#include <istream>
#include <iterator>
#include <itkCenteredEuler3DTransform.h>
+#include "clitkElastix.h"
namespace clitk
{
// Call UpdateWithDim
if(Dimension==2) UpdateWithDim<2>(PixelType, Components);
else
- if(Dimension==3) UpdateWithDim<3>(PixelType, Components);
- else if (Dimension==4)UpdateWithDim<4>(PixelType, Components);
- else {
- std::cout<<"Error, Only for 2, 3 or 4 Dimensions!!!"<<std::endl ;
- return;
- }
+ if(Dimension==3) UpdateWithDim<3>(PixelType, Components);
+ else if (Dimension==4)UpdateWithDim<4>(PixelType, Components);
+ else {
+ std::cout<<"Error, Only for 2, 3 or 4 Dimensions!!!"<<std::endl ;
+ return;
+ }
}
//-------------------------------------------------------------------
if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
UpdateWithDimAndPixelType<Dimension, signed short>();
}
- // else if(PixelType == "unsigned_short"){
- // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
- // UpdateWithDimAndPixelType<Dimension, unsigned short>();
- // }
+ else if(PixelType == "unsigned_short"){
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, unsigned short>();
+ }
else if (PixelType == "unsigned_char") {
if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
}
else {
if (m_ArgsInfo.elastix_given) {
- matrix = createMatrixFromElastixFile<Dimension,PixelType>(m_ArgsInfo.elastix_arg);
+ 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) );
typename itk::Vector<double,Dimension> invTrans = clitk::GetTranslationPartMatrix(invMatrix);
-
+
// Display warning
if (m_ArgsInfo.spacing_given)
std::cout << "Warning --spacing ignored (because --transform_grid_flag)" << std::endl;
}
+ if (m_ArgsInfo.spacinglike_given) {
+ typename InputReaderType::Pointer likeReader=InputReaderType::New();
+ likeReader->SetFileName(m_ArgsInfo.spacinglike_arg);
+ likeReader->Update();
+
+ // set the support like the image
+ if (m_ArgsInfo.like_given) {
+ typename OutputImageType::SizeType outputSize;
+ outputSize[0] = ceil(resampler->GetSize()[0]*resampler->GetOutputSpacing()[0]
+ /likeReader->GetOutput()->GetSpacing()[0]);
+ outputSize[1] = ceil(resampler->GetSize()[1]*resampler->GetOutputSpacing()[1]
+ /likeReader->GetOutput()->GetSpacing()[1]);
+ outputSize[2] = ceil(resampler->GetSize()[2]*resampler->GetOutputSpacing()[2]
+ /likeReader->GetOutput()->GetSpacing()[2]);
+ if (m_ArgsInfo.verbose_flag) {
+ std::cout << "Compute the number of pixels such as the support is like " << m_ArgsInfo.like_arg << std::endl;
+ }
+ resampler->SetSize( outputSize );
+ }
+
+ resampler->SetOutputSpacing( likeReader->GetOutput()->GetSpacing() );
+ }
+
if (m_ArgsInfo.verbose_flag) {
std::cout << "Setting the output size to " << resampler->GetSize() << "..." << std::endl;
std::cout << "Setting the output spacing to " << resampler->GetOutputSpacing() << "..." << std::endl;
}
//-------------------------------------------------------------------
-
-
- //-------------------------------------------------------------------
- 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::string filename)
- {
- if (Dimension != 3) {
- FATAL("Only 3D yet" << std::endl);
- }
- typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
-
- // Open file
- std::ifstream is;
- clitk::openFileForReading(is, filename);
-
- // Check Transform
- std::string s;
- bool b = GetElastixValueFromTag(is, "Transform ", s);
- if (!b) {
- FATAL("Error must read 'Transform' in " << filename << std::endl);
- }
- if (s != "EulerTransform") {
- FATAL("Sorry only 'EulerTransform'" << std::endl);
- }
-
- // FIXME check
- // (InitialTransformParametersFileName "NoInitialTransform")
-
- // Get CenterOfRotationPoint
- GetElastixValueFromTag(is, "CenterOfRotationPoint ", s); // space is needed
- if (!b) {
- FATAL("Error must read 'CenterOfRotationPoint' in " << filename << 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 << std::endl);
- }
- std::vector<std::string> results;
- GetValuesFromValue(s, results);
-
- // construct a stream from the string
- itk::CenteredEuler3DTransform<double>::Pointer mat = itk::CenteredEuler3DTransform<double>::New();
- 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 << "Translation (phy) : " << p[3] << " " << p[4] << " " << p[5] << std::endl;
- std::cout << "Center of rot (phy) : " << p[6] << " " << p[7] << " " << p[8] << std::endl;
- }
-
- 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