diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.cpp b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.cpp index 12da728a93..381ae30b54 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.cpp @@ -1,1169 +1,1175 @@ /*========================================================================= 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 <algorithm> // Blueberry #include <berryISelectionService.h> #include <berryIWorkbenchWindow.h> // Qmitk #include "QmitkIGTTrackingDataEvaluationView.h" #include "QmitkStdMultiWidget.h" // Qt #include <QMessageBox> #include <qfiledialog.h> #include <qstringlist.h> // MITK #include "mitkNavigationDataCSVSequentialPlayer.h" #include <mitkNavigationDataRecorderDeprecated.h> #include <mitkQuaternionAveraging.h> #include <mitkTransform.h> #include <mitkStaticIGTHelperFunctions.h> #include <mitkNodePredicateDataType.h> //ITK #include <itksys/SystemTools.hxx> //VNL #include <vnl/vnl_vector.h> //vtk headers #include <vtkPoints.h> #include <vtkSmartPointer.h> #include <vtkLandmarkTransform.h> const std::string QmitkIGTTrackingDataEvaluationView::VIEW_ID = "org.mitk.views.igttrackingdataevaluation"; QmitkIGTTrackingDataEvaluationView::QmitkIGTTrackingDataEvaluationView() : QmitkFunctionality() , m_Controls(0) , m_MultiWidget(nullptr) , m_scalingfactor(1) { m_CSVtoXMLInputFilenameVector = std::vector<std::string>(); m_CSVtoXMLOutputFilenameVector = std::vector<std::string>(); } QmitkIGTTrackingDataEvaluationView::~QmitkIGTTrackingDataEvaluationView() { } void QmitkIGTTrackingDataEvaluationView::CreateQtPartControl(QWidget *parent) { // build up qt view, unless already done if (!m_Controls) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkIGTTrackingDataEvaluationViewControls; m_Controls->setupUi(parent); connect(m_Controls->m_LoadInputFileList, SIGNAL(clicked()), this, SLOT(OnLoadFileList())); connect(m_Controls->m_StartEvaluation, SIGNAL(clicked()), this, SLOT(OnEvaluateData())); connect(m_Controls->m_AddToCurrentList, SIGNAL(clicked()), this, SLOT(OnAddToCurrentList())); connect(m_Controls->m_GeneratePointSetOfMeanPositions, SIGNAL(clicked()), this, SLOT(OnGeneratePointSet())); connect(m_Controls->m_GenerateRotationLines, SIGNAL(clicked()), this, SLOT(OnGenerateRotationLines())); connect(m_Controls->m_GeneratePointSet, SIGNAL(clicked()), this, SLOT(OnGenerateGroundTruthPointSet())); connect(m_Controls->m_Convert, SIGNAL(clicked()), this, SLOT(OnConvertCSVtoXMLFile())); connect(m_Controls->m_loadCSVtoXMLInputList, SIGNAL(clicked()), this, SLOT(OnCSVtoXMLLoadInputList())); connect(m_Controls->m_loadCSVtoXMLOutputList, SIGNAL(clicked()), this, SLOT(OnCSVtoXMLLoadOutputList())); connect(m_Controls->m_OrientationCalculationGenerateReference, SIGNAL(clicked()), this, SLOT(OnOrientationCalculation_CalcRef())); connect(m_Controls->m_OrientationCalculationWriteOrientationsToFile, SIGNAL(clicked()), this, SLOT(OnOrientationCalculation_CalcOrientandWriteToFile())); connect(m_Controls->m_GeneratePointSetsOfSinglePositions, SIGNAL(clicked()), this, SLOT(OnGeneratePointSetsOfSinglePositions())); connect(m_Controls->m_StartEvaluationAll, SIGNAL(clicked()), this, SLOT(OnEvaluateDataAll())); connect(m_Controls->m_GridMatching, SIGNAL(clicked()), this, SLOT(OnPerfomGridMatching())); connect(m_Controls->m_ComputeRotation, SIGNAL(clicked()), this, SLOT(OnComputeRotation())); //initialize data storage combo boxes m_Controls->m_ReferencePointSetComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_ReferencePointSetComboBox->SetAutoSelectNewItems(true); m_Controls->m_ReferencePointSetComboBox->SetPredicate(mitk::NodePredicateDataType::New("PointSet")); m_Controls->m_MeasurementPointSetComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_MeasurementPointSetComboBox->SetAutoSelectNewItems(true); m_Controls->m_MeasurementPointSetComboBox->SetPredicate(mitk::NodePredicateDataType::New("PointSet")); } } void QmitkIGTTrackingDataEvaluationView::OnComputeRotation() { //Get all data from UI auto EvaluationDataCollection = GetAllDataFromUIList(); //Compute mean Quaternions auto OrientationVector = GetMeanOrientationsOfAllData(EvaluationDataCollection); //Compute Rotations itk::Vector<double> rotationVec; //adapt for Aurora 5D tools: [0,0,1000] rotationVec[0] = m_Controls->m_rotVecX->value(); //X rotationVec[1] = m_Controls->m_rotVecY->value(); //Y rotationVec[2] = m_Controls->m_rotVecZ->value(); //Z std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> allOrientationErrors; for (std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError>::size_type i = 0; i < OrientationVector.size() - 1; ++i) { double AngleBetweenTwoQuaternions = mitk::StaticIGTHelperFunctions::GetAngleBetweenTwoQuaterions(OrientationVector.at(i), OrientationVector.at(i+1), rotationVec); double AngularError = fabs(AngleBetweenTwoQuaternions - 11.25); std::stringstream description; description << "Rotation Error ROT" << (i + 1) << " / ROT" << (i + 2); allOrientationErrors.push_back({ AngularError, description.str() }); MITK_INFO << description.str() << ": " << AngularError; } //compute statistics std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> orientationErrorStatistics; orientationErrorStatistics = mitk::HummelProtocolEvaluation::ComputeStatistics(allOrientationErrors); MITK_INFO << "## Rotation error statistics: ##"; for (auto stat : orientationErrorStatistics) { MITK_INFO << stat.description << ": " << stat.distanceError; } //write results to file allOrientationErrors.insert(allOrientationErrors.end(), orientationErrorStatistics.begin(), orientationErrorStatistics.end()); allOrientationErrors.push_back({rotationVec[0],"Rot Vector [x]"}); allOrientationErrors.push_back({rotationVec[1], "Rot Vector [y]"}); allOrientationErrors.push_back({rotationVec[2], "Rot Vector [z]"}); std::stringstream filenameOrientationStat; filenameOrientationStat << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".orientationStatistics.csv"; MITK_INFO << "Writing output to file " << filenameOrientationStat.str(); writeToFile(filenameOrientationStat.str(), allOrientationErrors); } void QmitkIGTTrackingDataEvaluationView::OnPerfomGridMatching() { mitk::PointSet::Pointer reference = dynamic_cast<mitk::PointSet*>(m_Controls->m_ReferencePointSetComboBox->GetSelectedNode()->GetData()); mitk::PointSet::Pointer measurement = dynamic_cast<mitk::PointSet*>(m_Controls->m_MeasurementPointSetComboBox->GetSelectedNode()->GetData()); //convert point sets to vtk poly data vtkSmartPointer<vtkPoints> sourcePoints = vtkSmartPointer<vtkPoints>::New(); vtkSmartPointer<vtkPoints> targetPoints = vtkSmartPointer<vtkPoints>::New(); for (int i = 0; i<reference->GetSize(); i++) { double point[3] = { reference->GetPoint(i)[0], reference->GetPoint(i)[1], reference->GetPoint(i)[2] }; sourcePoints->InsertNextPoint(point); double point_targets[3] = { measurement->GetPoint(i)[0], measurement->GetPoint(i)[1], measurement->GetPoint(i)[2] }; targetPoints->InsertNextPoint(point_targets); } //compute transform vtkSmartPointer<vtkLandmarkTransform> transform = vtkSmartPointer<vtkLandmarkTransform>::New(); transform->SetSourceLandmarks(sourcePoints); transform->SetTargetLandmarks(targetPoints); transform->SetModeToRigidBody(); transform->Modified(); transform->Update(); //compute FRE of transform double FRE = mitk::StaticIGTHelperFunctions::ComputeFRE(reference, measurement, transform); MITK_INFO << "FRE after grid matching: " + QString::number(FRE) + " mm"; //convert from vtk to itk data types itk::Matrix<float, 3, 3> rotationFloat = itk::Matrix<float, 3, 3>(); itk::Vector<float, 3> translationFloat = itk::Vector<float, 3>(); itk::Matrix<double, 3, 3> rotationDouble = itk::Matrix<double, 3, 3>(); itk::Vector<double, 3> translationDouble = itk::Vector<double, 3>(); vtkSmartPointer<vtkMatrix4x4> m = transform->GetMatrix(); for (int k = 0; k<3; k++) for (int l = 0; l<3; l++) { rotationFloat[k][l] = m->GetElement(k, l); rotationDouble[k][l] = m->GetElement(k, l); } for (int k = 0; k<3; k++) { translationFloat[k] = m->GetElement(k, 3); translationDouble[k] = m->GetElement(k, 3); } //create affine transform 3D mitk::AffineTransform3D::Pointer mitkTransform = mitk::AffineTransform3D::New(); mitkTransform->SetMatrix(rotationDouble); mitkTransform->SetOffset(translationDouble); mitk::NavigationData::Pointer transformNavigationData = mitk::NavigationData::New(mitkTransform); m_Controls->m_ReferencePointSetComboBox->GetSelectedNode()->GetData()->GetGeometry()->SetIndexToWorldTransform(mitkTransform); m_Controls->m_ReferencePointSetComboBox->GetSelectedNode()->GetData()->GetGeometry()->Modified(); //write to file std::stringstream filename; filename << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".GridMatchingResult.csv"; MITK_INFO << "Writing output to file " << filename.str(); std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> FRE_Error; FRE_Error.push_back({ FRE, "FRE after grid matching [mm]" }); writeToFile(filename.str(), FRE_Error); } void QmitkIGTTrackingDataEvaluationView::OnOrientationCalculation_CalcRef() { if (m_FilenameVector.size() != 3) { MessageBox("Need exactly three points as reference, aborting!"); return; } //start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector[i]); //check if the stream is valid and skip file if not //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++j) myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); //update pipline until number of samples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); ++j) myEvaluationFilter->Update(); //store mean position as reference switch (i) { case 0: m_RefPoint1 = myEvaluationFilter->GetPositionMean(0); break; case 1: m_RefPoint2 = myEvaluationFilter->GetPositionMean(0); break; case 2: m_RefPoint3 = myEvaluationFilter->GetPositionMean(0); break; } } MessageBox("Created Reference!"); } void QmitkIGTTrackingDataEvaluationView::OnOrientationCalculation_CalcOrientandWriteToFile() { //start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //open file header QString outputname = QString(m_FilenameVector.at(i).c_str()) + "_orientationFile.csv"; m_CurrentWriteFile.open(outputname.toStdString().c_str(), std::ios::out); if (m_CurrentWriteFile.bad()) { MessageBox("Error: Can't open output file!"); return; } //write header to file m_CurrentWriteFile << "Nr;Calypso_Time;Valid_Reference;MeasureTool_Measurement-Tool[x];MeasureTool_Measurement-Tool[y];MeasureTool_Measurement-Tool[z];MeasureTool_Measurement-Tool[qx];MeasureTool_Measurement-Tool[qy];MeasureTool_Measurement-Tool[qz];MeasureTool_Measurement-Tool[qr]\n"; //update pipeline until number of samples is reached int step = 0; mitk::Point3D point1, point2, point3; mitk::Quaternion current_orientation; for (int j = 0; !myPlayer->IsAtEnd(); j++) { myPlayer->Update(); mitk::NavigationData::Pointer currentNavData = myPlayer->GetOutput(0); switch (step) { case 0: step++; point1 = currentNavData->GetPosition(); break; case 1: step++; point2 = currentNavData->GetPosition(); break; case 2: step = 0; point3 = currentNavData->GetPosition(); //compute transform from reference to current points if (point1[0] == 0 && point1[1] == 0 && point1[2] == 0 && point2[0] == 0 && point2[1] == 0 && point2[2] == 0 && point3[0] == 0 && point3[1] == 0 && point3[2] == 0 ) current_orientation.fill(0); else { vtkSmartPointer<vtkLandmarkTransform> transform = vtkSmartPointer<vtkLandmarkTransform>::New(); vtkSmartPointer<vtkPoints> sourcePoints = vtkSmartPointer<vtkPoints>::New(); double sourcepoint1[3] = { point1[0], point1[1], point1[2] }; double sourcepoint2[3] = { point2[0], point2[1], point2[2] }; double sourcepoint3[3] = { point3[0], point3[1], point3[2] }; sourcePoints->InsertNextPoint(sourcepoint1); sourcePoints->InsertNextPoint(sourcepoint2); sourcePoints->InsertNextPoint(sourcepoint3); vtkSmartPointer<vtkPoints> targetPoints = vtkSmartPointer<vtkPoints>::New(); double targetpoint1[3] = { m_RefPoint1[0], m_RefPoint1[1], m_RefPoint1[2] }; double targetpoint2[3] = { m_RefPoint2[0], m_RefPoint2[1], m_RefPoint2[2] }; double targetpoint3[3] = { m_RefPoint3[0], m_RefPoint3[1], m_RefPoint3[2] }; targetPoints->InsertNextPoint(targetpoint1); targetPoints->InsertNextPoint(targetpoint2); targetPoints->InsertNextPoint(targetpoint3); transform->SetSourceLandmarks(sourcePoints); transform->SetTargetLandmarks(targetPoints); transform->Modified(); transform->Update(); mitk::Transform::Pointer newTransform = mitk::Transform::New(); newTransform->SetMatrix(transform->GetMatrix()); current_orientation = newTransform->GetOrientation(); //add pointset with the three positions if ((j > 15) && (j < 18)) { mitk::DataNode::Pointer newNode = mitk::DataNode::New(); mitk::PointSet::Pointer newPointSet = mitk::PointSet::New(); newPointSet->InsertPoint(0, point1); newPointSet->InsertPoint(1, point2); newPointSet->InsertPoint(2, point3); QString name = QString(m_FilenameVector.at(i).c_str()); newNode->SetName(name.toStdString().c_str()); newNode->SetData(newPointSet); newNode->SetFloatProperty("pointsize", 0.1); this->GetDataStorage()->Add(newNode); } } break; } m_CurrentWriteFile << i << ";"; m_CurrentWriteFile << currentNavData->GetTimeStamp() << ";"; //IMPORTANT: change to GetIGTTimeStamp in new version! m_CurrentWriteFile << "true;"; m_CurrentWriteFile << currentNavData->GetPosition()[0] << ";"; m_CurrentWriteFile << currentNavData->GetPosition()[1] << ";"; m_CurrentWriteFile << currentNavData->GetPosition()[2] << ";"; m_CurrentWriteFile << current_orientation.x() << ";"; m_CurrentWriteFile << current_orientation.y() << ";"; m_CurrentWriteFile << current_orientation.z() << ";"; m_CurrentWriteFile << current_orientation.r() << ";"; m_CurrentWriteFile << "\n"; } //close output file m_CurrentWriteFile.close(); } MessageBox("Finished!"); } void QmitkIGTTrackingDataEvaluationView::StdMultiWidgetAvailable(QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkIGTTrackingDataEvaluationView::StdMultiWidgetNotAvailable() { m_MultiWidget = nullptr; } void QmitkIGTTrackingDataEvaluationView::OnAddToCurrentList() { //read in files QStringList files = QFileDialog::getOpenFileNames(nullptr, "Select one or more files to open", "/", "CSV (*.csv)"); if (files.isEmpty()) return; for (int i = 0; i < files.size(); i++) { std::string tmp = files.at(i).toStdString().c_str(); m_FilenameVector.push_back(tmp); } //fill list at GUI m_Controls->m_FileList->clear(); for (unsigned int i = 0; i < m_FilenameVector.size(); i++) { new QListWidgetItem(tr(m_FilenameVector.at(i).c_str()), m_Controls->m_FileList); } } void QmitkIGTTrackingDataEvaluationView::OnLoadFileList() { m_FilenameVector = std::vector<std::string>(); m_FilenameVector.clear(); OnAddToCurrentList(); } void QmitkIGTTrackingDataEvaluationView::OnEvaluateDataAll() { std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> results5cm, results15cm, results30cm, resultsAccum; mitk::HummelProtocolEvaluation::HummelProtocolMeasurementVolume volume; if (m_Controls->m_standardVolume->isChecked()) { volume = mitk::HummelProtocolEvaluation::standard; mitk::HummelProtocolEvaluation::Evaluate5cmDistances(m_PointSetMeanPositions, volume, results5cm); mitk::HummelProtocolEvaluation::Evaluate15cmDistances(m_PointSetMeanPositions, volume, results15cm); mitk::HummelProtocolEvaluation::Evaluate30cmDistances(m_PointSetMeanPositions, volume, results30cm); mitk::HummelProtocolEvaluation::EvaluateAccumulatedDistances(m_PointSetMeanPositions, volume, resultsAccum); } else if (m_Controls->m_smallVolume->isChecked()) { volume = mitk::HummelProtocolEvaluation::small; mitk::HummelProtocolEvaluation::Evaluate5cmDistances(m_PointSetMeanPositions, volume, results5cm); } else if (m_Controls->m_mediumVolume->isChecked()) { volume = mitk::HummelProtocolEvaluation::medium; mitk::HummelProtocolEvaluation::Evaluate5cmDistances(m_PointSetMeanPositions, volume, results5cm); } + else if (m_Controls->m_medium5x6Volume->isChecked()) + { + volume = mitk::HummelProtocolEvaluation::medium5x6; + mitk::HummelProtocolEvaluation::Evaluate5cmDistances(m_PointSetMeanPositions, volume, results5cm); + } //write results to file std::stringstream filename5cm; filename5cm << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".results5cm.csv"; MITK_INFO << "Writing output to file " << filename5cm.str(); writeToFile(filename5cm.str(), results5cm); std::stringstream filename15cm; filename15cm << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".results15cm.csv"; MITK_INFO << "Writing output to file " << filename15cm.str(); writeToFile(filename15cm.str(), results15cm); std::stringstream filename30cm; filename30cm << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".results30cm.csv"; MITK_INFO << "Writing output to file " << filename30cm.str(); writeToFile(filename30cm.str(), results30cm); std::stringstream filenameAccum; filenameAccum << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".resultsAccumDist.csv"; MITK_INFO << "Writing output to file " << filenameAccum.str(); writeToFile(filenameAccum.str(), resultsAccum); } void QmitkIGTTrackingDataEvaluationView::OnEvaluateData() { //open output file m_CurrentWriteFile.open(std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str(), std::ios::out); if (m_CurrentWriteFile.bad()) { MessageBox("Error: Can't open output file!"); return; } std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> jitterValues; //write output file header WriteHeader(); //start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline - for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++i) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); } + myEvaluationFilter->SetInput(0, myPlayer->GetOutput(0)); if (myPlayer->GetNumberOfSnapshots() < m_Controls->m_NumberOfSamples->value()) { MITK_WARN << "Number of snapshots (" << myPlayer->GetNumberOfSnapshots() << ") smaller than number of samples to evaluate (" << m_Controls->m_NumberOfSamples->value() << ") ! Cannot proceed!"; return; } //update pipline until number of samples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); j++) myEvaluationFilter->Update(); + MITK_INFO << "Jitter (RMS) on position "<<i<<": " << myEvaluationFilter->GetPositionErrorRMS(0); + //store all jitter values in separate vector for statistics jitterValues.push_back({ myEvaluationFilter->GetPositionErrorRMS(0), "RMS" }); //write result to output file WriteDataSet(myEvaluationFilter, m_FilenameVector.at(i)); } //close output file for single data m_CurrentWriteFile.close(); //compute statistics std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> jitterStatistics = mitk::HummelProtocolEvaluation::ComputeStatistics(jitterValues); MITK_INFO << "## Jitter (RMS) statistics: ##"; for (auto jitterStat : jitterStatistics) {MITK_INFO << jitterStat.description << ": " << jitterStat.distanceError;} //write statistic results to separate file std::stringstream filenameJitterStat; filenameJitterStat << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".resultsJitterStatistics.csv"; MITK_INFO << "Writing output to file " << filenameJitterStat.str(); writeToFile(filenameJitterStat.str(), jitterStatistics); //calculate angles if option is on if (m_Controls->m_settingDifferenceAngles->isChecked() || m_Controls->m_DifferencesSLERP->isChecked()) CalculateDifferenceAngles(); MessageBox("Finished!"); } void QmitkIGTTrackingDataEvaluationView::OnGeneratePointSetsOfSinglePositions() { m_scalingfactor = m_Controls->m_ScalingFactor->value(); //start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { //create point set for this file mitk::PointSet::Pointer thisPointSet = mitk::PointSet::New(); //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //update pipline until number of samlples is reached and store every single point for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); j++) { myPlayer->Update(); mitk::Point3D thisPoint = myPlayer->GetOutput()->GetPosition(); thisPoint[0] *= m_scalingfactor; thisPoint[1] *= m_scalingfactor; thisPoint[2] *= m_scalingfactor; thisPointSet->InsertPoint(j, thisPoint); } //add point set to data storage mitk::DataNode::Pointer newNode = mitk::DataNode::New(); QString name = this->m_Controls->m_prefix->text() + QString("PointSet_of_All_Positions_") + QString::number(i); newNode->SetName(name.toStdString()); newNode->SetData(thisPointSet); this->GetDataStorage()->Add(newNode); } } void QmitkIGTTrackingDataEvaluationView::OnGeneratePointSet() { m_scalingfactor = m_Controls->m_ScalingFactor->value(); mitk::PointSet::Pointer generatedPointSet = mitk::PointSet::New(); //start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++j) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); } //update pipline until number of samlples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); ++j) { myEvaluationFilter->Update(); } //add mean position to point set mitk::Point3D meanPos = myEvaluationFilter->GetPositionMean(0); if (m_scalingfactor != 1) { meanPos[0] *= m_scalingfactor; meanPos[1] *= m_scalingfactor; meanPos[2] *= m_scalingfactor; } generatedPointSet->InsertPoint(i, meanPos); } //add point set to data storage mitk::DataNode::Pointer newNode = mitk::DataNode::New(); QString name = this->m_Controls->m_prefix->text() + "PointSet_of_Mean_Positions"; newNode->SetName(name.toStdString()); newNode->SetData(generatedPointSet); newNode->SetFloatProperty("pointsize", 5); this->GetDataStorage()->Add(newNode); m_PointSetMeanPositions = generatedPointSet; } void QmitkIGTTrackingDataEvaluationView::OnGenerateRotationLines() { m_scalingfactor = m_Controls->m_ScalingFactor->value(); //start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++j) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); } //update pipline until number of samlples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); ++j) myEvaluationFilter->Update(); //create line from mean pos to a second point which lies along the sensor (1,0,0 in tool coordinates for aurora) mitk::Point3D meanPos = myEvaluationFilter->GetPositionMean(0); if (m_scalingfactor != 1) { meanPos[0] *= m_scalingfactor; meanPos[1] *= m_scalingfactor; meanPos[2] *= m_scalingfactor; } mitk::Point3D secondPoint; mitk::Point3D thirdPoint; mitk::Point3D fourthPoint; mitk::FillVector3D(secondPoint, 2, 0, 0); //X vnl_vector<mitk::ScalarType> secondPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * secondPoint.GetVnlVector() + meanPos.GetVnlVector(); mitk::Point3D secondPointTransformedMITK; mitk::FillVector3D(secondPointTransformedMITK, secondPointTransformed[0], secondPointTransformed[1], secondPointTransformed[2]); mitk::FillVector3D(thirdPoint, 0, 4, 0); //Y vnl_vector<mitk::ScalarType> thirdPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * thirdPoint.GetVnlVector() + meanPos.GetVnlVector(); mitk::Point3D thirdPointTransformedMITK; mitk::FillVector3D(thirdPointTransformedMITK, thirdPointTransformed[0], thirdPointTransformed[1], thirdPointTransformed[2]); mitk::FillVector3D(fourthPoint, 0, 0, 6); //Z vnl_vector<mitk::ScalarType> fourthPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * fourthPoint.GetVnlVector() + meanPos.GetVnlVector(); mitk::Point3D fourthPointTransformedMITK; mitk::FillVector3D(fourthPointTransformedMITK, fourthPointTransformed[0], fourthPointTransformed[1], fourthPointTransformed[2]); mitk::PointSet::Pointer rotationLine = mitk::PointSet::New(); rotationLine->InsertPoint(0, secondPointTransformedMITK); rotationLine->InsertPoint(1, meanPos); rotationLine->InsertPoint(2, thirdPointTransformedMITK); rotationLine->InsertPoint(3, meanPos); rotationLine->InsertPoint(4, fourthPointTransformedMITK); mitk::DataNode::Pointer newNode = mitk::DataNode::New(); QString nodeName = this->m_Controls->m_prefix->text() + "RotationLineNumber" + QString::number(i); newNode->SetName(nodeName.toStdString()); newNode->SetData(rotationLine); newNode->SetBoolProperty("show contour", true); newNode->SetFloatProperty("pointsize", 0.5); this->GetDataStorage()->Add(newNode); } } void QmitkIGTTrackingDataEvaluationView::OnGenerateGroundTruthPointSet() { mitk::PointSet::Pointer generatedPointSet = mitk::PointSet::New(); int currentPointID = 0; mitk::Point3D currentPoint; mitk::FillVector3D(currentPoint, 0, 0, 0); for (int i = 0; i < m_Controls->m_PointNumber2->value(); i++) { for (int j = 0; j < m_Controls->m_PointNumber1->value(); j++) { generatedPointSet->InsertPoint(currentPointID, currentPoint); currentPointID++; currentPoint[1] += m_Controls->m_PointDistance->value(); } currentPoint[1] = 0; currentPoint[2] += m_Controls->m_PointDistance->value(); } mitk::DataNode::Pointer newNode = mitk::DataNode::New(); QString nodeName = "GroundTruthPointSet_" + QString::number(m_Controls->m_PointNumber1->value()) + "x" + QString::number(m_Controls->m_PointNumber2->value()) + "_(" + QString::number(m_Controls->m_PointDistance->value()) + "mm)"; newNode->SetName(nodeName.toStdString()); newNode->SetData(generatedPointSet); newNode->SetFloatProperty("pointsize", 5); this->GetDataStorage()->Add(newNode); } void QmitkIGTTrackingDataEvaluationView::OnConvertCSVtoXMLFile() { if (m_Controls->m_ConvertSingleFile->isChecked()) { //convert one file int lines = ConvertOneFile(this->m_Controls->m_InputCSV->text().toStdString(), this->m_Controls->m_OutputXML->text().toStdString()); QString result = "Converted one file with" + QString::number(lines) + " data sets"; MessageBox(result.toStdString()); } else //converte file list { if (m_CSVtoXMLInputFilenameVector.empty() || m_CSVtoXMLOutputFilenameVector.empty()) { MessageBox("Error: one list is not loaded!"); return; } else if (m_CSVtoXMLInputFilenameVector.size() != m_CSVtoXMLOutputFilenameVector.size()) { MessageBox("Error: lists do not have the same number of files!"); return; } for (std::size_t i = 0; i < m_CSVtoXMLInputFilenameVector.size(); ++i) { ConvertOneFile(m_CSVtoXMLInputFilenameVector.at(i), m_CSVtoXMLOutputFilenameVector.at(i)); } QString result = "Converted " + QString::number(m_CSVtoXMLInputFilenameVector.size()) + " files from file list!"; MessageBox(result.toStdString()); } } int QmitkIGTTrackingDataEvaluationView::ConvertOneFile(std::string inputFilename, std::string outputFilename) { std::vector<mitk::NavigationData::Pointer> myNavigationDatas = GetNavigationDatasFromFile(inputFilename); mitk::NavigationDataRecorderDeprecated::Pointer myRecorder = mitk::NavigationDataRecorderDeprecated::New(); myRecorder->SetFileName(outputFilename.c_str()); mitk::NavigationData::Pointer input = mitk::NavigationData::New(); if (m_Controls->m_ConvertCSV->isChecked()) myRecorder->SetOutputFormat(mitk::NavigationDataRecorderDeprecated::csv); myRecorder->AddNavigationData(input); myRecorder->StartRecording(); for (std::size_t i = 0; i < myNavigationDatas.size(); ++i) { input->Graft(myNavigationDatas.at(i)); myRecorder->Update(); } myRecorder->StopRecording(); return myNavigationDatas.size(); } void QmitkIGTTrackingDataEvaluationView::OnCSVtoXMLLoadInputList() { //read in filename QString filename = QFileDialog::getOpenFileName(nullptr, tr("Open Measurement Filename List"), "/", tr("All Files (*.*)")); if (filename.isNull()) return; m_CSVtoXMLInputFilenameVector = this->GetFileContentLineByLine(filename.toStdString()); m_Controls->m_labelCSVtoXMLInputList->setText("READY"); } void QmitkIGTTrackingDataEvaluationView::OnCSVtoXMLLoadOutputList() { //read in filename QString filename = QFileDialog::getOpenFileName(nullptr, tr("Open Measurement Filename List"), "/", tr("All Files (*.*)")); if (filename.isNull()) return; m_CSVtoXMLOutputFilenameVector = this->GetFileContentLineByLine(filename.toStdString()); m_Controls->m_labelCSVtoXMLOutputList->setText("READY"); } void QmitkIGTTrackingDataEvaluationView::MessageBox(std::string s) { QMessageBox msgBox; msgBox.setText(s.c_str()); msgBox.exec(); } void QmitkIGTTrackingDataEvaluationView::WriteHeader() { m_CurrentWriteFile << "Filename;"; m_CurrentWriteFile << "N;"; m_CurrentWriteFile << "N_invalid;"; m_CurrentWriteFile << "Percentage_invalid;"; if (m_Controls->m_settingPosMean->isChecked()) { m_CurrentWriteFile << "Position_Mean[x];"; m_CurrentWriteFile << "Position_Mean[y];"; m_CurrentWriteFile << "Position_Mean[z];"; } if (m_Controls->m_settingPosStabw->isChecked()) { m_CurrentWriteFile << "Position_StandDev[x];"; m_CurrentWriteFile << "Position_StandDev[y];"; m_CurrentWriteFile << "Position_StandDev[z];"; } if (m_Controls->m_settingPosSampleStabw->isChecked()) { m_CurrentWriteFile << "Position_SampleStandDev[x];"; m_CurrentWriteFile << "Position_SampleStandDev[y];"; m_CurrentWriteFile << "Position_SampleStandDev[z];"; } if (m_Controls->m_settingQuaternionMean->isChecked()) { m_CurrentWriteFile << "Quaternion_Mean[qx];"; m_CurrentWriteFile << "Quaternion_Mean[qy];"; m_CurrentWriteFile << "Quaternion_Mean[qz];"; m_CurrentWriteFile << "Quaternion_Mean[qr];"; } if (m_Controls->m_settionQuaternionStabw->isChecked()) { m_CurrentWriteFile << "Quaternion_StandDev[qx];"; m_CurrentWriteFile << "Quaternion_StandDev[qy];"; m_CurrentWriteFile << "Quaternion_StandDev[qz];"; m_CurrentWriteFile << "Quaternion_StandDev[qr];"; } if (m_Controls->m_settingPosErrorMean->isChecked()) m_CurrentWriteFile << "PositionError_Mean;"; if (m_Controls->m_settingPosErrorStabw->isChecked()) m_CurrentWriteFile << "PositionError_StandDev;"; if (m_Controls->m_settingPosErrorSampleStabw->isChecked()) m_CurrentWriteFile << "PositionError_SampleStandDev;"; if (m_Controls->m_settingPosErrorRMS->isChecked()) m_CurrentWriteFile << "PositionError_RMS;"; if (m_Controls->m_settingPosErrorMedian->isChecked()) m_CurrentWriteFile << "PositionError_Median;"; if (m_Controls->m_settingPosErrorMinMax->isChecked()) { m_CurrentWriteFile << "PositionError_Max;"; m_CurrentWriteFile << "PositionError_Min;"; } if (m_Controls->m_settingEulerMean->isChecked()) { m_CurrentWriteFile << "Euler_tx;"; m_CurrentWriteFile << "Euler_ty;"; m_CurrentWriteFile << "Euler_tz;"; } if (m_Controls->m_settingEulerRMS->isChecked()) { m_CurrentWriteFile << "EulerErrorRMS (rad);"; m_CurrentWriteFile << "EulerErrorRMS (grad);"; } m_CurrentWriteFile << "\n"; } void QmitkIGTTrackingDataEvaluationView::WriteDataSet(mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter, std::string dataSetName) { if (myEvaluationFilter->GetNumberOfOutputs() == 0) m_CurrentWriteFile << "Error: no input \n"; else { m_CurrentWriteFile << dataSetName << ";"; m_CurrentWriteFile << myEvaluationFilter->GetNumberOfAnalysedNavigationData(0) << ";"; m_CurrentWriteFile << myEvaluationFilter->GetNumberOfInvalidSamples(0) << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPercentageOfInvalidSamples(0) << ";"; if (m_Controls->m_settingPosMean->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetPositionMean(0)[0] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionMean(0)[1] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionMean(0)[2] << ";"; } if (m_Controls->m_settingPosStabw->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetPositionStandardDeviation(0)[0] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionStandardDeviation(0)[1] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionStandardDeviation(0)[2] << ";"; } if (m_Controls->m_settingPosSampleStabw->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetPositionSampleStandardDeviation(0)[0] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionSampleStandardDeviation(0)[1] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionSampleStandardDeviation(0)[2] << ";"; } if (m_Controls->m_settingQuaternionMean->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetQuaternionMean(0).x() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionMean(0).y() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionMean(0).z() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionMean(0).r() << ";"; } if (m_Controls->m_settionQuaternionStabw->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetQuaternionStandardDeviation(0).x() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionStandardDeviation(0).y() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionStandardDeviation(0).z() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionStandardDeviation(0).r() << ";"; } if (m_Controls->m_settingPosErrorMean->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorMean(0) << ";"; if (m_Controls->m_settingPosErrorStabw->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorStandardDeviation(0) << ";"; if (m_Controls->m_settingPosErrorSampleStabw->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorSampleStandardDeviation(0) << ";"; if (m_Controls->m_settingPosErrorRMS->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorRMS(0) << ";"; if (m_Controls->m_settingPosErrorMedian->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorMedian(0) << ";"; if (m_Controls->m_settingPosErrorMinMax->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorMax(0) << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorMin(0) << ";"; } if (m_Controls->m_settingEulerMean->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesMean(0)[0] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesMean(0)[1] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesMean(0)[2] << ";"; } if (m_Controls->m_settingEulerRMS->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesRMS(0) << ";"; m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesRMSDegree(0) << ";"; } m_CurrentWriteFile << "\n"; } } std::vector<mitk::Quaternion> QmitkIGTTrackingDataEvaluationView::GetMeanOrientationsOfAllData(std::vector<mitk::NavigationDataEvaluationFilter::Pointer> allData, bool useSLERP) { std::vector<mitk::Quaternion> returnValue; for (auto dataSet : allData) { if (useSLERP) returnValue.push_back(GetSLERPAverage(dataSet)); else returnValue.push_back(dataSet->GetQuaternionMean(0)); } return returnValue; } std::vector<mitk::NavigationDataEvaluationFilter::Pointer> QmitkIGTTrackingDataEvaluationView::GetAllDataFromUIList() { std::vector<mitk::NavigationDataEvaluationFilter::Pointer> EvaluationDataCollection; //start loop and iterate through all files of list: store the evaluation data for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++j) myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); //update pipline until number of samlples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); ++j) myEvaluationFilter->Update(); myEvaluationFilter->SetInput(nullptr); myPlayer = nullptr; EvaluationDataCollection.push_back(myEvaluationFilter); } return EvaluationDataCollection; } void QmitkIGTTrackingDataEvaluationView::CalculateDifferenceAngles() { //Get all data from UI std::vector<mitk::NavigationDataEvaluationFilter::Pointer> EvaluationDataCollection = GetAllDataFromUIList(); //calculation and writing of output data //open output file m_CurrentAngleDifferencesWriteFile.open(std::string((m_Controls->m_OutputFilename->text() + ".angledifferences.csv").toUtf8()).c_str(), std::ios::out); if (m_CurrentAngleDifferencesWriteFile.bad()) { MessageBox("Error: Can't open output file for angle differences calculation!"); return; } //write header WriteDifferenceAnglesHeader(); //compute angle differences QString pos1 = "invalid"; QString pos2 = "invalid"; //now iterate through all evaluation data and calculate the angles for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { pos1 = QString::fromStdString(itksys::SystemTools::GetFilenameWithoutLastExtension(m_FilenameVector.at(i))); for (std::size_t j = 0; j < m_FilenameVector.size(); ++j) { pos2 = QString::fromStdString(itksys::SystemTools::GetFilenameWithoutLastExtension(m_FilenameVector.at(j))); mitk::Quaternion q1; mitk::Quaternion q2; if (m_Controls->m_DifferencesSLERP->isChecked()) { //compute slerp average q1 = GetSLERPAverage(EvaluationDataCollection.at(i)); q2 = GetSLERPAverage(EvaluationDataCollection.at(j)); } else { //compute arithmetic average q1 = EvaluationDataCollection.at(i)->GetQuaternionMean(0); q2 = EvaluationDataCollection.at(j)->GetQuaternionMean(0); } itk::Vector<double> rotationVec; //adapt for Aurora 5D tools: [0,0,1000] rotationVec[0] = 10000; //X rotationVec[1] = 0; //Y rotationVec[2] = 0; //Z double AngleBetweenTwoQuaternions = mitk::StaticIGTHelperFunctions::GetAngleBetweenTwoQuaterions(q1, q2, rotationVec); //write data set WriteDifferenceAnglesDataSet(pos1.toStdString(), pos2.toStdString(), i, j, AngleBetweenTwoQuaternions); } } //close output file m_CurrentAngleDifferencesWriteFile.close(); } void QmitkIGTTrackingDataEvaluationView::WriteDifferenceAnglesHeader() { m_CurrentAngleDifferencesWriteFile << "Name;Idx1;Idx2;Angle [Degree]\n"; } void QmitkIGTTrackingDataEvaluationView::WriteDifferenceAnglesDataSet(std::string pos1, std::string pos2, int idx1, int idx2, double angle) { m_CurrentAngleDifferencesWriteFile << "Angle between " << pos1 << " and " << pos2 << ";" << idx1 << ";" << idx2 << ";" << angle << "\n"; MITK_INFO << "Angle: " << angle; } std::vector<mitk::NavigationData::Pointer> QmitkIGTTrackingDataEvaluationView::GetNavigationDatasFromFile(std::string filename) { std::vector<mitk::NavigationData::Pointer> returnValue = std::vector<mitk::NavigationData::Pointer>(); std::vector<std::string> fileContentLineByLine = GetFileContentLineByLine(filename); for (std::size_t i = 1; i < fileContentLineByLine.size(); ++i) //skip header so start at 1 { returnValue.push_back(GetNavigationDataOutOfOneLine(fileContentLineByLine.at(i))); } return returnValue; } std::vector<std::string> QmitkIGTTrackingDataEvaluationView::GetFileContentLineByLine(std::string filename) { std::vector<std::string> readData = std::vector<std::string>(); //save old locale char * oldLocale; oldLocale = setlocale(LC_ALL, 0); //define own locale std::locale C("C"); setlocale(LC_ALL, "C"); //read file std::ifstream file; file.open(filename.c_str(), std::ios::in); if (file.good()) { //read out file file.seekg(0L, std::ios::beg); // move to begin of file while (!file.eof()) { std::string buffer; std::getline(file, buffer); // read out file line by line if (buffer.size() > 0) readData.push_back(buffer); } } file.close(); //switch back to old locale setlocale(LC_ALL, oldLocale); return readData; } mitk::NavigationData::Pointer QmitkIGTTrackingDataEvaluationView::GetNavigationDataOutOfOneLine(std::string line) { mitk::NavigationData::Pointer returnValue = mitk::NavigationData::New(); QString myLine = QString(line.c_str()); QStringList myLineList = myLine.split(';'); mitk::Point3D position; mitk::Quaternion orientation; bool valid = false; if (myLineList.at(2).toStdString() == "1") valid = true; position[0] = myLineList.at(3).toDouble(); position[1] = myLineList.at(4).toDouble(); position[2] = myLineList.at(5).toDouble(); orientation[0] = myLineList.at(6).toDouble(); orientation[1] = myLineList.at(7).toDouble(); orientation[2] = myLineList.at(8).toDouble(); orientation[3] = myLineList.at(9).toDouble(); returnValue->SetDataValid(valid); returnValue->SetPosition(position); returnValue->SetOrientation(orientation); return returnValue; } mitk::Quaternion QmitkIGTTrackingDataEvaluationView::GetSLERPAverage(mitk::NavigationDataEvaluationFilter::Pointer evaluationFilter) { mitk::Quaternion average; //build a vector of quaternions from the evaulation filter (caution always takes the first (0) input of the filter std::vector<mitk::Quaternion> quaternions = std::vector<mitk::Quaternion>(); for (int i = 0; i < evaluationFilter->GetNumberOfAnalysedNavigationData(0); i++) { mitk::Quaternion currentq = evaluationFilter->GetLoggedOrientation(i, 0); quaternions.push_back(currentq); } //compute the slerp average using the quaternion averaging class mitk::QuaternionAveraging::Pointer myAverager = mitk::QuaternionAveraging::New(); average = myAverager->CalcAverage(quaternions); return average; } void QmitkIGTTrackingDataEvaluationView::writeToFile(std::string filename, std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> values) { std::fstream currentFile; currentFile.open(filename.c_str(), std::ios::out); if (currentFile.bad()) { MITK_WARN << "Cannot open file, aborting!"; return; } currentFile << "Description" << ";" << "Error[mm]" << "\n"; for (auto currentError : values) { currentFile << currentError.description << ";" << currentError.distanceError << "\n"; } currentFile.close(); } mitk::NavigationDataCSVSequentialPlayer::Pointer QmitkIGTTrackingDataEvaluationView::ConstructNewNavigationDataPlayer() { bool rightHanded = m_Controls->m_RigthHanded->isChecked(); QString separator = m_Controls->m_SeparatorSign->text(); QChar sepaSign = separator.at(0); //char separatorSign; char separatorSign = sepaSign.toLatin1(); //std::string separatorSign = m_Controls->m_SeparatorSign->text().toStdString(); int sampleCount = m_Controls->m_SampleCount->value(); bool headerRow = m_Controls->m_HeaderRow->isChecked(); int xPos = m_Controls->m_XPos->value(); int yPos = m_Controls->m_YPos->value(); int zPos = m_Controls->m_ZPos->value(); bool useQuats = m_Controls->m_UseQuats->isChecked(); int qx = m_Controls->m_Qx->value(); int qy = m_Controls->m_Qy->value(); int qz = m_Controls->m_Qz->value(); int qr = m_Controls->m_Qr->value(); int azimuth = m_Controls->m_Azimuth->value(); int elevation = m_Controls->m_Elevation->value(); int roll = m_Controls->m_Roll->value(); bool eulersInRad = m_Controls->m_Radiants->isChecked(); //need to find the biggest column number to determine the minimal number of columns the .csv file has to have int allInts[] = {xPos, yPos, zPos, qx, qy, qr, azimuth, elevation, roll}; int minNumberOfColumns = (*std::max_element(allInts, allInts+9)+1); //size needs to be +1 because columns start at 0 but size at 1 - mitk::NavigationDataCSVSequentialPlayer::Pointer navDataPlayer = mitk::NavigationDataCSVSequentialPlayer::New(); navDataPlayer->SetOptions(rightHanded, separatorSign, sampleCount, headerRow, xPos, yPos, zPos, useQuats, qx, qy, qz, qr, azimuth, elevation, roll, eulersInRad, minNumberOfColumns); return navDataPlayer; } diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationViewControls.ui b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationViewControls.ui index 2dd08f80f3..78393e3591 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationViewControls.ui +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationViewControls.ui @@ -1,1780 +1,1787 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>QmitkIGTTrackingDataEvaluationViewControls</class> <widget class="QWidget" name="QmitkIGTTrackingDataEvaluationViewControls"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>448</width> <height>955</height> </rect> </property> <property name="minimumSize"> <size> <width>0</width> <height>0</height> </size> </property> <property name="windowTitle"> <string>QmitkTemplate</string> </property> <layout class="QVBoxLayout" name="verticalLayout_2"> <item> <widget class="QTabWidget" name="tabWidget"> <property name="currentIndex"> <number>0</number> </property> <widget class="QWidget" name="tab"> <attribute name="title"> <string>Evaluation</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout"> <item> <widget class="QLabel" name="label"> <property name="text"> <string>Input File List (recorded NavigationData / *.csv):</string> </property> </widget> </item> <item> <widget class="QListWidget" name="m_FileList"/> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout"> <item> <spacer name="horizontalSpacer"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_LoadInputFileList"> <property name="minimumSize"> <size> <width>120</width> <height>0</height> </size> </property> <property name="text"> <string>Load New List</string> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_6"> <item> <spacer name="horizontalSpacer_4"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_AddToCurrentList"> <property name="minimumSize"> <size> <width>120</width> <height>0</height> </size> </property> <property name="text"> <string>Add To Current List</string> </property> </widget> </item> </layout> </item> <item> <widget class="Line" name="line_3"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QLabel" name="label_17"> <property name="text"> <string>(1) - VISUALIZATION - of all data sets:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_17"> <item> <widget class="QLabel" name="label_18"> <property name="text"> <string>Prefix for Data Nodes:</string> </property> </widget> </item> <item> <widget class="QLineEdit" name="m_prefix"/> </item> </layout> </item> <item> <widget class="QPushButton" name="m_GeneratePointSetOfMeanPositions"> <property name="text"> <string>Generate PointSet of Mean Positions</string> </property> </widget> </item> <item> <widget class="QPushButton" name="m_GeneratePointSetsOfSinglePositions"> <property name="text"> <string>Generate PointSets of Single Positions</string> </property> </widget> </item> <item> <widget class="QPushButton" name="m_GenerateRotationLines"> <property name="text"> <string>Generate Lines for Rotation</string> </property> </widget> </item> <item> <widget class="Line" name="line_4"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QLabel" name="label_19"> <property name="text"> <string>(3) - JITTER - Evaluation per file / data set:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_2"> <item> <widget class="QLabel" name="label_2"> <property name="text"> <string>Result CSV Filename:</string> </property> </widget> </item> <item> <widget class="QLineEdit" name="m_OutputFilename"> <property name="text"> <string>D:/tmp/output.csv</string> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_3"> <item> <spacer name="horizontalSpacer_2"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_StartEvaluation"> <property name="minimumSize"> <size> <width>220</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>200</width> <height>50</height> </size> </property> <property name="text"> <string>COMPUTE RESULTS PER DATA SET</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_3"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> </layout> </item> <item> <widget class="Line" name="line_5"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QLabel" name="label_20"> <property name="text"> <string>(3) - ACCURACY - Evaluation of all data sets:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_16"> <item> <spacer name="horizontalSpacer_16"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_StartEvaluationAll"> <property name="minimumSize"> <size> <width>220</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>200</width> <height>50</height> </size> </property> <property name="text"> <string>COMPUTE RESULTS OF ALL DATA</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_17"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> </layout> </item> <item> <widget class="Line" name="line_6"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QLabel" name="label_21"> <property name="text"> <string>(4) - GRID MATCHING - Evaluation of all data sets:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_19"> <item> <widget class="QLabel" name="label_22"> <property name="text"> <string>Reference PointSet:</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_20"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QmitkDataStorageComboBox" name="m_ReferencePointSetComboBox"> <property name="minimumSize"> <size> <width>150</width> <height>0</height> </size> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_20"> <item> <widget class="QLabel" name="label_23"> <property name="text"> <string>Measurement PointSet:</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_21"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QmitkDataStorageComboBox" name="m_MeasurementPointSetComboBox"> <property name="minimumSize"> <size> <width>150</width> <height>0</height> </size> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_18"> <item> <spacer name="horizontalSpacer_18"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_GridMatching"> <property name="minimumSize"> <size> <width>220</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>200</width> <height>50</height> </size> </property> <property name="text"> <string>PERFOM GRID MATCHING</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_19"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> </layout> </item> <item> <widget class="Line" name="line_7"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QLabel" name="label_24"> <property name="text"> <string>(5) - ROTATION - Evaluation of all data sets:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_21"> <item> <spacer name="horizontalSpacer_22"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_ComputeRotation"> <property name="minimumSize"> <size> <width>220</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>200</width> <height>50</height> </size> </property> <property name="text"> <string>COMPUTE ROTATION ERRORS</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_23"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> </layout> </item> <item> <spacer name="spacer1"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeType"> <enum>QSizePolicy::Expanding</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>220</height> </size> </property> </spacer> </item> </layout> </widget> <widget class="QWidget" name="tab_2"> <attribute name="title"> <string>Settings</string> </attribute> <layout class="QGridLayout" name="gridLayout_5"> <item row="0" column="0"> <widget class="QToolBox" name="toolBox"> <widget class="QWidget" name="page_5"> <property name="geometry"> <rect> <x>0</x> <y>0</y> - <width>409</width> - <height>768</height> + <width>420</width> + <height>843</height> </rect> </property> <attribute name="label"> <string>General</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_4"> <item> <widget class="QGroupBox" name="GeneralOptions"> <property name="title"> <string/> </property> <layout class="QVBoxLayout" name="verticalLayout_5"> <item> <layout class="QHBoxLayout" name="horizontalLayout_5"> <item> <widget class="QLabel" name="label_16"> <property name="text"> <string>Scaling Factor for Visualization:</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_15"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>38</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QDoubleSpinBox" name="m_ScalingFactor"> <property name="minimum"> <double>1.000000000000000</double> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_4"> <item> <widget class="QLabel" name="label_3"> <property name="text"> <string>Number of samples to analyze:</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_5"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>60</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QSpinBox" name="m_NumberOfSamples"> <property name="maximum"> <number>1000000</number> </property> <property name="value"> <number>150</number> </property> </widget> </item> </layout> </item> <item> <widget class="Line" name="line_8"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QLabel" name="label_15"> <property name="text"> <string>Tracking Volume:</string> </property> </widget> </item> <item> <widget class="QRadioButton" name="m_standardVolume"> <property name="text"> <string>Standard Volume (10 X 9 Positions)</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QRadioButton" name="m_mediumVolume"> <property name="text"> <string>Medium Volume (5 X 5 Positions)</string> </property> </widget> </item> + <item> + <widget class="QRadioButton" name="m_medium5x6Volume"> + <property name="text"> + <string>Medium Volume (5 X 6 Positions)</string> + </property> + </widget> + </item> <item> <widget class="QRadioButton" name="m_smallVolume"> <property name="text"> <string>Small Volume (3 X 4 Positions)</string> </property> </widget> </item> <item> <widget class="Line" name="line_9"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QLabel" name="label_40"> <property name="text"> <string>Rotation Evaluation:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_26"> <item> <widget class="QLabel" name="label_41"> <property name="text"> <string>Rotation Vector:</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_28"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QLabel" name="label_42"> <property name="text"> <string>X</string> </property> </widget> </item> <item> <widget class="QSpinBox" name="m_rotVecX"> <property name="maximum"> <number>99999</number> </property> </widget> </item> <item> <spacer name="horizontalSpacer_27"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QLabel" name="label_43"> <property name="text"> <string>Y</string> </property> </widget> </item> <item> <widget class="QSpinBox" name="m_rotVecY"> <property name="maximum"> <number>99999</number> </property> </widget> </item> <item> <spacer name="horizontalSpacer_26"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QLabel" name="label_44"> <property name="text"> <string>Z</string> </property> </widget> </item> <item> <widget class="QSpinBox" name="m_rotVecZ"> <property name="maximum"> <number>99999</number> </property> <property name="value"> <number>10000</number> </property> </widget> </item> </layout> </item> <item> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> </item> </layout> </widget> <widget class="QWidget" name="page"> <property name="geometry"> <rect> <x>0</x> <y>0</y> - <width>286</width> - <height>746</height> + <width>180</width> + <height>584</height> </rect> </property> <attribute name="label"> <string>.csv file input options</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_13"> <item> <widget class="QGroupBox" name="m_FileOptionsBox"> <property name="title"> <string>File Options:</string> </property> <layout class="QVBoxLayout" name="verticalLayout_12"> <item> <layout class="QHBoxLayout" name="horizontalLayout_23"> <item> <widget class="QLabel" name="label_26"> <property name="text"> <string>Separator in the csv file: </string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_25"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>60</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QLineEdit" name="m_SeparatorSign"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="maximumSize"> <size> <width>40</width> <height>16777215</height> </size> </property> <property name="text"> <string>;</string> </property> <property name="maxLength"> <number>1</number> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_25"> <item> <widget class="QLabel" name="label_25"> <property name="text"> <string>Use every n-th smaple n:</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_24"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QSpinBox" name="m_SampleCount"> <property name="value"> <number>1</number> </property> </widget> </item> </layout> </item> <item> <widget class="QCheckBox" name="m_HeaderRow"> <property name="text"> <string>The csv file has a header row</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="CoordinateType"> <property name="title"> <string>Type of Coordinate System:</string> </property> <layout class="QVBoxLayout" name="verticalLayout_19"> <item> <layout class="QHBoxLayout" name="horizontalLayout_24"> <item> <widget class="QRadioButton" name="m_LeftHanded"> <property name="text"> <string>Left handed </string> </property> </widget> </item> <item> <widget class="QRadioButton" name="m_RigthHanded"> <property name="text"> <string>Right handed</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> </layout> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="PositionAndOrientationOptions"> <property name="title"> <string>Position and Orientation Options:</string> </property> <layout class="QVBoxLayout" name="verticalLayout_11"> <item> <layout class="QGridLayout" name="gridLayout"> <item row="2" column="0"> <widget class="QLabel" name="label_28"> <property name="text"> <string>Y</string> </property> </widget> </item> <item row="2" column="1"> <widget class="QSpinBox" name="m_YPos"> <property name="value"> <number>4</number> </property> </widget> </item> <item row="3" column="0"> <widget class="QLabel" name="label_29"> <property name="text"> <string>Z</string> </property> </widget> </item> <item row="3" column="1"> <widget class="QSpinBox" name="m_ZPos"> <property name="value"> <number>5</number> </property> </widget> </item> <item row="1" column="0"> <widget class="QLabel" name="label_27"> <property name="text"> <string>X</string> </property> </widget> </item> <item row="1" column="1"> <widget class="QSpinBox" name="m_XPos"> <property name="value"> <number>3</number> </property> </widget> </item> <item row="0" column="0"> <widget class="QLabel" name="label_4"> <property name="text"> <string>Coordinate:</string> </property> </widget> </item> <item row="0" column="1"> <widget class="QLabel" name="label_5"> <property name="text"> <string>Colum number:</string> </property> </widget> </item> </layout> </item> <item> <widget class="QRadioButton" name="m_UseQuats"> <property name="text"> <string>Use Quaternions for Orientation</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <layout class="QGridLayout" name="gridLayout_2"> <item row="4" column="0"> <widget class="QLabel" name="label_35"> <property name="text"> <string>Qr</string> </property> </widget> </item> <item row="3" column="1"> <widget class="QSpinBox" name="m_Qz"> <property name="value"> <number>8</number> </property> </widget> </item> <item row="2" column="0"> <widget class="QLabel" name="label_33"> <property name="text"> <string>Qy</string> </property> </widget> </item> <item row="4" column="1"> <widget class="QSpinBox" name="m_Qr"> <property name="value"> <number>9</number> </property> </widget> </item> <item row="2" column="1"> <widget class="QSpinBox" name="m_Qy"> <property name="value"> <number>7</number> </property> </widget> </item> <item row="1" column="1"> <widget class="QSpinBox" name="m_Qx"> <property name="value"> <number>6</number> </property> </widget> </item> <item row="1" column="0"> <widget class="QLabel" name="label_32"> <property name="text"> <string>Qx</string> </property> </widget> </item> <item row="3" column="0"> <widget class="QLabel" name="label_34"> <property name="text"> <string>Qz</string> </property> </widget> </item> <item row="0" column="0"> <widget class="QLabel" name="label_6"> <property name="text"> <string>Quaternion component:</string> </property> </widget> </item> <item row="0" column="1"> <widget class="QLabel" name="label_36"> <property name="text"> <string>Column number:</string> </property> </widget> </item> </layout> </item> <item> <widget class="QRadioButton" name="m_UseEuler"> <property name="text"> <string>Use Euler Angles for Orientation</string> </property> </widget> </item> <item> <layout class="QGridLayout" name="gridLayout_3"> <item row="0" column="1"> <widget class="QLabel" name="label_30"> <property name="text"> <string>Column number:</string> </property> </widget> </item> <item row="1" column="0"> <widget class="QLabel" name="label_37"> <property name="text"> <string>Azimuth</string> </property> </widget> </item> <item row="2" column="1"> <widget class="QSpinBox" name="m_Elevation"> <property name="minimum"> <number>-1</number> </property> </widget> </item> <item row="3" column="0"> <widget class="QLabel" name="label_39"> <property name="text"> <string>Roll</string> </property> </widget> </item> <item row="0" column="0"> <widget class="QLabel" name="label_7"> <property name="text"> <string>Angle:</string> </property> </widget> </item> <item row="3" column="1"> <widget class="QSpinBox" name="m_Roll"> <property name="minimum"> <number>-1</number> </property> </widget> </item> <item row="2" column="0"> <widget class="QLabel" name="label_38"> <property name="text"> <string>Elevation</string> </property> </widget> </item> <item row="1" column="1"> <widget class="QSpinBox" name="m_Azimuth"> <property name="minimum"> <number>-1</number> </property> </widget> </item> </layout> </item> <item> <widget class="QWidget" name="EulerUnity" native="true"> <layout class="QVBoxLayout" name="verticalLayout_18"> <item> <widget class="QLabel" name="label_31"> <property name="text"> <string>Unity for Euler Angles:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_22"> <item> <widget class="QRadioButton" name="m_Radiants"> <property name="text"> <string>Radiants</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QRadioButton" name="m_Degrees"> <property name="text"> <string>Degrees</string> </property> <property name="checked"> <bool>false</bool> </property> </widget> </item> </layout> </item> </layout> </widget> </item> </layout> </widget> </item> </layout> </widget> <widget class="QWidget" name="toolBoxPage1"> <property name="geometry"> <rect> <x>0</x> <y>0</y> - <width>343</width> - <height>607</height> + <width>217</width> + <height>452</height> </rect> </property> <attribute name="label"> <string>Output per data set</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_17"> <item> <widget class="QGroupBox" name="groupBox"> <property name="title"> <string>Position</string> </property> <layout class="QVBoxLayout" name="verticalLayout_14"> <item> <widget class="QCheckBox" name="m_settingPosMean"> <property name="text"> <string>Mean (x,y,z)</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingPosStabw"> <property name="text"> <string>Standard Deviation (x,y,z)</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingPosSampleStabw"> <property name="text"> <string>Sample Standard Deviation (x,y,z)</string> </property> </widget> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBox_6"> <property name="title"> <string>Orientation</string> </property> <layout class="QVBoxLayout" name="verticalLayout_3"> <item> <widget class="QCheckBox" name="m_settingQuaternionMean"> <property name="text"> <string>Quaternion Mean (qx,qy,qz,qr)</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_QuaternionMeanSlerp"> <property name="text"> <string>Quaternion Mean (SLERP)</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settionQuaternionStabw"> <property name="text"> <string>Quaternion Standard Deviation (qx,qy,qz,qr)</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingEulerMean"> <property name="text"> <string>Euler Mean (tx,ty,tz)</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingDifferenceAngles"> <property name="text"> <string>Difference Angles to all other Positions</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_DifferencesSLERP"> <property name="text"> <string>Difference Angles to all other Positions (SLERP)</string> </property> </widget> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBox_7"> <property name="title"> <string>Position Error</string> </property> <layout class="QVBoxLayout" name="verticalLayout_15"> <item> <widget class="QCheckBox" name="m_settingPosErrorMean"> <property name="text"> <string>Mean</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingPosErrorStabw"> <property name="text"> <string>Standard Deviation</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingPosErrorSampleStabw"> <property name="text"> <string>Sample Standard Deviation</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingPosErrorRMS"> <property name="text"> <string>RMS</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingPosErrorMedian"> <property name="text"> <string>Median</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingPosErrorMinMax"> <property name="text"> <string>Min/Max</string> </property> </widget> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBox_8"> <property name="title"> <string>Orientation Error</string> </property> <layout class="QVBoxLayout" name="verticalLayout_16"> <item> <widget class="QCheckBox" name="m_settingEulerRMS"> <property name="text"> <string>Euler RMS</string> </property> </widget> </item> </layout> </widget> </item> </layout> </widget> </widget> </item> </layout> </widget> <widget class="QWidget" name="tab_3"> <attribute name="title"> <string>Tools</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_10"> <item> <widget class="QGroupBox" name="groupBox_2"> <property name="title"> <string>Point Set Ground Truth Generator</string> </property> <layout class="QVBoxLayout" name="verticalLayout_6"> <item> <layout class="QHBoxLayout" name="horizontalLayout_8"> <item> <widget class="QLabel" name="label_8"> <property name="text"> <string>Generate</string> </property> </widget> </item> <item> <widget class="QSpinBox" name="m_PointNumber1"> <property name="minimum"> <number>1</number> </property> <property name="maximum"> <number>999</number> </property> <property name="value"> <number>10</number> </property> </widget> </item> <item> <widget class="QLabel" name="label_9"> <property name="text"> <string>X</string> </property> </widget> </item> <item> <widget class="QSpinBox" name="m_PointNumber2"> <property name="minimum"> <number>1</number> </property> <property name="maximum"> <number>999</number> </property> <property name="value"> <number>9</number> </property> </widget> </item> <item> <widget class="QLabel" name="label_10"> <property name="text"> <string>Point Set</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_7"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_7"> <item> <widget class="QLabel" name="label_11"> <property name="text"> <string>Inter Point Distance (in mm):</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_8"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QSpinBox" name="m_PointDistance"> <property name="minimum"> <number>1</number> </property> <property name="maximum"> <number>99999</number> </property> <property name="value"> <number>50</number> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_9"> <item> <spacer name="horizontalSpacer_6"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_GeneratePointSet"> <property name="text"> <string>Generate</string> </property> </widget> </item> </layout> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBox_3"> <property name="title"> <string>Result CSV File to NavigationData Converter</string> </property> <layout class="QVBoxLayout" name="verticalLayout_7"> <item> <widget class="QRadioButton" name="m_ConvertSingleFile"> <property name="text"> <string>Convert Single File</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QLabel" name="label_12"> <property name="text"> <string>Input CSV Logging File:</string> </property> </widget> </item> <item> <widget class="QLineEdit" name="m_InputCSV"> <property name="text"> <string>C:/Tools/test.csv</string> </property> </widget> </item> <item> <widget class="QLabel" name="label_13"> <property name="text"> <string>Output Navigation Data File:</string> </property> </widget> </item> <item> <widget class="QLineEdit" name="m_OutputXML"> <property name="text"> <string>C:/Tools/testoutput.xml</string> </property> </widget> </item> <item> <widget class="Line" name="line_2"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QRadioButton" name="m_ConvertFileList"> <property name="text"> <string>Convert File List</string> </property> </widget> </item> <item> <widget class="QLabel" name="label_14"> <property name="text"> <string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:8pt; font-style:italic;">(use text files with a complete filename in every line)</span></p></body></html></string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_11"> <item> <widget class="QLabel" name="m_labelCSVtoXMLInputList"> <property name="text"> <string>not loaded</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_10"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_loadCSVtoXMLInputList"> <property name="minimumSize"> <size> <width>100</width> <height>0</height> </size> </property> <property name="text"> <string>Load Input List</string> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_12"> <item> <widget class="QLabel" name="m_labelCSVtoXMLOutputList"> <property name="text"> <string>not loaded</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_11"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_loadCSVtoXMLOutputList"> <property name="minimumSize"> <size> <width>100</width> <height>0</height> </size> </property> <property name="text"> <string>Load Output List</string> </property> </widget> </item> </layout> </item> <item> <widget class="Line" name="line"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_14"> <item> <spacer name="horizontalSpacer_12"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QGroupBox" name="groupBox_4"> <property name="title"> <string>Output Format</string> </property> <layout class="QVBoxLayout" name="verticalLayout_9"> <item> <widget class="QRadioButton" name="m_ConvertXML"> <property name="text"> <string>XML</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QRadioButton" name="m_ConvertCSV"> <property name="text"> <string>CSV</string> </property> </widget> </item> </layout> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_10"> <item> <spacer name="horizontalSpacer_9"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_Convert"> <property name="text"> <string>Convert</string> </property> </widget> </item> </layout> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBox_5"> <property name="title"> <string>Orientation Calculation (out of three positions)</string> </property> <layout class="QVBoxLayout" name="verticalLayout_8"> <item> <layout class="QHBoxLayout" name="horizontalLayout_13"> <item> <spacer name="horizontalSpacer_13"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_OrientationCalculationGenerateReference"> <property name="text"> <string>Generate Reference From Current List</string> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_15"> <item> <spacer name="horizontalSpacer_14"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_OrientationCalculationWriteOrientationsToFile"> <property name="text"> <string>Write Orientation Quaternions To File</string> </property> </widget> </item> </layout> </item> </layout> </widget> </item> <item> <spacer name="verticalSpacer_3"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>632</height> </size> </property> </spacer> </item> </layout> </widget> </widget> </item> </layout> </widget> <layoutdefault spacing="6" margin="11"/> <customwidgets> <customwidget> <class>QmitkDataStorageComboBox</class> <extends>QComboBox</extends> <header>QmitkDataStorageComboBox.h</header> </customwidget> </customwidgets> <resources/> <connections/> </ui> diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.cpp b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.cpp index d30c2104d8..da7e1f5177 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.cpp @@ -1,453 +1,521 @@ /*=================================================================== 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. ===================================================================*/ #define _USE_MATH_DEFINES #include "mitkHummelProtocolEvaluation.h" #include <boost/serialization/array_wrapper.hpp> #include <boost/accumulators/accumulators.hpp> #include <boost/accumulators/statistics.hpp> #include <boost/accumulators/statistics/stats.hpp> #include <boost/accumulators/statistics/mean.hpp> #include <boost/accumulators/statistics/moment.hpp> #include <boost/accumulators/statistics/tail_quantile.hpp> #include <boost/math/distributions/normal.hpp> #include <algorithm> bool mitk::HummelProtocolEvaluation::Evaluate15cmDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector<HummelProtocolDistanceError> &Results) { if (m != mitk::HummelProtocolEvaluation::standard) { MITK_WARN << "15 cm distances are only evaluated for standard volumes, aborting!"; return false; } MITK_INFO << "########### 15 cm distance errors #############"; //convert measurements to matrix std::array<std::array<mitk::Point3D, 10> ,9> matrix = ParseMatrixStandardVolume(p); //these are the variables for the results: std::vector<double> distances; std::vector<std::string> descriptions; //evaluation of rows int distanceCounter = 0; for (int row = 0; row < 9; row++) //rows for (int distance = 0; distance < 7; distance++) { distanceCounter++; mitk::Point3D point1 = p->GetPoint(row * 10 + distance); mitk::Point3D point2 = p->GetPoint(row * 10 + distance + 3); distances.push_back(point1.EuclideanDistanceTo(point2)); std::stringstream description; description << "Distance(" << distanceCounter << ") " << (row + 1) << "/" << (distance + 1) << " to " << (row + 1) << "/" << (distance + 4); descriptions.push_back(description.str()); } //evaluation of columns for (int column = 0; column < 10; column++) for (int row = 0; row < 6; row++) { distanceCounter++; mitk::Point3D point1 = matrix[row][column]; mitk::Point3D point2 = matrix[row + 3][column]; distances.push_back(point1.EuclideanDistanceTo(point2)); std::stringstream description; description << "Distance(" << distanceCounter << ") " << (row + 1) << "/" << (column + 1) << " to " << (row + 4) << "/" << (column + 1); descriptions.push_back(description.str()); } //compute all errors for (std::size_t i = 0; i < distances.size(); ++i) { HummelProtocolDistanceError currentError; currentError.distanceError = fabs(distances.at(i) - (double)150.0); currentError.description = descriptions.at(i); Results.push_back(currentError); MITK_INFO << "Error " << currentError.description << " : " << currentError.distanceError; } //compute statistics std::vector<HummelProtocolDistanceError> statistics = mitk::HummelProtocolEvaluation::ComputeStatistics(Results); for (auto currentError : statistics) { Results.push_back(currentError); MITK_INFO << currentError.description << " : " << currentError.distanceError; } return true; } bool mitk::HummelProtocolEvaluation::Evaluate30cmDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector<HummelProtocolDistanceError> &Results) { if (m != mitk::HummelProtocolEvaluation::standard) { MITK_WARN << "30 cm distances are only evaluated for standard volumes, aborting!"; return false; } MITK_INFO << "########### 30 cm distance errors #############"; //convert measurements to matrix std::array<std::array<mitk::Point3D, 10> ,9> matrix = ParseMatrixStandardVolume(p); //these are the variables for the results: std::vector<double> distances; std::vector<std::string> descriptions; //evaluation of rows int distanceCounter = 0; for (int row = 0; row < 9; row++) //rows for (int distance = 0; distance < 4; distance++) { distanceCounter++; mitk::Point3D point1 = p->GetPoint(row * 10 + distance); mitk::Point3D point2 = p->GetPoint(row * 10 + distance + 6); distances.push_back(point1.EuclideanDistanceTo(point2)); std::stringstream description; description << "Distance(" << distanceCounter << ") " << (row + 1) << "/" << (distance + 1) << " to " << (row + 1) << "/" << (distance + 7); descriptions.push_back(description.str()); } //evaluation of columns for (int column = 0; column < 10; column++) for (int row = 0; row < 3; row++) { distanceCounter++; mitk::Point3D point1 = matrix[row][column]; mitk::Point3D point2 = matrix[row + 6][column]; distances.push_back(point1.EuclideanDistanceTo(point2)); std::stringstream description; description << "Distance(" << distanceCounter << ") " << (row + 1) << "/" << (column + 1) << " to " << (row + 7) << "/" << (column + 1); descriptions.push_back(description.str()); } //compute all errors for (std::size_t i = 0; i < distances.size(); ++i) { HummelProtocolDistanceError currentError; currentError.distanceError = fabs(distances.at(i) - (double)300.0); currentError.description = descriptions.at(i); Results.push_back(currentError); MITK_INFO << "Error " << currentError.description << " : " << currentError.distanceError; } //compute statistics std::vector<HummelProtocolDistanceError> statistics = mitk::HummelProtocolEvaluation::ComputeStatistics(Results); for (auto currentError : statistics) { Results.push_back(currentError); MITK_INFO << currentError.description << " : " << currentError.distanceError; } return true; } bool mitk::HummelProtocolEvaluation::EvaluateAccumulatedDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector<HummelProtocolDistanceError> &Results) { if (m != mitk::HummelProtocolEvaluation::standard) { MITK_WARN << "Accumulated distances are only evaluated for standard volumes, aborting!"; return false; } MITK_INFO << "########### accumulated distance errors #############"; int distanceCounter = 0; //evaluation of rows for (int row = 0; row < 9; row++) //rows for (int distance = 0; distance < 9; distance++) { distanceCounter++; mitk::Point3D point1 = p->GetPoint(row * 10); mitk::Point3D point2 = p->GetPoint(row * 10 + distance + 1); std::stringstream description; description << "Distance(" << distanceCounter << ") " << (row + 1) << "/1 to " << (row + 1) << "/" << (distance + 2); //compute error HummelProtocolDistanceError currentError; currentError.distanceError = fabs(point1.EuclideanDistanceTo(point2) - (double)(50.0*(distance+1))); currentError.description = description.str(); Results.push_back(currentError); MITK_INFO << "Error " << currentError.description << " : " << currentError.distanceError; } //compute statistics std::vector<HummelProtocolDistanceError> statistics = mitk::HummelProtocolEvaluation::ComputeStatistics(Results); for (auto currentError : statistics) { Results.push_back(currentError); MITK_INFO << currentError.description << " : " << currentError.distanceError; } return true; } bool mitk::HummelProtocolEvaluation::Evaluate5cmDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector<HummelProtocolDistanceError> &Results) { MITK_INFO << "########### 5 cm distance errors #############"; std::vector<double> distances; std::vector<std::string> descriptions; switch (m) { case small: if (p->GetSize() != 12) { MITK_WARN << "Wrong number of points: " << p->GetSize() << " (expected 12), aborting"; return false; } MITK_INFO << "Computing Hummel protocol distance errors for small measurement volumes (12 points)..."; //row 1 distances.push_back(p->GetPoint(0).EuclideanDistanceTo(p->GetPoint(1))); //0 descriptions.push_back("Distance 4/4 to 4/5"); distances.push_back(p->GetPoint(1).EuclideanDistanceTo(p->GetPoint(2))); //1 descriptions.push_back("Distance 4/5 to 4/6"); distances.push_back(p->GetPoint(2).EuclideanDistanceTo(p->GetPoint(3))); //2 descriptions.push_back("Distance 4/6 to 4/7"); //row 2 distances.push_back(p->GetPoint(4).EuclideanDistanceTo(p->GetPoint(5))); //3 descriptions.push_back("Distance 5/4 to 5/5"); distances.push_back(p->GetPoint(5).EuclideanDistanceTo(p->GetPoint(6))); //4 descriptions.push_back("Distance 5/5 to 5/6"); distances.push_back(p->GetPoint(6).EuclideanDistanceTo(p->GetPoint(7))); //5 descriptions.push_back("Distance 5/6 to 5/7"); //row 3 distances.push_back(p->GetPoint(8).EuclideanDistanceTo(p->GetPoint(9))); //6 descriptions.push_back("Distance 6/4 to 6/5"); distances.push_back(p->GetPoint(9).EuclideanDistanceTo(p->GetPoint(10))); //7 descriptions.push_back("Distance 6/5 to 6/6"); distances.push_back(p->GetPoint(10).EuclideanDistanceTo(p->GetPoint(11))); //8 descriptions.push_back("Distance 6/6 to 6/7"); //column 1 distances.push_back(p->GetPoint(0).EuclideanDistanceTo(p->GetPoint(4))); //9 descriptions.push_back("Distance 4/4 to 5/4"); distances.push_back(p->GetPoint(4).EuclideanDistanceTo(p->GetPoint(8))); //10 descriptions.push_back("Distance 5/4 to 6/4"); //column 2 distances.push_back(p->GetPoint(1).EuclideanDistanceTo(p->GetPoint(5))); //11 descriptions.push_back("Distance 4/5 to 5/5"); distances.push_back(p->GetPoint(5).EuclideanDistanceTo(p->GetPoint(9))); //12 descriptions.push_back("Distance 5/5 to 6/5"); //column 3 distances.push_back(p->GetPoint(2).EuclideanDistanceTo(p->GetPoint(6))); //13 descriptions.push_back("Distance 4/6 to 5/6"); distances.push_back(p->GetPoint(6).EuclideanDistanceTo(p->GetPoint(10))); //14 descriptions.push_back("Distance 5/6 to 6/6"); //column 4 distances.push_back(p->GetPoint(3).EuclideanDistanceTo(p->GetPoint(7))); //15 descriptions.push_back("Distance 4/7 to 5/7"); distances.push_back(p->GetPoint(7).EuclideanDistanceTo(p->GetPoint(11))); //16 descriptions.push_back("Distance 5/7 to 6/7"); break; case medium: { if (p->GetSize() != 25) { MITK_WARN << "Wrong number of points (expected 25), aborting"; return false; } MITK_INFO << "Computing Hummel protocol distance errors for medium measurement volumes (25 points)..."; int distanceCounter = 0; //convert measurements to matrix std::array<std::array<mitk::Point3D, 5>, 5> matrix = ParseMatrixMediumVolume(p); //evaluation of rows for (int row = 0; row < 5; row++) //rows for (int distance = 0; distance < 4; distance++) { distanceCounter++; mitk::Point3D point1 = p->GetPoint(row * 5 + distance); mitk::Point3D point2 = p->GetPoint(row * 5 + distance + 1); distances.push_back(point1.EuclideanDistanceTo(point2)); std::stringstream description; description << "Distance(" << distanceCounter << ") " << (row + 1) << "/" << (distance + 1) << " to " << (row + 1) << "/" << (distance + 2); descriptions.push_back(description.str()); } //evaluation of columns for (int column = 0; column < 5; column++) for (int row = 0; row < 4; row++) { distanceCounter++; mitk::Point3D point1 = matrix[row][column]; mitk::Point3D point2 = matrix[row + 1][column]; MITK_INFO << "Point 1:" << point1 << "/Point 2:" << point2 << "/Distance:" << point1.EuclideanDistanceTo(point2); distances.push_back(point1.EuclideanDistanceTo(point2)); std::stringstream description; description << "Distance(" << distanceCounter << ") " << (row + 1) << "/" << (column + 1) << " to " << (row + 2) << "/" << (column + 1); descriptions.push_back(description.str()); } } break; +case medium5x6: +{ + if (p->GetSize() != 30) { + MITK_WARN << "Wrong number of points (expected 30), aborting"; + return false; + } + MITK_INFO << "Computing Hummel protocol distance errors for 5x6 medium measurement volumes (30 points)..."; + + int distanceCounter = 0; + + //convert measurements to matrix + std::array<std::array<mitk::Point3D, 6>, 5> matrix = ParseMatrixMedium5x6Volume(p); + + /* Print out matrix for debugging + for (int row = 0; row < 5; row++) + { + for (int column = 0; column < 6; column++) + { + std::cout << matrix.at(row).at(column); + } + std::cout << "\n"; + } + */ + + //evaluation of rows + for (int row = 0; row < 5; row++) //rows + for (int distance = 0; distance < 5; distance++) + { + distanceCounter++; + mitk::Point3D point1 = p->GetPoint(row * 6 + distance); + mitk::Point3D point2 = p->GetPoint(row * 6 + distance + 1); + distances.push_back(point1.EuclideanDistanceTo(point2)); + std::stringstream description; + description << "Distance(" << distanceCounter << ") " << (row + 1) << "/" << (distance + 1) << " to " << (row + 1) << "/" << (distance + 2); + descriptions.push_back(description.str()); + } + + //evaluation of columns + for (int column = 0; column < 6; column++) + for (int row = 0; row < 4; row++) + { + distanceCounter++; + mitk::Point3D point1 = matrix[row][column]; + mitk::Point3D point2 = matrix[row + 1][column]; + distances.push_back(point1.EuclideanDistanceTo(point2)); + std::stringstream description; + description << "Distance(" << distanceCounter << ") " << (row + 1) << "/" << (column + 1) << " to " << (row + 2) << "/" << (column + 1); + descriptions.push_back(description.str()); + } +} +break; + case standard: { if (p->GetSize() != 90) { MITK_WARN << "Wrong number of points (expected 90), aborting"; return false; } MITK_INFO << "Computing Hummel protocol distance errors for standard measurement volumes (90 points)..."; int distanceCounter = 0; //convert measurements to matrix std::array<std::array<mitk::Point3D, 10>, 9> matrix = ParseMatrixStandardVolume(p); //evaluation of rows for (int row = 0; row < 9; row++) //rows for (int distance = 0; distance < 9; distance++) { distanceCounter++; mitk::Point3D point1 = p->GetPoint(row * 10 + distance); mitk::Point3D point2 = p->GetPoint(row * 10 + distance + 1); distances.push_back(point1.EuclideanDistanceTo(point2)); std::stringstream description; description << "Distance(" << distanceCounter << ") " << (row + 1) << "/" << (distance + 1) << " to " << (row + 1) << "/" << (distance + 2); descriptions.push_back(description.str()); } //evaluation of columns for (int column = 0; column < 10; column++) for (int row = 0; row < 8; row++) { distanceCounter++; mitk::Point3D point1 = matrix[row][column]; mitk::Point3D point2 = matrix[row + 1][column]; distances.push_back(point1.EuclideanDistanceTo(point2)); std::stringstream description; description << "Distance(" << distanceCounter << ") " << (row + 1) << "/" << (column + 1) << " to " << (row + 2) << "/" << (column + 1); descriptions.push_back(description.str()); } } break; } //compute all errors for (std::size_t i = 0; i < distances.size(); ++i) { HummelProtocolDistanceError currentError; currentError.distanceError = fabs(distances.at(i) - (double)50.0); currentError.description = descriptions.at(i); Results.push_back(currentError); MITK_INFO << "Error " << currentError.description << " : " << currentError.distanceError; } //compute statistics std::vector<HummelProtocolDistanceError> statistics = mitk::HummelProtocolEvaluation::ComputeStatistics(Results); for (auto currentError : statistics) { Results.push_back(currentError); MITK_INFO << currentError.description << " : " << currentError.distanceError; } return true; } std::array<std::array<mitk::Point3D, 10>, 9> mitk::HummelProtocolEvaluation::ParseMatrixStandardVolume(mitk::PointSet::Pointer p) { std::array<std::array<mitk::Point3D, 10> ,9> returnValue; if (p->GetSize() != 90) { MITK_WARN << "PointSet does not have the right size. Expected 90 got " << p->GetSize() << " ... aborting!"; return returnValue; } for (int row = 0; row < 9; row++) for (int column = 0; column < 10; column++) returnValue[row][column] = p->GetPoint(row * 10 + column); return returnValue; } +std::array<std::array<mitk::Point3D, 6>, 5> mitk::HummelProtocolEvaluation::ParseMatrixMedium5x6Volume(mitk::PointSet::Pointer p) +{ + + std::array<std::array<mitk::Point3D, 6>, 5> returnValue; + + if (p->GetSize() != 30) + { + MITK_WARN << "PointSet does not have the right size. Expected 30 got " << p->GetSize() << " ... aborting!"; + return returnValue; + } + for (int row = 0; row < 5; row++) + for (int column = 0; column < 6; column++) + returnValue[row][column] = p->GetPoint(row * 6 + column); + return returnValue; +} + std::array<std::array<mitk::Point3D, 5>, 5> mitk::HummelProtocolEvaluation::ParseMatrixMediumVolume(mitk::PointSet::Pointer p) { std::array<std::array<mitk::Point3D, 5>, 5> returnValue; if (p->GetSize() != 25) { MITK_WARN << "PointSet does not have the right size. Expected 25 got " << p->GetSize() << " ... aborting!"; return returnValue; } for (int row = 0; row < 5; row++) for (int column = 0; column < 5; column++) { returnValue[row][column] = p->GetPoint(row * 5 + column); //MITK_INFO << "m " << row << "/" << column << ":" << p->GetPoint(row * 5 + column); } return returnValue; } std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> mitk::HummelProtocolEvaluation::ComputeStatistics(std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> values) { std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> returnValue; //convert input values to boost / using boost accumulators for statistics boost::accumulators::accumulator_set<double, boost::accumulators::features<boost::accumulators::tag::mean, //boost::accumulators::tag::median, boost::accumulators::tag::variance, boost::accumulators::tag::max, boost::accumulators::tag::min //boost::accumulators::tag::tail<boost::accumulators::left> > > acc; for (mitk::HummelProtocolEvaluation::HummelProtocolDistanceError each : values) { acc(each.distanceError); } returnValue.push_back({ static_cast<double>(values.size()), "N" }); returnValue.push_back({ boost::accumulators::mean(acc), "Mean" }); //double quantile25th = boost::accumulators::quantile(acc, boost::accumulators::quantile_probability = 0.25); //returnValue.push_back({ boost::accumulators::median(acc), "Median" }); //returnValue.push_back({ boost::accumulators::variance(acc), "Variance" }); returnValue.push_back({ boost::accumulators::min(acc), "Min" }); returnValue.push_back({ boost::accumulators::max(acc), "Max" }); //don't get the boost stuff working correctly, so computing the quantiles, median and standard deviation by myself: std::vector<double> quantile; for (mitk::HummelProtocolEvaluation::HummelProtocolDistanceError each : values) {quantile.push_back(each.distanceError);} auto const Q1 = quantile.size() / 4; auto const Q2 = quantile.size() / 2; auto const Q3 = Q1 + Q2; std::sort(quantile.begin(),quantile.end()); returnValue.push_back({ quantile[Q1], "Quartile 1" }); returnValue.push_back({ quantile[Q2], "Median" }); returnValue.push_back({ quantile[Q3], "Quartile 3" }); double mean = boost::accumulators::mean(acc); double errorSum = 0; for (mitk::HummelProtocolEvaluation::HummelProtocolDistanceError each : values) { double error = pow((each.distanceError - mean),2); errorSum += error; } double variance = errorSum / values.size(); double sampleVariance = errorSum / (values.size()-1); double standardDev = sqrt(variance); double sampleStandardDev = sqrt(sampleVariance); returnValue.push_back({ variance, "Variance" }); returnValue.push_back({ sampleVariance, "Sample Variance" }); returnValue.push_back({ standardDev, "Standard Deviation" }); returnValue.push_back({ sampleStandardDev, "Sample Standard Deviation" }); return returnValue; } diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.h b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.h index d08a7d1c8c..3ceff58312 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.h +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.h @@ -1,96 +1,98 @@ /*=================================================================== 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 MITKHummelProtocolEvaluation_H_HEADER_INCLUDED_ #define MITKHummelProtocolEvaluation_H_HEADER_INCLUDED_ #include <mitkPointSet.h> #include <array> namespace mitk { /**Documentation * \brief Static methods for evaluations according to the assessment protocol * for EM trackers published by Hummel et al. 2005 [1]. * * [1] Hummel, J. et al. - Design and application of an assessment protocol for electromagnetic tracking systems. Med Phys 32(7), July 2005 * * \ingroup IGT */ class HummelProtocolEvaluation { public: /** Distance error with description. */ struct HummelProtocolDistanceError {double distanceError; std::string description;}; /** Tracking volumes for evaluation. * standard: The standard volume of 9 x 10 measurment points as described in [1] * small: A small volume in the center 3 x 4 measurement points, for smaller field generators [2] * [2] Maier-Hein, L. et al. - Standardized assessment of new electromagnetic field generators in an interventional radiology setting. Med Phys 39(6), June 2012 */ - enum HummelProtocolMeasurementVolume { small, medium, standard }; + enum HummelProtocolMeasurementVolume { small, medium, medium5x6, standard }; /** Evaluates the 5 cm distances as defined by the Hummel protocol [1,2]. * @return Returns true if evaluation was successfull, false if not. * @param[out] Results Please give an empty vector. The results will be added to this vector. */ static bool Evaluate5cmDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector<HummelProtocolDistanceError> &Results); /** Evaluates the 15 cm distances as defined by the Hummel protocol [1,2]. * @return Returns true if evaluation was successfull, false if not. * @param[out] Results Please give an empty vector. The results will be added to this vector. */ static bool Evaluate15cmDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector<HummelProtocolDistanceError> &Results); /** Evaluates the 30 cm distances as defined by the Hummel protocol [1,2]. * @return Returns true if evaluation was successfull, false if not. * @param[out] Results Please give an empty vector. The results will be added to this vector. */ static bool Evaluate30cmDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector<HummelProtocolDistanceError> &Results); /** Evaluates the accumulated distances as defined by the Hummel protocol [1,2]. * @return Returns true if evaluation was successfull, false if not. * @param[out] Results Please give an empty vector. The results will be added to this vector. */ static bool EvaluateAccumulatedDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector<HummelProtocolDistanceError> &Results); /** Computes statistics (as mean, standard deviation, quantiles, min, max, etc.) on the given values. * The results are stored inside the return value. */ static std::vector<HummelProtocolDistanceError> ComputeStatistics(std::vector<HummelProtocolDistanceError> values); protected: /** Converts a pointset holding all measurement points of the hummel protocol in line-by-line order * to an array representing the hummel board. */ static std::array<std::array<mitk::Point3D, 10> ,9> ParseMatrixStandardVolume(mitk::PointSet::Pointer p); //It would be really wonderfull if we could replace std::array<std::array<mitk::Point3D, 10> ,9> by mitk::Matrix< mitk::Point3D, 9, 10 > but //unfortunatly this version does not compile under Linux. To be precise under Linux only matrices like this: mitk::Matriy<double, 9, 10> compile //even the usage of a double pointer (eg mitk::Matrix<double* , 9, 10>) does not compile. We always got an error message saying: //vnl_c_vector.h:42:49: error: invalid use of incomplete type ‘class vnl_numeric_traits<itk::Point<double, 3u> >’ //Under Windows this error does not appear there everything compiles fine. static std::array<std::array<mitk::Point3D, 5>, 5> ParseMatrixMediumVolume(mitk::PointSet::Pointer p); + static std::array<std::array<mitk::Point3D, 6>, 5> ParseMatrixMedium5x6Volume(mitk::PointSet::Pointer p); + }; } // namespace mitk #endif /* MITKHummelProtocolEvaluation_H_HEADER_INCLUDED_ */ diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.cpp b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.cpp index eaed0fb39c..0ee1bd0ac7 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.cpp @@ -1,315 +1,319 @@ /*=================================================================== 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. ===================================================================*/ #define _USE_MATH_DEFINES #include "mitkNavigationDataCSVSequentialPlayer.h" #include <QString> #include <QStringList> #include <iostream> #include <fstream> #include <math.h> mitk::NavigationDataCSVSequentialPlayer::NavigationDataCSVSequentialPlayer() : mitk::NavigationDataPlayerBase() { m_NavigationDatas = std::vector<mitk::NavigationData::Pointer>(); m_CurrentPos = 0; m_Filetype = mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV; } mitk::NavigationDataCSVSequentialPlayer::~NavigationDataCSVSequentialPlayer() { } bool mitk::NavigationDataCSVSequentialPlayer::IsAtEnd() { return m_CurrentPos >= static_cast<int>(m_NavigationDatas.size()); } void mitk::NavigationDataCSVSequentialPlayer:: SetFileName(const std::string& fileName) { this->SetNumberOfIndexedOutputs(1); FillOutputEmpty(0); MITK_INFO << "Reading file: " << fileName; m_NavigationDatas = GetNavigationDatasFromFile(fileName); this->Modified(); } void mitk::NavigationDataCSVSequentialPlayer::FillOutputEmpty(int number) { this->SetNthOutput(number, GetEmptyNavigationData()); } mitk::NavigationData::Pointer mitk::NavigationDataCSVSequentialPlayer::GetEmptyNavigationData() { mitk::NavigationData::Pointer emptyNd = mitk::NavigationData::New(); mitk::NavigationData::PositionType position; mitk::NavigationData::OrientationType orientation(0.0, 0.0, 0.0, 0.0); position.Fill(0.0); emptyNd->SetPosition(position); emptyNd->SetOrientation(orientation); emptyNd->SetDataValid(false); return emptyNd; } int mitk::NavigationDataCSVSequentialPlayer::GetNumberOfSnapshots() { return m_NavigationDatas.size(); } void mitk::NavigationDataCSVSequentialPlayer::GenerateData() { for (unsigned int index = 0; index < this->GetNumberOfOutputs(); index++) { mitk::NavigationData* output = this->GetOutput(index); if (m_CurrentPos > static_cast<int>(m_NavigationDatas.size())) { FillOutputEmpty(index); return; } output->Graft(this->m_NavigationDatas.at(m_CurrentPos)); m_CurrentPos++; } } void mitk::NavigationDataCSVSequentialPlayer::UpdateOutputInformation() { this->Modified(); // make sure that we need to be updated Superclass::UpdateOutputInformation(); } std::vector<mitk::NavigationData::Pointer> mitk::NavigationDataCSVSequentialPlayer::GetNavigationDatasFromFile(std::string filename) { std::vector<mitk::NavigationData::Pointer> returnValue = std::vector<mitk::NavigationData::Pointer>(); std::vector<std::string> fileContentLineByLine = GetFileContentLineByLine(filename); std::size_t i = m_HeaderRow ? 1 //file has a header row, so it has to be skipped when reading the NavigationDatas : 0; //file has no header row, so no need to skip the first row for ( ; i < fileContentLineByLine.size(); ++i) { returnValue.push_back(GetNavigationDataOutOfOneLine(fileContentLineByLine.at(i))); } return returnValue; } std::vector<std::string> mitk::NavigationDataCSVSequentialPlayer::GetFileContentLineByLine(std::string filename) { std::vector<std::string> readData = std::vector<std::string>(); //save old locale char * oldLocale; oldLocale = setlocale(LC_ALL, 0); //define own locale std::locale C("C"); setlocale(LC_ALL, "C"); //read file std::ifstream file; file.open(filename.c_str(), std::ios::in); if (file.good()) { //read out file file.seekg(0L, std::ios::beg); // move to begin of file int count = 0; while (!file.eof()) { std::string buffer; std::getline(file, buffer); // read out file line by line - readData.push_back(buffer); + if (!buffer.empty()) + { + readData.push_back(buffer); + //MITK_INFO << "Line: " << buffer; + } ++count; if (count == m_SampleCount) count = 0; } } file.close(); //switch back to old locale setlocale(LC_ALL, oldLocale); return readData; } mitk::NavigationData::Pointer mitk::NavigationDataCSVSequentialPlayer::GetNavigationDataOutOfOneLine(std::string line) { mitk::NavigationData::Pointer returnValue = mitk::NavigationData::New(); QString myLine = QString(line.c_str()); QStringList myLineList = myLine.split(m_SeparatorSign); mitk::Point3D position; mitk::Quaternion orientation; bool valid = false; //this is for custom csv files. You have adapt the column numbers to correctly //interpret your csv file. if (m_Filetype == mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV) { if (myLineList.size() < m_MinNumberOfColumns) { MITK_ERROR << "Error: cannot read line: only found " << myLineList.size() << " fields. Last field: " << myLineList.at(myLineList.size() - 1).toStdString(); returnValue = GetEmptyNavigationData(); return returnValue; } valid = true; //if no valid flag is given: simply set to true //############# Variant for the Aurora measurements ############### //############# (CUSTOM .csv files from MITK) ############### position[0] = myLineList.at(3).toDouble(); position[1] = myLineList.at(4).toDouble(); position[2] = myLineList.at(5).toDouble(); orientation[0] = myLineList.at(6).toDouble(); //qx orientation[1] = myLineList.at(7).toDouble(); //qy orientation[2] = myLineList.at(8).toDouble(); //qz orientation[3] = myLineList.at(9).toDouble(); //qr if(!m_RightHanded) //MITK uses a right handed coordinate system, so the position needs to be converted { position[0] = position[0]*(-1); } if (m_UseQuats) //Use Quaternions to construct the orientation of the NavigationData { orientation[0] = myLineList.at(m_Qx).toDouble(); //qx orientation[1] = myLineList.at(m_Qy).toDouble(); //qy orientation[2] = myLineList.at(m_Qz).toDouble(); //qz orientation[3] = myLineList.at(m_Qr).toDouble(); //qr } else //Use the Euler Angles to construct the orientation of the NavigationData { double azimuthAngle; double elevationAngle; double rollAngle; if(m_Azimuth < 0) //azimuth is not defined so set him to zero { azimuthAngle = 0; } else { azimuthAngle = myLineList.at(m_Azimuth).toDouble(); } if(m_Elevation < 0)// elevation is not defined so set him to zero { elevationAngle = 0; } else { elevationAngle = myLineList.at(m_Elevation).toDouble(); } if(m_Roll < 0) //roll is not defined so set him to zero { rollAngle = 0; } else { rollAngle = myLineList.at(m_Roll).toDouble(); } if (!m_EulersInRadiants) //the Euler Angles are in Degrees but MITK uses radiants so they need to be converted { azimuthAngle = azimuthAngle / 180 * M_PI; elevationAngle = elevationAngle / 180 * M_PI; rollAngle = rollAngle / 180 * M_PI; } vnl_quaternion<double> eulerQuat(rollAngle, elevationAngle, azimuthAngle); orientation = eulerQuat; } if(!m_RightHanded) //MITK uses a right handed coordinate system, so the orientation needs to be converted { //code block for conversion from left-handed to right-handed mitk::Quaternion linksZuRechtsdrehend; double rotationAngle = -M_PI; double rotationAxis[3]; rotationAxis[0] = 0; rotationAxis[1] = 0; rotationAxis[2] = 1; linksZuRechtsdrehend[3] = cos(rotationAngle / 2); linksZuRechtsdrehend[0] = rotationAxis[0] * sin(rotationAngle / 2); linksZuRechtsdrehend[1] = rotationAxis[1] * sin(rotationAngle / 2); linksZuRechtsdrehend[2] = rotationAxis[2] * sin(rotationAngle / 2); orientation = orientation * linksZuRechtsdrehend; } } //this is for MITK csv files that have been recorded with the MITK //navigation data recorder. You can also use the navigation data player //class from the MITK-IGT module instead. else if (m_Filetype == mitk::NavigationDataCSVSequentialPlayer::NavigationDataCSV) { if (myLineList.size() < 8) { MITK_ERROR << "Error: cannot read line: only found " << myLineList.size() << " fields. Last field: " << myLineList.at(myLineList.size() - 1).toStdString(); returnValue = GetEmptyNavigationData(); return returnValue; } if (myLineList.at(3).toStdString() == "1") valid = true; position[0] = myLineList.at(2).toDouble(); position[1] = myLineList.at(3).toDouble(); position[2] = myLineList.at(4).toDouble(); orientation[0] = myLineList.at(5).toDouble(); //qx orientation[1] = myLineList.at(6).toDouble(); //qy orientation[2] = myLineList.at(7).toDouble(); //qz orientation[3] = myLineList.at(8).toDouble(); //qr } returnValue->SetDataValid(valid); returnValue->SetPosition(position); returnValue->SetOrientation(orientation); return returnValue; } void mitk::NavigationDataCSVSequentialPlayer::SetOptions(bool rightHanded, char separatorSign, int sampleCount, bool headerRow, int xPos, int yPos, int zPos, bool useQuats, int qx, int qy, int qz, int qr, int azimuth, int elevation, int roll, bool eulerInRadiants, int minNumberOfColumns) { m_RightHanded = rightHanded; m_SeparatorSign = separatorSign; m_SampleCount = sampleCount; m_HeaderRow = headerRow; m_XPos = xPos; m_YPos = yPos; m_ZPos = zPos; m_UseQuats = useQuats; m_Qx = qx; m_Qy = qy; m_Qz = qz; m_Qr = qr; m_Azimuth = azimuth; m_Elevation = elevation; m_Roll = roll; m_EulersInRadiants = eulerInRadiants; m_MinNumberOfColumns = minNumberOfColumns; }