#include <istream>
#include <iterator>
#include <itkCenteredEuler3DTransform.h>
+#include "clitkElastix.h"
namespace clitk
{
{
if (m_ArgsInfo.matrix_given)
{
- std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
+ std::cerr << "You must use either rotate/translate or matrix options" << std::endl;
return;
}
itk::Array<double> transformParameters(2 * Dimension);
}
else {
if (m_ArgsInfo.elastix_given) {
- std::vector<std::string> s;
- for(uint i=0; i<m_ArgsInfo.elastix_given; i++) s.push_back(m_ArgsInfo.elastix_arg[i]);
- matrix = createMatrixFromElastixFile<Dimension,PixelType>(s);
+ std::string filename(m_ArgsInfo.elastix_arg);
+ matrix = createMatrixFromElastixFile<Dimension>(filename, m_Verbose);
}
else
matrix.SetIdentity();
likeReader->SetFileName(m_ArgsInfo.like_arg);
likeReader->Update();
resampler->SetOutputParametersFromImage(likeReader->GetOutput());
+ resampler->SetOutputDirection(likeReader->GetOutput()->GetDirection());
} else if(m_ArgsInfo.transform_grid_flag) {
typename itk::Matrix<double, Dimension+1, Dimension+1> invMatrix( matrix.GetInverse() );
typename itk::Matrix<double, Dimension, Dimension> invRotMatrix( clitk::GetRotationalPartMatrix(invMatrix) );
outputOrigin[i]=m_ArgsInfo.origin_arg[i];
} else outputOrigin=input->GetOrigin();
+ //Direction
+ typename OutputImageType::DirectionType outputDirection;
+ if (m_ArgsInfo.direction_given) {
+ for(unsigned int j=0; j< Dimension; j++)
+ for(unsigned int i=0; i< Dimension; i++)
+ outputDirection[j][i]=m_ArgsInfo.direction_arg[i+Dimension*j];
+ } else outputDirection=input->GetDirection();
+
// Set
resampler->SetSize( outputSize );
resampler->SetOutputSpacing( outputSpacing );
resampler->SetOutputOrigin( outputOrigin );
+ resampler->SetOutputDirection( outputDirection );
}
std::cout << "Setting the output size to " << resampler->GetSize() << "..." << std::endl;
std::cout << "Setting the output spacing to " << resampler->GetOutputSpacing() << "..." << std::endl;
std::cout << "Setting the output origin to " << resampler->GetOutputOrigin() << "..." << std::endl;
+ std::cout << "Setting the output direction to " << resampler->GetOutputDirection() << "..." << std::endl;
}
resampler->SetInput( input );
{
if (m_ArgsInfo.matrix_given)
{
- std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
+ std::cerr << "You must use either rotate/translate or matrix options" << std::endl;
return;
}
itk::Array<double> transformParameters(2 * Dimension);
resampler->SetSize( likeReader->GetOutput()->GetLargestPossibleRegion().GetSize() );
resampler->SetOutputSpacing( likeReader->GetOutput()->GetSpacing() );
resampler->SetOutputOrigin( likeReader->GetOutput()->GetOrigin() );
+ resampler->SetOutputDirection( likeReader->GetOutput()->GetDirection() );
} else {
//Size
typename OutputImageType::SizeType outputSize;
} else outputOrigin=input->GetOrigin();
std::cout<<"Setting the origin to "<<outputOrigin<<"..."<<std::endl;
+ //Direction
+ typename OutputImageType::DirectionType outputDirection;
+ if (m_ArgsInfo.direction_given) {
+ for(unsigned int j=0; j< Dimension; j++)
+ for(unsigned int i=0; i< Dimension; i++)
+ outputDirection[j][i]=m_ArgsInfo.direction_arg[i+Dimension*j];
+ } else outputDirection=input->GetDirection();
+ std::cout<<"Setting the direction to "<<outputDirection<<"..."<<std::endl;
+
// Set
resampler->SetSize( outputSize );
resampler->SetOutputSpacing( outputSpacing );
resampler->SetOutputOrigin( outputOrigin );
+ resampler->SetOutputDirection( outputDirection );
}
}
//-------------------------------------------------------------------
-
-
- //-------------------------------------------------------------------
- template<class args_info_type>
- template<unsigned int Dimension, class PixelType>
- typename itk::Matrix<double, Dimension+1, Dimension+1>
- AffineTransformGenericFilter<args_info_type>::createMatrixFromElastixFile(std::vector<std::string> & filename)
- {
- if (Dimension != 3) {
- FATAL("Only 3D yet" << std::endl);
- }
- typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
-
- itk::CenteredEuler3DTransform<double>::Pointer mat = itk::CenteredEuler3DTransform<double>::New();
- itk::CenteredEuler3DTransform<double>::Pointer previous;
- for(uint j=0; j<filename.size(); j++) {
-
- // Open file
- if (m_Verbose) std::cout << "Read elastix parameters in " << filename[j] << std::endl;
- std::ifstream is;
- clitk::openFileForReading(is, filename[j]);
-
- // Check Transform
- std::string s;
- bool b = GetElastixValueFromTag(is, "Transform ", s);
- if (!b) {
- FATAL("Error must read 'Transform' in " << filename[j] << std::endl);
- }
- if (s != "EulerTransform") {
- FATAL("Sorry only 'EulerTransform'" << std::endl);
- }
-
- // FIXME check
- // (InitialTransformParametersFilename[j] "NoInitialTransform")
-
- // Get CenterOfRotationPoint
- GetElastixValueFromTag(is, "CenterOfRotationPoint ", s); // space is needed
- if (!b) {
- FATAL("Error must read 'CenterOfRotationPoint' in " << filename[j] << std::endl);
- }
- std::vector<std::string> cor;
- GetValuesFromValue(s, cor);
-
- // Get Transformparameters
- GetElastixValueFromTag(is, "TransformParameters ", s); // space is needed
- if (!b) {
- FATAL("Error must read 'TransformParameters' in " << filename[j] << std::endl);
- }
- std::vector<std::string> results;
- GetValuesFromValue(s, results);
-
- // construct a stream from the string
- itk::CenteredEuler3DTransform<double>::ParametersType p;
- p.SetSize(9);
- for(uint i=0; i<3; i++)
- p[i] = atof(results[i].c_str()); // Rotation
- for(uint i=0; i<3; i++)
- p[i+3] = atof(cor[i].c_str()); // Centre of rotation
- for(uint i=0; i<3; i++)
- p[i+6] = atof(results[i+3].c_str()); // Translation
- mat->SetParameters(p);
-
- if (m_Verbose) {
- std::cout << "Rotation (deg) : " << rad2deg(p[0]) << " " << rad2deg(p[1]) << " " << rad2deg(p[2]) << std::endl;
- std::cout << "Center of rot (phy) : " << p[3] << " " << p[4] << " " << p[5] << std::endl;
- std::cout << "Translation (phy) : " << p[6] << " " << p[7] << " " << p[8] << std::endl;
- }
-
- // Compose with previous if needed
- if (j!=0) {
- mat->Compose(previous);
- if (m_Verbose) {
- std::cout << "Composed rotation (deg) : " << rad2deg(mat->GetAngleX()) << " " << rad2deg(mat->GetAngleY()) << " " << rad2deg(mat->GetAngleZ()) << std::endl;
- std::cout << "Composed center of rot (phy) : " << mat->GetCenter() << std::endl;
- std::cout << "Compsoed translation (phy) : " << mat->GetTranslation() << std::endl;
- }
- }
- // previous = mat->Clone(); // ITK4
- previous = itk::CenteredEuler3DTransform<double>::New();
- previous->SetParameters(mat->GetParameters());
- }
-
- mat = previous;
- for(uint i=0; i<3; i++)
- for(uint j=0; j<3; j++)
- matrix[i][j] = mat->GetMatrix()[i][j];
- // Offset is -Rc + t + c
- matrix[0][3] = mat->GetOffset()[0];
- matrix[1][3] = mat->GetOffset()[1];
- matrix[2][3] = mat->GetOffset()[2];
- matrix[3][3] = 1;
-
- return matrix;
- }
-
- //-------------------------------------------------------------------
- template<class args_info_type>
- bool
- AffineTransformGenericFilter<args_info_type>::GetElastixValueFromTag(std::ifstream & is,
- std::string tag,
- std::string & value)
- {
- std::string line;
- is.seekg (0, is.beg);
- while(std::getline(is, line)) {
- unsigned pos = line.find(tag);
- if (pos<line.size()) {
- value=line.substr(pos+tag.size(),line.size()-2);// remove last ')'
- value.erase (std::remove (value.begin(), value.end(), '"'), value.end());
- value.erase (std::remove (value.begin(), value.end(), ')'), value.end());
- return true;
- }
- }
- return false;
- }
- //-------------------------------------------------------------------
-
-
- //-------------------------------------------------------------------
- template<class args_info_type>
- void
- AffineTransformGenericFilter<args_info_type>::GetValuesFromValue(const std::string & s,
- std::vector<std::string> & values)
- {
- std::stringstream strstr(s);
- std::istream_iterator<std::string> it(strstr);
- std::istream_iterator<std::string> end;
- std::vector<std::string> results(it, end);
- values.clear();
- values.resize(results.size());
- for(uint i=0; i<results.size(); i++) values[i] = results[i];
- }
- //-------------------------------------------------------------------
-
} //end clitk