X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkCropImageGenericFilter.cxx;h=b062976b678b4dac3abe72804dd6dbda572c81aa;hb=fdc1613169b9725128ad19aaa4c4a5c39f2920d7;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..b062976
--- 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
@@ -14,7 +14,7 @@
 
   - 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
 
@@ -37,35 +37,131 @@ namespace clitk
   //-----------------------------------------------------------
   // Constructor
   //-----------------------------------------------------------
-  CropImageGenericFilter::CropImageGenericFilter()
+  CropImageGenericFilter::CropImageGenericFilter():
+    ImageToImageGenericFilter<Self>("CropImage")
   {
-    m_Verbose=false;
-    m_InputFileName="";
+    cmdline_parser_clitkCropImage_init(&mArgsInfo);
+    InitializeImageType<2>();
+    InitializeImageType<3>();
+    InitializeImageType<4>();
   }
 
-
-  //-----------------------------------------------------------
-  // Update
-  //-----------------------------------------------------------
-  void CropImageGenericFilter::Update()
+  //--------------------------------------------------------------------
+  template<unsigned int Dim>
+  void clitk::CropImageGenericFilter::InitializeImageType()
   {
-     // Read the Dimension and PixelType
-    int Dimension, Components;
-    std::string PixelType;
-    ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
+    ADD_DEFAULT_IMAGE_TYPES(Dim);
+    //ADD_IMAGE_TYPE(Dim, uchar);
+    //ADD_IMAGE_TYPE(Dim, short);
+    // ADD_IMAGE_TYPE(Dim, uint);
+    //  ADD_IMAGE_TYPE(Dim, ulong);
+    // ADD_IMAGE_TYPE(Dim, int);
+    // ADD_IMAGE_TYPE(Dim, float);
+  }
+  //--------------------------------------------------------------------
 
+  //--------------------------------------------------------------------
+  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);
+  }
+  //--------------------------------------------------------------------
+
+  //--------------------------------------------------------------------
+  // 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);
+
+    // Check options
+    if (mArgsInfo.BG_given && mArgsInfo.like_given)
+      clitkExceptionMacro("Do not use --BG and --like at the same time");    
+
+    // Prepare output
+    typename ImageType::Pointer output;
     
-    // 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.BG_given) { // AutoCrop filter
+      if (mArgsInfo.boundingBox_given) 
+        clitkExceptionMacro("Do not use --BG and --boundingBox at the same time");    
+      if (mArgsInfo.lower_given) 
+        clitkExceptionMacro("Do not use --BG and --lower at the same time");    
+      if (mArgsInfo.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(mArgsInfo.BG_arg);
+      filter->Update();
+      output = filter->GetOutput();
+    }
+    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.boundingBox_given) {
+          for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
+            lSize[i] = mArgsInfo.boundingBox_arg[2*i];
+            uSize[i] = input->GetLargestPossibleRegion().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);
+        }
+        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);
+    }
+
+    // Write/Save results
+    this->template SetNextOutput<ImageType>(output); 
+  }
+  //--------------------------------------------------------------------
 
 } //end clitk