X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkAffineTransformGenericFilter.txx;h=93d43571b11d170825ad6f31e09b5646e653f086;hb=71021d34bda3e0e61917cdc1780f7ed901714965;hp=03cf862e2ee261548d6707761648821823b9e1fb;hpb=14d6a55438749d14c04f32539b5bc76c6e0b97c8;p=clitk.git

diff --git a/tools/clitkAffineTransformGenericFilter.txx b/tools/clitkAffineTransformGenericFilter.txx
index 03cf862..93d4357 100644
--- a/tools/clitkAffineTransformGenericFilter.txx
+++ b/tools/clitkAffineTransformGenericFilter.txx
@@ -22,6 +22,7 @@
 #include <istream>
 #include <iterator>
 #include <itkCenteredEuler3DTransform.h>
+#include "clitkElastix.h"
 
 namespace clitk
 {
@@ -138,7 +139,7 @@ namespace clitk
       {
         if (m_ArgsInfo.matrix_given)
           {
-            std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
+            std::cerr << "You must use either rotate/translate or matrix options" << std::endl;
             return;
           }
         itk::Array<double> transformParameters(2 * Dimension);
@@ -181,9 +182,8 @@ namespace clitk
           }
         else {
           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);
+            std::string filename(m_ArgsInfo.elastix_arg);
+            matrix = createMatrixFromElastixFile<Dimension>(filename, m_Verbose);
           }
           else 
             matrix.SetIdentity();
@@ -212,6 +212,7 @@ namespace clitk
       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) );
@@ -368,7 +369,7 @@ namespace clitk
       {
         if (m_ArgsInfo.matrix_given)
           {
-            std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
+            std::cerr << "You must use either rotate/translate or matrix options" << std::endl;
             return;
           }
         itk::Array<double> transformParameters(2 * Dimension);
@@ -491,140 +492,6 @@ namespace clitk
 
   }
   //-------------------------------------------------------------------
-  
-  
-  //-------------------------------------------------------------------
-  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