diff --git a/Modules/IGTBase/src/mitkStaticIGTHelperFunctions.cpp b/Modules/IGTBase/src/mitkStaticIGTHelperFunctions.cpp index bdb6a32a72..c9872b6ebd 100644 --- a/Modules/IGTBase/src/mitkStaticIGTHelperFunctions.cpp +++ b/Modules/IGTBase/src/mitkStaticIGTHelperFunctions.cpp @@ -1,116 +1,120 @@ /*=================================================================== 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 #include double mitk::StaticIGTHelperFunctions::GetAngleBetweenTwoQuaterions(mitk::Quaternion a, mitk::Quaternion b, itk::Vector rotationVector) { double returnValue; itk::Vector point; //caution 5D-Tools: correct vector along the tool axis is needed point[0] = rotationVector[0]; point[1] = rotationVector[1]; point[2] = rotationVector[2]; //Quaternions used for rotations should alway be normalized, so just to be safe: a.normalize(); b.normalize(); itk::Matrix rotMatrixA; for(int i=0; i<3; i++) for(int j=0; j<3; j++) rotMatrixA[i][j] = a.rotation_matrix_transpose().transpose()[i][j]; itk::Matrix rotMatrixB; for(int i=0; i<3; i++) for(int j=0; j<3; j++) rotMatrixB[i][j] = b.rotation_matrix_transpose().transpose()[i][j]; itk::Vector pt1 = rotMatrixA * point; itk::Vector pt2 = rotMatrixB * point; returnValue = (pt1[0]*pt2[0]+pt1[1]*pt2[1]+pt1[2]*pt2[2]) / ( sqrt(pow(pt1[0],2.0)+pow(pt1[1],2.0)+pow(pt1[2],2.0)) * sqrt(pow(pt2[0],2.0)+pow(pt2[1],2.0)+pow(pt2[2],2.0))); returnValue = acos(returnValue) * 57.296; //57,296 = 180/Pi ; conversion to degrees return returnValue; } double mitk::StaticIGTHelperFunctions::GetAngleBetweenTwoQuaterions(mitk::Quaternion a, mitk::Quaternion b) { //formula returnValue = 2 * acos ( a b ) //(+ normalization because we need unit quaternions) //derivation from here: https://fgiesen.wordpress.com/2013/01/07/small-note-on-quaternion-distance-metrics/ double returnValue = ((a[0] * b[0] + a[1] * b[1] + a[2] * b[2] + a[3] * b[3]) / (sqrt(a[0] * a[0] + a[1] * a[1] + a[2] * a[2] + a[3] * a[3])*sqrt(b[0] * b[0] + b[1] * b[1] + b[2] * b[2] + b[3] * b[3]))); returnValue = 2 * acos(returnValue); return returnValue; } itk::Matrix mitk::StaticIGTHelperFunctions::ConvertEulerAnglesToRotationMatrix(double alpha, double beta, double gamma) { double PI = 3.141592653589793; alpha = alpha * PI / 180; beta = beta * PI / 180; gamma = gamma * PI / 180; //convert angles to matrix: itk::Matrix matrix; /* x-Konvention (Z, X, Z) matrix[0][0] = cos(alpha) * cos(gamma) - sin(alpha) * cos(beta) * sin(gamma); matrix[0][1] = -cos(alpha) * sin(gamma)- sin(alpha) * cos(beta) * cos(gamma); matrix[0][2] = sin(alpha) * sin(beta); matrix[1][0] = sin(alpha) * cos(gamma) + cos(alpha) * cos(beta) * sin(gamma); matrix[1][1] = cos(alpha) * cos(beta) * cos(gamma) - sin(alpha) * sin(gamma); matrix[1][2] = -cos(alpha) * sin(beta); matrix[2][0] = sin(beta) * sin(gamma); matrix[2][1] = sin(beta) * cos(gamma); matrix[2][2] = cos(beta); */ //Luftfahrtnorm (DIN 9300) (Yaw-Pitch-Roll, Z, Y, X) matrix[0][0] = cos(beta) * cos(alpha); matrix[0][1] = cos(beta) * sin(alpha); matrix[0][2] = -sin(beta); matrix[1][0] = sin(gamma) * sin(beta) * cos(alpha) - cos(gamma) * sin(alpha) ; matrix[1][1] = sin(gamma) * sin(beta) * sin(alpha) + cos(gamma) * cos(alpha); matrix[1][2] = sin(gamma) * cos(beta); matrix[2][0] = cos(gamma) * sin(beta) * cos(alpha) + sin(gamma) * sin(alpha); matrix[2][1] = cos(gamma) * sin(beta) * sin(alpha) - sin(gamma) * cos(alpha); matrix[2][2] = cos(gamma) * cos(beta); return matrix; } double mitk::StaticIGTHelperFunctions::ComputeFRE(mitk::PointSet::Pointer imageFiducials, mitk::PointSet::Pointer realWorldFiducials, vtkSmartPointer transform) { - if (imageFiducials->GetSize() != realWorldFiducials->GetSize()) return -1; + if (imageFiducials->GetSize() != realWorldFiducials->GetSize()) + { + MITK_WARN << "Cannot compute FRE, got different numbers of points (1: " << imageFiducials->GetSize() << " /2: " << realWorldFiducials->GetSize() << ")"; + return -1; + } double FRE = 0; for (int i = 0; i < imageFiducials->GetSize(); i++) { itk::Point current_image_fiducial_point = imageFiducials->GetPoint(i); if (transform != NULL) { current_image_fiducial_point = transform->TransformPoint(imageFiducials->GetPoint(i)[0], imageFiducials->GetPoint(i)[1], imageFiducials->GetPoint(i)[2]); } double cur_error_squared = current_image_fiducial_point.SquaredEuclideanDistanceTo(realWorldFiducials->GetPoint(i)); FRE += cur_error_squared; } FRE = sqrt(FRE / (double)imageFiducials->GetSize()); return FRE; } 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 e786efc119..eefc8e7643 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 @@ -1,1158 +1,1179 @@ /*========================================================================= The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. =========================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkIGTTrackingDataEvaluationView.h" #include "QmitkStdMultiWidget.h" // Qt #include #include #include // MITK #include "mitkNavigationDataCSVSequentialPlayer.h" #include #include #include #include #include //ITK #include //VNL #include //vtk headers #include #include #include const std::string QmitkIGTTrackingDataEvaluationView::VIEW_ID = "org.mitk.views.igttrackingdataevaluation"; QmitkIGTTrackingDataEvaluationView::QmitkIGTTrackingDataEvaluationView() : QmitkFunctionality() , m_Controls(0) , m_MultiWidget(NULL) , m_scalingfactor(1) { m_CSVtoXMLInputFilenameVector = std::vector(); m_CSVtoXMLOutputFilenameVector = std::vector(); } QmitkIGTTrackingDataEvaluationView::~QmitkIGTTrackingDataEvaluationView() { } void QmitkIGTTrackingDataEvaluationView::CreateQtPartControl(QWidget *parent) { // build up qt view, unless already done if (!m_Controls) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkIGTTrackingDataEvaluationViewControls; m_Controls->setupUi(parent); connect(m_Controls->m_LoadInputFileList, SIGNAL(clicked()), this, SLOT(OnLoadFileList())); connect(m_Controls->m_StartEvaluation, SIGNAL(clicked()), this, SLOT(OnEvaluateData())); connect(m_Controls->m_AddToCurrentList, SIGNAL(clicked()), this, SLOT(OnAddToCurrentList())); connect(m_Controls->m_GeneratePointSetOfMeanPositions, SIGNAL(clicked()), this, SLOT(OnGeneratePointSet())); connect(m_Controls->m_GenerateRotationLines, SIGNAL(clicked()), this, SLOT(OnGenerateRotationLines())); connect(m_Controls->m_GeneratePointSet, SIGNAL(clicked()), this, SLOT(OnGenerateGroundTruthPointSet())); connect(m_Controls->m_Convert, SIGNAL(clicked()), this, SLOT(OnConvertCSVtoXMLFile())); connect(m_Controls->m_loadCSVtoXMLInputList, SIGNAL(clicked()), this, SLOT(OnCSVtoXMLLoadInputList())); connect(m_Controls->m_loadCSVtoXMLOutputList, SIGNAL(clicked()), this, SLOT(OnCSVtoXMLLoadOutputList())); connect(m_Controls->m_OrientationCalculationGenerateReference, SIGNAL(clicked()), this, SLOT(OnOrientationCalculation_CalcRef())); connect(m_Controls->m_OrientationCalculationWriteOrientationsToFile, SIGNAL(clicked()), this, SLOT(OnOrientationCalculation_CalcOrientandWriteToFile())); connect(m_Controls->m_GeneratePointSetsOfSinglePositions, SIGNAL(clicked()), this, SLOT(OnGeneratePointSetsOfSinglePositions())); connect(m_Controls->m_StartEvaluationAll, SIGNAL(clicked()), this, SLOT(OnEvaluateDataAll())); connect(m_Controls->m_GridMatching, SIGNAL(clicked()), this, SLOT(OnPerfomGridMatching())); + connect(m_Controls->m_ComputeRotation, SIGNAL(clicked()), this, SLOT(OnComputeRotation())); //initialize data storage combo boxes m_Controls->m_ReferencePointSetComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_ReferencePointSetComboBox->SetAutoSelectNewItems(true); m_Controls->m_ReferencePointSetComboBox->SetPredicate(mitk::NodePredicateDataType::New("PointSet")); m_Controls->m_MeasurementPointSetComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_MeasurementPointSetComboBox->SetAutoSelectNewItems(true); m_Controls->m_MeasurementPointSetComboBox->SetPredicate(mitk::NodePredicateDataType::New("PointSet")); } } +void QmitkIGTTrackingDataEvaluationView::OnComputeRotation() +{ + +} + void QmitkIGTTrackingDataEvaluationView::OnPerfomGridMatching() { mitk::PointSet::Pointer reference = dynamic_cast(m_Controls->m_ReferencePointSetComboBox->GetSelectedNode()->GetData()); mitk::PointSet::Pointer measurement = dynamic_cast(m_Controls->m_MeasurementPointSetComboBox->GetSelectedNode()->GetData()); //convert point sets to vtk poly data vtkSmartPointer sourcePoints = vtkSmartPointer::New(); vtkSmartPointer targetPoints = vtkSmartPointer::New(); for (int i = 0; iGetSize(); i++) { - MITK_INFO << "Point added " << i; double point[3] = { reference->GetPoint(i)[0], reference->GetPoint(i)[1], reference->GetPoint(i)[2] }; sourcePoints->InsertNextPoint(point); double point_targets[3] = { measurement->GetPoint(i)[0], measurement->GetPoint(i)[1], measurement->GetPoint(i)[2] }; targetPoints->InsertNextPoint(point_targets); } //compute transform vtkSmartPointer transform = vtkSmartPointer::New(); transform->SetSourceLandmarks(sourcePoints); transform->SetTargetLandmarks(targetPoints); transform->SetModeToRigidBody(); transform->Modified(); transform->Update(); //compute FRE of transform double FRE = mitk::StaticIGTHelperFunctions::ComputeFRE(reference, measurement, transform); MITK_INFO << "FRE after grid matching: " + QString::number(FRE) + " mm"; //convert from vtk to itk data types itk::Matrix rotationFloat = itk::Matrix(); itk::Vector translationFloat = itk::Vector(); itk::Matrix rotationDouble = itk::Matrix(); itk::Vector translationDouble = itk::Vector(); vtkSmartPointer m = transform->GetMatrix(); for (int k = 0; k<3; k++) for (int l = 0; l<3; l++) { rotationFloat[k][l] = m->GetElement(k, l); rotationDouble[k][l] = m->GetElement(k, l); } for (int k = 0; k<3; k++) { translationFloat[k] = m->GetElement(k, 3); translationDouble[k] = m->GetElement(k, 3); } //create affine transform 3D mitk::AffineTransform3D::Pointer mitkTransform = mitk::AffineTransform3D::New(); mitkTransform->SetMatrix(rotationDouble); mitkTransform->SetOffset(translationDouble); mitk::NavigationData::Pointer transformNavigationData = mitk::NavigationData::New(mitkTransform); m_Controls->m_ReferencePointSetComboBox->GetSelectedNode()->GetData()->GetGeometry()->SetIndexToWorldTransform(mitkTransform); m_Controls->m_ReferencePointSetComboBox->GetSelectedNode()->GetData()->GetGeometry()->Modified(); } void QmitkIGTTrackingDataEvaluationView::OnOrientationCalculation_CalcRef() { if (m_FilenameVector.size() != 3) { MessageBox("Need exactly three points as reference, aborting!"); return; } //start loop and iterate through all files of list for (int i = 0; i < m_FilenameVector.size(); i++) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = mitk::NavigationDataCSVSequentialPlayer::New(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //check if the stream is valid and skip file if not /* if (!myPlayer->GetStreamValid()) { MITK_ERROR << "Error in file " << m_FilenameVector.at(i) << ": " << myPlayer->GetErrorMessage() << " ; Skipping file!"; continue; } */ //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (int j = 0; j < myPlayer->GetNumberOfOutputs(); j++) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); } //update pipline until number of samlples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); j++) { myEvaluationFilter->Update(); } //store mean position as reference switch (i) { case 0: m_RefPoint1 = myEvaluationFilter->GetPositionMean(0); break; case 1: m_RefPoint2 = myEvaluationFilter->GetPositionMean(0); break; case 2: m_RefPoint3 = myEvaluationFilter->GetPositionMean(0); break; } } MessageBox("Created Reference!"); } void QmitkIGTTrackingDataEvaluationView::OnOrientationCalculation_CalcOrientandWriteToFile() { //start loop and iterate through all files of list for (int i = 0; i < m_FilenameVector.size(); i++) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = mitk::NavigationDataCSVSequentialPlayer::New(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //check if the stream is valid and skip file if not /* if (!myPlayer->GetStreamValid()) { MITK_ERROR << "Error in file " << m_FilenameVector.at(i) << ": " << myPlayer->GetErrorMessage() << " ; Skipping file!"; continue; } */ //open file header QString outputname = QString(m_FilenameVector.at(i).c_str()) + "_orientationFile.csv"; m_CurrentWriteFile.open(outputname.toStdString().c_str(), std::ios::out); if (m_CurrentWriteFile.bad()) { MessageBox("Error: Can't open output file!"); return; } //write header to file m_CurrentWriteFile << "Nr;Calypso_Time;Valid_Reference;MeasureTool_Measurement-Tool[x];MeasureTool_Measurement-Tool[y];MeasureTool_Measurement-Tool[z];MeasureTool_Measurement-Tool[qx];MeasureTool_Measurement-Tool[qy];MeasureTool_Measurement-Tool[qz];MeasureTool_Measurement-Tool[qr]\n"; //update pipeline until number of samples is reached int step = 0; mitk::Point3D point1, point2, point3; mitk::Quaternion current_orientation; for (int j = 0; !myPlayer->IsAtEnd(); j++) { myPlayer->Update(); mitk::NavigationData::Pointer currentNavData = myPlayer->GetOutput(0); switch (step) { case 0: step++; point1 = currentNavData->GetPosition(); break; case 1: step++; point2 = currentNavData->GetPosition(); break; case 2: step = 0; point3 = currentNavData->GetPosition(); //compute transform from reference to current points if (point1[0] == 0 && point1[1] == 0 && point1[2] == 0 && point2[0] == 0 && point2[1] == 0 && point2[2] == 0 && point3[0] == 0 && point3[1] == 0 && point3[2] == 0 ) current_orientation.fill(0); else { /* Drehen um eine Achse um das "Umschlagen" zu vermeiden itk::Matrix rot180degreeAroundY; rot180degreeAroundY.Fill(0); rot180degreeAroundY[0][0] = -1; rot180degreeAroundY[1][1] = 1; rot180degreeAroundY[2][2] = -1; point1 = rot180degreeAroundY * point1; point2 = rot180degreeAroundY * point2; point3 = rot180degreeAroundY * point3; */ vtkSmartPointer transform = vtkSmartPointer::New(); vtkSmartPointer sourcePoints = vtkSmartPointer::New(); double sourcepoint1[3] = { point1[0], point1[1], point1[2] }; double sourcepoint2[3] = { point2[0], point2[1], point2[2] }; double sourcepoint3[3] = { point3[0], point3[1], point3[2] }; sourcePoints->InsertNextPoint(sourcepoint1); sourcePoints->InsertNextPoint(sourcepoint2); sourcePoints->InsertNextPoint(sourcepoint3); vtkSmartPointer targetPoints = vtkSmartPointer::New(); double targetpoint1[3] = { m_RefPoint1[0], m_RefPoint1[1], m_RefPoint1[2] }; double targetpoint2[3] = { m_RefPoint2[0], m_RefPoint2[1], m_RefPoint2[2] }; double targetpoint3[3] = { m_RefPoint3[0], m_RefPoint3[1], m_RefPoint3[2] }; targetPoints->InsertNextPoint(targetpoint1); targetPoints->InsertNextPoint(targetpoint2); targetPoints->InsertNextPoint(targetpoint3); transform->SetSourceLandmarks(sourcePoints); transform->SetTargetLandmarks(targetPoints); transform->Modified(); transform->Update(); mitk::Transform::Pointer newTransform = mitk::Transform::New(); newTransform->SetMatrix(transform->GetMatrix()); current_orientation = newTransform->GetOrientation(); //add pointset with the three positions if ((j > 15) && (j < 18)) { mitk::DataNode::Pointer newNode = mitk::DataNode::New(); mitk::PointSet::Pointer newPointSet = mitk::PointSet::New(); newPointSet->InsertPoint(0, point1); newPointSet->InsertPoint(1, point2); newPointSet->InsertPoint(2, point3); QString name = QString(m_FilenameVector.at(i).c_str()); newNode->SetName(name.toStdString().c_str()); newNode->SetData(newPointSet); newNode->SetFloatProperty("pointsize", 0.1); this->GetDataStorage()->Add(newNode); } } break; } m_CurrentWriteFile << i << ";"; m_CurrentWriteFile << currentNavData->GetTimeStamp() << ";"; //IMPORTANT: change to GetIGTTimeStamp in new version! m_CurrentWriteFile << "true;"; m_CurrentWriteFile << currentNavData->GetPosition()[0] << ";"; m_CurrentWriteFile << currentNavData->GetPosition()[1] << ";"; m_CurrentWriteFile << currentNavData->GetPosition()[2] << ";"; m_CurrentWriteFile << current_orientation.x() << ";"; m_CurrentWriteFile << current_orientation.y() << ";"; m_CurrentWriteFile << current_orientation.z() << ";"; m_CurrentWriteFile << current_orientation.r() << ";"; m_CurrentWriteFile << "\n"; } //close output file m_CurrentWriteFile.close(); } MessageBox("Finished!"); } void QmitkIGTTrackingDataEvaluationView::StdMultiWidgetAvailable(QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkIGTTrackingDataEvaluationView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkIGTTrackingDataEvaluationView::OnAddToCurrentList() { //read in files QStringList files = QFileDialog::getOpenFileNames(NULL, "Select one or more files to open", "/", "CSV (*.csv)"); if (files.isEmpty()) return; for (int i = 0; i < files.size(); i++){ std::string tmp = files.at(i).toStdString().c_str(); m_FilenameVector.push_back(tmp); } /* //save old locale char * oldLocale; oldLocale = setlocale( LC_ALL, 0 ); //define own locale std::locale C("C"); setlocale( LC_ALL, "C" ); */ //TODO: check if this is needed here, and load old locale if yes /* //read file std::ifstream file; file.open(filename.toStdString().c_str(), std::ios::in); if (file.good()) { //read out file file.seekg(0L, std::ios::beg); // move to begin of file while (!file.eof()) { std::string buffer; std::getline(file, buffer); // read out file line by line if (buffer.size() > 0) { std::string thisFilename = ""; if (m_Controls->m_AddPath->isChecked()) thisFilename = m_Controls->m_ListPath->text().toStdString(); thisFilename.append(buffer); m_FilenameVector.push_back(thisFilename); } } } */ //fill list at GUI m_Controls->m_FileList->clear(); for (unsigned int i = 0; i < m_FilenameVector.size(); i++) { new QListWidgetItem(tr(m_FilenameVector.at(i).c_str()), m_Controls->m_FileList); } } void QmitkIGTTrackingDataEvaluationView::OnLoadFileList() { m_FilenameVector = std::vector(); m_FilenameVector.clear(); OnAddToCurrentList(); } void QmitkIGTTrackingDataEvaluationView::OnEvaluateDataAll() { std::vector results5cm, results15cm, results30cm, resultsAccum; mitk::HummelProtocolEvaluation::HummelProtocolMeasurementVolume volume; if (m_Controls->m_standardVolume->isChecked()) { volume = mitk::HummelProtocolEvaluation::standard; mitk::HummelProtocolEvaluation::Evaluate5cmDistances(m_PointSetMeanPositions, volume, results5cm); mitk::HummelProtocolEvaluation::Evaluate15cmDistances(m_PointSetMeanPositions, volume, results15cm); - mitk::HummelProtocolEvaluation::Evaluate30cmDistances(m_PointSetMeanPositions, volume, results15cm); + mitk::HummelProtocolEvaluation::Evaluate30cmDistances(m_PointSetMeanPositions, volume, results30cm); mitk::HummelProtocolEvaluation::EvaluateAccumulatedDistances(m_PointSetMeanPositions, volume, resultsAccum); } else { volume = mitk::HummelProtocolEvaluation::small; mitk::HummelProtocolEvaluation::Evaluate5cmDistances(m_PointSetMeanPositions, volume, results5cm); } //write results to file std::stringstream filename5cm; filename5cm << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".results5cm.csv"; MITK_INFO << "Writing output to file " << filename5cm.str(); writeToFile(filename5cm.str(), results5cm); std::stringstream filename15cm; filename15cm << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".results15cm.csv"; MITK_INFO << "Writing output to file " << filename15cm.str(); writeToFile(filename15cm.str(), results15cm); std::stringstream filename30cm; filename30cm << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".results30cm.csv"; MITK_INFO << "Writing output to file " << filename30cm.str(); writeToFile(filename30cm.str(), results30cm); std::stringstream filenameAccum; filenameAccum << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".resultsAccumDist.csv"; MITK_INFO << "Writing output to file " << filenameAccum.str(); writeToFile(filenameAccum.str(), resultsAccum); } void QmitkIGTTrackingDataEvaluationView::OnEvaluateData() { //open output file m_CurrentWriteFile.open(std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str(), std::ios::out); if (m_CurrentWriteFile.bad()) { MessageBox("Error: Can't open output file!"); return; } + std::vector jitterValues; + //write output file header WriteHeader(); //start loop and iterate through all files of list for (int i = 0; i < m_FilenameVector.size(); i++) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = mitk::NavigationDataCSVSequentialPlayer::New(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //check if the stream is valid and skip file if not /* if (!myPlayer->GetStreamValid()) { MITK_ERROR << "Error in file " << m_FilenameVector.at(i) << ": " << myPlayer->GetErrorMessage() << " ; Skipping file!"; continue; } */ //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (int j = 0; j < myPlayer->GetNumberOfOutputs(); j++) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); } //update pipline until number of samlples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); j++) { myEvaluationFilter->Update(); //Debug output: //std::cout.precision(5); //std::cout << "Euler " << j << ";" << myPlayer->GetOutput()->GetOrientation().rotation_euler_angles()[0] << ";" << myPlayer->GetOutput()->GetOrientation().rotation_euler_angles()[1] << ";" << myPlayer->GetOutput()->GetOrientation().rotation_euler_angles()[2] << "\n"; } + //store all jitter values in separate vector for statistics + jitterValues.push_back({ myEvaluationFilter->GetPositionErrorRMS(0), "RMS" }); + //write result to output file WriteDataSet(myEvaluationFilter, m_FilenameVector.at(i)); } - //close output file + //close output file for single data m_CurrentWriteFile.close(); + //compute statistics + std::vector jitterStatistics = mitk::HummelProtocolEvaluation::ComputeStatistics(jitterValues); + MITK_INFO << "## Jitter (RMS) statistics: ##"; + for (auto jitterStat : jitterStatistics) {MITK_INFO << jitterStat.description << ": " << jitterStat.distanceError;} + + //write statistic results to separate file + std::stringstream filenameJitterStat; + filenameJitterStat << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".resultsJitterStatistics.csv"; + MITK_INFO << "Writing output to file " << filenameJitterStat.str(); + writeToFile(filenameJitterStat.str(), jitterStatistics); + //calculate angles if option is on if (m_Controls->m_settingDifferenceAngles->isChecked() || m_Controls->m_DifferencesSLERP->isChecked()) CalculateDifferenceAngles(); MessageBox("Finished!"); } void QmitkIGTTrackingDataEvaluationView::OnGeneratePointSetsOfSinglePositions() { m_scalingfactor = m_Controls->m_ScalingFactor->value(); //start loop and iterate through all files of list for (int i = 0; i < m_FilenameVector.size(); i++) { //create point set for this file mitk::PointSet::Pointer thisPointSet = mitk::PointSet::New(); //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = mitk::NavigationDataCSVSequentialPlayer::New(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //check if the stream is valid and skip file if not /* if (!myPlayer->GetStreamValid()) { MITK_ERROR << "Error in file " << m_FilenameVector.at(i) << ": " << myPlayer->GetErrorMessage() << " ; Skipping file!"; continue; } */ //update pipline until number of samlples is reached and store every single point for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); j++) { myPlayer->Update(); mitk::Point3D thisPoint = myPlayer->GetOutput()->GetPosition(); thisPoint[0] *= m_scalingfactor; thisPoint[1] *= m_scalingfactor; thisPoint[2] *= m_scalingfactor; thisPointSet->InsertPoint(j, thisPoint); } //add point set to data storage mitk::DataNode::Pointer newNode = mitk::DataNode::New(); QString name = this->m_Controls->m_prefix->text() + QString("PointSet_of_All_Positions_") + QString::number(i); newNode->SetName(name.toStdString()); newNode->SetData(thisPointSet); this->GetDataStorage()->Add(newNode); } } void QmitkIGTTrackingDataEvaluationView::OnGeneratePointSet() { m_scalingfactor = m_Controls->m_ScalingFactor->value(); mitk::PointSet::Pointer generatedPointSet = mitk::PointSet::New(); //start loop and iterate through all files of list for (int i = 0; i < m_FilenameVector.size(); i++) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = mitk::NavigationDataCSVSequentialPlayer::New(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //check if the stream is valid and skip file if not /* if (!myPlayer->GetStreamValid()) { MITK_ERROR << "Error in file " << m_FilenameVector.at(i) << ": " << myPlayer->GetErrorMessage() << " ; Skipping file!"; continue; } */ //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (int j = 0; j < myPlayer->GetNumberOfOutputs(); j++) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); } //update pipline until number of samlples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); j++) { myEvaluationFilter->Update(); } //add mean position to point set mitk::Point3D meanPos = myEvaluationFilter->GetPositionMean(0); if (m_scalingfactor != 1) { meanPos[0] *= m_scalingfactor; meanPos[1] *= m_scalingfactor; meanPos[2] *= m_scalingfactor; } generatedPointSet->InsertPoint(i, meanPos); } //add point set to data storage mitk::DataNode::Pointer newNode = mitk::DataNode::New(); QString name = this->m_Controls->m_prefix->text() + "PointSet_of_Mean_Positions"; newNode->SetName(name.toStdString()); newNode->SetData(generatedPointSet); newNode->SetFloatProperty("pointsize", 5); this->GetDataStorage()->Add(newNode); m_PointSetMeanPositions = generatedPointSet; } void QmitkIGTTrackingDataEvaluationView::OnGenerateRotationLines() { m_scalingfactor = m_Controls->m_ScalingFactor->value(); //start loop and iterate through all files of list for (int i = 0; i < m_FilenameVector.size(); i++) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = mitk::NavigationDataCSVSequentialPlayer::New(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //check if the stream is valid and skip file if not /* if (!myPlayer->GetStreamValid()) { MITK_ERROR << "Error in file " << m_FilenameVector.at(i) << ": " << myPlayer->GetErrorMessage() << " ; Skipping file!"; } else */ { //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (int j = 0; j < myPlayer->GetNumberOfOutputs(); j++) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); } //update pipline until number of samlples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); j++) { myEvaluationFilter->Update(); /* if (!myPlayer->GetStreamValid()) { MITK_ERROR << "Error in file " << m_FilenameVector.at(i) << ": " << myPlayer->GetErrorMessage() << " ; Skipping file!"; continue; } */ } //if (!myPlayer->IsAtEnd()) continue; //create line from mean pos to a second point which lies along the sensor (1,0,0 in tool coordinates for aurora) mitk::Point3D meanPos = myEvaluationFilter->GetPositionMean(0); if (m_scalingfactor != 1) { meanPos[0] *= m_scalingfactor; meanPos[1] *= m_scalingfactor; meanPos[2] *= m_scalingfactor; } mitk::Point3D secondPoint; mitk::Point3D thirdPoint; mitk::Point3D fourthPoint; mitk::FillVector3D(secondPoint, 2, 0, 0); //X vnl_vector secondPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * secondPoint.Get_vnl_vector() + meanPos.Get_vnl_vector(); mitk::Point3D secondPointTransformedMITK; mitk::FillVector3D(secondPointTransformedMITK, secondPointTransformed[0], secondPointTransformed[1], secondPointTransformed[2]); mitk::FillVector3D(thirdPoint, 0, 4, 0); //Y vnl_vector thirdPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * thirdPoint.Get_vnl_vector() + meanPos.Get_vnl_vector(); mitk::Point3D thirdPointTransformedMITK; mitk::FillVector3D(thirdPointTransformedMITK, thirdPointTransformed[0], thirdPointTransformed[1], thirdPointTransformed[2]); mitk::FillVector3D(fourthPoint, 0, 0, 6); //Z vnl_vector fourthPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * fourthPoint.Get_vnl_vector() + meanPos.Get_vnl_vector(); mitk::Point3D fourthPointTransformedMITK; mitk::FillVector3D(fourthPointTransformedMITK, fourthPointTransformed[0], fourthPointTransformed[1], fourthPointTransformed[2]); mitk::PointSet::Pointer rotationLine = mitk::PointSet::New(); rotationLine->InsertPoint(0, secondPointTransformedMITK); rotationLine->InsertPoint(1, meanPos); rotationLine->InsertPoint(2, thirdPointTransformedMITK); rotationLine->InsertPoint(3, meanPos); rotationLine->InsertPoint(4, fourthPointTransformedMITK); mitk::DataNode::Pointer newNode = mitk::DataNode::New(); QString nodeName = this->m_Controls->m_prefix->text() + "RotationLineNumber" + QString::number(i); newNode->SetName(nodeName.toStdString()); newNode->SetData(rotationLine); newNode->SetBoolProperty("show contour", true); newNode->SetFloatProperty("pointsize", 0.5); this->GetDataStorage()->Add(newNode); } } } void QmitkIGTTrackingDataEvaluationView::OnGenerateGroundTruthPointSet() { mitk::PointSet::Pointer generatedPointSet = mitk::PointSet::New(); int currentPointID = 0; mitk::Point3D currentPoint; mitk::FillVector3D(currentPoint, 0, 0, 0); for (int i = 0; i < m_Controls->m_PointNumber2->value(); i++) { for (int j = 0; j < m_Controls->m_PointNumber1->value(); j++) { generatedPointSet->InsertPoint(currentPointID, currentPoint); currentPointID++; currentPoint[1] += m_Controls->m_PointDistance->value(); } currentPoint[1] = 0; currentPoint[2] += m_Controls->m_PointDistance->value(); } mitk::DataNode::Pointer newNode = mitk::DataNode::New(); QString nodeName = "GroundTruthPointSet_" + QString::number(m_Controls->m_PointNumber1->value()) + "x" + QString::number(m_Controls->m_PointNumber2->value()) + "_(" + QString::number(m_Controls->m_PointDistance->value()) + "mm)"; newNode->SetName(nodeName.toStdString()); newNode->SetData(generatedPointSet); newNode->SetFloatProperty("pointsize", 5); this->GetDataStorage()->Add(newNode); } void QmitkIGTTrackingDataEvaluationView::OnConvertCSVtoXMLFile() { if (m_Controls->m_ConvertSingleFile->isChecked()) { //convert one file int lines = ConvertOneFile(this->m_Controls->m_InputCSV->text().toStdString(), this->m_Controls->m_OutputXML->text().toStdString()); QString result = "Converted one file with" + QString::number(lines) + " data sets"; MessageBox(result.toStdString()); } else //converte file list { if (m_CSVtoXMLInputFilenameVector.empty() || m_CSVtoXMLOutputFilenameVector.empty()) { MessageBox("Error: one list is not loaded!"); return; } else if (m_CSVtoXMLInputFilenameVector.size() != m_CSVtoXMLOutputFilenameVector.size()) { MessageBox("Error: lists do not have the same number of files!"); return; } for (int i = 0; i < m_CSVtoXMLInputFilenameVector.size(); i++) { int lines = ConvertOneFile(m_CSVtoXMLInputFilenameVector.at(i), m_CSVtoXMLOutputFilenameVector.at(i)); } QString result = "Converted " + QString::number(m_CSVtoXMLInputFilenameVector.size()) + " files from file list!"; MessageBox(result.toStdString()); } } int QmitkIGTTrackingDataEvaluationView::ConvertOneFile(std::string inputFilename, std::string outputFilename) { std::vector myNavigationDatas = GetNavigationDatasFromFile(inputFilename); mitk::NavigationDataRecorderDeprecated::Pointer myRecorder = mitk::NavigationDataRecorderDeprecated::New(); myRecorder->SetFileName(outputFilename.c_str()); mitk::NavigationData::Pointer input = mitk::NavigationData::New(); if (m_Controls->m_ConvertCSV->isChecked()) myRecorder->SetOutputFormat(mitk::NavigationDataRecorderDeprecated::csv); myRecorder->AddNavigationData(input); myRecorder->StartRecording(); for (int i = 0; i < myNavigationDatas.size(); i++) { input->Graft(myNavigationDatas.at(i)); myRecorder->Update(); } myRecorder->StopRecording(); return myNavigationDatas.size(); } void QmitkIGTTrackingDataEvaluationView::OnCSVtoXMLLoadInputList() { //read in filename QString filename = QFileDialog::getOpenFileName(NULL, tr("Open Measurement Filename List"), "/", tr("All Files (*.*)")); if (filename.isNull()) return; m_CSVtoXMLInputFilenameVector = this->GetFileContentLineByLine(filename.toStdString()); m_Controls->m_labelCSVtoXMLInputList->setText("READY"); } void QmitkIGTTrackingDataEvaluationView::OnCSVtoXMLLoadOutputList() { //read in filename QString filename = QFileDialog::getOpenFileName(NULL, tr("Open Measurement Filename List"), "/", tr("All Files (*.*)")); if (filename.isNull()) return; m_CSVtoXMLOutputFilenameVector = this->GetFileContentLineByLine(filename.toStdString()); m_Controls->m_labelCSVtoXMLOutputList->setText("READY"); } void QmitkIGTTrackingDataEvaluationView::MessageBox(std::string s) { QMessageBox msgBox; msgBox.setText(s.c_str()); msgBox.exec(); } void QmitkIGTTrackingDataEvaluationView::WriteHeader() { m_CurrentWriteFile << "Filename;"; m_CurrentWriteFile << "N;"; m_CurrentWriteFile << "N_invalid;"; m_CurrentWriteFile << "Percentage_invalid;"; if (m_Controls->m_settingPosMean->isChecked()) { m_CurrentWriteFile << "Position_Mean[x];"; m_CurrentWriteFile << "Position_Mean[y];"; m_CurrentWriteFile << "Position_Mean[z];"; } if (m_Controls->m_settingPosStabw->isChecked()) { m_CurrentWriteFile << "Position_StandDev[x];"; m_CurrentWriteFile << "Position_StandDev[y];"; m_CurrentWriteFile << "Position_StandDev[z];"; } if (m_Controls->m_settingPosSampleStabw->isChecked()) { m_CurrentWriteFile << "Position_SampleStandDev[x];"; m_CurrentWriteFile << "Position_SampleStandDev[y];"; m_CurrentWriteFile << "Position_SampleStandDev[z];"; } if (m_Controls->m_settingQuaternionMean->isChecked()) { m_CurrentWriteFile << "Quaternion_Mean[qx];"; m_CurrentWriteFile << "Quaternion_Mean[qy];"; m_CurrentWriteFile << "Quaternion_Mean[qz];"; m_CurrentWriteFile << "Quaternion_Mean[qr];"; } if (m_Controls->m_settionQuaternionStabw->isChecked()) { m_CurrentWriteFile << "Quaternion_StandDev[qx];"; m_CurrentWriteFile << "Quaternion_StandDev[qy];"; m_CurrentWriteFile << "Quaternion_StandDev[qz];"; m_CurrentWriteFile << "Quaternion_StandDev[qr];"; } if (m_Controls->m_settingPosErrorMean->isChecked()) m_CurrentWriteFile << "PositionError_Mean;"; if (m_Controls->m_settingPosErrorStabw->isChecked()) m_CurrentWriteFile << "PositionError_StandDev;"; if (m_Controls->m_settingPosErrorSampleStabw->isChecked()) m_CurrentWriteFile << "PositionError_SampleStandDev;"; if (m_Controls->m_settingPosErrorRMS->isChecked()) m_CurrentWriteFile << "PositionError_RMS;"; if (m_Controls->m_settingPosErrorMedian->isChecked()) m_CurrentWriteFile << "PositionError_Median;"; if (m_Controls->m_settingPosErrorMinMax->isChecked()) { m_CurrentWriteFile << "PositionError_Max;"; m_CurrentWriteFile << "PositionError_Min;"; } if (m_Controls->m_settingEulerMean->isChecked()) { m_CurrentWriteFile << "Euler_tx;"; m_CurrentWriteFile << "Euler_ty;"; m_CurrentWriteFile << "Euler_tz;"; } if (m_Controls->m_settingEulerRMS->isChecked()) { m_CurrentWriteFile << "EulerErrorRMS (rad);"; m_CurrentWriteFile << "EulerErrorRMS (grad);"; } m_CurrentWriteFile << "\n"; } void QmitkIGTTrackingDataEvaluationView::WriteDataSet(mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter, std::string dataSetName) { if (myEvaluationFilter->GetNumberOfOutputs() == 0) m_CurrentWriteFile << "Error: no input \n"; else { m_CurrentWriteFile << dataSetName << ";"; m_CurrentWriteFile << myEvaluationFilter->GetNumberOfAnalysedNavigationData(0) << ";"; m_CurrentWriteFile << myEvaluationFilter->GetNumberOfInvalidSamples(0) << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPercentageOfInvalidSamples(0) << ";"; if (m_Controls->m_settingPosMean->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetPositionMean(0)[0] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionMean(0)[1] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionMean(0)[2] << ";"; } if (m_Controls->m_settingPosStabw->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetPositionStandardDeviation(0)[0] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionStandardDeviation(0)[1] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionStandardDeviation(0)[2] << ";"; } if (m_Controls->m_settingPosSampleStabw->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetPositionSampleStandardDeviation(0)[0] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionSampleStandardDeviation(0)[1] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionSampleStandardDeviation(0)[2] << ";"; } if (m_Controls->m_settingQuaternionMean->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetQuaternionMean(0).x() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionMean(0).y() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionMean(0).z() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionMean(0).r() << ";"; } if (m_Controls->m_settionQuaternionStabw->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetQuaternionStandardDeviation(0).x() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionStandardDeviation(0).y() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionStandardDeviation(0).z() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionStandardDeviation(0).r() << ";"; } if (m_Controls->m_settingPosErrorMean->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorMean(0) << ";"; if (m_Controls->m_settingPosErrorStabw->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorStandardDeviation(0) << ";"; if (m_Controls->m_settingPosErrorSampleStabw->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorSampleStandardDeviation(0) << ";"; if (m_Controls->m_settingPosErrorRMS->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorRMS(0) << ";"; if (m_Controls->m_settingPosErrorMedian->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorMedian(0) << ";"; if (m_Controls->m_settingPosErrorMinMax->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorMax(0) << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorMin(0) << ";"; } if (m_Controls->m_settingEulerMean->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesMean(0)[0] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesMean(0)[1] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesMean(0)[2] << ";"; } if (m_Controls->m_settingEulerRMS->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesRMS(0) << ";"; m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesRMSDegree(0) << ";"; } m_CurrentWriteFile << "\n"; } } void QmitkIGTTrackingDataEvaluationView::CalculateDifferenceAngles() { std::vector EvaluationDataCollection; //start loop and iterate through all files of list: store the evaluation data for (int i = 0; i < m_FilenameVector.size(); i++) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = mitk::NavigationDataCSVSequentialPlayer::New(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //check if the stream is valid and skip file if not /* if (!myPlayer->GetStreamValid()) { MITK_ERROR << "Error in file " << m_FilenameVector.at(i) << ": " << myPlayer->GetErrorMessage() << " ; Skipping file!"; } else */ { //connect pipeline for (int j = 0; j < myPlayer->GetNumberOfOutputs(); j++) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); } //update pipline until number of samlples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); j++) { myEvaluationFilter->Update(); } } myEvaluationFilter->SetInput(NULL); myPlayer = NULL; EvaluationDataCollection.push_back(myEvaluationFilter); } //calculation and writing of output data //open output file m_CurrentAngleDifferencesWriteFile.open(std::string((m_Controls->m_OutputFilename->text() + ".angledifferences.csv").toUtf8()).c_str(), std::ios::out); if (m_CurrentAngleDifferencesWriteFile.bad()) { MessageBox("Error: Can't open output file for angle differences calculation!"); return; } //write header WriteDifferenceAnglesHeader(); //compute angle differences QString pos1 = "invalid"; QString pos2 = "invalid"; //now iterate through all evaluation data and calculate the angles for (int i = 0; i < m_FilenameVector.size(); i++) { pos1 = QString::fromStdString(itksys::SystemTools::GetFilenameWithoutLastExtension(m_FilenameVector.at(i))); for (int j = 0; j < m_FilenameVector.size(); j++) { pos2 = QString::fromStdString(itksys::SystemTools::GetFilenameWithoutLastExtension(m_FilenameVector.at(j))); mitk::Quaternion q1; mitk::Quaternion q2; if (m_Controls->m_DifferencesSLERP->isChecked()) { //compute slerp average q1 = GetSLERPAverage(EvaluationDataCollection.at(i)); q2 = GetSLERPAverage(EvaluationDataCollection.at(j)); } else { //compute arithmetic average q1 = EvaluationDataCollection.at(i)->GetQuaternionMean(0); q2 = EvaluationDataCollection.at(j)->GetQuaternionMean(0); } itk::Vector rotationVec; //adapt for Aurora 5D tools: [0,0,1000] rotationVec[0] = 10000; //X rotationVec[1] = 0; //Y rotationVec[2] = 0; //Z double AngleBetweenTwoQuaternions = mitk::StaticIGTHelperFunctions::GetAngleBetweenTwoQuaterions(q1, q2, rotationVec); //write data set WriteDifferenceAnglesDataSet(pos1.toStdString(), pos2.toStdString(), i, j, AngleBetweenTwoQuaternions); } } //close output file m_CurrentAngleDifferencesWriteFile.close(); } void QmitkIGTTrackingDataEvaluationView::WriteDifferenceAnglesHeader() { m_CurrentAngleDifferencesWriteFile << "Name;Idx1;Idx2;Angle [Degree]\n"; } void QmitkIGTTrackingDataEvaluationView::WriteDifferenceAnglesDataSet(std::string pos1, std::string pos2, int idx1, int idx2, double angle) { //double PI = 3.1415926535897932384626433832795; //double angle_degree = angle * 180 / PI; m_CurrentAngleDifferencesWriteFile << "Angle between " << pos1 << " and " << pos2 << ";" << idx1 << ";" << idx2 << ";" << angle << "\n";//<< ";" << angle_degree << "\n"; MITK_INFO << "Angle: " << angle; } std::vector QmitkIGTTrackingDataEvaluationView::GetNavigationDatasFromFile(std::string filename) { std::vector returnValue = std::vector(); std::vector fileContentLineByLine = GetFileContentLineByLine(filename); for (int i = 1; i < fileContentLineByLine.size(); i++) //skip header so start at 1 { returnValue.push_back(GetNavigationDataOutOfOneLine(fileContentLineByLine.at(i))); } return returnValue; } std::vector QmitkIGTTrackingDataEvaluationView::GetFileContentLineByLine(std::string filename) { std::vector readData = std::vector(); //save old locale char * oldLocale; oldLocale = setlocale(LC_ALL, 0); //define own locale std::locale C("C"); setlocale(LC_ALL, "C"); //read file std::ifstream file; file.open(filename.c_str(), std::ios::in); if (file.good()) { //read out file file.seekg(0L, std::ios::beg); // move to begin of file while (!file.eof()) { std::string buffer; std::getline(file, buffer); // read out file line by line if (buffer.size() > 0) readData.push_back(buffer); } } file.close(); //switch back to old locale setlocale(LC_ALL, oldLocale); return readData; } mitk::NavigationData::Pointer QmitkIGTTrackingDataEvaluationView::GetNavigationDataOutOfOneLine(std::string line) { mitk::NavigationData::Pointer returnValue = mitk::NavigationData::New(); QString myLine = QString(line.c_str()); QStringList myLineList = myLine.split(';'); mitk::Point3D position; mitk::Quaternion orientation; double time = myLineList.at(1).toDouble(); bool valid = false; if (myLineList.at(2).toStdString() == "1") valid = true; position[0] = myLineList.at(3).toDouble(); position[1] = myLineList.at(4).toDouble(); position[2] = myLineList.at(5).toDouble(); orientation[0] = myLineList.at(6).toDouble(); orientation[1] = myLineList.at(7).toDouble(); orientation[2] = myLineList.at(8).toDouble(); orientation[3] = myLineList.at(9).toDouble(); //returnValue->SetTimeStamp(time); returnValue->SetDataValid(valid); returnValue->SetPosition(position); returnValue->SetOrientation(orientation); return returnValue; } mitk::Quaternion QmitkIGTTrackingDataEvaluationView::GetSLERPAverage(mitk::NavigationDataEvaluationFilter::Pointer evaluationFilter) { mitk::Quaternion average; //build a vector of quaternions from the evaulation filter (caution always takes the first (0) input of the filter std::vector quaternions = std::vector(); for (int i = 0; i < evaluationFilter->GetNumberOfAnalysedNavigationData(0); i++) { mitk::Quaternion currentq = evaluationFilter->GetLoggedOrientation(i, 0); quaternions.push_back(currentq); } //compute the slerp average using the quaternion averaging class mitk::QuaternionAveraging::Pointer myAverager = mitk::QuaternionAveraging::New(); average = myAverager->CalcAverage(quaternions); return average; } void QmitkIGTTrackingDataEvaluationView::writeToFile(std::string filename, std::vector values) { std::fstream currentFile; currentFile.open(filename.c_str(), std::ios::out); if (currentFile.bad()) { MITK_WARN << "Cannot open file, aborting!"; return; } currentFile << "Description" << ";" << "Error[mm]" << "\n"; for (auto currentError : values) { currentFile << currentError.description << ";" << currentError.distanceError << "\n"; } currentFile.close(); } diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.h b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.h index f4d6342ef4..6918d4d078 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 @@ -1,131 +1,132 @@ /*=================================================================== 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 /*! \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(); /** 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); //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; }; #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 907459c9b6..c081daf5b1 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 @@ -1,1173 +1,1242 @@ QmitkIGTTrackingDataEvaluationViewControls 0 0 378 955 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 General Number of samples to analyze: Qt::Horizontal 40 20 1000000 150 Scaling Factor for Visualization: Qt::Horizontal 38 20 1.000000000000000 Tracking Volume: Standard Volume (10 X 9 Positions) true Small Volume (3 X 4 Positions) Output per data set <!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; text-decoration: underline;">Position</span></p></body></html> Mean (x,y,z) + + true + Standard Deviation (x,y,z) Sample Standard Deviation (x,y,z) <!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; text-decoration: underline;">Orientation</span></p></body></html> 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) <!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; text-decoration: underline;">Position Error</span></p></body></html> Mean Standard Deviation Sample Standard Deviation RMS + + true + Median Min/Max <!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; text-decoration: underline;">Orientation Error</span></p></body></html> Euler RMS Qt::Vertical 20 344 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
 diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.cpp b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.cpp index a45374a938..b2c9db94b0 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.cpp @@ -1,365 +1,383 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #define _USE_MATH_DEFINES #include "mitkHummelProtocolEvaluation.h" #include #include #include #include #include #include #include #include bool mitk::HummelProtocolEvaluation::Evaluate15cmDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector &Results) { if (m != mitk::HummelProtocolEvaluation::standard) { MITK_WARN << "15 cm distances are only evaluated for standard volumes, aborting!"; return false; } MITK_INFO << "########### 15 cm distance errors #############"; //convert measurements to matrix itk::Matrix, 9, 10> matrix = ParseMatrixStandardVolume(p); //these are the variables for the results: std::vector distances; std::vector descriptions; //evaluation of rows int distanceCounter = 0; for (int row = 0; row < 9; row++) //rows for (int distance = 0; distance < 7; distance++) { distanceCounter++; mitk::Point3D point1 = p->GetPoint(row * 10 + distance); mitk::Point3D point2 = p->GetPoint(row * 10 + distance + 3); distances.push_back(point1.EuclideanDistanceTo(point2)); std::stringstream description; description << "Distance(" << distanceCounter << ") " << (row + 1) << "/" << (distance + 1) << " to " << (row + 1) << "/" << (distance + 4); descriptions.push_back(description.str()); } //evaluation of columns for (int column = 0; column < 10; column++) for (int row = 0; row < 6; row++) { distanceCounter++; mitk::Point3D point1 = matrix[row][column]; mitk::Point3D point2 = matrix[row + 3][column]; distances.push_back(point1.EuclideanDistanceTo(point2)); std::stringstream description; description << "Distance(" << distanceCounter << ") " << (row + 1) << "/" << (column + 1) << " to " << (row + 4) << "/" << (column + 1); descriptions.push_back(description.str()); } //compute all errors for (int i = 0; i < distances.size(); i++) { HummelProtocolDistanceError currentError; currentError.distanceError = abs(distances.at(i) - (double)150.0); currentError.description = descriptions.at(i); Results.push_back(currentError); MITK_INFO << "Error " << currentError.description << " : " << currentError.distanceError; } //compute statistics std::vector statistics = mitk::HummelProtocolEvaluation::ComputeStatistics(Results); for (auto currentError : statistics) { Results.push_back(currentError); MITK_INFO << currentError.description << " : " << currentError.distanceError; } return true; } bool mitk::HummelProtocolEvaluation::Evaluate30cmDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector &Results) { if (m != mitk::HummelProtocolEvaluation::standard) { MITK_WARN << "30 cm distances are only evaluated for standard volumes, aborting!"; return false; } MITK_INFO << "########### 30 cm distance errors #############"; //convert measurements to matrix itk::Matrix, 9, 10> matrix = ParseMatrixStandardVolume(p); //these are the variables for the results: std::vector distances; std::vector descriptions; //evaluation of rows int distanceCounter = 0; for (int row = 0; row < 9; row++) //rows for (int distance = 0; distance < 4; distance++) { distanceCounter++; mitk::Point3D point1 = p->GetPoint(row * 10 + distance); mitk::Point3D point2 = p->GetPoint(row * 10 + distance + 6); distances.push_back(point1.EuclideanDistanceTo(point2)); std::stringstream description; description << "Distance(" << distanceCounter << ") " << (row + 1) << "/" << (distance + 1) << " to " << (row + 1) << "/" << (distance + 7); descriptions.push_back(description.str()); } //evaluation of columns for (int column = 0; column < 10; column++) for (int row = 0; row < 3; row++) { distanceCounter++; mitk::Point3D point1 = matrix[row][column]; mitk::Point3D point2 = matrix[row + 6][column]; distances.push_back(point1.EuclideanDistanceTo(point2)); std::stringstream description; description << "Distance(" << distanceCounter << ") " << (row + 1) << "/" << (column + 1) << " to " << (row + 7) << "/" << (column + 1); descriptions.push_back(description.str()); } //compute all errors for (int i = 0; i < distances.size(); i++) { HummelProtocolDistanceError currentError; currentError.distanceError = abs(distances.at(i) - (double)300.0); currentError.description = descriptions.at(i); Results.push_back(currentError); MITK_INFO << "Error " << currentError.description << " : " << currentError.distanceError; } //compute statistics std::vector statistics = mitk::HummelProtocolEvaluation::ComputeStatistics(Results); for (auto currentError : statistics) { Results.push_back(currentError); MITK_INFO << currentError.description << " : " << currentError.distanceError; } return true; } bool mitk::HummelProtocolEvaluation::EvaluateAccumulatedDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector &Results) { if (m != mitk::HummelProtocolEvaluation::standard) { MITK_WARN << "Accumulated distances are only evaluated for standard volumes, aborting!"; return false; } //convert measurements to matrix itk::Matrix, 9, 10> matrix = ParseMatrixStandardVolume(p); MITK_INFO << "########### accumulated distance errors #############"; int distanceCounter = 0; //evaluation of rows for (int row = 0; row < 9; row++) //rows for (int distance = 0; distance < 9; distance++) { distanceCounter++; mitk::Point3D point1 = p->GetPoint(row * 10); mitk::Point3D point2 = p->GetPoint(row * 10 + distance + 1); std::stringstream description; description << "Distance(" << distanceCounter << ") " << (row + 1) << "/1 to " << (row + 1) << "/" << (distance + 2); //compute error HummelProtocolDistanceError currentError; currentError.distanceError = abs(point1.EuclideanDistanceTo(point2) - (double)(50.0*(distance+1))); currentError.description = description.str(); Results.push_back(currentError); MITK_INFO << "Error " << currentError.description << " : " << currentError.distanceError; } //compute statistics std::vector statistics = mitk::HummelProtocolEvaluation::ComputeStatistics(Results); for (auto currentError : statistics) { Results.push_back(currentError); MITK_INFO << currentError.description << " : " << currentError.distanceError; } return true; } bool mitk::HummelProtocolEvaluation::Evaluate5cmDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector &Results) { MITK_INFO << "########### 5 cm distance errors #############"; std::vector distances; std::vector descriptions; switch (m) { case small: if (p->GetSize() != 12) { MITK_WARN << "Wrong number of points: " << p->GetSize() << " (expected 12), aborting"; return false; } MITK_INFO << "Computing Hummel protocol distance errors for small measurement volumes (12 points)..."; //row 1 distances.push_back(p->GetPoint(0).EuclideanDistanceTo(p->GetPoint(1))); //0 descriptions.push_back("Distance 4/4 to 4/5"); distances.push_back(p->GetPoint(1).EuclideanDistanceTo(p->GetPoint(2))); //1 descriptions.push_back("Distance 4/5 to 4/6"); distances.push_back(p->GetPoint(2).EuclideanDistanceTo(p->GetPoint(3))); //2 descriptions.push_back("Distance 4/6 to 4/7"); //row 2 distances.push_back(p->GetPoint(4).EuclideanDistanceTo(p->GetPoint(5))); //3 descriptions.push_back("Distance 5/4 to 5/5"); distances.push_back(p->GetPoint(5).EuclideanDistanceTo(p->GetPoint(6))); //4 descriptions.push_back("Distance 5/5 to 5/6"); distances.push_back(p->GetPoint(6).EuclideanDistanceTo(p->GetPoint(7))); //5 descriptions.push_back("Distance 5/6 to 5/7"); //row 3 distances.push_back(p->GetPoint(8).EuclideanDistanceTo(p->GetPoint(9))); //6 descriptions.push_back("Distance 6/4 to 6/5"); distances.push_back(p->GetPoint(9).EuclideanDistanceTo(p->GetPoint(10))); //7 descriptions.push_back("Distance 6/5 to 6/6"); distances.push_back(p->GetPoint(10).EuclideanDistanceTo(p->GetPoint(11))); //8 descriptions.push_back("Distance 6/6 to 6/7"); //column 1 distances.push_back(p->GetPoint(0).EuclideanDistanceTo(p->GetPoint(4))); //9 descriptions.push_back("Distance 4/4 to 5/4"); distances.push_back(p->GetPoint(4).EuclideanDistanceTo(p->GetPoint(8))); //10 descriptions.push_back("Distance 5/4 to 6/4"); //column 2 distances.push_back(p->GetPoint(1).EuclideanDistanceTo(p->GetPoint(5))); //11 descriptions.push_back("Distance 4/5 to 5/5"); distances.push_back(p->GetPoint(5).EuclideanDistanceTo(p->GetPoint(9))); //12 descriptions.push_back("Distance 5/5 to 6/5"); //column 3 distances.push_back(p->GetPoint(2).EuclideanDistanceTo(p->GetPoint(6))); //13 descriptions.push_back("Distance 4/6 to 5/6"); distances.push_back(p->GetPoint(6).EuclideanDistanceTo(p->GetPoint(10))); //14 descriptions.push_back("Distance 5/6 to 6/6"); //column 4 distances.push_back(p->GetPoint(3).EuclideanDistanceTo(p->GetPoint(7))); //15 descriptions.push_back("Distance 4/7 to 5/7"); distances.push_back(p->GetPoint(7).EuclideanDistanceTo(p->GetPoint(11))); //16 descriptions.push_back("Distance 5/7 to 6/7"); break; case standard: if (p->GetSize() != 90) { MITK_WARN << "Wrong number of points (expected 90), aborting"; return false; } MITK_INFO << "Computing Hummel protocol distance errors for standard measurement volumes (90 points)..."; int distanceCounter = 0; //convert measurements to matrix itk::Matrix, 9, 10> matrix = ParseMatrixStandardVolume(p); //evaluation of rows for (int row = 0; row < 9; row++) //rows for (int distance = 0; distance < 9; distance++) { distanceCounter++; mitk::Point3D point1 = p->GetPoint(row*10 + distance); mitk::Point3D point2 = p->GetPoint(row*10 + distance+1); distances.push_back(point1.EuclideanDistanceTo(point2)); std::stringstream description; description << "Distance(" << distanceCounter << ") " << (row + 1) << "/" << (distance + 1) << " to " << (row + 1) << "/" << (distance + 2); descriptions.push_back(description.str()); } //evaluation of columns for (int column = 0; column < 10; column++) for (int row = 0; row < 8; row++) { distanceCounter++; mitk::Point3D point1 = matrix[row][column]; mitk::Point3D point2 = matrix[row+1][column]; distances.push_back(point1.EuclideanDistanceTo(point2)); std::stringstream description; description << "Distance(" << distanceCounter << ") " << (row+1 )<< "/" << (column+1) << " to " << (row + 2) << "/" << (column + 1); descriptions.push_back(description.str()); } break; } //compute all errors for (int i = 0; i < distances.size(); i++) { HummelProtocolDistanceError currentError; currentError.distanceError = abs(distances.at(i) - (double)50.0); currentError.description = descriptions.at(i); Results.push_back(currentError); MITK_INFO << "Error " << currentError.description << " : " << currentError.distanceError; } //compute statistics std::vector statistics = mitk::HummelProtocolEvaluation::ComputeStatistics(Results); for (auto currentError : statistics) { Results.push_back(currentError); MITK_INFO << currentError.description << " : " << currentError.distanceError; } return true; } itk::Matrix, 9, 10> mitk::HummelProtocolEvaluation::ParseMatrixStandardVolume(mitk::PointSet::Pointer p) { itk::Matrix, 9, 10> returnValue = itk::Matrix, 9, 10>(); if (p->GetSize() != 90) { MITK_WARN << "PointSet does not have the right size. Expected 90 got " << p->GetSize() << " ... aborting!"; return returnValue; } for (int row = 0; row < 9; row++) for (int column = 0; column < 10; column++) returnValue[row][column] = p->GetPoint(row * 10 + column); } std::vector mitk::HummelProtocolEvaluation::ComputeStatistics(std::vector values) { std::vector returnValue; //convert input values to boost / using boost accumulators for statistics boost::accumulators::accumulator_set > > acc; for (mitk::HummelProtocolEvaluation::HummelProtocolDistanceError each : values) { acc(each.distanceError); } returnValue.push_back({ boost::accumulators::mean(acc), "Mean" }); //double quantile25th = boost::accumulators::quantile(acc, boost::accumulators::quantile_probability = 0.25); //returnValue.push_back({ boost::accumulators::median(acc), "Median" }); - returnValue.push_back({ boost::accumulators::variance(acc), "Variance" }); + //returnValue.push_back({ boost::accumulators::variance(acc), "Variance" }); returnValue.push_back({ boost::accumulators::min(acc), "Min" }); returnValue.push_back({ boost::accumulators::max(acc), "Max" }); - //don't get the boost stuff working correctly, so computing the quantiles and median by myself: + //don't get the boost stuff working correctly, so computing the quantiles, median and standard deviation by myself: std::vector quantile; for (mitk::HummelProtocolEvaluation::HummelProtocolDistanceError each : values) {quantile.push_back(each.distanceError);} auto const Q1 = quantile.size() / 4; auto const Q2 = quantile.size() / 2; auto const Q3 = Q1 + Q2; std::sort(quantile.begin(),quantile.end()); returnValue.push_back({ quantile[Q1], "Quartile 1" }); returnValue.push_back({ quantile[Q2], "Median" }); returnValue.push_back({ quantile[Q3], "Quartile 3" }); + double mean = boost::accumulators::mean(acc); + double errorSum = 0; + for (mitk::HummelProtocolEvaluation::HummelProtocolDistanceError each : values) + { + double error = pow((each.distanceError - mean),2); + errorSum += error; + } + double variance = errorSum / values.size(); + double sampleVariance = errorSum / (values.size()-1); + double standardDev = sqrt(variance); + double sampleStandardDev = sqrt(sampleVariance); + + returnValue.push_back({ variance, "Variance" }); + returnValue.push_back({ sampleVariance, "Sample Variance" }); + returnValue.push_back({ standardDev, "Standard Deviation" }); + returnValue.push_back({ sampleStandardDev, "Sample Standard Deviation" }); + + return returnValue; } diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.h b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.h index ba3b5c5001..9f20434e89 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.h +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.h @@ -1,87 +1,86 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef MITKHummelProtocolEvaluation_H_HEADER_INCLUDED_ #define MITKHummelProtocolEvaluation_H_HEADER_INCLUDED_ #include #include namespace mitk { /**Documentation * \brief Static methods for evaluations according to the assessment protocol * for EM trackers published by Hummel et al. 2005 [1]. * * [1] Hummel, J. et al. - Design and application of an assessment protocol for electromagnetic tracking systems. Med Phys 32(7), July 2005 * * \ingroup IGT */ class HummelProtocolEvaluation { public: /** Distance error with description. */ struct HummelProtocolDistanceError {double distanceError; std::string description;}; /** Tracking volumes for evaluation. * standard: The standard volume of 9 x 10 measurment points as described in [1] * small: A small volume in the center 3 x 4 measurement points, for smaller field generators [2] * [2] Maier-Hein, L. et al. - Standardized assessment of new electromagnetic field generators in an interventional radiology setting. Med Phys 39(6), June 2012 */ enum HummelProtocolMeasurementVolume { small, standard }; /** Evaluates the 5 cm distances as defined by the Hummel protocol [1,2]. * @return Returns true if evaluation was successfull, false if not. * @param[out] Results Please give an empty vector. The results will be added to this vector. */ static bool Evaluate5cmDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector &Results); /** Evaluates the 15 cm distances as defined by the Hummel protocol [1,2]. * @return Returns true if evaluation was successfull, false if not. * @param[out] Results Please give an empty vector. The results will be added to this vector. */ static bool Evaluate15cmDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector &Results); /** Evaluates the 30 cm distances as defined by the Hummel protocol [1,2]. * @return Returns true if evaluation was successfull, false if not. * @param[out] Results Please give an empty vector. The results will be added to this vector. */ static bool Evaluate30cmDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector &Results); /** Evaluates the accumulated distances as defined by the Hummel protocol [1,2]. * @return Returns true if evaluation was successfull, false if not. * @param[out] Results Please give an empty vector. The results will be added to this vector. */ static bool EvaluateAccumulatedDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector &Results); + /** Computes statistics (as mean, standard deviation, quantiles, min, max, etc.) on the given values. + * The results are stored inside the return value. + */ + static std::vector ComputeStatistics(std::vector values); + protected: /** Converts a pointset holding all measurement points of the hummel protocol in line-by-line order * to an array representing the hummel board. */ static itk::Matrix, 9, 10> ParseMatrixStandardVolume(mitk::PointSet::Pointer p); - - /** Computes statistics (as mean, standard deviation, quantiles, min, max, etc.) on the given values. - * The results are stored inside the return value. - */ - static std::vector ComputeStatistics(std::vector values); - }; } // namespace mitk #endif /* MITKHummelProtocolEvaluation_H_HEADER_INCLUDED_ */