--- /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
+======================================================================-====*/
+
+// clitk
+#include "clitkBinarizeImage_ggo.h"
+#include "clitkBinarizeImageGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+ // Init command line
+ GGO(clitkBinarizeImage, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::BinarizeImageGenericFilter<args_info_clitkBinarizeImage> FilterType;
+ FilterType::Pointer filter = FilterType::New();
+
+ filter->SetArgsInfo(args_info);
+ filter->Update();
+
+ if (filter->HasError()) {
+ std::cout << filter->GetLastError() << std::endl;
+ }
+
+ return EXIT_SUCCESS;
+} // This is the end, my friend
+//--------------------------------------------------------------------
--- /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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