GetExtension( this->GetInputLocation() ); ext = itksys::SystemTools::LowerCase( ext ); if (ext == ".hdwi" || ext == ".dwi" || ext == ".nrrd") { typedef itk::ImageFileReader FileReaderType; FileReaderType::Pointer reader = FileReaderType::New(); reader->SetFileName(this->GetInputLocation()); itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); reader->SetImageIO(io); reader->Update(); itkVectorImage = reader->GetOutput(); } // Diffusion Image information START GradientDirectionContainerType::Pointer DiffusionVectors = GradientDirectionContainerType::New(); GradientDirectionContainerType::Pointer OriginalDiffusionVectors = GradientDirectionContainerType::New(); MeasurementFrameType MeasurementFrame; float BValue = -1; // Diffusion Image information END if (ext == ".hdwi" || ext == ".dwi" || ext == ".nrrd") { itk::MetaDataDictionary imgMetaDictionary = itkVectorImage->GetMetaDataDictionary(); std::vector imgMetaKeys = imgMetaDictionary.GetKeys(); std::vector::const_iterator itKey = imgMetaKeys.begin(); std::string metaString; GradientDirectionType vect3d; int numberOfImages = 0; int numberOfGradientImages = 0; bool readb0 = false; double xx, xy, xz, yx, yy, yz, zx, zy, zz; for (; itKey != imgMetaKeys.end(); itKey ++) { double x,y,z; itk::ExposeMetaData (imgMetaDictionary, *itKey, metaString); if (itKey->find("DWMRI_gradient") != std::string::npos) { sscanf(metaString.c_str(), "%lf %lf %lf\n", &x, &y, &z); vect3d[0] = x; vect3d[1] = y; vect3d[2] = z; DiffusionVectors->InsertElement( numberOfImages, vect3d ); ++numberOfImages; // If the direction is 0.0, this is a reference image if (vect3d[0] == 0.0 && vect3d[1] == 0.0 && vect3d[2] == 0.0) { continue; } ++numberOfGradientImages;; } else if (itKey->find("DWMRI_b-value") != std::string::npos) { readb0 = true; BValue = atof(metaString.c_str()); } else if (itKey->find("measurement frame") != std::string::npos) { sscanf(metaString.c_str(), " ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) \n", &xx, &xy, &xz, &yx, &yy, &yz, &zx, &zy, &zz); if (xx>10e-10 || xy>10e-10 || xz>10e-10 || yx>10e-10 || yy>10e-10 || yz>10e-10 || zx>10e-10 || zy>10e-10 || zz>10e-10 ) { MeasurementFrame(0,0) = xx; MeasurementFrame(0,1) = xy; MeasurementFrame(0,2) = xz; MeasurementFrame(1,0) = yx; MeasurementFrame(1,1) = yy; MeasurementFrame(1,2) = yz; MeasurementFrame(2,0) = zx; MeasurementFrame(2,1) = zy; MeasurementFrame(2,2) = zz; } else { MeasurementFrame(0,0) = 1; MeasurementFrame(0,1) = 0; MeasurementFrame(0,2) = 0; MeasurementFrame(1,0) = 0; MeasurementFrame(1,1) = 1; MeasurementFrame(1,2) = 0; MeasurementFrame(2,0) = 0; MeasurementFrame(2,1) = 0; MeasurementFrame(2,2) = 1; } } } if(!readb0) { MITK_INFO << "BValue not specified in header file"; } } outputForCache = mitk::GrabItkImageMemory( itkVectorImage); // create BValueMap mitk::BValueMapProperty::BValueMap BValueMap = mitk::BValueMapProperty::CreateBValueMap(DiffusionVectors,BValue); outputForCache->SetProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( DiffusionVectors ) ); outputForCache->SetProperty( mitk::DiffusionPropertyHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( OriginalDiffusionVectors ) ); outputForCache->SetProperty( mitk::DiffusionPropertyHelper::MEASUREMENTFRAMEPROPERTYNAME.c_str(), mitk::MeasurementFrameProperty::New( MeasurementFrame ) ); outputForCache->SetProperty( mitk::DiffusionPropertyHelper::BVALUEMAPPROPERTYNAME.c_str(), mitk::BValueMapProperty::New( BValueMap ) ); outputForCache->SetProperty( mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( BValue ) ); // Since we have already read the tree, we can store it in a cache variable // so that it can be assigned to the DataObject in GenerateData(); m_OutputCache = outputForCache; m_CacheTime.Modified(); try { setlocale(LC_ALL, currLocale.c_str()); } catch(...) { MITK_INFO << "Could not reset locale " << currLocale; } } catch(std::exception& e) { MITK_INFO << "Std::Exception while reading file!!"; MITK_INFO << e.what(); throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what()); } catch(...) { MITK_INFO << "Exception while reading file!!"; throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested vessel tree file!"); } } } } //namespace MITK #endif diff --git a/Modules/IGTUI/Qmitk/QmitkNavigationToolCreationWidget.cpp b/Modules/IGTUI/Qmitk/QmitkNavigationToolCreationWidget.cpp index 879f0683ff..df6e5f0fbf 100644 --- a/Modules/IGTUI/Qmitk/QmitkNavigationToolCreationWidget.cpp +++ b/Modules/IGTUI/Qmitk/QmitkNavigationToolCreationWidget.cpp @@ -1,337 +1,336 @@ /*=================================================================== 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 "QmitkNavigationToolCreationWidget.h" //mitk headers #include -#include #include #include #include //qt headers #include #include #include #include //poco headers #include // vtk #include #include const std::string QmitkNavigationToolCreationWidget::VIEW_ID = "org.mitk.views.navigationtoolcreationwizardwidget"; QmitkNavigationToolCreationWidget::QmitkNavigationToolCreationWidget(QWidget* parent, Qt::WindowFlags f) : QWidget(parent, f) { m_Controls = NULL; m_AdvancedWidget = new QmitkNavigationToolCreationAdvancedWidget(this); m_AdvancedWidget->setWindowFlags(Qt::Tool | Qt::WindowStaysOnTopHint); m_AdvancedWidget->setWindowTitle("Tool Creation Advanced Options"); m_AdvancedWidget->setModal(false); CreateQtPartControl(this); CreateConnections(); } QmitkNavigationToolCreationWidget::~QmitkNavigationToolCreationWidget() { m_Controls->m_CalibrationLandmarksList->SetPointSetNode(NULL); m_Controls->m_RegistrationLandmarksList->SetPointSetNode(NULL); delete m_AdvancedWidget; } void QmitkNavigationToolCreationWidget::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkNavigationToolCreationWidgetControls; m_Controls->setupUi(parent); } } void QmitkNavigationToolCreationWidget::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(m_Controls->m_cancel), SIGNAL(clicked()), this, SLOT(OnCancel()) ); connect( (QObject*)(m_Controls->m_finished), SIGNAL(clicked()), this, SLOT(OnFinished()) ); connect( (QObject*)(m_Controls->m_LoadSurface), SIGNAL(clicked()), this, SLOT(OnLoadSurface()) ); connect( (QObject*)(m_Controls->m_LoadCalibrationFile), SIGNAL(clicked()), this, SLOT(OnLoadCalibrationFile()) ); connect( (QObject*)(m_Controls->m_ShowAdvancedOptionsPB), SIGNAL(toggled(bool)), this, SLOT(OnShowAdvancedOptions(bool)) ); connect( (QObject*)(m_AdvancedWidget), SIGNAL(DialogCloseRequested()), this, SLOT(OnProcessDialogCloseRequest()) ); connect( (QObject*)(m_AdvancedWidget), SIGNAL(RetrieveDataForManualToolTipManipulation()), this, SLOT(OnRetrieveDataForManualTooltipManipulation()) ); connect( m_Controls->m_Surface_Use_Other, SIGNAL(toggled(bool)), this, SLOT(OnSurfaceUseOtherToggled(bool))); } } void QmitkNavigationToolCreationWidget::Initialize(mitk::DataStorage* dataStorage, std::string supposedIdentifier, std::string supposedName) { m_DataStorage = dataStorage; //initialize UI components m_Controls->m_SurfaceChooser->SetDataStorage(m_DataStorage); m_Controls->m_SurfaceChooser->SetAutoSelectNewItems(true); m_Controls->m_SurfaceChooser->SetPredicate(mitk::NodePredicateDataType::New("Surface")); //set default data m_Controls->m_ToolNameEdit->setText(supposedName.c_str()); m_Controls->m_CalibrationFileName->setText("none"); m_Controls->m_Surface_Use_Sphere->setChecked(true); m_AdvancedWidget->SetDataStorage(m_DataStorage); m_Controls->m_IdentifierEdit->setText(supposedIdentifier.c_str()); this->InitializeUIToolLandmarkLists(); m_Controls->m_CalibrationLandmarksList->EnableEditButton(false); m_Controls->m_RegistrationLandmarksList->EnableEditButton(false); } void QmitkNavigationToolCreationWidget::SetTrackingDeviceType(mitk::TrackingDeviceType type, bool changeable) { switch(type) { case mitk::NDIAurora: m_Controls->m_TrackingDeviceTypeChooser->setCurrentIndex(0);break; case mitk::NDIPolaris: m_Controls->m_TrackingDeviceTypeChooser->setCurrentIndex(1);break; case mitk::ClaronMicron: m_Controls->m_TrackingDeviceTypeChooser->setCurrentIndex(2);break; case mitk::NPOptitrack: m_Controls->m_TrackingDeviceTypeChooser->setCurrentIndex(3);break; case mitk::VirtualTracker: m_Controls->m_TrackingDeviceTypeChooser->setCurrentIndex(4);break; default: m_Controls->m_TrackingDeviceTypeChooser->setCurrentIndex(4); } m_Controls->m_TrackingDeviceTypeChooser->setEnabled(changeable); } mitk::NavigationTool::Pointer QmitkNavigationToolCreationWidget::GetCreatedTool() { return m_CreatedTool; } //################################################################################## //############################## slots ############################ //################################################################################## void QmitkNavigationToolCreationWidget::OnFinished() { //here we create a new tool m_CreatedTool = mitk::NavigationTool::New(); //create DataNode... mitk::DataNode::Pointer newNode = mitk::DataNode::New(); if(m_Controls->m_Surface_Use_Sphere->isChecked()) { //create small sphere and use it as surface mitk::Surface::Pointer mySphere = mitk::Surface::New(); vtkConeSource *vtkData = vtkConeSource::New(); vtkData->SetAngle(5.0); vtkData->SetResolution(50); vtkData->SetHeight(6.0f); vtkData->SetRadius(2.0f); vtkData->SetCenter(0.0, 0.0, 0.0); vtkData->Update(); mySphere->SetVtkPolyData(vtkData->GetOutput()); vtkData->Delete(); newNode->SetData(mySphere); } else { newNode->SetData(m_Controls->m_SurfaceChooser->GetSelectedNode()->GetData()); } newNode->SetName(m_Controls->m_ToolNameEdit->text().toLatin1()); m_CreatedTool->SetDataNode(newNode); //fill NavigationTool object m_CreatedTool->SetCalibrationFile(m_Controls->m_CalibrationFileName->text().toLatin1().data()); m_CreatedTool->SetIdentifier(m_Controls->m_IdentifierEdit->text().toLatin1().data()); m_CreatedTool->SetSerialNumber(m_Controls->m_SerialNumberEdit->text().toLatin1().data()); //Tracking Device if (m_Controls->m_TrackingDeviceTypeChooser->currentText()=="NDI Aurora") m_CreatedTool->SetTrackingDeviceType(mitk::NDIAurora); else if (m_Controls->m_TrackingDeviceTypeChooser->currentText()=="NDI Polaris") m_CreatedTool->SetTrackingDeviceType(mitk::NDIPolaris); else if (m_Controls->m_TrackingDeviceTypeChooser->currentText()=="CT MicronTracker") m_CreatedTool->SetTrackingDeviceType(mitk::ClaronMicron); else if (m_Controls->m_TrackingDeviceTypeChooser->currentText()=="NP Optitrack") m_CreatedTool->SetTrackingDeviceType(mitk::NPOptitrack); else if (m_Controls->m_TrackingDeviceTypeChooser->currentText()=="Virtual Tracker") m_CreatedTool->SetTrackingDeviceType(mitk::VirtualTracker); else m_CreatedTool->SetTrackingDeviceType(mitk::TrackingSystemNotSpecified); //ToolType if (m_Controls->m_ToolTypeChooser->currentText()=="Instrument") m_CreatedTool->SetType(mitk::NavigationTool::Instrument); else if (m_Controls->m_ToolTypeChooser->currentText()=="Fiducial") m_CreatedTool->SetType(mitk::NavigationTool::Fiducial); else if (m_Controls->m_ToolTypeChooser->currentText()=="Skinmarker") m_CreatedTool->SetType(mitk::NavigationTool::Skinmarker); else m_CreatedTool->SetType(mitk::NavigationTool::Unknown); //Tool Tip mitk::NavigationData::Pointer tempND = mitk::NavigationData::New(m_AdvancedWidget->GetManipulatedToolTip()); m_CreatedTool->SetToolTipOrientation(tempND->GetOrientation()); m_CreatedTool->SetToolTipPosition(tempND->GetPosition()); //Tool Landmarks mitk::PointSet::Pointer toolCalLandmarks, toolRegLandmarks; GetUIToolLandmarksLists(toolCalLandmarks,toolRegLandmarks); m_CreatedTool->SetToolCalibrationLandmarks(toolCalLandmarks); m_CreatedTool->SetToolRegistrationLandmarks(toolRegLandmarks); emit NavigationToolFinished(); } void QmitkNavigationToolCreationWidget::OnCancel() { m_CreatedTool = NULL; emit Canceled(); } void QmitkNavigationToolCreationWidget::OnLoadSurface() { std::string filename = QFileDialog::getOpenFileName(NULL,tr("Open Surface"), "/", tr("STL (*.stl)")).toLatin1().data(); try { mitk::IOUtil::Load(filename.c_str(), *m_DataStorage); } catch (mitk::Exception &e) { MITK_ERROR << "Exception occured: " << e.what(); } } void QmitkNavigationToolCreationWidget::OnLoadCalibrationFile() { m_Controls->m_CalibrationFileName->setText(QFileDialog::getOpenFileName(NULL,tr("Open Calibration File"), "/", "*.*")); } void QmitkNavigationToolCreationWidget::SetDefaultData(mitk::NavigationTool::Pointer DefaultTool) { m_Controls->m_ToolNameEdit->setText(QString(DefaultTool->GetDataNode()->GetName().c_str())); m_Controls->m_IdentifierEdit->setText(QString(DefaultTool->GetIdentifier().c_str())); m_Controls->m_SerialNumberEdit->setText(QString(DefaultTool->GetSerialNumber().c_str())); m_AdvancedWidget->SetDefaultTooltip( DefaultTool->GetToolTipTransform() ); switch(DefaultTool->GetTrackingDeviceType()) { case mitk::NDIAurora: m_Controls->m_TrackingDeviceTypeChooser->setCurrentIndex(0);break; case mitk::NDIPolaris: m_Controls->m_TrackingDeviceTypeChooser->setCurrentIndex(1);break; case mitk::ClaronMicron: m_Controls->m_TrackingDeviceTypeChooser->setCurrentIndex(2);break; case mitk::NPOptitrack: m_Controls->m_TrackingDeviceTypeChooser->setCurrentIndex(3);break; case mitk::VirtualTracker: m_Controls->m_TrackingDeviceTypeChooser->setCurrentIndex(4);break; default: m_Controls->m_TrackingDeviceTypeChooser->setCurrentIndex(0); } m_Controls->m_CalibrationFileName->setText(QString(DefaultTool->GetCalibrationFile().c_str())); m_Controls->m_Surface_Use_Other->setChecked(true); switch(DefaultTool->GetType()) { case mitk::NavigationTool::Instrument: m_Controls->m_ToolTypeChooser->setCurrentIndex(0); break; case mitk::NavigationTool::Fiducial: m_Controls->m_ToolTypeChooser->setCurrentIndex(1); break; case mitk::NavigationTool::Skinmarker: m_Controls->m_ToolTypeChooser->setCurrentIndex(2); break; case mitk::NavigationTool::Unknown: m_Controls->m_ToolTypeChooser->setCurrentIndex(3); break; } m_Controls->m_SurfaceChooser->SetSelectedNode(DefaultTool->GetDataNode()); FillUIToolLandmarkLists(DefaultTool->GetToolCalibrationLandmarks(),DefaultTool->GetToolRegistrationLandmarks()); } //################################################################################## //############################## internal help methods ############################# //################################################################################## void QmitkNavigationToolCreationWidget::MessageBox(std::string s) { QMessageBox msgBox; msgBox.setText(s.c_str()); msgBox.exec(); } void QmitkNavigationToolCreationWidget::OnShowAdvancedOptions(bool state) { if(state) { m_AdvancedWidget->show(); m_AdvancedWidget->SetDefaultTooltip(m_AdvancedWidget->GetManipulatedToolTip()); //use the last one, if there is one m_AdvancedWidget->ReInitialize(); // reinit the views with the new nodes mitk::DataStorage::SetOfObjects::ConstPointer rs = m_DataStorage->GetAll(); mitk::TimeGeometry::Pointer bounds = m_DataStorage->ComputeBoundingGeometry3D(rs, "visible"); // initialize the views to the bounding geometry mitk::RenderingManager::GetInstance()->InitializeViews(bounds); } else { m_AdvancedWidget->hide(); } } void QmitkNavigationToolCreationWidget::OnProcessDialogCloseRequest() { m_AdvancedWidget->hide(); m_Controls->m_ShowAdvancedOptionsPB->setChecked(false); } void QmitkNavigationToolCreationWidget::OnRetrieveDataForManualTooltipManipulation() { if(m_Controls->m_Surface_Use_Sphere->isChecked()) { m_AdvancedWidget->SetToolTipSurface(true); } else { m_AdvancedWidget->SetToolTipSurface(false, dynamic_cast(m_Controls->m_SurfaceChooser->GetSelectedNode().GetPointer())); } } void QmitkNavigationToolCreationWidget::OnSurfaceUseOtherToggled(bool checked) { m_Controls->m_LoadSurface->setEnabled(checked); } void QmitkNavigationToolCreationWidget::FillUIToolLandmarkLists(mitk::PointSet::Pointer calLandmarks, mitk::PointSet::Pointer regLandmarks) { m_calLandmarkNode->SetData(calLandmarks); m_regLandmarkNode->SetData(regLandmarks); m_Controls->m_CalibrationLandmarksList->SetPointSetNode(m_calLandmarkNode); m_Controls->m_RegistrationLandmarksList->SetPointSetNode(m_regLandmarkNode); } void QmitkNavigationToolCreationWidget::GetUIToolLandmarksLists(mitk::PointSet::Pointer& calLandmarks, mitk::PointSet::Pointer& regLandmarks) { calLandmarks = dynamic_cast(m_calLandmarkNode->GetData()); regLandmarks = dynamic_cast(m_regLandmarkNode->GetData()); } void QmitkNavigationToolCreationWidget::InitializeUIToolLandmarkLists() { m_calLandmarkNode = mitk::DataNode::New(); m_regLandmarkNode = mitk::DataNode::New(); FillUIToolLandmarkLists(mitk::PointSet::New(),mitk::PointSet::New()); }