X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkCropImageGenericFilter.cxx;h=0e2818ac67e4d3584e20891545aa37d641ce0fba;hb=f49bf3a44e6deb7f840f4f63d5609206c0042b09;hp=7e37c1cfaf984660eeba18d666c1c63bbba40d10;hpb=a26cd8a19e1b9ad8344ab501436045f171a73713;p=clitk.git

diff --git a/tools/clitkCropImageGenericFilter.cxx b/tools/clitkCropImageGenericFilter.cxx
old mode 100755
new mode 100644
index 7e37c1c..0e2818a
--- a/tools/clitkCropImageGenericFilter.cxx
+++ b/tools/clitkCropImageGenericFilter.cxx
@@ -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
@@ -14,59 +14,186 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+===========================================================================**/
 #ifndef clitkCropImageGenericFilter_cxx
 #define clitkCropImageGenericFilter_cxx
 
-/* =================================================
- * @file   clitkCropImageGenericFilter.cxx
- * @author 
- * @date   
- * 
- * @brief 
- * 
- ===================================================*/
-
 #include "clitkCropImageGenericFilter.h"
 
+//-----------------------------------------------------------
+// Constructor
+//-----------------------------------------------------------
+clitk::CropImageGenericFilter::CropImageGenericFilter():
+  ImageToImageGenericFilter<Self>("CropImage")
+{
+  cmdline_parser_clitkCropImage_init(&mArgsInfo);
+  InitializeImageType<2>();
+  InitializeImageType<3>();
+  InitializeImageType<4>();
+}
+
+//--------------------------------------------------------------------
+template<unsigned int Dim>
+void clitk::CropImageGenericFilter::InitializeImageType()
+{
+  ADD_DEFAULT_IMAGE_TYPES(Dim);
+  ADD_DEFAULT_VEC_IMAGE_TYPES;
+}
+//--------------------------------------------------------------------
 
-namespace clitk
+//--------------------------------------------------------------------
+void clitk::CropImageGenericFilter::SetArgsInfo(const args_info_type& a)
+{
+  mArgsInfo=a;
+  SetIOVerbose(mArgsInfo.verbose_flag);
+  if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+  if (mArgsInfo.input_given)   AddInputFilename(mArgsInfo.input_arg);
+  if (mArgsInfo.output_given)  AddOutputFilename(mArgsInfo.output_arg);
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class ImageType>
+typename clitk::CropImageGenericFilter::AutoCrop<ImageType>::ImagePointer
+clitk::CropImageGenericFilter::AutoCrop<ImageType>::Do(args_info_type &argsInfo, ImagePointer input)
+{
+  static const unsigned int PixelDimension = itk::PixelTraits<typename ImageType::PixelType>::Dimension;
+  return this->Do(argsInfo, input, static_cast< PixelDimType<PixelDimension> *>(NULL) );
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class ImageType>
+template<unsigned int Dim>
+typename clitk::CropImageGenericFilter::AutoCrop<ImageType>::ImagePointer
+clitk::CropImageGenericFilter::AutoCrop<ImageType>::Do(args_info_type &, ImagePointer, PixelDimType<Dim> *)
+{
+  clitkExceptionMacro("Autocrop is not implemented for vector fields");
+  return NULL;
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class ImageType>
+typename clitk::CropImageGenericFilter::AutoCrop<ImageType>::ImagePointer
+clitk::CropImageGenericFilter::AutoCrop<ImageType>::Do(args_info_type &argsInfo, ImagePointer input, PixelDimType<1> *)
+{
+  if (argsInfo.boundingBox_given)
+    clitkExceptionMacro("Do not use --BG and --boundingBox at the same time");
+  if (argsInfo.lower_given)
+    clitkExceptionMacro("Do not use --BG and --lower at the same time");
+  if (argsInfo.upper_given)
+    clitkExceptionMacro("Do not use --BG and --upper at the same time");
+  typedef clitk::AutoCropFilter<ImageType> FilterType;
+  typename FilterType::Pointer filter = FilterType::New();
+  filter->SetInput(input);
+  filter->SetBackgroundValue(argsInfo.BG_arg);
+  filter->Update();
+  return filter->GetOutput();
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ImageType>
+void clitk::CropImageGenericFilter::UpdateWithInputImageType()
 {
+  // Reading input
+  typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
+  typename ImageType::RegionType input_region = input->GetLargestPossibleRegion();
 
+  // Check options
+  if (mArgsInfo.BG_given && mArgsInfo.like_given)
+    clitkExceptionMacro("Do not use --BG and --like at the same time");
 
-  //-----------------------------------------------------------
-  // Constructor
-  //-----------------------------------------------------------
-  CropImageGenericFilter::CropImageGenericFilter()
-  {
-    m_Verbose=false;
-    m_InputFileName="";
-  }
+  // Prepare output
+  typename ImageType::Pointer output;
 
+  // ------------------------------------------------
+  if (mArgsInfo.BG_given) { // AutoCrop filter
+    AutoCrop<ImageType> autoCrop;
+    output = autoCrop.Do(mArgsInfo, input);
+  }
+  else {
+    // ------------------------------------------------
+    if (mArgsInfo.like_given) { // CropLike filter
+    if (mArgsInfo.boundingBox_given)
+      clitkExceptionMacro("Do not use --like and --boundingBox at the same time");
+    if (mArgsInfo.lower_given)
+      clitkExceptionMacro("Do not use --like and --lower at the same time");
+    if (mArgsInfo.upper_given)
+      clitkExceptionMacro("Do not use --like and --upper at the same time");
+      typedef clitk::CropLikeImageFilter<ImageType> FilterType;
+      typename FilterType::Pointer filter = FilterType::New();
+      filter->SetInput(input);
+      filter->SetCropLikeFilename(mArgsInfo.like_arg);
+      filter->SetBackgroundValue(mArgsInfo.BGLike_arg);
+      filter->Update();
+      output = filter->GetOutput();
+    }
+    else {
+      // ------------------------------------------------
+      typename ImageType::SizeType lSize;
+      typename ImageType::SizeType uSize;
+      if (mArgsInfo.verbose_flag) std::cout << "input region " << input_region << std::endl;
+      if (mArgsInfo.boundingBox_given) {
+        for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
+          lSize[i] = mArgsInfo.boundingBox_arg[2*i];
+          uSize[i] = input_region.GetSize()[i]-mArgsInfo.boundingBox_arg[2*i+1]-1;
+        }
+      }
+      else {
+        if (mArgsInfo.lower_given) {
+          for(unsigned int i=0; i<ImageType::ImageDimension; i++)
+            lSize[i]=static_cast<unsigned int >(mArgsInfo.lower_arg[i]);
+        }
+        else lSize.Fill(0);
+        if (mArgsInfo.upper_given) {
+          for(unsigned int i=0; i<ImageType::ImageDimension; i++)
+            uSize[i]=static_cast<unsigned int >(mArgsInfo.upper_arg[i]);
+        }
+        else uSize.Fill(0);
+      }
 
-  //-----------------------------------------------------------
-  // Update
-  //-----------------------------------------------------------
-  void CropImageGenericFilter::Update()
-  {
-     // Read the Dimension and PixelType
-    int Dimension, Components;
-    std::string PixelType;
-    ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
-
-    
-    // Call UpdateWithDim
-    if(Dimension==2) UpdateWithDim<2>(PixelType, Components);
-    else if(Dimension==3) UpdateWithDim<3>(PixelType, Components);
-    else if (Dimension==4)UpdateWithDim<4>(PixelType, Components); 
-    else 
-      {
-	std::cout<<"Error, Only for 2, 3 or 4  Dimensions!!!"<<std::endl ;
-	return;
+      if (mArgsInfo.verbose_flag) {
+        std::cout << "lower " << lSize << " upper " << uSize << std::endl;
       }
+
+      typedef  itk::CropImageFilter<ImageType, ImageType> CropImageFilterType;
+      typename CropImageFilterType::Pointer filter=CropImageFilterType::New();
+      filter->SetInput(input);
+      filter->SetLowerBoundaryCropSize(lSize);
+      filter->SetUpperBoundaryCropSize(uSize);
+      filter->Update();
+      output = filter->GetOutput();
+    }
   }
 
+  // Force origin if needed
+  if (mArgsInfo.origin_flag) {
+    typename ImageType::PointType origin;
+    origin.Fill(itk::NumericTraits<double>::Zero);
+    output->SetOrigin(origin);
+  }
 
-} //end clitk
+  // adjust image origin and force index to zero
+  typename ImageType::RegionType region = output->GetLargestPossibleRegion();
+  typename ImageType::IndexType index = region.GetIndex();
+  typename ImageType::PointType origin = output->GetOrigin();
+  typename ImageType::SpacingType spacing = output->GetSpacing();
+  if (mArgsInfo.verbose_flag) std::cout << "origin before crop " << origin << std::endl;
+  input->TransformIndexToPhysicalPoint(index,origin);
+  if (mArgsInfo.verbose_flag) std::cout << "origin after crop " << origin << std::endl;
+  output->SetOrigin(origin);
+
+  index.Fill(itk::NumericTraits<double>::Zero);
+  region.SetIndex(index);
+  output->SetRegions(region);
+
+  // Write/Save results
+  this->template SetNextOutput<ImageType>(output);
+}
+//--------------------------------------------------------------------
 
 #endif  //#define clitkCropImageGenericFilter_cxx