// Matrix
typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
- if (m_ArgsInfo.matrix_given) {
- matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
- if (m_Verbose) std::cout<<"Reading the matrix..."<<std::endl;
- } else {
- matrix.SetIdentity();
+ if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given)
+ {
+ if (m_ArgsInfo.matrix_given)
+ {
+ std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
+ return;
+ }
+ itk::Array<double> transformParameters(2 * Dimension);
+ transformParameters.Fill(0.0);
+ if (m_ArgsInfo.rotate_given)
+ {
+ if (Dimension == 2)
+ transformParameters[0] = m_ArgsInfo.rotate_arg[0];
+ else
+ for (unsigned int i = 0; i < 3; i++)
+ transformParameters[i] = m_ArgsInfo.rotate_arg[i];
+ }
+ if (m_ArgsInfo.translate_given)
+ {
+ int pos = 3;
+ if (Dimension == 2)
+ pos = 1;
+ for (unsigned int i = 0; i < Dimension && i < 3; i++)
+ transformParameters[pos++] = m_ArgsInfo.translate_arg[i];
+ }
+ if (Dimension == 4)
+ {
+ matrix.SetIdentity();
+ itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
+ for (unsigned int i = 0; i < 3; ++i)
+ for (unsigned int j = 0; j < 3; ++j)
+ matrix[i][j] = tmp[i][j];
+ for (unsigned int i = 0; i < 3; ++i)
+ matrix[i][4] = tmp[i][3];
+ }
+ else
+ matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
}
- if (m_Verbose) std::cout<<"Using the following matrix:"<<std::endl;
- if (m_Verbose) std::cout<<matrix<<std::endl;
- typename itk::Matrix<double, Dimension, Dimension> rotationMatrix=clitk::GetRotationalPartMatrix(matrix);
- typename itk::Vector<double,Dimension> translationPart= clitk::GetTranslationPartMatrix(matrix);
+ else
+ {
+ if (m_ArgsInfo.matrix_given)
+ {
+ matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
+ if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
+ }
+ else
+ matrix.SetIdentity();
+ }
+ if (m_Verbose)
+ std::cout << "Using the following matrix:" << std::endl
+ << matrix << std::endl;
+ typename itk::Matrix<double, Dimension, Dimension> rotationMatrix = clitk::GetRotationalPartMatrix(matrix);
+ typename itk::Vector<double, Dimension> translationPart = clitk::GetTranslationPartMatrix(matrix);
// Transform
typedef itk::AffineTransform<double, Dimension> AffineTransformType;
likeReader->SetFileName(m_ArgsInfo.like_arg);
likeReader->Update();
resampler->SetOutputParametersFromImage(likeReader->GetOutput());
+ } 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);
+
+ // Spacing is influenced by affine transform matrix and input direction
+ typename InputImageType::SpacingType outputSpacing;
+ outputSpacing = invRotMatrix *
+ input->GetDirection() *
+ input->GetSpacing();
+
+ // Origin is influenced by translation but not by input direction
+ typename InputImageType::PointType outputOrigin;
+ outputOrigin = invRotMatrix *
+ input->GetOrigin() +
+ invTrans;
+
+ // Size is influenced by affine transform matrix and input direction
+ // Size is converted to double, transformed and converted back to size type.
+ vnl_vector<double> vnlOutputSize(Dimension);
+ for(unsigned int i=0; i< Dimension; i++) {
+ vnlOutputSize[i] = input->GetLargestPossibleRegion().GetSize()[i];
+ }
+ vnlOutputSize = invRotMatrix *
+ input->GetDirection().GetVnlMatrix() *
+ vnlOutputSize;
+ typename OutputImageType::SizeType outputSize;
+ for(unsigned int i=0; i< Dimension; i++) {
+ // If the size is negative, we have a flip and we must modify
+ // the origin and the spacing accordingly.
+ if(vnlOutputSize[i]<0.) {
+ vnlOutputSize[i] *= -1.;
+ outputOrigin[i] = outputOrigin[i] + outputSpacing[i] * (vnlOutputSize[i]-1);
+ outputSpacing[i] *= -1.;
+ }
+ outputSize[i] = lrint(vnlOutputSize[i]);
+ }
+ resampler->SetSize( outputSize );
+ resampler->SetOutputSpacing( outputSpacing );
+ resampler->SetOutputOrigin( outputOrigin );
} else {
//Size
typename OutputImageType::SizeType outputSize;
for(unsigned int i=0; i< Dimension; i++)
outputSize[i]=m_ArgsInfo.size_arg[i];
} else outputSize=input->GetLargestPossibleRegion().GetSize();
- std::cout<<"Setting the size to "<<outputSize<<"..."<<std::endl;
//Spacing
typename OutputImageType::SpacingType outputSpacing;
for(unsigned int i=0; i< Dimension; i++)
outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
} else outputSpacing=input->GetSpacing();
- std::cout<<"Setting the spacing to "<<outputSpacing<<"..."<<std::endl;
//Origin
typename OutputImageType::PointType outputOrigin;
for(unsigned int i=0; i< Dimension; i++)
outputOrigin[i]=m_ArgsInfo.origin_arg[i];
} else outputOrigin=input->GetOrigin();
- std::cout<<"Setting the origin to "<<outputOrigin<<"..."<<std::endl;
// Set
resampler->SetSize( outputSize );
}
+ 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;
+ std::cout << "Setting the output origin to " << resampler->GetOutputOrigin() << "..." << std::endl;
+ }
+
resampler->SetInput( input );
resampler->SetTransform( affineTransform );
resampler->SetInterpolator( genericInterpolator->GetInterpolatorPointer());
// Matrix
typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
- if (m_ArgsInfo.matrix_given)
- matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
+ if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given)
+ {
+ if (m_ArgsInfo.matrix_given)
+ {
+ std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
+ return;
+ }
+ itk::Array<double> transformParameters(2 * Dimension);
+ transformParameters.Fill(0.0);
+ if (m_ArgsInfo.rotate_given)
+ {
+ if (Dimension == 2)
+ transformParameters[0] = m_ArgsInfo.rotate_arg[0];
+ else
+ for (unsigned int i = 0; i < 3; i++)
+ transformParameters[i] = m_ArgsInfo.rotate_arg[i];
+ }
+ if (m_ArgsInfo.translate_given)
+ {
+ int pos = 3;
+ if (Dimension == 2)
+ pos = 1;
+ for (unsigned int i = 0; i < Dimension && i < 3; i++)
+ transformParameters[pos++] = m_ArgsInfo.translate_arg[i];
+ }
+ if (Dimension == 4)
+ {
+ matrix.SetIdentity();
+ itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
+ for (unsigned int i = 0; i < 3; ++i)
+ for (unsigned int j = 0; j < 3; ++j)
+ matrix[i][j] = tmp[i][j];
+ for (unsigned int i = 0; i < 3; ++i)
+ matrix[i][4] = tmp[i][3];
+ }
+ else
+ matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
+ }
else
- matrix.SetIdentity();
- if (m_Verbose) std::cout<<"Using the following matrix:"<<std::endl;
- if (m_Verbose) std::cout<<matrix<<std::endl;
- typename itk::Matrix<double, Dimension, Dimension> rotationMatrix=clitk::GetRotationalPartMatrix(matrix);
- typename itk::Vector<double, Dimension> translationPart= clitk::GetTranslationPartMatrix(matrix);
+ {
+ if (m_ArgsInfo.matrix_given)
+ {
+ matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
+ if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
+ }
+ else
+ matrix.SetIdentity();
+ }
+ if (m_Verbose)
+ std::cout << "Using the following matrix:" << std::endl
+ << matrix << std::endl;
+ typename itk::Matrix<double, Dimension, Dimension> rotationMatrix = clitk::GetRotationalPartMatrix(matrix);
+ typename itk::Vector<double, Dimension> translationPart = clitk::GetTranslationPartMatrix(matrix);
// Transform
typedef itk::AffineTransform<double, Dimension> AffineTransformType;
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff