X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=filters%2FclitkBinarizeImageGenericFilter.txx;h=61a427733a50876db4d6e4e2fc999c95b838d1a8;hb=f1016340d797dbe6e0672e6e06a583baaafc738b;hp=38f7725a06f8e47f46c5d89ae7b1743435659be9;hpb=62e27d7c139840bc8c62eff63792b6b765a10da2;p=clitk.git

diff --git a/filters/clitkBinarizeImageGenericFilter.txx b/filters/clitkBinarizeImageGenericFilter.txx
index 38f7725..61a4277 100644
--- a/filters/clitkBinarizeImageGenericFilter.txx
+++ b/filters/clitkBinarizeImageGenericFilter.txx
@@ -1,100 +1,168 @@
-#ifndef clitkBinarizeImageGenericFilter_txx
-#define clitkBinarizeImageGenericFilter_txx
-
-/* =================================================
- * @file   clitkBinarizeImageGenericFilter.txx
- * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
- * @date   29 june 2009
- * 
- * @brief 
- * 
- ===================================================*/
+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  Authors belong to:
+  - University of LYON              http://www.universite-lyon.fr/
+  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the copyright notices for more information.
+
+  It is distributed under dual licence
+
+  - BSD        See included LICENSE.txt file
+  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+======================================================================-====*/
+
+#ifndef CLITKBINARIZEIMAGEGENERICFILTER_TXX
+#define CLITKBINARIZEIMAGEGENERICFILTER_TXX
+
+// itk include
+#include "itkBinaryThresholdImageFilter.h"
+#include "itkMaskImageFilter.h"
+#include "itkMaskNegatedImageFilter.h"
+
+#include <clitkCommon.h>
+// #include <tiff.h>
 
 namespace clitk
 {
-  
-  //--------------------------------------------------------------------
-  template<class args_info_type>
-  BinarizeImageGenericFilter<args_info_type>::BinarizeImageGenericFilter():
-    ImageToImageGenericFilter<Self>("Binarize") {
-    InitializeImageType<2>();
-    InitializeImageType<3>();
-  }
-  //--------------------------------------------------------------------
 
+//--------------------------------------------------------------------
+template<class args_info_type>
+BinarizeImageGenericFilter<args_info_type>::BinarizeImageGenericFilter():
+  ImageToImageGenericFilter<Self>("Binarize")
+{
+  InitializeImageType<2>();
+  InitializeImageType<3>();
+  InitializeImageType<4>();
+}
+//--------------------------------------------------------------------
 
-  //--------------------------------------------------------------------
-  template<class args_info_type>
-  template<unsigned int Dim>
-  void BinarizeImageGenericFilter<args_info_type>::InitializeImageType() {      
-    ADD_IMAGE_TYPE(Dim, char);
-    ADD_IMAGE_TYPE(Dim, short);
-  }
-  //--------------------------------------------------------------------
-  
 
-  //--------------------------------------------------------------------
-  template<class args_info_type>
-  void BinarizeImageGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a) {
-    mArgsInfo=a;
-    SetIOVerbose(mArgsInfo.verbose_flag);
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<unsigned int Dim>
+void BinarizeImageGenericFilter<args_info_type>::InitializeImageType()
+{
+  ADD_DEFAULT_IMAGE_TYPES(Dim);
+}
+//--------------------------------------------------------------------
 
-    if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
 
-    if (mArgsInfo.input_given) {
-      SetInputFilename(mArgsInfo.input_arg);
-    }
-    if (mArgsInfo.output_given) {
-      SetOutputFilename(mArgsInfo.output_arg);
-    }
+//--------------------------------------------------------------------
+template<class args_info_type>
+void BinarizeImageGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
+{
+  mArgsInfo=a;
+  SetIOVerbose(mArgsInfo.verbose_flag);
+  if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+
+  if (mArgsInfo.input_given) {
+    SetInputFilename(mArgsInfo.input_arg);
   }
-  //--------------------------------------------------------------------
-
-  //--------------------------------------------------------------------
-  // Update with the number of dimensions and the pixeltype
-  //--------------------------------------------------------------------
-  template<class args_info_type>
-  template<class InputImageType>
-  void 
-  BinarizeImageGenericFilter<args_info_type>::UpdateWithInputImageType()
-  {
-
-    // Reading input
-    typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
-    
-    // Main filter
-    typedef typename InputImageType::PixelType PixelType;
-    typedef itk::Image<int, InputImageType::ImageDimension> OutputImageType;
-
-    // Filter
-    typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
-    typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
-    thresholdFilter->SetInput(input);
-    if(mArgsInfo.lower_given) thresholdFilter->SetLowerThreshold(static_cast<PixelType>(mArgsInfo.lower_arg));
-    if(mArgsInfo.upper_given) thresholdFilter->SetUpperThreshold(static_cast<PixelType>(mArgsInfo.upper_arg));
-
-    DD(mArgsInfo.lower_given);
-    DD(mArgsInfo.upper_given);
-    DD(mArgsInfo.lower_arg);
-    DD(mArgsInfo.upper_arg);
-
-    DD(mArgsInfo.inside_arg);
-    DD(mArgsInfo.outside_arg);
-    DD(mArgsInfo.inside_given);
-    DD(mArgsInfo.outside_given);
-
-    thresholdFilter->SetInsideValue(mArgsInfo.inside_arg);
-    thresholdFilter->SetOutsideValue(mArgsInfo.outside_arg);
+  if (mArgsInfo.output_given) {
+    SetOutputFilename(mArgsInfo.output_arg);
+  }
+}
+//--------------------------------------------------------------------
+
 
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<class InputImageType>
+void
+BinarizeImageGenericFilter<args_info_type>::UpdateWithInputImageType()
+{
+
+  // Reading input
+  typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
+
+  // Main filter
+  typedef typename InputImageType::PixelType PixelType;
+  typedef itk::Image<uchar, InputImageType::ImageDimension> OutputImageType;
+
+  // Filter
+  typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
+  typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
+  thresholdFilter->SetInput(input);
+  thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
+
+  if (mArgsInfo.lower_given) thresholdFilter->SetLowerThreshold(static_cast<PixelType>(mArgsInfo.lower_arg));
+  if (mArgsInfo.upper_given) thresholdFilter->SetUpperThreshold(static_cast<PixelType>(mArgsInfo.upper_arg));
+
+  // DD(mArgsInfo.lower_given);
+  // DD(mArgsInfo.upper_given);
+  // DD(mArgsInfo.lower_arg);
+  // DD(mArgsInfo.upper_arg);
+  // DD(mArgsInfo.fg_arg);
+  // DD(mArgsInfo.bg_arg);
+  // DD(mArgsInfo.fg_given);
+  // DD(mArgsInfo.bg_given);
+  // DD(mArgsInfo.mode_arg);
+
+//     DD(mArgsInfo.useFG_flag);
+//     DD(mArgsInfo.useBG_flag);
+
+//     thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
+
+//     // Keep BG value to 0 if maskFilterType is used after
+//     if (mArgsInfo.useBG_flag && mArgsInfo.useFG_flag) {
+//       thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
+//     }
+//     else {
+//       DD("0");
+//       thresholdFilter->SetOutsideValue(0);
+//     }
+
+//     // thresholdFilter->Update();
+
+//     // If no BG or no FG : new image, copy input with MaskImageFilter
+//     // If setFG -> FG BG have been changed
+//     if (mArgsInfo.useBG_flag && mArgsInfo.useFG_flag) {
+// =======
+  /* Three modes :
+     - FG -> only use FG value for pixel in the Foreground (or Inside), keep input values for outside
+     - BG -> only use BG value for pixel in the Background (or Outside), keep input values for inside
+     - both -> use FG and BG (real binary image)
+  */
+  if (mArgsInfo.mode_arg == std::string("both")) {
+    thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
     thresholdFilter->Update();
-  
-    // Write/Save results
+    //>>>>>>> 1.5
     typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
     this->template SetNextOutput<OutputImageType>(outputImage);
+  } else {
+    typename InputImageType::Pointer outputImage;
+    thresholdFilter->SetOutsideValue(0);
+    if (mArgsInfo.mode_arg == std::string("BG")) {
+      typedef itk::MaskImageFilter<InputImageType,OutputImageType> maskFilterType;
+      typename maskFilterType::Pointer maskFilter = maskFilterType::New();
+      maskFilter->SetInput1(input);
+      maskFilter->SetInput2(thresholdFilter->GetOutput());
+      maskFilter->SetOutsideValue(mArgsInfo.bg_arg);
+      maskFilter->Update();
+      outputImage = maskFilter->GetOutput();
+    } else {
+      typedef itk::MaskNegatedImageFilter<InputImageType,OutputImageType> maskFilterType;
+      typename maskFilterType::Pointer maskFilter = maskFilterType::New();
+      maskFilter->SetInput1(input);
+      maskFilter->SetInput2(thresholdFilter->GetOutput());
+      maskFilter->SetOutsideValue(mArgsInfo.fg_arg);
+      maskFilter->Update();
+      outputImage = maskFilter->GetOutput();
+    }
+    // Write/Save results
+    this->template SetNextOutput<InputImageType>(outputImage);
   }
-  //--------------------------------------------------------------------
+}
+//--------------------------------------------------------------------
 
 
 }//end clitk
- 
+
 #endif //#define clitkBinarizeImageGenericFilter_txx