Go from matrix to elastix file

diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index 77f12f9f863e301e089cc28c49aab05a20276fe8..899bd36926334450346382e69dcc510f657ad100 100644 (file)
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -113,6 +113,10 @@ IF (CLITK_BUILD_TOOLS)
   TARGET_LINK_LIBRARIES(clitkElastixTransformToMatrix clitkCommon )
   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkElastixTransformToMatrix)
 
+  WRAP_GGO(clitkMatrixToElastixTransform_GGO_C clitkMatrixToElastixTransform.ggo)
+  ADD_EXECUTABLE(clitkMatrixToElastixTransform clitkMatrixToElastixTransform.cxx ${clitkMatrixToElastixTransform_GGO_C})
+  TARGET_LINK_LIBRARIES(clitkMatrixToElastixTransform clitkCommon )
+  SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMatrixToElastixTransform)
 
   WRAP_GGO(clitkSetBackground_GGO_C clitkSetBackground.ggo)
   ADD_EXECUTABLE(clitkSetBackground clitkSetBackground.cxx clitkSetBackgroundGenericFilter.cxx ${clitkSetBackground_GGO_C})

diff --git a/tools/clitkMatrixToElastixTransform.cxx b/tools/clitkMatrixToElastixTransform.cxx
new file mode 100644 (file)
index 0000000..a8b7520
--- /dev/null
+++ b/tools/clitkMatrixToElastixTransform.cxx
@@ -0,0 +1,118 @@
+/*=========================================================================
+  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
+===========================================================================**/
+
+// clitk
+#include "clitkMatrixToElastixTransform_ggo.h"
+#include "clitkTransformUtilities.h"
+#include "clitkIO.h"
+
+// itk
+#include <itkEuler3DTransform.h>
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+  // Init command line
+  GGO(clitkMatrixToElastixTransform, args_info);
+  CLITK_INIT;
+
+  // Read matrix
+  itk::Matrix<double, 4, 4> matrix;
+  try {
+    matrix = clitk::ReadMatrix3D(args_info.input_arg);
+  }
+  catch (itk::ExceptionObject & err) {
+    std::cerr << "Error reading " << args_info.input_arg << std::endl;
+    std::cerr << err.GetDescription() << std::endl;
+    exit(-1);
+  }
+
+  // Compute parameters from transfer using itk Euler transform
+  itk::Euler3DTransform<double>::CenterType center;
+  center.Fill(0.);
+  if(args_info.center_given==3) {
+    center[0] = args_info.center_arg[0];
+    center[1] = args_info.center_arg[1];
+    center[2] = args_info.center_arg[2];
+  }
+  itk::Euler3DTransform<double>::MatrixType rotMat;
+  itk::Euler3DTransform<double>::OutputVectorType transVec;
+  for(int i=0; i<3; i++) {
+    transVec[i] = matrix[i][3];
+    for(int j=0; j<3; j++)
+      rotMat[i][j] = matrix[i][j];
+  }
+  itk::Euler3DTransform<double>::Pointer euler;
+  euler = itk::Euler3DTransform<double>::New();
+  euler->SetCenter(center);
+  euler->SetOffset(transVec);
+  euler->SetComputeZYX(false);
+  try {
+    euler->SetMatrix(rotMat);
+  }
+  catch (itk::ExceptionObject & err) {
+    std::cerr << "Error reading " << args_info.input_arg << std::endl;
+    std::cerr << err.GetDescription() << std::endl;
+    exit(-1);
+  }
+
+  // Write result
+  std::ofstream out;
+  clitk::openFileForWriting(out, args_info.output_arg);
+  out << "(Transform \"EulerTransform\")" << std::endl;
+  out << "(NumberOfParameters 6)" << std::endl;
+  out << "(TransformParameters ";
+  for(unsigned int i=0; i<6; i++)
+    out << euler->GetParameters()[i] << ' ';
+  out << ')' << std::endl;
+  out << "(InitialTransformParametersFileName \"NoInitialTransform\")" << std::endl;
+  out << "(HowToCombineTransforms \"Compose\")" << std::endl;
+
+  out << "// EulerTransform specific" << std::endl;
+  out << "(CenterOfRotationPoint "<< center[0] << ' ' << center[1] << ' ' << center[2] << ')' << std::endl;
+  out << "(ComputeZYX \"false\")" << std::endl;
+
+  // The rest is commented, up to the user to define it manually
+  out << "// Image specific" << std::endl;
+  out << "// (FixedImageDimension 3)" << std::endl;
+  out << "// (MovingImageDimension 3)" << std::endl;
+  out << "// (FixedInternalImagePixelType \"float\")" << std::endl;
+  out << "// (MovingInternalImagePixelType \"float\")" << std::endl;
+  out << "// (Size 1 1 1)" << std::endl;
+  out << "// (Index 0 0 0)" << std::endl;
+  out << "// (Spacing 1 1 1)" << std::endl;
+  out << "// (Origin -0.5 -0.5 -0.5)" << std::endl;
+  out << "// (Direction 1 0 0 0 1 0 0 0 1)" << std::endl;
+  out << "// (UseDirectionCosines \"true\")" << std::endl << std::endl;
+
+  out << "// ResampleInterpolator specific" << std::endl;
+  out << "// (ResampleInterpolator \"FinalBSplineInterpolator\")" << std::endl;
+  out << "// (FinalBSplineInterpolationOrder 3)" << std::endl << std::endl;
+
+  out << "// Resampler specific" << std::endl;
+  out << "// (Resampler \"DefaultResampler\")" << std::endl;
+  out << "// (DefaultPixelValue 0.000000)" << std::endl;
+  out << "// (ResultImageFormat \"mhd\")" << std::endl;
+  out << "// (ResultImagePixelType \"short\")" << std::endl;
+  out << "// (CompressResultImage \"false\")" << std::endl;
+  out.close();
+
+  return EXIT_SUCCESS;
+}// end main
+
+//--------------------------------------------------------------------

diff --git a/tools/clitkMatrixToElastixTransform.ggo b/tools/clitkMatrixToElastixTransform.ggo
new file mode 100644 (file)
index 0000000..38f73fa
--- /dev/null
+++ b/tools/clitkMatrixToElastixTransform.ggo
@@ -0,0 +1,10 @@
+#File clitkMatrixToElastixTransform.ggo
+package "clitkMatrixToElastixTransform"
+version "1.0"
+purpose ""
+
+option "config"  - "Config file"             string optional
+option "verbose" v "Verbose"                 flag   off
+option "input"   i "Input matrix filename"   string required
+option "output"  o "Output elastix filename" string required
+option "center"  - "Rotation center"         float     no multiple(3)