--- /dev/null
+/*=========================================================================
+ 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 clitkElastix_h
+#define clitkElastix_h
+
+//--------------------------------------------------------------------
+namespace clitk {
+
+//-------------------------------------------------------------------
+bool
+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;
+}
+//-------------------------------------------------------------------
+
+
+//-------------------------------------------------------------------
+void
+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];
+}
+//-------------------------------------------------------------------
+
+
+//-------------------------------------------------------------------
+template<unsigned int Dimension>
+typename itk::Matrix<double, Dimension+1, Dimension+1>
+createMatrixFromElastixFile(std::vector<std::string> & filename, bool verbose=true) {
+ 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 (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 (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 (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;
+}
+}
+//-------------------------------------------------------------------
+
+#endif
//----------------------------------------
void Update();
- template<unsigned int Dimension, class PixelType>
- static
- typename itk::Matrix<double, Dimension+1, Dimension+1>
- createMatrixFromElastixFile(std::vector<std::string> & filename, bool verbose=true);
-
protected:
//----------------------------------------
template <unsigned int Dimension, class PixelType> void UpdateWithDimAndPixelType();
template <unsigned int Dimension, class PixelType> void UpdateWithDimAndVectorType();
- static bool GetElastixValueFromTag(std::ifstream & is, std::string tag, std::string & value);
- static void GetValuesFromValue(const std::string & s,
- std::vector<std::string> & values);
-
//----------------------------------------
// Data members
//----------------------------------------
#include <istream>
#include <iterator>
#include <itkCenteredEuler3DTransform.h>
+#include "clitkElastix.h"
namespace clitk
{
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, m_Verbose);
+ matrix = createMatrixFromElastixFile<Dimension>(s, m_Verbose);
}
else
matrix.SetIdentity();
}
//-------------------------------------------------------------------
-
-
- //-------------------------------------------------------------------
- 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, bool verbose)
- {
- 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 (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 (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 (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
// clitk
#include "clitkElastixTransformToMatrix_ggo.h"
#include "clitkAffineTransformGenericFilter.h"
+#include "clitkElastix.h"
//--------------------------------------------------------------------
int main(int argc, char * argv[])
CLITK_INIT;
// Use static fct of AffineTransformGenericFilter
- typedef clitk::AffineTransformGenericFilter<args_info_clitkElastixTransformToMatrix> FilterType;
std::vector<std::string> l;
l.push_back(args_info.input_arg);
- itk::Matrix<double, 4, 4> m =
- FilterType::createMatrixFromElastixFile<3, int>(l, args_info.verbose_flag);
+ itk::Matrix<double, 4, 4> m = clitk::createMatrixFromElastixFile<3>(l, args_info.verbose_flag);
// Print matrix
std::ofstream os;
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff