X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=itk%2FclitkResampleImageWithOptionsFilter.txx;h=ddaa8a077b41f2ffcf2456836c2eeb7a4f0119fc;hb=299afce0c4c4cc3524dccecf4ecffd46d7a66328;hp=aa09f7129812ce2cc3065e85925d5d09faac173f;hpb=d8e6a6c0b380c2e7b542a2b9d922dc982a3d0d85;p=clitk.git

diff --git a/itk/clitkResampleImageWithOptionsFilter.txx b/itk/clitkResampleImageWithOptionsFilter.txx
index aa09f71..ddaa8a0 100644
--- a/itk/clitkResampleImageWithOptionsFilter.txx
+++ b/itk/clitkResampleImageWithOptionsFilter.txx
@@ -3,7 +3,7 @@
 
   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
@@ -14,10 +14,10 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-  ======================================================================-====*/
+  ===========================================================================**/
 
 // clitk
-#include "clitkCommon.h"
+#include "clitkDD.h"
 
 // itk include
 #include "itkImage.h"
@@ -35,9 +35,9 @@
 #include "itkCommand.h"
 
 //--------------------------------------------------------------------
-template <class TInputImage, class TOutputImage>
-clitk::ResampleImageWithOptionsFilter<TInputImage, TOutputImage>::
-ResampleImageWithOptionsFilter():itk::ImageToImageFilter<TInputImage, TOutputImage>() 
+template <class InputImageType, class OutputImageType>
+clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
+ResampleImageWithOptionsFilter():itk::ImageToImageFilter<InputImageType, OutputImageType>() 
 {
   static const unsigned int dim = InputImageType::ImageDimension;
   this->SetNumberOfRequiredInputs(1);
@@ -55,14 +55,15 @@ ResampleImageWithOptionsFilter():itk::ImageToImageFilter<TInputImage, TOutputIma
     m_GaussianSigma[i] = -1;
   }
   m_VerboseOptions = false;
+  SetDefaultPixelValue(0);
 }
 //--------------------------------------------------------------------
 
 
 //--------------------------------------------------------------------
-template <class TInputImage, class TOutputImage>
+template <class InputImageType, class OutputImageType>
 void
-clitk::ResampleImageWithOptionsFilter<TInputImage, TOutputImage>::
+clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
 SetInput(const InputImageType * image) 
 {
   // Process object is not const-correct so the const casting is required.
@@ -72,9 +73,9 @@ SetInput(const InputImageType * image)
 
 
 //--------------------------------------------------------------------
-template <class TInputImage, class TOutputImage>
+template <class InputImageType, class OutputImageType>
 void
-clitk::ResampleImageWithOptionsFilter<TInputImage, TOutputImage>::
+clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
 GenerateInputRequestedRegion() 
 {
   // call the superclass's implementation of this method
@@ -82,7 +83,7 @@ GenerateInputRequestedRegion()
 
   // get pointers to the input and output
   InputImagePointer  inputPtr  =
-    const_cast< TInputImage *>( this->GetInput() );
+    const_cast< InputImageType *>( this->GetInput() );
 
   // Request the entire input image
   InputImageRegionType inputRegion;
@@ -93,9 +94,9 @@ GenerateInputRequestedRegion()
 
 
 //--------------------------------------------------------------------
-template <class TInputImage, class TOutputImage>
+template <class InputImageType, class OutputImageType>
 void
-clitk::ResampleImageWithOptionsFilter<TInputImage, TOutputImage>::
+clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
 GenerateOutputInformation() 
 {
   static const unsigned int dim = InputImageType::ImageDimension;
@@ -121,12 +122,20 @@ GenerateOutputInformation()
   if (m_OutputIsoSpacing != -1) { // apply isoSpacing
     for(unsigned int i=0; i<dim; i++) {
       m_OutputSpacing[i] = m_OutputIsoSpacing;
-      m_OutputSize[i] = (int)lrint(inputSize[i]*inputSpacing[i]/m_OutputSpacing[i]);
+      // floor() is used to intentionally reduce the number of slices 
+      // because, from a clinical point of view, it's better to 
+      // remove data than to add data that privously didn't exist.
+      if(inputSpacing[i]*m_OutputSpacing[i]<0)
+        itkExceptionMacro( << "Input and output spacings don't have the same signs, can't cope with that" );
+      m_OutputSize[i] = (int)floor(inputSize[i]*inputSpacing[i]/m_OutputSpacing[i]);
     }
   } else {
     if (m_OutputSpacing[0] != -1) { // apply spacing, compute size
       for(unsigned int i=0; i<dim; i++) {
-        m_OutputSize[i] = (int)lrint(inputSize[i]*inputSpacing[i]/m_OutputSpacing[i]);
+        if(inputSpacing[i]*m_OutputSpacing[i]<0)
+          itkExceptionMacro( << "Input and output spacings don't have the same signs, can't cope with that" );
+	// see comment above for the use of floor()
+	m_OutputSize[i] = (int)floor(inputSize[i]*inputSpacing[i]/m_OutputSpacing[i]);
       }
     } else {
       if (m_OutputSize[0] != 0) { // apply size, compute spacing
@@ -146,7 +155,7 @@ GenerateOutputInformation()
     m_OutputSize[l] = inputSize[l];
     m_OutputSpacing[l] = inputSpacing[l];
   }
-    
+
   // Set Size/Spacing
   OutputImagePointer outputImage = this->GetOutput(0);
   // OutputImageRegionType region;
@@ -178,9 +187,9 @@ GenerateOutputInformation()
 
 
 //--------------------------------------------------------------------
-template <class TInputImage, class TOutputImage>
+template <class InputImageType, class OutputImageType>
 void 
-clitk::ResampleImageWithOptionsFilter<TInputImage, TOutputImage>::
+clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
 GenerateData() 
 {
    
@@ -188,18 +197,11 @@ GenerateData()
   InputImagePointer input = dynamic_cast<InputImageType*>(itk::ProcessObject::GetInput(0));
   static const unsigned int dim = InputImageType::ImageDimension;
 
-  // Set regions and allocate
-  //this->GetOutput()->SetRegions(m_OutputRegion);
-  //this->GetOutput()->Allocate();
-  // this->GetOutput()->FillBuffer(m_DefaultPixelValue);
-
   // Create main Resample Image Filter
   typedef itk::ResampleImageFilter<InputImageType,OutputImageType> FilterType;
   typename FilterType::Pointer filter = FilterType::New();
   filter->GraftOutput(this->GetOutput());
-  //     this->GetOutput()->Print(std::cout);
-  //     this->GetOutput()->SetBufferedRegion(this->GetOutput()->GetLargestPossibleRegion());
-  //     this->GetOutput()->Print(std::cout);
+  this->GetOutput()->SetBufferedRegion(this->GetOutput()->GetLargestPossibleRegion());
 
   // Print options if needed
   if (m_VerboseOptions) {
@@ -220,12 +222,19 @@ GenerateData()
     std::cout << "LastDimIsTime  = " << m_LastDimensionIsTime << std::endl;
   }
 
+  // Compute origin based on image corner
+  typename FilterType::OriginPointType origin = input->GetOrigin();
+  for(unsigned int i=0; i<OutputImageType::ImageDimension; i++) {
+    origin[i] -= 0.5 * input->GetSpacing()[i];
+    origin[i] += 0.5 * m_OutputSpacing[i];
+  }
+
   // Instance of the transform object to be passed to the resample
   // filter. By default, identity transform is applied
   filter->SetTransform(m_Transform);
   filter->SetSize(m_OutputSize);
   filter->SetOutputSpacing(m_OutputSpacing);
-  filter->SetOutputOrigin(input->GetOrigin());
+  filter->SetOutputOrigin(origin);
   filter->SetDefaultPixelValue(m_DefaultPixelValue);
   filter->SetNumberOfThreads(this->GetNumberOfThreads()); 
   filter->SetOutputDirection(input->GetDirection()); // <-- NEEDED if we want to keep orientation (in case of PermutAxes for example)
@@ -303,3 +312,30 @@ GenerateData()
   // DD("after Graft");
 }
 //--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class InputImageType>
+typename InputImageType::Pointer 
+clitk::ResampleImageSpacing(typename InputImageType::Pointer input, 
+                            typename InputImageType::SpacingType spacing, 
+                            int interpolationType)
+{
+  typedef clitk::ResampleImageWithOptionsFilter<InputImageType> ResampleFilterType;
+  typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
+  resampler->SetInput(input);
+  resampler->SetOutputSpacing(spacing);
+  typename ResampleFilterType::InterpolationTypeEnumeration inter=ResampleFilterType::NearestNeighbor;
+  switch(interpolationType) {
+  case 0: inter = ResampleFilterType::NearestNeighbor; break;
+  case 1: inter = ResampleFilterType::Linear; break;
+  case 2: inter = ResampleFilterType::BSpline; break;
+  case 3: inter = ResampleFilterType::B_LUT; break;
+  case 4: inter = ResampleFilterType::WSINC; break;
+  }
+  resampler->SetInterpolationType(inter);
+  resampler->SetGaussianFilteringEnabled(true);
+  resampler->Update();
+  return resampler->GetOutput();
+}
+//--------------------------------------------------------------------