diff --git a/Modules/IGT/Algorithms/mitkNavigationDataEvaluationFilter.cpp b/Modules/IGT/Algorithms/mitkNavigationDataEvaluationFilter.cpp index bf504724a0..e6b110c1e7 100644 --- a/Modules/IGT/Algorithms/mitkNavigationDataEvaluationFilter.cpp +++ b/Modules/IGT/Algorithms/mitkNavigationDataEvaluationFilter.cpp @@ -1,371 +1,371 @@ /*=================================================================== 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 "mitkNavigationDataEvaluationFilter.h" #include #define _USE_MATH_DEFINES #include mitk::NavigationDataEvaluationFilter::NavigationDataEvaluationFilter() : mitk::NavigationDataToNavigationDataFilter() { } mitk::NavigationDataEvaluationFilter::~NavigationDataEvaluationFilter() {} void mitk::NavigationDataEvaluationFilter::GenerateData() { this->CreateOutputsForAllInputs(); // make sure that we have the same number of outputs as inputs this->CreateMembersForAllInputs(); /* update outputs with tracking data from tools */ for (unsigned int i = 0; i < this->GetNumberOfOutputs(); ++i) { // first copy outputs to inputs mitk::NavigationData *output = this->GetOutput(i); assert(output); const mitk::NavigationData *input = this->GetInput(i); assert(input); if (input->IsDataValid() == false) { output->SetDataValid(false); } else { output->Graft(input); } // then save statistics if (input->IsDataValid()) { m_LoggedPositions[i].push_back(input->GetPosition()); m_LoggedQuaternions[i].push_back(input->GetOrientation()); } else { m_InvalidSamples[i]++; } } } void mitk::NavigationDataEvaluationFilter::CreateMembersForAllInputs() { while (this->m_LoggedPositions.size() < this->GetNumberOfInputs()) { std::pair> newElement(m_LoggedPositions.size(), std::vector()); m_LoggedPositions.insert(newElement); } while (this->m_LoggedQuaternions.size() < this->GetNumberOfInputs()) { std::pair> newElement(m_LoggedQuaternions.size(), std::vector()); m_LoggedQuaternions.insert(newElement); } while (this->m_InvalidSamples.size() < this->GetNumberOfInputs()) { std::pair newElement(m_InvalidSamples.size(), 0); m_InvalidSamples.insert(newElement); } } void mitk::NavigationDataEvaluationFilter::ResetStatistic() { for (unsigned int i = 0; i < m_LoggedPositions.size(); i++) m_LoggedPositions[i] = std::vector(); for (unsigned int i = 0; i < m_LoggedQuaternions.size(); i++) m_LoggedQuaternions[i] = std::vector(); for (unsigned int i = 0; i < m_InvalidSamples.size(); i++) m_InvalidSamples[i] = 0; } int mitk::NavigationDataEvaluationFilter::GetNumberOfAnalysedNavigationData(int input) { return this->m_LoggedPositions[input].size(); } mitk::Point3D mitk::NavigationDataEvaluationFilter::GetPositionMean(int input) { mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); return myCalculator->GetPositionMean(); } mitk::Vector3D mitk::NavigationDataEvaluationFilter::GetPositionStandardDeviation(int input) { mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); return myCalculator->GetPositionStandardDeviation(); } mitk::Vector3D mitk::NavigationDataEvaluationFilter::GetPositionSampleStandardDeviation(int input) { mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); return myCalculator->GetPositionSampleStandardDeviation(); } mitk::Quaternion mitk::NavigationDataEvaluationFilter::GetQuaternionMean(int input) { return GetMean(m_LoggedQuaternions[input]); } mitk::Quaternion mitk::NavigationDataEvaluationFilter::GetQuaternionStandardDeviation(int input) { mitk::Quaternion returnValue; std::vector list1 = std::vector(); std::vector list2 = std::vector(); std::vector list3 = std::vector(); std::vector list4 = std::vector(); for (unsigned int i = 0; i < m_LoggedQuaternions[input].size(); i++) { list1.push_back(m_LoggedQuaternions[input].at(i)[0]); list2.push_back(m_LoggedQuaternions[input].at(i)[1]); list3.push_back(m_LoggedQuaternions[input].at(i)[2]); list4.push_back(m_LoggedQuaternions[input].at(i)[3]); } mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(); returnValue[0] = myCalculator->GetStabw(list1); returnValue[1] = myCalculator->GetStabw(list2); returnValue[2] = myCalculator->GetStabw(list3); returnValue[3] = myCalculator->GetStabw(list4); return returnValue; } mitk::Vector3D mitk::NavigationDataEvaluationFilter::GetEulerAnglesMean(int input) { mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(QuaternionsToEulerAngles(m_LoggedQuaternions[input]))); mitk::Vector3D returnValue; returnValue[0] = myCalculator->GetPositionMean()[0]; returnValue[1] = myCalculator->GetPositionMean()[1]; returnValue[2] = myCalculator->GetPositionMean()[2]; return returnValue; } double mitk::NavigationDataEvaluationFilter::GetEulerAnglesRMS(int input) { mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(QuaternionsToEulerAngles(m_LoggedQuaternions[input]))); return myCalculator->GetPositionErrorRMS(); } double mitk::NavigationDataEvaluationFilter::GetEulerAnglesRMSDegree(int input) { mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(QuaternionsToEulerAnglesGrad(m_LoggedQuaternions[input]))); return myCalculator->GetPositionErrorRMS(); } double mitk::NavigationDataEvaluationFilter::GetToolAxisRSME(int input) { double returnValue = -1; mitk::Point3D evaluationPoint; mitk::FillVector3D(evaluationPoint, 0, 0, 1); //compute mean transformed point mitk::Point3D meanTransformedPoint; mitk::FillVector3D(meanTransformedPoint, 0, 0, 0); std::vector transformedPoints; - for (int i = 0; i < m_LoggedPositions[input].size(); i++) + for (unsigned int i = 0; i < m_LoggedPositions[input].size(); i++) { mitk::NavigationData::Pointer currentTransform = mitk::NavigationData::New(); currentTransform->SetPosition(m_LoggedPositions[input].at(i)); currentTransform->SetOrientation(m_LoggedQuaternions[input].at(i)); mitk::NavigationData::Pointer transformedPoint = mitk::NavigationData::New(); transformedPoint->SetPosition(evaluationPoint); transformedPoint->Compose(currentTransform); meanTransformedPoint[0] += transformedPoint->GetPosition()[0]; meanTransformedPoint[1] += transformedPoint->GetPosition()[1]; meanTransformedPoint[2] += transformedPoint->GetPosition()[2]; transformedPoints.push_back(transformedPoint->GetPosition()); } meanTransformedPoint[0] /= m_LoggedPositions[input].size(); meanTransformedPoint[1] /= m_LoggedPositions[input].size(); meanTransformedPoint[2] /= m_LoggedPositions[input].size(); //compute RMS of error values returnValue = 0; for (mitk::Point3D transformedPoint : transformedPoints) { double currentError = transformedPoint.EuclideanDistanceTo(meanTransformedPoint); returnValue += pow(currentError,2); } returnValue /= transformedPoints.size(); returnValue = sqrt(returnValue); return returnValue; } double mitk::NavigationDataEvaluationFilter::GetPositionErrorMean(int input) { mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); return myCalculator->GetPositionErrorMean(); } double mitk::NavigationDataEvaluationFilter::GetPositionErrorStandardDeviation(int input) { mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); return myCalculator->GetPositionErrorStandardDeviation(); } double mitk::NavigationDataEvaluationFilter::GetPositionErrorSampleStandardDeviation(int input) { mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); return myCalculator->GetPositionErrorSampleStandardDeviation(); } double mitk::NavigationDataEvaluationFilter::GetPositionErrorRMS(int input) { mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); return myCalculator->GetPositionErrorRMS(); } double mitk::NavigationDataEvaluationFilter::GetPositionErrorMedian(int input) { mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); return myCalculator->GetPositionErrorMedian(); } double mitk::NavigationDataEvaluationFilter::GetPositionErrorMax(int input) { mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); return myCalculator->GetPositionErrorMax(); } double mitk::NavigationDataEvaluationFilter::GetPositionErrorMin(int input) { mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); return myCalculator->GetPositionErrorMin(); } int mitk::NavigationDataEvaluationFilter::GetNumberOfInvalidSamples(int input) { return m_InvalidSamples[input]; } double mitk::NavigationDataEvaluationFilter::GetPercentageOfInvalidSamples(int input) { return (m_InvalidSamples[input] / (m_InvalidSamples[input] + ((double)m_LoggedPositions[input].size()))) * 100.0; } mitk::Quaternion mitk::NavigationDataEvaluationFilter::GetMean(std::vector list) { // calculate mean mitk::Quaternion mean; mean[0] = 0; mean[1] = 0; mean[2] = 0; mean[3] = 0; for (unsigned int i = 0; i < list.size(); i++) { mean[0] += list.at(i)[0]; mean[1] += list.at(i)[1]; mean[2] += list.at(i)[2]; mean[3] += list.at(i)[3]; } mean[0] /= list.size(); mean[1] /= list.size(); mean[2] /= list.size(); mean[3] /= list.size(); return mean; } mitk::PointSet::Pointer mitk::NavigationDataEvaluationFilter::VectorToPointSet(std::vector pSet) { mitk::PointSet::Pointer returnValue = mitk::PointSet::New(); for (unsigned int i = 0; i < pSet.size(); i++) returnValue->InsertPoint(i, pSet.at(i)); return returnValue; } mitk::PointSet::Pointer mitk::NavigationDataEvaluationFilter::VectorToPointSet(std::vector pSet) { mitk::PointSet::Pointer returnValue = mitk::PointSet::New(); for (unsigned int i = 0; i < pSet.size(); i++) { mitk::Point3D thisPoint; thisPoint[0] = pSet.at(i)[0]; thisPoint[1] = pSet.at(i)[1]; thisPoint[2] = pSet.at(i)[2]; returnValue->InsertPoint(i, thisPoint); } return returnValue; } std::vector mitk::NavigationDataEvaluationFilter::QuaternionsToEulerAngles( std::vector quaterions) { std::vector returnValue = std::vector(); for (unsigned int i = 0; i < quaterions.size(); i++) { mitk::Vector3D eulerAngles; mitk::Quaternion currentQuaternion = quaterions.at(i); currentQuaternion .normalize(); // must be normalized due to the documentation of the vnl method rotation_euler_angles() eulerAngles[0] = currentQuaternion.rotation_euler_angles()[0]; eulerAngles[1] = currentQuaternion.rotation_euler_angles()[1]; eulerAngles[2] = currentQuaternion.rotation_euler_angles()[2]; returnValue.push_back(eulerAngles); } return returnValue; } std::vector mitk::NavigationDataEvaluationFilter::QuaternionsToEulerAnglesGrad( std::vector quaterions) { std::vector returnValue = std::vector(); std::vector eulerAnglesRadians = QuaternionsToEulerAngles(quaterions); for (unsigned int i = 0; i < eulerAnglesRadians.size(); i++) { mitk::Vector3D currentAngles; currentAngles[0] = (eulerAnglesRadians.at(i)[0] / itk::Math::pi) * 180; currentAngles[1] = (eulerAnglesRadians.at(i)[1] / itk::Math::pi) * 180; currentAngles[2] = (eulerAnglesRadians.at(i)[2] / itk::Math::pi) * 180; returnValue.push_back(currentAngles); } return returnValue; } mitk::Point3D mitk::NavigationDataEvaluationFilter::GetLoggedPosition(unsigned int i, int input) { mitk::Point3D returnValue; if (m_LoggedPositions[input].size() <= i) returnValue.Fill(0); else returnValue = m_LoggedPositions[input].at(i); return returnValue; } mitk::Quaternion mitk::NavigationDataEvaluationFilter::GetLoggedOrientation(unsigned int i, int input) { mitk::Quaternion returnValue; if (m_LoggedQuaternions[input].size() <= i) returnValue.fill(0); else returnValue = m_LoggedQuaternions[input].at(i); return returnValue; } 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 ec2be18a1a..9adc10faf9 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 @@ -1,1370 +1,1370 @@ /*========================================================================= 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 #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(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_Degrees->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_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 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")); // initialize output filename std::stringstream outputFilename; outputFilename << mitk::IOUtil::GetTempPath() << "results"; m_Controls->m_OutputFilename->setText(outputFilename.str().c_str()); } } 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] = 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) { double AngleBetweenTwoQuaternions = mitk::StaticIGTHelperFunctions::GetAngleBetweenTwoQuaterions( OrientationVector.at(i), OrientationVector.at(i + 1), rotationVec); double AngularError = fabs(AngleBetweenTwoQuaternions - 11.25); std::stringstream description; description << "Rotation Error ROT" << (i + 1) << " / ROT" << (i + 2); allOrientationErrors.push_back({AngularError, description.str()}); MITK_INFO << description.str() << ": " << AngularError; } // compute statistics std::vector orientationErrorStatistics; orientationErrorStatistics = mitk::HummelProtocolEvaluation::ComputeStatistics(allOrientationErrors); MITK_INFO << "## Rotation error statistics: ##"; for (auto stat : orientationErrorStatistics) { MITK_INFO << stat.description << ": " << stat.distanceError; } // write results to file allOrientationErrors.insert( allOrientationErrors.end(), orientationErrorStatistics.begin(), orientationErrorStatistics.end()); allOrientationErrors.push_back({rotationVec[0], "Rot Vector [x]"}); allOrientationErrors.push_back({rotationVec[1], "Rot Vector [y]"}); allOrientationErrors.push_back({rotationVec[2], "Rot Vector [z]"}); std::stringstream filenameOrientationStat; filenameOrientationStat << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".orientationStatistics.csv"; MITK_INFO << "Writing output to file " << filenameOrientationStat.str(); writeToFile(filenameOrientationStat.str(), allOrientationErrors); } void QmitkIGTTrackingDataEvaluationView::OnPerfomGridMatching() { mitk::PointSet::Pointer reference = dynamic_cast(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; i < reference->GetSize(); i++) { double point[3] = {reference->GetPoint(i)[0], reference->GetPoint(i)[1], reference->GetPoint(i)[2]}; sourcePoints->InsertNextPoint(point); double point_targets[3] = {measurement->GetPoint(i)[0], measurement->GetPoint(i)[1], measurement->GetPoint(i)[2]}; targetPoints->InsertNextPoint(point_targets); } // compute transform vtkSmartPointer 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(); // 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]"}); writeToFile(filename.str(), FRE_Error); GlobalReinit(); } void QmitkIGTTrackingDataEvaluationView::OnOrientationCalculation_CalcRef() { if (m_FilenameVector.size() != 3) { MessageBox("Need exactly three points as reference, aborting!"); return; } // start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { // create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector[i]); // check if the stream is valid and skip file if not // create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); // connect pipeline for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++j) myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); // update pipline until number of samples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); ++j) myEvaluationFilter->Update(); // store mean position as reference switch (i) { case 0: m_RefPoint1 = myEvaluationFilter->GetPositionMean(0); break; case 1: m_RefPoint2 = myEvaluationFilter->GetPositionMean(0); break; case 2: m_RefPoint3 = myEvaluationFilter->GetPositionMean(0); break; } } MessageBox("Created Reference!"); } void QmitkIGTTrackingDataEvaluationView::OnOrientationCalculation_CalcOrientandWriteToFile() { // start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { // create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); // open file header QString outputname = QString(m_FilenameVector.at(i).c_str()) + "_orientationFile.csv"; m_CurrentWriteFile.open(outputname.toStdString().c_str(), std::ios::out); if (m_CurrentWriteFile.bad()) { MessageBox("Error: Can't open output file!"); return; } // write header to file m_CurrentWriteFile << "Nr;Calypso_Time;Valid_Reference;MeasureTool_Measurement-Tool[x];MeasureTool_Measurement-" "Tool[y];MeasureTool_Measurement-Tool[z];MeasureTool_Measurement-Tool[qx];MeasureTool_" "Measurement-Tool[qy];MeasureTool_Measurement-Tool[qz];MeasureTool_Measurement-Tool[qr]\n"; // update pipeline until number of samples is reached int step = 0; mitk::Point3D point1, point2, point3; mitk::Quaternion current_orientation; for (int j = 0; !myPlayer->IsAtEnd(); j++) { myPlayer->Update(); mitk::NavigationData::Pointer currentNavData = myPlayer->GetOutput(0); switch (step) { case 0: step++; point1 = currentNavData->GetPosition(); break; case 1: step++; point2 = currentNavData->GetPosition(); break; case 2: step = 0; point3 = currentNavData->GetPosition(); // compute transform from reference to current points if (point1[0] == 0 && point1[1] == 0 && point1[2] == 0 && point2[0] == 0 && point2[1] == 0 && point2[2] == 0 && point3[0] == 0 && point3[1] == 0 && point3[2] == 0) current_orientation.fill(0); else { vtkSmartPointer 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 = nullptr; } bool QmitkIGTTrackingDataEvaluationView::OnAddToCurrentList() { // read in files QStringList files = QFileDialog::getOpenFileNames(nullptr, "Select one or more files to open", "/", "CSV (*.csv)"); if (files.isEmpty()) return false; // reset results this->GetDataStorage()->Remove(m_PointSetDataNode); m_PointSetDataNode = nullptr; m_PointSetMeanPositions = nullptr; for (mitk::DataNode::Pointer d : m_rotationLines) { this->GetDataStorage()->Remove(d); } m_rotationLines = std::vector(); for (int i = 0; i < files.size(); i++) { std::string tmp = files.at(i).toStdString().c_str(); m_FilenameVector.push_back(tmp); } // fill list at GUI m_Controls->m_FileList->clear(); for (unsigned int i = 0; i < m_FilenameVector.size(); i++) { new QListWidgetItem(tr(m_FilenameVector.at(i).c_str()), m_Controls->m_FileList); } return true; } void QmitkIGTTrackingDataEvaluationView::OnLoadFileList() { std::vector tempOld = m_FilenameVector; m_FilenameVector = std::vector(); m_FilenameVector.clear(); // load/add new data if (!OnAddToCurrentList()) { m_FilenameVector = tempOld; } } void QmitkIGTTrackingDataEvaluationView::OnEvaluateDataAll() { if (m_PointSetMeanPositions.IsNull()) { this->OnGeneratePointSet(); } 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 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 std::stringstream outputfilename; outputfilename << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".csv"; m_CurrentWriteFile.open(outputfilename.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 (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { // create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); // create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); // connect pipeline myEvaluationFilter->SetInput(0, myPlayer->GetOutput(0)); if (myPlayer->GetNumberOfSnapshots() < m_Controls->m_NumberOfSamples->value()) { MITK_WARN << "Number of snapshots (" << myPlayer->GetNumberOfSnapshots() << ") smaller than number of samples to evaluate (" << m_Controls->m_NumberOfSamples->value() << ") ! Cannot proceed!"; return; } // update pipline until number of samples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); j++) myEvaluationFilter->Update(); MITK_INFO << "Jitter (RMS) on position " << i << ": " << myEvaluationFilter->GetPositionErrorRMS(0); // store all jitter values in separate vector for statistics jitterValues.push_back({myEvaluationFilter->GetPositionErrorRMS(0), "RMS"}); // write result to output file WriteDataSet(myEvaluationFilter, m_FilenameVector.at(i)); } // close output file for single data m_CurrentWriteFile.close(); // compute statistics std::vector jitterStatistics = mitk::HummelProtocolEvaluation::ComputeStatistics(jitterValues); MITK_INFO << "## Jitter (RMS) statistics: ##"; for (auto jitterStat : jitterStatistics) { MITK_INFO << jitterStat.description << ": " << jitterStat.distanceError; } // write statistic results to separate file std::stringstream filenameJitterStat; filenameJitterStat << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".resultsJitterStatistics.csv"; MITK_INFO << "Writing output to file " << filenameJitterStat.str(); writeToFile(filenameJitterStat.str(), jitterStatistics); // calculate angles if option is on if (m_Controls->m_settingDifferenceAngles->isChecked() || m_Controls->m_DifferencesSLERP->isChecked()) CalculateDifferenceAngles(); // MessageBox("Finished!"); } void QmitkIGTTrackingDataEvaluationView::OnGeneratePointSetsOfSinglePositions() { m_scalingfactor = m_Controls->m_ScalingFactor->value(); // start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { // create point set for this file mitk::PointSet::Pointer thisPointSet = mitk::PointSet::New(); // create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); // update pipline until number of samlples is reached and store every single point for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); j++) { myPlayer->Update(); mitk::Point3D thisPoint = myPlayer->GetOutput()->GetPosition(); thisPoint[0] *= m_scalingfactor; thisPoint[1] *= m_scalingfactor; thisPoint[2] *= m_scalingfactor; thisPointSet->InsertPoint(j, thisPoint); } // add point set to data storage mitk::DataNode::Pointer newNode = mitk::DataNode::New(); QString name = this->m_Controls->m_prefix->text() + QString("PointSet_of_All_Positions_") + QString::number(i); newNode->SetName(name.toStdString()); newNode->SetData(thisPointSet); this->GetDataStorage()->Add(newNode); } } void QmitkIGTTrackingDataEvaluationView::OnGeneratePointSet() { m_scalingfactor = m_Controls->m_ScalingFactor->value(); mitk::PointSet::Pointer generatedPointSet = mitk::PointSet::New(); // start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { // create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); // create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); // connect pipeline for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++j) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); } // update pipline until number of samlples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); ++j) { myEvaluationFilter->Update(); } // add mean position to point set mitk::Point3D meanPos = myEvaluationFilter->GetPositionMean(0); if (m_scalingfactor != 1) { meanPos[0] *= m_scalingfactor; meanPos[1] *= m_scalingfactor; meanPos[2] *= m_scalingfactor; } generatedPointSet->InsertPoint(i, meanPos); } // add point set to data storage m_PointSetDataNode = mitk::DataNode::New(); QString name = this->m_Controls->m_prefix->text() + "PointSet_of_Mean_Positions"; m_PointSetDataNode->SetName(name.toStdString()); m_PointSetDataNode->SetData(generatedPointSet); m_PointSetDataNode->SetFloatProperty("pointsize", 5); this->GetDataStorage()->Add(m_PointSetDataNode); m_PointSetMeanPositions = generatedPointSet; GlobalReinit(); } void QmitkIGTTrackingDataEvaluationView::OnGenerateRotationLines() { m_scalingfactor = m_Controls->m_ScalingFactor->value(); for (mitk::DataNode::Pointer d : m_rotationLines) { this->GetDataStorage()->Remove(d); } m_rotationLines = std::vector(); // start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { // create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); // create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); // connect pipeline for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++j) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); } // update pipline until number of samlples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); ++j) myEvaluationFilter->Update(); // create line from mean pos to a second point which lies along the sensor (1,0,0 in tool coordinates for aurora) mitk::Point3D meanPos = myEvaluationFilter->GetPositionMean(0); if (m_scalingfactor != 1) { meanPos[0] *= m_scalingfactor; meanPos[1] *= m_scalingfactor; meanPos[2] *= m_scalingfactor; } mitk::Point3D secondPoint; mitk::Point3D thirdPoint; mitk::Point3D fourthPoint; mitk::FillVector3D(secondPoint, 2, 0, 0); // X vnl_vector secondPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * secondPoint.GetVnlVector() + meanPos.GetVnlVector(); mitk::Point3D secondPointTransformedMITK; mitk::FillVector3D( secondPointTransformedMITK, secondPointTransformed[0], secondPointTransformed[1], secondPointTransformed[2]); mitk::FillVector3D(thirdPoint, 0, 4, 0); // Y vnl_vector thirdPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * thirdPoint.GetVnlVector() + meanPos.GetVnlVector(); mitk::Point3D thirdPointTransformedMITK; mitk::FillVector3D( thirdPointTransformedMITK, thirdPointTransformed[0], thirdPointTransformed[1], thirdPointTransformed[2]); mitk::FillVector3D(fourthPoint, 0, 0, 6); // Z vnl_vector fourthPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * fourthPoint.GetVnlVector() + meanPos.GetVnlVector(); mitk::Point3D fourthPointTransformedMITK; mitk::FillVector3D( fourthPointTransformedMITK, fourthPointTransformed[0], fourthPointTransformed[1], fourthPointTransformed[2]); mitk::PointSet::Pointer rotationLine = mitk::PointSet::New(); rotationLine->InsertPoint(0, secondPointTransformedMITK); rotationLine->InsertPoint(1, meanPos); rotationLine->InsertPoint(2, thirdPointTransformedMITK); rotationLine->InsertPoint(3, meanPos); rotationLine->InsertPoint(4, fourthPointTransformedMITK); mitk::DataNode::Pointer newNode = mitk::DataNode::New(); QString nodeName = this->m_Controls->m_prefix->text() + "RotationLineNumber" + QString::number(i); newNode->SetName(nodeName.toStdString()); newNode->SetData(rotationLine); newNode->SetBoolProperty("show contour", true); newNode->SetFloatProperty("pointsize", 0.5); this->GetDataStorage()->Add(newNode); m_rotationLines.push_back(newNode); } this->GlobalReinit(); } void QmitkIGTTrackingDataEvaluationView::OnGenerateGroundTruthPointSet() { mitk::PointSet::Pointer generatedPointSet = mitk::PointSet::New(); int currentPointID = 0; mitk::Point3D currentPoint; mitk::FillVector3D(currentPoint, 0, 0, 0); for (int i = 0; i < m_Controls->m_PointNumber2->value(); i++) { for (int j = 0; j < m_Controls->m_PointNumber1->value(); j++) { generatedPointSet->InsertPoint(currentPointID, currentPoint); currentPointID++; currentPoint[1] += m_Controls->m_PointDistance->value(); } currentPoint[1] = 0; currentPoint[2] += m_Controls->m_PointDistance->value(); } mitk::DataNode::Pointer newNode = mitk::DataNode::New(); QString nodeName = "GroundTruthPointSet_" + QString::number(m_Controls->m_PointNumber1->value()) + "x" + QString::number(m_Controls->m_PointNumber2->value()) + "_(" + QString::number(m_Controls->m_PointDistance->value()) + "mm)"; newNode->SetName(nodeName.toStdString()); newNode->SetData(generatedPointSet); newNode->SetFloatProperty("pointsize", 5); this->GetDataStorage()->Add(newNode); } void QmitkIGTTrackingDataEvaluationView::OnConvertCSVtoXMLFile() { if (m_Controls->m_ConvertSingleFile->isChecked()) { // convert one file int lines = ConvertOneFile(this->m_Controls->m_InputCSV->text().toStdString(), this->m_Controls->m_OutputXML->text().toStdString()); QString result = "Converted one file with" + QString::number(lines) + " data sets"; MessageBox(result.toStdString()); } else // converte file list { if (m_CSVtoXMLInputFilenameVector.empty() || m_CSVtoXMLOutputFilenameVector.empty()) { MessageBox("Error: one list is not loaded!"); return; } else if (m_CSVtoXMLInputFilenameVector.size() != m_CSVtoXMLOutputFilenameVector.size()) { MessageBox("Error: lists do not have the same number of files!"); return; } for (std::size_t i = 0; i < m_CSVtoXMLInputFilenameVector.size(); ++i) { ConvertOneFile(m_CSVtoXMLInputFilenameVector.at(i), m_CSVtoXMLOutputFilenameVector.at(i)); } QString result = "Converted " + QString::number(m_CSVtoXMLInputFilenameVector.size()) + " files from file list!"; MessageBox(result.toStdString()); } } int QmitkIGTTrackingDataEvaluationView::ConvertOneFile(std::string inputFilename, std::string outputFilename) { std::vector myNavigationDatas = GetNavigationDatasFromFile(inputFilename); mitk::NavigationDataRecorderDeprecated::Pointer myRecorder = mitk::NavigationDataRecorderDeprecated::New(); myRecorder->SetFileName(outputFilename.c_str()); mitk::NavigationData::Pointer input = mitk::NavigationData::New(); if (m_Controls->m_ConvertCSV->isChecked()) myRecorder->SetOutputFormat(mitk::NavigationDataRecorderDeprecated::csv); myRecorder->AddNavigationData(input); myRecorder->StartRecording(); for (std::size_t i = 0; i < myNavigationDatas.size(); ++i) { input->Graft(myNavigationDatas.at(i)); myRecorder->Update(); } myRecorder->StopRecording(); return myNavigationDatas.size(); } void QmitkIGTTrackingDataEvaluationView::OnCSVtoXMLLoadInputList() { // read in filename QString filename = QFileDialog::getOpenFileName(nullptr, tr("Open Measurement Filename List"), "/", tr("All Files (*.*)")); if (filename.isNull()) return; m_CSVtoXMLInputFilenameVector = this->GetFileContentLineByLine(filename.toStdString()); m_Controls->m_labelCSVtoXMLInputList->setText("READY"); } void QmitkIGTTrackingDataEvaluationView::OnCSVtoXMLLoadOutputList() { // read in filename QString filename = QFileDialog::getOpenFileName(nullptr, tr("Open Measurement Filename List"), "/", tr("All Files (*.*)")); if (filename.isNull()) return; m_CSVtoXMLOutputFilenameVector = this->GetFileContentLineByLine(filename.toStdString()); m_Controls->m_labelCSVtoXMLOutputList->setText("READY"); } void QmitkIGTTrackingDataEvaluationView::MessageBox(std::string s) { QMessageBox msgBox; msgBox.setText(s.c_str()); msgBox.exec(); } void QmitkIGTTrackingDataEvaluationView::WriteHeader() { m_CurrentWriteFile << "Filename;"; m_CurrentWriteFile << "N;"; m_CurrentWriteFile << "N_invalid;"; m_CurrentWriteFile << "Percentage_invalid;"; if (m_Controls->m_settingPosMean->isChecked()) { m_CurrentWriteFile << "Position_Mean[x];"; m_CurrentWriteFile << "Position_Mean[y];"; m_CurrentWriteFile << "Position_Mean[z];"; } if (m_Controls->m_settingPosStabw->isChecked()) { m_CurrentWriteFile << "Position_StandDev[x];"; m_CurrentWriteFile << "Position_StandDev[y];"; m_CurrentWriteFile << "Position_StandDev[z];"; } if (m_Controls->m_settingPosSampleStabw->isChecked()) { m_CurrentWriteFile << "Position_SampleStandDev[x];"; m_CurrentWriteFile << "Position_SampleStandDev[y];"; m_CurrentWriteFile << "Position_SampleStandDev[z];"; } if (m_Controls->m_settingQuaternionMean->isChecked()) { m_CurrentWriteFile << "Quaternion_Mean[qx];"; m_CurrentWriteFile << "Quaternion_Mean[qy];"; m_CurrentWriteFile << "Quaternion_Mean[qz];"; m_CurrentWriteFile << "Quaternion_Mean[qr];"; } if (m_Controls->m_settionQuaternionStabw->isChecked()) { m_CurrentWriteFile << "Quaternion_StandDev[qx];"; m_CurrentWriteFile << "Quaternion_StandDev[qy];"; m_CurrentWriteFile << "Quaternion_StandDev[qz];"; m_CurrentWriteFile << "Quaternion_StandDev[qr];"; } if (m_Controls->m_settingPosErrorMean->isChecked()) m_CurrentWriteFile << "PositionError_Mean;"; if (m_Controls->m_settingPosErrorStabw->isChecked()) m_CurrentWriteFile << "PositionError_StandDev;"; if (m_Controls->m_settingPosErrorSampleStabw->isChecked()) m_CurrentWriteFile << "PositionError_SampleStandDev;"; if (m_Controls->m_settingPosErrorRMS->isChecked()) m_CurrentWriteFile << "PositionError_RMS;"; if (m_Controls->m_settingPosErrorMedian->isChecked()) m_CurrentWriteFile << "PositionError_Median;"; if (m_Controls->m_settingPosErrorMinMax->isChecked()) { m_CurrentWriteFile << "PositionError_Max;"; m_CurrentWriteFile << "PositionError_Min;"; } if (m_Controls->m_settingEulerMean->isChecked()) { m_CurrentWriteFile << "Euler_tx;"; m_CurrentWriteFile << "Euler_ty;"; m_CurrentWriteFile << "Euler_tz;"; } if (m_Controls->m_toolAxisRSME->isChecked()) { m_CurrentWriteFile << "Tool Axis RMS Error [mm];"; } 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_toolAxisRSME->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetToolAxisRSME(0) << ";"; } 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 (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { // create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); // create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); // connect pipeline for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++j) myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); // update pipline until number of samlples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); ++j) myEvaluationFilter->Update(); myEvaluationFilter->SetInput(nullptr); myPlayer = nullptr; EvaluationDataCollection.push_back(myEvaluationFilter); } return EvaluationDataCollection; } void QmitkIGTTrackingDataEvaluationView::CalculateDifferenceAngles() { // Get all data from UI std::vector EvaluationDataCollection = GetAllDataFromUIList(); // calculation and writing of output data // open output file m_CurrentAngleDifferencesWriteFile.open( std::string((m_Controls->m_OutputFilename->text() + ".angledifferences.csv").toUtf8()).c_str(), std::ios::out); if (m_CurrentAngleDifferencesWriteFile.bad()) { MessageBox("Error: Can't open output file for angle differences calculation!"); return; } // write header WriteDifferenceAnglesHeader(); // compute angle differences QString pos1 = "invalid"; QString pos2 = "invalid"; // now iterate through all evaluation data and calculate the angles for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { pos1 = QString::fromStdString(itksys::SystemTools::GetFilenameWithoutLastExtension(m_FilenameVector.at(i))); for (std::size_t j = 0; j < m_FilenameVector.size(); ++j) { pos2 = QString::fromStdString(itksys::SystemTools::GetFilenameWithoutLastExtension(m_FilenameVector.at(j))); mitk::Quaternion q1; mitk::Quaternion q2; if (m_Controls->m_DifferencesSLERP->isChecked()) { // compute slerp average q1 = GetSLERPAverage(EvaluationDataCollection.at(i)); q2 = GetSLERPAverage(EvaluationDataCollection.at(j)); } else { // compute arithmetic average q1 = EvaluationDataCollection.at(i)->GetQuaternionMean(0); q2 = EvaluationDataCollection.at(j)->GetQuaternionMean(0); } itk::Vector rotationVec; // adapt for Aurora 5D tools: [0,0,1000] rotationVec[0] = 10000; // X rotationVec[1] = 0; // Y rotationVec[2] = 0; // Z double AngleBetweenTwoQuaternions = mitk::StaticIGTHelperFunctions::GetAngleBetweenTwoQuaterions(q1, q2, rotationVec); // write data set WriteDifferenceAnglesDataSet(pos1.toStdString(), pos2.toStdString(), i, j, AngleBetweenTwoQuaternions); } } // close output file m_CurrentAngleDifferencesWriteFile.close(); } void QmitkIGTTrackingDataEvaluationView::WriteDifferenceAnglesHeader() { m_CurrentAngleDifferencesWriteFile << "Name;Idx1;Idx2;Angle [Degree]\n"; } void QmitkIGTTrackingDataEvaluationView::WriteDifferenceAnglesDataSet( std::string pos1, std::string pos2, int idx1, int idx2, double angle) { m_CurrentAngleDifferencesWriteFile << "Angle between " << pos1 << " and " << pos2 << ";" << idx1 << ";" << idx2 << ";" << angle << "\n"; MITK_INFO << "Angle: " << angle; } std::vector 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 { 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; bool valid = false; if (myLineList.at(2).toStdString() == "1") valid = true; position[0] = myLineList.at(3).toDouble(); position[1] = myLineList.at(4).toDouble(); position[2] = myLineList.at(5).toDouble(); orientation[0] = myLineList.at(6).toDouble(); orientation[1] = myLineList.at(7).toDouble(); orientation[2] = myLineList.at(8).toDouble(); orientation[3] = myLineList.at(9).toDouble(); returnValue->SetDataValid(valid); returnValue->SetPosition(position); returnValue->SetOrientation(orientation); return returnValue; } mitk::Quaternion QmitkIGTTrackingDataEvaluationView::GetSLERPAverage( mitk::NavigationDataEvaluationFilter::Pointer evaluationFilter) { mitk::Quaternion average; // build a vector of quaternions from the evaulation filter (caution always takes the first (0) input of the filter std::vector 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(); } 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; } void QmitkIGTTrackingDataEvaluationView::GlobalReinit() { // Global reinit // get all nodes that have not set "includeInBoundingBox" to false mitk::NodePredicateNot::Pointer pred = mitk::NodePredicateNot::New( mitk::NodePredicateProperty::New("includeInBoundingBox", mitk::BoolProperty::New(false))); mitk::DataStorage::SetOfObjects::ConstPointer rs = this->GetDataStorage()->GetSubset(pred); // calculate bounding geometry of these nodes - mitk::TimeGeometry::Pointer bounds = this->GetDataStorage()->ComputeBoundingGeometry3D(rs, "visible"); + auto bounds = this->GetDataStorage()->ComputeBoundingGeometry3D(rs, "visible"); // initialize the views to the bounding geometry mitk::RenderingManager::GetInstance()->InitializeViews(bounds); } 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 3fb0acbb95..a59f8ef6c3 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 @@ -1,323 +1,323 @@ /*=================================================================== 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 "mitkNavigationDataCSVSequentialPlayer.h" #include #include #include #include mitk::NavigationDataCSVSequentialPlayer::NavigationDataCSVSequentialPlayer() - : mitk::NavigationDataPlayerBase(), - m_numberOfReadErrorsInARow(0), - m_NavigationDatas(std::vector()), - m_CurrentPos(0), - m_Filetype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV) + : mitk::NavigationDataPlayerBase() { + m_numberOfReadErrorsInARow = 0; + m_NavigationDatas = std::vector(); + m_CurrentPos = 0; + m_Filetype = mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV; } mitk::NavigationDataCSVSequentialPlayer::~NavigationDataCSVSequentialPlayer() { } bool mitk::NavigationDataCSVSequentialPlayer::IsAtEnd() { return m_CurrentPos >= static_cast(m_NavigationDatas.size()); } void mitk::NavigationDataCSVSequentialPlayer:: SetFileName(const std::string& fileName) { this->SetNumberOfIndexedOutputs(1); FillOutputEmpty(0); MITK_INFO << "Reading file: " << fileName; m_NavigationDatas = GetNavigationDatasFromFile(fileName); this->Modified(); } void mitk::NavigationDataCSVSequentialPlayer::FillOutputEmpty(int number) { this->SetNthOutput(number, GetEmptyNavigationData()); } mitk::NavigationData::Pointer mitk::NavigationDataCSVSequentialPlayer::GetEmptyNavigationData() { mitk::NavigationData::Pointer emptyNd = mitk::NavigationData::New(); mitk::NavigationData::PositionType position; mitk::NavigationData::OrientationType orientation(0.0, 0.0, 0.0, 0.0); position.Fill(0.0); emptyNd->SetPosition(position); emptyNd->SetOrientation(orientation); emptyNd->SetDataValid(false); return emptyNd; } int mitk::NavigationDataCSVSequentialPlayer::GetNumberOfSnapshots() { return m_NavigationDatas.size(); } void mitk::NavigationDataCSVSequentialPlayer::GenerateData() { for (unsigned int index = 0; index < this->GetNumberOfOutputs(); index++) { mitk::NavigationData* output = this->GetOutput(index); if (m_CurrentPos >= static_cast(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); std::size_t i = m_HeaderRow ? 1 //file has a header row, so it has to be skipped when reading the NavigationDatas : 0; //file has no header row, so no need to skip the first row for ( ; i < fileContentLineByLine.size(); ++i) { returnValue.push_back(GetNavigationDataOutOfOneLine(fileContentLineByLine.at(i))); if (m_numberOfReadErrorsInARow>5) { MITK_ERROR << "More than 5 read errors in a row, aborting! Is the csv file reader configured correctly?"; m_numberOfReadErrorsInARow = 0; return returnValue; } } 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; while (!file.eof()) { std::string buffer; std::getline(file, buffer); // read out file line by line if (!buffer.empty()) { readData.push_back(buffer); //MITK_INFO << "Line: " << buffer; } ++count; if (count == m_SampleCount) count = 0; } } file.close(); //switch back to old locale setlocale(LC_ALL, oldLocale); return readData; } mitk::NavigationData::Pointer mitk::NavigationDataCSVSequentialPlayer::GetNavigationDataOutOfOneLine(std::string line) { mitk::NavigationData::Pointer returnValue = mitk::NavigationData::New(); QString myLine = QString(line.c_str()); QStringList myLineList = myLine.split(m_SeparatorSign); mitk::Point3D position; mitk::Quaternion orientation; bool valid = false; //this is for custom csv files. You have adapt the column numbers to correctly //interpret your csv file. if (m_Filetype == mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV) { if (myLineList.size() < m_MinNumberOfColumns) { MITK_WARN << "Cannot read line: only found " << myLineList.size() << " fields. Last field: " << myLineList.at(myLineList.size() - 1).toStdString(); returnValue = GetEmptyNavigationData(); m_numberOfReadErrorsInARow++; return returnValue; } m_numberOfReadErrorsInARow = 0; valid = true; //if no valid flag is given: simply set to true position[0] = myLineList.at(m_XPos).toDouble(); position[1] = myLineList.at(m_YPos).toDouble(); position[2] = myLineList.at(m_ZPos).toDouble(); orientation[0] = myLineList.at(m_Qx).toDouble(); // qx orientation[1] = myLineList.at(m_Qy).toDouble(); // qy orientation[2] = myLineList.at(m_Qz).toDouble(); // qz orientation[3] = myLineList.at(m_Qr).toDouble(); // qr if(!m_RightHanded) //MITK uses a right handed coordinate system, so the position needs to be converted { position[0] = position[0]*(-1); } if (m_UseQuats) //Use Quaternions to construct the orientation of the NavigationData { orientation[0] = myLineList.at(m_Qx).toDouble(); //qx orientation[1] = myLineList.at(m_Qy).toDouble(); //qy orientation[2] = myLineList.at(m_Qz).toDouble(); //qz orientation[3] = myLineList.at(m_Qr).toDouble(); //qr } else //Use the Euler Angles to construct the orientation of the NavigationData { double azimuthAngle; double elevationAngle; double rollAngle; if(m_Azimuth < 0) //azimuth is not defined so set him to zero { azimuthAngle = 0; } else { azimuthAngle = myLineList.at(m_Azimuth).toDouble(); } if(m_Elevation < 0)// elevation is not defined so set him to zero { elevationAngle = 0; } else { elevationAngle = myLineList.at(m_Elevation).toDouble(); } if(m_Roll < 0) //roll is not defined so set him to zero { rollAngle = 0; } else { rollAngle = myLineList.at(m_Roll).toDouble(); } if (!m_EulersInRadiants) //the Euler Angles are in Degrees but MITK uses radiants so they need to be converted { azimuthAngle = azimuthAngle / 180 * itk::Math::pi; elevationAngle = elevationAngle / 180 * itk::Math::pi; rollAngle = rollAngle / 180 * itk::Math::pi; } vnl_quaternion eulerQuat(rollAngle, elevationAngle, azimuthAngle); orientation = eulerQuat; } if(!m_RightHanded) //MITK uses a right handed coordinate system, so the orientation needs to be converted { //code block for conversion from left-handed to right-handed mitk::Quaternion linksZuRechtsdrehend; double rotationAngle = -itk::Math::pi; double rotationAxis[3]; rotationAxis[0] = 0; rotationAxis[1] = 0; rotationAxis[2] = 1; linksZuRechtsdrehend[3] = cos(rotationAngle / 2); linksZuRechtsdrehend[0] = rotationAxis[0] * sin(rotationAngle / 2); linksZuRechtsdrehend[1] = rotationAxis[1] * sin(rotationAngle / 2); linksZuRechtsdrehend[2] = rotationAxis[2] * sin(rotationAngle / 2); orientation = orientation * linksZuRechtsdrehend; } } //this is for MITK csv files that have been recorded with the MITK //navigation data recorder. You can also use the navigation data player //class from the MITK-IGT module instead. else if (m_Filetype == mitk::NavigationDataCSVSequentialPlayer::NavigationDataCSV) { if (myLineList.size() < 8) { MITK_ERROR << "Error: cannot read line: only found " << myLineList.size() << " fields. Last field: " << myLineList.at(myLineList.size() - 1).toStdString(); returnValue = GetEmptyNavigationData(); return returnValue; } if (myLineList.at(3).toStdString() == "1") valid = true; position[0] = myLineList.at(2).toDouble(); position[1] = myLineList.at(3).toDouble(); position[2] = myLineList.at(4).toDouble(); orientation[0] = myLineList.at(5).toDouble(); //qx orientation[1] = myLineList.at(6).toDouble(); //qy orientation[2] = myLineList.at(7).toDouble(); //qz orientation[3] = myLineList.at(8).toDouble(); //qr } returnValue->SetDataValid(valid); returnValue->SetPosition(position); returnValue->SetOrientation(orientation); return returnValue; } void mitk::NavigationDataCSVSequentialPlayer::SetOptions(bool rightHanded, char separatorSign, int sampleCount, bool headerRow, int xPos, int yPos, int zPos, bool useQuats, int qx, int qy, int qz, int qr, int azimuth, int elevation, int roll, bool eulerInRadiants, int minNumberOfColumns) { m_RightHanded = rightHanded; m_SeparatorSign = separatorSign; m_SampleCount = sampleCount; m_HeaderRow = headerRow; m_XPos = xPos; m_YPos = yPos; m_ZPos = zPos; m_UseQuats = useQuats; m_Qx = qx; m_Qy = qy; m_Qz = qz; m_Qr = qr; m_Azimuth = azimuth; m_Elevation = elevation; m_Roll = roll; m_EulersInRadiants = eulerInRadiants; m_MinNumberOfColumns = minNumberOfColumns; }