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 clitkMorphoMathGenericFilter_txx
-#define clitkMorphoMathGenericFilter_txx
-/**
- =================================================
- * @file clitkMorphoMathGenericFilter.txx
- * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
- * @date 5 May 2009
- *
- * @brief
- *
- =================================================*/
-
-
-namespace clitk
+ ===========================================================================**/
+
+#include "clitkSegmentationUtils.h"
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+clitk::MorphoMathGenericFilter<ArgsInfoType>::
+MorphoMathGenericFilter():
+ ImageToImageGenericFilter<MorphoMathGenericFilter<ArgsInfoType> >("MorphMath")
{
+ // Default values
+ cmdline_parser_clitkMorphoMath_init(&mArgsInfo);
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+ InitializeImageType<4>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<unsigned int Dim>
+void clitk::MorphoMathGenericFilter<ArgsInfoType>::
+InitializeImageType()
+{
+ ADD_DEFAULT_IMAGE_TYPES(Dim);
+ //ADD_IMAGE_TYPE(Dim, short); //
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+void clitk::MorphoMathGenericFilter<ArgsInfoType>::
+SetArgsInfo(const ArgsInfoType & a)
+{
+ mArgsInfo=a;
+ this->SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+ if (mArgsInfo.input_given) this->AddInputFilename(mArgsInfo.input_arg);
+ if (mArgsInfo.output_given) this->AddOutputFilename(mArgsInfo.output_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class FilterType>
+void clitk::MorphoMathGenericFilter<ArgsInfoType>::
+SetOptionsFromArgsInfoToFilter(FilterType * f)
+{
+ f->SetVerboseFlag(mArgsInfo.verbose_flag);
+ f->SetExtendSupportFlag(mArgsInfo.extend_flag);
+ f->SetOperationType(mArgsInfo.type_arg);
+ f->SetBackgroundValue(mArgsInfo.bg_arg);
+ f->SetForegroundValue(mArgsInfo.fg_arg);
+ f->SetBoundaryToForegroundFlag(mArgsInfo.bound_flag);
+ if (mArgsInfo.radius_given && mArgsInfo.radiusInMM_given) {
+ clitkExceptionMacro("Please give --radius OR --radiusInMM, not both.");
+ }
- //==============================================================================
- // Update with the number of dimensions
- //==============================================================================
- template<unsigned int Dimension>
- void
- MorphoMathGenericFilter::UpdateWithDim(std::string PixelType)
- {
- if(PixelType == "short"){
- if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, signed short>();
- }
- // else if(PixelType == "unsigned_short"){
- // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
- // UpdateWithDimAndPixelType<Dimension, unsigned short>();
- // }
-
- else if (PixelType == "unsigned_char"){
- if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, unsigned char>();
+ if (mArgsInfo.radiusInMM_given) {
+ typename FilterType::PointType p;
+ if (mArgsInfo.radiusInMM_given) {
+ ConvertOptionMacro(mArgsInfo.radiusInMM, p, FilterType::ImageDimension, false);
+ f->SetRadiusInMM(p);
}
-
- // else if (PixelType == "char"){
- // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
- // UpdateWithDimAndPixelType<Dimension, signed char>();
- // }
- else {
- if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, float>();
+ }
+ else {
+ typename FilterType::SizeType r;
+ if (mArgsInfo.radius_given) {
+ ConvertOptionMacro(mArgsInfo.radius, r, FilterType::ImageDimension, false);
+ f->SetRadius(r);
}
}
-
-
- //==============================================================================
- // Update with the pixel type
- //==============================================================================
- template <unsigned int Dimension, class InputPixelType>
- void
- MorphoMathGenericFilter::UpdateWithDimAndPixelType()
- {
-
- //---------------------------------
- // Define the images
- //---------------------------------
- typedef float InternalPixelType;
- typedef itk::Image<InputPixelType, Dimension> InputImageType;
- typedef itk::Image<InternalPixelType, Dimension> InternalImageType;
- typedef itk::Image<InputPixelType, Dimension> OutputImageType;
- typedef itk::ImageFileReader<InputImageType> FileReaderType;
- typename FileReaderType::Pointer fileReader=FileReaderType::New();
- fileReader->SetFileName(m_InputFileName);
- typedef itk::CastImageFilter<InputImageType, InternalImageType> InputCastImageFilterType;
- typename InputCastImageFilterType::Pointer caster = InputCastImageFilterType::New();
- caster->SetInput(fileReader->GetOutput());
- caster->Update();
- typename InternalImageType::Pointer input =caster->GetOutput();
-
-
- //---------------------------------
- // Find the type of action
- //---------------------------------
- typedef itk::ImageToImageFilter<InternalImageType, InternalImageType> ImageFilterType;
- typename ImageFilterType::Pointer filter;
-
- typedef itk::BinaryBallStructuringElement<InputPixelType,Dimension > KernelType;
- KernelType structuringElement;
- typename InternalImageType::SizeType radius;
- if (m_ArgsInfo.radius_given==Dimension)
- for (unsigned int i=0;i<Dimension;i++)
- {radius[i]=m_ArgsInfo.radius_arg[i];}
- else
- for (unsigned int i=0;i<Dimension;i++)
- radius[i]=m_ArgsInfo.radius_arg[0];
-
- structuringElement.SetRadius(radius);
- structuringElement.CreateStructuringElement();
-
- switch(m_ArgsInfo.type_arg)
- {
-
- case 0:
- {
- typedef itk::BinaryErodeImageFilter<InternalImageType, InternalImageType , KernelType> FilterType;
- typename FilterType::Pointer m = FilterType::New();
- m->SetBackgroundValue(m_ArgsInfo.bg_arg);
- m->SetForegroundValue(m_ArgsInfo.fg_arg);
- m->SetBoundaryToForeground(m_ArgsInfo.bound_flag);
- m->SetKernel(structuringElement);
-
- filter=m;
- if(m_Verbose) std::cout<<"Using the erode filter..."<<std::endl;
- break;
- }
-
- case 1:
- {
- typedef itk::BinaryDilateImageFilter<InternalImageType, InternalImageType , KernelType> FilterType;
- typename FilterType::Pointer m = FilterType::New();
- m->SetBackgroundValue(m_ArgsInfo.bg_arg);
- m->SetForegroundValue(m_ArgsInfo.fg_arg);
- m->SetBoundaryToForeground(m_ArgsInfo.bound_flag);
- m->SetKernel(structuringElement);
-
- filter=m;
- if(m_Verbose) std::cout<<"Using the dilate filter..."<<std::endl;
- break;
- }
-
- case 2:
- {
- typedef itk::BinaryMorphologicalClosingImageFilter<InternalImageType, InternalImageType , KernelType> FilterType;
- typename FilterType::Pointer m = FilterType::New();
- m->SetForegroundValue(m_ArgsInfo.fg_arg);
- m->SetSafeBorder(m_ArgsInfo.bound_flag);
- m->SetKernel(structuringElement);
-
- filter=m;
- if(m_Verbose) std::cout<<"Using the closing filter..."<<std::endl;
- break;
- }
-
- case 3:
- {
- typedef itk::BinaryMorphologicalOpeningImageFilter<InternalImageType, InternalImageType , KernelType> FilterType;
- typename FilterType::Pointer m = FilterType::New();
- m->SetBackgroundValue(m_ArgsInfo.bg_arg);
- m->SetForegroundValue(m_ArgsInfo.fg_arg);
- m->SetKernel(structuringElement);
-
- filter=m;
- if(m_Verbose) std::cout<<"Using the opening filter..."<<std::endl;
- break;
- }
-
- case 4:
- {
- typedef clitk::ConditionalBinaryErodeImageFilter<InternalImageType, InternalImageType , KernelType> FilterType;
- typename FilterType::Pointer m = FilterType::New();
- m->SetBackgroundValue(m_ArgsInfo.bg_arg);
- m->SetForegroundValue(m_ArgsInfo.fg_arg);
- m->SetBoundaryToForeground(m_ArgsInfo.bound_flag);
- m->SetKernel(structuringElement);
-
- filter=m;
- if(m_Verbose) std::cout<<"Using the conditional erode filter..."<<std::endl;
- break;
- }
-
- case 5:
- {
- typedef clitk::ConditionalBinaryDilateImageFilter<InternalImageType, InternalImageType , KernelType> FilterType;
- typename FilterType::Pointer m = FilterType::New();
- m->SetBackgroundValue(m_ArgsInfo.bg_arg);
- m->SetForegroundValue(m_ArgsInfo.fg_arg);
- m->SetBoundaryToForeground(m_ArgsInfo.bound_flag);
- m->SetKernel(structuringElement);
-
- filter=m;
- if(m_Verbose) std::cout<<"Using the conditional dilate filter..."<<std::endl;
- break;
- }
-
- }
-
-
- //---------------------------------
- // Execute the filter
- //---------------------------------
- filter->SetInput(input);
+}
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class ImageType>
+void clitk::MorphoMathGenericFilter<ArgsInfoType>::
+UpdateWithInputImageType()
+{
+ // Reading input
+ typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
+
+ // Create filter
+ typedef clitk::MorphoMathFilter<ImageType> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
- try
- {
- filter->Update();
- }
- catch( itk::ExceptionObject & err )
- {
- std::cerr << "ExceptionObject caught executing the filter!" << std::endl;
- std::cerr << err << std::endl;
- return;
- }
+ // Set the filter (needed for example for threaded monitoring)
+ this->SetFilterBase(filter);
+ // Set global Options
+ filter->SetInput(input);
+ SetOptionsFromArgsInfoToFilter<FilterType>(filter);
+
+ // Go !
+ filter->Update();
+
+ // Write/Save results
+ typename ImageType::Pointer output = filter->GetOutput();
+ this->template SetNextOutput<ImageType>(output);
+}
+//--------------------------------------------------------------------
- //---------------------------------
- // Write the output
- //---------------------------------
- typedef itk::CastImageFilter< InternalImageType, OutputImageType > OutputCastImageFilterType;
- typename OutputCastImageFilterType::Pointer oCaster = OutputCastImageFilterType::New();
- oCaster->SetInput(filter->GetOutput());
- typedef itk::ImageFileWriter<OutputImageType> FileWriterType;
- typename FileWriterType::Pointer writer=FileWriterType::New();
- writer->SetInput(oCaster->GetOutput());
- writer->SetFileName(m_ArgsInfo.output_arg);
- writer->Update();
-
- }
-}//end namespace
-
-#endif //#define clitkMorphoMathGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff