+++ /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_h
-#define clitkRegionGrowingGenericFilter_h
-
-/* =================================================
- * @file clitkRegionGrowingGenericFilter.h
- * @author
- * @date
- *
- * @brief
- *
- ===================================================*/
-
-
-// clitk include
-#include "clitkIO.h"
-#include "clitkCommon.h"
-#include "clitkImageCommon.h"
-#include "clitkRegionGrowing_ggo.h"
-#include "clitkLocallyAdaptiveThresholdConnectedImageFilter.h"
-#include "clitkExplosionControlledThresholdConnectedImageFilter.h"
-
-//itk include
-#include "itkLightObject.h"
-#include "itkConnectedThresholdImageFilter.h"
-#include "itkNeighborhoodConnectedImageFilter.h"
-#include "itkConfidenceConnectedImageFilter.h"
-#include "itkConfidenceConnectedImageFilter.h"
-
-namespace clitk
-{
-
-
- class ITK_EXPORT RegionGrowingGenericFilter : public itk::LightObject
- {
- public:
- //----------------------------------------
- // ITK
- //----------------------------------------
- typedef RegionGrowingGenericFilter Self;
- typedef itk::LightObject Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
-
- // Method for creation through the object factory
- itkNewMacro(Self);
-
- // Run-time type information (and related methods)
- itkTypeMacro( RegionGrowingGenericFilter, LightObject );
-
-
- //----------------------------------------
- // Typedefs
- //----------------------------------------
-
-
- //----------------------------------------
- // Set & Get
- //----------------------------------------
- void SetArgsInfo(const args_info_clitkRegionGrowing & a)
- {
- m_ArgsInfo=a;
- m_Verbose=m_ArgsInfo.verbose_flag;
- m_InputFileName=m_ArgsInfo.input_arg;
- }
-
-
- //----------------------------------------
- // Update
- //----------------------------------------
- void Update();
-
- protected:
-
- //----------------------------------------
- // Constructor & Destructor
- //----------------------------------------
- RegionGrowingGenericFilter();
- ~RegionGrowingGenericFilter() {};
-
-
- //----------------------------------------
- // Templated members
- //----------------------------------------
- template <unsigned int Dimension> void UpdateWithDim(std::string PixelType);
- template <unsigned int Dimension, class PixelType> void UpdateWithDimAndPixelType();
-
-
- //----------------------------------------
- // Data members
- //----------------------------------------
- args_info_clitkRegionGrowing m_ArgsInfo;
- bool m_Verbose;
- std::string m_InputFileName;
-
- };
-
-
-} // end namespace clitk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "clitkRegionGrowingGenericFilter.txx"
-#endif
-
-#endif // #define clitkRegionGrowingGenericFilter_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://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 / commitdiff