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 clitkRegionGrowingGenericFilter_txx
-#define clitkRegionGrowingGenericFilter_txx
+ ===========================================================================**/
-namespace clitk
+#ifndef CLITKREGIONGROWINGGENERICFILTER_TXX
+#define CLITKREGIONGROWINGGENERICFILTER_TXX
+
+#include <itkBinaryBallStructuringElement.h>
+#include <itkConstShapedNeighborhoodIterator.h>
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+clitk::RegionGrowingGenericFilter<ArgsInfoType>::RegionGrowingGenericFilter():
+ ImageToImageGenericFilter<Self>("RegionGrowing")
{
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+ //InitializeImageType<4>();
+}
+//--------------------------------------------------------------------
- //-------------------------------------------------------------------
- // Update with the number of dimensions
- //-------------------------------------------------------------------
- template<unsigned int Dimension>
- void
- RegionGrowingGenericFilter::UpdateWithDim(std::string PixelType)
- {
- if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
-
- 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>();
- }
-
- // 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>();
- }
- }
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<unsigned int Dim>
+void clitk::RegionGrowingGenericFilter<ArgsInfoType>::InitializeImageType()
+{
+ ADD_IMAGE_TYPE(Dim, uchar);
+ ADD_IMAGE_TYPE(Dim, short);
+ // ADD_IMAGE_TYPE(Dim, int);
+ ADD_IMAGE_TYPE(Dim, float);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+void clitk::RegionGrowingGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a)
+{
+ mArgsInfo=a;
+ this->SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.input_given) this->AddInputFilename(mArgsInfo.input_arg);
+ if (mArgsInfo.output_given) this->SetOutputFilename(mArgsInfo.output_arg);
+}
+//--------------------------------------------------------------------
- //-------------------------------------------------------------------
- // Update with the number of dimensions and the pixeltype
- //-------------------------------------------------------------------
- template <unsigned int Dimension, class PixelType>
- void
- RegionGrowingGenericFilter::UpdateWithDimAndPixelType()
- {
- // ImageTypes
- typedef itk::Image<PixelType, Dimension> InputImageType;
- typedef itk::Image<PixelType, Dimension> OutputImageType;
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class ImageType>
+void clitk::RegionGrowingGenericFilter<ArgsInfoType>::UpdateWithInputImageType()
+{
+ DD("UpdateWithInputImageType");
+ const int Dimension = ImageType::ImageDimension;
+
+ // ImageTypes
+ typedef ImageType InputImageType;
+ typedef ImageType OutputImageType;
+ typedef typename ImageType::PixelType PixelType;
- // Read the input
- typedef itk::ImageFileReader<InputImageType> InputReaderType;
- typename InputReaderType::Pointer reader = InputReaderType::New();
- reader->SetFileName( m_InputFileName);
- reader->Update();
- typename InputImageType::Pointer input= reader->GetOutput();
-
- // Seed
- typename InputImageType::IndexType index;
- if(m_ArgsInfo.seed_given==Dimension)
- for (unsigned int i=0; i<Dimension;i++)
- index[i]=m_ArgsInfo.seed_arg[i];
+ // Reading input
+ typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
+
+ // Seed
+ typedef typename std::vector<typename InputImageType::IndexType> SeedsType;
+ SeedsType seeds(1);
+ if (mArgsInfo.seed_given==Dimension)
+ for (unsigned int i=0; i<Dimension;i++)
+ seeds[0][i]=mArgsInfo.seed_arg[i];
- else if ( m_ArgsInfo.seed_given==1)
- index.Fill(m_ArgsInfo.seed_arg[0]);
+ else if ( mArgsInfo.seed_given==1)
+ seeds[0].Fill(mArgsInfo.seed_arg[0]);
- else index.Fill(m_ArgsInfo.seed_arg[0]);
- if(m_Verbose)std::cout<<"Setting seed index to "<<index<<"..."<<std::endl;
+ else seeds[0].Fill(mArgsInfo.seed_arg[0]);
+ if (mArgsInfo.verbose_flag) std::cout<<"Setting seed seeds to "<<seeds[0]<<"..."<<std::endl;
+
+ if (mArgsInfo.seedRadius_given)
+ {
+ typedef itk::BinaryBallStructuringElement<PixelType, Dimension> BallType;
+ typename BallType::RadiusType r;
+ if (mArgsInfo.seedRadius_given == Dimension)
+ for (unsigned i = 0; i < Dimension; i++)
+ r[i] = mArgsInfo.seedRadius_arg[i];
+ else
+ r.Fill(mArgsInfo.seedRadius_arg[0]);
- // Filter
- typedef itk::ImageToImageFilter<InputImageType, OutputImageType> ImageToImageFilterType;
- typename ImageToImageFilterType::Pointer filter;
+ BallType ball;
+ ball.SetRadius(r);
+ ball.CreateStructuringElement();
- switch (m_ArgsInfo.type_arg)
- {
- case 0: {
+ typedef itk::ConstShapedNeighborhoodIterator<InputImageType> IteratorType;
+ IteratorType it(ball.GetRadius(),
+ input,
+ input->GetLargestPossibleRegion());
+ it.CreateActiveListFromNeighborhood(ball);
+ it.NeedToUseBoundaryConditionOff();
+
+ it.SetLocation(seeds[0]);
+ for (typename IteratorType::ConstIterator i = it.Begin(); !i.IsAtEnd(); ++i)
+ {
+ typename InputImageType::IndexType id = seeds[0] + i.GetNeighborhoodOffset();
+ if (id != seeds[0] && input->GetLargestPossibleRegion().IsInside(id))
+ seeds.push_back(id);
+ }
+ }
+
+ // Filter
+ typedef itk::ImageToImageFilter<InputImageType, OutputImageType> ImageToImageFilterType;
+ typename ImageToImageFilterType::Pointer filter;
+
+ switch (mArgsInfo.type_arg)
+ {
+ case 0: {
- typedef itk::ConnectedThresholdImageFilter<InputImageType, OutputImageType> ImageFilterType;
- typename ImageFilterType::Pointer f= ImageFilterType::New();
+ typedef itk::ConnectedThresholdImageFilter<InputImageType, OutputImageType> ImageFilterType;
+ typename ImageFilterType::Pointer f= ImageFilterType::New();
- f->SetLower(m_ArgsInfo.lower_arg);
- f->SetUpper(m_ArgsInfo.upper_arg);
- f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
- f->SetSeed(index);
- filter=f;
- if(m_Verbose)std::cout<<"Using the connected threshold image filter..."<<std::endl;
+ f->SetLower(mArgsInfo.lower_arg);
+ f->SetUpper(mArgsInfo.upper_arg);
+ f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
+ for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+ f->AddSeed(*it);
+ filter=f;
+ if (mArgsInfo.verbose_flag) std::cout<<"Using the connected threshold image filter..."<<std::endl;
- break;
- }
+ break;
+ }
- case 1: {
+ case 1: {
- typedef itk::NeighborhoodConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
- typename ImageFilterType::Pointer f= ImageFilterType::New();
+ typedef itk::NeighborhoodConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
+ typename ImageFilterType::Pointer f= ImageFilterType::New();
- // Radius
- typename InputImageType::SizeType size;
- if(m_ArgsInfo.radius_given==Dimension)
- for (unsigned int i=0; i<Dimension;i++)
- size[i]=m_ArgsInfo.radius_arg[i];
+ // Radius
+ typename InputImageType::SizeType size;
+ if (mArgsInfo.radius_given==Dimension)
+ for (unsigned int i=0; i<Dimension;i++)
+ size[i]=mArgsInfo.radius_arg[i];
- else if ( m_ArgsInfo.radius_given==1)
- size.Fill(m_ArgsInfo.radius_arg[0]);
+ else if ( mArgsInfo.radius_given==1)
+ size.Fill(mArgsInfo.radius_arg[0]);
- else size.Fill(m_ArgsInfo.radius_arg[0]);
- if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
+ else size.Fill(mArgsInfo.radius_arg[0]);
+ if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
- f->SetLower(m_ArgsInfo.lower_arg);
- f->SetUpper(m_ArgsInfo.upper_arg);
- f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
- f->AddSeed(index);
- f->SetRadius(size);
- filter=f;
- if(m_Verbose)std::cout<<"Using the neighborhood threshold connected image filter..."<<std::endl;
+ f->SetLower(mArgsInfo.lower_arg);
+ f->SetUpper(mArgsInfo.upper_arg);
+ f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
+ for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+ f->AddSeed(*it);
+ f->SetRadius(size);
+ filter=f;
+ if (mArgsInfo.verbose_flag) std::cout<<"Using the neighborhood threshold connected image filter..."<<std::endl;
- break;
- }
+ break;
+ }
- case 2: {
+ case 2: {
- typedef itk::ConfidenceConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
- typename ImageFilterType::Pointer f= ImageFilterType::New();
+ typedef itk::ConfidenceConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
+ typename ImageFilterType::Pointer f= ImageFilterType::New();
- // Radius
- typename InputImageType::SizeType size;
- if(m_ArgsInfo.radius_given==Dimension)
- for (unsigned int i=0; i<Dimension;i++)
- size[i]=m_ArgsInfo.radius_arg[i];
+ // Radius
+ typename InputImageType::SizeType size;
+ if (mArgsInfo.radius_given==Dimension)
+ for (unsigned int i=0; i<Dimension;i++)
+ size[i]=mArgsInfo.radius_arg[i];
- else if ( m_ArgsInfo.radius_given==1)
- size.Fill(m_ArgsInfo.radius_arg[0]);
+ else if ( mArgsInfo.radius_given==1)
+ size.Fill(mArgsInfo.radius_arg[0]);
- else size.Fill(m_ArgsInfo.radius_arg[0]);
- if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
-
- f->SetMultiplier( m_ArgsInfo.multiplier_arg );
- f->SetNumberOfIterations( m_ArgsInfo.multiplier_arg );
- f->AddSeed( index );
- f->SetNumberOfIterations( m_ArgsInfo.iter_arg);
- f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
- f->SetInitialNeighborhoodRadius(size[0]);
- filter=f;
- if(m_Verbose)std::cout<<"Using the confidence threshold connected image filter..."<<std::endl;
+ else size.Fill(mArgsInfo.radius_arg[0]);
+ if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
+
+ f->SetMultiplier( mArgsInfo.multiplier_arg );
+ f->SetNumberOfIterations( mArgsInfo.multiplier_arg );
+ for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+ f->AddSeed(*it);
+ f->SetNumberOfIterations( mArgsInfo.iter_arg);
+ f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
+ f->SetInitialNeighborhoodRadius(size[0]);
+ filter=f;
+ if (mArgsInfo.verbose_flag) std::cout<<"Using the confidence threshold connected image filter..."<<std::endl;
- break;
- }
+ break;
+ }
- case 3: {
+ case 3: {
- typedef clitk::LocallyAdaptiveThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
- typename ImageFilterType::Pointer f= ImageFilterType::New();
+ typedef clitk::LocallyAdaptiveThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
+ typename ImageFilterType::Pointer f= ImageFilterType::New();
- // Radius
- typename InputImageType::SizeType size;
- if(m_ArgsInfo.radius_given==Dimension)
- for (unsigned int i=0; i<Dimension;i++)
- size[i]=m_ArgsInfo.radius_arg[i];
- else size.Fill(m_ArgsInfo.radius_arg[0]);
- if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
-
- // params
- f->SetLower(m_ArgsInfo.lower_arg);
- f->SetUpper(m_ArgsInfo.upper_arg);
- f->SetLowerBorderIsGiven(m_ArgsInfo.adaptLower_flag);
- f->SetLowerBorderIsGiven(m_ArgsInfo.adaptUpper_flag);
- f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
- f->SetMultiplier(m_ArgsInfo.multiplier_arg);
- f->SetMaximumSDIsGiven(m_ArgsInfo.maxSD_given);
- if (m_ArgsInfo.maxSD_given) f->SetMaximumSD(m_ArgsInfo.maxSD_arg);
- f->AddSeed(index);
- f->SetRadius(size);
- filter=f;
- if(m_Verbose)std::cout<<"Using the locally adaptive threshold connected image filter..."<<std::endl;
-
- break;
- }
+ // Radius
+ typename InputImageType::SizeType size;
+ if (mArgsInfo.radius_given==Dimension)
+ for (unsigned int i=0; i<Dimension;i++)
+ size[i]=mArgsInfo.radius_arg[i];
+ else size.Fill(mArgsInfo.radius_arg[0]);
+ if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
+
+ // params
+ f->SetLower(mArgsInfo.lower_arg);
+ f->SetUpper(mArgsInfo.upper_arg);
+ f->SetLowerBorderIsGiven(mArgsInfo.adaptLower_flag);
+ f->SetLowerBorderIsGiven(mArgsInfo.adaptUpper_flag);
+ f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
+ f->SetMultiplier(mArgsInfo.multiplier_arg);
+ f->SetMaximumSDIsGiven(mArgsInfo.maxSD_given);
+ if (mArgsInfo.maxSD_given) f->SetMaximumSD(mArgsInfo.maxSD_arg);
+ for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+ f->AddSeed(*it);
+ f->SetRadius(size);
+ filter=f;
+ if (mArgsInfo.verbose_flag) std::cout<<"Using the locally adaptive threshold connected image filter..."<<std::endl;
+
+ break;
+ }
- case 4: {
+ case 4: {
- typedef clitk::ExplosionControlledThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
- typename ImageFilterType::Pointer f= ImageFilterType::New();
+ typedef clitk::ExplosionControlledThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
+ typename ImageFilterType::Pointer f= ImageFilterType::New();
- // // Radius
- // typename InputImageType::SizeType size;
- // if(m_ArgsInfo.radius_given==Dimension)
- // for (unsigned int i=0; i<Dimension;i++)
- // size[i]=m_ArgsInfo.radius_arg[i];
- // else size.Fill(m_ArgsInfo.radius_arg[0]);
- // if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
+ // // Radius
+ // typename InputImageType::SizeType size;
+ // if (mArgsInfo.radius_given==Dimension)
+ // for (unsigned int i=0; i<Dimension;i++)
+ // size[i]=mArgsInfo.radius_arg[i];
+ // else size.Fill(mArgsInfo.radius_arg[0]);
+ // if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
- // params
- f->SetVerbose(m_ArgsInfo.verbose_flag);
- f->SetLower(m_ArgsInfo.lower_arg);
- f->SetUpper(m_ArgsInfo.upper_arg);
- f->SetMinimumLowerThreshold(m_ArgsInfo.minLower_arg);
- f->SetMaximumUpperThreshold(m_ArgsInfo.maxUpper_arg);
- f->SetAdaptLowerBorder(m_ArgsInfo.adaptLower_flag);
- f->SetAdaptUpperBorder(m_ArgsInfo.adaptUpper_flag);
- f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
- f->SetMultiplier(m_ArgsInfo.multiplier_arg);
- f->SetThresholdStepSize(m_ArgsInfo.step_arg);
- f->SetMinimumThresholdStepSize(m_ArgsInfo.minStep_arg);
- f->SetFullyConnected(m_ArgsInfo.full_flag);
- f->AddSeed(index);
- filter=f;
- if(m_Verbose)std::cout<<"Using the explosion controlled threshold connected image filter..."<<std::endl;
-
- break;
- }
+ // params
+ f->SetVerbose(mArgsInfo.verbose_flag);
+ f->SetLower(mArgsInfo.lower_arg);
+ f->SetUpper(mArgsInfo.upper_arg);
+ f->SetMinimumLowerThreshold(mArgsInfo.minLower_arg);
+ f->SetMaximumUpperThreshold(mArgsInfo.maxUpper_arg);
+ f->SetAdaptLowerBorder(mArgsInfo.adaptLower_flag);
+ f->SetAdaptUpperBorder(mArgsInfo.adaptUpper_flag);
+ f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
+ f->SetMultiplier(mArgsInfo.multiplier_arg);
+ f->SetThresholdStepSize(mArgsInfo.step_arg);
+ f->SetMinimumThresholdStepSize(mArgsInfo.minStep_arg);
+ f->SetFullyConnected(mArgsInfo.full_flag);
+ for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+ f->AddSeed(*it);
+ filter=f;
+ if (mArgsInfo.verbose_flag) std::cout<<"Using the explosion controlled threshold connected image filter..."<<std::endl;
+
+ break;
+ }
}
- filter->SetInput(input);
- filter->Update();
- typename OutputImageType::Pointer output=filter->GetOutput();
+ filter->SetInput(input);
+ filter->Update();
+ typename OutputImageType::Pointer output=filter->GetOutput();
- // Output
- typedef itk::ImageFileWriter<OutputImageType> WriterType;
- typename WriterType::Pointer writer = WriterType::New();
- writer->SetFileName(m_ArgsInfo.output_arg);
- writer->SetInput(output);
- writer->Update();
- }
+ // Write/Save results
+ this->template SetNextOutput<OutputImageType>(output);
+}
+//--------------------------------------------------------------------
-}//end clitk
-#endif //#define clitkRegionGrowingGenericFilter_txx
+#endif //#define CLITKREGIONGROWINGGENERICFILTER_TXX
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff