--- /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://www.centreleonberard.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 clitkRegionGrowingGenericFilter_txx
+#define clitkRegionGrowingGenericFilter_txx
+#include <itkBinaryBallStructuringElement.h>
+#include <itkConstShapedNeighborhoodIterator.h>
+
+namespace clitk
+{
+
+ //-------------------------------------------------------------------
+ // 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>();
+ }
+ }
+
+
+ //-------------------------------------------------------------------
+ // 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;
+
+ // 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
+ typedef typename std::vector<typename InputImageType::IndexType> SeedsType;
+ SeedsType seeds(1);
+ if(m_ArgsInfo.seed_given==Dimension)
+ for (unsigned int i=0; i<Dimension;i++)
+ seeds[0][i]=m_ArgsInfo.seed_arg[i];
+
+ else if ( m_ArgsInfo.seed_given==1)
+ seeds[0].Fill(m_ArgsInfo.seed_arg[0]);
+
+ else seeds[0].Fill(m_ArgsInfo.seed_arg[0]);
+ if(m_Verbose)std::cout<<"Setting seed seeds to "<<seeds[0]<<"..."<<std::endl;
+
+ if (m_ArgsInfo.seedRadius_given)
+ {
+ typedef itk::BinaryBallStructuringElement<PixelType, Dimension> BallType;
+ typename BallType::RadiusType r;
+
+ if (m_ArgsInfo.seedRadius_given == Dimension)
+ for (unsigned i = 0; i < Dimension; i++)
+ r[i] = m_ArgsInfo.seedRadius_arg[i];
+ else
+ r.Fill(m_ArgsInfo.seedRadius_arg[0]);
+
+ BallType ball;
+ ball.SetRadius(r);
+ ball.CreateStructuringElement();
+
+ typedef itk::ConstShapedNeighborhoodIterator<InputImageType> IteratorType;
+ IteratorType it(ball.GetRadius(),
+ input,
+ input->GetLargestPossibleRegion());
+#if ITK_VERSION_MAJOR < 4
+ typename BallType::ConstIterator nit;
+ unsigned idx = 0;
+ for (nit = ball.Begin(); nit != ball.End(); ++nit, ++idx)
+ {
+ if (*nit)
+ {
+ it.ActivateOffset(it.GetOffset(idx));
+ }
+ else
+ {
+ it.DeactivateOffset(it.GetOffset(idx));
+ }
+ }
+#else
+ it.CreateActiveListFromNeighborhood(ball);
+ it.NeedToUseBoundaryConditionOff();
+#endif
+
+ 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 (m_ArgsInfo.type_arg)
+ {
+ case 0: {
+
+ 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));
+ for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+ f->AddSeed(*it);
+ filter=f;
+ if(m_Verbose)std::cout<<"Using the connected threshold image filter..."<<std::endl;
+
+ break;
+ }
+
+ case 1: {
+
+ 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];
+
+ else if ( m_ArgsInfo.radius_given==1)
+ size.Fill(m_ArgsInfo.radius_arg[0]);
+
+ else size.Fill(m_ArgsInfo.radius_arg[0]);
+ if(m_Verbose)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));
+ for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+ f->AddSeed(*it);
+ f->SetRadius(size);
+ filter=f;
+ if(m_Verbose)std::cout<<"Using the neighborhood threshold connected image filter..."<<std::endl;
+
+ break;
+ }
+
+ case 2: {
+
+ 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];
+
+ else if ( m_ArgsInfo.radius_given==1)
+ size.Fill(m_ArgsInfo.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 );
+ for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+ f->AddSeed(*it);
+ 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;
+
+ break;
+ }
+
+ case 3: {
+
+ 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);
+ for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+ f->AddSeed(*it);
+ f->SetRadius(size);
+ filter=f;
+ if(m_Verbose)std::cout<<"Using the locally adaptive threshold connected image filter..."<<std::endl;
+
+ break;
+ }
+
+ case 4: {
+
+ 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;
+
+ // 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);
+ for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+ f->AddSeed(*it);
+ filter=f;
+ if(m_Verbose)std::cout<<"Using the explosion controlled threshold connected image filter..."<<std::endl;
+
+ break;
+ }
+
+ }
+
+
+ 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();
+ }
+
+}//end clitk
+
+#endif //#define clitkRegionGrowingGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff