X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkWarpImageGenericFilter.txx;h=84bfbaaec7148cc5f133180c3b5290ca608eb491;hb=543b72e23ad001ac2a7743b9beacf48e2d0054ac;hp=3d73221de9ad4e72193e0a02853ce36ce93531f1;hpb=0b7c9b1e1215634b02cbd38d4e4ba101d6111ba8;p=clitk.git

diff --git a/tools/clitkWarpImageGenericFilter.txx b/tools/clitkWarpImageGenericFilter.txx
index 3d73221..84bfbaa 100644
--- a/tools/clitkWarpImageGenericFilter.txx
+++ b/tools/clitkWarpImageGenericFilter.txx
@@ -1,9 +1,9 @@
 /*=========================================================================
   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
 
-  Authors belong to: 
+  Authors belong to:
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.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
@@ -14,227 +14,236 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+===========================================================================**/
 #ifndef clitkWarpImageGenericFilter_txx
 #define clitkWarpImageGenericFilter_txx
 
 /* =================================================
  * @file   clitkWarpImageGenericFilter.txx
- * @author 
- * @date   
- * 
- * @brief 
- * 
+ * @author
+ * @date
+ *
+ * @brief
+ *
  ===================================================*/
 
+#include "itkVectorResampleImageFilter.h"
+#include "clitkConvertBLUTCoeffsToVFFilter.h"
 
 namespace clitk
 {
 
-  //-------------------------------------------------------------------
-  // Update with the number of dimensions
-  //-------------------------------------------------------------------
-  template<unsigned int Dimension>
-  void 
-  WarpImageGenericFilter::UpdateWithDim(std::string PixelType)
-  {
-    if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
-
-    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>();
-    }
+//-------------------------------------------------------------------
+// Update with the number of dimensions
+//-------------------------------------------------------------------
+template<unsigned int Dimension>
+void
+WarpImageGenericFilter::UpdateWithDim(std::string PixelType)
+{
+  if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
+
+  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>();
+  }
+}
 
 
-  //-------------------------------------------------------------------
-  // Update with the number of dimensions and the pixeltype
-  //-------------------------------------------------------------------
-  template <unsigned int Dimension, class  PixelType> 
-  void 
-  WarpImageGenericFilter::UpdateWithDimAndPixelType()
-  {
-
-    // ImageTypes
-    typedef itk::Image<PixelType, Dimension> InputImageType;
-    typedef itk::Image<PixelType, Dimension> OutputImageType;
-    typedef itk::Vector<float, Dimension> DisplacementType;
-    typedef itk::Image<DisplacementType, Dimension> DeformationFieldType;
-    
-
-    // Read the input
-    typedef itk::ImageFileReader<InputImageType> InputReaderType;
-    typename InputReaderType::Pointer reader = InputReaderType::New();
-    reader->SetFileName( m_InputFileName);
-    reader->Update();
-    typename InputImageType::Pointer input= reader->GetOutput();
- 
+//-------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//-------------------------------------------------------------------
+template <unsigned int Dimension, class  PixelType>
+void
+WarpImageGenericFilter::UpdateWithDimAndPixelType()
+{
+
+  // ImageTypes
+  typedef itk::Image<PixelType, Dimension> InputImageType;
+  typedef itk::Image<PixelType, Dimension> OutputImageType;
+  typedef itk::Vector<float, Dimension> DisplacementType;
+  typedef itk::Image<DisplacementType, Dimension> DeformationFieldType;
+  
+  // Read the input
+  typedef itk::ImageFileReader<InputImageType> InputReaderType;
+  typename InputReaderType::Pointer reader = InputReaderType::New();
+  reader->SetFileName( m_InputFileName);
+  reader->Update();
+  typename InputImageType::Pointer input= reader->GetOutput();
+  
+  typename DeformationFieldType::Pointer deformationField;
+  if (m_ArgsInfo.coeff_given) {
+    typedef ConvertBLUTCoeffsToVFFilter<DeformationFieldType> FilterType;
+    typename FilterType::Pointer filter = FilterType::New();
+    filter->SetInputFileName(m_ArgsInfo.coeff_arg);
+    filter->SetLikeFileName(m_InputFileName);
+    filter->SetVerbose(m_Verbose);
+    filter->Update();
+    deformationField = filter->GetOutput();
+  }
+  else {
     //Read the deformation field
     typedef itk::ImageFileReader<DeformationFieldType> DeformationFieldReaderType;
     typename  DeformationFieldReaderType::Pointer deformationFieldReader= DeformationFieldReaderType::New();
     deformationFieldReader->SetFileName(m_ArgsInfo.vf_arg);
     deformationFieldReader->Update();
-    typename DeformationFieldType::Pointer deformationField =deformationFieldReader->GetOutput();
+    deformationField =deformationFieldReader->GetOutput();
+  }
+
+  // Intensity interpolator
+  typedef clitk::GenericVectorInterpolator<args_info_clitkWarpImage, DeformationFieldType, double> GenericInterpolatorType;
+  typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
+  genericInterpolator->SetArgsInfo(m_ArgsInfo);
+
+
+  // -------------------------------------------
+  // Spacing like DVF
+  // -------------------------------------------
+  if (m_ArgsInfo.spacing_arg == 0) {
+    // Calculate the region
+    typename DeformationFieldType::SizeType newSize;
+    for (unsigned int i=0 ; i <Dimension; i++)
+      newSize[i]=(unsigned int) (input->GetLargestPossibleRegion().GetSize()[i]*input->GetSpacing()[i]/deformationField->GetSpacing()[i]);
 
-    // Intensity interpolator
+    // Get the interpolator
     typedef clitk::GenericVectorInterpolator<args_info_clitkWarpImage, DeformationFieldType, double> GenericInterpolatorType;
     typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
     genericInterpolator->SetArgsInfo(m_ArgsInfo);
-    
-
-    // -------------------------------------------
-    // Spacing like DVF
-    // -------------------------------------------
-    if (m_ArgsInfo.spacing_arg == 0)
-      {
-	// Calculate the region
-	typename DeformationFieldType::SizeType newSize;
-	for (unsigned int i=0 ; i <Dimension; i++)
-	  newSize[i]=(unsigned int) (input->GetLargestPossibleRegion().GetSize()[i]*input->GetSpacing()[i]/deformationField->GetSpacing()[i]);
-	
-	// Get the interpolator
-	typedef clitk::GenericVectorInterpolator<args_info_clitkWarpImage, DeformationFieldType, double> GenericInterpolatorType;
-	typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
-	genericInterpolator->SetArgsInfo(m_ArgsInfo);
-	
-	// Resample to match the extent of the input
-	typename itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::Pointer 
-	  resampler =itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::New();
-	resampler->SetInput(deformationField);
-	resampler->SetOutputSpacing(deformationField->GetSpacing());
-	resampler->SetSize(newSize);
-	resampler->SetOutputOrigin(input->GetOrigin());
-	resampler->SetInterpolator(genericInterpolator->GetInterpolatorPointer());
-
-	// Update
-	if (m_Verbose) std::cout<< "Resampling the VF..." <<std::endl;
-	try {
-	  resampler->Update();
-	}
-	catch( itk::ExceptionObject & excp ) {
-	  std::cerr << "Problem resampling the input vector field file" << std::endl;
-	  std::cerr << excp << std::endl;
-	  return;
-	}	  
-	deformationField= resampler->GetOutput();
-	
-      }
-    
-    // -------------------------------------------
-    // Spacing like input
-    // -------------------------------------------
-    else
-      {
-	// Get size
-	typename DeformationFieldType::SizeType newSize;
-	for (unsigned int i=0 ; i <Dimension; i++)
-	  newSize[i]=input->GetLargestPossibleRegion().GetSize()[i];
-
-	// Resample to match the extent of the input
-	typename itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::Pointer 
-	  resampler =itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::New();
-	resampler->SetInput(deformationField);
-	resampler->SetOutputSpacing(input->GetSpacing());
-	resampler->SetSize(newSize);
-	resampler->SetOutputOrigin(input->GetOrigin());
-	resampler->SetInterpolator(genericInterpolator->GetInterpolatorPointer());
-
-	// Update
-	if (m_Verbose) std::cout<< "Resampling the VF..." <<std::endl;
-	try {
-	  resampler->Update();
-	}
-	catch( itk::ExceptionObject & excp ) {
-	  std::cerr << "Problem resampling the input vector field file" << std::endl;
-	  std::cerr << excp << std::endl;
-	  return;
-	}  
-	deformationField= resampler->GetOutput();
-      }
-
-
-    // -------------------------------------------
-    // Forward Warp
-    // -------------------------------------------
-    typename    itk::ImageToImageFilter<InputImageType, InputImageType>::Pointer warpFilter;
-    if (m_ArgsInfo.forward_flag)
-      {
-    	//Forward warping: always linear
-	typedef clitk::ForwardWarpImageFilter<InputImageType, InputImageType, DeformationFieldType> ForwardWarpFilterType;
-	typename ForwardWarpFilterType::Pointer forwardWarpFilter= ForwardWarpFilterType::New();
-	forwardWarpFilter->SetDeformationField( deformationField );
-	forwardWarpFilter->SetEdgePaddingValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
-	warpFilter=forwardWarpFilter;
-      }
-
-    // -------------------------------------------
-    // Backward Warp
-    // -------------------------------------------
-    else
-      {
-	// Get the interpolator
-	typedef clitk::GenericInterpolator<args_info_clitkWarpImage, InputImageType, double> GenericInterpolatorType;
-	typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
-	genericInterpolator->SetArgsInfo(m_ArgsInfo);
-
-	//Backward mapping
-	typedef itk::WarpImageFilter<InputImageType, InputImageType, DeformationFieldType> BackwardWarpFilterType;
-	typename BackwardWarpFilterType::Pointer backwardWarpFilter= BackwardWarpFilterType::New();
-	backwardWarpFilter->SetDeformationField( deformationField );
-	backwardWarpFilter->SetEdgePaddingValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
-	backwardWarpFilter->SetOutputSpacing( deformationField->GetSpacing() );
-	backwardWarpFilter->SetOutputOrigin( input->GetOrigin() );
-	backwardWarpFilter->SetOutputSize( deformationField->GetLargestPossibleRegion().GetSize() );
-	typename itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::Pointer 
-	  resampler =itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::New();
-	backwardWarpFilter->SetInterpolator(genericInterpolator->GetInterpolatorPointer());
-	warpFilter=backwardWarpFilter;
-      }
-
-
-    // -------------------------------------------
+
+    // Resample to match the extent of the input
+    typename itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::Pointer
+    resampler =itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::New();
+    resampler->SetInput(deformationField);
+    resampler->SetOutputSpacing(deformationField->GetSpacing());
+    resampler->SetOutputDirection(deformationField->GetDirection());
+    resampler->SetSize(newSize);
+    resampler->SetOutputOrigin(input->GetOrigin());
+    resampler->SetInterpolator(genericInterpolator->GetInterpolatorPointer());
+
     // Update
-    // -------------------------------------------
-    warpFilter->SetInput(input);
-    if (m_Verbose) std::cout<< "Warping the input..." <<std::endl;
+    if (m_Verbose) std::cout<< "Resampling the VF..." <<std::endl;
     try {
-      warpFilter->Update();
+      resampler->Update();
+    } catch( itk::ExceptionObject & excp ) {
+      std::cerr << "Problem resampling the input vector field file" << std::endl;
+      std::cerr << excp << std::endl;
+      return;
     }
-    catch( itk::ExceptionObject & excp ) {
-      std::cerr << "Problem warping the input image" << std::endl;
+    deformationField= resampler->GetOutput();
+
+  }
+
+  // -------------------------------------------
+  // Spacing like input
+  // -------------------------------------------
+  else if (!m_ArgsInfo.coeff_given) {
+    // Get size
+    typename DeformationFieldType::SizeType newSize;
+    for (unsigned int i=0 ; i <Dimension; i++)
+      newSize[i]=input->GetLargestPossibleRegion().GetSize()[i];
+
+    // Resample to match the extent of the input
+    typename itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::Pointer
+    resampler =itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::New();
+    resampler->SetInput(deformationField);
+    resampler->SetOutputSpacing(input->GetSpacing());
+    resampler->SetOutputDirection(deformationField->GetDirection());
+    resampler->SetSize(newSize);
+    resampler->SetOutputOrigin(input->GetOrigin());
+    resampler->SetInterpolator(genericInterpolator->GetInterpolatorPointer());
+
+    // Update
+    if (m_Verbose) std::cout<< "Resampling the VF..." <<std::endl;
+    try {
+      resampler->Update();
+    } catch( itk::ExceptionObject & excp ) {
+      std::cerr << "Problem resampling the input vector field file" << std::endl;
       std::cerr << excp << std::endl;
       return;
-    } 
-    
+    }
+    deformationField= resampler->GetOutput();
+  }
 
-    // Output
-    typedef itk::ImageFileWriter<OutputImageType> WriterType;
-    typename WriterType::Pointer writer = WriterType::New();
-    writer->SetFileName(m_ArgsInfo.output_arg);
-    writer->SetInput(warpFilter->GetOutput());
-    writer->Update();
 
+  // -------------------------------------------
+  // Forward Warp
+  // -------------------------------------------
+  typename    itk::ImageToImageFilter<InputImageType, InputImageType>::Pointer warpFilter;
+  if (m_ArgsInfo.forward_flag) {
+    //Forward warping: always linear
+    typedef clitk::ForwardWarpImageFilter<InputImageType, InputImageType, DeformationFieldType> ForwardWarpFilterType;
+    typename ForwardWarpFilterType::Pointer forwardWarpFilter= ForwardWarpFilterType::New();
+    forwardWarpFilter->SetDeformationField( deformationField );
+    forwardWarpFilter->SetEdgePaddingValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
+    warpFilter=forwardWarpFilter;
   }
 
+  // -------------------------------------------
+  // Backward Warp
+  // -------------------------------------------
+  else {
+    // Get the interpolator
+    typedef clitk::GenericInterpolator<args_info_clitkWarpImage, InputImageType, double> GenericInterpolatorType;
+    typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
+    genericInterpolator->SetArgsInfo(m_ArgsInfo);
+
+    //Backward mapping
+    typedef itk::WarpImageFilter<InputImageType, InputImageType, DeformationFieldType> BackwardWarpFilterType;
+    typename BackwardWarpFilterType::Pointer backwardWarpFilter= BackwardWarpFilterType::New();
+    backwardWarpFilter->SetDisplacementField( deformationField );
+    backwardWarpFilter->SetEdgePaddingValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
+    backwardWarpFilter->SetOutputSpacing( deformationField->GetSpacing() );
+    backwardWarpFilter->SetOutputOrigin( input->GetOrigin() );
+    backwardWarpFilter->SetOutputSize( deformationField->GetLargestPossibleRegion().GetSize() );
+    backwardWarpFilter->SetOutputDirection( input->GetDirection() );
+    typename itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::Pointer
+    resampler =itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::New();
+    backwardWarpFilter->SetInterpolator(genericInterpolator->GetInterpolatorPointer());
+    warpFilter=backwardWarpFilter;
+  }
+
+
+  // -------------------------------------------
+  // Update
+  // -------------------------------------------
+  warpFilter->SetInput(input);
+  if (m_Verbose) std::cout<< "Warping the input..." <<std::endl;
+  try {
+    warpFilter->Update();
+  } catch( itk::ExceptionObject & excp ) {
+    std::cerr << "Problem warping the input image" << std::endl;
+    std::cerr << excp << std::endl;
+    return;
+  }
+
+
+  // Output
+  typedef itk::ImageFileWriter<OutputImageType> WriterType;
+  typename WriterType::Pointer writer = WriterType::New();
+  writer->SetFileName(m_ArgsInfo.output_arg);
+  writer->SetInput(warpFilter->GetOutput());
+  writer->Update();
+
+}
+
 
 }//end clitk
- 
+
 #endif //#define clitkWarpImageGenericFilter_txx