diff --git a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/NavigationStepWidgets/QmitkUSNavigationStepMarkerIntervention.cpp b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/NavigationStepWidgets/QmitkUSNavigationStepMarkerIntervention.cpp index 8324642e18..01997b4002 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/NavigationStepWidgets/QmitkUSNavigationStepMarkerIntervention.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/NavigationStepWidgets/QmitkUSNavigationStepMarkerIntervention.cpp @@ -1,1020 +1,1020 @@ /*=================================================================== 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 "QmitkUSNavigationStepMarkerIntervention.h" #include "ui_QmitkUSNavigationStepMarkerIntervention.h" #include "mitkBaseRenderer.h" #include "mitkContourModel.h" #include "mitkNeedleProjectionFilter.h" #include "mitkNodeDisplacementFilter.h" #include "mitkSurface.h" #include "mitkTextAnnotation2D.h" #include #include #include "../Filter/mitkUSNavigationTargetIntersectionFilter.h" #include "../Filter/mitkUSNavigationTargetOcclusionFilter.h" #include "../Filter/mitkUSNavigationTargetUpdateFilter.h" #include "../USNavigationMarkerPlacement.h" #include "../Widgets/QmitkZoneProgressBar.h" #include "../mitkUSTargetPlacementQualityCalculator.h" #include "../Interactors/mitkUSPointMarkInteractor.h" #include "usModuleRegistry.h" #include "mitkLookupTable.h" #include "mitkLookupTableProperty.h" #include "mitkSurface.h" // VTK #include "vtkCellLocator.h" #include "vtkDataSet.h" #include "vtkDoubleArray.h" #include "vtkFloatArray.h" #include "vtkIdList.h" #include "vtkLinearTransform.h" #include "vtkLookupTable.h" #include "vtkMath.h" #include "vtkOBBTree.h" #include "vtkPointData.h" #include "vtkPointData.h" #include "vtkPolyData.h" #include "vtkSelectEnclosedPoints.h" #include "vtkSmartPointer.h" #include "vtkSphereSource.h" #include "vtkTransformPolyDataFilter.h" #include "vtkWarpScalar.h" QmitkUSNavigationStepMarkerIntervention::QmitkUSNavigationStepMarkerIntervention(QWidget *parent) : QmitkUSAbstractNavigationStep(parent), m_NumberOfTargets(0), m_TargetProgressBar(0), m_PlannedTargetProgressBar(0), m_CurrentTargetIndex(0), m_CurrentTargetReached(false), m_ShowPlanningColors(false), m_NeedleProjectionFilter(mitk::NeedleProjectionFilter::New()), m_NodeDisplacementFilter(mitk::NodeDisplacementFilter::New()), m_TargetUpdateFilter(mitk::USNavigationTargetUpdateFilter::New()), m_TargetOcclusionFilter(mitk::USNavigationTargetOcclusionFilter::New()), m_TargetIntersectionFilter(mitk::USNavigationTargetIntersectionFilter::New()), m_PlacementQualityCalculator(mitk::USTargetPlacementQualityCalculator::New()), - m_ListenerTargetCoordinatesChanged(this, &QmitkUSNavigationStepMarkerIntervention::UpdateTargetCoordinates), m_TargetStructureWarnOverlay(mitk::TextAnnotation2D::New()), m_ReferenceSensorIndex(1), m_NeedleSensorIndex(0), + m_ListenerTargetCoordinatesChanged(this, &QmitkUSNavigationStepMarkerIntervention::UpdateTargetCoordinates), ui(new Ui::QmitkUSNavigationStepMarkerIntervention) { m_ActiveTargetColor[0] = 1; m_ActiveTargetColor[1] = 1; m_ActiveTargetColor[2] = 0; m_InactiveTargetColor[0] = 1; m_InactiveTargetColor[1] = 1; m_InactiveTargetColor[2] = 0.5; m_ReachedTargetColor[0] = 0.6; m_ReachedTargetColor[1] = 1; m_ReachedTargetColor[2] = 0.6; ui->setupUi(this); connect(ui->freezeImageButton, SIGNAL(SignalFreezed(bool)), this, SLOT(OnFreeze(bool))); connect(ui->backToLastTargetButton, SIGNAL(clicked()), this, SLOT(OnBackToLastTargetClicked())); connect(ui->targetReachedButton, SIGNAL(clicked()), this, SLOT(OnTargetLeft())); connect(this, SIGNAL(TargetReached(int)), this, SLOT(OnTargetReached())); connect(this, SIGNAL(TargetLeft(int)), this, SLOT(OnTargetLeft())); connect(ui->riskStructuresRangeWidget, SIGNAL(SignalZoneViolated(const mitk::DataNode *, mitk::Point3D)), this, SLOT(OnRiskZoneViolated(const mitk::DataNode *, mitk::Point3D))); m_PointMarkInteractor = mitk::USPointMarkInteractor::New(); m_PointMarkInteractor->CoordinatesChangedEvent.AddListener(m_ListenerTargetCoordinatesChanged); this->GenerateTargetColorLookupTable(); m_TargetProgressBar = new QmitkZoneProgressBar(QString::fromStdString("Target: %1 mm"), 200, 0, this); m_TargetProgressBar->SetTextFormatInvalid("Target is not on Needle Path"); ui->targetStructuresRangeLayout->addWidget(m_TargetProgressBar); m_TargetUpdateFilter->SetScalarArrayIdentifier("USNavigation::ReachedTargetScores"); } QmitkUSNavigationStepMarkerIntervention::~QmitkUSNavigationStepMarkerIntervention() { mitk::DataStorage::Pointer dataStorage = this->GetDataStorage(false); if (dataStorage.IsNotNull()) { // remove the node for the needle path mitk::DataNode::Pointer node = this->GetNamedDerivedNode("Needle Path", QmitkUSAbstractNavigationStep::DATANAME_BASENODE); if (node.IsNotNull()) { dataStorage->Remove(node); } } if (m_SegmentationNode.IsNotNull()) { this->GetDataStorage()->Remove(m_SegmentationNode); } if (m_ForegroundModelPointsNode.IsNotNull()) { this->GetDataStorage()->Remove(m_ForegroundModelPointsNode); } delete ui; m_PointMarkInteractor->CoordinatesChangedEvent.RemoveListener(m_ListenerTargetCoordinatesChanged); } bool QmitkUSNavigationStepMarkerIntervention::OnStartStep() { m_NeedleProjectionFilter->SelectInput(m_NeedleSensorIndex); // create node for Needle Projection mitk::DataNode::Pointer node = this->GetNamedDerivedNodeAndCreate("Needle Path", QmitkUSAbstractNavigationStep::DATANAME_BASENODE); node->SetData(m_NeedleProjectionFilter->GetProjection()); node->SetBoolProperty("show contour", true); // initialize warning overlay (and do not display it, yet) m_TargetStructureWarnOverlay->SetText("Warning: Needle is Inside the Target Structure."); m_TargetStructureWarnOverlay->SetVisibility(false); // set position and font size for the text overlay mitk::Point2D overlayPosition; overlayPosition.SetElement(0, 10.0f); overlayPosition.SetElement(1, 10.0f); m_TargetStructureWarnOverlay->SetPosition2D(overlayPosition); m_TargetStructureWarnOverlay->SetFontSize(18); // overlay should be red mitk::Color color; color[0] = 1; color[1] = 0; color[2] = 0; m_TargetStructureWarnOverlay->SetColor(color); mitk::ManualPlacementAnnotationRenderer::AddAnnotation(m_TargetStructureWarnOverlay.GetPointer(), "stdmulti.widget4"); return true; } bool QmitkUSNavigationStepMarkerIntervention::OnStopStep() { mitk::DataStorage::Pointer dataStorage = this->GetDataStorage(); // remove all reached nodes from the data storage for (QVector>::iterator it = m_ReachedTargetsNodes.begin(); it != m_ReachedTargetsNodes.end(); ++it) { dataStorage->Remove(*it); } m_ReachedTargetsNodes.clear(); m_CurrentTargetIndex = 0; // reset button states ui->freezeImageButton->setEnabled(false); ui->backToLastTargetButton->setEnabled(false); ui->targetReachedButton->setEnabled(true); // make sure that it is unfreezed after stopping the step ui->freezeImageButton->Unfreeze(); // remove base node for reached targets from the data storage mitk::DataNode::Pointer reachedTargetsNode = this->GetNamedDerivedNode( QmitkUSAbstractNavigationStep::DATANAME_BASENODE, USNavigationMarkerPlacement::DATANAME_REACHED_TARGETS); if (reachedTargetsNode.IsNotNull()) { dataStorage->Remove(reachedTargetsNode); } return true; } bool QmitkUSNavigationStepMarkerIntervention::OnFinishStep() { return true; } bool QmitkUSNavigationStepMarkerIntervention::OnActivateStep() { this->ClearZones(); // clear risk zones before adding new ones // get target node from data storage and make sure that it contains data m_TargetNode = this->GetNamedDerivedNode(USNavigationMarkerPlacement::DATANAME_TARGETSURFACE, USNavigationMarkerPlacement::DATANAME_TUMOUR); if (m_TargetNode.IsNull() || m_TargetNode->GetData() == 0) { mitkThrow() << "Target node (" << USNavigationMarkerPlacement::DATANAME_TARGETSURFACE << ") must not be null."; } // get target data and make sure that it is a surface m_TargetSurface = dynamic_cast(m_TargetNode->GetData()); if (m_TargetSurface.IsNull()) { mitkThrow() << "Target node (" << USNavigationMarkerPlacement::DATANAME_TARGETSURFACE << ") data must be of type mitk::Surface"; } // delete progress bars for reinitializing them again afterwards if (m_PlannedTargetProgressBar) { ui->targetStructuresRangeLayout->removeWidget(m_PlannedTargetProgressBar); delete m_PlannedTargetProgressBar; m_PlannedTargetProgressBar = 0; } m_NodeDisplacementFilter->SelectInput(m_ReferenceSensorIndex); this->UpdateTargetProgressDisplay(); mitk::DataNode::Pointer tumourNode = this->GetNamedDerivedNode(USNavigationMarkerPlacement::DATANAME_TUMOUR, QmitkUSAbstractNavigationStep::DATANAME_BASENODE); if (tumourNode.IsNotNull()) { // do not show tumour node during intervention (target surface is shown) tumourNode->SetBoolProperty("visible", false); // add tumour as a risk structure ui->riskStructuresRangeWidget->AddZone(tumourNode); } // set target structure for target update filter m_TargetUpdateFilter->SetTargetStructure(m_TargetNode); m_TargetOcclusionFilter->SetTargetStructure(m_TargetNode); // set lookup table of tumour node m_TargetNode->SetProperty("LookupTable", m_TargetColorLookupTableProperty); // mitk::DataNode::Pointer targetsBaseNode = this->GetNamedDerivedNode(USNavigationMarkerPlacement::DATANAME_TARGETS, QmitkUSAbstractNavigationStep::DATANAME_BASENODE); mitk::DataStorage::SetOfObjects::ConstPointer plannedTargetNodes; if (targetsBaseNode.IsNotNull()) { plannedTargetNodes = this->GetDataStorage()->GetDerivations(targetsBaseNode); } if (plannedTargetNodes.IsNotNull() && plannedTargetNodes->Size() > 0) { for (mitk::DataStorage::SetOfObjects::ConstIterator it = plannedTargetNodes->Begin(); it != plannedTargetNodes->End(); ++it) { m_PlannedTargetsNodes.push_back(it->Value()); } m_PlannedTargetProgressBar = new QmitkZoneProgressBar(QString::fromStdString("Planned Target"), 200, 0); ui->targetStructuresRangeLayout->addWidget(m_PlannedTargetProgressBar); } // add progress bars for risk zone nodes mitk::DataNode::Pointer zonesBaseNode = this->GetNamedDerivedNode(USNavigationMarkerPlacement::DATANAME_ZONES, QmitkUSAbstractNavigationStep::DATANAME_BASENODE); // only add progress bars if the base node for zones was created if (zonesBaseNode.IsNotNull()) { mitk::DataStorage::SetOfObjects::ConstPointer zoneNodes = this->GetDataStorage()->GetDerivations(zonesBaseNode); for (mitk::DataStorage::SetOfObjects::ConstIterator it = zoneNodes->Begin(); it != zoneNodes->End(); ++it) { ui->riskStructuresRangeWidget->AddZone(it->Value()); } m_TargetOcclusionFilter->SelectStartPositionInput(m_NeedleSensorIndex); m_TargetOcclusionFilter->SetObstacleStructures(zoneNodes); } return true; } bool QmitkUSNavigationStepMarkerIntervention::OnDeactivateStep() { ui->freezeImageButton->Unfreeze(); return true; } void QmitkUSNavigationStepMarkerIntervention::OnUpdate() { // get navigation data source and make sure that it is not null mitk::NavigationDataSource::Pointer navigationDataSource = this->GetCombinedModality()->GetNavigationDataSource(); if (navigationDataSource.IsNull()) { MITK_ERROR("QmitkUSAbstractNavigationStep") ("QmitkUSNavigationStepMarkerIntervention") << "Navigation Data Source of Combined Modality must not be null."; mitkThrow() << "Navigation Data Source of Combined Modality must not be null."; } ui->riskStructuresRangeWidget->UpdateDistancesToNeedlePosition(navigationDataSource->GetOutput(m_NeedleSensorIndex)); this->UpdateBodyMarkerStatus(navigationDataSource->GetOutput(m_ReferenceSensorIndex)); this->UpdateTargetColors(); this->UpdateTargetScore(); this->UpdateTargetViolationStatus(); } void QmitkUSNavigationStepMarkerIntervention::OnSettingsChanged(const itk::SmartPointer settingsNode) { if (settingsNode.IsNull()) { return; } int numberOfTargets; if (settingsNode->GetIntProperty("settings.number-of-targets", numberOfTargets)) { m_NumberOfTargets = numberOfTargets; m_TargetUpdateFilter->SetNumberOfTargets(numberOfTargets); m_PlacementQualityCalculator->SetOptimalAngle(m_TargetUpdateFilter->GetOptimalAngle()); } std::string referenceSensorName; if (settingsNode->GetStringProperty("settings.reference-name-selected", referenceSensorName)) { m_ReferenceSensorName = referenceSensorName; } std::string needleSensorName; if (settingsNode->GetStringProperty("settings.needle-name-selected", needleSensorName)) { m_NeedleSensorName = needleSensorName; } this->UpdateSensorsNames(); } QString QmitkUSNavigationStepMarkerIntervention::GetTitle() { return "Computer-assisted Intervention"; } bool QmitkUSNavigationStepMarkerIntervention::GetIsRestartable() { return true; } QmitkUSAbstractNavigationStep::FilterVector QmitkUSNavigationStepMarkerIntervention::GetFilter() { FilterVector filter; filter.push_back(m_NeedleProjectionFilter.GetPointer()); filter.push_back(m_NodeDisplacementFilter.GetPointer()); filter.push_back(m_TargetOcclusionFilter.GetPointer()); return filter; } void QmitkUSNavigationStepMarkerIntervention::OnSetCombinedModality() { mitk::USCombinedModality::Pointer combinedModality = this->GetCombinedModality(false); if (combinedModality.IsNotNull()) { mitk::AffineTransform3D::Pointer calibration = combinedModality->GetCalibration(); if (calibration.IsNotNull()) { m_NeedleProjectionFilter->SetTargetPlane(calibration); } } ui->freezeImageButton->SetCombinedModality(combinedModality, m_ReferenceSensorIndex); this->UpdateSensorsNames(); } void QmitkUSNavigationStepMarkerIntervention::OnTargetReached() { m_CurrentTargetReached = true; } void QmitkUSNavigationStepMarkerIntervention::OnTargetLeft() { m_CurrentTargetReached = false; m_CurrentTargetIndex++; if (m_CurrentTargetIndex >= 0 && static_cast(m_CurrentTargetIndex) >= m_NumberOfTargets) { ui->targetReachedButton->setDisabled(true); } ui->backToLastTargetButton->setEnabled(true); ui->freezeImageButton->setEnabled(true); this->UpdateTargetProgressDisplay(); if (m_ReachedTargetsNodes.size() < m_CurrentTargetIndex) { mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetName( (QString("Target ") + QString("%1").arg(m_CurrentTargetIndex, 2, 10, QLatin1Char('0'))).toStdString()); this->GetDataStorage()->Add( node, this->GetNamedDerivedNodeAndCreate(USNavigationMarkerPlacement::DATANAME_REACHED_TARGETS, QmitkUSAbstractNavigationStep::DATANAME_BASENODE)); m_ReachedTargetsNodes.push_back(node); } mitk::DataNode::Pointer node = m_ReachedTargetsNodes.at(m_CurrentTargetIndex - 1); mitk::Surface::Pointer zone = mitk::Surface::New(); // create a vtk sphere with given radius vtkSphereSource *vtkData = vtkSphereSource::New(); vtkData->SetRadius(5); vtkData->SetCenter(0, 0, 0); vtkData->Update(); zone->SetVtkPolyData(vtkData->GetOutput()); vtkData->Delete(); // set vtk sphere and origin to data node node->SetData(zone); node->GetData()->GetGeometry()->SetOrigin( this->GetCombinedModality()->GetNavigationDataSource()->GetOutput(m_NeedleSensorIndex)->GetPosition()); node->SetColor(0.2, 0.9, 0.2); this->UpdateTargetCoordinates(node); } void QmitkUSNavigationStepMarkerIntervention::OnBackToLastTargetClicked() { if (m_CurrentTargetIndex < 1) { MITK_WARN << "Cannot go back to last target as there is no last target."; return; } m_CurrentTargetIndex--; if (m_ReachedTargetsNodes.size() > m_CurrentTargetIndex) { this->GetDataStorage()->Remove(m_ReachedTargetsNodes.last()); MITK_INFO("QmitkUSAbstractNavigationStep") ("QmitkUSNavigationStepMarkerIntervention") << "Removed Target " << m_ReachedTargetsNodes.size(); m_ReachedTargetsNodes.pop_back(); } if (m_CurrentTargetIndex == 0) { ui->backToLastTargetButton->setDisabled(true); } if (m_CurrentTargetIndex >= 0 && static_cast(m_CurrentTargetIndex) < m_NumberOfTargets) { ui->targetReachedButton->setEnabled(true); } ui->freezeImageButton->setEnabled(false); ui->freezeImageButton->Unfreeze(); this->UpdateTargetProgressDisplay(); m_TargetUpdateFilter->RemovePositionOfTarget(m_CurrentTargetIndex); } void QmitkUSNavigationStepMarkerIntervention::OnFreeze(bool freezed) { if (freezed) { this->GetCombinedModality()->SetIsFreezed(true); // load state machine and event config for data interactor m_PointMarkInteractor->LoadStateMachine("USPointMarkInteractions.xml", us::ModuleRegistry::GetModule("MitkUS")); m_PointMarkInteractor->SetEventConfig("globalConfig.xml"); if (m_CurrentTargetIndex < 1) { mitkThrow() << "Current target index has to be greater zero when freeze button is clicked."; } if (m_ReachedTargetsNodes.size() < m_CurrentTargetIndex) { mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetName( (QString("Target ") + QString("%1").arg(m_CurrentTargetIndex, 2, 10, QLatin1Char('0'))).toStdString()); this->GetDataStorage()->Add( node, this->GetNamedDerivedNodeAndCreate(USNavigationMarkerPlacement::DATANAME_REACHED_TARGETS, QmitkUSAbstractNavigationStep::DATANAME_BASENODE)); m_ReachedTargetsNodes.push_back(node); } m_PointMarkInteractor->SetDataNode(m_ReachedTargetsNodes.last()); } else { m_PointMarkInteractor->SetDataNode(0); this->GetCombinedModality()->SetIsFreezed(false); } } void QmitkUSNavigationStepMarkerIntervention::OnShowPlanningView(bool show) { m_ShowPlanningColors = show; } void QmitkUSNavigationStepMarkerIntervention::OnRiskZoneViolated(const mitk::DataNode *node, mitk::Point3D position) { MITK_INFO << "Risk zone (" << node->GetName() << ") violated at position " << position << "."; } void QmitkUSNavigationStepMarkerIntervention::ClearZones() { ui->riskStructuresRangeWidget->ClearZones(); // remove all reached target nodes from the data storage and clear the list mitk::DataStorage::Pointer dataStorage = this->GetDataStorage(); for (QVector::iterator it = m_ReachedTargetsNodes.begin(); it != m_ReachedTargetsNodes.end(); ++it) { if (it->IsNotNull()) { dataStorage->Remove(*it); } } m_ReachedTargetsNodes.clear(); } void QmitkUSNavigationStepMarkerIntervention::UpdateTargetCoordinates(mitk::DataNode *dataNode) { m_NodeDisplacementFilter->ResetNodes(); for (QVector>::iterator it = m_ReachedTargetsNodes.begin(); it != m_ReachedTargetsNodes.end(); ++it) { if (it->IsNotNull() && (*it)->GetData() != 0) { m_NodeDisplacementFilter->AddNode(*it); } } mitk::BaseData *baseData = dataNode->GetData(); if (!baseData) { mitkThrow() << "Data of the data node must not be null."; } mitk::BaseGeometry::Pointer geometry = baseData->GetGeometry(); if (geometry.IsNull()) { mitkThrow() << "Geometry of the data node must not be null."; } m_TargetUpdateFilter->SetControlNode(m_CurrentTargetIndex - 1, dataNode); if (m_PlannedTargetsNodes.size() > m_CurrentTargetIndex - 1) { m_PlannedTargetsNodes.at(m_CurrentTargetIndex - 1)->SetVisibility(false); } MITK_INFO("QmitkUSAbstractNavigationStep") ("QmitkUSNavigationStepMarkerIntervention") << "Target " << m_CurrentTargetIndex << " reached at position " << geometry->GetOrigin(); this->CalculateTargetPlacementQuality(); } void QmitkUSNavigationStepMarkerIntervention::UpdateBodyMarkerStatus(mitk::NavigationData::Pointer bodyMarker) { if (bodyMarker.IsNull()) { MITK_ERROR("QmitkUSAbstractNavigationStep") ("QmitkUSNavigationStepMarkerIntervention") << "Current Navigation Data for body marker of Combined Modality must not be null."; mitkThrow() << "Current Navigation Data for body marker of Combined Modality must not be null."; } bool valid = bodyMarker->IsDataValid(); // update body marker status label if (valid) { ui->bodyMarkerTrackingStatusLabel->setStyleSheet( "background-color: #8bff8b; margin-right: 1em; margin-left: 1em; border: 1px solid grey"); ui->bodyMarkerTrackingStatusLabel->setText("Body marker is inside the tracking volume."); } else { ui->bodyMarkerTrackingStatusLabel->setStyleSheet( "background-color: #ff7878; margin-right: 1em; margin-left: 1em; border: 1px solid grey"); ui->bodyMarkerTrackingStatusLabel->setText("Body marker is not inside the tracking volume."); } ui->targetStructuresRangeGroupBox->setEnabled(valid); ui->riskStructuresRangeGroupBox->setEnabled(valid); } void QmitkUSNavigationStepMarkerIntervention::GenerateTargetColorLookupTable() { vtkSmartPointer lookupTable = vtkSmartPointer::New(); lookupTable->SetHueRange(0.0, 0.33); lookupTable->SetSaturationRange(1.0, 1.0); lookupTable->SetValueRange(1.0, 1.0); lookupTable->SetTableRange(0.0, 1.0); lookupTable->Build(); mitk::LookupTable::Pointer lut = mitk::LookupTable::New(); lut->SetVtkLookupTable(lookupTable); m_TargetColorLookupTableProperty = mitk::LookupTableProperty::New(lut); } void QmitkUSNavigationStepMarkerIntervention::UpdateTargetColors() { if (m_TargetNode.IsNull()) { return; } m_TargetNode->SetColor(1, 1, 1); mitk::BaseData *targetNodeData = m_TargetNode->GetData(); if (targetNodeData == 0) { return; } mitk::Surface::Pointer targetNodeSurface = dynamic_cast(targetNodeData); vtkSmartPointer targetNodeSurfaceVtk = targetNodeSurface->GetVtkPolyData(); vtkPointData *targetPointData = targetNodeSurface->GetVtkPolyData()->GetPointData(); vtkFloatArray *scalars = dynamic_cast(targetPointData->GetScalars("USNavigation::Occlusion")); vtkFloatArray *targetScoreScalars; if (m_ShowPlanningColors) { targetScoreScalars = dynamic_cast(targetPointData->GetScalars("USNavigation::PlanningScalars")); } else { targetScoreScalars = dynamic_cast(targetPointData->GetScalars("USNavigation::ReachedTargetScores")); } if (!scalars || !targetScoreScalars) { return; } unsigned int numberOfTupels = scalars->GetNumberOfTuples(); vtkSmartPointer colors = vtkSmartPointer::New(); colors->SetNumberOfComponents(1); colors->SetNumberOfTuples(numberOfTupels); colors->SetName("Colors"); double color, intersection, markerScore; for (unsigned int n = 0; n < numberOfTupels; n++) { scalars->GetTuple(n, &intersection); targetScoreScalars->GetTuple(n, &markerScore); if (intersection > 0) { color = 0; } else { color = markerScore; } colors->SetTuple(n, &color); } if (numberOfTupels > 0) { targetNodeSurfaceVtk->GetPointData()->SetScalars(colors); targetNodeSurfaceVtk->GetPointData()->Update(); } } void QmitkUSNavigationStepMarkerIntervention::UpdateTargetScore() { if (m_NeedleProjectionFilter->GetProjection()->GetSize() != 2) { return; } vtkSmartPointer targetSurfaceVtk = m_TargetSurface->GetVtkPolyData(); m_TargetIntersectionFilter->SetTargetSurface(m_TargetSurface); m_TargetIntersectionFilter->SetLine(m_NeedleProjectionFilter->GetProjection()); m_TargetIntersectionFilter->CalculateIntersection(); if (m_TargetIntersectionFilter->GetIsIntersecting()) { vtkFloatArray *scalars = dynamic_cast(targetSurfaceVtk->GetPointData()->GetScalars("USNavigation::ReachedTargetScores")); double score; scalars->GetTuple(m_TargetIntersectionFilter->GetIntersectionNearestSurfacePointId(), &score); double color[3]; m_TargetColorLookupTableProperty->GetLookupTable()->GetVtkLookupTable()->GetColor(score, color); float colorF[3]; colorF[0] = color[0]; colorF[1] = color[1]; colorF[2] = color[2]; m_TargetProgressBar->SetColor(colorF); m_TargetProgressBar->SetBorderColor(colorF); m_TargetProgressBar->setValue(m_TargetIntersectionFilter->GetDistanceToIntersection()); if (m_PlannedTargetProgressBar) { vtkFloatArray *scalars = dynamic_cast(targetSurfaceVtk->GetPointData()->GetScalars("USNavigation::PlanningScalars")); if (scalars) { double score; scalars->GetTuple(m_TargetIntersectionFilter->GetIntersectionNearestSurfacePointId(), &score); double color[3]; m_TargetColorLookupTableProperty->GetLookupTable()->GetVtkLookupTable()->GetColor(score, color); float colorF[3]; colorF[0] = color[0]; colorF[1] = color[1]; colorF[2] = color[2]; m_PlannedTargetProgressBar->SetColor(colorF); m_PlannedTargetProgressBar->SetBorderColor(colorF); m_PlannedTargetProgressBar->SetTextFormatValid("Planned Target: %1 mm"); mitk::Point3D intersectionPoint = m_TargetIntersectionFilter->GetIntersectionPoint(); mitk::ScalarType minDistance = -1; for (QVector>::iterator it = m_PlannedTargetsNodes.begin(); it != m_PlannedTargetsNodes.end(); ++it) { mitk::ScalarType distance = intersectionPoint.EuclideanDistanceTo((*it)->GetData()->GetGeometry()->GetOrigin()); if (minDistance < 0 || distance < minDistance) { minDistance = distance; } } m_PlannedTargetProgressBar->setValue(minDistance); } } } else { m_TargetProgressBar->setValueInvalid(); } } void QmitkUSNavigationStepMarkerIntervention::UpdateTargetProgressDisplay() { QString description; if (m_CurrentTargetIndex >= static_cast(m_NumberOfTargets)) { description = "All Targets Reached"; if (m_TargetProgressBar) { m_TargetProgressBar->hide(); } } else { description = QString("Distance to Target ") + QString::number(m_CurrentTargetIndex + 1) + QString(" of ") + QString::number(m_NumberOfTargets); if (m_TargetProgressBar) { m_TargetProgressBar->show(); } } ui->targetStructuresRangeGroupBox->setTitle(description); } void QmitkUSNavigationStepMarkerIntervention::UpdatePlannedTargetProgressDisplay() { // make sure that the needle projection consists of two points if (m_NeedleProjectionFilter->GetProjection()->GetSize() != 2) { return; } vtkSmartPointer targetSurfaceVtk = m_TargetSurface->GetVtkPolyData(); m_TargetIntersectionFilter->SetTargetSurface(m_TargetSurface); m_TargetIntersectionFilter->SetLine(m_NeedleProjectionFilter->GetProjection()); m_TargetIntersectionFilter->CalculateIntersection(); // update target progress bar according to the color of the intersection // point on the target surface and the distance to the intersection if (m_TargetIntersectionFilter->GetIsIntersecting()) { vtkFloatArray *scalars = dynamic_cast(targetSurfaceVtk->GetPointData()->GetScalars("Colors")); double score; scalars->GetTuple(m_TargetIntersectionFilter->GetIntersectionNearestSurfacePointId(), &score); double color[3]; m_TargetColorLookupTableProperty->GetLookupTable()->GetVtkLookupTable()->GetColor(score, color); float colorF[3]; colorF[0] = color[0]; colorF[1] = color[1]; colorF[2] = color[2]; m_TargetProgressBar->SetColor(colorF); m_TargetProgressBar->SetBorderColor(colorF); m_TargetProgressBar->setValue(m_TargetIntersectionFilter->GetDistanceToIntersection()); } else { float red[3] = {0.6, 0, 0}; m_TargetProgressBar->SetBorderColor(red); m_TargetProgressBar->setValueInvalid(); } } void QmitkUSNavigationStepMarkerIntervention::UpdateTargetViolationStatus() { // transform vtk polydata according to mitk geometry vtkSmartPointer transformFilter = vtkSmartPointer::New(); transformFilter->SetInputData(0, m_TargetSurface->GetVtkPolyData()); transformFilter->SetTransform(m_TargetSurface->GetGeometry()->GetVtkTransform()); transformFilter->Update(); vtkSmartPointer enclosedPoints = vtkSmartPointer::New(); enclosedPoints->Initialize(transformFilter->GetOutput()); mitk::Point3D needleTip = m_NeedleProjectionFilter->GetProjection()->GetPoint(0); // show warning if the needle tip is inside the target surface if (enclosedPoints->IsInsideSurface(needleTip[0], needleTip[1], needleTip[2])) { if (!m_TargetStructureWarnOverlay->IsVisible(NULL)) { m_TargetStructureWarnOverlay->SetVisibility(true); mitk::DataNode::Pointer targetViolationResult = mitk::DataNode::New(); targetViolationResult->SetName("TargetViolation"); targetViolationResult->SetProperty("USNavigation::TargetViolationPoint", mitk::Point3dProperty::New(needleTip)); emit SignalIntermediateResult(targetViolationResult); } MITK_INFO("QmitkUSAbstractNavigationStep") ("QmitkUSNavigationStepMarkerIntervention") << "Target surface violated at " << needleTip << "."; } else { m_TargetStructureWarnOverlay->SetVisibility(false); } } void QmitkUSNavigationStepMarkerIntervention::CalculateTargetPlacementQuality() { // clear quality display if there aren't all targets reached if (m_ReachedTargetsNodes.size() != static_cast(m_NumberOfTargets)) { ui->placementQualityGroupBox->setEnabled(false); ui->angleDifferenceValue->setText(""); ui->centersOfMassValue->setText(""); return; } ui->placementQualityGroupBox->setEnabled(true); mitk::Surface::Pointer targetSurface = dynamic_cast(m_TargetNode->GetData()); if (targetSurface.IsNull()) { mitkThrow() << "Target surface must not be null."; } m_PlacementQualityCalculator->SetTargetSurface(targetSurface); mitk::PointSet::Pointer targetPointSet = mitk::PointSet::New(); // copy the origins of all reached target nodes into a point set // for the quality calculator mitk::PointSet::PointIdentifier n = 0; for (QVector>::iterator it = m_ReachedTargetsNodes.begin(); it != m_ReachedTargetsNodes.end(); ++it) { targetPointSet->InsertPoint(n++, (*it)->GetData()->GetGeometry()->GetOrigin()); } m_PlacementQualityCalculator->SetTargetPoints(targetPointSet); m_PlacementQualityCalculator->Update(); double centersOfMassDistance = m_PlacementQualityCalculator->GetCentersOfMassDistance(); ui->centersOfMassValue->setText(QString::number(centersOfMassDistance, 103, 2) + " mm"); double meanAnglesDifference = m_PlacementQualityCalculator->GetMeanAngleDifference(); ui->angleDifferenceValue->setText(QString::number(meanAnglesDifference, 103, 2) + QString::fromLatin1(" °")); // create an intermediate result of the placement quality mitk::DataNode::Pointer placementQualityResult = mitk::DataNode::New(); placementQualityResult->SetName("PlacementQuality"); placementQualityResult->SetFloatProperty("USNavigation::CentersOfMassDistance", centersOfMassDistance); placementQualityResult->SetFloatProperty("USNavigation::MeanAngleDifference", meanAnglesDifference); placementQualityResult->SetProperty( "USNavigation::AngleDifferences", mitk::GenericProperty::New(m_PlacementQualityCalculator->GetAngleDifferences())); if (m_PlannedTargetsNodes.size() == static_cast(m_NumberOfTargets)) { mitk::VnlVector reachedPlannedDifferences; double reachedPlannedDifferencesSum = 0; double reachedPlannedDifferencesMax = 0; reachedPlannedDifferences.set_size(m_NumberOfTargets); // get sum and maximum of the planning / reality differences for (unsigned int n = 0; n < m_NumberOfTargets; ++n) { mitk::ScalarType distance = m_PlannedTargetsNodes.at(n)->GetData()->GetGeometry()->GetOrigin().EuclideanDistanceTo( m_ReachedTargetsNodes.at(n)->GetData()->GetGeometry()->GetOrigin()); reachedPlannedDifferences.put(n, distance); reachedPlannedDifferencesSum += distance; if (distance > reachedPlannedDifferencesMax) { reachedPlannedDifferencesMax = distance; } } // add distances between planning and reality to the quality intermediate result placementQualityResult->SetProperty("USNavigation::PlanningRealityDistances", mitk::GenericProperty::New(reachedPlannedDifferences)); placementQualityResult->SetProperty( "USNavigation::MeanPlanningRealityDistance", mitk::DoubleProperty::New(reachedPlannedDifferencesSum / static_cast(m_NumberOfTargets))); placementQualityResult->SetProperty("USNavigation::MaximumPlanningRealityDistance", mitk::DoubleProperty::New(reachedPlannedDifferencesMax)); } emit SignalIntermediateResult(placementQualityResult); } void QmitkUSNavigationStepMarkerIntervention::UpdateSensorsNames() { mitk::USCombinedModality::Pointer combinedModality = this->GetCombinedModality(false); if (combinedModality.IsNull()) { return; } mitk::NavigationDataSource::Pointer navigationDataSource = combinedModality->GetNavigationDataSource(); if (navigationDataSource.IsNull()) { return; } if (!m_NeedleSensorName.empty()) { try { m_NeedleSensorIndex = navigationDataSource->GetOutputIndex(m_NeedleSensorName); } catch (const std::exception &e) { MITK_WARN("QmitkUSAbstractNavigationStep") ("QmitkUSNavigationStepPlacementPlanning") << "Cannot get index for needle sensor name: " << e.what(); } } if (this->GetNavigationStepState() >= QmitkUSAbstractNavigationStep::State_Active) { m_NeedleProjectionFilter->SelectInput(m_NeedleSensorIndex); } if (!m_ReferenceSensorName.empty()) { try { m_ReferenceSensorIndex = navigationDataSource->GetOutputIndex(m_ReferenceSensorName); } catch (const std::exception &e) { MITK_WARN("QmitkUSAbstractNavigationStep") ("QmitkUSNavigationStepPlacementPlanning") << "Cannot get index for reference sensor name: " << e.what(); } } if (this->GetNavigationStepState() >= QmitkUSAbstractNavigationStep::State_Active) { m_NodeDisplacementFilter->SelectInput(m_ReferenceSensorIndex); } ui->freezeImageButton->SetCombinedModality(combinedModality, m_ReferenceSensorIndex); } diff --git a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.cpp b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.cpp index add64852a0..a582d7a530 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.cpp @@ -1,286 +1,286 @@ /*=================================================================== 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 "QmitkUSNavigationStepPunctuationIntervention.h" #include "ui_QmitkUSNavigationStepPunctuationIntervention.h" #include "mitkNeedleProjectionFilter.h" #include "../Widgets/QmitkZoneProgressBar.h" #include "../USNavigationMarkerPlacement.h" #include "usModuleRegistry.h" #include QmitkUSNavigationStepPunctuationIntervention::QmitkUSNavigationStepPunctuationIntervention(QWidget *parent) : QmitkUSAbstractNavigationStep(parent), + m_Ui(new Ui::QmitkUSNavigationStepPunctuationIntervention), m_NeedleProjectionFilter(mitk::NeedleProjectionFilter::New()), - ui(new Ui::QmitkUSNavigationStepPunctuationIntervention), m_SphereSource(vtkSmartPointer::New()), m_OBBTree(vtkSmartPointer::New()), m_IntersectPoints(vtkSmartPointer::New()) { - ui->setupUi(this); - connect(ui->m_AddNewAblationZone, SIGNAL(clicked()), this, SLOT(OnAddAblationZoneClicked())); - connect(ui->m_EnableAblationMarking, SIGNAL(clicked()), this, SLOT(OnEnableAblationZoneMarkingClicked())); - connect(ui->m_AblationZoneSizeSlider, SIGNAL(valueChanged(int)), this, SLOT(OnAblationZoneSizeSliderChanged(int))); - ui->m_AblationZonesBox->setVisible(false); + m_Ui->setupUi(this); + connect(m_Ui->m_AddNewAblationZone, SIGNAL(clicked()), this, SLOT(OnAddAblationZoneClicked())); + connect(m_Ui->m_EnableAblationMarking, SIGNAL(clicked()), this, SLOT(OnEnableAblationZoneMarkingClicked())); + connect(m_Ui->m_AblationZoneSizeSlider, SIGNAL(valueChanged(int)), this, SLOT(OnAblationZoneSizeSliderChanged(int))); + m_Ui->m_AblationZonesBox->setVisible(false); } QmitkUSNavigationStepPunctuationIntervention::QmitkUSNavigationStepPunctuationIntervention(mitk::Point3D toolAxis, QWidget *parent) : QmitkUSAbstractNavigationStep(parent), -m_NeedleProjectionFilter(mitk::NeedleProjectionFilter::New()), -ui(new Ui::QmitkUSNavigationStepPunctuationIntervention), -m_SphereSource(vtkSmartPointer::New()), -m_OBBTree(vtkSmartPointer::New()), -m_IntersectPoints(vtkSmartPointer::New()) + m_Ui(new Ui::QmitkUSNavigationStepPunctuationIntervention), + m_NeedleProjectionFilter(mitk::NeedleProjectionFilter::New()), + m_SphereSource(vtkSmartPointer::New()), + m_OBBTree(vtkSmartPointer::New()), + m_IntersectPoints(vtkSmartPointer::New()) { m_ToolAxis.SetElement(0, (toolAxis.GetElement(0))); m_ToolAxis.SetElement(1, (toolAxis.GetElement(1))); m_ToolAxis.SetElement(2, (toolAxis.GetElement(2))); m_NeedleProjectionFilter->SetToolAxisForFilter(m_ToolAxis); - ui->setupUi(this); - connect(ui->m_AddNewAblationZone, SIGNAL(clicked()), this, SLOT(OnAddAblationZoneClicked())); - connect(ui->m_EnableAblationMarking, SIGNAL(clicked()), this, SLOT(OnEnableAblationZoneMarkingClicked())); - connect(ui->m_AblationZoneSizeSlider, SIGNAL(valueChanged(int)), this, SLOT(OnAblationZoneSizeSliderChanged(int))); - ui->m_AblationZonesBox->setVisible(false); + m_Ui->setupUi(this); + connect(m_Ui->m_AddNewAblationZone, SIGNAL(clicked()), this, SLOT(OnAddAblationZoneClicked())); + connect(m_Ui->m_EnableAblationMarking, SIGNAL(clicked()), this, SLOT(OnEnableAblationZoneMarkingClicked())); + connect(m_Ui->m_AblationZoneSizeSlider, SIGNAL(valueChanged(int)), this, SLOT(OnAblationZoneSizeSliderChanged(int))); + m_Ui->m_AblationZonesBox->setVisible(false); } void QmitkUSNavigationStepPunctuationIntervention::OnEnableAblationZoneMarkingClicked() { - if(ui->m_EnableAblationMarking->isChecked()) - ui->m_AblationZonesBox->setVisible(true); + if(m_Ui->m_EnableAblationMarking->isChecked()) + m_Ui->m_AblationZonesBox->setVisible(true); else - ui->m_AblationZonesBox->setVisible(false); + m_Ui->m_AblationZonesBox->setVisible(false); } void QmitkUSNavigationStepPunctuationIntervention::OnAblationZoneSizeSliderChanged(int size) { -int id = ui->m_AblationZonesList->currentRow(); +int id = m_Ui->m_AblationZonesList->currentRow(); if (id!=-1) {emit AblationZoneChanged(id,size);} }// void QmitkUSNavigationStepPunctuationIntervention::OnAddAblationZoneClicked() { - QListWidgetItem* newItem = new QListWidgetItem("Ablation Zone (initial size: " + QString::number(ui->m_AblationZoneSizeSlider->value()) + " mm)", ui->m_AblationZonesList); + QListWidgetItem* newItem = new QListWidgetItem("Ablation Zone (initial size: " + QString::number(m_Ui->m_AblationZoneSizeSlider->value()) + " mm)", m_Ui->m_AblationZonesList); newItem->setSelected(true); - emit AddAblationZoneClicked(ui->m_AblationZoneSizeSlider->value()); + emit AddAblationZoneClicked(m_Ui->m_AblationZoneSizeSlider->value()); } QmitkUSNavigationStepPunctuationIntervention::~QmitkUSNavigationStepPunctuationIntervention() { mitk::DataStorage::Pointer dataStorage = this->GetDataStorage(false); if ( dataStorage.IsNotNull() ) { // remove needle path from data storage if it is there mitk::DataNode::Pointer node = this->GetNamedDerivedNode ("Needle Path", QmitkUSAbstractNavigationStep::DATANAME_BASENODE); if ( node.IsNotNull() ) { dataStorage->Remove(node); } } - delete ui; + delete m_Ui; } bool QmitkUSNavigationStepPunctuationIntervention::OnStartStep() { // create node for Needle Projection mitk::DataNode::Pointer node = this->GetNamedDerivedNodeAndCreate ("Needle Path", QmitkUSAbstractNavigationStep::DATANAME_BASENODE); node->SetData(m_NeedleProjectionFilter->GetProjection()); node->SetBoolProperty("show contour", true); return true; } bool QmitkUSNavigationStepPunctuationIntervention::OnRestartStep() { return this->OnActivateStep(); } bool QmitkUSNavigationStepPunctuationIntervention::OnFinishStep() { mitk::DataNode::Pointer finishPunctionResult = mitk::DataNode::New(); finishPunctionResult->SetName("PunctionResult"); mitk::Point3D needlePos = m_NeedleProjectionFilter->GetOutput(0)->GetPosition(); mitk::Quaternion needleRot = m_NeedleProjectionFilter->GetOutput(0)->GetOrientation(); finishPunctionResult->SetProperty("USNavigation::TipPositionEnd", mitk::Point3dProperty::New(needlePos)); MITK_INFO("USNavigationLogging") << "Instrument tip at end: " <ClearZones(); mitk::DataStorage::Pointer dataStorage = this->GetDataStorage(); // add progress bars for risk zone nodes m_ZoneNodes = dataStorage->GetDerivations(dataStorage->GetNamedNode(USNavigationMarkerPlacement::DATANAME_ZONES)); // add zones to the widgets for risk structures for (mitk::DataStorage::SetOfObjects::ConstIterator it = m_ZoneNodes->Begin(); it != m_ZoneNodes->End(); ++it) { - ui->riskStructuresRangeWidget->AddZone(it->Value()); + m_Ui->riskStructuresRangeWidget->AddZone(it->Value()); float rgb[3]; it->Value()->GetColor(rgb); mitk::Color color; color.SetRed(rgb[0]); color.SetGreen(rgb[1]); color.SetBlue(rgb[2]); m_OldColors[it->Value()] = color; } m_NeedleProjectionFilter->SelectInput(0); return true; } void QmitkUSNavigationStepPunctuationIntervention::OnUpdate() { // get navigation data source and make sure that it is not null mitk::NavigationDataSource::Pointer navigationDataSource = this->GetCombinedModality()->GetNavigationDataSource(); if ( navigationDataSource.IsNull() ) { MITK_ERROR("QmitkUSAbstractNavigationStep")("QmitkUSNavigationStepPunctuationIntervention") << "Navigation Data Source of Combined Modality must not be null."; mitkThrow() << "Navigation Data Source of Combined Modality must not be null."; } // update body marker this->UpdateBodyMarkerStatus(navigationDataSource->GetOutput(1)); // update critical structures this->UpdateCriticalStructures(navigationDataSource->GetOutput(0),m_NeedleProjectionFilter->GetProjection()); //Update Distance to US image mitk::Point3D point1 = m_NeedleProjectionFilter->GetProjection()->GetPoint(0); mitk::Point3D point2 = m_NeedleProjectionFilter->GetProjection()->GetPoint(1); double distance = point1.EuclideanDistanceTo(point2); - ui->m_DistanceToUSPlane->setText(QString::number(distance) + " mm"); + m_Ui->m_DistanceToUSPlane->setText(QString::number(distance) + " mm"); } void QmitkUSNavigationStepPunctuationIntervention::OnSettingsChanged(const itk::SmartPointer settingsNode) { if ( settingsNode.IsNull() ) { return; } } QString QmitkUSNavigationStepPunctuationIntervention::GetTitle() { return "Computer-assisted Intervention"; } bool QmitkUSNavigationStepPunctuationIntervention::GetIsRestartable() { return false; } QmitkUSNavigationStepPunctuationIntervention::FilterVector QmitkUSNavigationStepPunctuationIntervention::GetFilter() { return FilterVector(1, m_NeedleProjectionFilter.GetPointer()); } void QmitkUSNavigationStepPunctuationIntervention::OnSetCombinedModality() { mitk::USCombinedModality::Pointer combinedModality = this->GetCombinedModality(false); if ( combinedModality.IsNotNull() ) { // set calibration of the combined modality to the needle projection filter mitk::AffineTransform3D::Pointer calibration = combinedModality->GetCalibration(); if ( calibration.IsNotNull() ) { m_NeedleProjectionFilter->SetTargetPlane(calibration); } } } void QmitkUSNavigationStepPunctuationIntervention::ClearZones() { - ui->riskStructuresRangeWidget->ClearZones(); + m_Ui->riskStructuresRangeWidget->ClearZones(); } void QmitkUSNavigationStepPunctuationIntervention::UpdateBodyMarkerStatus(mitk::NavigationData::Pointer bodyMarker) { if ( bodyMarker.IsNull() ) { MITK_ERROR("QmitkUSAbstractNavigationStep")("QmitkUSNavigationStepPunctuationIntervention") << "Current Navigation Data for body marker of Combined Modality must not be null."; mitkThrow() << "Current Navigation Data for body marker of Combined Modality must not be null."; } bool valid = bodyMarker->IsDataValid(); // update body marker status label if (valid) { - ui->bodyMarkerTrackingStatusLabel->setStyleSheet( + m_Ui->bodyMarkerTrackingStatusLabel->setStyleSheet( "background-color: #8bff8b; margin-right: 1em; margin-left: 1em; border: 1px solid grey"); - ui->bodyMarkerTrackingStatusLabel->setText("Body marker is inside the tracking volume."); + m_Ui->bodyMarkerTrackingStatusLabel->setText("Body marker is inside the tracking volume."); } else { - ui->bodyMarkerTrackingStatusLabel->setStyleSheet( + m_Ui->bodyMarkerTrackingStatusLabel->setStyleSheet( "background-color: #ff7878; margin-right: 1em; margin-left: 1em; border: 1px solid grey"); - ui->bodyMarkerTrackingStatusLabel->setText("Body marker is not inside the tracking volume."); + m_Ui->bodyMarkerTrackingStatusLabel->setText("Body marker is not inside the tracking volume."); } - ui->riskStructuresRangeGroupBox->setEnabled(valid); + m_Ui->riskStructuresRangeGroupBox->setEnabled(valid); } void QmitkUSNavigationStepPunctuationIntervention::UpdateCriticalStructures(mitk::NavigationData::Pointer needle, mitk::PointSet::Pointer path) { // update the distances for the risk structures widget - ui->riskStructuresRangeWidget->UpdateDistancesToNeedlePosition(needle); + m_Ui->riskStructuresRangeWidget->UpdateDistancesToNeedlePosition(needle); //iterate through all zones for (mitk::DataStorage::SetOfObjects::ConstIterator it = m_ZoneNodes->Begin(); it != m_ZoneNodes->End(); ++it) { mitk::DataNode::Pointer currentNode = it->Value(); //get center point and radius float radius = -1; mitk::Point3D center; currentNode->GetFloatProperty("zone.size", radius); center = currentNode->GetData()->GetGeometry()->GetIndexToWorldTransform()->GetTranslation(); mitk::Point3D point0 = path->GetPoint(0); mitk::Point3D point1 = path->GetPoint(1); if (CheckSphereLineIntersection(center,radius,point0,point1)) {currentNode->SetColor(mitk::IGTColor_WARNING);} else {currentNode->SetColor(m_OldColors[currentNode]);} } } bool QmitkUSNavigationStepPunctuationIntervention::CheckSphereLineIntersection(mitk::Point3D& sphereOrigin, float& sphereRadius, mitk::Point3D& lineStart, mitk::Point3D& lineEnd) { double center[3] = {sphereOrigin[0],sphereOrigin[1],sphereOrigin[2]}; m_SphereSource->SetCenter(center); m_SphereSource->SetRadius(sphereRadius); m_SphereSource->Update(); m_OBBTree->SetDataSet(m_SphereSource->GetOutput()); m_OBBTree->BuildLocator(); double lineP0[3] = {lineStart[0], lineStart[1], lineStart[2]}; double lineP1[3] = {lineEnd[0], lineEnd[1], lineEnd[2]}; m_OBBTree->IntersectWithLine(lineP0, lineP1, m_IntersectPoints, nullptr); if (m_IntersectPoints->GetNumberOfPoints() > 0) {return true;} else {return false;} } diff --git a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.h b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.h index 9c6e54b87f..a41339d019 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.h +++ b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.h @@ -1,119 +1,119 @@ /*=================================================================== 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 QMITKUSNAVIGATIONSTEPPUNCTUATIONINTERVENTION_H #define QMITKUSNAVIGATIONSTEPPUNCTUATIONINTERVENTION_H #include "QmitkUSAbstractNavigationStep.h" #include #include #include #include #include namespace mitk { class DataNode; class NeedleProjectionFilter; class NodeDisplacementFilter; class USNavigationGrabCutSegmentationUpdateFilter; class USNavigationTargetUpdateFilter; class USNavigationTargetOcclusionFilter; class USPointMarkInteractor; class LookupTableProperty; class Surface; } namespace Ui { class QmitkUSNavigationStepPunctuationIntervention; } class QmitkZoneProgressBar; /** * \brief Navigations step for the actual punctuation intervention. * The needle path is projected onto the image plane and the distances to all * risk structures are displayed in the widget. * * The risk structures are expected to be in the data storage under * DATANAME_BASENODE -> DATANAME_ZONES. They should contain a property named * "zone.size" and it is assumed that they are spherical. */ class QmitkUSNavigationStepPunctuationIntervention : public QmitkUSAbstractNavigationStep { Q_OBJECT public: explicit QmitkUSNavigationStepPunctuationIntervention(QWidget *parent = 0); explicit QmitkUSNavigationStepPunctuationIntervention(mitk::Point3D toolAxis, QWidget *parent = 0); ~QmitkUSNavigationStepPunctuationIntervention(); virtual bool OnStartStep(); virtual bool OnRestartStep(); virtual bool OnFinishStep(); virtual bool OnActivateStep(); virtual void OnUpdate(); virtual void OnSettingsChanged(const itk::SmartPointer); virtual QString GetTitle(); virtual bool GetIsRestartable(); virtual FilterVector GetFilter(); signals: void AddAblationZoneClicked(int); void AblationZoneChanged(int,int); protected slots: void OnAddAblationZoneClicked(); void OnEnableAblationZoneMarkingClicked(); void OnAblationZoneSizeSliderChanged(int size); protected: virtual void OnSetCombinedModality(); void ClearZones(); void UpdateBodyMarkerStatus(mitk::NavigationData::Pointer bodyMarker); /** Updates the critical structures which means that the distance to the needle tip is updated and also the color changes to red if the path projection intersects the critical structure. */ void UpdateCriticalStructures(mitk::NavigationData::Pointer needle, mitk::PointSet::Pointer path); /** Checks if the given line intersects the given sphere. */ bool CheckSphereLineIntersection(mitk::Point3D& sphereOrigin, float& sphereRadius, mitk::Point3D& lineStart, mitk::Point3D& lineEnd); +private: + Ui::QmitkUSNavigationStepPunctuationIntervention *m_Ui; + mitk::DataStorage::SetOfObjects::ConstPointer m_ZoneNodes; /** * \brief Creates a Pointset that projects the needle's path */ itk::SmartPointer m_NeedleProjectionFilter; mitk::Point3D m_ToolAxis; std::map m_OldColors; //stores the original color of the critical structrue nodes //some help variables for the CheckSphereLineIntersection()-Method vtkSmartPointer m_SphereSource; vtkSmartPointer m_OBBTree; vtkSmartPointer m_IntersectPoints; - -private: - Ui::QmitkUSNavigationStepPunctuationIntervention *ui; }; #endif // QMITKUSNAVIGATIONSTEPPUNCTUATIONINTERVENTION_H diff --git a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/QmitkUSNavigationCalibrationsDataModel.h b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/QmitkUSNavigationCalibrationsDataModel.h index 72a3303239..358b15fb10 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/QmitkUSNavigationCalibrationsDataModel.h +++ b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/QmitkUSNavigationCalibrationsDataModel.h @@ -1,73 +1,74 @@ /*=================================================================== 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 QMITKUSNAVIGATIONCALIBRATIONSDATAMODEL_H #define QMITKUSNAVIGATIONCALIBRATIONSDATAMODEL_H #include #include #include namespace mitk { class USCombinedModality; class USControlInterfaceBMode; class USControlInterfaceProbes; } class QmitkUSNavigationCalibrationsDataModel : public QAbstractTableModel { Q_OBJECT public: explicit QmitkUSNavigationCalibrationsDataModel(QObject *parent = 0); virtual ~QmitkUSNavigationCalibrationsDataModel(); void SetCombinedModality(itk::SmartPointer combinedModality); void OnDeviceChanged(const std::string&, const std::string&); /** \brief Return number of rows of the model. */ virtual int rowCount ( const QModelIndex & parent = QModelIndex() ) const; /** \brief Return number of columns (3) of the model. */ virtual int columnCount ( const QModelIndex & parent = QModelIndex() ) const; /** \brief Return names for the columns, numbers for the rows and invalid for DisplayRole. */ virtual QVariant headerData ( int section, Qt::Orientation orientation, int role = Qt::DisplayRole ) const; /** \brief Return selectable and enabled for column 1 (size); selectable, enabled and editable for every other column. */ virtual Qt::ItemFlags flags ( const QModelIndex & index ) const; /** \brief Return model data of the selected cell. */ virtual QVariant data ( const QModelIndex & index, int role = Qt::DisplayRole ) const; /** \brief Set model data for the selected cell. */ virtual bool setData ( const QModelIndex & index, const QVariant & value, int role = Qt::EditRole ); + using QAbstractTableModel::removeRows; /** \brief Remove given rows from the model. * \param removeFromDataStorage zone nodes are removed from the data storage too, if this is set to true */ virtual bool removeRows ( int row, int count, const QModelIndex& parent, bool removeFromDataStorage ); private: itk::SmartPointer m_CombinedModality; itk::SmartPointer m_ControlInterfaceBMode; mitk::MessageDelegate2 m_ListenerDeviceChanged; }; #endif // QMITKUSNAVIGATIONCALIBRATIONSDATAMODEL_H diff --git a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/USNavigationMarkerPlacement.cpp b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/USNavigationMarkerPlacement.cpp index 380c84b225..9fc49abbf6 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/USNavigationMarkerPlacement.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/USNavigationMarkerPlacement.cpp @@ -1,809 +1,809 @@ /*=================================================================== 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 "USNavigationMarkerPlacement.h" #include "ui_USNavigationMarkerPlacement.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 "mitkIRenderingManager.h" #include "mitkNodeDisplacementFilter.h" #include "mitkUSCombinedModality.h" #include #include "IO/mitkUSNavigationExperimentLogging.h" #include "IO/mitkUSNavigationStepTimer.h" #include #include #include #include #include #include #include "QmitkRenderWindow.h" #include "QmitkStdMultiWidget.h" #include "QmitkStdMultiWidgetEditor.h" #include "mitkLayoutAnnotationRenderer.h" // scene serialization #include #include #include #include #include const std::string USNavigationMarkerPlacement::VIEW_ID = "org.mitk.views.usmarkerplacement"; const char *USNavigationMarkerPlacement::DATANAME_TUMOUR = "Tumour"; const char *USNavigationMarkerPlacement::DATANAME_TARGETSURFACE = "Target Surface"; const char *USNavigationMarkerPlacement::DATANAME_ZONES = "Zones"; const char *USNavigationMarkerPlacement::DATANAME_TARGETS = "Targets"; const char *USNavigationMarkerPlacement::DATANAME_TARGETS_PATHS = "Target Paths"; const char *USNavigationMarkerPlacement::DATANAME_REACHED_TARGETS = "Reached Targets"; USNavigationMarkerPlacement::USNavigationMarkerPlacement() : m_Parent(nullptr), m_UpdateTimer(new QTimer(this)), m_ImageAndNavigationDataLoggingTimer(new QTimer(this)), - m_StdMultiWidget(0), + m_StdMultiWidget(nullptr), m_ReinitAlreadyDone(false), m_IsExperimentRunning(false), m_NavigationStepTimer(mitk::USNavigationStepTimer::New()), m_ExperimentLogging(mitk::USNavigationExperimentLogging::New()), m_AblationZonesDisplacementFilter(mitk::NodeDisplacementFilter::New()), m_IconRunning(QPixmap(":/USNavigation/record.png")), m_IconNotRunning(QPixmap(":/USNavigation/record-gray.png")), m_USImageLoggingFilter(mitk::USImageLoggingFilter::New()), m_NavigationDataRecorder(mitk::NavigationDataRecorder::New()), m_SceneNumber(1), m_WarnOverlay(mitk::TextAnnotation2D::New()), - m_ListenerDeviceChanged(this, &USNavigationMarkerPlacement::OnCombinedModalityPropertyChanged), m_NeedleIndex(0), m_MarkerIndex(1), + m_ListenerDeviceChanged(this, &USNavigationMarkerPlacement::OnCombinedModalityPropertyChanged), ui(new Ui::USNavigationMarkerPlacement) { 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); // set prefix for experiment logging (only keys with this prefix are taken // into consideration m_ExperimentLogging->SetKeyPrefix("USNavigation::"); m_UpdateTimer->start(33); // every 33 Milliseconds = 30 Frames/Second } USNavigationMarkerPlacement::~USNavigationMarkerPlacement() { // remove listener for ultrasound device changes if (m_CombinedModality.IsNotNull() && m_CombinedModality->GetUltrasoundDevice().IsNotNull()) { m_CombinedModality->GetUltrasoundDevice()->RemovePropertyChangedListener(m_ListenerDeviceChanged); } // remove listener for ultrasound device changes if (m_CombinedModality.IsNotNull() && m_CombinedModality->GetUltrasoundDevice().IsNotNull()) { m_CombinedModality->GetUltrasoundDevice()->RemovePropertyChangedListener(m_ListenerDeviceChanged); } delete ui; } void USNavigationMarkerPlacement::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 vtkSphereSource *vtkData = vtkSphereSource::New(); vtkData->SetRadius(newSize / 2); vtkData->SetCenter(0, 0, 0); vtkData->SetPhiResolution(20); vtkData->SetThetaResolution(20); vtkData->Update(); mitk::Surface::Pointer zoneSurface = dynamic_cast(m_AblationZonesVector.at(id)->GetData()); zoneSurface->SetVtkPolyData(vtkData->GetOutput()); vtkData->Delete(); } void USNavigationMarkerPlacement::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 vtkSphereSource *vtkData = vtkSphereSource::New(); vtkData->SetRadius(size / 2); vtkData->SetCenter(0, 0, 0); vtkData->SetPhiResolution(20); vtkData->SetThetaResolution(20); vtkData->Update(); zone->SetVtkPolyData(vtkData->GetOutput()); vtkData->Delete(); // 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 USNavigationMarkerPlacement::CreateQtPartControl(QWidget *parent) { m_Parent = parent; ui->setupUi(parent); connect(ui->navigationProcessWidget, SIGNAL(SignalCombinedModalityChanged(itk::SmartPointer)), this, SLOT(OnCombinedModalityChanged(itk::SmartPointer))); connect(ui->navigationProcessWidget, SIGNAL(SignalSettingsChanged(itk::SmartPointer)), this, SLOT(OnSettingsChanged(itk::SmartPointer))); connect(ui->navigationProcessWidget, SIGNAL(SignalActiveNavigationStepChanged(int)), this, SLOT(OnActiveNavigationStepChanged(int))); 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->navigationProcessWidget, SIGNAL(SignalIntermediateResult(const itk::SmartPointer)), this, SLOT(OnIntermediateResultProduced(const itk::SmartPointer))); ui->navigationProcessWidget->SetDataStorage(this->GetDataStorage()); // indicate that no experiment is running at start ui->runningLabel->setPixmap(m_IconNotRunning); ui->navigationProcessWidget->SetSettingsWidget(new QmitkUSNavigationCombinedSettingsWidget(m_Parent)); } void USNavigationMarkerPlacement::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 USNavigationMarkerPlacement::SetToolAxisMarkerPlacement() { m_NavigationDataSource = m_CombinedModality->GetNavigationDataSource(); m_ToolAxis.SetElement(0, 0); m_ToolAxis.SetElement(1, 0); m_ToolAxis.SetElement(2, 1); if (m_NavigationDataSource.IsNull()) { MITK_WARN << "Cannot retrieve tool axis as tracking source is null."; } else { 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(); m_CurrentStorage = context->GetService(refs.front()); if (m_CurrentStorage.IsNull()) { MITK_WARN << "Found an invalid storage object!"; } - if (m_CurrentStorage->GetToolCount() != m_NavigationDataSource->GetNumberOfOutputs()) //there is something wrong with the storage + if (m_CurrentStorage->GetToolCount() != static_cast(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."; m_CurrentStorage = NULL; } //getting the first tool in the tool storage, assuming this is the needle mitk::NavigationTool::Pointer needle; needle = m_CurrentStorage->GetTool(0); m_ToolAxis.SetElement(0, (needle->GetToolAxis().GetElement(0))); m_ToolAxis.SetElement(1, (needle->GetToolAxis().GetElement(1))); m_ToolAxis.SetElement(2, (needle->GetToolAxis().GetElement(2))); } } void USNavigationMarkerPlacement::SetFocus() { this->ReinitOnImage(); } void USNavigationMarkerPlacement::OnTimeout() { 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(); if (m_StdMultiWidget) { m_StdMultiWidget->DisableStandardLevelWindow(); m_StdMultiWidget->changeLayoutTo2DUpAnd3DDown(); } } this->CreateOverlays(); } if (m_CombinedModality.IsNotNull() && !this->m_CombinedModality->GetIsFreezed()) // if the combined modality is freezed: do nothing { ui->navigationProcessWidget->UpdateNavigationProgress(); 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 USNavigationMarkerPlacement::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(); if (m_StdMultiWidget) { m_StdMultiWidget->DisableStandardLevelWindow(); m_StdMultiWidget->changeLayoutTo2DUpAnd3DDown(); this->GetDataStorage()->GetNamedNode("stdmulti.widget1.plane")->SetVisibility(false); this->GetDataStorage()->GetNamedNode("stdmulti.widget3.plane")->SetVisibility(false); } } } void USNavigationMarkerPlacement::OnResetStandardLayout() { //reset render windows mitk::DataNode::Pointer widget1 = this->GetDataStorage()->GetNamedNode("stdmulti.widget1.plane"); if (widget1.IsNotNull()) { widget1->SetVisibility(true); } mitk::DataNode::Pointer widget3 = this->GetDataStorage()->GetNamedNode("stdmulti.widget3.plane"); if (widget3.IsNotNull()) { widget3->SetVisibility(true); } m_StdMultiWidget->changeLayoutToDefault(); } void USNavigationMarkerPlacement::OnChangeLayoutClicked() { if (ui->m_enableNavigationLayout->isChecked()) OnEnableNavigationLayout(); else OnResetStandardLayout(); } void USNavigationMarkerPlacement::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 USNavigationMarkerPlacement::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()); } 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); ui->navigationProcessWidget->EnableInteraction(true); // (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, m_NavigationSteps.at(0)->GetTitle().toStdString()); 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); // (re)start experiment logging and set output file name m_ExperimentLogging->Reset(); m_ExperimentLogging->SetFileName( QString(m_ExperimentResultsSubDirectory + QDir::separator() + "experiment-logging.xml").toStdString()); } } } void USNavigationMarkerPlacement::OnFinishExperiment() { this->WaitCursorOn(); MITK_INFO("USNavigationLogging") << "Experiment finished!"; MITK_INFO("USNavigationLogging") << "Position/Orientation of needle tip: " << (dynamic_cast(m_CombinedModality->GetTrackingDevice()->GetOutput(0)))->GetPosition(); MITK_INFO("USNavigationLogging") << "Position of target: " << m_TargetNodeDisplacementFilter->GetRawDisplacementNavigationData(0)->GetPosition(); MITK_INFO("USNavigationLogging") << "Total duration: " << m_NavigationStepTimer->GetTotalDuration(); ui->navigationProcessWidget->FinishCurrentNavigationStep(); m_ImageAndNavigationDataLoggingTimer->stop(); ui->runningLabel->setPixmap(m_IconNotRunning); ui->navigationProcessWidget->EnableInteraction(false); m_NavigationStepTimer->Stop(); // make sure that the navigation process will be start from beginning at the // next experiment ui->navigationProcessWidget->ResetNavigationProcess(); 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"; MITK_INFO("USNavigationLogging") << "Writing logged navigation messages to separate csv file: " << csvNavigationMessagesFilename.str(); m_LoggingBackend.WriteCSVFileWithNavigationMessages(csvNavigationMessagesFilename.str()); mbilog::UnregisterBackend(&m_LoggingBackend); m_IsExperimentRunning = false; m_ImageAndNavigationDataLoggingTimer->stop(); m_CombinedModality = 0; // reset scene number for next experiment m_SceneNumber = 1; this->WaitCursorOff(); MITK_INFO("USNavigationLogging") << "Finished!"; } void USNavigationMarkerPlacement::OnCombinedModalityChanged( itk::SmartPointer combinedModality) { // remove old listener for ultrasound device changes if (m_CombinedModality.IsNotNull() && m_CombinedModality->GetUltrasoundDevice().IsNotNull()) { m_CombinedModality->GetUltrasoundDevice()->RemovePropertyChangedListener(m_ListenerDeviceChanged); } m_CombinedModality = combinedModality; m_ReinitAlreadyDone = false; // add a listener for ultrasound device changes if (m_CombinedModality.IsNotNull() && m_CombinedModality->GetUltrasoundDevice().IsNotNull()) { m_CombinedModality->GetUltrasoundDevice()->AddPropertyChangedListener(m_ListenerDeviceChanged); } // update navigation data recorder for using the new combined modality mitk::NavigationDataSource::Pointer navigationDataSource = combinedModality->GetNavigationDataSource(); m_NavigationDataRecorder->ConnectTo(navigationDataSource); m_NavigationDataRecorder->ResetRecording(); //upate stored tool axis for current tool this->SetToolAxisMarkerPlacement(); //store new tool axis QmitkUSNavigationStepPunctuationIntervention* stepIntervention = new QmitkUSNavigationStepPunctuationIntervention(m_ToolAxis, m_Parent); m_NavigationSteps.pop_back(); m_NavigationSteps.push_back(stepIntervention); // TODO check for correct connection // for (unsigned int n = 0; n < navigationDataSource->GetNumberOfIndexedOutputs(); ++n) // { // m_NavigationDataRecorder->AddNavigationData(navigationDataSource->GetOutput(n)); // } // update ultrasound image logging filter for using the new combined modality mitk::USDevice::Pointer ultrasoundImageSource = combinedModality->GetUltrasoundDevice(); for (unsigned int n = 0; n < ultrasoundImageSource->GetNumberOfIndexedOutputs(); ++n) { m_USImageLoggingFilter->SetInput(n, ultrasoundImageSource->GetOutput(n)); } // update ablation zone filter for using the new combined modality for (unsigned int n = 0; n < navigationDataSource->GetNumberOfIndexedOutputs(); ++n) { m_AblationZonesDisplacementFilter->SetInput(n, navigationDataSource->GetOutput(n)); } m_AblationZonesDisplacementFilter->SelectInput(m_MarkerIndex); // make sure that a reinit is done for the new images this->ReinitOnImage(); } void USNavigationMarkerPlacement::OnSettingsChanged(itk::SmartPointer settings) { std::string applicationName; if (!settings->GetStringProperty("settings.application", applicationName)) { // set default application if the string property is not available applicationName = "Marker Placement"; } // create navigation step widgets according to the selected application if (applicationName != m_CurrentApplicationName) { m_CurrentApplicationName = applicationName; QmitkUSNavigationProcessWidget::NavigationStepVector navigationSteps; if (applicationName == "Puncture") { QmitkUSNavigationStepCombinedModality* stepCombinedModality = new QmitkUSNavigationStepCombinedModality(m_Parent); QmitkUSNavigationStepTumourSelection* stepTumourSelection = new QmitkUSNavigationStepTumourSelection(m_Parent); stepTumourSelection->SetTargetSelectionOptional(true); m_TargetNodeDisplacementFilter = stepTumourSelection->GetTumourNodeDisplacementFilter(); QmitkUSNavigationStepZoneMarking* stepZoneMarking = new QmitkUSNavigationStepZoneMarking(m_Parent); QmitkUSNavigationStepPunctuationIntervention* stepIntervention = new QmitkUSNavigationStepPunctuationIntervention(m_Parent); connect(stepIntervention, SIGNAL(AddAblationZoneClicked(int)), this, SLOT(OnAddAblationZone(int))); connect(stepIntervention, SIGNAL(AblationZoneChanged(int, int)), this, SLOT(OnChangeAblationZone(int, int))); m_NavigationStepNames = std::vector(); navigationSteps.push_back(stepCombinedModality); m_NavigationStepNames.push_back("Combined Modality Initialization"); navigationSteps.push_back(stepTumourSelection); m_NavigationStepNames.push_back("Target Selection"); navigationSteps.push_back(stepZoneMarking); m_NavigationStepNames.push_back("Critical Structure Marking"); navigationSteps.push_back(stepIntervention); m_NavigationStepNames.push_back("Intervention"); } else if (applicationName == "Marker Placement") { QmitkUSNavigationStepCombinedModality *stepCombinedModality = new QmitkUSNavigationStepCombinedModality(m_Parent); QmitkUSNavigationStepTumourSelection *stepTumourSelection = new QmitkUSNavigationStepTumourSelection(m_Parent); m_TargetNodeDisplacementFilter = stepTumourSelection->GetTumourNodeDisplacementFilter(); QmitkUSNavigationStepZoneMarking *stepZoneMarking = new QmitkUSNavigationStepZoneMarking(m_Parent); QmitkUSNavigationStepPlacementPlanning *stepPlacementPlanning = new QmitkUSNavigationStepPlacementPlanning(m_Parent); QmitkUSNavigationStepMarkerIntervention *stepMarkerIntervention = new QmitkUSNavigationStepMarkerIntervention(m_Parent); m_NavigationStepNames = std::vector(); navigationSteps.push_back(stepCombinedModality); m_NavigationStepNames.push_back("Combined Modality Initialization"); navigationSteps.push_back(stepTumourSelection); m_NavigationStepNames.push_back("Target Selection"); navigationSteps.push_back(stepZoneMarking); m_NavigationStepNames.push_back("Critical Structure Marking"); navigationSteps.push_back(stepPlacementPlanning); m_NavigationStepNames.push_back("Placement Planning"); navigationSteps.push_back(stepMarkerIntervention); m_NavigationStepNames.push_back("Marker Intervention"); } // set navigation step widgets to the process widget ui->navigationProcessWidget->SetNavigationSteps(navigationSteps); for (QmitkUSNavigationProcessWidget::NavigationStepIterator it = m_NavigationSteps.begin(); it != m_NavigationSteps.end(); ++it) { delete *it; } m_NavigationSteps.clear(); m_NavigationSteps = navigationSteps; } // 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->navigationProcessWidget->ResetNavigationProcess(); ui->navigationProcessWidget->EnableInteraction(false); ui->runningLabel->setPixmap(m_IconNotRunning); } else if (!experimentMode) { if (m_IsExperimentRunning) { this->OnFinishExperiment(); } ui->navigationProcessWidget->EnableInteraction(true); } // 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 << "Results Directory: " << m_ResultsDirectory.toStdString(); } void USNavigationMarkerPlacement::OnActiveNavigationStepChanged(int index) { // update navigation step timer each time the active navigation step changes m_NavigationStepTimer->SetActiveIndex(index, m_NavigationSteps.at(index)->GetTitle().toStdString()); if (static_cast(m_NavigationStepNames.size()) <= index) { MITK_INFO("USNavigationLogging") << "Someting went wrong: unknown navigation step!"; } else { MITK_INFO("USNavigationLogging") << "Navigation step finished/changed, next step: " << this->m_NavigationStepNames.at(index).toStdString() << "; duration until now: " << m_NavigationStepTimer->GetTotalDuration(); } } void USNavigationMarkerPlacement::OnIntermediateResultProduced(const itk::SmartPointer resultsNode) { // intermediate results only matter during an experiment if (!m_IsExperimentRunning) { return; } this->WaitCursorOn(); // set results node to the experiment logging (for saving contents to the // file system) m_ExperimentLogging->SetResult(resultsNode); std::string resultsName; if (!resultsNode->GetName(resultsName)) { MITK_WARN << "Could not get name of current results node."; return; } // save the mitk scene std::string scenefile = QString(m_ExperimentResultsSubDirectory + QDir::separator() + QString("Scene %1 - ").arg(m_SceneNumber++, 2, 10, QChar('0')) + QString::fromStdString(resultsName).replace(":", "_") + ".mitk") .toStdString(); MITK_INFO << "Saving Scene File: " << scenefile; mitk::SceneIO::Pointer sceneIO = mitk::SceneIO::New(); mitk::NodePredicateNot::Pointer isNotHelperObject = mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object", mitk::BoolProperty::New(true))); mitk::DataStorage::SetOfObjects::ConstPointer nodesToBeSaved = this->GetDataStorage()->GetSubset(isNotHelperObject); this->Convert2DImagesTo3D(nodesToBeSaved); sceneIO->SaveScene(nodesToBeSaved, this->GetDataStorage(), scenefile); this->WaitCursorOff(); } void USNavigationMarkerPlacement::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 USNavigationMarkerPlacement::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 USNavigationMarkerPlacement::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 } diff --git a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/USNavigationMarkerPlacement.h b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/USNavigationMarkerPlacement.h index 550c100edf..3fe0f4156c 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/USNavigationMarkerPlacement.h +++ b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/USNavigationMarkerPlacement.h @@ -1,206 +1,198 @@ /*=================================================================== 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 USNAVIGATIONMARKERPLACEMENT_H #define USNAVIGATIONMARKERPLACEMENT_H #include #include "IO/mitkUSNavigationLoggingBackend.h" #include "Widgets/QmitkUSNavigationProcessWidget.h" #include "mitkNavigationDataRecorder.h" #include "mitkNodeDisplacementFilter.h" #include "mitkUSImageLoggingFilter.h" #include #include #include #include namespace itk { - template - class SmartPointer; + template + class SmartPointer; } namespace mitk { - class USNavigationStepTimer; - class USNavigationExperimentLogging; + class USNavigationStepTimer; + class USNavigationExperimentLogging; } namespace Ui { - class USNavigationMarkerPlacement; + class USNavigationMarkerPlacement; } class QmitkUSAbstractNavigationStep; 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 USNavigationMarkerPlacement : public QmitkAbstractView { - Q_OBJECT - - protected slots: - /** - * \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(); - - void OnCombinedModalityChanged(itk::SmartPointer); - - /** - * \brief Switches the navigation step widgets if the navigation application was changed. - */ - void OnSettingsChanged(itk::SmartPointer); - - /** - * \brief Updates the timer for the navigation steps durations every time the active navigation step changes. - */ - void OnActiveNavigationStepChanged(int); - - /** - * \brief The data node is given to the experiment logging and scene is saved to the file system. - */ - void OnIntermediateResultProduced(const itk::SmartPointer); - - void OnAddAblationZone(int size); + Q_OBJECT + + protected slots: + /** + * \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(); + + void OnCombinedModalityChanged(itk::SmartPointer); + + /** + * \brief Switches the navigation step widgets if the navigation application was changed. + */ + void OnSettingsChanged(itk::SmartPointer); + + /** + * \brief Updates the timer for the navigation steps durations every time the active navigation step changes. + */ + void OnActiveNavigationStepChanged(int); + + /** + * \brief The data node is given to the experiment logging and scene is saved to the file system. + */ + void OnIntermediateResultProduced(const itk::SmartPointer); + + void OnAddAblationZone(int size); void OnEnableNavigationLayout(); void OnResetStandardLayout(); void OnChangeLayoutClicked(); - void OnChangeAblationZone(int id, int newSize); + void OnChangeAblationZone(int id, int newSize); 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; + 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 USNavigationMarkerPlacement(); - ~USNavigationMarkerPlacement(); + explicit USNavigationMarkerPlacement(); + ~USNavigationMarkerPlacement(); - virtual void CreateQtPartControl(QWidget *parent); + virtual void CreateQtPartControl(QWidget *parent); - static const std::string VIEW_ID; + static const std::string VIEW_ID; - void OnCombinedModalityPropertyChanged(const std::string &, const std::string &); + void OnCombinedModalityPropertyChanged(const std::string &, const std::string &); /** * \returns the point defining the needle axis in the tool storage */ void SetToolAxisMarkerPlacement(); mitk::Point3D m_ToolAxis; 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 Helper function for being able to serialize the 2d ultrasound image. - */ - void Convert2DImagesTo3D(mitk::DataStorage::SetOfObjects::ConstPointer nodes); - - void CreateOverlays(); - - QWidget *m_Parent; - QmitkUSNavigationProcessWidget::NavigationStepVector m_NavigationSteps; - QTimer *m_UpdateTimer; - QTimer *m_ImageAndNavigationDataLoggingTimer; - QmitkStdMultiWidget *m_StdMultiWidget; - itk::SmartPointer m_CombinedModality; - bool m_ReinitAlreadyDone; - bool m_IsExperimentRunning; - std::string m_CurrentApplicationName; - - itk::SmartPointer m_NavigationStepTimer; - itk::SmartPointer m_ExperimentLogging; - - 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; - std::vector m_AblationZonesVector; - - int m_NeedleIndex; - int m_MarkerIndex; - - int m_SceneNumber; - - itk::SmartPointer m_WarnOverlay; + /** + * \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 Helper function for being able to serialize the 2d ultrasound image. + */ + void Convert2DImagesTo3D(mitk::DataStorage::SetOfObjects::ConstPointer nodes); + + void CreateOverlays(); + + QmitkUSNavigationProcessWidget::NavigationStepVector m_NavigationSteps; + itk::SmartPointer m_CombinedModality; + std::string m_CurrentApplicationName; + 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::NodeDisplacementFilter::Pointer m_TargetNodeDisplacementFilter; + std::vector m_AblationZonesVector; //To get tool storage mitk::NavigationDataSource::Pointer m_NavigationDataSource; mitk::NavigationToolStorage::Pointer m_CurrentStorage; + QWidget *m_Parent; + QTimer *m_UpdateTimer; + QTimer *m_ImageAndNavigationDataLoggingTimer; + QmitkStdMultiWidget *m_StdMultiWidget; + bool m_ReinitAlreadyDone; + bool m_IsExperimentRunning; + itk::SmartPointer m_NavigationStepTimer; + itk::SmartPointer m_ExperimentLogging; + mitk::NodeDisplacementFilter::Pointer m_AblationZonesDisplacementFilter; + QPixmap m_IconRunning; + QPixmap m_IconNotRunning; + mitk::USImageLoggingFilter::Pointer m_USImageLoggingFilter; + mitk::NavigationDataRecorder::Pointer m_NavigationDataRecorder; // records navigation data files + int m_SceneNumber; + itk::SmartPointer m_WarnOverlay; + int m_NeedleIndex; + int m_MarkerIndex; + private: - mitk::MessageDelegate2 m_ListenerDeviceChanged; + mitk::MessageDelegate2 m_ListenerDeviceChanged; - Ui::USNavigationMarkerPlacement *ui; + Ui::USNavigationMarkerPlacement *ui; }; #endif // USNAVIGATIONMARKERPLACEMENT_H