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
- 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
#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