diff --git a/Modules/IGT/Algorithms/mitkNavigationDataEvaluationFilter.cpp b/Modules/IGT/Algorithms/mitkNavigationDataEvaluationFilter.cpp index 4fcef91f9c..89ec5d87a7 100644 --- a/Modules/IGT/Algorithms/mitkNavigationDataEvaluationFilter.cpp +++ b/Modules/IGT/Algorithms/mitkNavigationDataEvaluationFilter.cpp @@ -1,314 +1,302 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkNavigationDataEvaluationFilter.h" #include #define _USE_MATH_DEFINES #include mitk::NavigationDataEvaluationFilter::NavigationDataEvaluationFilter() -: mitk::NavigationDataToNavigationDataFilter() + : mitk::NavigationDataToNavigationDataFilter() { - } - mitk::NavigationDataEvaluationFilter::~NavigationDataEvaluationFilter() { - } void mitk::NavigationDataEvaluationFilter::GenerateData() { + this->CreateOutputsForAllInputs(); // make sure that we have the same number of outputs as inputs + this->CreateMembersForAllInputs(); - this->CreateOutputsForAllInputs(); // make sure that we have the same number of outputs as inputs - this->CreateMembersForAllInputs(); - - /* update outputs with tracking data from tools */ - for (unsigned int i = 0; i < this->GetNumberOfOutputs() ; ++i) + /* update outputs with tracking data from tools */ + for (unsigned int i = 0; i < this->GetNumberOfOutputs(); ++i) + { + //first copy outputs to inputs + mitk::NavigationData* output = this->GetOutput(i); + assert(output); + const mitk::NavigationData* input = this->GetInput(i); + assert(input); + if (input->IsDataValid() == false) { output->SetDataValid(false); } + else { output->Graft(input); } + + //then save statistics + if (input->IsDataValid()) { - //first copy outputs to inputs - mitk::NavigationData* output = this->GetOutput(i); - assert(output); - const mitk::NavigationData* input = this->GetInput(i); - assert(input); - if (input->IsDataValid() == false) {output->SetDataValid(false);} - else {output->Graft(input);} - - //then save statistics - if(input->IsDataValid()) - { - m_LoggedPositions[i].push_back(input->GetPosition()); - m_LoggedQuaternions[i].push_back(input->GetOrientation()); - } - else - { - m_InvalidSamples[i]++; - } + m_LoggedPositions[i].push_back(input->GetPosition()); + m_LoggedQuaternions[i].push_back(input->GetOrientation()); } - + else + { + m_InvalidSamples[i]++; + } + } } void mitk::NavigationDataEvaluationFilter::CreateMembersForAllInputs() { - while(this->m_LoggedPositions.size() < this->GetNumberOfInputs()) - { - std::pair > newElement(m_LoggedPositions.size(),std::vector()); + while (this->m_LoggedPositions.size() < this->GetNumberOfInputs()) + { + std::pair > newElement(m_LoggedPositions.size(), std::vector()); m_LoggedPositions.insert(newElement); - } - while(this->m_LoggedQuaternions.size() < this->GetNumberOfInputs()) - { - std::pair > newElement(m_LoggedQuaternions.size(),std::vector()); + } + while (this->m_LoggedQuaternions.size() < this->GetNumberOfInputs()) + { + std::pair > newElement(m_LoggedQuaternions.size(), std::vector()); m_LoggedQuaternions.insert(newElement); - } - while(this->m_InvalidSamples.size() < this->GetNumberOfInputs()) - { - std::pair newElement(m_InvalidSamples.size(),0); + } + while (this->m_InvalidSamples.size() < this->GetNumberOfInputs()) + { + std::pair newElement(m_InvalidSamples.size(), 0); m_InvalidSamples.insert(newElement); - } - - + } } void mitk::NavigationDataEvaluationFilter::ResetStatistic() { -for (unsigned int i = 0; i < m_LoggedPositions.size(); i++) m_LoggedPositions[i] = std::vector(); -for (unsigned int i = 0; i < m_LoggedQuaternions.size(); i++) m_LoggedQuaternions[i] = std::vector(); -for (unsigned int i = 0; i < m_InvalidSamples.size(); i++) m_InvalidSamples[i] = 0; + for (unsigned int i = 0; i < m_LoggedPositions.size(); i++) m_LoggedPositions[i] = std::vector(); + for (unsigned int i = 0; i < m_LoggedQuaternions.size(); i++) m_LoggedQuaternions[i] = std::vector(); + for (unsigned int i = 0; i < m_InvalidSamples.size(); i++) m_InvalidSamples[i] = 0; } int mitk::NavigationDataEvaluationFilter::GetNumberOfAnalysedNavigationData(int input) { -return this->m_LoggedPositions[input].size(); + return this->m_LoggedPositions[input].size(); } - mitk::Point3D mitk::NavigationDataEvaluationFilter::GetPositionMean(int input) { -mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); -return myCalculator->GetPositionMean(); + mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); + return myCalculator->GetPositionMean(); } mitk::Vector3D mitk::NavigationDataEvaluationFilter::GetPositionStandardDeviation(int input) { -mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); -return myCalculator->GetPositionStandardDeviation(); + mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); + return myCalculator->GetPositionStandardDeviation(); } mitk::Vector3D mitk::NavigationDataEvaluationFilter::GetPositionSampleStandardDeviation(int input) { -mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); -return myCalculator->GetPositionSampleStandardDeviation(); + mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); + return myCalculator->GetPositionSampleStandardDeviation(); } mitk::Quaternion mitk::NavigationDataEvaluationFilter::GetQuaternionMean(int input) { -return GetMean(m_LoggedQuaternions[input]); + return GetMean(m_LoggedQuaternions[input]); } mitk::Quaternion mitk::NavigationDataEvaluationFilter::GetQuaternionStandardDeviation(int input) { -mitk::Quaternion returnValue; -std::vector list1 = std::vector(); -std::vector list2 = std::vector(); -std::vector list3 = std::vector(); -std::vector list4 = std::vector(); -for (unsigned int i=0; i list1 = std::vector(); + std::vector list2 = std::vector(); + std::vector list3 = std::vector(); + std::vector list4 = std::vector(); + for (unsigned int i = 0; i < m_LoggedQuaternions[input].size(); i++) { - list1.push_back(m_LoggedQuaternions[input].at(i)[0]); - list2.push_back(m_LoggedQuaternions[input].at(i)[1]); - list3.push_back(m_LoggedQuaternions[input].at(i)[2]); - list4.push_back(m_LoggedQuaternions[input].at(i)[3]); + list1.push_back(m_LoggedQuaternions[input].at(i)[0]); + list2.push_back(m_LoggedQuaternions[input].at(i)[1]); + list3.push_back(m_LoggedQuaternions[input].at(i)[2]); + list4.push_back(m_LoggedQuaternions[input].at(i)[3]); } -mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(); -returnValue[0] = myCalculator->GetStabw(list1); -returnValue[1] = myCalculator->GetStabw(list2); -returnValue[2] = myCalculator->GetStabw(list3); -returnValue[3] = myCalculator->GetStabw(list4); -return returnValue; + mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(); + returnValue[0] = myCalculator->GetStabw(list1); + returnValue[1] = myCalculator->GetStabw(list2); + returnValue[2] = myCalculator->GetStabw(list3); + returnValue[3] = myCalculator->GetStabw(list4); + return returnValue; } mitk::Vector3D mitk::NavigationDataEvaluationFilter::GetEulerAnglesMean(int input) { -mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(QuaternionsToEulerAngles(m_LoggedQuaternions[input]))); -mitk::Vector3D returnValue; -returnValue[0] = myCalculator->GetPositionMean()[0]; -returnValue[1] = myCalculator->GetPositionMean()[1]; -returnValue[2] = myCalculator->GetPositionMean()[2]; -return returnValue; + mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(QuaternionsToEulerAngles(m_LoggedQuaternions[input]))); + mitk::Vector3D returnValue; + returnValue[0] = myCalculator->GetPositionMean()[0]; + returnValue[1] = myCalculator->GetPositionMean()[1]; + returnValue[2] = myCalculator->GetPositionMean()[2]; + return returnValue; } double mitk::NavigationDataEvaluationFilter::GetEulerAnglesRMS(int input) { -mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(QuaternionsToEulerAngles(m_LoggedQuaternions[input]))); -return myCalculator->GetPositionErrorRMS(); + mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(QuaternionsToEulerAngles(m_LoggedQuaternions[input]))); + return myCalculator->GetPositionErrorRMS(); } double mitk::NavigationDataEvaluationFilter::GetEulerAnglesRMSDegree(int input) { -mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(QuaternionsToEulerAnglesGrad(m_LoggedQuaternions[input]))); -return myCalculator->GetPositionErrorRMS(); + mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(QuaternionsToEulerAnglesGrad(m_LoggedQuaternions[input]))); + return myCalculator->GetPositionErrorRMS(); } - - double mitk::NavigationDataEvaluationFilter::GetPositionErrorMean(int input) { -mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); -return myCalculator->GetPositionErrorMean(); + mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); + return myCalculator->GetPositionErrorMean(); } double mitk::NavigationDataEvaluationFilter::GetPositionErrorStandardDeviation(int input) { -mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); -return myCalculator->GetPositionErrorStandardDeviation(); + mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); + return myCalculator->GetPositionErrorStandardDeviation(); } double mitk::NavigationDataEvaluationFilter::GetPositionErrorSampleStandardDeviation(int input) { -mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); -return myCalculator->GetPositionErrorSampleStandardDeviation(); + mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); + return myCalculator->GetPositionErrorSampleStandardDeviation(); } - double mitk::NavigationDataEvaluationFilter::GetPositionErrorRMS(int input) { -mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); -return myCalculator->GetPositionErrorRMS(); + mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); + return myCalculator->GetPositionErrorRMS(); } double mitk::NavigationDataEvaluationFilter::GetPositionErrorMedian(int input) { -mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); -return myCalculator->GetPositionErrorMedian(); + mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); + return myCalculator->GetPositionErrorMedian(); } double mitk::NavigationDataEvaluationFilter::GetPositionErrorMax(int input) { -mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); -return myCalculator->GetPositionErrorMax(); + mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); + return myCalculator->GetPositionErrorMax(); } double mitk::NavigationDataEvaluationFilter::GetPositionErrorMin(int input) { -mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); -return myCalculator->GetPositionErrorMin(); + mitk::PointSetStatisticsCalculator::Pointer myCalculator = mitk::PointSetStatisticsCalculator::New(VectorToPointSet(m_LoggedPositions[input])); + return myCalculator->GetPositionErrorMin(); } int mitk::NavigationDataEvaluationFilter::GetNumberOfInvalidSamples(int input) { -return m_InvalidSamples[input]; + return m_InvalidSamples[input]; } double mitk::NavigationDataEvaluationFilter::GetPercentageOfInvalidSamples(int input) { -return (m_InvalidSamples[input]/(m_InvalidSamples[input]+((double)m_LoggedPositions[input].size())))*100.0; + return (m_InvalidSamples[input] / (m_InvalidSamples[input] + ((double)m_LoggedPositions[input].size())))*100.0; } mitk::Quaternion mitk::NavigationDataEvaluationFilter::GetMean(std::vector list) { -//calculate mean -mitk::Quaternion mean; -mean[0] = 0; -mean[1] = 0; -mean[2] = 0; -mean[3] = 0; - -for (unsigned int i=0; i pSet) { mitk::PointSet::Pointer returnValue = mitk::PointSet::New(); - for (unsigned int i=0; iInsertPoint(i,pSet.at(i)); + for (unsigned int i = 0; i < pSet.size(); i++) returnValue->InsertPoint(i, pSet.at(i)); return returnValue; } mitk::PointSet::Pointer mitk::NavigationDataEvaluationFilter::VectorToPointSet(std::vector pSet) { mitk::PointSet::Pointer returnValue = mitk::PointSet::New(); - for (unsigned int i=0; iInsertPoint(i,thisPoint); - } + returnValue->InsertPoint(i, thisPoint); + } return returnValue; } std::vector mitk::NavigationDataEvaluationFilter::QuaternionsToEulerAngles(std::vector quaterions) { std::vector returnValue = std::vector(); - for (unsigned int i=0; i mitk::NavigationDataEvaluationFilter::QuaternionsToEulerAnglesGrad(std::vector quaterions) { double PI = M_PI; std::vector returnValue = std::vector(); std::vector eulerAnglesRadians = QuaternionsToEulerAngles(quaterions); - for (unsigned int i=0; i + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/resources/QmitkIGTTrackingSemiAutomaticMeasurementView.qrc b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/resources/QmitkIGTTrackingSemiAutomaticMeasurementView.qrc new file mode 100644 index 0000000000..4222814e5c --- /dev/null +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/resources/QmitkIGTTrackingSemiAutomaticMeasurementView.qrc @@ -0,0 +1,8 @@ + + + icon.xpm + + + icon-eval.xpm + + diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/resources/icon-eval.xpm b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/resources/icon-eval.xpm new file mode 100644 index 0000000000..dd04f91df1 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/resources/icon-eval.xpm @@ -0,0 +1,107 @@ +/* XPM */ +static char * icon_xpm[] = { +"100 100 4 1", +" c None", +". c #FFFFFF", +"+ c #000000", +"@ c #22B14C", +"....................................................................................................", +"....................................................................................................", +"....................................................................................................", +"....................................................................................................", +"....................................................................................................", +"....................................................................................................", +"....................................................................................................", +"....................................................................................................", +"....................................................................................................", +"....................................................................................................", +"....................................................................................................", +".............................++++...................................................................", +"...........................++++++...................................................................", +"..........................+++++++...................................................................", +".........................+++.++++...................................................................", +".........................++..++++...................................................................", +".............................++++...................................................................", +".............................++++...........................+++++++.................................", +".............................++++.........................++++++++++................................", +".............................++++.........................+++++++++++...............................", +".............................++++.........................++....+++++...............................", +".............................++++................................++++...............................", +".............................++++................................++++...............................", +".............................++++...............................++++................................", +".............................++++...........................+++++++.................................", +".............................++++...........................+++++++.................................", +".........................++++++++++++.......................+++++++++...............................", +".........................++++++++++++............................+++++..............................", +".........................++++++++++++.............................++++..............................", +"..................................................................++++..............................", +"..................................................................++++..............................", +"..........................................................++.....+++++..............................", +"..........................................................+++++++++++...............................", +"..........................................................++++++++++................................", 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+"........................................++++++++++..................................................", +"........................................++++++++++..................................................", +"........................................++....+++++.................................................", +"...............................................++++.................................................", +"...............................................++++.................................................", +"...............................................++++.................................................", +"..............................................++++..................................................", +"..............................................++++..................................................", +".............................................++++...................................................", 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+".......................+++++@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@+++++++++++++.................", +".......................+++++@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@++++++++++++++..................", +".......................++++++++++++++++++++++++++++++++@@@@@@@@@@++++++++++++++.....................", +".......................+++++++++++++++++++++++++++++++++@@@@@@+++++++++++++++.......................", +".......................+++++++++++++++++++++++++++++++++@@@@++++++++++++++..........................", +".......................+++++++++++++++++++++++++++++++++@++++++++++++++.............................", +"........................+++++++++++++++++++++++++++++++++++++++++++++...............................", +"...................................................+++++++++++++++..................................", +"...................................................++++++++++++.....................................", +"...................................................++++++++++.......................................", +"...................................................+++++++..........................................", +"....................................................+++.............................................", +"....................................................................................................", +"....................................................................................................", +"....................................................................................................", +"....................................................................................................", +"....................................................................................................", +"....................................................................................................", +"....................................................................................................", +"....................................................................................................", +"...................................................................................................."}; diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/resources/icon.xpm b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/resources/icon.xpm new file mode 100644 index 0000000000..76b97458fd --- /dev/null +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/resources/icon.xpm @@ -0,0 +1,6640 @@ +/* XPM */ +static char * icon_xpm[] = { +"130 130 6507 2", +" c None", +". c #FFFFFF", +"+ c #FCFCFC", +"@ c #FDFDFD", +"# c #FDFFFF", +"$ c #FDFDFF", +"% c #FFFDFF", +"& c #FCFDFC", +"* c #FBFBFB", +"= c #FAFAFA", +"- c #FAF9F9", +"; c #FBF9FB", +"> c #FCFAFB", +", c #F9F7F9", +"' c #F8F7F9", +") c #F6F6F6", +"! c #F8F7F7", +"~ c #F8F8F8", 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QmitkToolTrackingStatusWidget.h
+ 1 + + + QmitkTrackingDeviceConfigurationWidget + QWidget +
QmitkTrackingDeviceConfigurationWidget.h
+ 1 + + + + + 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 new file mode 100644 index 0000000000..a7fca9f3ca --- /dev/null +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.cpp @@ -0,0 +1,210 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ +#define _USE_MATH_DEFINES +#include "mitkNavigationDataCSVSequentialPlayer.h" +#include +#include +#include +#include +#include + +mitk::NavigationDataCSVSequentialPlayer::NavigationDataCSVSequentialPlayer() + : mitk::NavigationDataPlayerBase() +{ + m_NavigationDatas = std::vector(); + m_CurrentPos = 0; + m_Filetype = mitk::NavigationDataCSVSequentialPlayer::NavigationDataCSV; +} + +mitk::NavigationDataCSVSequentialPlayer::~NavigationDataCSVSequentialPlayer() +{ +} + +bool mitk::NavigationDataCSVSequentialPlayer::IsAtEnd() +{ + if (m_CurrentPos >= m_NavigationDatas.size()) return true; + else return false; +} + +void mitk::NavigationDataCSVSequentialPlayer:: +SetFileName(const std::string& fileName) +{ + this->SetNumberOfOutputs(1); + FillOutputEmpty(0); + + MITK_INFO << "Reading file: " << fileName; + m_NavigationDatas = GetNavigationDatasFromFile(fileName); + + this->Modified(); +} + +void mitk::NavigationDataCSVSequentialPlayer::FillOutputEmpty(int number) +{ + this->SetNthOutput(number, GetEmptyNavigationData()); +} + +mitk::NavigationData::Pointer mitk::NavigationDataCSVSequentialPlayer::GetEmptyNavigationData() +{ + mitk::NavigationData::Pointer emptyNd = mitk::NavigationData::New(); + mitk::NavigationData::PositionType position; + mitk::NavigationData::OrientationType orientation(0.0, 0.0, 0.0, 0.0); + position.Fill(0.0); + + emptyNd->SetPosition(position); + emptyNd->SetOrientation(orientation); + emptyNd->SetDataValid(false); + return emptyNd; +} + +void mitk::NavigationDataCSVSequentialPlayer::GenerateData() +{ + for (unsigned int index = 0; index < this->GetNumberOfOutputs(); index++) + { + mitk::NavigationData* output = this->GetOutput(index); + + if (m_CurrentPos > m_NavigationDatas.size()) + { + FillOutputEmpty(index); + return; + } + + output->Graft(this->m_NavigationDatas.at(m_CurrentPos)); + m_CurrentPos++; + } +} + +void mitk::NavigationDataCSVSequentialPlayer::UpdateOutputInformation() +{ + this->Modified(); // make sure that we need to be updated + Superclass::UpdateOutputInformation(); +} + +std::vector mitk::NavigationDataCSVSequentialPlayer::GetNavigationDatasFromFile(std::string filename) +{ + std::vector returnValue = std::vector(); + std::vector fileContentLineByLine = GetFileContentLineByLine(filename); + for (int i = 1; (i < fileContentLineByLine.size()); i = i + 24) //skip header so start at 1 + { + returnValue.push_back(GetNavigationDataOutOfOneLine(fileContentLineByLine.at(i))); + } + + return returnValue; +} + +std::vector mitk::NavigationDataCSVSequentialPlayer::GetFileContentLineByLine(std::string filename) +{ + std::vector readData = std::vector(); + + //save old locale + char * oldLocale; + oldLocale = setlocale(LC_ALL, 0); + + //define own locale + std::locale C("C"); + setlocale(LC_ALL, "C"); + + //read file + std::ifstream file; + file.open(filename.c_str(), std::ios::in); + if (file.good()) + { + //read out file + file.seekg(0L, std::ios::beg); // move to begin of file + 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 mitk::NavigationDataCSVSequentialPlayer::GetNavigationDataOutOfOneLine(std::string line) +{ + mitk::NavigationData::Pointer returnValue = mitk::NavigationData::New(); + + QString myLine = QString(line.c_str()); + + QStringList myLineList = myLine.split(';'); + + mitk::Point3D position; + mitk::Quaternion orientation; + bool valid = false; + double time; + + if (m_Filetype = mitk::NavigationDataCSVSequentialPlayer::NavigationDataCSV) + { + if (myLineList.size() < 10) + { + MITK_ERROR << "Error: cannot read line: only found " << myLineList.size() << " fields. Last field: " << myLineList.at(myLineList.size() - 1).toStdString(); + returnValue = GetEmptyNavigationData(); + return returnValue; + } + + time = myLineList.at(2).toDouble(); + + if (myLineList.at(3).toStdString() == "1") valid = true; + + position[0] = myLineList.at(4).toDouble(); + position[1] = myLineList.at(5).toDouble(); + position[2] = myLineList.at(6).toDouble(); + + double euler1 = (myLineList.at(11).toDouble() / 180 * M_PI); + double euler2 = (myLineList.at(12).toDouble() / 180 * M_PI); + double euler3 = (myLineList.at(13).toDouble() / 180 * M_PI); + mitk::Quaternion eulerQuat(euler3, euler2, euler1); + orientation = eulerQuat; + } + else + { + if (myLineList.size() < 10) + { + MITK_ERROR << "Error: cannot read line: only found " << myLineList.size() << " fields. Last field: " << myLineList.at(myLineList.size() - 1).toStdString(); + returnValue = GetEmptyNavigationData(); + return returnValue; + } + + //time = myLineList.at(2).toDouble(); + + //if (myLineList.at(2).toStdString() == "true") + //valid-flag wurde hier nicht gespeichert + valid = true; + + position[0] = myLineList.at(4).toDouble(); + position[1] = myLineList.at(5).toDouble(); + position[2] = myLineList.at(6).toDouble(); + + double euler1 = (myLineList.at(11).toDouble() / 180 * M_PI); + double euler2 = (myLineList.at(12).toDouble() / 180 * M_PI); + double euler3 = (myLineList.at(13).toDouble() / 180 * M_PI); + mitk::Quaternion eulerQuat(euler3, euler2, euler1); + orientation = eulerQuat; + } + + //returnValue->SetTimeStamp(time); //DOES NOT WORK ANY MORE... CANNOT SET TIME TO itk::timestamp CLASS + returnValue->SetDataValid(valid); + returnValue->SetPosition(position); + returnValue->SetOrientation(orientation); + + return returnValue; +} diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.h b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.h new file mode 100644 index 0000000000..457ae7771c --- /dev/null +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.h @@ -0,0 +1,97 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + + +#ifndef MITKNavigationDataCSVSequentialPlayer_H_HEADER_INCLUDED_ +#define MITKNavigationDataCSVSequentialPlayer_H_HEADER_INCLUDED_ + +#include +#include "tinyxml.h" + + +namespace mitk +{ + + /**Documentation + * \brief This class is a NavigationDataPlayer which can play CSV formatted + * files in sequential order, which means it doesn't + * care about timestamps and just + * outputs the navigationdatas in their sequential order + * + * \ingroup IGT + */ + class NavigationDataCSVSequentialPlayer + : public NavigationDataPlayerBase + { + public: + + enum Filetype + { + NavigationDataCSV, + ManualLoggingCSV + }; + + mitkClassMacro(NavigationDataCSVSequentialPlayer, NavigationDataPlayerBase); + itkNewMacro(Self); + + /** + * \brief sets the file name and path (if XMLString is set, this is neglected) + */ + void SetFileName(const std::string& _FileName); + + /** + * \brief returns the file name and path + */ + itkGetStringMacro(FileName); + + itkSetMacro(Filetype,Filetype); + + bool IsAtEnd(); + + /** + * \brief Used for pipeline update just to tell the pipeline + * that we always have to update + */ + virtual void UpdateOutputInformation(); + + protected: + NavigationDataCSVSequentialPlayer(); + virtual ~NavigationDataCSVSequentialPlayer(); + + /// + /// do the work here + /// + virtual void GenerateData(); + + std::string m_FileName; + + int m_CurrentPos; + Filetype m_Filetype; + + //member for the navigation datas which were read (only one output is supported at the moment) + std::vector m_NavigationDatas; + + std::vector GetNavigationDatasFromFile(std::string filename); + std::vector GetFileContentLineByLine(std::string filename); + mitk::NavigationData::Pointer GetNavigationDataOutOfOneLine(std::string line); + + void FillOutputEmpty(int number); + mitk::NavigationData::Pointer GetEmptyNavigationData(); + + }; +} // namespace mitk + +#endif /* MITKNavigationDataCSVSequentialPlayer_H_HEADER_INCLUDED_ */ diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkPluginActivator.cpp new file mode 100644 index 0000000000..daf9692487 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkPluginActivator.cpp @@ -0,0 +1,39 @@ +/*========================================================================= + +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 "mitkPluginActivator.h" + +#include + +#include "QmitkIGTTrackingSemiAutomaticMeasurementView.h" +#include "QmitkIGTTrackingDataEvaluationView.h" + +namespace mitk { + void PluginActivator::start(ctkPluginContext* context) + { + BERRY_REGISTER_EXTENSION_CLASS(QmitkIGTTrackingSemiAutomaticMeasurementView, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkIGTTrackingDataEvaluationView, context) + } + + void PluginActivator::stop(ctkPluginContext* context) + { + Q_UNUSED(context) + } +} + +#if QT_VERSION < QT_VERSION_CHECK(5, 0, 0) +Q_EXPORT_PLUGIN2(org_mitk_gui_qt_igttrackingsemiautomaticmeasurement, mitk::PluginActivator) +#endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkPluginActivator.h new file mode 100644 index 0000000000..08f307e628 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkPluginActivator.h @@ -0,0 +1,43 @@ +/*=================================================================== + +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 MITKPLUGINACTIVATOR_H +#define MITKPLUGINACTIVATOR_H + +#include + +namespace mitk { + +class PluginActivator : + public QObject, public ctkPluginActivator +{ + Q_OBJECT + #if QT_VERSION >= QT_VERSION_CHECK(5, 0, 0) + Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_igtapphummelprotocolmeasurements") + #endif + Q_INTERFACES(ctkPluginActivator) + +public: + + void start(ctkPluginContext* context); + void stop(ctkPluginContext* context); + +}; // PluginActivator + +} + +#endif // MITKPLUGINACTIVATOR_H

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J ,DsFtFuFvFwFxF +#include + +// Qmitk +#include "QmitkIGTTrackingDataEvaluationView.h" +#include "QmitkStdMultiWidget.h" + +// Qt +#include +#include +#include + +// MITK +#include "mitkNavigationDataCSVSequentialPlayer.h" +#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())); + } +} + +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::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; + } + + //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"; + } + + //write result to output file + WriteDataSet(myEvaluationFilter, m_FilenameVector.at(i)); + } + + //close output file + m_CurrentWriteFile.close(); + + //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); + this->GetDataStorage()->Add(newNode); +} + +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_PointNumber1->value(); i++) + { + for (int j = 0; j < m_Controls->m_PointNumber2->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); + 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); + } + + double AngleBetweenTwoQuaternions = GetAngleBetweenTwoQuaterions(q1, q2); + + //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 [-PI..+PI]; 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 << ";" << angle_degree << "\n"; + MITK_INFO << "Angle: " << angle_degree; +} + +double QmitkIGTTrackingDataEvaluationView::GetAngleBetweenTwoQuaterions(mitk::Quaternion a, mitk::Quaternion b) +{ + double returnValue; + + //variant to work with the data received from the polhemus tracker + 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); + + /* + //another variant + mitk::Quaternion combinedRotation = b * a; + + itk::Vector pt1; //caution 5D-Tools: Vector must lie in the YZ-plane for a correct result. + pt1[0] = 0.0; + pt1[1] = 0.0; + pt1[2] = 100000.0; + + itk::Matrix rotMatrixA; + for (int i = 0; i < 3; i++) for (int j = 0; j < 3; j++) rotMatrixA[i][j] = combinedRotation.rotation_matrix_transpose().transpose()[i][j]; + itk::Vector pt2 = rotMatrixA*pt1; + + //compute angle between the two vectors + returnValue = (pt1[0] * pt2[0] + pt1[1] * pt2[1] + pt1[2] * pt2[2]) / (sqrt(pow(pt1[0], 2) + pow(pt1[1], 2) + pow(pt1[2], 2)) * sqrt(pow(pt2[0], 2) + pow(pt2[1], 2) + pow(pt2[2], 2))); + returnValue = acos(returnValue); + */ + /* + //variant with double precision + + itk::Vector point; //caution 5D-Tools: Vector must lie in the YZ-plane for a correct result. + //TODO: welchen Vektor hier nehmen? + point[0] = 0; + point[1] = 100000.0; + point[2] = 100000.0; + + //OB DAS HILFT? + 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); + */ + /* + // same code with float precision: + mitk::Point3D point; + mitk::FillVector3D(point, 0, 0, 100); //caution 5D-Tools: Vector must lie in the YZ-plane for a correct result. + vnl_vector pt1 = a.rotate(point.Get_vnl_vector()); + vnl_vector pt2 = b.rotate(point.Get_vnl_vector()); + + //compute angle between the two vectors + returnValue = (pt1[0] * pt2[0] + pt1[1] * pt2[1] + pt1[2] * pt2[2]) / (sqrt(pow(pt1[0], 2) + pow(pt1[1], 2) + pow(pt1[2], 2)) * sqrt(pow(pt2[0], 2) + pow(pt2[1], 2) + pow(pt2[2], 2))); + returnValue = acos(returnValue); + //angle(pt1,pt2); + */ + return returnValue; +} + +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; +} 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 new file mode 100644 index 0000000000..8a5a688a51 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.h @@ -0,0 +1,123 @@ +/*=================================================================== + +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 + + + +/*! + \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 OnGeneratePointSet(); + void OnGeneratePointSetsOfSinglePositions(); + void OnGenerateRotationLines(); + void OnGenerateGroundTruthPointSet(); + void OnConvertCSVtoXMLFile(); + void OnCSVtoXMLLoadInputList(); + void OnCSVtoXMLLoadOutputList(); + + /** 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); + + //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); +}; + + + +#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 new file mode 100644 index 0000000000..e2b4e65966 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationViewControls.ui @@ -0,0 +1,941 @@ + + + QmitkIGTTrackingDataEvaluationViewControls + + + + 0 + 0 + 378 + 955 + + + + + 0 + 0 + + + + QmitkTemplate + + + + + + 0 + + + + Evaluation + + + + + + Input File List (recorded NavigationData / *.csv): + + + + + + + + + + + + Add Path: + + + + + + + D:/Experimente/ + + + + + + + + + <!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> + + + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + 110 + 0 + + + + Load New List + + + + + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + 110 + 0 + + + + Add To Current List + + + + + + + + + + + Number of samples to analyze: + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + 1000000 + + + 150 + + + + + + + + + + + Result CSV Filename: + + + + + + + D:/tmp/output.csv + + + + + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + 200 + 50 + + + + + 200 + 50 + + + + START EVALUATION + + + + + + + + + Qt::Horizontal + + + + + + + Visualization Tools: + + + + + + + Generate PointSet of Mean Positions + + + + + + + Generate PointSets of Single Positions + + + + + + + Generate Lines for Rotation + + + + + + + + + Prefix for Data Nodes: + + + + + + + + + + + + Qt::Vertical + + + QSizePolicy::Expanding + + + + 20 + 220 + + + + + + + + + Settings + + + + + + Output Settings + + + + + + <!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) + + + + + + + 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 + + + + + + + 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 + + + + + + + + + + + + Scaling Factor for Visualization: + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + 1.000000000000000 + + + + + + + + + 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 + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementView.cpp b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementView.cpp new file mode 100644 index 0000000000..4d9416ddea --- /dev/null +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementView.cpp @@ -0,0 +1,666 @@ +/*=================================================================== + +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 "QmitkIGTTrackingSemiAutomaticMeasurementView.h" +#include "QmitkStdMultiWidget.h" + +// Qt +#include +#include +#include +#include + +// MITK +#include +#include +#include + +// POCO +#include +#include + +const std::string QmitkIGTTrackingSemiAutomaticMeasurementView::VIEW_ID = "org.mitk.views.igttrackingsemiautomaticmeasurement"; + +QmitkIGTTrackingSemiAutomaticMeasurementView::QmitkIGTTrackingSemiAutomaticMeasurementView() + : QmitkFunctionality() + , m_Controls(0) + , m_MultiWidget(NULL) +{ + m_NextFile = 0; + m_FilenameVector = std::vector(); + m_Timer = new QTimer(this); + m_logging = false; + m_referenceValid = true; + m_tracking = false; + m_EvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); +} + +QmitkIGTTrackingSemiAutomaticMeasurementView::~QmitkIGTTrackingSemiAutomaticMeasurementView() +{ +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::CreateResults() +{ + QString LogFileName = m_Controls->m_OutputPath->text() + "_results.log"; + mitk::LoggingBackend::Unregister(); + mitk::LoggingBackend::SetLogFile(LogFileName.toStdString().c_str()); + mitk::LoggingBackend::Register(); + + double RMSmean = 0; + for (int i = 0; i < m_RMSValues.size(); i++) + { + MITK_INFO << "RMS at " << this->m_FilenameVector.at(i) << ": " << m_RMSValues.at(i); + RMSmean += m_RMSValues.at(i); + } + RMSmean /= m_RMSValues.size(); + MITK_INFO << "RMS mean over " << m_RMSValues.size() << " values: " << RMSmean; + + mitk::DataNode::Pointer newNode = mitk::DataNode::New(); + newNode->SetName("Tracking Results"); + newNode->SetData(this->m_MeanPoints); + this->GetDataStorage()->Add(newNode); + + if (m_MeanPoints->GetSize() == 12) + { + MITK_INFO << "Computing distance error for Compact FG..."; + std::vector distances; + mitk::Point3D test; + //row 1 + distances.push_back(m_MeanPoints->GetPoint(0).EuclideanDistanceTo(m_MeanPoints->GetPoint(1))); //0 + distances.push_back(m_MeanPoints->GetPoint(1).EuclideanDistanceTo(m_MeanPoints->GetPoint(2))); //1 + distances.push_back(m_MeanPoints->GetPoint(2).EuclideanDistanceTo(m_MeanPoints->GetPoint(3))); //2 + //row 2 + distances.push_back(m_MeanPoints->GetPoint(4).EuclideanDistanceTo(m_MeanPoints->GetPoint(5))); //3 + distances.push_back(m_MeanPoints->GetPoint(5).EuclideanDistanceTo(m_MeanPoints->GetPoint(6))); //4 + distances.push_back(m_MeanPoints->GetPoint(6).EuclideanDistanceTo(m_MeanPoints->GetPoint(7))); //5 + //row 3 + distances.push_back(m_MeanPoints->GetPoint(8).EuclideanDistanceTo(m_MeanPoints->GetPoint(9))); //6 + distances.push_back(m_MeanPoints->GetPoint(9).EuclideanDistanceTo(m_MeanPoints->GetPoint(10))); //7 + distances.push_back(m_MeanPoints->GetPoint(10).EuclideanDistanceTo(m_MeanPoints->GetPoint(11))); //8 + //column 1 + distances.push_back(m_MeanPoints->GetPoint(0).EuclideanDistanceTo(m_MeanPoints->GetPoint(4))); //9 + distances.push_back(m_MeanPoints->GetPoint(4).EuclideanDistanceTo(m_MeanPoints->GetPoint(8))); //10 + //column 2 + distances.push_back(m_MeanPoints->GetPoint(1).EuclideanDistanceTo(m_MeanPoints->GetPoint(5))); //11 + distances.push_back(m_MeanPoints->GetPoint(5).EuclideanDistanceTo(m_MeanPoints->GetPoint(9))); //12 + //column 3 + distances.push_back(m_MeanPoints->GetPoint(2).EuclideanDistanceTo(m_MeanPoints->GetPoint(6))); //13 + distances.push_back(m_MeanPoints->GetPoint(6).EuclideanDistanceTo(m_MeanPoints->GetPoint(10))); //14 + //column 4 + distances.push_back(m_MeanPoints->GetPoint(3).EuclideanDistanceTo(m_MeanPoints->GetPoint(7))); //15 + distances.push_back(m_MeanPoints->GetPoint(7).EuclideanDistanceTo(m_MeanPoints->GetPoint(11))); //16 + + std::vector errors; + double meanError = 0; + for (int i = 0; i < distances.size(); i++) + { + double currentError = distances.at(i) - (double)50.0; + errors.push_back(currentError); + meanError += currentError; + MITK_INFO << "Error" << i << " : " << currentError; + } + meanError /= distances.size(); + MITK_INFO << "Mean error : " << meanError; + } +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::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::QmitkIGTTrackingSemiAutomaticMeasurementViewControls; + m_Controls->setupUi(parent); + + //buttons + connect(m_Controls->m_LoadMeasurementToolStorage, SIGNAL(clicked()), this, SLOT(OnLoadMeasurementStorage())); + connect(m_Controls->m_LoadReferenceToolStorage, SIGNAL(clicked()), this, SLOT(OnLoadReferenceStorage())); + connect(m_Controls->m_StartTracking, SIGNAL(clicked()), this, SLOT(OnStartTracking())); + connect(m_Controls->m_LoadList, SIGNAL(clicked()), this, SLOT(OnMeasurementLoadFile())); + connect(m_Controls->m_StartNextMeasurement, SIGNAL(clicked()), this, SLOT(StartNextMeasurement())); + connect(m_Controls->m_ReapeatLastMeasurement, SIGNAL(clicked()), this, SLOT(RepeatLastMeasurement())); + connect(m_Controls->m_SetReference, SIGNAL(clicked()), this, SLOT(OnSetReference())); + connect(m_Controls->m_UseReferenceTrackingSystem, SIGNAL(toggled(bool)), this, SLOT(OnUseReferenceToggled(bool))); + connect(m_Controls->m_CreateResults, SIGNAL(clicked()), this, SLOT(CreateResults())); + + //event filter + qApp->installEventFilter(this); + + //timers + connect(m_Timer, SIGNAL(timeout()), this, SLOT(UpdateTimer())); + } + + //initialize some view + m_Controls->m_StopTracking->setEnabled(false); +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::StdMultiWidgetAvailable(QmitkStdMultiWidget &stdMultiWidget) +{ + m_MultiWidget = &stdMultiWidget; +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::OnUseReferenceToggled(bool state) +{ + if (state) + { + m_Controls->m_ReferenceBox->setEnabled(true); + m_Controls->m_SetReference->setEnabled(true); + } + + else + { + m_Controls->m_ReferenceBox->setEnabled(false); + m_Controls->m_SetReference->setEnabled(false); + } +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::StdMultiWidgetNotAvailable() +{ + m_MultiWidget = NULL; +} + +mitk::NavigationToolStorage::Pointer QmitkIGTTrackingSemiAutomaticMeasurementView::ReadStorage(std::string file) +{ + mitk::NavigationToolStorage::Pointer returnValue; + + //initialize tool storage + returnValue = mitk::NavigationToolStorage::New(); + + //read tool storage from disk + mitk::NavigationToolStorageDeserializer::Pointer myDeserializer = mitk::NavigationToolStorageDeserializer::New(GetDataStorage()); + returnValue = myDeserializer->Deserialize(file); + if (returnValue.IsNull()) + { + QMessageBox msgBox; + msgBox.setText(myDeserializer->GetErrorMessage().c_str()); + msgBox.exec(); + + returnValue = NULL; + } + + return returnValue; +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::OnSetReference() +{ + //initialize reference + m_ReferenceStartPositions = std::vector(); + m_ReferenceTrackingDeviceSource->Update(); + QString Label = "Positions At Start: "; + for (int i = 0; i < m_ReferenceTrackingDeviceSource->GetNumberOfOutputs(); i++) + { + mitk::Point3D position = m_ReferenceTrackingDeviceSource->GetOutput(i)->GetPosition(); + Label = Label + "Tool" + QString::number(i) + ":[" + QString::number(position[0]) + ":" + QString::number(position[1]) + ":" + QString::number(position[1]) + "] "; + m_ReferenceStartPositions.push_back(position); + } + m_Controls->m_ReferencePosAtStart->setText(Label); +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::OnLoadMeasurementStorage() +{ + //read in filename + QString filename = QFileDialog::getOpenFileName(NULL, tr("Open Toolfile"), "/", tr("All Files (*.*)")); + if (filename.isNull()) return; + + m_MeasurementStorage = ReadStorage(filename.toStdString()); + + //update label + Poco::Path myPath = Poco::Path(filename.toStdString()); //use this to seperate filename from path + QString toolLabel = QString("Tool Storage: ") + QString::number(m_MeasurementStorage->GetToolCount()) + " Tools from " + myPath.getFileName().c_str(); + m_Controls->m_MeasurementToolStorageLabel->setText(toolLabel); + + //update status widget + m_Controls->m_ToolStatusWidget->RemoveStatusLabels(); + m_Controls->m_ToolStatusWidget->PreShowTools(m_MeasurementStorage); +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::OnLoadReferenceStorage() +{ + //read in filename + static QString oldFile; + if (oldFile.isNull()) oldFile = "/"; + QString filename = QFileDialog::getOpenFileName(NULL, tr("Open Toolfile"), oldFile, tr("All Files (*.*)")); + if (filename.isNull()) return; + oldFile = filename; + + m_ReferenceStorage = ReadStorage(filename.toStdString()); + + //update label + Poco::Path myPath = Poco::Path(filename.toStdString()); //use this to seperate filename from path + QString toolLabel = QString("Tool Storage: ") + QString::number(m_ReferenceStorage->GetToolCount()) + " Tools from " + myPath.getFileName().c_str(); + m_Controls->m_ReferenceToolStorageLabel->setText(toolLabel); +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::OnStartTracking() +{ + //check if everything is ready to start tracking + if (m_MeasurementStorage.IsNull()) + { + MessageBox("Error: No measurement tools loaded yet!"); + return; + } + else if (m_ReferenceStorage.IsNull() && m_Controls->m_UseReferenceTrackingSystem->isChecked()) + { + MessageBox("Error: No refernce tools loaded yet!"); + return; + } + else if (m_MeasurementStorage->GetToolCount() == 0) + { + MessageBox("Error: No way to track without tools!"); + return; + } + else if (m_Controls->m_UseReferenceTrackingSystem->isChecked() && (m_ReferenceStorage->GetToolCount() == 0)) + { + MessageBox("Error: No way to track without tools!"); + return; + } + + //build the first IGT pipeline (MEASUREMENT) + mitk::TrackingDeviceSourceConfigurator::Pointer myTrackingDeviceSourceFactory1 = mitk::TrackingDeviceSourceConfigurator::New(this->m_MeasurementStorage, this->m_Controls->m_MeasurementTrackingDeviceConfigurationWidget->GetTrackingDevice()); + m_MeasurementTrackingDeviceSource = myTrackingDeviceSourceFactory1->CreateTrackingDeviceSource(this->m_MeasurementToolVisualizationFilter); + if (m_MeasurementTrackingDeviceSource.IsNull()) + { + MessageBox(myTrackingDeviceSourceFactory1->GetErrorMessage()); + return; + } + //connect the tool visualization widget + for (int i = 0; i < m_MeasurementTrackingDeviceSource->GetNumberOfOutputs(); i++) + { + m_Controls->m_ToolStatusWidget->AddNavigationData(m_MeasurementTrackingDeviceSource->GetOutput(i)); + m_EvaluationFilter->SetInput(i, m_MeasurementTrackingDeviceSource->GetOutput(i)); + } + m_Controls->m_ToolStatusWidget->ShowStatusLabels(); + m_Controls->m_ToolStatusWidget->SetShowPositions(true); + m_Controls->m_ToolStatusWidget->SetShowQuaternions(true); + + //build the second IGT pipeline (REFERENCE) + if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) + { + mitk::TrackingDeviceSourceConfigurator::Pointer myTrackingDeviceSourceFactory2 = mitk::TrackingDeviceSourceConfigurator::New(this->m_ReferenceStorage, this->m_Controls->m_ReferenceDeviceConfigurationWidget->GetTrackingDevice()); + m_ReferenceTrackingDeviceSource = myTrackingDeviceSourceFactory2->CreateTrackingDeviceSource(); + if (m_ReferenceTrackingDeviceSource.IsNull()) + { + MessageBox(myTrackingDeviceSourceFactory2->GetErrorMessage()); + return; + } + } + + //initialize tracking + try + { + m_MeasurementTrackingDeviceSource->Connect(); + m_MeasurementTrackingDeviceSource->StartTracking(); + if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) + { + m_ReferenceTrackingDeviceSource->Connect(); + m_ReferenceTrackingDeviceSource->StartTracking(); + } + } + catch (...) + { + MessageBox("Error while starting the tracking device!"); + return; + } + + //set reference + if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) OnSetReference(); + + //start timer + m_Timer->start(1000 / (m_Controls->m_SamplingRate->value())); + + m_Controls->m_StartTracking->setEnabled(false); + m_Controls->m_StartTracking->setEnabled(true); + + m_tracking = true; +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::OnStopTracking() +{ + if (this->m_logging) FinishMeasurement(); + m_MeasurementTrackingDeviceSource->Disconnect(); + m_MeasurementTrackingDeviceSource->StopTracking(); + if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) + { + m_ReferenceTrackingDeviceSource->Disconnect(); + m_ReferenceTrackingDeviceSource->StopTracking(); + } + m_Timer->stop(); + m_Controls->m_StartTracking->setEnabled(true); + m_Controls->m_StartTracking->setEnabled(false); + m_tracking = false; +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::OnMeasurementLoadFile() +{ + m_FilenameVector = std::vector(); + m_FilenameVector.clear(); + m_NextFile = 0; + + //read in filename + QString filename = QFileDialog::getOpenFileName(NULL, tr("Open Measurement Filename List"), "/", tr("All Files (*.*)")); + if (filename.isNull()) return; + + //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.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) m_FilenameVector.push_back(buffer); + } + } + + //fill list at GUI + m_Controls->m_MeasurementList->clear(); + for (unsigned int i = 0; i < m_FilenameVector.size(); i++) { new QListWidgetItem(tr(m_FilenameVector.at(i).c_str()), m_Controls->m_MeasurementList); } + + //update label next measurement + std::stringstream label; + label << "Next Measurement: " << m_FilenameVector.at(0); + m_Controls->m_NextMeasurement->setText(label.str().c_str()); + + //reset results files + m_MeanPoints = mitk::PointSet::New(); + m_RMSValues = std::vector(); + m_EvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); + if (m_MeasurementToolVisualizationFilter.IsNotNull()) m_EvaluationFilter->SetInput(0, m_MeasurementToolVisualizationFilter->GetOutput(0)); +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::UpdateTimer() +{ + if (m_EvaluationFilter.IsNotNull() && m_logging) m_EvaluationFilter->Update(); + else m_MeasurementToolVisualizationFilter->Update(); + + m_Controls->m_ToolStatusWidget->Refresh(); + + //update reference + if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) + { + m_ReferenceTrackingDeviceSource->Update(); + QString Label = "Current Positions: "; + bool distanceThresholdExceeded = false; + for (int i = 0; i < m_ReferenceTrackingDeviceSource->GetNumberOfOutputs(); i++) + { + mitk::Point3D position = m_ReferenceTrackingDeviceSource->GetOutput(i)->GetPosition(); + Label = Label + "Tool" + QString::number(i) + ":[" + QString::number(position[0]) + ":" + QString::number(position[1]) + ":" + QString::number(position[1]) + "] "; + if (position.EuclideanDistanceTo(m_ReferenceStartPositions.at(i)) > m_Controls->m_ReferenceThreshold->value()) distanceThresholdExceeded = true; + } + m_Controls->m_ReferenceCurrentPos->setText(Label); + if (distanceThresholdExceeded) + { + m_Controls->m_ReferenceOK->setText("NOT OK!"); + m_referenceValid = false; + } + else + { + m_Controls->m_ReferenceOK->setText("OK"); + m_referenceValid = true; + } + } + + //update logging + if (m_logging) + { + //check for missing objects + if (m_MeasurementLoggingFilterXML.IsNull() || + m_MeasurementLoggingFilterCSV.IsNull() + ) + { + return; + } + + //log/measure + m_MeasurementLoggingFilterXML->Update(); + m_MeasurementLoggingFilterCSV->Update(); + + if (m_Controls->m_UseReferenceTrackingSystem->isChecked() && + m_ReferenceLoggingFilterXML.IsNotNull() && + m_ReferenceLoggingFilterCSV.IsNotNull()) + { + m_ReferenceLoggingFilterXML->Update(); + m_ReferenceLoggingFilterCSV->Update(); + } + m_loggedFrames++; + LogAdditionalCSVFile(); + + //check if all frames are logged ... if yes finish the measurement + if (m_loggedFrames > m_Controls->m_SamplesPerMeasurement->value()) { FinishMeasurement(); } + + //update logging label + QString loggingLabel = "Collected Samples: " + QString::number(m_loggedFrames); + m_Controls->m_CollectedSamples->setText(loggingLabel); + } +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::StartNextMeasurement() +{ + if (this->m_NextFile >= m_FilenameVector.size()) + { + MessageBox("Last Measurement reached!"); + return; + } + + m_loggedFrames = 0; + m_logging = true; + + //check if directory exists, if not create one + Poco::File myPath(std::string(m_Controls->m_OutputPath->text().toUtf8()).c_str()); + if (!myPath.exists()) myPath.createDirectory(); + + QString LogFileName = m_Controls->m_OutputPath->text() + QString(m_FilenameVector.at(m_NextFile).c_str()) + ".log"; + mitk::LoggingBackend::Unregister(); + mitk::LoggingBackend::SetLogFile(LogFileName.toStdString().c_str()); + mitk::LoggingBackend::Register(); + + //initialize logging filters + m_MeasurementLoggingFilterXML = mitk::NavigationDataRecorderDeprecated::New(); + m_MeasurementLoggingFilterXML->SetRecordingMode(mitk::NavigationDataRecorderDeprecated::NormalFile); + m_MeasurementLoggingFilterCSV = mitk::NavigationDataRecorderDeprecated::New(); + m_MeasurementLoggingFilterCSV->SetRecordingMode(mitk::NavigationDataRecorderDeprecated::NormalFile); + m_MeasurementLoggingFilterXML->SetOutputFormat(mitk::NavigationDataRecorderDeprecated::xml); + m_MeasurementLoggingFilterCSV->SetOutputFormat(mitk::NavigationDataRecorderDeprecated::csv); + QString MeasurementFilenameXML = m_Controls->m_OutputPath->text() + QString(m_FilenameVector.at(m_NextFile).c_str()) + ".xml"; + QString MeasurementFilenameCSV = m_Controls->m_OutputPath->text() + QString(m_FilenameVector.at(m_NextFile).c_str()) + ".csv"; + m_MeasurementLoggingFilterXML->SetFileName(MeasurementFilenameXML.toStdString()); + m_MeasurementLoggingFilterCSV->SetFileName(MeasurementFilenameCSV.toStdString()); + m_MeasurementLoggingFilterXML->SetRecordCountLimit(m_Controls->m_SamplesPerMeasurement->value()); + m_MeasurementLoggingFilterCSV->SetRecordCountLimit(m_Controls->m_SamplesPerMeasurement->value()); + + if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) + { + m_ReferenceLoggingFilterXML = mitk::NavigationDataRecorderDeprecated::New(); + m_ReferenceLoggingFilterXML->SetRecordingMode(mitk::NavigationDataRecorderDeprecated::NormalFile); + m_ReferenceLoggingFilterCSV = mitk::NavigationDataRecorderDeprecated::New(); + m_ReferenceLoggingFilterCSV->SetRecordingMode(mitk::NavigationDataRecorderDeprecated::NormalFile); + m_ReferenceLoggingFilterXML->SetOutputFormat(mitk::NavigationDataRecorderDeprecated::xml); + m_ReferenceLoggingFilterCSV->SetOutputFormat(mitk::NavigationDataRecorderDeprecated::csv); + QString ReferenceFilenameXML = m_Controls->m_OutputPath->text() + "Reference_" + QString(m_FilenameVector.at(m_NextFile).c_str()) + ".xml"; + QString ReferenceFilenameCSV = m_Controls->m_OutputPath->text() + "Reference_" + QString(m_FilenameVector.at(m_NextFile).c_str()) + ".csv"; + m_ReferenceLoggingFilterXML->SetFileName(ReferenceFilenameXML.toStdString()); + m_ReferenceLoggingFilterCSV->SetFileName(ReferenceFilenameCSV.toStdString()); + m_ReferenceLoggingFilterXML->SetRecordCountLimit(m_Controls->m_SamplesPerMeasurement->value()); + m_ReferenceLoggingFilterCSV->SetRecordCountLimit(m_Controls->m_SamplesPerMeasurement->value()); + } + + //start additional csv logging + StartLoggingAdditionalCSVFile(m_FilenameVector.at(m_NextFile)); + + //connect filter + for (int i = 0; i < m_MeasurementToolVisualizationFilter->GetNumberOfOutputs(); i++) + { + m_MeasurementLoggingFilterXML->AddNavigationData(m_MeasurementToolVisualizationFilter->GetOutput(i)); + m_MeasurementLoggingFilterCSV->AddNavigationData(m_MeasurementToolVisualizationFilter->GetOutput(i)); + } + if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) for (int i = 0; i < m_ReferenceTrackingDeviceSource->GetNumberOfOutputs(); i++) + { + m_ReferenceLoggingFilterXML->AddNavigationData(m_ReferenceTrackingDeviceSource->GetOutput(i)); + m_ReferenceLoggingFilterCSV->AddNavigationData(m_ReferenceTrackingDeviceSource->GetOutput(i)); + } + + //start filter + m_MeasurementLoggingFilterXML->StartRecording(); + m_MeasurementLoggingFilterCSV->StartRecording(); + if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) + { + m_ReferenceLoggingFilterXML->StartRecording(); + m_ReferenceLoggingFilterCSV->StartRecording(); + } + + //disable all buttons + DisableAllButtons(); + + //update label next measurement + std::stringstream label; + if ((m_NextFile + 1) >= m_FilenameVector.size()) label << "Next Measurement: "; + else label << "Next Measurement: " << m_FilenameVector.at(m_NextFile + 1); + m_Controls->m_NextMeasurement->setText(label.str().c_str()); + + //update label last measurement + std::stringstream label2; + label2 << "Last Measurement: " << m_FilenameVector.at(m_NextFile); + m_Controls->m_LastMeasurement->setText(label2.str().c_str()); + + m_NextFile++; +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::RepeatLastMeasurement() +{ + m_NextFile--; + StartNextMeasurement(); +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::MessageBox(std::string s) +{ + QMessageBox msgBox; + msgBox.setText(s.c_str()); + msgBox.exec(); +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::DisableAllButtons() +{ + m_Controls->m_LoadList->setEnabled(false); + m_Controls->m_StartNextMeasurement->setEnabled(false); + m_Controls->m_ReapeatLastMeasurement->setEnabled(false); + m_Controls->m_SamplingRate->setEnabled(false); + m_Controls->m_SamplesPerMeasurement->setEnabled(false); + m_Controls->m_ReferenceThreshold->setEnabled(false); +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::EnableAllButtons() +{ + m_Controls->m_LoadList->setEnabled(true); + m_Controls->m_StartNextMeasurement->setEnabled(true); + m_Controls->m_ReapeatLastMeasurement->setEnabled(true); + m_Controls->m_SamplingRate->setEnabled(true); + m_Controls->m_SamplesPerMeasurement->setEnabled(true); + m_Controls->m_ReferenceThreshold->setEnabled(true); +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::FinishMeasurement() +{ + m_logging = false; + + m_MeasurementLoggingFilterXML->StopRecording(); + m_MeasurementLoggingFilterCSV->StopRecording(); + if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) + { + m_ReferenceLoggingFilterXML->StopRecording(); + m_ReferenceLoggingFilterCSV->StopRecording(); + } + StopLoggingAdditionalCSVFile(); + + int id = m_NextFile - 1; + mitk::Point3D positionMean = m_EvaluationFilter->GetPositionMean(0); + MITK_INFO << "Evaluated " << m_EvaluationFilter->GetNumberOfAnalysedNavigationData(0) << " samples."; + double rms = m_EvaluationFilter->GetPositionErrorRMS(0); + MITK_INFO << "RMS: " << rms; + MITK_INFO << "Position Mean: " << positionMean; + m_MeanPoints->SetPoint(id, positionMean); + if (m_RMSValues.size() <= id) m_RMSValues.push_back(rms); + else m_RMSValues[id] = rms; + + m_EvaluationFilter->ResetStatistic(); + + EnableAllButtons(); +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::StartLoggingAdditionalCSVFile(std::string filePostfix) +{ + //write logfile header + QString header = "Nr;MITK_Time;Valid_Reference;"; + QString tool = QString("MeasureTool_") + QString(m_MeasurementTrackingDeviceSource->GetOutput(0)->GetName()); + header = header + tool + "[x];" + tool + "[y];" + tool + "[z];" + tool + "[qx];" + tool + "[qy];" + tool + "[qz];" + tool + "[qr]\n"; + + //open logfile and write header + m_logFileCSV.open(std::string(m_Controls->m_OutputPath->text().toUtf8()).append("/LogFileCombined").append(filePostfix.c_str()).append(".csv").c_str(), std::ios::out); + m_logFileCSV << header.toStdString().c_str(); +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::LogAdditionalCSVFile() +{ + mitk::Point3D pos = m_MeasurementTrackingDeviceSource->GetOutput(0)->GetPosition(); + mitk::Quaternion rot = m_MeasurementTrackingDeviceSource->GetOutput(0)->GetOrientation(); + std::string valid = ""; + if (m_referenceValid) valid = "true"; + else valid = "false"; + std::stringstream timestamp; + timestamp << m_MeasurementTrackingDeviceSource->GetOutput(0)->GetTimeStamp(); + QString dataSet = QString::number(m_loggedFrames) + ";" + QString(timestamp.str().c_str()) + ";" + QString(valid.c_str()) + ";" + QString::number(pos[0]) + ";" + QString::number(pos[1]) + ";" + QString::number(pos[2]) + ";" + QString::number(rot.x()) + ";" + QString::number(rot.y()) + ";" + QString::number(rot.z()) + ";" + QString::number(rot.r()) + "\n"; + m_logFileCSV << dataSet.toStdString(); +} + +void QmitkIGTTrackingSemiAutomaticMeasurementView::StopLoggingAdditionalCSVFile() +{ + m_logFileCSV.close(); +} + +bool QmitkIGTTrackingSemiAutomaticMeasurementView::eventFilter(QObject *obj, QEvent *ev) +{ + if (ev->type() == QEvent::KeyPress) + { + QKeyEvent *k = (QKeyEvent *)ev; + bool up = false; + bool down = false; + if (k->key() == 16777238) up = true; //page up + else if (k->key() == 16777239) down = true; //page down + + if (down && m_tracking && !m_logging) + { + StartNextMeasurement(); + } + } + + return false; +} diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementView.h b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementView.h new file mode 100644 index 0000000000..3ec59713ba --- /dev/null +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementView.h @@ -0,0 +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 QmitkIGTTrackingSemiAutomaticMeasurementView_h +#define QmitkIGTTrackingSemiAutomaticMeasurementView_h + +#include + +#include + +//QT +#include + +//MITK +#include +#include +#include +#include +#include + +#include "ui_QmitkIGTTrackingSemiAutomaticMeasurementViewControls.h" + +/*! + \brief QmitkIGTTrackingSemiAutomaticMeasurementView + + \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 QmitkIGTTrackingSemiAutomaticMeasurementView : 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; + + QmitkIGTTrackingSemiAutomaticMeasurementView(); + virtual ~QmitkIGTTrackingSemiAutomaticMeasurementView(); + + virtual void CreateQtPartControl(QWidget *parent); + + virtual void StdMultiWidgetAvailable(QmitkStdMultiWidget &stdMultiWidget); + virtual void StdMultiWidgetNotAvailable(); + + protected slots: + + void OnLoadMeasurementStorage(); + void OnLoadReferenceStorage(); + void OnStartTracking(); + void OnStopTracking(); + void OnMeasurementLoadFile(); + void OnSetReference(); + void StartNextMeasurement(); + void RepeatLastMeasurement(); + void UpdateTimer(); + void CreateResults(); + void OnUseReferenceToggled(bool state); + +protected: + + Ui::QmitkIGTTrackingSemiAutomaticMeasurementViewControls* m_Controls; + + QmitkStdMultiWidget* m_MultiWidget; + + //the tool storages + mitk::NavigationToolStorage::Pointer m_MeasurementStorage; + mitk::NavigationToolStorage::Pointer m_ReferenceStorage; + + //members for the filter pipeline + mitk::TrackingDeviceSource::Pointer m_MeasurementTrackingDeviceSource; + mitk::NavigationDataObjectVisualizationFilter::Pointer m_MeasurementToolVisualizationFilter; + mitk::NavigationDataRecorderDeprecated::Pointer m_MeasurementLoggingFilterXML; + mitk::NavigationDataRecorderDeprecated::Pointer m_MeasurementLoggingFilterCSV; + mitk::TrackingDeviceSource::Pointer m_ReferenceTrackingDeviceSource; + mitk::NavigationDataRecorderDeprecated::Pointer m_ReferenceLoggingFilterXML; + mitk::NavigationDataRecorderDeprecated::Pointer m_ReferenceLoggingFilterCSV; + + //members for file name list + std::vector m_FilenameVector; + int m_NextFile; + + //help methods + mitk::NavigationToolStorage::Pointer ReadStorage(std::string file); + void MessageBox(std::string s); + void DisableAllButtons(); + void EnableAllButtons(); + void FinishMeasurement(); + void StartLoggingAdditionalCSVFile(std::string filePostfix); + void LogAdditionalCSVFile(); + void StopLoggingAdditionalCSVFile(); + + //timer + QTimer* m_Timer; + + //memebers for reference checking + std::vector m_ReferenceStartPositions; + bool m_referenceValid; + + //logging members + int m_loggedFrames; + bool m_logging; + std::fstream m_logFileCSV; + + //event filter for key presses + bool eventFilter(QObject *obj, QEvent *ev); + + //results members + mitk::PointSet::Pointer m_MeanPoints; + std::vector m_RMSValues; + mitk::NavigationDataEvaluationFilter::Pointer m_EvaluationFilter; + + bool m_tracking; +}; + +#endif // _QMITKIGTTRACKINGSEMIAUTOMATICMEASUREMENTVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementViewControls.ui b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementViewControls.ui new file mode 100644 index 0000000000..50168cb767 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementViewControls.ui @@ -0,0 +1,555 @@ + + + QmitkIGTTrackingSemiAutomaticMeasurementViewControls + + + + 0 + 0 + 419 + 931 + + + + + 0 + 0 + + + + QmitkTemplate + + + + + + 0 + + + + Tracking Initialization + + + + + + Measurement Tracking System + + + + + + + + + + + Tool Storage: <none> + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + Load Tool Storage + + + + + + + + + + + + Reference Trackingsystem + + + + + + + + + + + Tool Storage: <none> + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + Load Tool Storage + + + + + + + + + + + + Start Tracking + + + + + + + Stop Tracking + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + Measurement + + + + + + Measurement List: + + + + + + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + Load List + + + + + + + + + + + Output Path: + + + + + + + C:/temp/ + + + + + + + + + Last Measurement: <none> + + + + + + + Next Measurement: <none> + + + + + + + Collected Samples: <none> + + + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + 200 + 0 + + + + Start Next Measurement + + + + + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + 200 + 0 + + + + Repeat Last Measurement + + + + + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + 200 + 0 + + + + Create Results + + + + + + + + + Qt::Vertical + + + + 20 + 281 + + + + + + + + Qt::Horizontal + + + + + + + <!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-weight:600; text-decoration: underline;">Measurement Sensors:</span></p></body></html> + + + + + + + + + + Qt::Horizontal + + + + + + + <!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-weight:600; text-decoration: underline;">Reference Sensors:</span></p></body></html> + + + + + + + Set Reference + + + + + + + Reference Postion: <none> + + + + + + + Current Positions: <none> + + + + + + + <!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:28pt; font-weight:600;">OK</span></p></body></html> + + + Qt::AlignCenter + + + + + + + + Settings + + + + + + + + Sampling Rate (Times Per Second): + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + 999.000000000000000 + + + 15.000000000000000 + + + + + + + + + + + Samples Per Measurement: + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + 1000 + + + 150 + + + + + + + + + + + Threshold For Reference Tools: + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + 1.000000000000000 + + + + + + + + + Use Reference Tracking System + + + true + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + + + + + + QmitkToolTrackingStatusWidget + QWidget +