+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+ ===========================================================================**/
#ifndef clitkAffineTransformGenericFilter_txx
#define clitkAffineTransformGenericFilter_txx
-/* =================================================
- * @file clitkAffineTransformGenericFilter.txx
- * @author
- * @date
- *
- * @brief
- *
- ===================================================*/
-
+#include <sstream>
+#include <istream>
+#include <iterator>
+#include <itkCenteredEuler3DTransform.h>
+#include <itkRecursiveGaussianImageFilter.h>
+#include "clitkElastix.h"
+#include "clitkResampleImageWithOptionsFilter.h"
namespace clitk
{
m_Verbose=false;
m_InputFileName="";
}
-
+ //-------------------------------------------------------------------
+
//-----------------------------------------------------------
// Update
std::string PixelType;
ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
-
// 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;
}
}
+ //-------------------------------------------------------------------
+
//-------------------------------------------------------------------
// Update with the number of dimensions
//-------------------------------------------------------------------
template<class args_info_type>
template<unsigned int Dimension>
- void
+ void
AffineTransformGenericFilter<args_info_type>::UpdateWithDim(std::string PixelType, int Components)
{
if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<<Components<<" component(s) of "<< PixelType<<"..."<<std::endl;
- if (Components==1)
- {
- if(PixelType == "short"){
- 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_char"){
- if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, unsigned char>();
- }
-
- // else if (PixelType == "char"){
- // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
- // UpdateWithDimAndPixelType<Dimension, signed char>();
- // }
- else {
- if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, float>();
- }
- }
-
- else if (Components==3)
- {
- if (m_Verbose) std::cout << "Launching transform in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
- UpdateWithDimAndVectorType<Dimension, itk::Vector<float, Dimension> >();
+ if (Components==1) {
+ if(PixelType == "short") {
+ 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_char") {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, unsigned char>();
+ }
+
+ // else if (PixelType == "char"){
+ // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
+ // UpdateWithDimAndPixelType<Dimension, signed char>();
+ // }
+ else if(PixelType == "double"){
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and double..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, double>();
+ }
+ else {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, float>();
+ }
+ }
+
+ else if (Components==3) {
+ if (m_Verbose) std::cout << "Launching transform in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
+ UpdateWithDimAndVectorType<Dimension, itk::Vector<float, Dimension> >();
+ }
else std::cerr<<"Number of components is "<<Components<<", not supported!"<<std::endl;
}
+ //-------------------------------------------------------------------
+
+
+ //-------------------------------------------------------------------
+ // Compute updated bounding box
+ //-------------------------------------------------------------------
+ template<class args_info_type>
+ vnl_vector<double>
+ AffineTransformGenericFilter<args_info_type>::ComputeSize(vnl_vector<double> inputSize, vnl_matrix<double> transformationMatrix, bool returnMin)
+ {
+ //Compute input corners
+ int Dimension = inputSize.size();
+ vnl_matrix<double> vnlOutputSize(std::pow(2, Dimension), Dimension);
+ vnlOutputSize.fill(0);
+ if (Dimension == 2) {
+ for(unsigned int i=0; i< Dimension; i++)
+ vnlOutputSize[3][i] = inputSize[i];
+ vnlOutputSize[1][0] = inputSize[0];
+ vnlOutputSize[2][1] = inputSize[1];
+ } else if (Dimension == 3) {
+ for(unsigned int i=0; i< Dimension; i++)
+ vnlOutputSize[7][i] = inputSize[i];
+ vnlOutputSize[1][0] = inputSize[0];
+ vnlOutputSize[2][1] = inputSize[1];
+ vnlOutputSize[3][2] = inputSize[2];
+ vnlOutputSize[4][0] = inputSize[0];
+ vnlOutputSize[4][1] = inputSize[1];
+ vnlOutputSize[5][1] = inputSize[1];
+ vnlOutputSize[5][2] = inputSize[2];
+ vnlOutputSize[6][0] = inputSize[0];
+ vnlOutputSize[6][2] = inputSize[2];
+ } else { //Dimension ==4
+ for(unsigned int i=0; i< Dimension; i++)
+ vnlOutputSize[15][i] = inputSize[i];
+ vnlOutputSize[1][0] = inputSize[0];
+ vnlOutputSize[2][1] = inputSize[1];
+ vnlOutputSize[3][2] = inputSize[2];
+ vnlOutputSize[4][3] = inputSize[3];
+ vnlOutputSize[5][0] = inputSize[0];
+ vnlOutputSize[5][1] = inputSize[1];
+ vnlOutputSize[6][0] = inputSize[0];
+ vnlOutputSize[6][2] = inputSize[2];
+ vnlOutputSize[7][0] = inputSize[0];
+ vnlOutputSize[7][3] = inputSize[3];
+ vnlOutputSize[8][1] = inputSize[1];
+ vnlOutputSize[8][2] = inputSize[2];
+ vnlOutputSize[9][1] = inputSize[1];
+ vnlOutputSize[9][3] = inputSize[3];
+ vnlOutputSize[10][2] = inputSize[2];
+ vnlOutputSize[10][3] = inputSize[3];
+ vnlOutputSize[11][0] = inputSize[0];
+ vnlOutputSize[11][1] = inputSize[1];
+ vnlOutputSize[11][2] = inputSize[2];
+ vnlOutputSize[12][0] = inputSize[0];
+ vnlOutputSize[12][1] = inputSize[1];
+ vnlOutputSize[12][3] = inputSize[3];
+ vnlOutputSize[13][0] = inputSize[0];
+ vnlOutputSize[13][2] = inputSize[2];
+ vnlOutputSize[13][3] = inputSize[3];
+ vnlOutputSize[14][1] = inputSize[1];
+ vnlOutputSize[14][2] = inputSize[2];
+ vnlOutputSize[14][3] = inputSize[3];
+ }
+
+ //Compute the transformation of all corner
+ for (unsigned int i=0; i< std::pow(2, Dimension); ++i)
+ vnlOutputSize.set_row(i, transformationMatrix*vnlOutputSize.get_row(i));
+
+ //Compute the bounding box taking the max and the min
+ vnl_vector<double> minBB(vnlOutputSize.get_row(0)), maxBB(vnlOutputSize.get_row(0));
+ for (unsigned int i=0; i< std::pow(2, Dimension); ++i) {
+ for (unsigned int j=0; j< Dimension; ++j) {
+ if (vnlOutputSize[i][j] < minBB[j])
+ minBB[j] = vnlOutputSize[i][j];
+ if (vnlOutputSize[i][j] > maxBB[j])
+ maxBB[j] = vnlOutputSize[i][j];
+ }
+ }
+ //Compute the size
+ if (returnMin)
+ return minBB;
+ else {
+ vnl_vector<double> size;
+ size = maxBB - minBB;
+
+ return size;
+ }
+ }
+ //-------------------------------------------------------------------
+
//-------------------------------------------------------------------
// Update with the number of dimensions and the pixeltype
//-------------------------------------------------------------------
template<class args_info_type>
- template <unsigned int Dimension, class PixelType>
- void
+ template <unsigned int Dimension, class PixelType>
+ void
AffineTransformGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
{
// ImageTypes
typedef itk::Image<PixelType, Dimension> InputImageType;
typedef itk::Image<PixelType, Dimension> OutputImageType;
-
+
// Read the input
typedef itk::ImageFileReader<InputImageType> InputReaderType;
typename InputReaderType::Pointer reader = InputReaderType::New();
reader->Update();
typename InputImageType::Pointer input= reader->GetOutput();
+ //Adaptative size, spacing origin (use previous clitkResampleImage)
+ if (m_ArgsInfo.adaptive_given) {
+ // Filter
+ typedef clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType> ResampleImageFilterType;
+ typename ResampleImageFilterType::Pointer filter = ResampleImageFilterType::New();
+ filter->SetInput(input);
+
+ // Set Verbose
+ filter->SetVerboseOptions(m_ArgsInfo.verbose_flag);
+
+ // Set size / spacing
+ static const unsigned int dim = OutputImageType::ImageDimension;
+ typename OutputImageType::SpacingType spacing;
+ typename OutputImageType::SizeType size;
+ typename OutputImageType::PointType origin;
+ typename OutputImageType::DirectionType direction;
+
+ if (m_ArgsInfo.like_given) {
+ itk::ImageIOBase::Pointer header = clitk::readImageHeader(m_ArgsInfo.like_arg);
+ if (header) {
+ for(unsigned int i=0; i<dim; i++){
+ spacing[i] = header->GetSpacing(i);
+ size[i] = header->GetDimensions(i);
+ origin[i] = header->GetOrigin(i);
+ }
+ for(unsigned int i=0; i<dim; i++) {
+ for(unsigned int j=0;j<dim;j++) {
+ direction(i,j) = header->GetDirection(i)[j];
+ }
+ }
+ filter->SetOutputSpacing(spacing);
+ filter->SetOutputSize(size);
+ filter->SetOutputOrigin(origin);
+ filter->SetOutputDirection(direction);
+ }
+ else {
+ std::cerr << "*** Warning : I could not read '" << m_ArgsInfo.like_arg << "' ***" << std::endl;
+ exit(0);
+ }
+ }
+ else {
+ if (m_ArgsInfo.spacing_given == 1) {
+ filter->SetOutputIsoSpacing(m_ArgsInfo.spacing_arg[0]);
+ }
+ else if ((m_ArgsInfo.spacing_given != 0) && (m_ArgsInfo.size_given != 0)) {
+ std::cerr << "Error: use spacing or size, not both." << std::endl;
+ exit(0);
+ }
+ else if (m_ArgsInfo.spacing_given) {
+ if ((m_ArgsInfo.spacing_given != 0) && (m_ArgsInfo.spacing_given != dim)) {
+ std::cerr << "Error: spacing should have one or " << dim << " values." << std::endl;
+ exit(0);
+ }
+ for(unsigned int i=0; i<dim; i++)
+ spacing[i] = m_ArgsInfo.spacing_arg[i];
+ filter->SetOutputSpacing(spacing);
+ }
+ else if (m_ArgsInfo.size_given) {
+ if ((m_ArgsInfo.size_given != 0) && (m_ArgsInfo.size_given != dim)) {
+ std::cerr << "Error: size should have " << dim << " values." << std::endl;
+ exit(0);
+ }
+ for(unsigned int i=0; i<dim; i++)
+ size[i] = m_ArgsInfo.size_arg[i];
+ filter->SetOutputSize(size);
+ }
+ for(unsigned int i=0; i<dim; i++){
+ origin[i] = input->GetOrigin()[i];
+ }
+ for(unsigned int i=0; i<dim; i++) {
+ for(unsigned int j=0;j<dim;j++) {
+ direction(i,j) = input->GetDirection()[i][j];
+ }
+ }
+ filter->SetOutputOrigin(origin);
+ filter->SetOutputDirection(direction);
+ }
+
+ // Set temporal dimension
+ //filter->SetLastDimensionIsTime(m_ArgsInfo.time_flag);
+
+ // Set Gauss
+ filter->SetGaussianFilteringEnabled(m_ArgsInfo.autogauss_flag);
+ if (m_ArgsInfo.gauss_given != 0) {
+ typename ResampleImageFilterType::GaussianSigmaType g;
+ for(unsigned int i=0; i<dim; i++) {
+ g[i] = m_ArgsInfo.gauss_arg[i];
+ }
+ filter->SetGaussianSigma(g);
+ }
+
+ // Set Interpolation
+ int interp = m_ArgsInfo.interp_arg;
+ if (interp == 0) {
+ filter->SetInterpolationType(ResampleImageFilterType::NearestNeighbor);
+ } else {
+ if (interp == 1) {
+ filter->SetInterpolationType(ResampleImageFilterType::Linear);
+ } else {
+ if (interp == 2) {
+ filter->SetInterpolationType(ResampleImageFilterType::BSpline);
+ } else {
+ if (interp == 3) {
+ filter->SetInterpolationType(ResampleImageFilterType::B_LUT);
+ } else {
+ std::cerr << "Error. I do not know interpolation '" << m_ArgsInfo.interp_arg
+ << "'. Choose among: nn, linear, bspline, blut, windowed sinc" << std::endl;
+ exit(0);
+ }
+ }
+ }
+ }
+
+ // Set default pixel value
+ filter->SetDefaultPixelValue(m_ArgsInfo.pad_arg);
+
+ // Set thread
+ //if (m_ArgsInfo.thread_given) {
+ // filter->SetNumberOfThreads(m_ArgsInfo.thread_arg);
+ //}
+
+ // Go !
+ filter->Update();
+ typename OutputImageType::Pointer output = filter->GetOutput();
+ //this->template SetNextOutput<OutputImageType>(outputImage);
+
+ // Output
+ typedef itk::ImageFileWriter<OutputImageType> WriterType;
+ typename WriterType::Pointer writer = WriterType::New();
+ writer->SetFileName(m_ArgsInfo.output_arg);
+ writer->SetInput(output);
+ writer->Update();
+
+ return;
+ }
+
+ //Gaussian pre-filtering
+ typename itk::Vector<double, Dimension> gaussianSigma;
+ gaussianSigma.Fill(0);
+ bool gaussianFilteringEnabled(false);
+ bool autoGaussEnabled(false);
+ if (m_ArgsInfo.autogauss_given) { // Gaussian filter auto
+ autoGaussEnabled = m_ArgsInfo.autogauss_flag;
+ }
+ if (m_ArgsInfo.gauss_given) { // Gaussian filter set by user
+ gaussianFilteringEnabled = true;
+ if (m_ArgsInfo.gauss_given == 1)
+ {
+ for (unsigned int i=0; i<Dimension; i++)
+ {
+ gaussianSigma[i] = m_ArgsInfo.gauss_arg[0];
+ }
+ }
+ else if (m_ArgsInfo.gauss_given == Dimension)
+ {
+ for (unsigned int i=0; i<Dimension; i++)
+ {
+ gaussianSigma[i] = m_ArgsInfo.gauss_arg[i];
+ }
+ }
+ else
+ {
+ std::cerr << "Gaussian sigma dimension is incorrect" << std::endl;
+ return;
+ }
+ }
+
//Filter
typedef itk::ResampleImageFilter< InputImageType,OutputImageType > ResampleFilterType;
typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
-
+
// Matrix
typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
- if (m_ArgsInfo.matrix_given)
+ if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given)
{
- matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
- if (m_Verbose) std::cout<<"Reading the matrix..."<<std::endl;
+ if (m_ArgsInfo.matrix_given)
+ {
+ std::cerr << "You must use either rotate/translate or matrix options" << std::endl;
+ 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_ArgsInfo.matrix_given)
+ {
+ matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
+ if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
+ }
+ else {
+ if (m_ArgsInfo.elastix_given) {
+ std::string filename(m_ArgsInfo.elastix_arg);
+ matrix = createMatrixFromElastixFile<Dimension>(filename, m_Verbose);
+ }
+ 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_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;
typename AffineTransformType::Pointer affineTransform=AffineTransformType::New();
affineTransform->SetMatrix(rotationMatrix);
affineTransform->SetTranslation(translationPart);
- // Interp
+ // Interp
typedef clitk::GenericInterpolator<args_info_type, InputImageType, double> GenericInterpolatorType;
typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
genericInterpolator->SetArgsInfo(m_ArgsInfo);
-
+
// Properties
- if (m_ArgsInfo.like_given)
- {
- typename InputReaderType::Pointer likeReader=InputReaderType::New();
- likeReader->SetFileName(m_ArgsInfo.like_arg);
- likeReader->Update();
- resampler->SetOutputParametersFromImage(likeReader->GetOutput());
+ if (m_ArgsInfo.like_given) {
+ typename InputReaderType::Pointer likeReader=InputReaderType::New();
+ likeReader->SetFileName(m_ArgsInfo.like_arg);
+ likeReader->Update();
+ resampler->SetOutputParametersFromImage(likeReader->GetOutput());
+ resampler->SetOutputDirection(likeReader->GetOutput()->GetDirection());
+ if (autoGaussEnabled) { // Automated sigma when downsample
+ for(unsigned int i=0; i<Dimension; i++) {
+ if (likeReader->GetOutput()->GetSpacing()[i] > input->GetSpacing()[i]) { // downsample
+ gaussianSigma[i] = 0.5*likeReader->GetOutput()->GetSpacing()[i];// / inputSpacing[i]);
+ }
+ else gaussianSigma[i] = 0; // will be ignore after
+ }
+ }
+ } 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.origin_given)
+ std::cout << "Warning --origin ignored (because --transform_grid_flag)" << std::endl;
+
+ // 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.
+ // Determine the bounding box tranforming all corners
+ vnl_vector<double> vnlOutputSize(Dimension), vnlOutputmmSize(Dimension), vnlOutputOffset(Dimension);
+ typename InputImageType::SpacingType outputSpacing;
+ for(unsigned int i=0; i< Dimension; i++) {
+ vnlOutputSize[i] = input->GetLargestPossibleRegion().GetSize()[i];
+ vnlOutputmmSize[i] = input->GetLargestPossibleRegion().GetSize()[i]*input->GetSpacing()[i];
+ vnlOutputOffset[i] = input->GetLargestPossibleRegion().GetSize()[i]*input->GetSpacing()[i];
+ }
+ vnlOutputSize = ComputeSize(vnlOutputSize, invRotMatrix.GetVnlMatrix() * input->GetDirection().GetVnlMatrix(), 0);
+ vnlOutputmmSize = ComputeSize(vnlOutputmmSize, invRotMatrix.GetVnlMatrix() * input->GetDirection().GetVnlMatrix(), 0);
+ vnlOutputOffset = ComputeSize(vnlOutputOffset, invRotMatrix.GetVnlMatrix() * input->GetDirection().GetVnlMatrix(), 1);
+ for(unsigned int i=0; i< Dimension; i++) {
+ outputSpacing[i] = vnlOutputmmSize[i]/lrint(vnlOutputSize[i]);
+ outputOrigin[i] += vnlOutputOffset[i];
+ }
+ if (autoGaussEnabled) { // Automated sigma when downsample
+ for(unsigned int i=0; i<Dimension; i++) {
+ if (outputSpacing[i] > input->GetSpacing()[i]) { // downsample
+ gaussianSigma[i] = 0.5*outputSpacing[i];// / inputSpacing[i]);
+ }
+ else gaussianSigma[i] = 0; // will be ignore after
+ }
}
- else
- {
- //Size
- typename OutputImageType::SizeType outputSize;
- if (m_ArgsInfo.size_given)
- {
- 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;
- if (m_ArgsInfo.spacing_given)
- {
- 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;
- if (m_ArgsInfo.origin_given)
- {
- 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 );
- resampler->SetOutputSpacing( outputSpacing );
- resampler->SetOutputOrigin( outputOrigin );
+ 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;
+ if (m_ArgsInfo.size_given) {
+ for(unsigned int i=0; i< Dimension; i++)
+ outputSize[i]=m_ArgsInfo.size_arg[i];
+ } else outputSize=input->GetLargestPossibleRegion().GetSize();
+
+ //Spacing
+ typename OutputImageType::SpacingType outputSpacing;
+ if (m_ArgsInfo.spacing_given) {
+ for(unsigned int i=0; i< Dimension; i++)
+ outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
+ } else outputSpacing=input->GetSpacing();
+ if (autoGaussEnabled) { // Automated sigma when downsample
+ for(unsigned int i=0; i<Dimension; i++) {
+ if (outputSpacing[i] > input->GetSpacing()[i]) { // downsample
+ gaussianSigma[i] = 0.5*outputSpacing[i];// / inputSpacing[i]);
+ }
+ else gaussianSigma[i] = 0; // will be ignore after
+ }
}
- resampler->SetInput( input );
+ //Origin
+ typename OutputImageType::PointType outputOrigin;
+ if (m_ArgsInfo.origin_given) {
+ for(unsigned int i=0; i< Dimension; i++)
+ 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 );
+
+ }
+
+ 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;
+ std::cout << "Setting the output origin to " << resampler->GetOutputOrigin() << "..." << std::endl;
+ std::cout << "Setting the output direction to " << resampler->GetOutputDirection() << "..." << std::endl;
+ }
+
+ typedef itk::RecursiveGaussianImageFilter<InputImageType, InputImageType> GaussianFilterType;
+ std::vector<typename GaussianFilterType::Pointer> gaussianFilters;
+ if (gaussianFilteringEnabled || autoGaussEnabled) {
+ for(unsigned int i=0; i<Dimension; i++) {
+ if (gaussianSigma[i] != 0) {
+ gaussianFilters.push_back(GaussianFilterType::New());
+ gaussianFilters[i]->SetDirection(i);
+ gaussianFilters[i]->SetOrder(GaussianFilterType::ZeroOrder);
+ gaussianFilters[i]->SetNormalizeAcrossScale(false);
+ gaussianFilters[i]->SetSigma(gaussianSigma[i]); // in millimeter !
+ if (gaussianFilters.size() == 1) { // first
+ gaussianFilters[0]->SetInput(input);
+ } else {
+ gaussianFilters[i]->SetInput(gaussianFilters[i-1]->GetOutput());
+ }
+ }
+ }
+ if (gaussianFilters.size() > 0) {
+ resampler->SetInput(gaussianFilters[gaussianFilters.size()-1]->GetOutput());
+ } else resampler->SetInput(input);
+ } else resampler->SetInput(input);
+
resampler->SetTransform( affineTransform );
resampler->SetInterpolator( genericInterpolator->GetInterpolatorPointer());
resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
- try
- {
- resampler->Update();
- }
- catch(itk::ExceptionObject)
- {
- std::cerr<<"Error resampling the image"<<std::endl;
- }
+ try {
+ resampler->Update();
+ } catch(itk::ExceptionObject) {
+ std::cerr<<"Error resampling the image"<<std::endl;
+ }
typename OutputImageType::Pointer output = resampler->GetOutput();
writer->Update();
}
+ //-------------------------------------------------------------------
+
//-------------------------------------------------------------------
// Update with the number of dimensions and the pixeltype (components)
// ImageTypes
typedef itk::Image<PixelType, Dimension> InputImageType;
typedef itk::Image<PixelType, Dimension> OutputImageType;
-
+
// Read the input
typedef itk::ImageFileReader<InputImageType> InputReaderType;
typename InputReaderType::Pointer reader = InputReaderType::New();
reader->Update();
typename InputImageType::Pointer input= reader->GetOutput();
+ //Gaussian pre-filtering
+ typename itk::Vector<double, Dimension> gaussianSigma;
+ gaussianSigma.Fill(0);
+ bool gaussianFilteringEnabled(false);
+ bool autoGaussEnabled(false);
+ if (m_ArgsInfo.autogauss_given) { // Gaussian filter auto
+ autoGaussEnabled = m_ArgsInfo.autogauss_flag;
+ }
+ if (m_ArgsInfo.gauss_given) { // Gaussian filter set by user
+ gaussianFilteringEnabled = true;
+ if (m_ArgsInfo.gauss_given == 1)
+ {
+ for (unsigned int i=0; i<Dimension; i++)
+ {
+ gaussianSigma[i] = m_ArgsInfo.gauss_arg[0];
+ }
+ }
+ else if (m_ArgsInfo.gauss_given == Dimension)
+ {
+ for (unsigned int i=0; i<Dimension; i++)
+ {
+ gaussianSigma[i] = m_ArgsInfo.gauss_arg[i];
+ }
+ }
+ else
+ {
+ std::cerr << "Gaussian sigma dimension is incorrect" << std::endl;
+ return;
+ }
+ }
+
//Filter
+#if ( ITK_VERSION_MAJOR < 5 )
typedef itk::VectorResampleImageFilter< InputImageType,OutputImageType, double > ResampleFilterType;
+#else
+ typedef itk::ResampleImageFilter< InputImageType,OutputImageType, double > ResampleFilterType;
+#endif
typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
-
+
// Matrix
typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
- if (m_ArgsInfo.matrix_given)
- matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
- 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.rotate_given || m_ArgsInfo.translate_given)
+ {
+ if (m_ArgsInfo.matrix_given)
+ {
+ std::cerr << "You must use either rotate/translate or matrix options" << std::endl;
+ 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
+ {
+ 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;
typename AffineTransformType::Pointer affineTransform=AffineTransformType::New();
affineTransform->SetMatrix(rotationMatrix);
affineTransform->SetTranslation(translationPart);
- // Interp
+ // Interp
typedef clitk::GenericVectorInterpolator<args_info_type, InputImageType, double> GenericInterpolatorType;
typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
genericInterpolator->SetArgsInfo(m_ArgsInfo);
-
+
// Properties
- if (m_ArgsInfo.like_given)
- {
- typename InputReaderType::Pointer likeReader=InputReaderType::New();
- likeReader->SetFileName(m_ArgsInfo.like_arg);
- likeReader->Update();
- resampler->SetSize( likeReader->GetOutput()->GetLargestPossibleRegion().GetSize() );
- resampler->SetOutputSpacing( likeReader->GetOutput()->GetSpacing() );
- resampler->SetOutputOrigin( likeReader->GetOutput()->GetOrigin() );
+ if (m_ArgsInfo.like_given) {
+ typename InputReaderType::Pointer likeReader=InputReaderType::New();
+ likeReader->SetFileName(m_ArgsInfo.like_arg);
+ likeReader->Update();
+ resampler->SetSize( likeReader->GetOutput()->GetLargestPossibleRegion().GetSize() );
+ resampler->SetOutputSpacing( likeReader->GetOutput()->GetSpacing() );
+ resampler->SetOutputOrigin( likeReader->GetOutput()->GetOrigin() );
+ resampler->SetOutputDirection( likeReader->GetOutput()->GetDirection() );
+ if (autoGaussEnabled) { // Automated sigma when downsample
+ for(unsigned int i=0; i<Dimension; i++) {
+ if (likeReader->GetOutput()->GetSpacing()[i] > input->GetSpacing()[i]) { // downsample
+ gaussianSigma[i] = 0.5*likeReader->GetOutput()->GetSpacing()[i];// / inputSpacing[i]);
+ }
+ else gaussianSigma[i] = 0; // will be ignore after
+ }
}
- else
- {
- //Size
- typename OutputImageType::SizeType outputSize;
- if (m_ArgsInfo.size_given)
- {
- 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;
- if (m_ArgsInfo.spacing_given)
- {
- 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;
- if (m_ArgsInfo.origin_given)
- {
- 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 );
- resampler->SetOutputSpacing( outputSpacing );
- resampler->SetOutputOrigin( outputOrigin );
-
+ } else {
+ //Size
+ typename OutputImageType::SizeType outputSize;
+ if (m_ArgsInfo.size_given) {
+ 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;
+ if (m_ArgsInfo.spacing_given) {
+ for(unsigned int i=0; i< Dimension; i++)
+ outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
+ } else outputSpacing=input->GetSpacing();
+ if (autoGaussEnabled) { // Automated sigma when downsample
+ for(unsigned int i=0; i<Dimension; i++) {
+ if (outputSpacing[i] > input->GetSpacing()[i]) { // downsample
+ gaussianSigma[i] = 0.5*outputSpacing[i];// / inputSpacing[i]);
+ }
+ else gaussianSigma[i] = 0; // will be ignore after
+ }
}
+ std::cout<<"Setting the spacing to "<<outputSpacing<<"..."<<std::endl;
+
+ //Origin
+ typename OutputImageType::PointType outputOrigin;
+ if (m_ArgsInfo.origin_given) {
+ 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;
+
+ //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 );
+
+ }
+
+ typedef itk::RecursiveGaussianImageFilter<InputImageType, InputImageType> GaussianFilterType;
+ std::vector<typename GaussianFilterType::Pointer> gaussianFilters;
+ if (gaussianFilteringEnabled || autoGaussEnabled) {
+ for(unsigned int i=0; i<Dimension; i++) {
+ if (gaussianSigma[i] != 0) {
+ gaussianFilters.push_back(GaussianFilterType::New());
+ gaussianFilters[i]->SetDirection(i);
+ gaussianFilters[i]->SetOrder(GaussianFilterType::ZeroOrder);
+ gaussianFilters[i]->SetNormalizeAcrossScale(false);
+ gaussianFilters[i]->SetSigma(gaussianSigma[i]); // in millimeter !
+ if (gaussianFilters.size() == 1) { // first
+ gaussianFilters[0]->SetInput(input);
+ } else {
+ gaussianFilters[i]->SetInput(gaussianFilters[i-1]->GetOutput());
+ }
+ }
+ }
+ if (gaussianFilters.size() > 0) {
+ resampler->SetInput(gaussianFilters[gaussianFilters.size()-1]->GetOutput());
+ } else resampler->SetInput(input);
+ } else resampler->SetInput(input);
resampler->SetInput( input );
resampler->SetTransform( affineTransform );
resampler->SetInterpolator( genericInterpolator->GetInterpolatorPointer());
resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
- try
- {
- resampler->Update();
- }
- catch(itk::ExceptionObject)
- {
- std::cerr<<"Error resampling the image"<<std::endl;
- }
+ try {
+ resampler->Update();
+ } catch(itk::ExceptionObject) {
+ std::cerr<<"Error resampling the image"<<std::endl;
+ }
typename OutputImageType::Pointer output = resampler->GetOutput();
writer->Update();
}
-
+ //-------------------------------------------------------------------
} //end clitk
-
+
#endif //#define clitkAffineTransformGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff