From: David Sarrut Date: Mon, 22 Jul 2013 12:10:26 +0000 (+0200) Subject: Remove itk filter which is now inside itk X-Git-Tag: v1.4.0~164^2~49 X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=f4854864b1e9dacf51ffee720eeb4c72edb59e4f;p=clitk.git Remove itk filter which is now inside itk --- diff --git a/itk/itkLabelOverlapMeasuresImageFilter.h b/itk/itkLabelOverlapMeasuresImageFilter.h deleted file mode 100644 index 978fed3..0000000 --- a/itk/itkLabelOverlapMeasuresImageFilter.h +++ /dev/null @@ -1,212 +0,0 @@ -/*========================================================================= - - Program: Insight Segmentation & Registration Toolkit - Module: $RCSfile: itkLabelOverlapMeasuresImageFilter.h,v $ - Language: C++ - Date: $Date: $ - Version: $Revision: $ - - Copyright (c) Insight Software Consortium. All rights reserved. - See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. - - This software is distributed WITHOUT ANY WARRANTY; without even - the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR - PURPOSE. See the above copyright notices for more information. - -=========================================================================*/ -#ifndef __itkLabelOverlapMeasuresImageFilter_h -#define __itkLabelOverlapMeasuresImageFilter_h - -#include "itkImageToImageFilter.h" -#include "itkFastMutexLock.h" -#include "itkNumericTraits.h" - -//#include "itk_hash_map.h" -#include "itksys/hash_map.hxx" - -namespace itk { - -/** \class LabelOverlapMeasuresImageFilter - * \brief Computes overlap measures between the set same set of labels of - * pixels of two images. Background is assumed to be 0. - * - * \sa LabelOverlapMeasuresImageFilter - * - * \ingroup MultiThreaded - */ -template -class ITK_EXPORT LabelOverlapMeasuresImageFilter : - public ImageToImageFilter -{ -public: - /** Standard Self typedef */ - typedef LabelOverlapMeasuresImageFilter Self; - typedef ImageToImageFilter Superclass; - typedef SmartPointer Pointer; - typedef SmartPointer ConstPointer; - - /** Method for creation through the object factory. */ - itkNewMacro( Self ); - - /** Runtime information support. */ - itkTypeMacro( LabelOverlapMeasuresImageFilter, ImageToImageFilter ); - - virtual void VerifyInputInformation() { } - - - /** Image related typedefs. */ - typedef TLabelImage LabelImageType; - typedef typename TLabelImage::Pointer LabelImagePointer; - typedef typename TLabelImage::ConstPointer LabelImageConstPointer; - - typedef typename TLabelImage::RegionType RegionType; - typedef typename TLabelImage::SizeType SizeType; - typedef typename TLabelImage::IndexType IndexType; - - typedef typename TLabelImage::PixelType LabelType; - - /** Type to use form computations. */ - typedef typename NumericTraits::RealType RealType; - - /** \class LabelLabelOverlapMeasuress - * \brief Metrics stored per label */ - class LabelSetMeasures - { - public: - // default constructor - LabelSetMeasures() - { - m_Source = 0; - m_Target = 0; - m_Union = 0; - m_Intersection = 0; - m_SourceComplement = 0; - m_TargetComplement = 0; - } - - // added for completeness - LabelSetMeasures& operator=( const LabelSetMeasures& l ) - { - m_Source = l.m_Source; - m_Target = l.m_Target; - m_Union = l.m_Union; - m_Intersection = l.m_Intersection; - m_SourceComplement = l.m_SourceComplement; - m_TargetComplement = l.m_TargetComplement; - } - - unsigned long m_Source; - unsigned long m_Target; - unsigned long m_Union; - unsigned long m_Intersection; - unsigned long m_SourceComplement; - unsigned long m_TargetComplement; - }; - - /** Type of the map used to store data per label */ - typedef itksys::hash_map MapType; - typedef typename MapType::iterator MapIterator; - typedef typename MapType::const_iterator MapConstIterator; - - /** Image related typedefs. */ - itkStaticConstMacro( ImageDimension, unsigned int, - TLabelImage::ImageDimension ); - - /** Set the source image. */ - void SetSourceImage( const LabelImageType * image ) - { this->SetNthInput( 0, const_cast( image ) ); } - - /** Set the target image. */ - void SetTargetImage( const LabelImageType * image ) - { this->SetNthInput( 1, const_cast( image ) ); } - - /** Get the source image. */ - const LabelImageType * GetSourceImage( void ) - { return this->GetInput( 0 ); } - - /** Get the target image. */ - const LabelImageType * GetTargetImage( void ) - { return this->GetInput( 1 ); } - - /** Get the label set measures */ - MapType GetLabelSetMeasures() - { return this->m_LabelSetMeasures; } - - /** - * tric overlap measures - */ - /** measures over all labels */ - RealType GetTotalOverlap(); - RealType GetUnionOverlap(); - RealType GetMeanOverlap(); - RealType GetVolumeSimilarity(); - RealType GetFalseNegativeError(); - RealType GetFalsePositiveError(); - /** measures over individual labels */ - RealType GetTargetOverlap( LabelType ); - RealType GetUnionOverlap( LabelType ); - RealType GetMeanOverlap( LabelType ); - RealType GetVolumeSimilarity( LabelType ); - RealType GetFalseNegativeError( LabelType ); - RealType GetFalsePositiveError( LabelType ); - /** alternative names */ - RealType GetJaccardCoefficient() - { return this->GetUnionOverlap(); } - RealType GetJaccardCoefficient( LabelType label ) - { return this->GetUnionOverlap( label ); } - RealType GetDiceCoefficient() - { return this->GetMeanOverlap(); } - RealType GetDiceCoefficient( LabelType label ) - { return this->GetMeanOverlap( label ); } - - -#ifdef ITK_USE_CONCEPT_CHECKING - /** Begin concept checking */ - itkConceptMacro( Input1HasNumericTraitsCheck, - ( Concept::HasNumericTraits ) ); - /** End concept checking */ -#endif - -protected: - LabelOverlapMeasuresImageFilter(); - ~LabelOverlapMeasuresImageFilter(){}; - void PrintSelf( std::ostream& os, Indent indent ) const; - - /** - * Pass the input through unmodified. Do this by setting the output to the - * source this by setting the output to the source image in the - * AllocateOutputs() method. - */ - void AllocateOutputs(); - - void BeforeThreadedGenerateData(); - - void AfterThreadedGenerateData(); - - /** Multi-thread version GenerateData. */ - void ThreadedGenerateData( const RegionType&, int ); - - // Override since the filter needs all the data for the algorithm - void GenerateInputRequestedRegion(); - - // Override since the filter produces all of its output - void EnlargeOutputRequestedRegion( DataObject *data ); - -private: - LabelOverlapMeasuresImageFilter( const Self& ); //purposely not implemented - void operator=( const Self& ); //purposely not implemented - - std::vector m_LabelSetMeasuresPerThread; - MapType m_LabelSetMeasures; - - SimpleFastMutexLock m_Mutex; - -}; // end of class - -} // end namespace itk - -#ifndef ITK_MANUAL_INSTANTIATION -#include "itkLabelOverlapMeasuresImageFilter.txx" -#endif - -#endif diff --git a/itk/itkLabelOverlapMeasuresImageFilter.txx b/itk/itkLabelOverlapMeasuresImageFilter.txx deleted file mode 100644 index ced277b..0000000 --- a/itk/itkLabelOverlapMeasuresImageFilter.txx +++ /dev/null @@ -1,437 +0,0 @@ -/*========================================================================= - - Program: Insight Segmentation & Registration Toolkit - Module: $RCSfile: itkLabelOverlapMeasuresImageFilter.txx,v $ - Language: C++ - Date: $Date: $ - Version: $Revision: $ - - Copyright (c) Insight Software Consortium. All rights reserved. - See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. - - This software is distributed WITHOUT ANY WARRANTY; without even - the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR - PURPOSE. See the above copyright notices for more information. - -=========================================================================*/ -#ifndef _itkLabelOverlapMeasuresImageFilter_txx -#define _itkLabelOverlapMeasuresImageFilter_txx - -#include "itkLabelOverlapMeasuresImageFilter.h" - -#include "itkImageRegionConstIterator.h" -#include "itkProgressReporter.h" - -namespace itk { - -#if defined(__GNUC__) && (__GNUC__ <= 2) //NOTE: This class needs a mutex for gnu 2.95 -/** Used for mutex locking */ -#define LOCK_HASHMAP this->m_Mutex.Lock() -#define UNLOCK_HASHMAP this->m_Mutex.Unlock() -#else -#define LOCK_HASHMAP -#define UNLOCK_HASHMAP -#endif - -template -LabelOverlapMeasuresImageFilter -::LabelOverlapMeasuresImageFilter() -{ - // this filter requires two input images - this->SetNumberOfRequiredInputs( 2 ); -} - -template -void -LabelOverlapMeasuresImageFilter -::GenerateInputRequestedRegion() -{ - Superclass::GenerateInputRequestedRegion(); - if( this->GetSourceImage() ) - { - LabelImagePointer source = const_cast - ( this->GetSourceImage() ); - source->SetRequestedRegionToLargestPossibleRegion(); - } - if( this->GetTargetImage() ) - { - LabelImagePointer target = const_cast - ( this->GetTargetImage() ); - target->SetRequestedRegionToLargestPossibleRegion(); - } -} - -template -void -LabelOverlapMeasuresImageFilter -::EnlargeOutputRequestedRegion( DataObject *data ) -{ - Superclass::EnlargeOutputRequestedRegion( data ); - data->SetRequestedRegionToLargestPossibleRegion(); -} - - -template -void -LabelOverlapMeasuresImageFilter -::AllocateOutputs() -{ - // Pass the source through as the output - LabelImagePointer image = - const_cast( this->GetSourceImage() ); - this->SetNthOutput( 0, image ); - - // Nothing that needs to be allocated for the remaining outputs -} - -template -void -LabelOverlapMeasuresImageFilter -::BeforeThreadedGenerateData() -{ - int numberOfThreads = this->GetNumberOfThreads(); - - // Resize the thread temporaries - this->m_LabelSetMeasuresPerThread.resize( numberOfThreads ); - - // Initialize the temporaries - for( int n = 0; n < numberOfThreads; n++ ) - { - this->m_LabelSetMeasuresPerThread[n].clear(); - } - - // Initialize the final map - this->m_LabelSetMeasures.clear(); -} - -template -void -LabelOverlapMeasuresImageFilter -::AfterThreadedGenerateData() -{ - // Run through the map for each thread and accumulate the set measures. - for( int n = 0; n < this->GetNumberOfThreads(); n++ ) - { - // iterate over the map for this thread - for( MapConstIterator threadIt = this->m_LabelSetMeasuresPerThread[n].begin(); - threadIt != this->m_LabelSetMeasuresPerThread[n].end(); - ++threadIt ) - { - // does this label exist in the cumulative stucture yet? - MapIterator mapIt = this->m_LabelSetMeasures.find( ( *threadIt ).first ); - if( mapIt == this->m_LabelSetMeasures.end() ) - { - // create a new entry - typedef typename MapType::value_type MapValueType; - mapIt = this->m_LabelSetMeasures.insert( MapValueType( - (*threadIt).first, LabelSetMeasures() ) ).first; - } - - // accumulate the information from this thread - (*mapIt).second.m_Source += (*threadIt).second.m_Source; - (*mapIt).second.m_Target += (*threadIt).second.m_Target; - (*mapIt).second.m_Union += (*threadIt).second.m_Union; - (*mapIt).second.m_Intersection += - (*threadIt).second.m_Intersection; - (*mapIt).second.m_SourceComplement += - (*threadIt).second.m_SourceComplement; - (*mapIt).second.m_TargetComplement += - (*threadIt).second.m_TargetComplement; - } // end of thread map iterator loop - } // end of thread loop -} - -template -void -LabelOverlapMeasuresImageFilter -::ThreadedGenerateData( const RegionType& outputRegionForThread, - int threadId ) -{ - ImageRegionConstIterator ItS( this->GetSourceImage(), - outputRegionForThread ); - ImageRegionConstIterator ItT( this->GetTargetImage(), - outputRegionForThread ); - - // support progress methods/callbacks - ProgressReporter progress( this, threadId, - 2*outputRegionForThread.GetNumberOfPixels() ); - - for( ItS.GoToBegin(), ItT.GoToBegin(); !ItS.IsAtEnd(); ++ItS, ++ItT ) - { - LabelType sourceLabel = ItS.Get(); - LabelType targetLabel = ItT.Get(); - - // is the label already in this thread? - MapIterator mapItS = - this->m_LabelSetMeasuresPerThread[threadId].find( sourceLabel ); - MapIterator mapItT = - this->m_LabelSetMeasuresPerThread[threadId].find( targetLabel ); - - if( mapItS == this->m_LabelSetMeasuresPerThread[threadId].end() ) - { - // create a new label set measures object - typedef typename MapType::value_type MapValueType; - LOCK_HASHMAP; - mapItS = this->m_LabelSetMeasuresPerThread[threadId].insert( - MapValueType( sourceLabel, LabelSetMeasures() ) ).first; - UNLOCK_HASHMAP; - } - - if( mapItT == this->m_LabelSetMeasuresPerThread[threadId].end() ) - { - // create a new label set measures object - typedef typename MapType::value_type MapValueType; - LOCK_HASHMAP; - mapItT = this->m_LabelSetMeasuresPerThread[threadId].insert( - MapValueType( targetLabel, LabelSetMeasures() ) ).first; - UNLOCK_HASHMAP; - } - - (*mapItS).second.m_Source++; - (*mapItT).second.m_Target++; - - if( sourceLabel == targetLabel ) - { - (*mapItS).second.m_Intersection++; - (*mapItS).second.m_Union++; - } - else - { - (*mapItS).second.m_Union++; - (*mapItT).second.m_Union++; - - (*mapItS).second.m_SourceComplement++; - (*mapItT).second.m_TargetComplement++; - } - - progress.CompletedPixel(); - } -} - -/** - * measures - */ -template -typename LabelOverlapMeasuresImageFilter::RealType -LabelOverlapMeasuresImageFilter -::GetTotalOverlap() -{ - RealType numerator = 0.0; - RealType denominator = 0.0; - for( MapIterator mapIt = this->m_LabelSetMeasures.begin(); - mapIt != this->m_LabelSetMeasures.end(); ++mapIt ) - { - // Do not include the background in the final value. - if( (*mapIt).first == NumericTraits::Zero ) - { - continue; - } - numerator += static_cast( (*mapIt).second.m_Intersection ); - denominator += static_cast( (*mapIt).second.m_Target ); - } - return ( numerator / denominator ); -} - -template -typename LabelOverlapMeasuresImageFilter::RealType -LabelOverlapMeasuresImageFilter -::GetTargetOverlap( LabelType label ) -{ - MapIterator mapIt = this->m_LabelSetMeasures.find( label ); - if( mapIt == this->m_LabelSetMeasures.end() ) - { - itkWarningMacro( "Label " << label << " not found." ); - return 0.0; - } - RealType value = - static_cast( (*mapIt).second.m_Intersection ) / - static_cast( (*mapIt).second.m_Target ); - return value; -} - -template -typename LabelOverlapMeasuresImageFilter::RealType -LabelOverlapMeasuresImageFilter -::GetUnionOverlap() -{ - RealType numerator = 0.0; - RealType denominator = 0.0; - for( MapIterator mapIt = this->m_LabelSetMeasures.begin(); - mapIt != this->m_LabelSetMeasures.end(); ++mapIt ) - { - // Do not include the background in the final value. - if( (*mapIt).first == NumericTraits::Zero ) - { - continue; - } - numerator += static_cast( (*mapIt).second.m_Intersection ); - denominator += static_cast( (*mapIt).second.m_Union ); - } - return ( numerator / denominator ); -} - -template -typename LabelOverlapMeasuresImageFilter::RealType -LabelOverlapMeasuresImageFilter -::GetUnionOverlap( LabelType label ) -{ - MapIterator mapIt = this->m_LabelSetMeasures.find( label ); - if( mapIt == this->m_LabelSetMeasures.end() ) - { - itkWarningMacro( "Label " << label << " not found." ); - return 0.0; - } - RealType value = - static_cast( (*mapIt).second.m_Intersection ) / - static_cast( (*mapIt).second.m_Union ); - return value; -} - -template -typename LabelOverlapMeasuresImageFilter::RealType -LabelOverlapMeasuresImageFilter -::GetMeanOverlap() -{ - RealType uo = this->GetUnionOverlap(); - return ( 2.0 * uo / ( 1.0 + uo ) ); -} - -template -typename LabelOverlapMeasuresImageFilter::RealType -LabelOverlapMeasuresImageFilter -::GetMeanOverlap( LabelType label ) -{ - RealType uo = this->GetUnionOverlap( label ); - return ( 2.0 * uo / ( 1.0 + uo ) ); -} - -template -typename LabelOverlapMeasuresImageFilter::RealType -LabelOverlapMeasuresImageFilter -::GetVolumeSimilarity() -{ - RealType numerator = 0.0; - RealType denominator = 0.0; - for( MapIterator mapIt = this->m_LabelSetMeasures.begin(); - mapIt != this->m_LabelSetMeasures.end(); ++mapIt ) - { - // Do not include the background in the final value. - if( (*mapIt).first == NumericTraits::Zero ) - { - continue; - } - numerator += ( ( static_cast( (*mapIt).second.m_Source ) - - static_cast( (*mapIt).second.m_Target ) ) ); - denominator += ( ( static_cast( (*mapIt).second.m_Source ) + - static_cast( (*mapIt).second.m_Target ) ) ); - } - return ( 2.0 * numerator / denominator ); -} - -template -typename LabelOverlapMeasuresImageFilter::RealType -LabelOverlapMeasuresImageFilter -::GetVolumeSimilarity( LabelType label ) -{ - MapIterator mapIt = this->m_LabelSetMeasures.find( label ); - if( mapIt == this->m_LabelSetMeasures.end() ) - { - itkWarningMacro( "Label " << label << " not found." ); - return 0.0; - } - RealType value = 2.0 * - ( static_cast( (*mapIt).second.m_Source ) - - static_cast( (*mapIt).second.m_Target ) ) / - ( static_cast( (*mapIt).second.m_Source ) + - static_cast( (*mapIt).second.m_Target ) ); - return value; -} - -template -typename LabelOverlapMeasuresImageFilter::RealType -LabelOverlapMeasuresImageFilter -::GetFalseNegativeError() -{ - RealType numerator = 0.0; - RealType denominator = 0.0; - for( MapIterator mapIt = this->m_LabelSetMeasures.begin(); - mapIt != this->m_LabelSetMeasures.end(); ++mapIt ) - { - // Do not include the background in the final value. - if( (*mapIt).first == NumericTraits::Zero ) - { - continue; - } - numerator += static_cast( (*mapIt).second.m_TargetComplement ); - denominator += static_cast( (*mapIt).second.m_Target ); - } - return ( numerator / denominator ); -} - -template -typename LabelOverlapMeasuresImageFilter::RealType -LabelOverlapMeasuresImageFilter -::GetFalseNegativeError( LabelType label ) -{ - MapIterator mapIt = this->m_LabelSetMeasures.find( label ); - if( mapIt == this->m_LabelSetMeasures.end() ) - { - itkWarningMacro( "Label " << label << " not found." ); - return 0.0; - } - RealType value = - static_cast( (*mapIt).second.m_TargetComplement ) / - static_cast( (*mapIt).second.m_Target ); - return value; -} - -template -typename LabelOverlapMeasuresImageFilter::RealType -LabelOverlapMeasuresImageFilter -::GetFalsePositiveError() -{ - RealType numerator = 0.0; - RealType denominator = 0.0; - for( MapIterator mapIt = this->m_LabelSetMeasures.begin(); - mapIt != this->m_LabelSetMeasures.end(); ++mapIt ) - { - // Do not include the background in the final value. - if( (*mapIt).first == NumericTraits::Zero ) - { - continue; - } - numerator += static_cast( (*mapIt).second.m_SourceComplement ); - denominator += static_cast( (*mapIt).second.m_Source ); - } - return ( numerator / denominator ); -} - -template -typename LabelOverlapMeasuresImageFilter::RealType -LabelOverlapMeasuresImageFilter -::GetFalsePositiveError( LabelType label ) -{ - MapIterator mapIt = this->m_LabelSetMeasures.find( label ); - if( mapIt == this->m_LabelSetMeasures.end() ) - { - itkWarningMacro( "Label " << label << " not found." ); - return 0.0; - } - RealType value = - static_cast( (*mapIt).second.m_SourceComplement ) / - static_cast( (*mapIt).second.m_Source ); - return value; -} - -template -void -LabelOverlapMeasuresImageFilter -::PrintSelf( std::ostream& os, Indent indent ) const -{ - Superclass::PrintSelf( os, indent ); - -} - - -}// end namespace itk -#endif