X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=filters%2FclitkBinarizeImageGenericFilter.txx;h=747412acde44b85ea32f0b6627a4af3e2c312d45;hb=0410cde2a749710c2659d4c582d9fc0c332aced6;hp=6b993e56ae97e7f73656a29e615823013150d847;hpb=894303629c17b343135c71a151bc911e96aedfb8;p=clitk.git

diff --git a/filters/clitkBinarizeImageGenericFilter.txx b/filters/clitkBinarizeImageGenericFilter.txx
index 6b993e5..747412a 100644
--- a/filters/clitkBinarizeImageGenericFilter.txx
+++ b/filters/clitkBinarizeImageGenericFilter.txx
@@ -10,7 +10,10 @@
  * 
  ===================================================*/
 
+// itk include
+#include "itkBinaryThresholdImageFilter.h"
 #include "itkMaskImageFilter.h"
+#include "itkMaskNegatedImageFilter.h"
 
 namespace clitk
 {
@@ -19,9 +22,9 @@ 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>();
   }
   //--------------------------------------------------------------------
 
@@ -30,10 +33,10 @@ 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, char);
     ADD_IMAGE_TYPE(Dim, short);
-    //ADD_IMAGE_TYPE(Dim, int);
-    //ADD_IMAGE_TYPE(Dim, float);
+    ADD_IMAGE_TYPE(Dim, int);
+    ADD_IMAGE_TYPE(Dim, float);
   }
   //--------------------------------------------------------------------
   
@@ -43,7 +46,6 @@ 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) {
@@ -66,60 +68,86 @@ namespace clitk
 
     // 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;
+    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.setFG_flag) {
-      double fg = mArgsInfo.fg_arg;
-      mArgsInfo.fg_arg = mArgsInfo.bg_arg;
-      mArgsInfo.bg_arg = fg;
-    }
-
-    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);
-
     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 (0) {
-      if (mArgsInfo.setBG_flag || mArgsInfo.setFG_flag) {
-        DD("set BG!!!!");
-        //if ()
-        typedef itk::MaskImageFilter<InputImageType,OutputImageType> maskFilterType;
-        typename maskFilterType::Pointer maskFilter = maskFilterType::New();
-        maskFilter->SetInput1(input);
-        maskFilter->SetInput2(thresholdFilter->GetOutput());
-        maskFilter->Update();
-        typename InputImageType::Pointer outputImage = maskFilter->GetOutput();
-        // Write/Save results
-        this->template SetNextOutput<InputImageType>(outputImage);
-      }
+ 
+    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);
+
+// <<<<<<< 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();
+      this->template SetNextOutput<OutputImageType>(outputImage);
     }
     else {
-      typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
+      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<OutputImageType>(outputImage);
+      this->template SetNextOutput<InputImageType>(outputImage);
     }
   }
   //--------------------------------------------------------------------