diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.cpp b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.cpp
index a595f8877a..038653921c 100644
--- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.cpp
+++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.cpp
@@ -1,315 +1,324 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#define _USE_MATH_DEFINES
#include "mitkNavigationDataCSVSequentialPlayer.h"
#include <QString>
#include <QStringList>
#include <iostream>
#include <fstream>
#include <math.h>
mitk::NavigationDataCSVSequentialPlayer::NavigationDataCSVSequentialPlayer()
- : mitk::NavigationDataPlayerBase()
+ : mitk::NavigationDataPlayerBase(),
+ m_numberOfReadErrorsInARow(0),
+ m_NavigationDatas(std::vector<mitk::NavigationData::Pointer>()),
+ m_CurrentPos(0),
+ m_Filetype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV)
{
- m_NavigationDatas = std::vector<mitk::NavigationData::Pointer>();
- m_CurrentPos = 0;
- m_Filetype = mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV;
-
}
mitk::NavigationDataCSVSequentialPlayer::~NavigationDataCSVSequentialPlayer()
{
}
bool mitk::NavigationDataCSVSequentialPlayer::IsAtEnd()
{
return m_CurrentPos >= static_cast<int>(m_NavigationDatas.size());
}
void mitk::NavigationDataCSVSequentialPlayer::
SetFileName(const std::string& fileName)
{
this->SetNumberOfIndexedOutputs(1);
FillOutputEmpty(0);
MITK_INFO << "Reading file: " << fileName;
m_NavigationDatas = GetNavigationDatasFromFile(fileName);
this->Modified();
}
void mitk::NavigationDataCSVSequentialPlayer::FillOutputEmpty(int number)
{
this->SetNthOutput(number, GetEmptyNavigationData());
}
mitk::NavigationData::Pointer mitk::NavigationDataCSVSequentialPlayer::GetEmptyNavigationData()
{
mitk::NavigationData::Pointer emptyNd = mitk::NavigationData::New();
mitk::NavigationData::PositionType position;
mitk::NavigationData::OrientationType orientation(0.0, 0.0, 0.0, 0.0);
position.Fill(0.0);
emptyNd->SetPosition(position);
emptyNd->SetOrientation(orientation);
emptyNd->SetDataValid(false);
return emptyNd;
}
int mitk::NavigationDataCSVSequentialPlayer::GetNumberOfSnapshots()
{
return m_NavigationDatas.size();
}
void mitk::NavigationDataCSVSequentialPlayer::GenerateData()
{
for (unsigned int index = 0; index < this->GetNumberOfOutputs(); index++)
{
mitk::NavigationData* output = this->GetOutput(index);
- if (m_CurrentPos > static_cast<int>(m_NavigationDatas.size()))
+ if (m_CurrentPos >= static_cast<int>(m_NavigationDatas.size()))
{
FillOutputEmpty(index);
return;
}
output->Graft(this->m_NavigationDatas.at(m_CurrentPos));
m_CurrentPos++;
}
}
void mitk::NavigationDataCSVSequentialPlayer::UpdateOutputInformation()
{
this->Modified(); // make sure that we need to be updated
Superclass::UpdateOutputInformation();
}
std::vector<mitk::NavigationData::Pointer> mitk::NavigationDataCSVSequentialPlayer::GetNavigationDatasFromFile(std::string filename)
{
std::vector<mitk::NavigationData::Pointer> returnValue = std::vector<mitk::NavigationData::Pointer>();
std::vector<std::string> fileContentLineByLine = GetFileContentLineByLine(filename);
std::size_t i = m_HeaderRow
? 1 //file has a header row, so it has to be skipped when reading the NavigationDatas
: 0; //file has no header row, so no need to skip the first row
for ( ; i < fileContentLineByLine.size(); ++i)
{
returnValue.push_back(GetNavigationDataOutOfOneLine(fileContentLineByLine.at(i)));
+ if (m_numberOfReadErrorsInARow>5)
+ {
+ MITK_ERROR << "More than 5 read errors in a row, aborting! Is the csv file reader configured correctly?";
+ m_numberOfReadErrorsInARow = 0;
+ return returnValue;
+ }
}
return returnValue;
}
std::vector<std::string> mitk::NavigationDataCSVSequentialPlayer::GetFileContentLineByLine(std::string filename)
{
std::vector<std::string> readData = std::vector<std::string>();
//save old locale
char * oldLocale;
oldLocale = setlocale(LC_ALL, 0);
//define own locale
std::locale C("C");
setlocale(LC_ALL, "C");
//read file
std::ifstream file;
file.open(filename.c_str(), std::ios::in);
if (file.good())
{
//read out file
file.seekg(0L, std::ios::beg); // move to begin of file
int count = 0;
while (!file.eof())
{
std::string buffer;
std::getline(file, buffer); // read out file line by line
if (!buffer.empty())
{
readData.push_back(buffer);
//MITK_INFO << "Line: " << buffer;
}
++count; if (count == m_SampleCount) count = 0;
}
}
file.close();
//switch back to old locale
setlocale(LC_ALL, oldLocale);
return readData;
}
mitk::NavigationData::Pointer mitk::NavigationDataCSVSequentialPlayer::GetNavigationDataOutOfOneLine(std::string line)
{
mitk::NavigationData::Pointer returnValue = mitk::NavigationData::New();
QString myLine = QString(line.c_str());
QStringList myLineList = myLine.split(m_SeparatorSign);
mitk::Point3D position;
mitk::Quaternion orientation;
bool valid = false;
//this is for custom csv files. You have adapt the column numbers to correctly
//interpret your csv file.
if (m_Filetype == mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV)
{
if (myLineList.size() < m_MinNumberOfColumns)
{
- MITK_ERROR << "Error: cannot read line: only found " << myLineList.size() << " fields. Last field: " << myLineList.at(myLineList.size() - 1).toStdString();
+ MITK_WARN << "Error: cannot read line: only found " << myLineList.size() << " fields. Last field: " << myLineList.at(myLineList.size() - 1).toStdString();
returnValue = GetEmptyNavigationData();
+ m_numberOfReadErrorsInARow++;
return returnValue;
}
+ m_numberOfReadErrorsInARow = true;
+
valid = true; //if no valid flag is given: simply set to true
position[0] = myLineList.at(m_XPos).toDouble();
position[1] = myLineList.at(m_YPos).toDouble();
position[2] = myLineList.at(m_ZPos).toDouble();
orientation[0] = myLineList.at(m_Qx).toDouble(); // qx
orientation[1] = myLineList.at(m_Qy).toDouble(); // qy
orientation[2] = myLineList.at(m_Qz).toDouble(); // qz
orientation[3] = myLineList.at(m_Qr).toDouble(); // qr
if(!m_RightHanded) //MITK uses a right handed coordinate system, so the position needs to be converted
{
position[0] = position[0]*(-1);
}
if (m_UseQuats) //Use Quaternions to construct the orientation of the NavigationData
{
orientation[0] = myLineList.at(m_Qx).toDouble(); //qx
orientation[1] = myLineList.at(m_Qy).toDouble(); //qy
orientation[2] = myLineList.at(m_Qz).toDouble(); //qz
orientation[3] = myLineList.at(m_Qr).toDouble(); //qr
}
else //Use the Euler Angles to construct the orientation of the NavigationData
{
double azimuthAngle;
double elevationAngle;
double rollAngle;
if(m_Azimuth < 0) //azimuth is not defined so set him to zero
{
azimuthAngle = 0;
}
else
{
azimuthAngle = myLineList.at(m_Azimuth).toDouble();
}
if(m_Elevation < 0)// elevation is not defined so set him to zero
{
elevationAngle = 0;
}
else
{
elevationAngle = myLineList.at(m_Elevation).toDouble();
}
if(m_Roll < 0) //roll is not defined so set him to zero
{
rollAngle = 0;
}
else
{
rollAngle = myLineList.at(m_Roll).toDouble();
}
if (!m_EulersInRadiants) //the Euler Angles are in Degrees but MITK uses radiants so they need to be converted
{
azimuthAngle = azimuthAngle / 180 * M_PI;
elevationAngle = elevationAngle / 180 * M_PI;
rollAngle = rollAngle / 180 * M_PI;
}
vnl_quaternion<double> eulerQuat(rollAngle, elevationAngle, azimuthAngle);
orientation = eulerQuat;
}
if(!m_RightHanded) //MITK uses a right handed coordinate system, so the orientation needs to be converted
{
//code block for conversion from left-handed to right-handed
mitk::Quaternion linksZuRechtsdrehend;
double rotationAngle = -M_PI;
double rotationAxis[3];
rotationAxis[0] = 0;
rotationAxis[1] = 0;
rotationAxis[2] = 1;
linksZuRechtsdrehend[3] = cos(rotationAngle / 2);
linksZuRechtsdrehend[0] = rotationAxis[0] * sin(rotationAngle / 2);
linksZuRechtsdrehend[1] = rotationAxis[1] * sin(rotationAngle / 2);
linksZuRechtsdrehend[2] = rotationAxis[2] * sin(rotationAngle / 2);
orientation = orientation * linksZuRechtsdrehend;
}
}
//this is for MITK csv files that have been recorded with the MITK
//navigation data recorder. You can also use the navigation data player
//class from the MITK-IGT module instead.
else if (m_Filetype == mitk::NavigationDataCSVSequentialPlayer::NavigationDataCSV)
{
if (myLineList.size() < 8)
{
MITK_ERROR << "Error: cannot read line: only found " << myLineList.size() << " fields. Last field: " << myLineList.at(myLineList.size() - 1).toStdString();
returnValue = GetEmptyNavigationData();
return returnValue;
}
if (myLineList.at(3).toStdString() == "1") valid = true;
position[0] = myLineList.at(2).toDouble();
position[1] = myLineList.at(3).toDouble();
position[2] = myLineList.at(4).toDouble();
orientation[0] = myLineList.at(5).toDouble(); //qx
orientation[1] = myLineList.at(6).toDouble(); //qy
orientation[2] = myLineList.at(7).toDouble(); //qz
orientation[3] = myLineList.at(8).toDouble(); //qr
}
returnValue->SetDataValid(valid);
returnValue->SetPosition(position);
returnValue->SetOrientation(orientation);
return returnValue;
}
void mitk::NavigationDataCSVSequentialPlayer::SetOptions(bool rightHanded, char separatorSign, int sampleCount, bool headerRow, int xPos, int yPos,
int zPos, bool useQuats, int qx, int qy, int qz, int qr, int azimuth, int elevation, int roll,
bool eulerInRadiants, int minNumberOfColumns)
{
m_RightHanded = rightHanded;
m_SeparatorSign = separatorSign;
m_SampleCount = sampleCount;
m_HeaderRow = headerRow;
m_XPos = xPos;
m_YPos = yPos;
m_ZPos = zPos;
m_UseQuats = useQuats;
m_Qx = qx;
m_Qy = qy;
m_Qz = qz;
m_Qr = qr;
m_Azimuth = azimuth;
m_Elevation = elevation;
m_Roll = roll;
m_EulersInRadiants = eulerInRadiants;
m_MinNumberOfColumns = minNumberOfColumns;
}
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
index 6976f05997..6cc89a61ad 100644
--- 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
@@ -1,154 +1,155 @@
/*===================================================================
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 <mitkNavigationDataPlayerBase.h>
#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.
*
* It is thought to interpret custom csv files. To do so please adapt the column
* numbers of position and orientation in the internal method GetNavigationDataOutOfOneLine().
*
* So far only one (the first) tool is read in as required for the hummel protocol measurements.
*
* This class can also interpret MITK style csv files (set filetype to NavigationDataCSV), but
* you can also use the MITK navigation data player class inside the MITK-IGT module which
* is newer and better maintained.
*
* \ingroup IGT
*/
class NavigationDataCSVSequentialPlayer
: public NavigationDataPlayerBase
{
public:
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 SetOptions sets the options for reading out the data out of the correct postions of the file. They need to be set before using the player
* @param rightHanded true if the used coordinate System is right handed, false if it is left handed
* @param seperatorSign symbol that is used to separate the values in the .csv file
* @param sampleCount every n-th sample in the file that should be used
* @param headerRow true if the .csv file has a header row otherwise false
* @param xPos number of the colum in the .csv file for the x-coordinates of the position
* @param yPos number of the colum in the .csv file for the y-coordinates of the position
* @param zPos number of the colum in the .csv file for the z-coordinates of the position
* @param useQuats true if Quaternions are used to construct the orientation, false if Euler Angles are used
* @param qx number of the column in the .csv file for the x component of the quaternion
* @param qy number of the column in the .csv file for the y component of the quaternion
* @param qz number of the column in the .csv file for the z component of the quaternion
* @param qr number of the column in the .csv file for the r component of the quaternion
* @param azimuth number of the colum in the .csv file for Azimuth (Euler Angles). Set < 0 if angle is not defined
* @param elevatino number of the colum in the .csv file for Elevation (Euler Angles) Set < 0 if angle is not defined
* @param roll number of the colum in the .csv file for Roll (Euler Angles) Set < 0 if angle is not defined
* @param eulerInRadiants true if the Euler Angles in the .csv file are in radiants, false if they are in degrees
* @param minNumberOfColumns
*/
void SetOptions(bool rightHanded, char seperatorSign, int sampleCount, bool headerRow, int xPos, int yPos, int zPos, bool useQuats,
int qx, int qy, int qz, int qr, int azimuth, int elevatino, int roll, bool eulerInRadiants, int minNumberOfColums);
/**
* \brief returns the file name and path
*/
itkGetStringMacro(FileName);
enum Filetype
{
NavigationDataCSV, //for csv files from the MITK navigation data player
ManualLoggingCSV //for custum csv files
};
/**
* \brief Sets the file type. ManualLoggingCSV is default and is thought for your
* custom csv files. You can also set it to NavigationDataCSV, then this
* player interprets MITK style csv files.
*/
itkSetMacro(Filetype, Filetype);
/**
* \return Returns true if the player reached the end of the file.
*/
bool IsAtEnd();
/**
* \brief Used for pipeline update just to tell the pipeline
* that we always have to update
*/
virtual void UpdateOutputInformation();
int GetNumberOfSnapshots();
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<mitk::NavigationData::Pointer> m_NavigationDatas;
std::vector<mitk::NavigationData::Pointer> GetNavigationDatasFromFile(std::string filename);
std::vector<std::string> GetFileContentLineByLine(std::string filename);
mitk::NavigationData::Pointer GetNavigationDataOutOfOneLine(std::string line);
+ short m_numberOfReadErrorsInARow; //after a certain number of read errors, the software will abort
void FillOutputEmpty(int number);
mitk::NavigationData::Pointer GetEmptyNavigationData();
bool m_RightHanded; //true if the used coordinate System is right handed, false if it is left handed
char m_SeparatorSign; //symbol that is used to separate the values in the .csv file
int m_SampleCount; //every n-th sample in the file that should be used
bool m_HeaderRow; //true if the .csv file has a header row otherwise false
int m_XPos; //number of the colum in the .csv file for the x-coordinates of the position
int m_YPos; //number of the colum in the .csv file for the y-coordinates of the position
int m_ZPos; //number of the colum in the .csv file for the z-coordinates of the position
bool m_UseQuats; //true if Quaternions are used to construct the orientation, false if Euler Angles are used
int m_Qx; //number of the column in the .csv file for the x component of the quaternion
int m_Qy; //number of the column in the .csv file for the y component of the quaternion
int m_Qz; //number of the column in the .csv file for the z component of the quaternion
int m_Qr; //number of the column in the .csv file for the r component of the quaternion
int m_Azimuth; //number of the colum in the .csv file for Azimuth (Euler Angles)
int m_Elevation; //number of the colum in the .csv file for Elevation (Euler Angles)
int m_Roll; //number of the colum in the .csv file for Roll (Euler Angles)
bool m_EulersInRadiants; // true if the Euler Angles in the .csv file are in radiants, false if they are in degrees
int m_MinNumberOfColumns; //minimal number of columns the file has to have (e.g. if you read data from column 8 the file has to have at least 8 columns)
};
} // namespace mitk
#endif /* MITKNavigationDataCSVSequentialPlayer_H_HEADER_INCLUDED_ */