Merge branch 'master' of git.creatis.insa-lyon.fr:clitk

[clitk.git] / tools / clitkBinarizeImageGenericFilter.cxx

diff --git a/tools/clitkBinarizeImageGenericFilter.cxx b/tools/clitkBinarizeImageGenericFilter.cxx
index 6e5a5f4c409a210e96ce3826ee39bd711c720d2d..46f846b0e772cc2ed3aad24ac683b445f5225da7 100644 (file)
--- a/tools/clitkBinarizeImageGenericFilter.cxx
+++ b/tools/clitkBinarizeImageGenericFilter.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 clitkBinarizeImageGenericFilter_cxx
 #define clitkBinarizeImageGenericFilter_cxx
 
@@ -29,4 +29,116 @@
 
 #include "clitkBinarizeImageGenericFilter.h"
 
+// itk include
+#include "itkBinaryThresholdImageFilter.h"
+#include "itkMaskImageFilter.h"
+#include "itkMaskNegatedImageFilter.h"
+
+#include <clitkCommon.h>
+
+namespace clitk
+{
+
+//--------------------------------------------------------------------
+BinarizeImageGenericFilter::BinarizeImageGenericFilter():
+  ImageToImageGenericFilter<Self>("BinarizeImage")
+{
+  InitializeImageType<2>();
+  InitializeImageType<3>();
+  InitializeImageType<4>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<unsigned int Dim>
+void BinarizeImageGenericFilter::InitializeImageType()
+{
+  ADD_DEFAULT_IMAGE_TYPES(Dim);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void BinarizeImageGenericFilter::SetArgsInfo(const args_info_type & a)
+{
+  mArgsInfo=a;
+  if (mArgsInfo.verbose_given)
+    SetIOVerbose(mArgsInfo.verbose_flag);
+  if (mArgsInfo.imagetypes_given && mArgsInfo.imagetypes_flag)
+    this->PrintAvailableImageTypes();
+
+  if (mArgsInfo.input_given) {
+    SetInputFilename(mArgsInfo.input_arg);
+  }
+  if (mArgsInfo.output_given) {
+    SetOutputFilename(mArgsInfo.output_arg);
+  }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class InputImageType>
+void
+BinarizeImageGenericFilter::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));
+
+  /* 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();
+    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_cxx