void Transform::FromCSVFile(const std::string& file)
{
std::ifstream csvFile (file.c_str());
endoAssert ( csvFile.fail() == false );
mitk::Transform::Pointer transform = mitk::Transform::New();
vnl_matrix_fixed<mitk::ScalarType, 4, 4> mat;
std::string line;
mitk::ScalarType d = 0.0f;
int row=0,column = 0;
while (std::getline (csvFile, line))
{
std::istringstream linestream(line);
std::string item;
column = 0;
while (std::getline (linestream, item, ','))
{
std::istringstream number;
number.str(item);
number >> d;
mat(row, column) = d;
++column;
}
++row;
}
endoAssert( row == 4 && column == 4 );
transform->SetMatrix( mat );
this->SetNavigationData( transform->GetNavigationData() );
// modified is called in SetNavigationData
}
void Transform::ToCSVFile(const std::string& file) const
{
std::ofstream csvFile;
csvFile.open(file.c_str());
endoAssert ( csvFile.fail() == false );
csvFile << this->ToCSVString();
csvFile.close();
}
void Transform::ToMatlabFile(const std::string& file
, const std::string& varname) const
{
std::ofstream csvFile;
csvFile.open(file.c_str());
endoAssert ( csvFile.fail() == false );
csvFile << this->ToMatlabString(varname);
csvFile.close();
}
void mitk::CameraIntrinsics::FromGMLCalibrationXML(TiXmlElement* elem)
{
assert( elem );
assert( elem->ValueStr() == "results" );
cv::Mat CameraMatrix = cv::Mat::zeros(3, 3, cv::DataType<double>::type);
CameraMatrix.at<double>(2,2) = 1.0;
cv::Mat DistorsionCoeffs = cv::Mat::zeros(1, 5, cv::DataType<double>::type);
TiXmlElement* focus_lenXElem = elem->FirstChildElement("focus_lenX");
endoAssert( focus_lenXElem != 0 );
CameraMatrix.at<double>(0,0) = atof( focus_lenXElem->GetText() );
TiXmlElement* focus_lenYElem = elem->FirstChildElement("focus_lenY");
endoAssert( focus_lenYElem != 0 );
CameraMatrix.at<double>(1,1) = atof( focus_lenYElem->GetText() );
TiXmlElement* PrincipalXElem = elem->FirstChildElement("PrincipalX");
endoAssert( PrincipalXElem != 0 );
CameraMatrix.at<double>(0,2) = atof( PrincipalXElem->GetText() );
TiXmlElement* PrincipalYElem = elem->FirstChildElement("PrincipalY");
endoAssert( PrincipalYElem != 0 );
CameraMatrix.at<double>(1,2) = atof( PrincipalYElem->GetText() );
// DISTORSION COEFFS
TiXmlElement* Dist1Elem = elem->FirstChildElement("Dist1");
endoAssert( Dist1Elem != 0 );
DistorsionCoeffs.at<double>(0,0) = atof( Dist1Elem->GetText() );
TiXmlElement* Dist2Elem = elem->FirstChildElement("Dist2");
endoAssert( Dist2Elem != 0 );
DistorsionCoeffs.at<double>(0,1) = atof( Dist2Elem->GetText() );
TiXmlElement* Dist3Elem = elem->FirstChildElement("Dist3");
endoAssert( Dist3Elem != 0 );
DistorsionCoeffs.at<double>(0,2) = atof( Dist3Elem->GetText() );
TiXmlElement* Dist4Elem = elem->FirstChildElement("Dist4");
endoAssert( Dist4Elem != 0 );
DistorsionCoeffs.at<double>(0,3) = atof( Dist4Elem->GetText() );
int valid = 0;
elem->QueryIntAttribute("Valid", &valid);
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
m_Valid = static_cast<bool>(valid);
m_CameraMatrix = CameraMatrix;
m_DistorsionCoeffs = DistorsionCoeffs;
}
this->Modified();
}
void mitk::CameraIntrinsics::FromXML(TiXmlElement* elem)
{
endoAssert ( elem );
MITK_DEBUG << elem->Value();
std::string filename;
if(elem->QueryStringAttribute("file", &filename) == TIXML_SUCCESS)
{
this->FromXMLFile(filename);
return;
}
else if(strcmp(elem->Value(), "CalibrationProject") == 0)
{
this->FromGMLCalibrationXML(elem->FirstChildElement("results"));
return;
}
assert ( elem );
if(strcmp(elem->Value(), this->GetNameOfClass()) != 0)
elem = elem->FirstChildElement(this->GetNameOfClass());
std::ostringstream err;
// CAMERA MATRIX
cv::Mat CameraMatrix = cv::Mat::zeros(3, 3, cv::DataType<double>::type);
CameraMatrix.at<double>(2,2) = 1.0;
float val = 0.0f;
if(elem->QueryFloatAttribute("fx", &val) == TIXML_SUCCESS)
CameraMatrix.at<double>(0,0) = val;
else
err << "fx, ";
if(elem->QueryFloatAttribute("fy", &val) == TIXML_SUCCESS)
CameraMatrix.at<double>(1,1) = val;
else
err << "fy, ";
if(elem->QueryFloatAttribute("cx", &val) == TIXML_SUCCESS)
CameraMatrix.at<double>(0,2) = val;
else
err << "cx, ";
if(elem->QueryFloatAttribute("cy", &val) == TIXML_SUCCESS)
CameraMatrix.at<double>(1,2) = val;
else
err << "cy, ";
// DISTORSION COEFFS
endodebug( "creating DistorsionCoeffs from XML file")
cv::Mat DistorsionCoeffs = cv::Mat::zeros(1, 5, cv::DataType<double>::type);
if(elem->QueryFloatAttribute("k1", &val) == TIXML_SUCCESS)
DistorsionCoeffs.at<double>(0,0) = val;
else
err << "k1, ";
if(elem->QueryFloatAttribute("k2", &val) == TIXML_SUCCESS)
DistorsionCoeffs.at<double>(0,1) = val;
else
err << "k2, ";
if(elem->QueryFloatAttribute("p1", &val) == TIXML_SUCCESS)
DistorsionCoeffs.at<double>(0,2) = val;
else
err << "p1, ";
if(elem->QueryFloatAttribute("p2", &val) == TIXML_SUCCESS)
DistorsionCoeffs.at<double>(0,3) = val;
else
err << "p2, ";
DistorsionCoeffs.at<double>(0,4) = 0.0;
/*if(elem->QueryFloatAttribute("k3", &val) == TIXML_SUCCESS)
DistorsionCoeffs.at<double>(4,0) = val;
else
err << "k3, ";*/
std::string errorStr = err.str();
int errLength = errorStr.length();
if(errLength > 0)
{
errorStr = errorStr.substr(0, errLength-2);
errorStr.append(" not found");
throw std::invalid_argument(err.str());
}
int valid = 0;
elem->QueryIntAttribute("Valid", &valid);
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
m_Valid = static_cast<bool>(valid);
m_CameraMatrix = CameraMatrix;
m_DistorsionCoeffs = DistorsionCoeffs;
}
this->Modified();
}
void Transform::SetNavigationData( const mitk::NavigationData* naviData )
{
endoAssert( naviData != 0 );
m_NavData->Graft( naviData );
this->Modified();
}
