+++ /dev/null
-/*=========================================================================
-
- 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 TLabelImage>
-class ITK_EXPORT LabelOverlapMeasuresImageFilter :
- public ImageToImageFilter<TLabelImage, TLabelImage>
-{
-public:
- /** Standard Self typedef */
- typedef LabelOverlapMeasuresImageFilter Self;
- typedef ImageToImageFilter<TLabelImage,TLabelImage> Superclass;
- typedef SmartPointer<Self> Pointer;
- typedef SmartPointer<const Self> 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<LabelType>::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<LabelType, LabelSetMeasures> 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<LabelImageType *>( image ) ); }
-
- /** Set the target image. */
- void SetTargetImage( const LabelImageType * image )
- { this->SetNthInput( 1, const_cast<LabelImageType *>( 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<LabelType> ) );
- /** 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<MapType> m_LabelSetMeasuresPerThread;
- MapType m_LabelSetMeasures;
-
- SimpleFastMutexLock m_Mutex;
-
-}; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkLabelOverlapMeasuresImageFilter.txx"
-#endif
-
-#endif
+++ /dev/null
-/*=========================================================================
-
- 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<class TLabelImage>
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::LabelOverlapMeasuresImageFilter()
-{
- // this filter requires two input images
- this->SetNumberOfRequiredInputs( 2 );
-}
-
-template<class TLabelImage>
-void
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::GenerateInputRequestedRegion()
-{
- Superclass::GenerateInputRequestedRegion();
- if( this->GetSourceImage() )
- {
- LabelImagePointer source = const_cast
- <LabelImageType *>( this->GetSourceImage() );
- source->SetRequestedRegionToLargestPossibleRegion();
- }
- if( this->GetTargetImage() )
- {
- LabelImagePointer target = const_cast
- <LabelImageType *>( this->GetTargetImage() );
- target->SetRequestedRegionToLargestPossibleRegion();
- }
-}
-
-template<class TLabelImage>
-void
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::EnlargeOutputRequestedRegion( DataObject *data )
-{
- Superclass::EnlargeOutputRequestedRegion( data );
- data->SetRequestedRegionToLargestPossibleRegion();
-}
-
-
-template<class TLabelImage>
-void
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::AllocateOutputs()
-{
- // Pass the source through as the output
- LabelImagePointer image =
- const_cast<TLabelImage *>( this->GetSourceImage() );
- this->SetNthOutput( 0, image );
-
- // Nothing that needs to be allocated for the remaining outputs
-}
-
-template<class TLabelImage>
-void
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::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<class TLabelImage>
-void
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::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<class TLabelImage>
-void
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::ThreadedGenerateData( const RegionType& outputRegionForThread,
- int threadId )
-{
- ImageRegionConstIterator<LabelImageType> ItS( this->GetSourceImage(),
- outputRegionForThread );
- ImageRegionConstIterator<LabelImageType> 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<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::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<LabelType>::Zero )
- {
- continue;
- }
- numerator += static_cast<RealType>( (*mapIt).second.m_Intersection );
- denominator += static_cast<RealType>( (*mapIt).second.m_Target );
- }
- return ( numerator / denominator );
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::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<RealType>( (*mapIt).second.m_Intersection ) /
- static_cast<RealType>( (*mapIt).second.m_Target );
- return value;
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::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<LabelType>::Zero )
- {
- continue;
- }
- numerator += static_cast<RealType>( (*mapIt).second.m_Intersection );
- denominator += static_cast<RealType>( (*mapIt).second.m_Union );
- }
- return ( numerator / denominator );
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::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<RealType>( (*mapIt).second.m_Intersection ) /
- static_cast<RealType>( (*mapIt).second.m_Union );
- return value;
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::GetMeanOverlap()
-{
- RealType uo = this->GetUnionOverlap();
- return ( 2.0 * uo / ( 1.0 + uo ) );
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::GetMeanOverlap( LabelType label )
-{
- RealType uo = this->GetUnionOverlap( label );
- return ( 2.0 * uo / ( 1.0 + uo ) );
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::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<LabelType>::Zero )
- {
- continue;
- }
- numerator += ( ( static_cast<RealType>( (*mapIt).second.m_Source ) -
- static_cast<RealType>( (*mapIt).second.m_Target ) ) );
- denominator += ( ( static_cast<RealType>( (*mapIt).second.m_Source ) +
- static_cast<RealType>( (*mapIt).second.m_Target ) ) );
- }
- return ( 2.0 * numerator / denominator );
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::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<RealType>( (*mapIt).second.m_Source ) -
- static_cast<RealType>( (*mapIt).second.m_Target ) ) /
- ( static_cast<RealType>( (*mapIt).second.m_Source ) +
- static_cast<RealType>( (*mapIt).second.m_Target ) );
- return value;
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::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<LabelType>::Zero )
- {
- continue;
- }
- numerator += static_cast<RealType>( (*mapIt).second.m_TargetComplement );
- denominator += static_cast<RealType>( (*mapIt).second.m_Target );
- }
- return ( numerator / denominator );
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::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<RealType>( (*mapIt).second.m_TargetComplement ) /
- static_cast<RealType>( (*mapIt).second.m_Target );
- return value;
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::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<LabelType>::Zero )
- {
- continue;
- }
- numerator += static_cast<RealType>( (*mapIt).second.m_SourceComplement );
- denominator += static_cast<RealType>( (*mapIt).second.m_Source );
- }
- return ( numerator / denominator );
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::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<RealType>( (*mapIt).second.m_SourceComplement ) /
- static_cast<RealType>( (*mapIt).second.m_Source );
- return value;
-}
-
-template<class TLabelImage>
-void
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::PrintSelf( std::ostream& os, Indent indent ) const
-{
- Superclass::PrintSelf( os, indent );
-
-}
-
-
-}// end namespace itk
-#endif
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