X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=itk%2FclitkResampleImageWithOptionsFilter.txx;h=4c949cec33eff1ade7b4fe43cfac3f4bf313a1fe;hb=7ae042efea7b958dc573948b4e27981bafa9957e;hp=7c05dc5b018644848ded74469216017e23b3769a;hpb=ff7b62d284bd4f5eadce3aff4b217ae722b369a7;p=clitk.git

diff --git a/itk/clitkResampleImageWithOptionsFilter.txx b/itk/clitkResampleImageWithOptionsFilter.txx
index 7c05dc5..4c949ce 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
@@ -14,7 +14,7 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-  ======================================================================-====*/
+  ===========================================================================**/
 
 // clitk
 #include "clitkDD.h"
@@ -37,7 +37,7 @@
 //--------------------------------------------------------------------
 template <class InputImageType, class OutputImageType>
 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
-ResampleImageWithOptionsFilter():itk::ImageToImageFilter<InputImageType, OutputImageType>() 
+ResampleImageWithOptionsFilter():itk::ImageToImageFilter<InputImageType, OutputImageType>()
 {
   static const unsigned int dim = InputImageType::ImageDimension;
   this->SetNumberOfRequiredInputs(1);
@@ -54,7 +54,10 @@ ResampleImageWithOptionsFilter():itk::ImageToImageFilter<InputImageType, OutputI
     m_OutputSpacing[i] = -1;
     m_GaussianSigma[i] = -1;
   }
+  m_OutputOrigin.Fill(0);
+  m_OutputDirection.SetIdentity();
   m_VerboseOptions = false;
+  SetDefaultPixelValue(0);
 }
 //--------------------------------------------------------------------
 
@@ -63,7 +66,7 @@ ResampleImageWithOptionsFilter():itk::ImageToImageFilter<InputImageType, OutputI
 template <class InputImageType, class OutputImageType>
 void
 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
-SetInput(const InputImageType * image) 
+SetInput(const InputImageType * image)
 {
   // Process object is not const-correct so the const casting is required.
   this->SetNthInput(0, const_cast<InputImageType *>(image));
@@ -75,7 +78,7 @@ SetInput(const InputImageType * image)
 template <class InputImageType, class OutputImageType>
 void
 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
-GenerateInputRequestedRegion() 
+GenerateInputRequestedRegion()
 {
   // call the superclass's implementation of this method
   Superclass::GenerateInputRequestedRegion();
@@ -96,7 +99,7 @@ GenerateInputRequestedRegion()
 template <class InputImageType, class OutputImageType>
 void
 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
-GenerateOutputInformation() 
+GenerateOutputInformation()
 {
   static const unsigned int dim = InputImageType::ImageDimension;
 
@@ -121,19 +124,31 @@ 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 {
+  }
+  else if(m_OutputSpacing[0]==-1 ||  m_OutputSize[0]==0){
     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 {
+    }
+    else {
       if (m_OutputSize[0] != 0) { // apply size, compute spacing
         for(unsigned int i=0; i<dim; i++) {
           m_OutputSpacing[i] = (double)inputSize[i]*inputSpacing[i]/(double)m_OutputSize[i];
         }
-      } else { // copy input size/spacing ... (no resampling)
+      }
+      else { // copy input size/spacing ... (no resampling)
         m_OutputSize = inputSize;
         m_OutputSpacing = inputSpacing;
       }
@@ -146,7 +161,7 @@ GenerateOutputInformation()
     m_OutputSize[l] = inputSize[l];
     m_OutputSpacing[l] = inputSpacing[l];
   }
-    
+
   // Set Size/Spacing
   OutputImagePointer outputImage = this->GetOutput(0);
   // OutputImageRegionType region;
@@ -179,28 +194,20 @@ GenerateOutputInformation()
 
 //--------------------------------------------------------------------
 template <class InputImageType, class OutputImageType>
-void 
+void
 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
-GenerateData() 
+GenerateData()
 {
-   
+
   // Get input pointer
   InputImagePointer input = dynamic_cast<InputImageType*>(itk::ProcessObject::GetInput(0));
   static const unsigned int dim = InputImageType::ImageDimension;
 
-  // Set regions and allocate
-  //DD(this->GetOutput()->GetLargestPossibleRegion());
-  //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);
 
   // Print options if needed
   if (m_VerboseOptions) {
@@ -221,15 +228,21 @@ GenerateData()
     std::cout << "LastDimIsTime  = " << m_LastDimensionIsTime << std::endl;
   }
 
+  // Compute origin based on image corner
+  for(unsigned int i=0; i<OutputImageType::ImageDimension; i++) {
+    m_OutputOrigin[i] -= 0.5 * input->GetSpacing()[i];
+    m_OutputOrigin[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(m_OutputOrigin);
   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)
+  filter->SetNumberOfThreads(this->GetNumberOfThreads());
+  filter->SetOutputDirection(m_OutputDirection); // <-- NEEDED if we want to keep orientation (in case of PermutAxes for example)
 
   // Select interpolator
   switch (m_InterpolationType) {
@@ -296,21 +309,16 @@ GenerateData()
   filter->Update();
 
   // Set output
-  // DD("before Graft");
-
-  //this->GraftOutput(filter->GetOutput());
-  this->SetNthOutput(0, filter->GetOutput());
-
-  // DD("after Graft");
+  this->GraftOutput(filter->GetOutput());
 }
 //--------------------------------------------------------------------
 
 
 //--------------------------------------------------------------------
 template<class InputImageType>
-typename InputImageType::Pointer 
-clitk::ResampleImageSpacing(typename InputImageType::Pointer input, 
-                            typename InputImageType::SpacingType spacing, 
+typename InputImageType::Pointer
+clitk::ResampleImageSpacing(typename InputImageType::Pointer input,
+                            typename InputImageType::SpacingType spacing,
                             int interpolationType)
 {
   typedef clitk::ResampleImageWithOptionsFilter<InputImageType> ResampleFilterType;