diff --git a/Modules/US/USNavigation/mitkAbstractUltrasoundTrackerDevice.cpp b/Modules/US/USNavigation/mitkAbstractUltrasoundTrackerDevice.cpp index 8bb5a8975b..19e989ad48 100644 --- a/Modules/US/USNavigation/mitkAbstractUltrasoundTrackerDevice.cpp +++ b/Modules/US/USNavigation/mitkAbstractUltrasoundTrackerDevice.cpp @@ -1,473 +1,474 @@ /*=================================================================== 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 "mitkAbstractUltrasoundTrackerDevice.h" #include "mitkImageReadAccessor.h" #include "mitkNavigationDataSmoothingFilter.h" #include "mitkNavigationDataDelayFilter.h" #include "mitkNavigationDataDisplacementFilter.h" #include "mitkTrackingDeviceSource.h" // US Control Interfaces #include "mitkUSControlInterfaceProbes.h" #include "mitkUSControlInterfaceBMode.h" #include "mitkUSControlInterfaceDoppler.h" //Microservices #include #include #include #include #include //TempIncludes #include const std::string mitk::AbstractUltrasoundTrackerDevice::DeviceClassIdentifier = "org.mitk.modules.us.AbstractUltrasoundTrackerDevice"; const char* mitk::AbstractUltrasoundTrackerDevice::DefaultProbeIdentifier = "default"; const char* mitk::AbstractUltrasoundTrackerDevice::ProbeAndDepthSeperator = "_"; const std::string mitk::AbstractUltrasoundTrackerDevice::US_INTERFACE_NAME = "org.mitk.services.AbstractUltrasoundTrackerDevice"; const std::string mitk::AbstractUltrasoundTrackerDevice::US_PROPKEY_DEVICENAME = US_INTERFACE_NAME + ".devicename"; const std::string mitk::AbstractUltrasoundTrackerDevice::US_PROPKEY_CLASS = US_INTERFACE_NAME + ".class"; const std::string mitk::AbstractUltrasoundTrackerDevice::US_PROPKEY_ID = US_INTERFACE_NAME + ".id"; //____ mitk::AbstractUltrasoundTrackerDevice::AbstractUltrasoundTrackerDevice( USDevice::Pointer usDevice, NavigationDataSource::Pointer trackingDevice, bool trackedUltrasoundActive ) : m_UltrasoundDevice(usDevice), m_TrackingDeviceDataSource(trackingDevice), m_SmoothingFilter(mitk::NavigationDataSmoothingFilter::New()), m_DelayFilter(mitk::NavigationDataDelayFilter::New(0)), m_DisplacementFilter(mitk::NavigationDataDisplacementFilter::New()), m_LastFilterOfIGTPipeline(nullptr), m_NumberOfSmoothingValues(0), m_DelayCount(0), m_IsTrackedUltrasoundActive( trackedUltrasoundActive ) { m_DisplacementFilter->SetTransform6DOF(true); this->RebuildFilterPipeline(); //create a new output (for the image data) //___ mitk::Image::Pointer newOutput = mitk::Image::New(); //___ this->SetNthOutput(0, newOutput); // Combined Modality should not spawn an own acquire thread, because // image acquiring is done by the included us device //___ m_UltrasoundDevice->SetSpawnAcquireThread(false); } mitk::AbstractUltrasoundTrackerDevice::~AbstractUltrasoundTrackerDevice() { if (m_ServiceRegistration != nullptr) { m_ServiceRegistration.Unregister(); } m_ServiceRegistration = 0; } mitk::AffineTransform3D::Pointer mitk::AbstractUltrasoundTrackerDevice::GetCalibration() { return this->GetCalibration( this->GetCurrentDepthValue(), this->GetIdentifierForCurrentProbe() ); } mitk::AffineTransform3D::Pointer mitk::AbstractUltrasoundTrackerDevice::GetCalibration(std::string depth) { return this->GetCalibration(depth, this->GetIdentifierForCurrentProbe()); } mitk::AffineTransform3D::Pointer mitk::AbstractUltrasoundTrackerDevice::GetCalibration( std::string depth, std::string probe ) { // make sure that there is no '/' which would cause problems for TinyXML std::replace(probe.begin(), probe.end(), '/', '-'); // create identifier for calibration from probe and depth std::string calibrationKey = probe + mitk::AbstractUltrasoundTrackerDevice::ProbeAndDepthSeperator + depth; // find calibration for combination of probe identifier and depth std::map::iterator calibrationIterator = m_Calibrations.find(calibrationKey); if (calibrationIterator == m_Calibrations.end()) { return 0; } return calibrationIterator->second; } void mitk::AbstractUltrasoundTrackerDevice::SetCalibration( mitk::AffineTransform3D::Pointer calibration ) { if( calibration.IsNull() ) { MITK_WARN << "Null pointer passed to SetCalibration of mitk::USDevice. Ignoring call."; return; } std::string calibrationKey = this->GetIdentifierForCurrentCalibration(); if( calibrationKey.empty() ) { MITK_WARN << "Could not get a key for the calibration -> Calibration cannot be set."; return; } m_Calibrations[calibrationKey] = calibration; } bool mitk::AbstractUltrasoundTrackerDevice::RemoveCalibration() { return this->RemoveCalibration( this->GetCurrentDepthValue(), this->GetIdentifierForCurrentProbe() ); } bool mitk::AbstractUltrasoundTrackerDevice::RemoveCalibration(std::string depth) { return this->RemoveCalibration( depth, this->GetIdentifierForCurrentProbe() ); } bool mitk::AbstractUltrasoundTrackerDevice::RemoveCalibration( std::string depth, std::string probe ) { // make sure that there is no '/' which would cause problems for TinyXML std::replace(probe.begin(), probe.end(), '/', '-'); // create identifier for calibration from probe and depth std::string calibrationKey = probe + mitk::AbstractUltrasoundTrackerDevice::ProbeAndDepthSeperator + depth; return m_Calibrations.erase(calibrationKey) > 0; } std::string mitk::AbstractUltrasoundTrackerDevice::GetDeviceClass() { return DeviceClassIdentifier; } mitk::USImageSource::Pointer mitk::AbstractUltrasoundTrackerDevice::GetUSImageSource() { if (m_UltrasoundDevice.IsNull()) { MITK_ERROR("AbstractUltrasoundTrackerDevice")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } return m_UltrasoundDevice->GetUSImageSource(); } mitk::NavigationDataSource::Pointer mitk::AbstractUltrasoundTrackerDevice::GetNavigationDataSource() { if( m_LastFilterOfIGTPipeline.IsNull() ) { this->RebuildFilterPipeline(); } + m_LastFilterOfIGTPipeline->SetToolMetaDataCollection(this->m_TrackingDeviceDataSource->GetToolMetaDataCollection()); return m_LastFilterOfIGTPipeline; } bool mitk::AbstractUltrasoundTrackerDevice::GetIsCalibratedForCurrentStatus() { return m_Calibrations.find(this->GetIdentifierForCurrentCalibration()) != m_Calibrations.end(); } bool mitk::AbstractUltrasoundTrackerDevice::GetContainsAtLeastOneCalibration() { return !m_Calibrations.empty(); } std::string mitk::AbstractUltrasoundTrackerDevice::SerializeCalibration() { std::stringstream result; result << "" << std::endl; // For each calibration in the set for( std::map::iterator it = m_Calibrations.begin(); it != m_Calibrations.end(); it++ ) { mitk::AffineTransform3D::MatrixType matrix = it->second->GetMatrix(); mitk::AffineTransform3D::TranslationType translation = it->second->GetTranslation(); TiXmlElement elem(it->first); // Serialize Matrix elem.SetDoubleAttribute("M00", matrix[0][0]); elem.SetDoubleAttribute("M01", matrix[0][1]); elem.SetDoubleAttribute("M02", matrix[0][2]); elem.SetDoubleAttribute("M10", matrix[1][0]); elem.SetDoubleAttribute("M11", matrix[1][1]); elem.SetDoubleAttribute("M12", matrix[1][2]); elem.SetDoubleAttribute("M20", matrix[2][0]); elem.SetDoubleAttribute("M21", matrix[2][1]); elem.SetDoubleAttribute("M22", matrix[2][2]); // Serialize Offset elem.SetDoubleAttribute("T0", translation[0]); elem.SetDoubleAttribute("T1", translation[1]); elem.SetDoubleAttribute("T2", translation[2]); result << elem << std::endl; } result << "" << std::endl; return result.str(); } void mitk::AbstractUltrasoundTrackerDevice::DeserializeCalibration( const std::string& xmlString, bool clearPreviousCalibrations ) { // Sanitize Input if (xmlString == "") { MITK_ERROR << "Empty string passed to Deserialize() method of CombinedModality. Aborting..."; mitkThrow() << "Empty string passed to Deserialize() method of CombinedModality. Aborting..."; return; } // Clear previous calibrations if necessary if (clearPreviousCalibrations) m_Calibrations.clear(); // Parse Input TiXmlDocument doc; if (!doc.Parse(xmlString.c_str())) { MITK_ERROR << "Unable to deserialize calibrations in CombinedModality. Error was: " << doc.ErrorDesc(); mitkThrow() << "Unable to deserialize calibrations in CombinedModality. Error was: " << doc.ErrorDesc(); return; } TiXmlElement* root = doc.FirstChildElement(); if (root == nullptr) { MITK_ERROR << "Unable to deserialize calibrations in CombinedModality. String contained no root element."; mitkThrow() << "Unable to deserialize calibrations in CombinedModality. String contained no root element."; return; } // Read Calibrations for (TiXmlElement* elem = root->FirstChildElement(); elem != nullptr; elem = elem->NextSiblingElement()) { mitk::AffineTransform3D::MatrixType matrix; mitk::AffineTransform3D::OffsetType translation; std::string calibName = elem->Value(); // Deserialize Matrix elem->QueryDoubleAttribute("M00", &matrix[0][0]); elem->QueryDoubleAttribute("M01", &matrix[0][1]); elem->QueryDoubleAttribute("M02", &matrix[0][2]); elem->QueryDoubleAttribute("M10", &matrix[1][0]); elem->QueryDoubleAttribute("M11", &matrix[1][1]); elem->QueryDoubleAttribute("M12", &matrix[1][2]); elem->QueryDoubleAttribute("M20", &matrix[2][0]); elem->QueryDoubleAttribute("M21", &matrix[2][1]); elem->QueryDoubleAttribute("M22", &matrix[2][2]); // Deserialize Offset elem->QueryDoubleAttribute("T0", &translation[0]); elem->QueryDoubleAttribute("T1", &translation[1]); elem->QueryDoubleAttribute("T2", &translation[2]); mitk::AffineTransform3D::Pointer calibration = mitk::AffineTransform3D::New(); calibration->SetMatrix(matrix); calibration->SetTranslation(translation); m_Calibrations[calibName] = calibration; } } void mitk::AbstractUltrasoundTrackerDevice::SetNumberOfSmoothingValues( unsigned int numberOfSmoothingValues ) { unsigned int oldNumber = m_NumberOfSmoothingValues; m_NumberOfSmoothingValues = numberOfSmoothingValues; // if filter should be activated or deactivated if ((oldNumber == 0 && numberOfSmoothingValues != 0) || (oldNumber != 0 && numberOfSmoothingValues == 0)) { this->RebuildFilterPipeline(); } m_SmoothingFilter->SetNumerOfValues(numberOfSmoothingValues); } void mitk::AbstractUltrasoundTrackerDevice::SetDelayCount( unsigned int delayCount ) { unsigned int oldCount = m_DelayCount; m_DelayCount = delayCount; // if filter should be activated or deactivated if ((oldCount == 0 && delayCount != 0) || (oldCount != 0 && delayCount == 0)) { this->RebuildFilterPipeline(); } m_DelayFilter->SetDelay(delayCount); } void mitk::AbstractUltrasoundTrackerDevice::GenerateData() { } std::string mitk::AbstractUltrasoundTrackerDevice::GetIdentifierForCurrentCalibration() { return this->GetIdentifierForCurrentProbe() + mitk::AbstractUltrasoundTrackerDevice::ProbeAndDepthSeperator + this->GetCurrentDepthValue(); } std::string mitk::AbstractUltrasoundTrackerDevice::GetIdentifierForCurrentProbe() { us::ServiceProperties usdeviceProperties = m_UltrasoundDevice->GetServiceProperties(); us::ServiceProperties::const_iterator probeIt = usdeviceProperties.find( mitk::USDevice::GetPropertyKeys().US_PROPKEY_PROBES_SELECTED); // get probe identifier from control interface for probes std::string probeName = mitk::AbstractUltrasoundTrackerDevice::DefaultProbeIdentifier; if (probeIt != usdeviceProperties.end()) { probeName = (probeIt->second).ToString(); } // make sure that there is no '/' which would cause problems for TinyXML std::replace(probeName.begin(), probeName.end(), '/', '-'); return probeName; } std::string mitk::AbstractUltrasoundTrackerDevice::GetCurrentDepthValue() { us::ServiceProperties usdeviceProperties = m_UltrasoundDevice->GetServiceProperties(); // get string for depth value from the micro service properties std::string depth; us::ServiceProperties::iterator depthIterator = usdeviceProperties.find( mitk::USDevice::GetPropertyKeys().US_PROPKEY_BMODE_DEPTH); if (depthIterator != usdeviceProperties.end()) { depth = depthIterator->second.ToString(); } else { depth = "0"; } return depth; } void mitk::AbstractUltrasoundTrackerDevice::RebuildFilterPipeline() { m_LastFilterOfIGTPipeline = m_TrackingDeviceDataSource; if( m_NumberOfSmoothingValues > 0 ) { m_SmoothingFilter->ConnectTo(m_LastFilterOfIGTPipeline.GetPointer()); m_LastFilterOfIGTPipeline = m_SmoothingFilter; } if( m_DelayCount > 0 ) { m_DelayFilter->ConnectTo(m_LastFilterOfIGTPipeline.GetPointer()); m_LastFilterOfIGTPipeline = m_DelayFilter; } if( m_IsTrackedUltrasoundActive ) { m_DisplacementFilter->ConnectTo(m_LastFilterOfIGTPipeline.GetPointer()); m_LastFilterOfIGTPipeline = m_DisplacementFilter; } } void mitk::AbstractUltrasoundTrackerDevice::UnregisterOnService() { if (m_UltrasoundDevice->GetDeviceState() == USDevice::State_Activated) { m_UltrasoundDevice->Deactivate(); } if (m_UltrasoundDevice->GetDeviceState() == USDevice::State_Connected) { m_UltrasoundDevice->Disconnect(); } if (m_ServiceRegistration != nullptr) m_ServiceRegistration.Unregister(); m_ServiceRegistration = 0; } void mitk::AbstractUltrasoundTrackerDevice::RegisterAsMicroservice() { //Get Context us::ModuleContext* context = us::GetModuleContext(); //Define ServiceProps //us::ServiceProperties props; mitk::UIDGenerator uidGen = mitk::UIDGenerator("org.mitk.services.AbstractUltrasoundTrackerDevice", 16); m_ServiceProperties[US_PROPKEY_ID] = uidGen.GetUID(); m_ServiceProperties[US_PROPKEY_DEVICENAME] = m_UltrasoundDevice->GetName(); m_ServiceProperties[US_PROPKEY_CLASS] = mitk::AbstractUltrasoundTrackerDevice::DeviceClassIdentifier; m_ServiceRegistration = context->RegisterService(this, m_ServiceProperties); } mitk::USAbstractControlInterface::Pointer mitk::AbstractUltrasoundTrackerDevice::GetControlInterfaceCustom() { if (m_UltrasoundDevice.IsNull()) { MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } return m_UltrasoundDevice->GetControlInterfaceCustom(); } mitk::USControlInterfaceBMode::Pointer mitk::AbstractUltrasoundTrackerDevice::GetControlInterfaceBMode() { if (m_UltrasoundDevice.IsNull()) { MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } return m_UltrasoundDevice->GetControlInterfaceBMode(); } mitk::USControlInterfaceProbes::Pointer mitk::AbstractUltrasoundTrackerDevice::GetControlInterfaceProbes() { if (m_UltrasoundDevice.IsNull()) { MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } return m_UltrasoundDevice->GetControlInterfaceProbes(); } mitk::USControlInterfaceDoppler::Pointer mitk::AbstractUltrasoundTrackerDevice::GetControlInterfaceDoppler() { if (m_UltrasoundDevice.IsNull()) { MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } return m_UltrasoundDevice->GetControlInterfaceDoppler(); } diff --git a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/QmitkUSNavigationMarkerPlacement.cpp b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/QmitkUSNavigationMarkerPlacement.cpp index 877b8848f2..7cbe1a69bf 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/QmitkUSNavigationMarkerPlacement.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/QmitkUSNavigationMarkerPlacement.cpp @@ -1,698 +1,760 @@ /*=================================================================== 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 "QmitkUSNavigationMarkerPlacement.h" #include "ui_QmitkUSNavigationMarkerPlacement.h" #include "NavigationStepWidgets/QmitkUSNavigationStepCombinedModality.h" #include "NavigationStepWidgets/QmitkUSNavigationStepMarkerIntervention.h" #include "NavigationStepWidgets/QmitkUSNavigationStepPlacementPlanning.h" #include "NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.h" #include "NavigationStepWidgets/QmitkUSNavigationStepTumourSelection.h" #include "NavigationStepWidgets/QmitkUSNavigationStepZoneMarking.h" #include "SettingsWidgets/QmitkUSNavigationCombinedSettingsWidget.h" +#include "mitkAbstractUltrasoundTrackerDevice.h" #include "mitkIRenderingManager.h" #include "mitkNodeDisplacementFilter.h" -#include "mitkAbstractUltrasoundTrackerDevice.h" +#include "mitkTrackedUltrasound.h" #include #include "IO/mitkUSNavigationStepTimer.h" #include #include #include #include #include #include #include "QmitkRenderWindow.h" #include "QmitkStdMultiWidget.h" #include "QmitkStdMultiWidgetEditor.h" -#include "mitkLayoutAnnotationRenderer.h" #include "mitkCameraController.h" +#include "mitkLayoutAnnotationRenderer.h" #include // scene serialization #include #include #include #include #include const std::string QmitkUSNavigationMarkerPlacement::VIEW_ID = "org.mitk.views.usmarkerplacement"; const char *QmitkUSNavigationMarkerPlacement::DATANAME_TUMOUR = "Tumour"; const char *QmitkUSNavigationMarkerPlacement::DATANAME_TARGETSURFACE = "Target Surface"; const char *QmitkUSNavigationMarkerPlacement::DATANAME_ZONES = "Zones"; const char *QmitkUSNavigationMarkerPlacement::DATANAME_TARGETS = "Targets"; const char *QmitkUSNavigationMarkerPlacement::DATANAME_TARGETS_PATHS = "Target Paths"; const char *QmitkUSNavigationMarkerPlacement::DATANAME_REACHED_TARGETS = "Reached Targets"; QmitkUSNavigationMarkerPlacement::QmitkUSNavigationMarkerPlacement() : m_Parent(nullptr), - m_UpdateTimer(new QTimer(this)), - m_ImageAndNavigationDataLoggingTimer(new QTimer(this)), - m_StdMultiWidget(nullptr), - m_CombinedModality(nullptr), - m_ImageStreamNode(nullptr), - m_ReinitAlreadyDone(false), - m_IsExperimentRunning(false), - m_CurrentApplicationName(), - m_NavigationStepTimer(mitk::USNavigationStepTimer::New()), - m_IconRunning(QPixmap(":/USNavigation/record.png")), - m_IconNotRunning(QPixmap(":/USNavigation/record-gray.png")), - m_ResultsDirectory(), - m_ExperimentName(), - m_ExperimentResultsSubDirectory(), - m_NavigationStepNames(), - m_LoggingBackend(), - m_USImageLoggingFilter(mitk::USImageLoggingFilter::New()), - m_NavigationDataRecorder(mitk::NavigationDataRecorder::New()), - m_TargetNodeDisplacementFilter(nullptr), - m_AblationZonesDisplacementFilter(mitk::NodeDisplacementFilter::New()), - m_AblationZonesVector(), - m_NeedleIndex(0), - m_MarkerIndex(1), - m_SceneNumber(1), - m_WarnOverlay(mitk::TextAnnotation2D::New()), - m_NavigationDataSource(nullptr), - m_CurrentStorage(nullptr), - ui(new Ui::QmitkUSNavigationMarkerPlacement ) + m_UpdateTimer(new QTimer(this)), + m_ImageAndNavigationDataLoggingTimer(new QTimer(this)), + m_StdMultiWidget(nullptr), + m_CombinedModality(nullptr), + m_ImageStreamNode(nullptr), + m_ReinitAlreadyDone(false), + m_IsExperimentRunning(false), + m_CurrentApplicationName(), + m_NavigationStepTimer(mitk::USNavigationStepTimer::New()), + m_IconRunning(QPixmap(":/USNavigation/record.png")), + m_IconNotRunning(QPixmap(":/USNavigation/record-gray.png")), + m_ResultsDirectory(), + m_ExperimentName(), + m_ExperimentResultsSubDirectory(), + m_NavigationStepNames(), + m_LoggingBackend(), + m_USImageLoggingFilter(mitk::USImageLoggingFilter::New()), + m_NavigationDataRecorder(mitk::NavigationDataRecorder::New()), + m_TargetNodeDisplacementFilter(nullptr), + m_AblationZonesDisplacementFilter(mitk::NodeDisplacementFilter::New()), + m_AblationZonesVector(), + m_NeedleIndex(0), + m_MarkerIndex(1), + m_SceneNumber(1), + m_WarnOverlay(mitk::TextAnnotation2D::New()), + m_NavigationDataSource(nullptr), + m_CurrentStorage(nullptr), + ui(new Ui::QmitkUSNavigationMarkerPlacement), + m_ToolVisualizationFilter(nullptr) { connect(m_UpdateTimer, SIGNAL(timeout()), this, SLOT(OnTimeout())); connect( m_ImageAndNavigationDataLoggingTimer, SIGNAL(timeout()), this, SLOT(OnImageAndNavigationDataLoggingTimeout())); // scale running (and not running) icon the specific height m_IconRunning = m_IconRunning.scaledToHeight(20, Qt::SmoothTransformation); m_IconNotRunning = m_IconNotRunning.scaledToHeight(20, Qt::SmoothTransformation); - m_UpdateTimer->start(33); // every 33 Milliseconds = 30 Frames/Second + m_UpdateTimer->start(50); // every 50 Milliseconds = 20 Frames/Second } QmitkUSNavigationMarkerPlacement::~QmitkUSNavigationMarkerPlacement() { + this->GetDataStorage()->Remove(m_InstrumentNode); delete ui; } void QmitkUSNavigationMarkerPlacement::OnChangeAblationZone(int id, int newSize) { if ((static_cast(m_AblationZonesVector.size()) < id) || (id < 0)) { return; } MITK_INFO << "Ablation Zone " << id << " changed, new size: " << newSize; // create a vtk sphere with given radius vtkSmartPointer vtkSphere = vtkSmartPointer::New(); vtkSphere->SetRadius(newSize / 2); vtkSphere->SetCenter(0, 0, 0); vtkSphere->SetPhiResolution(20); vtkSphere->SetThetaResolution(20); vtkSphere->Update(); mitk::Surface::Pointer zoneSurface = dynamic_cast(m_AblationZonesVector.at(id)->GetData()); zoneSurface->SetVtkPolyData(vtkSphere->GetOutput()); } void QmitkUSNavigationMarkerPlacement::OnAddAblationZone(int size) { m_AblationZonesDisplacementFilter->SetInitialReferencePose( m_CombinedModality->GetNavigationDataSource()->GetOutput(m_MarkerIndex)); mitk::DataNode::Pointer NewAblationZone = mitk::DataNode::New(); mitk::Point3D origin = m_CombinedModality->GetNavigationDataSource()->GetOutput(m_NeedleIndex)->GetPosition(); MITK_INFO("USNavigationLogging") << "Ablation Zone Added, initial size: " << size << ", origin: " << origin; mitk::Surface::Pointer zone = mitk::Surface::New(); // create a vtk sphere with given radius vtkSmartPointer vtkSphere = vtkSmartPointer::New(); vtkSphere->SetRadius(size / 2); vtkSphere->SetCenter(0, 0, 0); vtkSphere->SetPhiResolution(20); vtkSphere->SetThetaResolution(20); vtkSphere->Update(); zone->SetVtkPolyData(vtkSphere->GetOutput()); // set vtk sphere and origin to data node (origin must be set // again, because of the new sphere set as data) NewAblationZone->SetData(zone); NewAblationZone->GetData()->GetGeometry()->SetOrigin(origin); mitk::Color SphereColor = mitk::Color(); // default color SphereColor[0] = 102; SphereColor[1] = 0; SphereColor[2] = 204; NewAblationZone->SetColor(SphereColor); NewAblationZone->SetOpacity(0.3); // set name of zone std::stringstream name; name << "Ablation Zone" << m_AblationZonesVector.size(); NewAblationZone->SetName(name.str()); // add zone to filter m_AblationZonesDisplacementFilter->AddNode(NewAblationZone); m_AblationZonesVector.push_back(NewAblationZone); this->GetDataStorage()->Add(NewAblationZone); } void QmitkUSNavigationMarkerPlacement::CreateQtPartControl(QWidget *parent) { m_Parent = parent; ui->setupUi(parent); connect(ui->startExperimentButton, SIGNAL(clicked()), this, SLOT(OnStartExperiment())); connect(ui->finishExperimentButton, SIGNAL(clicked()), this, SLOT(OnFinishExperiment())); connect(ui->m_enableNavigationLayout, SIGNAL(clicked()), this, SLOT(OnChangeLayoutClicked())); connect(ui->m_RenderWindowSelection, SIGNAL(valueChanged(int)), this, SLOT(OnRenderWindowSelection())); connect(ui->m_RefreshView, SIGNAL(clicked()), this, SLOT(OnRefreshView())); m_BaseNode = this->GetDataStorage()->GetNamedNode(QmitkUSAbstractNavigationStep::DATANAME_BASENODE); if (m_BaseNode.IsNull()) { m_BaseNode = mitk::DataNode::New(); m_BaseNode->SetName(QmitkUSAbstractNavigationStep::DATANAME_BASENODE); this->GetDataStorage()->Add(m_BaseNode); } connect(ui->m_initializeTargetMarking, SIGNAL(clicked()), this, SLOT(OnInitializeTargetMarking())); connect(ui->m_initializeCritStructureMarking, SIGNAL(clicked()), this, SLOT(OnInitializeCriticalStructureMarking())); connect(ui->m_initializeNavigation, SIGNAL(clicked()), this, SLOT(OnInitializeNavigation())); // indicate that no experiment is running at start ui->runningLabel->setPixmap(m_IconNotRunning); - connect(ui->m_settingsWidget, SIGNAL(SettingsChanged(itk::SmartPointer)), this, SLOT(OnSettingsChanged(itk::SmartPointer))); - + connect(ui->m_settingsWidget, + SIGNAL(SettingsChanged(itk::SmartPointer)), + this, + SLOT(OnSettingsChanged(itk::SmartPointer))); } void QmitkUSNavigationMarkerPlacement::ReInitializeSettingsNodesAndImageStream() { m_SettingsNode = mitk::DataNode::New(); ui->m_settingsWidget->OnSetSettingsNode(m_SettingsNode, true); InitImageStream(); m_CombinedModality = ui->m_CombinedModalityCreationWidget->GetSelectedCombinedModality(); } void QmitkUSNavigationMarkerPlacement::OnInitializeTargetMarking() { ReInitializeSettingsNodesAndImageStream(); ui->m_TargetMarkingWidget->SetCombinedModality(m_CombinedModality); ui->m_TargetMarkingWidget->SetDataStorage(this->GetDataStorage()); ui->m_TargetMarkingWidget->OnSettingsChanged(m_SettingsNode); ui->m_TargetMarkingWidget->OnActivateStep(); ui->m_TargetMarkingWidget->OnStartStep(); ui->m_TargetMarkingWidget->Update(); - } void QmitkUSNavigationMarkerPlacement::OnInitializeCriticalStructureMarking() { ReInitializeSettingsNodesAndImageStream(); ui->m_CriticalStructuresWidget->SetCombinedModality(m_CombinedModality); ui->m_CriticalStructuresWidget->SetDataStorage(this->GetDataStorage()); ui->m_CriticalStructuresWidget->OnSettingsChanged(m_SettingsNode); ui->m_CriticalStructuresWidget->OnActivateStep(); ui->m_CriticalStructuresWidget->OnStartStep(); ui->m_CriticalStructuresWidget->Update(); } void QmitkUSNavigationMarkerPlacement::OnInitializeNavigation() { - ReInitializeSettingsNodesAndImageStream(); ui->m_NavigationWidget->SetCombinedModality(m_CombinedModality); ui->m_NavigationWidget->SetDataStorage(this->GetDataStorage()); ui->m_NavigationWidget->OnSettingsChanged(m_SettingsNode); ui->m_NavigationWidget->OnActivateStep(); ui->m_NavigationWidget->OnStartStep(); ui->m_NavigationWidget->Update(); + // test if it is tracked US, if yes add visualization filter + if (m_CombinedModality->GetIsTrackedUltrasoundActive()) + { + mitk::TrackedUltrasound *test = dynamic_cast(this->m_CombinedModality.GetPointer()); + m_InstrumentNode = mitk::DataNode::New(); + m_InstrumentNode->SetName("Tracked US Instrument"); + m_InstrumentNode->SetData( + m_CombinedModality->GetNavigationDataSource()->GetToolMetaData(0)->GetToolSurface()->Clone()); + this->GetDataStorage()->Add(m_InstrumentNode); + m_ToolVisualizationFilter = mitk::NavigationDataObjectVisualizationFilter::New(); + m_ToolVisualizationFilter->ConnectTo(m_CombinedModality->GetNavigationDataSource()); + m_ToolVisualizationFilter->SetRepresentationObject(0, m_InstrumentNode->GetData()); + } } void QmitkUSNavigationMarkerPlacement::InitImageStream() { if (m_ImageStreamNode.IsNull()) { m_ImageStreamNode = mitk::DataNode::New(); m_ImageStreamNode->SetName("US Navigation Viewing Stream"); this->GetDataStorage()->Add(m_ImageStreamNode); } } void QmitkUSNavigationMarkerPlacement::OnCombinedModalityPropertyChanged(const std::string &key, const std::string &) { if (key == mitk::USDevice::GetPropertyKeys().US_PROPKEY_BMODE_DEPTH) { m_ReinitAlreadyDone = false; this->ReinitOnImage(); if (m_CombinedModality.IsNotNull() && !m_CombinedModality->GetIsCalibratedForCurrentStatus()) { mitk::LayoutAnnotationRenderer::AddAnnotation( m_WarnOverlay.GetPointer(), "stdmulti.widget1", mitk::LayoutAnnotationRenderer::TopLeft); MITK_WARN << "No calibration available for the selected ultrasound image depth."; } } } void QmitkUSNavigationMarkerPlacement::SetFocus() { this->ReinitOnImage(); } void QmitkUSNavigationMarkerPlacement::OnTimeout() { - if (m_CombinedModality.IsNull()) return; - m_CombinedModality->Modified(); //shouldn't be nessecary ... fix in abstract ultrasound tracker device! + if (m_CombinedModality.IsNull()) + return; + m_CombinedModality->Modified(); // shouldn't be nessecary ... fix in abstract ultrasound tracker device! m_CombinedModality->Update(); + if (m_ToolVisualizationFilter.IsNotNull()) + { + m_ToolVisualizationFilter->Update(); + } ui->m_TargetMarkingWidget->Update(); ui->m_CriticalStructuresWidget->Update(); ui->m_NavigationWidget->Update(); mitk::Image::Pointer image = m_CombinedModality->GetOutput(); // make sure that always the current image is set to the data node if (image.IsNotNull() && m_ImageStreamNode->GetData() != image.GetPointer() && image->IsInitialized()) { m_ImageStreamNode->SetData(image); } if (!m_StdMultiWidget) { // try to get the standard multi widget if it couldn't be got before mitk::IRenderWindowPart *renderWindow = this->GetRenderWindowPart(); QmitkStdMultiWidgetEditor *multiWidgetEditor = dynamic_cast(renderWindow); // if there is a standard multi widget now, disable the level window and // change the layout to 2D up and 3d down if (multiWidgetEditor) { m_StdMultiWidget = multiWidgetEditor->GetStdMultiWidget(); SetTwoWindowView(); } this->CreateOverlays(); } - if (m_CombinedModality.IsNotNull() && - !this->m_CombinedModality->GetUltrasoundDevice()->GetIsFreezed()) // if the combined modality is freezed: do nothing + if (m_CombinedModality.IsNotNull() && !this->m_CombinedModality->GetUltrasoundDevice() + ->GetIsFreezed()) // if the combined modality is freezed: do nothing { m_AblationZonesDisplacementFilter->Update(); - - // update the 3D window only every fourth time to speed up the rendering (at least in 2D) this->RequestRenderWindowUpdate(mitk::RenderingManager::REQUEST_UPDATE_2DWINDOWS); // make sure that a reinit was performed on the image this->ReinitOnImage(); } } void QmitkUSNavigationMarkerPlacement::OnEnableNavigationLayout() { MITK_INFO << "Navigation Layout"; // try to get the standard multi widget if it couldn't be got before mitk::IRenderWindowPart *renderWindow = this->GetRenderWindowPart(); QmitkStdMultiWidgetEditor *multiWidgetEditor = dynamic_cast(renderWindow); // if there is a standard multi widget now, disable the level window and // change the layout to 2D up and 3d down if (multiWidgetEditor) { m_StdMultiWidget = multiWidgetEditor->GetStdMultiWidget(); SetTwoWindowView(); } } void QmitkUSNavigationMarkerPlacement::OnRenderWindowSelection() { SetTwoWindowView(); } void QmitkUSNavigationMarkerPlacement::OnRefreshView() { if (!ui->m_enableNavigationLayout->isChecked()) OnResetStandardLayout(); else { - //Reinit the US Image Stream (this might be broken if there was a global reinit somewhere...) + // Reinit the US Image Stream (this might be broken if there was a global reinit somewhere...) try { - mitk::RenderingManager::GetInstance()->InitializeViews(//Reinit - this->GetDataStorage()//GetDataStorage - ->GetNamedNode("US Support Viewing Stream")->GetData()->GetTimeGeometry());//GetNode + mitk::RenderingManager::GetInstance()->InitializeViews( // Reinit + this + ->GetDataStorage() // GetDataStorage + ->GetNamedNode("US Support Viewing Stream") + ->GetData() + ->GetTimeGeometry()); // GetNode } catch (...) { MITK_DEBUG << "No reinit possible"; } SetTwoWindowView(); } } void QmitkUSNavigationMarkerPlacement::SetTwoWindowView() { if (m_StdMultiWidget) { m_StdMultiWidget->DisableStandardLevelWindow(); int i, j, k; switch (this->ui->m_RenderWindowSelection->value()) { - case 1: - mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget4"))->GetCameraController()->SetViewToCaudal(); - i = 2; j = 3; //other windows - k = 1; - break; - case 2: - mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget4"))->GetCameraController()->SetViewToSinister(); - i = 1; j = 3; - k = 2; - break; - case 3: - mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget4"))->GetCameraController()->SetViewToAnterior(); - i = 2; j = 1; - k = 3; - break; - default: - return; + case 1: + mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget4")) + ->GetCameraController() + ->SetViewToCaudal(); + i = 2; + j = 3; // other windows + k = 1; + break; + case 2: + mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget4")) + ->GetCameraController() + ->SetViewToSinister(); + i = 1; + j = 3; + k = 2; + break; + case 3: + mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget4")) + ->GetCameraController() + ->SetViewToAnterior(); + i = 2; + j = 1; + k = 3; + break; + default: + return; } m_StdMultiWidget->changeLayoutTo2DUpAnd3DDown(k); ////Crosshair invisible in 3D view - this->GetDataStorage()->GetNamedNode("stdmulti.widget" + std::to_string(i) + ".plane")-> - SetBoolProperty("visible", false, mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget4"))); - this->GetDataStorage()->GetNamedNode("stdmulti.widget" + std::to_string(j) + ".plane")-> - SetBoolProperty("visible", false, mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget4"))); - this->GetDataStorage()->GetNamedNode("stdmulti.widget" + std::to_string(k) + ".plane")-> - SetBoolProperty("visible", true, mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget4"))); - this->GetDataStorage()->GetNamedNode("stdmulti.widget" + std::to_string(i) + ".plane")-> - SetIntProperty("Crosshair.Gap Size", 0); - this->GetDataStorage()->GetNamedNode("stdmulti.widget" + std::to_string(j) + ".plane")-> - SetIntProperty("Crosshair.Gap Size", 0); + this->GetDataStorage() + ->GetNamedNode("stdmulti.widget" + std::to_string(i) + ".plane") + ->SetBoolProperty("visible", + false, + mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget4"))); + this->GetDataStorage() + ->GetNamedNode("stdmulti.widget" + std::to_string(j) + ".plane") + ->SetBoolProperty("visible", + false, + mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget4"))); + this->GetDataStorage() + ->GetNamedNode("stdmulti.widget" + std::to_string(k) + ".plane") + ->SetBoolProperty("visible", + true, + mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget4"))); + this->GetDataStorage() + ->GetNamedNode("stdmulti.widget" + std::to_string(i) + ".plane") + ->SetIntProperty("Crosshair.Gap Size", 0); + this->GetDataStorage() + ->GetNamedNode("stdmulti.widget" + std::to_string(j) + ".plane") + ->SetIntProperty("Crosshair.Gap Size", 0); } } void QmitkUSNavigationMarkerPlacement::OnResetStandardLayout() { - //reset render windows + // reset render windows mitk::DataNode::Pointer widget1 = this->GetDataStorage()->GetNamedNode("stdmulti.widget1.plane"); - if (widget1.IsNotNull()) { widget1->SetVisibility(true); } + if (widget1.IsNotNull()) + { + widget1->SetVisibility(true); + } mitk::DataNode::Pointer widget2 = this->GetDataStorage()->GetNamedNode("stdmulti.widget2.plane"); - if (widget2.IsNotNull()) { widget2->SetVisibility(true); } + if (widget2.IsNotNull()) + { + widget2->SetVisibility(true); + } mitk::DataNode::Pointer widget3 = this->GetDataStorage()->GetNamedNode("stdmulti.widget3.plane"); - if (widget3.IsNotNull()) { widget3->SetVisibility(true); } + if (widget3.IsNotNull()) + { + widget3->SetVisibility(true); + } m_StdMultiWidget->changeLayoutToDefault(); } void QmitkUSNavigationMarkerPlacement::OnChangeLayoutClicked() { - if (ui->m_enableNavigationLayout->isChecked()) OnEnableNavigationLayout(); - else OnResetStandardLayout(); + if (ui->m_enableNavigationLayout->isChecked()) + OnEnableNavigationLayout(); + else + OnResetStandardLayout(); } void QmitkUSNavigationMarkerPlacement::OnImageAndNavigationDataLoggingTimeout() { // update filter for logging navigation data and ultrasound images if (m_CombinedModality.IsNotNull()) { m_NavigationDataRecorder->Update(); // get last messages for logging filer and store them std::vector messages = m_LoggingBackend.GetNavigationMessages(); std::string composedMessage = ""; for (std::size_t i = 0; i < messages.size(); i++) { composedMessage += messages.at(i); } m_USImageLoggingFilter->AddMessageToCurrentImage(composedMessage); m_LoggingBackend.ClearNavigationMessages(); // update logging filter m_USImageLoggingFilter->Update(); } } void QmitkUSNavigationMarkerPlacement::OnStartExperiment() { // get name for the experiment by a QInputDialog bool ok; if (m_ExperimentName.isEmpty()) { // default: current date m_ExperimentName = QString::number(QDateTime::currentDateTime().date().year()) + "_" + - QString::number(QDateTime::currentDateTime().date().month()) + "_" + - QString::number(QDateTime::currentDateTime().date().day()) + "_experiment_" + - QString::number(QDateTime::currentDateTime().time().hour()) + "." + - QString::number(QDateTime::currentDateTime().time().minute()); + QString::number(QDateTime::currentDateTime().date().month()) + "_" + + QString::number(QDateTime::currentDateTime().date().day()) + "_experiment_" + + QString::number(QDateTime::currentDateTime().time().hour()) + "." + + QString::number(QDateTime::currentDateTime().time().minute()); } m_ExperimentName = QInputDialog::getText( m_Parent, QString("Experiment Name"), QString("Name of the Experiment"), QLineEdit::Normal, m_ExperimentName, &ok); MITK_INFO("USNavigationLogging") << "Experiment started: " << m_ExperimentName.toStdString(); if (ok && !m_ExperimentName.isEmpty()) { // display error message and call the function recursivly if a directory // with the given name already exists QDir experimentResultsDir(m_ResultsDirectory + QDir::separator() + m_ExperimentName); if (experimentResultsDir.exists()) { QMessageBox::critical( m_Parent, "Results Directory Exists", "The result directory already exists.\nPlease choose an other name."); this->OnStartExperiment(); } else { QDir(m_ResultsDirectory).mkdir(m_ExperimentName); m_ExperimentResultsSubDirectory = m_ResultsDirectory + QDir::separator() + m_ExperimentName; // experiment is running now ui->runningLabel->setPixmap(m_IconRunning); // (re)start timer for navigation step durations m_NavigationStepTimer->Reset(); m_NavigationStepTimer->SetOutputFileName( QString(m_ExperimentResultsSubDirectory + QDir::separator() + QString("durations.cvs")).toStdString()); m_NavigationStepTimer->SetActiveIndex(0, "Initialization"); ui->finishExperimentButton->setEnabled(true); ui->startExperimentButton->setDisabled(true); // initialize and register logging backend QString loggingFilename = m_ExperimentResultsSubDirectory + QDir::separator() + "logging.txt"; m_LoggingBackend.SetOutputFileName(loggingFilename.toStdString()); mbilog::RegisterBackend(&m_LoggingBackend); // initialize and start navigation data recorder form xml recording m_NavigationDataRecorder->StartRecording(); m_IsExperimentRunning = true; m_ImageAndNavigationDataLoggingTimer->start(1000); } } } void QmitkUSNavigationMarkerPlacement::OnFinishExperiment() { this->WaitCursorOn(); MITK_INFO("USNavigationLogging") << "Experiment finished!"; - MITK_INFO("USNavigationLogging") - << "Position/Orientation of needle tip: " - << (dynamic_cast(m_CombinedModality->GetTrackingDeviceDataSource()->GetOutput(0)))->GetPosition(); + MITK_INFO("USNavigationLogging") << "Position/Orientation of needle tip: " + << (dynamic_cast( + m_CombinedModality->GetTrackingDeviceDataSource()->GetOutput(0))) + ->GetPosition(); MITK_INFO("USNavigationLogging") << "Position of target: " << m_TargetNodeDisplacementFilter->GetRawDisplacementNavigationData(0)->GetPosition(); MITK_INFO("USNavigationLogging") << "Total duration: " << m_NavigationStepTimer->GetTotalDuration(); m_ImageAndNavigationDataLoggingTimer->stop(); ui->runningLabel->setPixmap(m_IconNotRunning); m_NavigationStepTimer->Stop(); - ui->finishExperimentButton->setDisabled(true); ui->startExperimentButton->setEnabled(true); MITK_INFO("USNavigationLogging") << "Writing logging data to " << m_ExperimentResultsSubDirectory.toStdString(); // save ultrasound images to the file system QDir(m_ExperimentResultsSubDirectory).mkdir("ImageStream"); m_USImageLoggingFilter->Update(); m_USImageLoggingFilter->SetImageFilesExtension(".jpg"); m_USImageLoggingFilter->SaveImages( QString(m_ExperimentResultsSubDirectory + QDir::separator() + "ImageStream" + QDir::separator()).toStdString()); m_USImageLoggingFilter = mitk::USImageLoggingFilter::New(); m_NavigationDataRecorder->StopRecording(); // Write data to csv and xml file mitk::IOUtil::Save( m_NavigationDataRecorder->GetNavigationDataSet(), (QString(m_ExperimentResultsSubDirectory + QDir::separator() + "navigation-data.xml").toStdString().c_str())); mitk::IOUtil::Save( m_NavigationDataRecorder->GetNavigationDataSet(), (QString(m_ExperimentResultsSubDirectory + QDir::separator() + "navigation-data.csv").toStdString().c_str())); // write logged navigation data messages to separate file std::stringstream csvNavigationMessagesFilename; csvNavigationMessagesFilename << m_ExperimentResultsSubDirectory.toStdString() << QDir::separator().toLatin1() - << "CSVNavigationMessagesLogFile.csv"; + << "CSVNavigationMessagesLogFile.csv"; MITK_INFO("USNavigationLogging") << "Writing logged navigation messages to separate csv file: " - << csvNavigationMessagesFilename.str(); + << csvNavigationMessagesFilename.str(); m_LoggingBackend.WriteCSVFileWithNavigationMessages(csvNavigationMessagesFilename.str()); mbilog::UnregisterBackend(&m_LoggingBackend); m_IsExperimentRunning = false; m_ImageAndNavigationDataLoggingTimer->stop(); m_CombinedModality = nullptr; // reset scene number for next experiment m_SceneNumber = 1; this->WaitCursorOff(); MITK_INFO("USNavigationLogging") << "Finished!"; } void QmitkUSNavigationMarkerPlacement::OnSettingsChanged(itk::SmartPointer settings) { // initialize gui according to the experiment mode setting bool experimentMode = false; settings->GetBoolProperty("settings.experiment-mode", experimentMode); ui->startExperimentButton->setVisible(experimentMode); ui->finishExperimentButton->setVisible(experimentMode); ui->runningLabel->setVisible(experimentMode); if (experimentMode && !m_IsExperimentRunning) { ui->runningLabel->setPixmap(m_IconNotRunning); } else if (!experimentMode) { if (m_IsExperimentRunning) { this->OnFinishExperiment(); } } // get the results directory from the settings and use home directory if // there is no results directory configured std::string resultsDirectory; if (settings->GetStringProperty("settings.experiment-results-directory", resultsDirectory)) { m_ResultsDirectory = QString::fromStdString(resultsDirectory); } else { m_ResultsDirectory = QDir::homePath(); } // make sure that the results directory exists QDir resultsDirectoryQDir = QDir(m_ResultsDirectory); if (!resultsDirectoryQDir.exists()) { resultsDirectoryQDir.mkpath(m_ResultsDirectory); } MITK_INFO("USNavigation") << "Results Directory: " << m_ResultsDirectory.toStdString(); } void QmitkUSNavigationMarkerPlacement::ReinitOnImage() { if (!m_ReinitAlreadyDone && m_CombinedModality.IsNotNull()) { // make sure that the output is already calibrated correctly // (if the zoom level was changed recently) m_CombinedModality->Modified(); m_CombinedModality->Update(); mitk::Image::Pointer image = m_CombinedModality->GetOutput(); if (image.IsNotNull() && image->IsInitialized()) { // make a reinit on the ultrasound image mitk::IRenderWindowPart *renderWindow = this->GetRenderWindowPart(); if (renderWindow != NULL && image->GetTimeGeometry()->IsValid()) { renderWindow->GetRenderingManager()->InitializeViews( image->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); renderWindow->GetRenderingManager()->RequestUpdateAll(); } this->RequestRenderWindowUpdate(); m_ReinitAlreadyDone = true; } } } void QmitkUSNavigationMarkerPlacement::Convert2DImagesTo3D(mitk::DataStorage::SetOfObjects::ConstPointer nodes) { for (mitk::DataStorage::SetOfObjects::ConstIterator it = nodes->Begin(); it != nodes->End(); ++it) { if (it->Value()->GetData() && strcmp(it->Value()->GetData()->GetNameOfClass(), "Image") == 0) { // convert image to 3d image if it is 2d at the moment mitk::Image::Pointer image = dynamic_cast(it->Value()->GetData()); if (image.IsNotNull() && image->GetDimension() == 2 && !image->GetGeometry()->Is2DConvertable()) { mitk::Convert2Dto3DImageFilter::Pointer convert2DTo3DImageFilter = mitk::Convert2Dto3DImageFilter::New(); convert2DTo3DImageFilter->SetInput(image); convert2DTo3DImageFilter->Update(); it->Value()->SetData(convert2DTo3DImageFilter->GetOutput()); } } } } void QmitkUSNavigationMarkerPlacement::CreateOverlays() { // initialize warning overlay (and do not display it, yet) m_WarnOverlay->SetText("Warning: No calibration available for current depth."); // set position and font size for the text overlay // (nonesense postition as a layouter is used, but it ignored // the overlay without setting a position here) mitk::Point2D overlayPosition; overlayPosition.SetElement(0, -50.0f); overlayPosition.SetElement(1, -50.0f); m_WarnOverlay->SetPosition2D(overlayPosition); m_WarnOverlay->SetFontSize(22); m_WarnOverlay->SetColor(1, 0, 0); // overlay should be red } void QmitkUSNavigationMarkerPlacement::UpdateToolStorage() { - if (m_NavigationDataSource.IsNull()) { m_NavigationDataSource = m_CombinedModality->GetNavigationDataSource(); } - if (m_NavigationDataSource.IsNull()) { MITK_WARN << "Found an invalid navigation data source object!"; } - us::ModuleContext* context = us::GetModuleContext(); + if (m_NavigationDataSource.IsNull()) + { + m_NavigationDataSource = m_CombinedModality->GetNavigationDataSource(); + } + if (m_NavigationDataSource.IsNull()) + { + MITK_WARN << "Found an invalid navigation data source object!"; + } + us::ModuleContext *context = us::GetModuleContext(); std::string id = m_NavigationDataSource->US_PROPKEY_ID; std::string filter = "(" + mitk::NavigationToolStorage::US_PROPKEY_SOURCE_ID + "=" + id + ")"; // Get Storage - std::vector > refs = context->GetServiceReferences(); + std::vector> refs = + context->GetServiceReferences(); m_CurrentStorage = context->GetService(refs.front()); if (m_CurrentStorage.IsNull()) { MITK_WARN << "Found an invalid storage object!"; } - else if (m_CurrentStorage->GetToolCount() != m_NavigationDataSource->GetNumberOfOutputs()) //there is something wrong with the storage + else if (m_CurrentStorage->GetToolCount() != + m_NavigationDataSource->GetNumberOfOutputs()) // there is something wrong with the storage { - MITK_WARN << "Found a tool storage, but it has not the same number of tools like the NavigationDataSource. This storage won't be used because it isn't the right one."; + MITK_WARN << "Found a tool storage, but it has not the same number of tools like the NavigationDataSource. This " + "storage won't be used because it isn't the right one."; m_CurrentStorage = NULL; } } diff --git a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/QmitkUSNavigationMarkerPlacement.h b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/QmitkUSNavigationMarkerPlacement.h index c58dfad0ba..68b9b8217b 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/QmitkUSNavigationMarkerPlacement.h +++ b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/QmitkUSNavigationMarkerPlacement.h @@ -1,207 +1,210 @@ /*=================================================================== 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 QmitkUSNAVIGATIONMARKERPLACEMENT_H #define QmitkUSNAVIGATIONMARKERPLACEMENT_H #include #include "IO/mitkUSNavigationLoggingBackend.h" #include "mitkNavigationDataRecorder.h" #include "mitkNodeDisplacementFilter.h" #include "mitkUSImageLoggingFilter.h" #include #include #include #include +#include namespace itk { template class SmartPointer; } namespace mitk { class USNavigationStepTimer; } namespace Ui { class QmitkUSNavigationMarkerPlacement; } class QmitkUSAbstractNavigationStep; class QmitkUSNavigationStepPunctuationIntervention; class QmitkStdMultiWidget; class QTimer; class QSignalMapper; /** * \brief View for navigated marker placement using the combined modality. * This view utilizes the QmitkUSNavigationProcessWidget to do the navigation * process. It can be switched between widgets for marker placement and widgets * for punctuation. * * An experiment mode allows for logging results, durations and the ultrasound * images. */ class QmitkUSNavigationMarkerPlacement : public QmitkAbstractView { Q_OBJECT protected slots: void OnInitializeTargetMarking(); void OnInitializeCriticalStructureMarking(); void OnInitializeNavigation(); /** * \brief Called periodically to update the rendering. * The standard multi widget is changed to fit the navigation process once it * is available and a reinit on the ultrasound image is done for a new image * node. */ void OnTimeout(); /** * \brief Called periodically during an experiment for logging the ultrasound images. */ void OnImageAndNavigationDataLoggingTimeout(); /** * \brief Initializes anything neccessary for an experiment. * The user is asked for a directory for storing the results and the logging * is started. */ void OnStartExperiment(); /** * \brief Stops logging and saves everything to the file system. */ void OnFinishExperiment(); /** * \brief Switches the navigation step widgets if the navigation application was changed. */ void OnSettingsChanged(itk::SmartPointer); void OnAddAblationZone(int size); void OnEnableNavigationLayout(); void OnResetStandardLayout(); void OnChangeLayoutClicked(); void OnChangeAblationZone(int id, int newSize); void OnRenderWindowSelection(); void OnRefreshView(); public: static const char *DATANAME_TUMOUR; static const char *DATANAME_TARGETSURFACE; static const char *DATANAME_ZONES; static const char *DATANAME_TARGETS; static const char *DATANAME_TARGETS_PATHS; static const char *DATANAME_REACHED_TARGETS; explicit QmitkUSNavigationMarkerPlacement(); ~QmitkUSNavigationMarkerPlacement(); virtual void CreateQtPartControl(QWidget *parent); static const std::string VIEW_ID; void OnCombinedModalityPropertyChanged(const std::string &, const std::string &); protected: /** * \brief A reinit on the ultrasound image is performed every time the view gets the focus. */ virtual void SetFocus(); /** * \brief Helper function which performs a reinit on the ultrasound image. */ void ReinitOnImage(); /** * \brief Sets the multiwidget to two windows, axial on top and 3D render window on the bottom. */ virtual void SetTwoWindowView(); /** * \brief Helper function for being able to serialize the 2d ultrasound image. */ void Convert2DImagesTo3D(mitk::DataStorage::SetOfObjects::ConstPointer nodes); void ReInitializeSettingsNodesAndImageStream(); void UpdateToolStorage(); void CreateOverlays(); void InitImageStream(); QWidget *m_Parent; QTimer *m_UpdateTimer; QTimer *m_ImageAndNavigationDataLoggingTimer; QmitkStdMultiWidget *m_StdMultiWidget; itk::SmartPointer m_CombinedModality; itk::SmartPointer m_SettingsNode; bool m_ReinitAlreadyDone; bool m_IsExperimentRunning; std::string m_CurrentApplicationName; itk::SmartPointer m_NavigationStepTimer; QPixmap m_IconRunning; QPixmap m_IconNotRunning; QString m_ResultsDirectory; QString m_ExperimentName; QString m_ExperimentResultsSubDirectory; std::vector m_NavigationStepNames; // stores the names of the navigation steps which are currently used (for logging purposes) mitk::USNavigationLoggingBackend m_LoggingBackend; mitk::USImageLoggingFilter::Pointer m_USImageLoggingFilter; mitk::NavigationDataRecorder::Pointer m_NavigationDataRecorder; // records navigation data files mitk::NodeDisplacementFilter::Pointer m_TargetNodeDisplacementFilter; mitk::NodeDisplacementFilter::Pointer m_AblationZonesDisplacementFilter; + mitk::NavigationDataObjectVisualizationFilter::Pointer m_ToolVisualizationFilter; + mitk::DataNode::Pointer m_InstrumentNode; std::vector m_AblationZonesVector; int m_NeedleIndex; int m_MarkerIndex; int m_SceneNumber; itk::SmartPointer m_WarnOverlay; //To get tool storage mitk::NavigationDataSource::Pointer m_NavigationDataSource; mitk::NavigationToolStorage::Pointer m_CurrentStorage; itk::SmartPointer m_BaseNode; itk::SmartPointer m_ImageStreamNode; private: Ui::QmitkUSNavigationMarkerPlacement *ui; }; #endif // USNAVIGATIONMARKERPLACEMENT_H diff --git a/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkMITKIGTTrackingToolboxViewControls.ui b/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkMITKIGTTrackingToolboxViewControls.ui index 8e043ac2f8..4c4ff80a50 100644 --- a/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkMITKIGTTrackingToolboxViewControls.ui +++ b/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkMITKIGTTrackingToolboxViewControls.ui @@ -1,954 +1,954 @@ QmitkMITKIGTTrackingToolboxViewControls 0 0 370 739 0 0 QmitkTemplate 0 Tracking QFrame::NoFrame QFrame::Raised 0 0 QFrame::NoFrame QFrame::Raised 10 75 true true Tracking Tools Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop 0 0 ToolStorage: <none> Qt::Horizontal 40 20 0 0 Qt::Horizontal 13 49 120 0 Auto Detection 120 0 Add Single Tool 120 0 Load Tool Storage 120 0 Reset QFrame::NoFrame QFrame::Raised 10 75 true Tracking Control Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop Status: disconnected Qt::Horizontal 40 20 142 0 Connect Qt::Horizontal 40 20 142 0 Start Tracking Qt::Horizontal 40 20 <html><head/><body><p><span style=" color:#ff0000;">Tracking Frozen!</span></p></body></html> true 142 0 Freeze Tracking Qt::Vertical 20 40 Options Update Rate Options Update Rate [per second] Qt::Horizontal 40 20 100 - 30 + 10 Use different Render and Log Update Rates false Render Update Rate [fps] Qt::Horizontal 40 20 false 0 100 30 false Log Update Rate [per second] Qt::Horizontal 40 20 false 1 120 10 60 Other Options Show Tool Quaternions Simple UI Caution, only for backward compatibility: Inverse mode (Quaternions are stored inverse) Tracking Volume Options true Show Tracking Volume false Select Model: Tool Visualization Options true Show Tool Projection false Show Tool Axis Open IGT Link Enable Open IGT Link MicroService true Select Open IGT Link Data Format: TRANSFORM QTDATA TDATA POSITION Disable All Timers true <html><head/><body><p align="right"><span style=" color:#ff0000;">Rendering Disabled!</span></p></body></html> Qt::AutoText Qt::Vertical 20 40 Logging Filename: Choose File Limit Number Of Logged Frames: Qt::Horizontal 40 20 1 9999 300 CSV format true XML format Skip invalid data Logging Status Logging OFF Logged Frames: 0 Qt::Horizontal 40 20 Start Logging Stop Logging Qt::Vertical 20 40 9 742 303 70 70 50 Connect 70 50 Start Tracking Qt::Horizontal 40 20 70 50 Advanced Mode QmitkToolTrackingStatusWidget QWidget
QmitkToolTrackingStatusWidget.h
1
QmitkTrackingDeviceConfigurationWidget QWidget
QmitkTrackingDeviceConfigurationWidget.h
1
QmitkNavigationToolCreationWidget QWidget
QmitkNavigationToolCreationWidget.h
1