Add Direction options in clitkAffineTransform

[clitk.git] / tools / clitkAffineTransformGenericFilter.txx

diff --git a/tools/clitkAffineTransformGenericFilter.txx b/tools/clitkAffineTransformGenericFilter.txx
index 1fa58b582919d4d7b03447f4be7aecb14a8738ac..15baf2d7a41c2b99068bc52b331634545cd993c4 100644 (file)
--- a/tools/clitkAffineTransformGenericFilter.txx
+++ b/tools/clitkAffineTransformGenericFilter.txx
@@ -139,7 +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);
@@ -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) );
@@ -280,10 +281,19 @@ namespace clitk
           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 );
 
     }
 
@@ -314,6 +324,7 @@ namespace clitk
       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;
     }
 
     resampler->SetInput( input );
@@ -368,7 +379,7 @@ 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);
@@ -437,6 +448,7 @@ namespace clitk
       resampler->SetSize( likeReader->GetOutput()->GetLargestPossibleRegion().GetSize() );
       resampler->SetOutputSpacing( likeReader->GetOutput()->GetSpacing() );
       resampler->SetOutputOrigin(  likeReader->GetOutput()->GetOrigin() );
+      resampler->SetOutputDirection( likeReader->GetOutput()->GetDirection() );
     } else {
       //Size
       typename OutputImageType::SizeType outputSize;
@@ -462,10 +474,20 @@ namespace clitk
       } 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 );
 
     }