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 381ae30b54..284e7fa363 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 @@ -1,1175 +1,1305 @@ /*========================================================================= 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 // Blueberry #include #include // Qmitk #include "QmitkIGTTrackingDataEvaluationView.h" #include "QmitkStdMultiWidget.h" // Qt #include #include #include // MITK #include "mitkNavigationDataCSVSequentialPlayer.h" #include +#include #include -#include #include -#include - +#include -//ITK +// ITK #include -//VNL +// VNL #include -//vtk headers +// vtk headers +#include #include #include -#include const std::string QmitkIGTTrackingDataEvaluationView::VIEW_ID = "org.mitk.views.igttrackingdataevaluation"; QmitkIGTTrackingDataEvaluationView::QmitkIGTTrackingDataEvaluationView() - : QmitkFunctionality() - , m_Controls(0) - , m_MultiWidget(nullptr) - , m_scalingfactor(1) + : QmitkFunctionality(), m_Controls(0), m_MultiWidget(nullptr), m_scalingfactor(1) { m_CSVtoXMLInputFilenameVector = std::vector(); m_CSVtoXMLOutputFilenameVector = std::vector(); } QmitkIGTTrackingDataEvaluationView::~QmitkIGTTrackingDataEvaluationView() +{} + +void QmitkIGTTrackingDataEvaluationView::OnLoadMITKPresets() +{ + m_Controls->m_ScalingFactor->setValue(1.0); + m_Controls->m_SeparatorSign->setText(";"); + m_Controls->m_SampleCount->setValue(1.0); + m_Controls->m_HeaderRow->setChecked(true); + m_Controls->m_RigthHanded->setChecked(true); + m_Controls->m_XPos->setValue(3); + m_Controls->m_YPos->setValue(4); + m_Controls->m_ZPos->setValue(5); + m_Controls->m_UseQuats->setChecked(true); + m_Controls->m_Qx->setValue(6); + m_Controls->m_Qy->setValue(7); + m_Controls->m_Qz->setValue(8); + m_Controls->m_Qr->setValue(9); +} + +void QmitkIGTTrackingDataEvaluationView::OnLoadPolhemusPresets() { + m_Controls->m_ScalingFactor->setValue(10.0); + m_Controls->m_SeparatorSign->setText(","); + m_Controls->m_SampleCount->setValue(24.0); + m_Controls->m_HeaderRow->setChecked(false); + m_Controls->m_RigthHanded->setChecked(true); + m_Controls->m_XPos->setValue(4); + m_Controls->m_YPos->setValue(5); + m_Controls->m_ZPos->setValue(6); + m_Controls->m_UseEuler->setChecked(true); + m_Controls->m_Azimuth->setValue(11); + m_Controls->m_Elevation->setValue(12); + m_Controls->m_Roll->setValue(13); + m_Controls->m_Radiants->setChecked(true); } 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_loadMITKPresets, SIGNAL(clicked()), this, SLOT(OnLoadMITKPresets())); + connect(m_Controls->m_loadPolhemusPresets, SIGNAL(clicked()), this, SLOT(OnLoadPolhemusPresets())); + 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 + // 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 + // Get all data from UI auto EvaluationDataCollection = GetAllDataFromUIList(); - //Compute mean Quaternions + // Compute mean Quaternions auto OrientationVector = GetMeanOrientationsOfAllData(EvaluationDataCollection); - //Compute Rotations + // Compute Rotations itk::Vector 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 + // 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 allOrientationErrors; - for (std::vector::size_type i = 0; i < OrientationVector.size() - 1; ++i) + for (std::vector::size_type i = 0; + i < OrientationVector.size() - 1; + ++i) { - double AngleBetweenTwoQuaternions = mitk::StaticIGTHelperFunctions::GetAngleBetweenTwoQuaterions(OrientationVector.at(i), OrientationVector.at(i+1), rotationVec); + 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() }); + allOrientationErrors.push_back({AngularError, description.str()}); MITK_INFO << description.str() << ": " << AngularError; } - //compute statistics + // 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; } + 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]"}); + // 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"; + 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 + 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++) + for (int i = 0; i < reference->GetSize(); i++) { - double point[3] = { reference->GetPoint(i)[0], reference->GetPoint(i)[1], reference->GetPoint(i)[2] }; + 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] }; + double point_targets[3] = {measurement->GetPoint(i)[0], measurement->GetPoint(i)[1], measurement->GetPoint(i)[2]}; targetPoints->InsertNextPoint(point_targets); } - //compute transform + // compute transform vtkSmartPointer transform = vtkSmartPointer::New(); transform->SetSourceLandmarks(sourcePoints); transform->SetTargetLandmarks(targetPoints); transform->SetModeToRigidBody(); transform->Modified(); transform->Update(); - //compute FRE of transform + // 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 + // 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++) + 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 + // 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()->SetIndexToWorldTransform( + mitkTransform); m_Controls->m_ReferencePointSetComboBox->GetSelectedNode()->GetData()->GetGeometry()->Modified(); - //write to file + // 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 FRE_Error; - FRE_Error.push_back({ FRE, "FRE after grid matching [mm]" }); + 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 + // start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { - //create navigation data player + // 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 + // check if the stream is valid and skip file if not - //create evaluation filter + // create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); - //connect pipeline + // 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 + // 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 + // 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; + 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 + // start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { - //create navigation data player + // create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); - //open file header + // 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"; + // 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 + // 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 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)) + 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 { - 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); + 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; + break; } m_CurrentWriteFile << i << ";"; - m_CurrentWriteFile << currentNavData->GetTimeStamp() << ";"; //IMPORTANT: change to GetIGTTimeStamp in new version! + 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 + // 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 + // read in files QStringList files = QFileDialog::getOpenFileNames(nullptr, "Select one or more files to open", "/", "CSV (*.csv)"); - if (files.isEmpty()) return; + 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 + // 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); } + 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; + 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 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 + // 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 + // 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 + // write output file header WriteHeader(); - //start loop and iterate through all files of list + // start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { - //create navigation data player + // create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); - //create evaluation filter + // create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); - //connect pipeline + // connect pipeline 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!"; + 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 + // 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 "<GetPositionErrorRMS(0); + 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" }); + // store all jitter values in separate vector for statistics + jitterValues.push_back({myEvaluationFilter->GetPositionErrorRMS(0), "RMS"}); - //write result to output file + // write result to output file WriteDataSet(myEvaluationFilter, m_FilenameVector.at(i)); } - //close output file for single data + // close output file for single data m_CurrentWriteFile.close(); - //compute statistics - std::vector jitterStatistics = mitk::HummelProtocolEvaluation::ComputeStatistics(jitterValues); + // compute statistics + std::vector jitterStatistics = + mitk::HummelProtocolEvaluation::ComputeStatistics(jitterValues); MITK_INFO << "## Jitter (RMS) statistics: ##"; - for (auto jitterStat : jitterStatistics) {MITK_INFO << jitterStat.description << ": " << jitterStat.distanceError;} + for (auto jitterStat : jitterStatistics) + { + MITK_INFO << jitterStat.description << ": " << jitterStat.distanceError; + } - //write statistic results to separate file + // write statistic results to separate file std::stringstream filenameJitterStat; - filenameJitterStat << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".resultsJitterStatistics.csv"; + 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(); + // 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 + // 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 + // create point set for this file mitk::PointSet::Pointer thisPointSet = mitk::PointSet::New(); - //create navigation data player + // 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 + // 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 + // 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 + // start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { - //create navigation data player + // create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); - //create evaluation filter + // 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)); } + // 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(); } + // 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 + // 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 + // 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 + // start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { - //create navigation data player + // create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); - //create evaluation filter + // 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)); } + // 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 + // 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) + // 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.GetVnlVector() + meanPos.GetVnlVector(); + mitk::FillVector3D(secondPoint, 2, 0, 0); // X + vnl_vector 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( + 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.GetVnlVector() + meanPos.GetVnlVector(); + mitk::FillVector3D(thirdPoint, 0, 4, 0); // Y + vnl_vector 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( + 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.GetVnlVector() + meanPos.GetVnlVector(); + mitk::FillVector3D(fourthPoint, 0, 0, 6); // Z + vnl_vector 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::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)"; + 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()); + { // 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 + 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 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); + 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; + // 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; + // 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_settingPosErrorMean->isChecked()) + m_CurrentWriteFile << "PositionError_Mean;"; - if (m_Controls->m_settingPosErrorStabw->isChecked()) m_CurrentWriteFile << "PositionError_StandDev;"; + if (m_Controls->m_settingPosErrorStabw->isChecked()) + m_CurrentWriteFile << "PositionError_StandDev;"; - if (m_Controls->m_settingPosErrorSampleStabw->isChecked()) m_CurrentWriteFile << "PositionError_SampleStandDev;"; + if (m_Controls->m_settingPosErrorSampleStabw->isChecked()) + m_CurrentWriteFile << "PositionError_SampleStandDev;"; - if (m_Controls->m_settingPosErrorRMS->isChecked()) m_CurrentWriteFile << "PositionError_RMS;"; + if (m_Controls->m_settingPosErrorRMS->isChecked()) + m_CurrentWriteFile << "PositionError_RMS;"; - if (m_Controls->m_settingPosErrorMedian->isChecked()) m_CurrentWriteFile << "PositionError_Median;"; + 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) +void QmitkIGTTrackingDataEvaluationView::WriteDataSet(mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter, + std::string dataSetName) { - if (myEvaluationFilter->GetNumberOfOutputs() == 0) m_CurrentWriteFile << "Error: no input \n"; + 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_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 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)); + 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 + // 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 + // create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); - //create evaluation filter + // create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); - //connect pipeline + // 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 + // 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 + // 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); + // 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 + // write header WriteDifferenceAnglesHeader(); - //compute angle differences + // compute angle differences QString pos1 = "invalid"; QString pos2 = "invalid"; - //now iterate through all evaluation data and calculate the angles + // 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 + // compute slerp average q1 = GetSLERPAverage(EvaluationDataCollection.at(i)); q2 = GetSLERPAverage(EvaluationDataCollection.at(j)); } else { - //compute arithmetic average + // 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 + // 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 + // 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) +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"; + m_CurrentAngleDifferencesWriteFile << "Angle between " << pos1 << " and " << pos2 << ";" << idx1 << ";" << idx2 << ";" + << angle << "\n"; MITK_INFO << "Angle: " << angle; } -std::vector QmitkIGTTrackingDataEvaluationView::GetNavigationDatasFromFile(std::string filename) +std::vector QmitkIGTTrackingDataEvaluationView::GetNavigationDatasFromFile( + std::string filename) { std::vector returnValue = std::vector(); std::vector fileContentLineByLine = GetFileContentLineByLine(filename); - for (std::size_t i = 1; i < fileContentLineByLine.size(); ++i) //skip header so start at 1 + 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 QmitkIGTTrackingDataEvaluationView::GetFileContentLineByLine(std::string filename) { std::vector readData = std::vector(); - //save old locale - char * oldLocale; + // save old locale + char *oldLocale; oldLocale = setlocale(LC_ALL, 0); - //define own locale + // define own locale std::locale C("C"); setlocale(LC_ALL, "C"); - //read file + // 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 + // 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); + 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 + // 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; + 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 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 + // 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 + // 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) +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"; + 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; + 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/QmitkIGTTrackingDataEvaluationView.h b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.h index 28271da295..2240d0d872 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.h +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.h @@ -1,142 +1,144 @@ /*=================================================================== 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 QmitkIGTTrackingDataEvaluationView_h #define QmitkIGTTrackingDataEvaluationView_h #include #include #include "ui_QmitkIGTTrackingDataEvaluationViewControls.h" #include "mitkHummelProtocolEvaluation.h" #include #include "mitkNavigationDataCSVSequentialPlayer.h" /*! \brief QmitkIGTTrackingDataEvaluationView \warning This application module is not yet documented. Use "svn blame/praise/annotate" and ask the author to provide basic documentation. \sa QmitkFunctionality \ingroup Functionalities */ class QmitkIGTTrackingDataEvaluationView : public QmitkFunctionality { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; QmitkIGTTrackingDataEvaluationView(); virtual ~QmitkIGTTrackingDataEvaluationView(); virtual void CreateQtPartControl(QWidget *parent); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); protected slots: void OnLoadFileList(); void OnAddToCurrentList(); void OnEvaluateData(); void OnEvaluateDataAll(); void OnGeneratePointSet(); void OnGeneratePointSetsOfSinglePositions(); void OnGenerateRotationLines(); void OnGenerateGroundTruthPointSet(); void OnConvertCSVtoXMLFile(); void OnCSVtoXMLLoadInputList(); void OnCSVtoXMLLoadOutputList(); void OnPerfomGridMatching(); void OnComputeRotation(); + void OnLoadMITKPresets(); + void OnLoadPolhemusPresets(); /** Reads in exactly three position files als reference. */ void OnOrientationCalculation_CalcRef(); /** Uses always three positions (1,2,3: first orientation; 4,5,6: second orientation; and so on) in every file to calcualte a orientation. */ void OnOrientationCalculation_CalcOrientandWriteToFile(); protected: Ui::QmitkIGTTrackingDataEvaluationViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; std::vector m_FilenameVector; void MessageBox(std::string s); std::fstream m_CurrentWriteFile; void WriteHeader(); void WriteDataSet(mitk::NavigationDataEvaluationFilter::Pointer evaluationFilter, std::string dataSetName); //members for orientation calculation mitk::Point3D m_RefPoint1; mitk::Point3D m_RefPoint2; mitk::Point3D m_RefPoint3; double m_scalingfactor; //scaling factor for visualization, 1 by default //angle diffrences: seperated file std::fstream m_CurrentAngleDifferencesWriteFile; void CalculateDifferenceAngles(); void WriteDifferenceAnglesHeader(); void WriteDifferenceAnglesDataSet(std::string pos1, std::string pos2, int idx1, int idx2, double angle); void writeToFile(std::string filename, std::vector values); //different help methods to read a csv logging file std::vector GetNavigationDatasFromFile(std::string filename); std::vector GetFileContentLineByLine(std::string filename); mitk::NavigationData::Pointer GetNavigationDataOutOfOneLine(std::string line); //help method to sonstruct the NavigationDataCSVSequentialPlayer filled with all the options from the UI mitk::NavigationDataCSVSequentialPlayer::Pointer ConstructNewNavigationDataPlayer(); //CSV to XML members std::vector m_CSVtoXMLInputFilenameVector; std::vector m_CSVtoXMLOutputFilenameVector; //returns the number of converted lines int ConvertOneFile(std::string inputFilename, std::string outputFilename); /** @brief calculates the angle in the plane perpendicular to the rotation axis of the two quaterions. */ double GetAngleBetweenTwoQuaterions(mitk::Quaternion a, mitk::Quaternion b); /** @brief calculates the slerp average of a set of quaternions which is stored in the navigation data evaluation filter */ mitk::Quaternion GetSLERPAverage(mitk::NavigationDataEvaluationFilter::Pointer); /** @brief Stores the mean positions of all evaluated data */ mitk::PointSet::Pointer m_PointSetMeanPositions; /** @return returns the mean orientation of all given data */ std::vector GetMeanOrientationsOfAllData(std::vector allData, bool useSLERP = false); /** @return returns all data read from the data list as NavigationDataEvaluationFilters */ std::vector GetAllDataFromUIList(); }; #endif // _QMITKIGTTRACKINGDATAEVALUATIONVIEW_H_INCLUDED 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 78393e3591..f7b42b6a64 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 @@ -1,1787 +1,1810 @@ QmitkIGTTrackingDataEvaluationViewControls 0 0 448 955 0 0 QmitkTemplate 0 Evaluation Input File List (recorded NavigationData / *.csv): Qt::Horizontal 40 20 120 0 Load New List Qt::Horizontal 40 20 120 0 Add To Current List Qt::Horizontal (1) - VISUALIZATION - of all data sets: Prefix for Data Nodes: Generate PointSet of Mean Positions Generate PointSets of Single Positions Generate Lines for Rotation Qt::Horizontal (3) - JITTER - Evaluation per file / data set: Result CSV Filename: D:/tmp/output.csv Qt::Horizontal 40 20 220 0 200 50 COMPUTE RESULTS PER DATA SET Qt::Horizontal 40 20 Qt::Horizontal (3) - ACCURACY - Evaluation of all data sets: Qt::Horizontal 40 20 220 0 200 50 COMPUTE RESULTS OF ALL DATA Qt::Horizontal 40 20 Qt::Horizontal (4) - GRID MATCHING - Evaluation of all data sets: Reference PointSet: Qt::Horizontal 40 20 150 0 Measurement PointSet: Qt::Horizontal 40 20 150 0 Qt::Horizontal 40 20 220 0 200 50 PERFOM GRID MATCHING Qt::Horizontal 40 20 Qt::Horizontal (5) - ROTATION - Evaluation of all data sets: Qt::Horizontal 40 20 220 0 200 50 COMPUTE ROTATION ERRORS Qt::Horizontal 40 20 Qt::Vertical QSizePolicy::Expanding 20 220 Settings 0 0 - 420 - 843 + 406 + 812 General - - - - - - Scaling Factor for Visualization: - - - - - - - Qt::Horizontal - - - - 38 - 20 - - - - - - - - 1.000000000000000 - - - - - Number of samples to analyze: Qt::Horizontal 60 20 1000000 150 Qt::Horizontal Tracking Volume: Standard Volume (10 X 9 Positions) true Medium Volume (5 X 5 Positions) Medium Volume (5 X 6 Positions) Small Volume (3 X 4 Positions) Qt::Horizontal Rotation Evaluation: Rotation Vector: Qt::Horizontal 40 20 X 99999 Qt::Horizontal 40 20 Y 99999 Qt::Horizontal 40 20 Z 99999 10000 Qt::Vertical 20 40 0 0 - 180 - 584 + 406 + 812 .csv file input options + + + + Presets + + + + + + Load MITK tracking data csv file presets + + + + + + + Load Polhemus csv file presets + + + + + + File Options: + + + + + + Scaling factor to convert to mm : + + + + + + + Qt::Horizontal + + + + 38 + 20 + + + + + + + + 1.000000000000000 + + + + + Separator in the csv file: Qt::Horizontal 60 20 0 0 40 16777215 ; 1 Use every n-th smaple n: Qt::Horizontal 40 20 1 The csv file has a header row true Type of Coordinate System: Left handed Right handed true Position and Orientation Options: Y 4 Z 5 X 3 Coordinate: Colum number: Use Quaternions for Orientation true Qr 8 Qy 9 7 6 Qx Qz Quaternion component: Column number: Use Euler Angles for Orientation Column number: Azimuth -1 Roll Angle: -1 Elevation -1 Unity for Euler Angles: Radiants true Degrees false 0 0 - 217 - 452 + 287 + 512 Output per data set Position Mean (x,y,z) true Standard Deviation (x,y,z) Sample Standard Deviation (x,y,z) Orientation Quaternion Mean (qx,qy,qz,qr) Quaternion Mean (SLERP) Quaternion Standard Deviation (qx,qy,qz,qr) Euler Mean (tx,ty,tz) Difference Angles to all other Positions Difference Angles to all other Positions (SLERP) Position Error Mean Standard Deviation Sample Standard Deviation RMS true Median Min/Max Orientation Error Euler RMS Tools Point Set Ground Truth Generator Generate 1 999 10 X 1 999 9 Point Set Qt::Horizontal 40 20 Inter Point Distance (in mm): Qt::Horizontal 40 20 1 99999 50 Qt::Horizontal 40 20 Generate Result CSV File to NavigationData Converter Convert Single File true Input CSV Logging File: C:/Tools/test.csv Output Navigation Data File: C:/Tools/testoutput.xml Qt::Horizontal Convert File List <!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> not loaded Qt::Horizontal 40 20 100 0 Load Input List not loaded Qt::Horizontal 40 20 100 0 Load Output List Qt::Horizontal Qt::Horizontal 40 20 Output Format XML true CSV Qt::Horizontal 40 20 Convert Orientation Calculation (out of three positions) Qt::Horizontal 40 20 Generate Reference From Current List Qt::Horizontal 40 20 Write Orientation Quaternions To File Qt::Vertical 20 632 QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h