#with long compilation times that are used by vv
ADD_LIBRARY(clitkImageConvertLib clitkImageConvertGenericFilter.cxx)
ADD_LIBRARY(clitkImageResampleLib clitkImageResampleGenericFilter.cxx)
+ADD_LIBRARY(clitkBinarizeImageLib clitkBinarizeImageGenericFilter.cxx)
IF (CLITK_BUILD_TOOLS)
WRAP_GGO(clitkDicomInfo_GGO_C clitkDicomInfo.ggo)
ADD_EXECUTABLE(clitkImageConvert clitkImageConvert.cxx ${clitkImageConvert_GGO_C})
TARGET_LINK_LIBRARIES(clitkImageConvert clitkImageConvertLib clitkCommon ITKIO)
+ ADD_EXECUTABLE(clitkBinarizeImage clitkBinarizeImage.cxx
+ ${clitkBinarizeImage_GGO_C})
+ TARGET_LINK_LIBRARIES(clitkBinarizeImage clitkBinarizeImageLib clitkCommon ITKIO)
+
# ADD_EXECUTABLE(clitkImageResample clitkImageResample.cxx
# ${clitkImageResample_GGO_C})
# TARGET_LINK_LIBRARIES(clitkImageResample clitkImageResampleLib clitkCommon ITKIO )
CLITK_INIT;
// Filter
- typedef clitk::BinarizeImageGenericFilter<args_info_clitkBinarizeImage> FilterType;
+ typedef clitk::BinarizeImageGenericFilter FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetArgsInfo(args_info);
#include "clitkBinarizeImageGenericFilter.h"
+// itk include
+#include "itkBinaryThresholdImageFilter.h"
+#include "itkMaskImageFilter.h"
+#include "itkMaskNegatedImageFilter.h"
+
+#include <clitkCommon.h>
+
+namespace clitk
+{
+
+//--------------------------------------------------------------------
+BinarizeImageGenericFilter::BinarizeImageGenericFilter():
+ ImageToImageGenericFilter<Self>("Binarize")
+{
+ 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;
+ 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 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
#include "clitkIO.h"
#include "clitkImageToImageGenericFilter.h"
+#include "clitkBinarizeImage_ggo.h"
//--------------------------------------------------------------------
namespace clitk
{
- template<class args_info_type>
class ITK_EXPORT BinarizeImageGenericFilter:
- public ImageToImageGenericFilter<BinarizeImageGenericFilter<args_info_type> >
+ public ImageToImageGenericFilter<BinarizeImageGenericFilter>
{
public:
typedef BinarizeImageGenericFilter Self;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
+ typedef args_info_clitkBinarizeImage args_info_type;
//--------------------------------------------------------------------
// Method for creation through the object factory
} // 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
#Libs for generic filters with long compilation times
clitkImageConvertLib
clitkImageResampleLib
+clitkBinarizeImageLib
#Libs for _ggo.c files
clitkSegmentationGgoLib clitkToolsGgoLib
clitkRegistrationGgoLib
mBGSlider->SetText("Background value");
// Main filter
- mFilter = new clitk::BinarizeImageGenericFilter<args_info_clitkBinarizeImage>;
+ mFilter = new clitk::BinarizeImageGenericFilter;
// Set how many inputs are needed for this tool
AddInputSelector("Select one image", mFilter);
GetArgsInfoFromGUI();
// Main filter
- clitk::BinarizeImageGenericFilter<args_info_clitkBinarizeImage>::Pointer filter =
- clitk::BinarizeImageGenericFilter<args_info_clitkBinarizeImage>::New();
+ clitk::BinarizeImageGenericFilter::Pointer filter =
+ clitk::BinarizeImageGenericFilter::New();
filter->SetInputVVImage(mCurrentImage);
filter->SetArgsInfo(mArgsInfo);
filter->EnableReadOnDisk(false);
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff