VF composition with BSpline coefficients

[clitk.git] / tools / clitkComposeVFGenericFilter.txx

diff --git a/tools/clitkComposeVFGenericFilter.txx b/tools/clitkComposeVFGenericFilter.txx
index 80d1d001a9bdf172a8df55a572ed7c4fb8e770e7..07df9882fe573cafd268b4b78a83d9e914cc80f7 100644 (file)
--- a/tools/clitkComposeVFGenericFilter.txx
+++ b/tools/clitkComposeVFGenericFilter.txx
@@ -19,6 +19,13 @@
 #define __clitkComposeVFGenericFilter_txx
 #include "clitkComposeVFGenericFilter.h"
 
+#include "clitkBSplineDeformableTransform.h"
+#include "clitkBSplineDeformableTransformInitializer.h"
+#if ITK_VERSION_MAJOR >= 4
+#include "itkTransformToDisplacementFieldSource.h"
+#else
+#include "itkTransformToDeformationFieldSource.h"
+#endif
 
 namespace clitk
 {
@@ -36,43 +43,102 @@ namespace clitk
       }
   }
 
+  template<class DisplacementFieldType>
+  typename DisplacementFieldType::Pointer ComposeVFGenericFilter::CoeffsToDVF(std::string fileName, std::string likeFileName)
+  {
+    typedef clitk::BSplineDeformableTransform<double, DisplacementFieldType::ImageDimension, DisplacementFieldType::ImageDimension> TransformType;
+    typedef typename TransformType::CoefficientImageType CoefficientImageType;
+
+    typedef itk::ImageFileReader<CoefficientImageType> CoeffReaderType;
+    typename CoeffReaderType::Pointer reader = CoeffReaderType::New();
+    reader->SetFileName(fileName);
+    reader->Update();
+
+    typename TransformType::Pointer transform = TransformType::New();
+    transform->SetCoefficientImage(reader->GetOutput());
+    
+#if ITK_VERSION_MAJOR >= 4
+        typedef itk::TransformToDisplacementFieldSource<DisplacementFieldType, double> ConvertorType;
+#else
+        typedef itk::TransformToDeformationFieldSource<DisplacementFieldType, double> ConvertorType;
+#endif
+
+    typedef itk::ImageIOBase ImageIOType;
+    typename ImageIOType::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(likeFileName.c_str(), itk::ImageIOFactory::ReadMode);
+    imageIO->SetFileName(likeFileName);
+    imageIO->ReadImageInformation();
+
+    typename ConvertorType::Pointer convertor= ConvertorType::New();
+    typename ConvertorType::SizeType output_size;
+    typename ConvertorType::SpacingType output_spacing;
+    typename ConvertorType::OriginType output_origin;
+    typename ConvertorType::DirectionType output_direction;
+    for (unsigned int i = 0; i < DisplacementFieldType::ImageDimension; i++) {
+      output_size[i] = imageIO->GetDimensions(i);
+      output_spacing[i] = imageIO->GetSpacing(i);
+      output_origin[i] = imageIO->GetOrigin(i);
+      for (unsigned int j = 0; j < DisplacementFieldType::ImageDimension; j++)
+        output_direction[i][j] = imageIO->GetDirection(i)[j];
+    }
+    
+    if (m_Verbose) {
+      std::cout << "Interpolating coefficients with grid:" << std::endl;
+      std::cout << output_size << output_spacing << std::endl;
+    }
+    
+    convertor->SetNumberOfThreads(1);
+    convertor->SetTransform(transform);
+    convertor->SetOutputOrigin(output_origin);
+    convertor->SetOutputSpacing(output_spacing);
+    convertor->SetOutputSize(output_size);
+    convertor->SetOutputDirection(output_direction);
+    convertor->Update();
 
+    return convertor->GetOutput();
+  }
+  
   template<unsigned int Dimension, class PixelType>
   void ComposeVFGenericFilter::UpdateWithDimAndPixelType()
   {
-
-    //Define the image type
     typedef itk::Vector<PixelType, Dimension> DisplacementType;
     typedef itk::Image<DisplacementType, Dimension> ImageType;
+    typename ImageType::Pointer input1, input2;
 
-    //Read the input1
-    typedef itk::ImageFileReader<ImageType> ImageReaderType;
-    typename  ImageReaderType::Pointer reader1= ImageReaderType::New();
-    reader1->SetFileName(m_InputName1);
-    reader1->Update();
-    typename ImageType::Pointer input1 =reader1->GetOutput();
- 
-    //Read the input2
-    typename  ImageReaderType::Pointer reader2= ImageReaderType::New();
-    reader2->SetFileName(m_InputName2);
-    reader2->Update();
-    typename ImageType::Pointer input2=reader2->GetOutput();
-
-    //Create the ComposeVFFilter
-    typedef clitk::ComposeVFFilter<ImageType,ImageType> FilterType;
-    typename FilterType::Pointer filter =FilterType::New();
-    filter->SetInput1(input1);
-    filter->SetInput2(input2);
-    filter->SetVerbose(m_Verbose);
-    filter->Update();
-    
-    //Write the output
-    typedef itk::ImageFileWriter<ImageType> WriterType;
-    typename WriterType::Pointer writer = WriterType::New();
-    writer->SetFileName(m_OutputName);
-    writer->SetInput(filter->GetOutput());
-    writer->Update();
+    //Define the image type
+    if (m_Type == 1) {
+      input1 = this->CoeffsToDVF<ImageType>(m_InputName1, m_LikeImage);
+      input2 = this->CoeffsToDVF<ImageType>(m_InputName2, m_LikeImage);
+    }
+    else {
+      //Read the input1
+      typedef itk::ImageFileReader<ImageType> ImageReaderType;
+      typename  ImageReaderType::Pointer reader1= ImageReaderType::New();
+      reader1->SetFileName(m_InputName1);
+      reader1->Update();
+      input1 =reader1->GetOutput();
+
+      //Read the input2
+      typename  ImageReaderType::Pointer reader2= ImageReaderType::New();
+      reader2->SetFileName(m_InputName2);
+      reader2->Update();
+      input2=reader2->GetOutput();
+    }
 
+      //Create the ComposeVFFilter
+      typedef clitk::ComposeVFFilter<ImageType,ImageType> FilterType;
+      typename FilterType::Pointer filter =FilterType::New();
+      filter->SetInput1(input1);
+      filter->SetInput2(input2);
+      filter->SetVerbose(m_Verbose);
+      filter->Update();
+
+      //Write the output
+      typedef itk::ImageFileWriter<ImageType> WriterType;
+      typename WriterType::Pointer writer = WriterType::New();
+      writer->SetFileName(m_OutputName);
+      writer->SetInput(filter->GetOutput());
+      writer->Update();
+    
   }
 }