// 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::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);
}
else
matrix.SetIdentity();
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)
+ 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;
- // 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);
+ 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 << "Translation (phy) : " << p[3] << " " << p[4] << " " << p[5] << std::endl;
- std::cout << "Center of rot (phy) : " << p[6] << " " << p[7] << " " << p[8] << std::endl;
+ 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];
value.erase (std::remove (value.begin(), value.end(), ')'), value.end());
return true;
}
- }
+ }
return false;
}
//-------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff