X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=itk%2FclitkCropLikeImageFilter.txx;h=e7e342fce498464947a9dd841aad4cb54da0cf29;hb=HEAD;hp=8b90fe30e704a1b1b61454608b01c477ceda89d6;hpb=709d3deddba827afcff948a7ebfe8d4908e72f8f;p=clitk.git

diff --git a/itk/clitkCropLikeImageFilter.txx b/itk/clitkCropLikeImageFilter.txx
index 8b90fe3..e7e342f 100644
--- a/itk/clitkCropLikeImageFilter.txx
+++ b/itk/clitkCropLikeImageFilter.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
@@ -14,16 +14,14 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-  ======================================================================-====*/
+  ===========================================================================**/
 
 #ifndef CLITKCROPLIKEIMAGEFILTER_TXX
 #define CLITKCROPLIKEIMAGEFILTER_TXX
 
 // clitk
 #include "clitkCommon.h"
-
-// itk
-#include "itkPasteImageFilter.h"
+#include "clitkPasteImageFilter.h"
 
 //--------------------------------------------------------------------
 template <class ImageType>
@@ -32,7 +30,7 @@ CropLikeImageFilter():itk::ImageToImageFilter<ImageType, ImageType>() {
   this->SetNumberOfRequiredInputs(1);
   m_LikeImage = NULL;
   m_LikeFilenameIsGiven = false;
-  this->SetBackgroundValue(0);
+  this->SetBackgroundValue(typename PixelTraits<typename ImageType::PixelType>::ValueType(0));
   m_CropAlongThisDimension.resize(ImageType::ImageDimension);
   for(uint i=0; i<ImageType::ImageDimension; i++)
     m_CropAlongThisDimension[i] = true;
@@ -93,8 +91,7 @@ GenerateInputRequestedRegion() {
 template <class ImageType>
 void 
 clitk::CropLikeImageFilter<ImageType>::
-GenerateOutputInformation() {    
-  DD("GenerateOutputInformation");
+GenerateOutputInformation() {   
   // Get input pointers
   ImageConstPointer input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
     
@@ -106,11 +103,17 @@ GenerateOutputInformation() {
   typename ImageType::IndexType likeStart;
   typename ImageType::PointType likeOrigin;  
   typename ImageType::SpacingType likeSpacing;  
+  typename ImageType::DirectionType likeDirection;
+  typename ImageType::DirectionType like_invDirection;
   if (m_LikeImage) {   
     likeSize = m_LikeImage->GetLargestPossibleRegion().GetSize();
     likeStart = m_LikeImage->GetLargestPossibleRegion().GetIndex();
     likeOrigin = m_LikeImage->GetOrigin();
     likeSpacing = m_LikeImage->GetSpacing();
+    likeDirection = m_LikeImage->GetDirection();
+    //I don't know really why I need the inverse...
+    like_invDirection = likeDirection.GetInverse();
+    //output->CopyInformation(m_LikeImage);
   }
   else {
     // Only load the header (allows to use 'like' with any image type)
@@ -121,8 +124,12 @@ GenerateOutputInformation() {
         likeStart[i] = 0;//header->GetIORegion().GetIndex()[i];
         likeOrigin[i] = header->GetOrigin(i);
         likeSpacing[i] = header->GetSpacing(i);
+        for(unsigned int j=0; j<ImageType::ImageDimension; j++)
+            likeDirection[i][j] = header->GetDirection(i)[j];
+       }
+      //I don't know really why I need the inverse...
+      like_invDirection = likeDirection.GetInverse();
       }
-    }
     else {
       clitkExceptionMacro("You should provide SetCropLikeFilename or SetCropLike to CropLikeImageFilter");
     }
@@ -132,10 +139,20 @@ GenerateOutputInformation() {
   for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
     if (likeSpacing[i] != input->GetSpacing()[i]) {
       clitkExceptionMacro("Images must have the same spacing, but input's spacing(" << i
-                          <<") is " << input->GetSpacing()[i] << " while like's spacing(" << i 
-                          << ") is " << likeSpacing[i] << ".");
+                          <<") is " << input->GetSpacing()[i] << " while the spacing(" << i 
+                          << ") of 'like' is " << likeSpacing[i] << ".");
+    }
+  }
+
+  // Check that we must crop along each dimension. If not, we use the
+  // size of the input image
+  for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
+    if (m_CropAlongThisDimension[i] == false) {
+      likeStart[i] = input->GetLargestPossibleRegion().GetIndex()[i];
+      likeSize[i] = input->GetLargestPossibleRegion().GetSize()[i];
     }
   }
+
   // Define output region 
   m_OutputRegion.SetIndex(likeStart);
   m_OutputRegion.SetSize(likeSize);
@@ -144,6 +161,8 @@ GenerateOutputInformation() {
   output->SetBufferedRegion(m_OutputRegion);
   output->SetSpacing(likeSpacing);  
   output->SetOrigin(likeOrigin);
+  output->SetDirection(like_invDirection);
+  output->Allocate(); // Needed ?
 
   // get startpoint source/dest
   // for each dim
@@ -199,6 +218,7 @@ GenerateOutputInformation() {
   for(int i=0; i<ImageType::ImageDimension; i++)
     s[i] = m_StopSourceIndex[i]-m_StartSourceIndex[i];
   m_Region.SetSize(s);
+
 }
 //--------------------------------------------------------------------
    
@@ -212,12 +232,14 @@ GenerateData() {
 
   // Get output pointer, fill with Background
   ImagePointer output = this->GetOutput(0);
-  output->Allocate();
+  
   output->FillBuffer(GetBackgroundValue());
   
   // Paste image inside
-  typedef itk::PasteImageFilter<ImageType,ImageType> PasteFilterType;
+  typedef clitk::PasteImageFilter<ImageType,ImageType> PasteFilterType;
   typename PasteFilterType::Pointer pasteFilter = PasteFilterType::New();
+  //pasteFilter->ReleaseDataFlagOn(); // change nothing ?
+  //  pasteFilter->InPlaceOn(); // makt it seg fault
   pasteFilter->SetSourceImage(input);
   pasteFilter->SetDestinationImage(output);
   pasteFilter->SetDestinationIndex(m_StartDestIndex);
@@ -225,10 +247,63 @@ GenerateData() {
   pasteFilter->Update();
 
   // Get (graft) output (SetNthOutput does not fit here because of Origin).
-  //  this->GraftOutput(cropFilter->GetOutput());
   this->GraftOutput(pasteFilter->GetOutput());
 }
 //--------------------------------------------------------------------
    
- 
-#endif //#define CLITKAUTOCROPFILTER
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer
+clitk::ResizeImageLike(const ImageType * input,                       
+                       const itk::ImageBase<ImageType::ImageDimension> * like, 
+                       typename ImageType::PixelType backgroundValue) 
+{
+  typedef clitk::CropLikeImageFilter<ImageType> CropFilterType;
+  typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+  cropFilter->SetInput(input);
+  cropFilter->SetCropLikeImage(like);
+  cropFilter->SetBackgroundValue(backgroundValue);
+  cropFilter->Update();
+  return cropFilter->GetOutput();  
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer
+clitk::ResizeImageLike(const ImageType * input,                       
+                       typename itk::ImageBase<ImageType::ImageDimension>::RegionType * region, 
+                       typename ImageType::PixelType backgroundValue) 
+{
+  typename ImageType::Pointer output = ImageType::New();
+  output->CopyInformation(input);
+  typename ImageType::RegionType reg;
+  reg.SetIndex(region->GetIndex());
+  reg.SetSize(region->GetSize());
+  output->SetRegions(reg);
+  output->Allocate();
+  return clitk::ResizeImageLike<ImageType>(input, output, backgroundValue);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer
+clitk::ResizeImageLike(const ImageType * input, 
+                       typename itk::BoundingBox<unsigned long, ImageType::ImageDimension>::Pointer bb, 
+                       typename ImageType::PixelType BG)
+{
+  typename ImageType::RegionType region;
+  clitk::ComputeRegionFromBB<ImageType>(input, bb, region);
+  typename ImageType::Pointer output = ImageType::New();
+  output->CopyInformation(input);
+  output->SetRegions(region);
+  output->Allocate();
+  return clitk::ResizeImageLike<ImageType>(input, output, BG);   
+}
+//--------------------------------------------------------------------
+
+#endif //#define CLITKCROPLIKEIMAGEFILTER_TXX