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 d148ecc33f..381ae30b54 100644
--- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.cpp
+++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.cpp
@@ -1,1174 +1,1175 @@
/*=========================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
=========================================================================*/
#include <algorithm>
// Blueberry
#include <berryISelectionService.h>
#include <berryIWorkbenchWindow.h>
// Qmitk
#include "QmitkIGTTrackingDataEvaluationView.h"
#include "QmitkStdMultiWidget.h"
// Qt
#include <QMessageBox>
#include <qfiledialog.h>
#include <qstringlist.h>
// MITK
#include "mitkNavigationDataCSVSequentialPlayer.h"
#include <mitkNavigationDataRecorderDeprecated.h>
#include <mitkQuaternionAveraging.h>
#include <mitkTransform.h>
#include <mitkStaticIGTHelperFunctions.h>
#include <mitkNodePredicateDataType.h>
//ITK
#include <itksys/SystemTools.hxx>
//VNL
#include <vnl/vnl_vector.h>
//vtk headers
#include <vtkPoints.h>
#include <vtkSmartPointer.h>
#include <vtkLandmarkTransform.h>
const std::string QmitkIGTTrackingDataEvaluationView::VIEW_ID = "org.mitk.views.igttrackingdataevaluation";
QmitkIGTTrackingDataEvaluationView::QmitkIGTTrackingDataEvaluationView()
: QmitkFunctionality()
, m_Controls(0)
, m_MultiWidget(nullptr)
, m_scalingfactor(1)
{
m_CSVtoXMLInputFilenameVector = std::vector<std::string>();
m_CSVtoXMLOutputFilenameVector = std::vector<std::string>();
}
QmitkIGTTrackingDataEvaluationView::~QmitkIGTTrackingDataEvaluationView()
{
}
void QmitkIGTTrackingDataEvaluationView::CreateQtPartControl(QWidget *parent)
{
// build up qt view, unless already done
if (!m_Controls)
{
// create GUI widgets from the Qt Designer's .ui file
m_Controls = new Ui::QmitkIGTTrackingDataEvaluationViewControls;
m_Controls->setupUi(parent);
connect(m_Controls->m_LoadInputFileList, SIGNAL(clicked()), this, SLOT(OnLoadFileList()));
connect(m_Controls->m_StartEvaluation, SIGNAL(clicked()), this, SLOT(OnEvaluateData()));
connect(m_Controls->m_AddToCurrentList, SIGNAL(clicked()), this, SLOT(OnAddToCurrentList()));
connect(m_Controls->m_GeneratePointSetOfMeanPositions, SIGNAL(clicked()), this, SLOT(OnGeneratePointSet()));
connect(m_Controls->m_GenerateRotationLines, SIGNAL(clicked()), this, SLOT(OnGenerateRotationLines()));
connect(m_Controls->m_GeneratePointSet, SIGNAL(clicked()), this, SLOT(OnGenerateGroundTruthPointSet()));
connect(m_Controls->m_Convert, SIGNAL(clicked()), this, SLOT(OnConvertCSVtoXMLFile()));
connect(m_Controls->m_loadCSVtoXMLInputList, SIGNAL(clicked()), this, SLOT(OnCSVtoXMLLoadInputList()));
connect(m_Controls->m_loadCSVtoXMLOutputList, SIGNAL(clicked()), this, SLOT(OnCSVtoXMLLoadOutputList()));
connect(m_Controls->m_OrientationCalculationGenerateReference, SIGNAL(clicked()), this, SLOT(OnOrientationCalculation_CalcRef()));
connect(m_Controls->m_OrientationCalculationWriteOrientationsToFile, SIGNAL(clicked()), this, SLOT(OnOrientationCalculation_CalcOrientandWriteToFile()));
connect(m_Controls->m_GeneratePointSetsOfSinglePositions, SIGNAL(clicked()), this, SLOT(OnGeneratePointSetsOfSinglePositions()));
connect(m_Controls->m_StartEvaluationAll, SIGNAL(clicked()), this, SLOT(OnEvaluateDataAll()));
connect(m_Controls->m_GridMatching, SIGNAL(clicked()), this, SLOT(OnPerfomGridMatching()));
connect(m_Controls->m_ComputeRotation, SIGNAL(clicked()), this, SLOT(OnComputeRotation()));
//initialize data storage combo boxes
m_Controls->m_ReferencePointSetComboBox->SetDataStorage(this->GetDataStorage());
m_Controls->m_ReferencePointSetComboBox->SetAutoSelectNewItems(true);
m_Controls->m_ReferencePointSetComboBox->SetPredicate(mitk::NodePredicateDataType::New("PointSet"));
m_Controls->m_MeasurementPointSetComboBox->SetDataStorage(this->GetDataStorage());
m_Controls->m_MeasurementPointSetComboBox->SetAutoSelectNewItems(true);
m_Controls->m_MeasurementPointSetComboBox->SetPredicate(mitk::NodePredicateDataType::New("PointSet"));
}
}
void QmitkIGTTrackingDataEvaluationView::OnComputeRotation()
{
//Get all data from UI
auto EvaluationDataCollection = GetAllDataFromUIList();
//Compute mean Quaternions
auto OrientationVector = GetMeanOrientationsOfAllData(EvaluationDataCollection);
//Compute Rotations
itk::Vector<double> rotationVec;
//adapt for Aurora 5D tools: [0,0,1000]
rotationVec[0] = m_Controls->m_rotVecX->value(); //X
rotationVec[1] = m_Controls->m_rotVecY->value(); //Y
rotationVec[2] = m_Controls->m_rotVecZ->value(); //Z
std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> allOrientationErrors;
for (std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError>::size_type i = 0; i < OrientationVector.size() - 1; ++i)
{
double AngleBetweenTwoQuaternions = mitk::StaticIGTHelperFunctions::GetAngleBetweenTwoQuaterions(OrientationVector.at(i), OrientationVector.at(i+1), rotationVec);
double AngularError = fabs(AngleBetweenTwoQuaternions - 11.25);
std::stringstream description;
description << "Rotation Error ROT" << (i + 1) << " / ROT" << (i + 2);
allOrientationErrors.push_back({ AngularError, description.str() });
MITK_INFO << description.str() << ": " << AngularError;
}
//compute statistics
std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> orientationErrorStatistics;
orientationErrorStatistics = mitk::HummelProtocolEvaluation::ComputeStatistics(allOrientationErrors);
MITK_INFO << "## Rotation error statistics: ##";
for (auto stat : orientationErrorStatistics) { MITK_INFO << stat.description << ": " << stat.distanceError; }
//write results to file
allOrientationErrors.insert(allOrientationErrors.end(), orientationErrorStatistics.begin(), orientationErrorStatistics.end());
allOrientationErrors.push_back({rotationVec[0],"Rot Vector [x]"});
allOrientationErrors.push_back({rotationVec[1], "Rot Vector [y]"});
allOrientationErrors.push_back({rotationVec[2], "Rot Vector [z]"});
std::stringstream filenameOrientationStat;
filenameOrientationStat << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".orientationStatistics.csv";
MITK_INFO << "Writing output to file " << filenameOrientationStat.str();
writeToFile(filenameOrientationStat.str(), allOrientationErrors);
}
void QmitkIGTTrackingDataEvaluationView::OnPerfomGridMatching()
{
mitk::PointSet::Pointer reference = dynamic_cast<mitk::PointSet*>(m_Controls->m_ReferencePointSetComboBox->GetSelectedNode()->GetData());
mitk::PointSet::Pointer measurement = dynamic_cast<mitk::PointSet*>(m_Controls->m_MeasurementPointSetComboBox->GetSelectedNode()->GetData());
//convert point sets to vtk poly data
vtkSmartPointer<vtkPoints> sourcePoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkPoints> targetPoints = vtkSmartPointer<vtkPoints>::New();
for (int i = 0; i<reference->GetSize(); i++)
{
double point[3] = { reference->GetPoint(i)[0], reference->GetPoint(i)[1], reference->GetPoint(i)[2] };
sourcePoints->InsertNextPoint(point);
double point_targets[3] = { measurement->GetPoint(i)[0], measurement->GetPoint(i)[1], measurement->GetPoint(i)[2] };
targetPoints->InsertNextPoint(point_targets);
}
//compute transform
vtkSmartPointer<vtkLandmarkTransform> transform = vtkSmartPointer<vtkLandmarkTransform>::New();
transform->SetSourceLandmarks(sourcePoints);
transform->SetTargetLandmarks(targetPoints);
transform->SetModeToRigidBody();
transform->Modified();
transform->Update();
//compute FRE of transform
double FRE = mitk::StaticIGTHelperFunctions::ComputeFRE(reference, measurement, transform);
MITK_INFO << "FRE after grid matching: " + QString::number(FRE) + " mm";
//convert from vtk to itk data types
itk::Matrix<float, 3, 3> rotationFloat = itk::Matrix<float, 3, 3>();
itk::Vector<float, 3> translationFloat = itk::Vector<float, 3>();
itk::Matrix<double, 3, 3> rotationDouble = itk::Matrix<double, 3, 3>();
itk::Vector<double, 3> translationDouble = itk::Vector<double, 3>();
vtkSmartPointer<vtkMatrix4x4> m = transform->GetMatrix();
for (int k = 0; k<3; k++) for (int l = 0; l<3; l++)
{
rotationFloat[k][l] = m->GetElement(k, l);
rotationDouble[k][l] = m->GetElement(k, l);
}
for (int k = 0; k<3; k++)
{
translationFloat[k] = m->GetElement(k, 3);
translationDouble[k] = m->GetElement(k, 3);
}
//create affine transform 3D
mitk::AffineTransform3D::Pointer mitkTransform = mitk::AffineTransform3D::New();
mitkTransform->SetMatrix(rotationDouble);
mitkTransform->SetOffset(translationDouble);
mitk::NavigationData::Pointer transformNavigationData = mitk::NavigationData::New(mitkTransform);
m_Controls->m_ReferencePointSetComboBox->GetSelectedNode()->GetData()->GetGeometry()->SetIndexToWorldTransform(mitkTransform);
m_Controls->m_ReferencePointSetComboBox->GetSelectedNode()->GetData()->GetGeometry()->Modified();
//write to file
std::stringstream filename;
filename << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".GridMatchingResult.csv";
MITK_INFO << "Writing output to file " << filename.str();
std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> FRE_Error;
FRE_Error.push_back({ FRE, "FRE after grid matching [mm]" });
writeToFile(filename.str(), FRE_Error);
}
void QmitkIGTTrackingDataEvaluationView::OnOrientationCalculation_CalcRef()
{
if (m_FilenameVector.size() != 3)
{
MessageBox("Need exactly three points as reference, aborting!");
return;
}
//start loop and iterate through all files of list
for (std::size_t i = 0; i < m_FilenameVector.size(); ++i)
{
//create navigation data player
mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer();
myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV);
myPlayer->SetFileName(m_FilenameVector[i]);
//check if the stream is valid and skip file if not
//create evaluation filter
mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New();
//connect pipeline
for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++j)
myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j));
//update pipline until number of samples is reached
for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); ++j)
myEvaluationFilter->Update();
//store mean position as reference
switch (i)
{
case 0:
m_RefPoint1 = myEvaluationFilter->GetPositionMean(0);
break;
case 1:
m_RefPoint2 = myEvaluationFilter->GetPositionMean(0);
break;
case 2:
m_RefPoint3 = myEvaluationFilter->GetPositionMean(0);
break;
}
}
MessageBox("Created Reference!");
}
void QmitkIGTTrackingDataEvaluationView::OnOrientationCalculation_CalcOrientandWriteToFile()
{
//start loop and iterate through all files of list
for (std::size_t i = 0; i < m_FilenameVector.size(); ++i)
{
//create navigation data player
mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer();
myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV);
myPlayer->SetFileName(m_FilenameVector.at(i));
//open file header
QString outputname = QString(m_FilenameVector.at(i).c_str()) + "_orientationFile.csv";
m_CurrentWriteFile.open(outputname.toStdString().c_str(), std::ios::out);
if (m_CurrentWriteFile.bad())
{
MessageBox("Error: Can't open output file!");
return;
}
//write header to file
m_CurrentWriteFile << "Nr;Calypso_Time;Valid_Reference;MeasureTool_Measurement-Tool[x];MeasureTool_Measurement-Tool[y];MeasureTool_Measurement-Tool[z];MeasureTool_Measurement-Tool[qx];MeasureTool_Measurement-Tool[qy];MeasureTool_Measurement-Tool[qz];MeasureTool_Measurement-Tool[qr]\n";
//update pipeline until number of samples is reached
int step = 0;
mitk::Point3D point1, point2, point3;
mitk::Quaternion current_orientation;
for (int j = 0; !myPlayer->IsAtEnd(); j++)
{
myPlayer->Update();
mitk::NavigationData::Pointer currentNavData = myPlayer->GetOutput(0);
switch (step)
{
case 0:
step++;
point1 = currentNavData->GetPosition();
break;
case 1:
step++;
point2 = currentNavData->GetPosition();
break;
case 2:
step = 0;
point3 = currentNavData->GetPosition();
//compute transform from reference to current points
if (point1[0] == 0 &&
point1[1] == 0 &&
point1[2] == 0 &&
point2[0] == 0 &&
point2[1] == 0 &&
point2[2] == 0 &&
point3[0] == 0 &&
point3[1] == 0 &&
point3[2] == 0
) current_orientation.fill(0);
else
{
vtkSmartPointer<vtkLandmarkTransform> transform = vtkSmartPointer<vtkLandmarkTransform>::New();
vtkSmartPointer<vtkPoints> sourcePoints = vtkSmartPointer<vtkPoints>::New();
double sourcepoint1[3] = { point1[0], point1[1], point1[2] };
double sourcepoint2[3] = { point2[0], point2[1], point2[2] };
double sourcepoint3[3] = { point3[0], point3[1], point3[2] };
sourcePoints->InsertNextPoint(sourcepoint1);
sourcePoints->InsertNextPoint(sourcepoint2);
sourcePoints->InsertNextPoint(sourcepoint3);
vtkSmartPointer<vtkPoints> targetPoints = vtkSmartPointer<vtkPoints>::New();
double targetpoint1[3] = { m_RefPoint1[0], m_RefPoint1[1], m_RefPoint1[2] };
double targetpoint2[3] = { m_RefPoint2[0], m_RefPoint2[1], m_RefPoint2[2] };
double targetpoint3[3] = { m_RefPoint3[0], m_RefPoint3[1], m_RefPoint3[2] };
targetPoints->InsertNextPoint(targetpoint1);
targetPoints->InsertNextPoint(targetpoint2);
targetPoints->InsertNextPoint(targetpoint3);
transform->SetSourceLandmarks(sourcePoints);
transform->SetTargetLandmarks(targetPoints);
transform->Modified();
transform->Update();
mitk::Transform::Pointer newTransform = mitk::Transform::New();
newTransform->SetMatrix(transform->GetMatrix());
current_orientation = newTransform->GetOrientation();
//add pointset with the three positions
if ((j > 15) && (j < 18))
{
mitk::DataNode::Pointer newNode = mitk::DataNode::New();
mitk::PointSet::Pointer newPointSet = mitk::PointSet::New();
newPointSet->InsertPoint(0, point1);
newPointSet->InsertPoint(1, point2);
newPointSet->InsertPoint(2, point3);
QString name = QString(m_FilenameVector.at(i).c_str());
newNode->SetName(name.toStdString().c_str());
newNode->SetData(newPointSet);
newNode->SetFloatProperty("pointsize", 0.1);
this->GetDataStorage()->Add(newNode);
}
}
break;
}
m_CurrentWriteFile << i << ";";
m_CurrentWriteFile << currentNavData->GetTimeStamp() << ";"; //IMPORTANT: change to GetIGTTimeStamp in new version!
m_CurrentWriteFile << "true;";
m_CurrentWriteFile << currentNavData->GetPosition()[0] << ";";
m_CurrentWriteFile << currentNavData->GetPosition()[1] << ";";
m_CurrentWriteFile << currentNavData->GetPosition()[2] << ";";
m_CurrentWriteFile << current_orientation.x() << ";";
m_CurrentWriteFile << current_orientation.y() << ";";
m_CurrentWriteFile << current_orientation.z() << ";";
m_CurrentWriteFile << current_orientation.r() << ";";
m_CurrentWriteFile << "\n";
}
//close output file
m_CurrentWriteFile.close();
}
MessageBox("Finished!");
}
void QmitkIGTTrackingDataEvaluationView::StdMultiWidgetAvailable(QmitkStdMultiWidget &stdMultiWidget)
{
m_MultiWidget = &stdMultiWidget;
}
void QmitkIGTTrackingDataEvaluationView::StdMultiWidgetNotAvailable()
{
m_MultiWidget = nullptr;
}
void QmitkIGTTrackingDataEvaluationView::OnAddToCurrentList()
{
//read in files
QStringList files = QFileDialog::getOpenFileNames(nullptr, "Select one or more files to open", "/", "CSV (*.csv)");
if (files.isEmpty()) return;
for (int i = 0; i < files.size(); i++)
{
std::string tmp = files.at(i).toStdString().c_str();
m_FilenameVector.push_back(tmp);
}
//fill list at GUI
m_Controls->m_FileList->clear();
for (unsigned int i = 0; i < m_FilenameVector.size(); i++) { new QListWidgetItem(tr(m_FilenameVector.at(i).c_str()), m_Controls->m_FileList); }
}
void QmitkIGTTrackingDataEvaluationView::OnLoadFileList()
{
m_FilenameVector = std::vector<std::string>();
m_FilenameVector.clear();
OnAddToCurrentList();
}
void QmitkIGTTrackingDataEvaluationView::OnEvaluateDataAll()
{
std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> results5cm, results15cm, results30cm, resultsAccum;
mitk::HummelProtocolEvaluation::HummelProtocolMeasurementVolume volume;
if (m_Controls->m_standardVolume->isChecked())
{
volume = mitk::HummelProtocolEvaluation::standard;
mitk::HummelProtocolEvaluation::Evaluate5cmDistances(m_PointSetMeanPositions, volume, results5cm);
mitk::HummelProtocolEvaluation::Evaluate15cmDistances(m_PointSetMeanPositions, volume, results15cm);
mitk::HummelProtocolEvaluation::Evaluate30cmDistances(m_PointSetMeanPositions, volume, results30cm);
mitk::HummelProtocolEvaluation::EvaluateAccumulatedDistances(m_PointSetMeanPositions, volume, resultsAccum);
}
else if (m_Controls->m_smallVolume->isChecked())
{
volume = mitk::HummelProtocolEvaluation::small;
mitk::HummelProtocolEvaluation::Evaluate5cmDistances(m_PointSetMeanPositions, volume, results5cm);
}
else if (m_Controls->m_mediumVolume->isChecked())
{
volume = mitk::HummelProtocolEvaluation::medium;
mitk::HummelProtocolEvaluation::Evaluate5cmDistances(m_PointSetMeanPositions, volume, results5cm);
}
else if (m_Controls->m_medium5x6Volume->isChecked())
{
volume = mitk::HummelProtocolEvaluation::medium5x6;
mitk::HummelProtocolEvaluation::Evaluate5cmDistances(m_PointSetMeanPositions, volume, results5cm);
}
//write results to file
std::stringstream filename5cm;
filename5cm << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".results5cm.csv";
MITK_INFO << "Writing output to file " << filename5cm.str();
writeToFile(filename5cm.str(), results5cm);
std::stringstream filename15cm;
filename15cm << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".results15cm.csv";
MITK_INFO << "Writing output to file " << filename15cm.str();
writeToFile(filename15cm.str(), results15cm);
std::stringstream filename30cm;
filename30cm << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".results30cm.csv";
MITK_INFO << "Writing output to file " << filename30cm.str();
writeToFile(filename30cm.str(), results30cm);
std::stringstream filenameAccum;
filenameAccum << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".resultsAccumDist.csv";
MITK_INFO << "Writing output to file " << filenameAccum.str();
writeToFile(filenameAccum.str(), resultsAccum);
}
void QmitkIGTTrackingDataEvaluationView::OnEvaluateData()
{
//open output file
m_CurrentWriteFile.open(std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str(), std::ios::out);
if (m_CurrentWriteFile.bad())
{
MessageBox("Error: Can't open output file!");
return;
}
std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> jitterValues;
//write output file header
WriteHeader();
//start loop and iterate through all files of list
for (std::size_t i = 0; i < m_FilenameVector.size(); ++i)
{
//create navigation data player
mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer();
myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV);
myPlayer->SetFileName(m_FilenameVector.at(i));
//create evaluation filter
mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New();
//connect pipeline
- for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++i) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); }
+ myEvaluationFilter->SetInput(0, myPlayer->GetOutput(0));
if (myPlayer->GetNumberOfSnapshots() < m_Controls->m_NumberOfSamples->value())
{
MITK_WARN << "Number of snapshots (" << myPlayer->GetNumberOfSnapshots() << ") smaller than number of samples to evaluate (" << m_Controls->m_NumberOfSamples->value() << ") ! Cannot proceed!";
return;
}
//update pipline until number of samples is reached
for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); j++)
myEvaluationFilter->Update();
+ MITK_INFO << "Jitter (RMS) on position "<<i<<": " << myEvaluationFilter->GetPositionErrorRMS(0);
+
//store all jitter values in separate vector for statistics
jitterValues.push_back({ myEvaluationFilter->GetPositionErrorRMS(0), "RMS" });
//write result to output file
WriteDataSet(myEvaluationFilter, m_FilenameVector.at(i));
}
//close output file for single data
m_CurrentWriteFile.close();
//compute statistics
std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> jitterStatistics = mitk::HummelProtocolEvaluation::ComputeStatistics(jitterValues);
MITK_INFO << "## Jitter (RMS) statistics: ##";
for (auto jitterStat : jitterStatistics) {MITK_INFO << jitterStat.description << ": " << jitterStat.distanceError;}
//write statistic results to separate file
std::stringstream filenameJitterStat;
filenameJitterStat << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".resultsJitterStatistics.csv";
MITK_INFO << "Writing output to file " << filenameJitterStat.str();
writeToFile(filenameJitterStat.str(), jitterStatistics);
//calculate angles if option is on
if (m_Controls->m_settingDifferenceAngles->isChecked() || m_Controls->m_DifferencesSLERP->isChecked()) CalculateDifferenceAngles();
MessageBox("Finished!");
}
void QmitkIGTTrackingDataEvaluationView::OnGeneratePointSetsOfSinglePositions()
{
m_scalingfactor = m_Controls->m_ScalingFactor->value();
//start loop and iterate through all files of list
for (std::size_t i = 0; i < m_FilenameVector.size(); ++i)
{
//create point set for this file
mitk::PointSet::Pointer thisPointSet = mitk::PointSet::New();
//create navigation data player
mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer();
myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV);
myPlayer->SetFileName(m_FilenameVector.at(i));
//update pipline until number of samlples is reached and store every single point
for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); j++)
{
myPlayer->Update();
mitk::Point3D thisPoint = myPlayer->GetOutput()->GetPosition();
thisPoint[0] *= m_scalingfactor;
thisPoint[1] *= m_scalingfactor;
thisPoint[2] *= m_scalingfactor;
thisPointSet->InsertPoint(j, thisPoint);
}
//add point set to data storage
mitk::DataNode::Pointer newNode = mitk::DataNode::New();
QString name = this->m_Controls->m_prefix->text() + QString("PointSet_of_All_Positions_") + QString::number(i);
newNode->SetName(name.toStdString());
newNode->SetData(thisPointSet);
this->GetDataStorage()->Add(newNode);
}
}
void QmitkIGTTrackingDataEvaluationView::OnGeneratePointSet()
{
m_scalingfactor = m_Controls->m_ScalingFactor->value();
mitk::PointSet::Pointer generatedPointSet = mitk::PointSet::New();
//start loop and iterate through all files of list
for (std::size_t i = 0; i < m_FilenameVector.size(); ++i)
{
//create navigation data player
mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer();
myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV);
myPlayer->SetFileName(m_FilenameVector.at(i));
//create evaluation filter
mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New();
//connect pipeline
for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++j) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); }
//update pipline until number of samlples is reached
for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); ++j) { myEvaluationFilter->Update(); }
//add mean position to point set
mitk::Point3D meanPos = myEvaluationFilter->GetPositionMean(0);
if (m_scalingfactor != 1)
{
meanPos[0] *= m_scalingfactor;
meanPos[1] *= m_scalingfactor;
meanPos[2] *= m_scalingfactor;
}
generatedPointSet->InsertPoint(i, meanPos);
}
//add point set to data storage
mitk::DataNode::Pointer newNode = mitk::DataNode::New();
QString name = this->m_Controls->m_prefix->text() + "PointSet_of_Mean_Positions";
newNode->SetName(name.toStdString());
newNode->SetData(generatedPointSet);
newNode->SetFloatProperty("pointsize", 5);
this->GetDataStorage()->Add(newNode);
m_PointSetMeanPositions = generatedPointSet;
}
void QmitkIGTTrackingDataEvaluationView::OnGenerateRotationLines()
{
m_scalingfactor = m_Controls->m_ScalingFactor->value();
//start loop and iterate through all files of list
for (std::size_t i = 0; i < m_FilenameVector.size(); ++i)
{
//create navigation data player
mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer();
myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV);
myPlayer->SetFileName(m_FilenameVector.at(i));
//create evaluation filter
mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New();
//connect pipeline
for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++j) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); }
//update pipline until number of samlples is reached
for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); ++j)
myEvaluationFilter->Update();
//create line from mean pos to a second point which lies along the sensor (1,0,0 in tool coordinates for aurora)
mitk::Point3D meanPos = myEvaluationFilter->GetPositionMean(0);
if (m_scalingfactor != 1)
{
meanPos[0] *= m_scalingfactor;
meanPos[1] *= m_scalingfactor;
meanPos[2] *= m_scalingfactor;
}
mitk::Point3D secondPoint;
mitk::Point3D thirdPoint;
mitk::Point3D fourthPoint;
mitk::FillVector3D(secondPoint, 2, 0, 0); //X
vnl_vector<mitk::ScalarType> secondPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * secondPoint.GetVnlVector() + meanPos.GetVnlVector();
mitk::Point3D secondPointTransformedMITK;
mitk::FillVector3D(secondPointTransformedMITK, secondPointTransformed[0], secondPointTransformed[1], secondPointTransformed[2]);
mitk::FillVector3D(thirdPoint, 0, 4, 0); //Y
vnl_vector<mitk::ScalarType> thirdPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * thirdPoint.GetVnlVector() + meanPos.GetVnlVector();
mitk::Point3D thirdPointTransformedMITK;
mitk::FillVector3D(thirdPointTransformedMITK, thirdPointTransformed[0], thirdPointTransformed[1], thirdPointTransformed[2]);
mitk::FillVector3D(fourthPoint, 0, 0, 6); //Z
vnl_vector<mitk::ScalarType> fourthPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * fourthPoint.GetVnlVector() + meanPos.GetVnlVector();
mitk::Point3D fourthPointTransformedMITK;
mitk::FillVector3D(fourthPointTransformedMITK, fourthPointTransformed[0], fourthPointTransformed[1], fourthPointTransformed[2]);
mitk::PointSet::Pointer rotationLine = mitk::PointSet::New();
rotationLine->InsertPoint(0, secondPointTransformedMITK);
rotationLine->InsertPoint(1, meanPos);
rotationLine->InsertPoint(2, thirdPointTransformedMITK);
rotationLine->InsertPoint(3, meanPos);
rotationLine->InsertPoint(4, fourthPointTransformedMITK);
mitk::DataNode::Pointer newNode = mitk::DataNode::New();
QString nodeName = this->m_Controls->m_prefix->text() + "RotationLineNumber" + QString::number(i);
newNode->SetName(nodeName.toStdString());
newNode->SetData(rotationLine);
newNode->SetBoolProperty("show contour", true);
newNode->SetFloatProperty("pointsize", 0.5);
this->GetDataStorage()->Add(newNode);
}
}
void QmitkIGTTrackingDataEvaluationView::OnGenerateGroundTruthPointSet()
{
mitk::PointSet::Pointer generatedPointSet = mitk::PointSet::New();
int currentPointID = 0;
mitk::Point3D currentPoint;
mitk::FillVector3D(currentPoint, 0, 0, 0);
for (int i = 0; i < m_Controls->m_PointNumber2->value(); i++)
{
for (int j = 0; j < m_Controls->m_PointNumber1->value(); j++)
{
generatedPointSet->InsertPoint(currentPointID, currentPoint);
currentPointID++;
currentPoint[1] += m_Controls->m_PointDistance->value();
}
currentPoint[1] = 0;
currentPoint[2] += m_Controls->m_PointDistance->value();
}
mitk::DataNode::Pointer newNode = mitk::DataNode::New();
QString nodeName = "GroundTruthPointSet_" + QString::number(m_Controls->m_PointNumber1->value()) + "x" + QString::number(m_Controls->m_PointNumber2->value()) + "_(" + QString::number(m_Controls->m_PointDistance->value()) + "mm)";
newNode->SetName(nodeName.toStdString());
newNode->SetData(generatedPointSet);
newNode->SetFloatProperty("pointsize", 5);
this->GetDataStorage()->Add(newNode);
}
void QmitkIGTTrackingDataEvaluationView::OnConvertCSVtoXMLFile()
{
if (m_Controls->m_ConvertSingleFile->isChecked())
{ //convert one file
int lines = ConvertOneFile(this->m_Controls->m_InputCSV->text().toStdString(), this->m_Controls->m_OutputXML->text().toStdString());
QString result = "Converted one file with" + QString::number(lines) + " data sets";
MessageBox(result.toStdString());
}
else //converte file list
{
if (m_CSVtoXMLInputFilenameVector.empty() || m_CSVtoXMLOutputFilenameVector.empty())
{
MessageBox("Error: one list is not loaded!");
return;
}
else if (m_CSVtoXMLInputFilenameVector.size() != m_CSVtoXMLOutputFilenameVector.size())
{
MessageBox("Error: lists do not have the same number of files!");
return;
}
for (std::size_t i = 0; i < m_CSVtoXMLInputFilenameVector.size(); ++i)
{
ConvertOneFile(m_CSVtoXMLInputFilenameVector.at(i), m_CSVtoXMLOutputFilenameVector.at(i));
}
QString result = "Converted " + QString::number(m_CSVtoXMLInputFilenameVector.size()) + " files from file list!";
MessageBox(result.toStdString());
}
}
int QmitkIGTTrackingDataEvaluationView::ConvertOneFile(std::string inputFilename, std::string outputFilename)
{
std::vector<mitk::NavigationData::Pointer> myNavigationDatas = GetNavigationDatasFromFile(inputFilename);
mitk::NavigationDataRecorderDeprecated::Pointer myRecorder = mitk::NavigationDataRecorderDeprecated::New();
myRecorder->SetFileName(outputFilename.c_str());
mitk::NavigationData::Pointer input = mitk::NavigationData::New();
if (m_Controls->m_ConvertCSV->isChecked()) myRecorder->SetOutputFormat(mitk::NavigationDataRecorderDeprecated::csv);
myRecorder->AddNavigationData(input);
myRecorder->StartRecording();
for (std::size_t i = 0; i < myNavigationDatas.size(); ++i)
{
input->Graft(myNavigationDatas.at(i));
myRecorder->Update();
}
myRecorder->StopRecording();
return myNavigationDatas.size();
}
void QmitkIGTTrackingDataEvaluationView::OnCSVtoXMLLoadInputList()
{
//read in filename
QString filename = QFileDialog::getOpenFileName(nullptr, tr("Open Measurement Filename List"), "/", tr("All Files (*.*)"));
if (filename.isNull()) return;
m_CSVtoXMLInputFilenameVector = this->GetFileContentLineByLine(filename.toStdString());
m_Controls->m_labelCSVtoXMLInputList->setText("READY");
}
void QmitkIGTTrackingDataEvaluationView::OnCSVtoXMLLoadOutputList()
{
//read in filename
QString filename = QFileDialog::getOpenFileName(nullptr, tr("Open Measurement Filename List"), "/", tr("All Files (*.*)"));
if (filename.isNull()) return;
m_CSVtoXMLOutputFilenameVector = this->GetFileContentLineByLine(filename.toStdString());
m_Controls->m_labelCSVtoXMLOutputList->setText("READY");
}
void QmitkIGTTrackingDataEvaluationView::MessageBox(std::string s)
{
QMessageBox msgBox;
msgBox.setText(s.c_str());
msgBox.exec();
}
void QmitkIGTTrackingDataEvaluationView::WriteHeader()
{
m_CurrentWriteFile << "Filename;";
m_CurrentWriteFile << "N;";
m_CurrentWriteFile << "N_invalid;";
m_CurrentWriteFile << "Percentage_invalid;";
if (m_Controls->m_settingPosMean->isChecked())
{
m_CurrentWriteFile << "Position_Mean[x];";
m_CurrentWriteFile << "Position_Mean[y];";
m_CurrentWriteFile << "Position_Mean[z];";
}
if (m_Controls->m_settingPosStabw->isChecked())
{
m_CurrentWriteFile << "Position_StandDev[x];";
m_CurrentWriteFile << "Position_StandDev[y];";
m_CurrentWriteFile << "Position_StandDev[z];";
}
if (m_Controls->m_settingPosSampleStabw->isChecked())
{
m_CurrentWriteFile << "Position_SampleStandDev[x];";
m_CurrentWriteFile << "Position_SampleStandDev[y];";
m_CurrentWriteFile << "Position_SampleStandDev[z];";
}
if (m_Controls->m_settingQuaternionMean->isChecked())
{
m_CurrentWriteFile << "Quaternion_Mean[qx];";
m_CurrentWriteFile << "Quaternion_Mean[qy];";
m_CurrentWriteFile << "Quaternion_Mean[qz];";
m_CurrentWriteFile << "Quaternion_Mean[qr];";
}
if (m_Controls->m_settionQuaternionStabw->isChecked())
{
m_CurrentWriteFile << "Quaternion_StandDev[qx];";
m_CurrentWriteFile << "Quaternion_StandDev[qy];";
m_CurrentWriteFile << "Quaternion_StandDev[qz];";
m_CurrentWriteFile << "Quaternion_StandDev[qr];";
}
if (m_Controls->m_settingPosErrorMean->isChecked()) m_CurrentWriteFile << "PositionError_Mean;";
if (m_Controls->m_settingPosErrorStabw->isChecked()) m_CurrentWriteFile << "PositionError_StandDev;";
if (m_Controls->m_settingPosErrorSampleStabw->isChecked()) m_CurrentWriteFile << "PositionError_SampleStandDev;";
if (m_Controls->m_settingPosErrorRMS->isChecked()) m_CurrentWriteFile << "PositionError_RMS;";
if (m_Controls->m_settingPosErrorMedian->isChecked()) m_CurrentWriteFile << "PositionError_Median;";
if (m_Controls->m_settingPosErrorMinMax->isChecked())
{
m_CurrentWriteFile << "PositionError_Max;";
m_CurrentWriteFile << "PositionError_Min;";
}
if (m_Controls->m_settingEulerMean->isChecked())
{
m_CurrentWriteFile << "Euler_tx;";
m_CurrentWriteFile << "Euler_ty;";
m_CurrentWriteFile << "Euler_tz;";
}
if (m_Controls->m_settingEulerRMS->isChecked())
{
m_CurrentWriteFile << "EulerErrorRMS (rad);";
m_CurrentWriteFile << "EulerErrorRMS (grad);";
}
m_CurrentWriteFile << "\n";
}
void QmitkIGTTrackingDataEvaluationView::WriteDataSet(mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter, std::string dataSetName)
{
if (myEvaluationFilter->GetNumberOfOutputs() == 0) m_CurrentWriteFile << "Error: no input \n";
else
{
m_CurrentWriteFile << dataSetName << ";";
m_CurrentWriteFile << myEvaluationFilter->GetNumberOfAnalysedNavigationData(0) << ";";
m_CurrentWriteFile << myEvaluationFilter->GetNumberOfInvalidSamples(0) << ";";
m_CurrentWriteFile << myEvaluationFilter->GetPercentageOfInvalidSamples(0) << ";";
if (m_Controls->m_settingPosMean->isChecked())
{
m_CurrentWriteFile << myEvaluationFilter->GetPositionMean(0)[0] << ";";
m_CurrentWriteFile << myEvaluationFilter->GetPositionMean(0)[1] << ";";
m_CurrentWriteFile << myEvaluationFilter->GetPositionMean(0)[2] << ";";
}
if (m_Controls->m_settingPosStabw->isChecked())
{
m_CurrentWriteFile << myEvaluationFilter->GetPositionStandardDeviation(0)[0] << ";";
m_CurrentWriteFile << myEvaluationFilter->GetPositionStandardDeviation(0)[1] << ";";
m_CurrentWriteFile << myEvaluationFilter->GetPositionStandardDeviation(0)[2] << ";";
}
if (m_Controls->m_settingPosSampleStabw->isChecked())
{
m_CurrentWriteFile << myEvaluationFilter->GetPositionSampleStandardDeviation(0)[0] << ";";
m_CurrentWriteFile << myEvaluationFilter->GetPositionSampleStandardDeviation(0)[1] << ";";
m_CurrentWriteFile << myEvaluationFilter->GetPositionSampleStandardDeviation(0)[2] << ";";
}
if (m_Controls->m_settingQuaternionMean->isChecked())
{
m_CurrentWriteFile << myEvaluationFilter->GetQuaternionMean(0).x() << ";";
m_CurrentWriteFile << myEvaluationFilter->GetQuaternionMean(0).y() << ";";
m_CurrentWriteFile << myEvaluationFilter->GetQuaternionMean(0).z() << ";";
m_CurrentWriteFile << myEvaluationFilter->GetQuaternionMean(0).r() << ";";
}
if (m_Controls->m_settionQuaternionStabw->isChecked())
{
m_CurrentWriteFile << myEvaluationFilter->GetQuaternionStandardDeviation(0).x() << ";";
m_CurrentWriteFile << myEvaluationFilter->GetQuaternionStandardDeviation(0).y() << ";";
m_CurrentWriteFile << myEvaluationFilter->GetQuaternionStandardDeviation(0).z() << ";";
m_CurrentWriteFile << myEvaluationFilter->GetQuaternionStandardDeviation(0).r() << ";";
}
if (m_Controls->m_settingPosErrorMean->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorMean(0) << ";";
if (m_Controls->m_settingPosErrorStabw->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorStandardDeviation(0) << ";";
if (m_Controls->m_settingPosErrorSampleStabw->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorSampleStandardDeviation(0) << ";";
if (m_Controls->m_settingPosErrorRMS->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorRMS(0) << ";";
if (m_Controls->m_settingPosErrorMedian->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorMedian(0) << ";";
if (m_Controls->m_settingPosErrorMinMax->isChecked())
{
m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorMax(0) << ";";
m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorMin(0) << ";";
}
if (m_Controls->m_settingEulerMean->isChecked())
{
m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesMean(0)[0] << ";";
m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesMean(0)[1] << ";";
m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesMean(0)[2] << ";";
}
if (m_Controls->m_settingEulerRMS->isChecked())
{
m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesRMS(0) << ";";
m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesRMSDegree(0) << ";";
}
m_CurrentWriteFile << "\n";
}
}
std::vector<mitk::Quaternion> QmitkIGTTrackingDataEvaluationView::GetMeanOrientationsOfAllData(std::vector<mitk::NavigationDataEvaluationFilter::Pointer> allData, bool useSLERP)
{
std::vector<mitk::Quaternion> returnValue;
for (auto dataSet : allData)
{
if (useSLERP) returnValue.push_back(GetSLERPAverage(dataSet));
else returnValue.push_back(dataSet->GetQuaternionMean(0));
}
return returnValue;
}
std::vector<mitk::NavigationDataEvaluationFilter::Pointer> QmitkIGTTrackingDataEvaluationView::GetAllDataFromUIList()
{
std::vector<mitk::NavigationDataEvaluationFilter::Pointer> EvaluationDataCollection;
//start loop and iterate through all files of list: store the evaluation data
for (std::size_t i = 0; i < m_FilenameVector.size(); ++i)
{
//create navigation data player
mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer();
myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV);
myPlayer->SetFileName(m_FilenameVector.at(i));
//create evaluation filter
mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New();
//connect pipeline
for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++j)
myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j));
//update pipline until number of samlples is reached
for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); ++j)
myEvaluationFilter->Update();
myEvaluationFilter->SetInput(nullptr);
myPlayer = nullptr;
EvaluationDataCollection.push_back(myEvaluationFilter);
}
return EvaluationDataCollection;
}
void QmitkIGTTrackingDataEvaluationView::CalculateDifferenceAngles()
{
//Get all data from UI
std::vector<mitk::NavigationDataEvaluationFilter::Pointer> EvaluationDataCollection = GetAllDataFromUIList();
//calculation and writing of output data
//open output file
m_CurrentAngleDifferencesWriteFile.open(std::string((m_Controls->m_OutputFilename->text() + ".angledifferences.csv").toUtf8()).c_str(), std::ios::out);
if (m_CurrentAngleDifferencesWriteFile.bad())
{
MessageBox("Error: Can't open output file for angle differences calculation!");
return;
}
//write header
WriteDifferenceAnglesHeader();
//compute angle differences
QString pos1 = "invalid";
QString pos2 = "invalid";
//now iterate through all evaluation data and calculate the angles
for (std::size_t i = 0; i < m_FilenameVector.size(); ++i)
{
pos1 = QString::fromStdString(itksys::SystemTools::GetFilenameWithoutLastExtension(m_FilenameVector.at(i)));
for (std::size_t j = 0; j < m_FilenameVector.size(); ++j)
{
pos2 = QString::fromStdString(itksys::SystemTools::GetFilenameWithoutLastExtension(m_FilenameVector.at(j)));
mitk::Quaternion q1;
mitk::Quaternion q2;
if (m_Controls->m_DifferencesSLERP->isChecked())
{
//compute slerp average
q1 = GetSLERPAverage(EvaluationDataCollection.at(i));
q2 = GetSLERPAverage(EvaluationDataCollection.at(j));
}
else
{
//compute arithmetic average
q1 = EvaluationDataCollection.at(i)->GetQuaternionMean(0);
q2 = EvaluationDataCollection.at(j)->GetQuaternionMean(0);
}
itk::Vector<double> rotationVec;
//adapt for Aurora 5D tools: [0,0,1000]
rotationVec[0] = 10000; //X
rotationVec[1] = 0; //Y
rotationVec[2] = 0; //Z
double AngleBetweenTwoQuaternions = mitk::StaticIGTHelperFunctions::GetAngleBetweenTwoQuaterions(q1, q2, rotationVec);
//write data set
WriteDifferenceAnglesDataSet(pos1.toStdString(), pos2.toStdString(), i, j, AngleBetweenTwoQuaternions);
}
}
//close output file
m_CurrentAngleDifferencesWriteFile.close();
}
void QmitkIGTTrackingDataEvaluationView::WriteDifferenceAnglesHeader()
{
m_CurrentAngleDifferencesWriteFile << "Name;Idx1;Idx2;Angle [Degree]\n";
}
void QmitkIGTTrackingDataEvaluationView::WriteDifferenceAnglesDataSet(std::string pos1, std::string pos2, int idx1, int idx2, double angle)
{
m_CurrentAngleDifferencesWriteFile << "Angle between " << pos1 << " and " << pos2 << ";" << idx1 << ";" << idx2 << ";" << angle << "\n";
MITK_INFO << "Angle: " << angle;
}
std::vector<mitk::NavigationData::Pointer> QmitkIGTTrackingDataEvaluationView::GetNavigationDatasFromFile(std::string filename)
{
std::vector<mitk::NavigationData::Pointer> returnValue = std::vector<mitk::NavigationData::Pointer>();
std::vector<std::string> fileContentLineByLine = GetFileContentLineByLine(filename);
for (std::size_t i = 1; i < fileContentLineByLine.size(); ++i) //skip header so start at 1
{
returnValue.push_back(GetNavigationDataOutOfOneLine(fileContentLineByLine.at(i)));
}
return returnValue;
}
std::vector<std::string> QmitkIGTTrackingDataEvaluationView::GetFileContentLineByLine(std::string filename)
{
std::vector<std::string> readData = std::vector<std::string>();
//save old locale
char * oldLocale;
oldLocale = setlocale(LC_ALL, 0);
//define own locale
std::locale C("C");
setlocale(LC_ALL, "C");
//read file
std::ifstream file;
file.open(filename.c_str(), std::ios::in);
if (file.good())
{
//read out file
file.seekg(0L, std::ios::beg); // move to begin of file
while (!file.eof())
{
std::string buffer;
std::getline(file, buffer); // read out file line by line
if (buffer.size() > 0) readData.push_back(buffer);
}
}
file.close();
//switch back to old locale
setlocale(LC_ALL, oldLocale);
return readData;
}
mitk::NavigationData::Pointer QmitkIGTTrackingDataEvaluationView::GetNavigationDataOutOfOneLine(std::string line)
{
mitk::NavigationData::Pointer returnValue = mitk::NavigationData::New();
QString myLine = QString(line.c_str());
QStringList myLineList = myLine.split(';');
mitk::Point3D position;
mitk::Quaternion orientation;
bool valid = false;
if (myLineList.at(2).toStdString() == "1") valid = true;
position[0] = myLineList.at(3).toDouble();
position[1] = myLineList.at(4).toDouble();
position[2] = myLineList.at(5).toDouble();
orientation[0] = myLineList.at(6).toDouble();
orientation[1] = myLineList.at(7).toDouble();
orientation[2] = myLineList.at(8).toDouble();
orientation[3] = myLineList.at(9).toDouble();
returnValue->SetDataValid(valid);
returnValue->SetPosition(position);
returnValue->SetOrientation(orientation);
return returnValue;
}
mitk::Quaternion QmitkIGTTrackingDataEvaluationView::GetSLERPAverage(mitk::NavigationDataEvaluationFilter::Pointer evaluationFilter)
{
mitk::Quaternion average;
//build a vector of quaternions from the evaulation filter (caution always takes the first (0) input of the filter
std::vector<mitk::Quaternion> quaternions = std::vector<mitk::Quaternion>();
for (int i = 0; i < evaluationFilter->GetNumberOfAnalysedNavigationData(0); i++)
{
mitk::Quaternion currentq = evaluationFilter->GetLoggedOrientation(i, 0);
quaternions.push_back(currentq);
}
//compute the slerp average using the quaternion averaging class
mitk::QuaternionAveraging::Pointer myAverager = mitk::QuaternionAveraging::New();
average = myAverager->CalcAverage(quaternions);
return average;
}
void QmitkIGTTrackingDataEvaluationView::writeToFile(std::string filename, std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> values)
{
std::fstream currentFile;
currentFile.open(filename.c_str(), std::ios::out);
if (currentFile.bad()) { MITK_WARN << "Cannot open file, aborting!"; return; }
currentFile << "Description" << ";" << "Error[mm]" << "\n";
for (auto currentError : values)
{
currentFile << currentError.description << ";" << currentError.distanceError << "\n";
}
currentFile.close();
}
mitk::NavigationDataCSVSequentialPlayer::Pointer QmitkIGTTrackingDataEvaluationView::ConstructNewNavigationDataPlayer()
{
bool rightHanded = m_Controls->m_RigthHanded->isChecked();
QString separator = m_Controls->m_SeparatorSign->text();
QChar sepaSign = separator.at(0);
//char separatorSign;
char separatorSign = sepaSign.toLatin1();
//std::string separatorSign = m_Controls->m_SeparatorSign->text().toStdString();
int sampleCount = m_Controls->m_SampleCount->value();
bool headerRow = m_Controls->m_HeaderRow->isChecked();
int xPos = m_Controls->m_XPos->value();
int yPos = m_Controls->m_YPos->value();
int zPos = m_Controls->m_ZPos->value();
bool useQuats = m_Controls->m_UseQuats->isChecked();
int qx = m_Controls->m_Qx->value();
int qy = m_Controls->m_Qy->value();
int qz = m_Controls->m_Qz->value();
int qr = m_Controls->m_Qr->value();
int azimuth = m_Controls->m_Azimuth->value();
int elevation = m_Controls->m_Elevation->value();
int roll = m_Controls->m_Roll->value();
bool eulersInRad = m_Controls->m_Radiants->isChecked();
//need to find the biggest column number to determine the minimal number of columns the .csv file has to have
int allInts[] = {xPos, yPos, zPos, qx, qy, qr, azimuth, elevation, roll};
int minNumberOfColumns = (*std::max_element(allInts, allInts+9)+1); //size needs to be +1 because columns start at 0 but size at 1
-
mitk::NavigationDataCSVSequentialPlayer::Pointer navDataPlayer = mitk::NavigationDataCSVSequentialPlayer::New();
navDataPlayer->SetOptions(rightHanded, separatorSign, sampleCount, headerRow, xPos, yPos, zPos, useQuats,
qx, qy, qz, qr, azimuth, elevation, roll, eulersInRad, minNumberOfColumns);
return navDataPlayer;
}
diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.cpp b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.cpp
index c6ab8b87ca..0ee1bd0ac7 100644
--- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.cpp
+++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.cpp
@@ -1,319 +1,319 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#define _USE_MATH_DEFINES
#include "mitkNavigationDataCSVSequentialPlayer.h"
#include <QString>
#include <QStringList>
#include <iostream>
#include <fstream>
#include <math.h>
mitk::NavigationDataCSVSequentialPlayer::NavigationDataCSVSequentialPlayer()
: mitk::NavigationDataPlayerBase()
{
m_NavigationDatas = std::vector<mitk::NavigationData::Pointer>();
m_CurrentPos = 0;
m_Filetype = mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV;
}
mitk::NavigationDataCSVSequentialPlayer::~NavigationDataCSVSequentialPlayer()
{
}
bool mitk::NavigationDataCSVSequentialPlayer::IsAtEnd()
{
return m_CurrentPos >= static_cast<int>(m_NavigationDatas.size());
}
void mitk::NavigationDataCSVSequentialPlayer::
SetFileName(const std::string& fileName)
{
this->SetNumberOfIndexedOutputs(1);
FillOutputEmpty(0);
MITK_INFO << "Reading file: " << fileName;
m_NavigationDatas = GetNavigationDatasFromFile(fileName);
this->Modified();
}
void mitk::NavigationDataCSVSequentialPlayer::FillOutputEmpty(int number)
{
this->SetNthOutput(number, GetEmptyNavigationData());
}
mitk::NavigationData::Pointer mitk::NavigationDataCSVSequentialPlayer::GetEmptyNavigationData()
{
mitk::NavigationData::Pointer emptyNd = mitk::NavigationData::New();
mitk::NavigationData::PositionType position;
mitk::NavigationData::OrientationType orientation(0.0, 0.0, 0.0, 0.0);
position.Fill(0.0);
emptyNd->SetPosition(position);
emptyNd->SetOrientation(orientation);
emptyNd->SetDataValid(false);
return emptyNd;
}
int mitk::NavigationDataCSVSequentialPlayer::GetNumberOfSnapshots()
{
return m_NavigationDatas.size();
}
void mitk::NavigationDataCSVSequentialPlayer::GenerateData()
{
for (unsigned int index = 0; index < this->GetNumberOfOutputs(); index++)
{
mitk::NavigationData* output = this->GetOutput(index);
if (m_CurrentPos > static_cast<int>(m_NavigationDatas.size()))
{
FillOutputEmpty(index);
return;
}
output->Graft(this->m_NavigationDatas.at(m_CurrentPos));
m_CurrentPos++;
}
}
void mitk::NavigationDataCSVSequentialPlayer::UpdateOutputInformation()
{
this->Modified(); // make sure that we need to be updated
Superclass::UpdateOutputInformation();
}
std::vector<mitk::NavigationData::Pointer> mitk::NavigationDataCSVSequentialPlayer::GetNavigationDatasFromFile(std::string filename)
{
std::vector<mitk::NavigationData::Pointer> returnValue = std::vector<mitk::NavigationData::Pointer>();
std::vector<std::string> fileContentLineByLine = GetFileContentLineByLine(filename);
std::size_t i = m_HeaderRow
? 1 //file has a header row, so it has to be skipped when reading the NavigationDatas
: 0; //file has no header row, so no need to skip the first row
for ( ; i < fileContentLineByLine.size(); ++i)
{
returnValue.push_back(GetNavigationDataOutOfOneLine(fileContentLineByLine.at(i)));
}
return returnValue;
}
std::vector<std::string> mitk::NavigationDataCSVSequentialPlayer::GetFileContentLineByLine(std::string filename)
{
std::vector<std::string> readData = std::vector<std::string>();
//save old locale
char * oldLocale;
oldLocale = setlocale(LC_ALL, 0);
//define own locale
std::locale C("C");
setlocale(LC_ALL, "C");
//read file
std::ifstream file;
file.open(filename.c_str(), std::ios::in);
if (file.good())
{
//read out file
file.seekg(0L, std::ios::beg); // move to begin of file
int count = 0;
while (!file.eof())
{
std::string buffer;
std::getline(file, buffer); // read out file line by line
if (!buffer.empty())
{
readData.push_back(buffer);
- MITK_INFO << "Line: " << buffer;
+ //MITK_INFO << "Line: " << buffer;
}
++count; if (count == m_SampleCount) count = 0;
}
}
file.close();
//switch back to old locale
setlocale(LC_ALL, oldLocale);
return readData;
}
mitk::NavigationData::Pointer mitk::NavigationDataCSVSequentialPlayer::GetNavigationDataOutOfOneLine(std::string line)
{
mitk::NavigationData::Pointer returnValue = mitk::NavigationData::New();
QString myLine = QString(line.c_str());
QStringList myLineList = myLine.split(m_SeparatorSign);
mitk::Point3D position;
mitk::Quaternion orientation;
bool valid = false;
//this is for custom csv files. You have adapt the column numbers to correctly
//interpret your csv file.
if (m_Filetype == mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV)
{
if (myLineList.size() < m_MinNumberOfColumns)
{
MITK_ERROR << "Error: cannot read line: only found " << myLineList.size() << " fields. Last field: " << myLineList.at(myLineList.size() - 1).toStdString();
returnValue = GetEmptyNavigationData();
return returnValue;
}
valid = true; //if no valid flag is given: simply set to true
//############# Variant for the Aurora measurements ###############
//############# (CUSTOM .csv files from MITK) ###############
position[0] = myLineList.at(3).toDouble();
position[1] = myLineList.at(4).toDouble();
position[2] = myLineList.at(5).toDouble();
orientation[0] = myLineList.at(6).toDouble(); //qx
orientation[1] = myLineList.at(7).toDouble(); //qy
orientation[2] = myLineList.at(8).toDouble(); //qz
orientation[3] = myLineList.at(9).toDouble(); //qr
if(!m_RightHanded) //MITK uses a right handed coordinate system, so the position needs to be converted
{
position[0] = position[0]*(-1);
}
if (m_UseQuats) //Use Quaternions to construct the orientation of the NavigationData
{
orientation[0] = myLineList.at(m_Qx).toDouble(); //qx
orientation[1] = myLineList.at(m_Qy).toDouble(); //qy
orientation[2] = myLineList.at(m_Qz).toDouble(); //qz
orientation[3] = myLineList.at(m_Qr).toDouble(); //qr
}
else //Use the Euler Angles to construct the orientation of the NavigationData
{
double azimuthAngle;
double elevationAngle;
double rollAngle;
if(m_Azimuth < 0) //azimuth is not defined so set him to zero
{
azimuthAngle = 0;
}
else
{
azimuthAngle = myLineList.at(m_Azimuth).toDouble();
}
if(m_Elevation < 0)// elevation is not defined so set him to zero
{
elevationAngle = 0;
}
else
{
elevationAngle = myLineList.at(m_Elevation).toDouble();
}
if(m_Roll < 0) //roll is not defined so set him to zero
{
rollAngle = 0;
}
else
{
rollAngle = myLineList.at(m_Roll).toDouble();
}
if (!m_EulersInRadiants) //the Euler Angles are in Degrees but MITK uses radiants so they need to be converted
{
azimuthAngle = azimuthAngle / 180 * M_PI;
elevationAngle = elevationAngle / 180 * M_PI;
rollAngle = rollAngle / 180 * M_PI;
}
vnl_quaternion<double> eulerQuat(rollAngle, elevationAngle, azimuthAngle);
orientation = eulerQuat;
}
if(!m_RightHanded) //MITK uses a right handed coordinate system, so the orientation needs to be converted
{
//code block for conversion from left-handed to right-handed
mitk::Quaternion linksZuRechtsdrehend;
double rotationAngle = -M_PI;
double rotationAxis[3];
rotationAxis[0] = 0;
rotationAxis[1] = 0;
rotationAxis[2] = 1;
linksZuRechtsdrehend[3] = cos(rotationAngle / 2);
linksZuRechtsdrehend[0] = rotationAxis[0] * sin(rotationAngle / 2);
linksZuRechtsdrehend[1] = rotationAxis[1] * sin(rotationAngle / 2);
linksZuRechtsdrehend[2] = rotationAxis[2] * sin(rotationAngle / 2);
orientation = orientation * linksZuRechtsdrehend;
}
}
//this is for MITK csv files that have been recorded with the MITK
//navigation data recorder. You can also use the navigation data player
//class from the MITK-IGT module instead.
else if (m_Filetype == mitk::NavigationDataCSVSequentialPlayer::NavigationDataCSV)
{
if (myLineList.size() < 8)
{
MITK_ERROR << "Error: cannot read line: only found " << myLineList.size() << " fields. Last field: " << myLineList.at(myLineList.size() - 1).toStdString();
returnValue = GetEmptyNavigationData();
return returnValue;
}
if (myLineList.at(3).toStdString() == "1") valid = true;
position[0] = myLineList.at(2).toDouble();
position[1] = myLineList.at(3).toDouble();
position[2] = myLineList.at(4).toDouble();
orientation[0] = myLineList.at(5).toDouble(); //qx
orientation[1] = myLineList.at(6).toDouble(); //qy
orientation[2] = myLineList.at(7).toDouble(); //qz
orientation[3] = myLineList.at(8).toDouble(); //qr
}
returnValue->SetDataValid(valid);
returnValue->SetPosition(position);
returnValue->SetOrientation(orientation);
return returnValue;
}
void mitk::NavigationDataCSVSequentialPlayer::SetOptions(bool rightHanded, char separatorSign, int sampleCount, bool headerRow, int xPos, int yPos,
int zPos, bool useQuats, int qx, int qy, int qz, int qr, int azimuth, int elevation, int roll,
bool eulerInRadiants, int minNumberOfColumns)
{
m_RightHanded = rightHanded;
m_SeparatorSign = separatorSign;
m_SampleCount = sampleCount;
m_HeaderRow = headerRow;
m_XPos = xPos;
m_YPos = yPos;
m_ZPos = zPos;
m_UseQuats = useQuats;
m_Qx = qx;
m_Qy = qy;
m_Qz = qz;
m_Qr = qr;
m_Azimuth = azimuth;
m_Elevation = elevation;
m_Roll = roll;
m_EulersInRadiants = eulerInRadiants;
m_MinNumberOfColumns = minNumberOfColumns;
}