+++ /dev/null
-/*=========================================================================
- 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_cxx
-#define clitkBinarizeImageGenericFilter_cxx
-
-/* =================================================
- * @file clitkBinarizeImageGenericFilter.cxx
- * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
- * @date 29 june 2009
- *
- * @brief
- *
- ===================================================*/
-
-#include "clitkBinarizeImageGenericFilter.h"
-
-#endif //#define clitkBinarizeImageGenericFilter_cxx
+++ /dev/null
-/*=========================================================================
- 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_H
-#define CLITKBINARIZEIMAGEGENERICFILTER_H
-
-#include "clitkIO.h"
-#include "clitkImageToImageGenericFilter.h"
-
-//--------------------------------------------------------------------
-namespace clitk
-{
-
- template<class args_info_type>
- class ITK_EXPORT BinarizeImageGenericFilter:
- public ImageToImageGenericFilter<BinarizeImageGenericFilter<args_info_type> >
- {
-
- public:
-
- //--------------------------------------------------------------------
- BinarizeImageGenericFilter();
-
- //--------------------------------------------------------------------
- typedef BinarizeImageGenericFilter Self;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
-
- //--------------------------------------------------------------------
- // Method for creation through the object factory
- // and Run-time type information (and related methods)
- itkNewMacro(Self);
- itkTypeMacro(BinarizeImageGenericFilter, LightObject);
-
- //--------------------------------------------------------------------
- void SetArgsInfo(const args_info_type & a);
-
- //--------------------------------------------------------------------
- // Main function called each time the filter is updated
- template<class InputImageType>
- void UpdateWithInputImageType();
-
- protected:
- template<unsigned int Dim> void InitializeImageType();
- args_info_type mArgsInfo;
-
- }; // end class
- //--------------------------------------------------------------------
-
-} // end namespace clitk
-//--------------------------------------------------------------------
-
-//--------------------------------------------------------------------
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "clitkBinarizeImageGenericFilter.txx"
-#endif
-//--------------------------------------------------------------------
-
-#endif // #define clitkBinarizeImageGenericFilter_h
+++ /dev/null
-/*=========================================================================
- 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>();
- InitializeImageType<4>();
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class args_info_type>
-template<unsigned int Dim>
-void BinarizeImageGenericFilter<args_info_type>::InitializeImageType()
-{
- ADD_DEFAULT_IMAGE_TYPES(Dim);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-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);
- }
- 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();
- //>>>>>>> 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
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