X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=itk%2FclitkAutoCropFilter.txx;h=e31e424d43bb2ce99d25889edf74b25464aa048b;hb=ad4ece7dc0107e7ed2dfff895321a02f5051bce9;hp=46e35879d61866db3a03c38b6dc6fd856e31b0b4;hpb=13ddd066e351ce733c75d38d0fb018bb6dba34b9;p=clitk.git

diff --git a/itk/clitkAutoCropFilter.txx b/itk/clitkAutoCropFilter.txx
index 46e3587..e31e424 100644
--- a/itk/clitkAutoCropFilter.txx
+++ b/itk/clitkAutoCropFilter.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
@@ -14,14 +14,13 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-  ======================================================================-====*/
+  ===========================================================================**/
 
 #ifndef CLITKAUTOCROPFILTER_TXX
 #define CLITKAUTOCROPFILTER_TXX
 
 // clitk
 #include "clitkCommon.h"
-#include "clitkSegmentationUtils.h"
 
 // itk
 #include "itkAutoCropLabelMapFilter.h"
@@ -29,34 +28,36 @@
 #include "itkLabelImageToLabelMapFilter.h"
 #include "itkLabelMapToLabelImageFilter.h"
 #include "itkRegionOfInterestImageFilter.h"
+#include "itkExtractImageFilter.h"
 
 namespace clitk {
 
   //--------------------------------------------------------------------
-  template <class TImageType>
-  AutoCropFilter<TImageType>::
-  AutoCropFilter():itk::ImageToImageFilter<TImageType, TImageType>() {
+  template <class ImageType>
+  AutoCropFilter<ImageType>::
+  AutoCropFilter():itk::ImageToImageFilter<ImageType, ImageType>() {
     this->SetNumberOfRequiredInputs(1);
     m_BackgroundValue  = 0;
+    UseBorderOff();
   }
   //--------------------------------------------------------------------
 
 
   //--------------------------------------------------------------------
-  template <class TImageType>
+  template <class ImageType>
   void 
-  AutoCropFilter<TImageType>::
-  SetInput(const TImageType * image) {
+  AutoCropFilter<ImageType>::
+  SetInput(const ImageType * image) {
     // Process object is not const-correct so the const casting is required.
-    this->SetNthInput(0, const_cast<TImageType *>( image ));
+    this->SetNthInput(0, const_cast<ImageType *>( image ));
   }
   //--------------------------------------------------------------------
   
 
   //--------------------------------------------------------------------
-  template <class TImageType>
+  template <class ImageType>
   void 
-  AutoCropFilter<TImageType>::  
+  AutoCropFilter<ImageType>::  
   SetBackgroundValue(ImagePixelType p) {
     m_BackgroundValue = p;
   }
@@ -64,9 +65,9 @@ namespace clitk {
 
 
   //--------------------------------------------------------------------
-  template <class TImageType>
+  template <class ImageType>
   void 
-  AutoCropFilter<TImageType>::
+  AutoCropFilter<ImageType>::
   GenerateOutputInformation() {    
 
     // Superclass
@@ -94,6 +95,16 @@ namespace clitk {
     typedef itk::AutoCropLabelMapFilter<LabelMapType> AutoCropFilterType;
     typename AutoCropFilterType::Pointer autoCropFilter = AutoCropFilterType::New();
     autoCropFilter->SetInput(imageToLabelFilter->GetOutput());
+    //    autoCropFilter->ReleaseDataFlagOff(); 
+    if (GetUseBorder()) {
+      DD("Crop UseBorder : not correctly implemented do not use (use PadLabelMapFilter)");
+      // http://www.itk.org/Doxygen/html/classitk_1_1AutoCropLabelMapFilter.html#a54f49fdff8d9f2d2313134109d510285
+      exit(0); 
+      typename ImageType::SizeType s;
+      for(uint i=0; i<ImageType::ImageDimension; i++) s[i] = 1;
+      autoCropFilter->SetCropBorder(s);
+    }
+    autoCropFilter->ReleaseDataFlagOn(); 
 
     // Convert to LabelImage
     typedef itk::LabelMapToLabelImageFilter<LabelMapType, ImageType> MapToImageFilterType;
@@ -106,6 +117,15 @@ namespace clitk {
 
     // Update the output size
     m_Region = m_labeImage->GetLargestPossibleRegion();
+    // Sometimes the index is 9223372036854775807 ???
+    if (m_Region.GetIndex()[0] > 99999) {
+      std::cerr << "Warning !! BUG int clitkAutoCropFilter ?" << std::endl;
+      typename ImageType::IndexType index; 
+      index.Fill(0);
+      m_Region.SetIndex(index);
+    }
+
+    // Set the region to output
     output->SetLargestPossibleRegion(m_Region);
     output->SetRequestedRegion(m_Region);
     output->SetBufferedRegion(m_Region);
@@ -114,18 +134,24 @@ namespace clitk {
   //--------------------------------------------------------------------
    
   //--------------------------------------------------------------------
-  template <class TImageType>
+  template <class ImageType>
   void 
-  AutoCropFilter<TImageType>::
+  AutoCropFilter<ImageType>::
   GenerateData() {
     // Get input pointers
     ImageConstPointer input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
   
-    // Extract the region
+    // Extract the region with RegionOfInterestImageFilter or ExtractImageFilter ? 
+    // The second is when reducing the nb of dimension (index always zero)
+    // The first keep index. 
+    // OLD : typedef itk::ExtractImageFilter<ImageType, ImageType> CropFilterType;
+    // OLD : cropFilter->SetExtractionRegion(m_Region);
+
     typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
     m_labeImage->SetRequestedRegion(m_labeImage->GetLargestPossibleRegion());
     typename CropFilterType::Pointer cropFilter = CropFilterType::New();
     cropFilter->SetInput(m_labeImage);
+    cropFilter->SetReleaseDataFlag(this->GetReleaseDataFlag());
     cropFilter->SetRegionOfInterest(m_Region);
 
     // Go !