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 defd89e62d..7b8d6d8729 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 @@ -1,1237 +1,1243 @@ /*========================================================================= 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. =========================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkIGTTrackingDataEvaluationView.h" #include "QmitkStdMultiWidget.h" // Qt #include #include #include // MITK #include "mitkNavigationDataCSVSequentialPlayer.h" #include #include #include #include #include //ITK #include //VNL #include //vtk headers #include #include #include const std::string QmitkIGTTrackingDataEvaluationView::VIEW_ID = "org.mitk.views.igttrackingdataevaluation"; QmitkIGTTrackingDataEvaluationView::QmitkIGTTrackingDataEvaluationView() : QmitkFunctionality() , m_Controls(0) , m_MultiWidget(NULL) , m_scalingfactor(1) { m_CSVtoXMLInputFilenameVector = std::vector(); m_CSVtoXMLOutputFilenameVector = std::vector(); } 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 rotationVec; //adapt for Aurora 5D tools: [0,0,1000] rotationVec[0] = 0; //X rotationVec[1] = 0; //Y rotationVec[2] = 10000; //Z std::vector allOrientationErrors; for (int i = 0; i < (OrientationVector.size() - 1); i++) { double AngleBetweenTwoQuaternions = mitk::StaticIGTHelperFunctions::GetAngleBetweenTwoQuaterions(OrientationVector.at(i), OrientationVector.at(i+1), rotationVec); double AngularError = abs(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 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()); 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(m_Controls->m_ReferencePointSetComboBox->GetSelectedNode()->GetData()); mitk::PointSet::Pointer measurement = dynamic_cast(m_Controls->m_MeasurementPointSetComboBox->GetSelectedNode()->GetData()); //convert point sets to vtk poly data vtkSmartPointer sourcePoints = vtkSmartPointer::New(); vtkSmartPointer targetPoints = vtkSmartPointer::New(); for (int i = 0; iGetSize(); 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 transform = vtkSmartPointer::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 rotationFloat = itk::Matrix(); itk::Vector translationFloat = itk::Vector(); itk::Matrix rotationDouble = itk::Matrix(); itk::Vector translationDouble = itk::Vector(); vtkSmartPointer 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(); } 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 (int i = 0; i < m_FilenameVector.size(); i++) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = mitk::NavigationDataCSVSequentialPlayer::New(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //check if the stream is valid and skip file if not /* if (!myPlayer->GetStreamValid()) { MITK_ERROR << "Error in file " << m_FilenameVector.at(i) << ": " << myPlayer->GetErrorMessage() << " ; Skipping file!"; continue; } */ //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (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(); } //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 (int i = 0; i < m_FilenameVector.size(); i++) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = mitk::NavigationDataCSVSequentialPlayer::New(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //check if the stream is valid and skip file if not /* if (!myPlayer->GetStreamValid()) { MITK_ERROR << "Error in file " << m_FilenameVector.at(i) << ": " << myPlayer->GetErrorMessage() << " ; Skipping file!"; continue; } */ //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 { /* Drehen um eine Achse um das "Umschlagen" zu vermeiden itk::Matrix rot180degreeAroundY; rot180degreeAroundY.Fill(0); rot180degreeAroundY[0][0] = -1; rot180degreeAroundY[1][1] = 1; rot180degreeAroundY[2][2] = -1; point1 = rot180degreeAroundY * point1; point2 = rot180degreeAroundY * point2; point3 = rot180degreeAroundY * point3; */ vtkSmartPointer transform = vtkSmartPointer::New(); vtkSmartPointer sourcePoints = vtkSmartPointer::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 targetPoints = vtkSmartPointer::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 = NULL; } void QmitkIGTTrackingDataEvaluationView::OnAddToCurrentList() { //read in files QStringList files = QFileDialog::getOpenFileNames(NULL, "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); } /* //save old locale char * oldLocale; oldLocale = setlocale( LC_ALL, 0 ); //define own locale std::locale C("C"); setlocale( LC_ALL, "C" ); */ //TODO: check if this is needed here, and load old locale if yes /* //read file std::ifstream file; file.open(filename.toStdString().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) { std::string thisFilename = ""; if (m_Controls->m_AddPath->isChecked()) thisFilename = m_Controls->m_ListPath->text().toStdString(); thisFilename.append(buffer); m_FilenameVector.push_back(thisFilename); } } } */ //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(); m_FilenameVector.clear(); OnAddToCurrentList(); } void QmitkIGTTrackingDataEvaluationView::OnEvaluateDataAll() { std::vector 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 { volume = mitk::HummelProtocolEvaluation::small; 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 jitterValues; //write output file header WriteHeader(); //start loop and iterate through all files of list for (int i = 0; i < m_FilenameVector.size(); i++) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = mitk::NavigationDataCSVSequentialPlayer::New(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //check if the stream is valid and skip file if not /* if (!myPlayer->GetStreamValid()) { MITK_ERROR << "Error in file " << m_FilenameVector.at(i) << ": " << myPlayer->GetErrorMessage() << " ; Skipping file!"; continue; } */ //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (int j = 0; j < myPlayer->GetNumberOfOutputs(); j++) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); } - //update pipline until number of samlples is reached + 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(); //Debug output: //std::cout.precision(5); //std::cout << "Euler " << j << ";" << myPlayer->GetOutput()->GetOrientation().rotation_euler_angles()[0] << ";" << myPlayer->GetOutput()->GetOrientation().rotation_euler_angles()[1] << ";" << myPlayer->GetOutput()->GetOrientation().rotation_euler_angles()[2] << "\n"; } //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 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 (int 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 = mitk::NavigationDataCSVSequentialPlayer::New(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //check if the stream is valid and skip file if not /* if (!myPlayer->GetStreamValid()) { MITK_ERROR << "Error in file " << m_FilenameVector.at(i) << ": " << myPlayer->GetErrorMessage() << " ; Skipping file!"; continue; } */ //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 (int i = 0; i < m_FilenameVector.size(); i++) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = mitk::NavigationDataCSVSequentialPlayer::New(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //check if the stream is valid and skip file if not /* if (!myPlayer->GetStreamValid()) { MITK_ERROR << "Error in file " << m_FilenameVector.at(i) << ": " << myPlayer->GetErrorMessage() << " ; Skipping file!"; continue; } */ //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (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 (int i = 0; i < m_FilenameVector.size(); i++) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = mitk::NavigationDataCSVSequentialPlayer::New(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //check if the stream is valid and skip file if not /* if (!myPlayer->GetStreamValid()) { MITK_ERROR << "Error in file " << m_FilenameVector.at(i) << ": " << myPlayer->GetErrorMessage() << " ; Skipping file!"; } else */ { //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (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(); /* if (!myPlayer->GetStreamValid()) { MITK_ERROR << "Error in file " << m_FilenameVector.at(i) << ": " << myPlayer->GetErrorMessage() << " ; Skipping file!"; continue; } */ } //if (!myPlayer->IsAtEnd()) continue; //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 secondPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * secondPoint.Get_vnl_vector() + meanPos.Get_vnl_vector(); mitk::Point3D secondPointTransformedMITK; mitk::FillVector3D(secondPointTransformedMITK, secondPointTransformed[0], secondPointTransformed[1], secondPointTransformed[2]); mitk::FillVector3D(thirdPoint, 0, 4, 0); //Y vnl_vector thirdPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * thirdPoint.Get_vnl_vector() + meanPos.Get_vnl_vector(); mitk::Point3D thirdPointTransformedMITK; mitk::FillVector3D(thirdPointTransformedMITK, thirdPointTransformed[0], thirdPointTransformed[1], thirdPointTransformed[2]); mitk::FillVector3D(fourthPoint, 0, 0, 6); //Z vnl_vector fourthPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * fourthPoint.Get_vnl_vector() + meanPos.Get_vnl_vector(); 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 (int i = 0; i < m_CSVtoXMLInputFilenameVector.size(); i++) { int lines = 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 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 (int 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(NULL, 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(NULL, 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 QmitkIGTTrackingDataEvaluationView::GetMeanOrientationsOfAllData(std::vector allData, bool useSLERP) { std::vector returnValue; for (auto dataSet : allData) { if (useSLERP) returnValue.push_back(GetSLERPAverage(dataSet)); else returnValue.push_back(dataSet->GetQuaternionMean(0)); } return returnValue; } std::vector QmitkIGTTrackingDataEvaluationView::GetAllDataFromUIList() { std::vector EvaluationDataCollection; //start loop and iterate through all files of list: store the evaluation data for (int i = 0; i < m_FilenameVector.size(); i++) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = mitk::NavigationDataCSVSequentialPlayer::New(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //check if the stream is valid and skip file if not /* if (!myPlayer->GetStreamValid()) { MITK_ERROR << "Error in file " << m_FilenameVector.at(i) << ": " << myPlayer->GetErrorMessage() << " ; Skipping file!"; } else */ { //connect pipeline for (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(NULL); myPlayer = NULL; EvaluationDataCollection.push_back(myEvaluationFilter); } return EvaluationDataCollection; } void QmitkIGTTrackingDataEvaluationView::CalculateDifferenceAngles() { //Get all data from UI std::vector 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 (int i = 0; i < m_FilenameVector.size(); i++) { pos1 = QString::fromStdString(itksys::SystemTools::GetFilenameWithoutLastExtension(m_FilenameVector.at(i))); for (int 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 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) { //double PI = 3.1415926535897932384626433832795; //double angle_degree = angle * 180 / PI; m_CurrentAngleDifferencesWriteFile << "Angle between " << pos1 << " and " << pos2 << ";" << idx1 << ";" << idx2 << ";" << angle << "\n";//<< ";" << angle_degree << "\n"; MITK_INFO << "Angle: " << angle; } std::vector QmitkIGTTrackingDataEvaluationView::GetNavigationDatasFromFile(std::string filename) { std::vector returnValue = std::vector(); std::vector fileContentLineByLine = GetFileContentLineByLine(filename); for (int i = 1; i < fileContentLineByLine.size(); i++) //skip header so start at 1 { returnValue.push_back(GetNavigationDataOutOfOneLine(fileContentLineByLine.at(i))); } return returnValue; } std::vector QmitkIGTTrackingDataEvaluationView::GetFileContentLineByLine(std::string filename) { std::vector readData = std::vector(); //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; double time = myLineList.at(1).toDouble(); 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->SetTimeStamp(time); 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 quaternions = std::vector(); 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 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(); } 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 c0b5a5463e..667811220a 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 @@ -1,309 +1,325 @@ /*=================================================================== 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 #include #include #include #include mitk::NavigationDataCSVSequentialPlayer::NavigationDataCSVSequentialPlayer() : mitk::NavigationDataPlayerBase() { m_NavigationDatas = std::vector(); m_CurrentPos = 0; m_Filetype = mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV; } mitk::NavigationDataCSVSequentialPlayer::~NavigationDataCSVSequentialPlayer() { } bool mitk::NavigationDataCSVSequentialPlayer::IsAtEnd() { if (m_CurrentPos >= m_NavigationDatas.size()) return true; else return false; } void mitk::NavigationDataCSVSequentialPlayer:: SetFileName(const std::string& fileName) { this->SetNumberOfOutputs(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 > 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::NavigationDataCSVSequentialPlayer::GetNavigationDatasFromFile(std::string filename) { std::vector returnValue = std::vector(); std::vector fileContentLineByLine = GetFileContentLineByLine(filename); for (int i = 1; (i < fileContentLineByLine.size()); i++) //skip header so start at 1 { returnValue.push_back(GetNavigationDataOutOfOneLine(fileContentLineByLine.at(i))); } return returnValue; } std::vector mitk::NavigationDataCSVSequentialPlayer::GetFileContentLineByLine(std::string filename) { std::vector readData = std::vector(); //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; + int count2 = 0; while (!file.eof()) { std::string buffer; std::getline(file, buffer); // read out file line by line - if (buffer.size() > 0) readData.push_back(buffer); + + //for Polhemus tracker: just take every 24th sample + if (count == 0) if (buffer.size() > 0) + { + MITK_INFO << "read(" << count2 << "): " << buffer.substr(0,30); + count2++; + readData.push_back(buffer); + } + + count++; if (count == 24) 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(','); mitk::Point3D position; mitk::Quaternion orientation; bool valid = false; double time; //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() < 10) { 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 */ //Variant for the polhemus measurements in August 2016 //(.csv files from the polhemus software) //Important: due to the documentation, Polhemus uses //a left handed coordinate system while MITK uses a //right handed. A conversion is not included in this //read in method yet, because this is not required //for this special rotation evaliation (no matter //if it turns 11.25 degree to left or right). For //other usage this might be important to adapt! + position[0] = myLineList.at(4).toDouble(); position[1] = myLineList.at(5).toDouble(); position[2] = myLineList.at(6).toDouble(); //Doesn't work... don't know how to interpret the //Polhemus quaternions. They are seem to different //different to other quaternions (NDI, Claron, etc.) //http://www.mathepedia.de/Quaternionen.aspx /* double qr = myLineList.at(7).toDouble(); double qx = myLineList.at(8).toDouble(); double qy = myLineList.at(9).toDouble(); double qz = myLineList.at(10).toDouble(); vnl_quaternion newQuat(qx, qy, qz, qr); orientation = newQuat; orientation.normalize();*/ /* orientation[3] = qr; //qr orientation[0] = qx; //qx orientation[1] = qy; //qy orientation[2] = qz; //qz orientation.normalize(); */ //Using Euler angles instead does work //azimuth: rotation about Z axis of reference frame double azimuthAngle = (myLineList.at(11).toDouble() / 180 * M_PI); //elevation: rotation about Y' axis (transformed Y axis of sonsor frame) double elevationAngle = (myLineList.at(12).toDouble() / 180 * M_PI); //roll: rotation about X axis of sensor frame double rollAngle = (myLineList.at(13).toDouble() / 180 * M_PI); vnl_quaternion eulerQuat(rollAngle, elevationAngle, azimuthAngle); orientation = eulerQuat; /* //code block for conversion from axis-angular representation double rotationAngle = myLineList.at(7).toDouble(); double rotationAxis[3]; rotationAxis[0] = myLineList.at(8).toDouble(); rotationAxis[1] = myLineList.at(9).toDouble(); rotationAxis[2] = myLineList.at(10).toDouble(); double betragRotationAxis = sqrt(pow(rotationAxis[0], 2) + pow(rotationAxis[1], 2) + pow(rotationAxis[2], 2)); rotationAngle /= betragRotationAxis; rotationAxis[0] /= betragRotationAxis; rotationAxis[1] /= betragRotationAxis; rotationAxis[2] /= betragRotationAxis; double qr = cos(rotationAngle/2); double qx = rotationAxis[0] * sin(rotationAngle/2); double qy = rotationAxis[1] * sin(rotationAngle/2); double qz = rotationAxis[1] * sin(rotationAngle/2); */ /* //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; } time = myLineList.at(2).toDouble(); 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->SetTimeStamp(time); //DOES NOT WORK ANY MORE... CANNOT SET TIME TO itk::timestamp CLASS returnValue->SetDataValid(valid); returnValue->SetPosition(position); returnValue->SetOrientation(orientation); return returnValue; } diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.h b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.h index eb46af805c..011e75f06b 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.h +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.h @@ -1,112 +1,114 @@ /*=================================================================== 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 MITKNavigationDataCSVSequentialPlayer_H_HEADER_INCLUDED_ #define MITKNavigationDataCSVSequentialPlayer_H_HEADER_INCLUDED_ #include #include "tinyxml.h" namespace mitk { /**Documentation * \brief This class is a NavigationDataPlayer which can play CSV formatted * files in sequential order, which means it doesn't care about timestamps and just * outputs the navigationdatas in their sequential order. * * It is thought to interpret custom csv files. To do so please adapt the column * numbers of position and orientation in the internal method GetNavigationDataOutOfOneLine(). * * So far only one (the first) tool is read in as required for the hummel protocol measurements. * * This class can also interpret MITK style csv files (set filetype to NavigationDataCSV), but * you can also use the MITK navigation data player class inside the MITK-IGT module which * is newer and better maintained. * * \ingroup IGT */ class NavigationDataCSVSequentialPlayer : public NavigationDataPlayerBase { public: mitkClassMacro(NavigationDataCSVSequentialPlayer, NavigationDataPlayerBase); itkNewMacro(Self); /** * \brief sets the file name and path (if XMLString is set, this is neglected) */ void SetFileName(const std::string& _FileName); /** * \brief returns the file name and path */ itkGetStringMacro(FileName); enum Filetype { NavigationDataCSV, //for csv files from the MITK navigation data player ManualLoggingCSV //for custum csv files }; /** * \brief Sets the file type. ManualLoggingCSV is default and is thought for your * custom csv files. You can also set it to NavigationDataCSV, then this * player interprets MITK style csv files. */ itkSetMacro(Filetype, Filetype); /** * \return Returns true if the player reached the end of the file. */ bool IsAtEnd(); /** * \brief Used for pipeline update just to tell the pipeline * that we always have to update */ virtual void UpdateOutputInformation(); + int mitk::NavigationDataCSVSequentialPlayer::GetNumberOfSnapshots(); + protected: NavigationDataCSVSequentialPlayer(); virtual ~NavigationDataCSVSequentialPlayer(); /// /// do the work here /// virtual void GenerateData(); std::string m_FileName; int m_CurrentPos; Filetype m_Filetype; //member for the navigation datas which were read (only one output is supported at the moment) std::vector m_NavigationDatas; std::vector GetNavigationDatasFromFile(std::string filename); std::vector GetFileContentLineByLine(std::string filename); mitk::NavigationData::Pointer GetNavigationDataOutOfOneLine(std::string line); void FillOutputEmpty(int number); mitk::NavigationData::Pointer GetEmptyNavigationData(); }; } // namespace mitk #endif /* MITKNavigationDataCSVSequentialPlayer_H_HEADER_INCLUDED_ */