X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=filters%2FclitkBinarizeImageGenericFilter.txx;h=a35a7304c802c4e5e63b2e6418af4a74afdbcf5f;hb=32def8dc2a3a571a7e34ac76355800c9e69c4f6a;hp=6d8d4e7b7d0e5622d3fbea866a7bb89730f3f568;hpb=2b7d488baad476881e322f58ceab4669ebe961f9;p=clitk.git

diff --git a/filters/clitkBinarizeImageGenericFilter.txx b/filters/clitkBinarizeImageGenericFilter.txx
index 6d8d4e7..a35a730 100644
--- a/filters/clitkBinarizeImageGenericFilter.txx
+++ b/filters/clitkBinarizeImageGenericFilter.txx
@@ -1,19 +1,30 @@
-#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
 {
@@ -22,9 +33,9 @@ namespace clitk
   template<class args_info_type>
   BinarizeImageGenericFilter<args_info_type>::BinarizeImageGenericFilter():
     ImageToImageGenericFilter<Self>("Binarize") {
-    //    InitializeImageType<2>();
+    InitializeImageType<2>();
     InitializeImageType<3>();
-    //InitializeImageType<4>();
+    InitializeImageType<4>();
   }
   //--------------------------------------------------------------------
 
@@ -33,10 +44,7 @@ namespace clitk
   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);
-    //ADD_IMAGE_TYPE(Dim, int);
-    //ADD_IMAGE_TYPE(Dim, float);
+    ADD_DEFAULT_IMAGE_TYPES(Dim);
   }
   //--------------------------------------------------------------------
   
@@ -46,7 +54,6 @@ namespace clitk
   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) {
@@ -70,75 +77,75 @@ namespace clitk
     // Reading input
     typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
 
-    // Check option
-    if (!mArgsInfo.useFG_flag && !mArgsInfo.useBG_flag) {
-      // Do nothing !!
-      std::cerr << "Warning : FG and BG are not used ! Do nothing." << std::endl;
-      this->template SetNextOutput<InputImageType>(input);
-      return;
-    }
-
     // Main filter
     typedef typename InputImageType::PixelType PixelType;
-    typedef itk::Image<int, InputImageType::ImageDimension> OutputImageType;
+    typedef itk::Image<char, InputImageType::ImageDimension> OutputImageType;
 
     // Filter
     typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
     typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
     thresholdFilter->SetInput(input);
-
-    /*    if (mArgsInfo.useFG_flag && !mArgsInfo.useBG_flag) {
-      DD("inverse");
-      // double fg = mArgsInfo.fg_arg;
-      //mArgsInfo.fg_arg = mArgsInfo.bg_arg;
-      // mArgsInfo.bg_arg = fg;
-       //   bool lo = mArgsInfo.lower_given;
-       //mArgsInfo.lower_given = mArgsInfo.upper_given;
-       //mArgsInfo.upper_given = lo;
-       }*/
-
+    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.useFG_flag);
-    DD(mArgsInfo.useBG_flag);
-
-    thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
-    thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
-
-    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) {
+    // 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);
+
+// <<<<<<< clitkBinarizeImageGenericFilter.txx
+//     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();
+      //>>>>>>> 1.5
       typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
-      // Write/Save results
       this->template SetNextOutput<OutputImageType>(outputImage);
     }
     else {
       typename InputImageType::Pointer outputImage;
-      if (mArgsInfo.useBG_flag) {
-	DD("use BG");
+      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->Update();
 	maskFilter->SetOutsideValue(mArgsInfo.bg_arg);
+	maskFilter->Update();
 	outputImage = maskFilter->GetOutput();
       }
       else {
-	DD("use FG");
 	typedef itk::MaskNegatedImageFilter<InputImageType,OutputImageType> maskFilterType;
 	typename maskFilterType::Pointer maskFilter = maskFilterType::New();
 	maskFilter->SetInput1(input);