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/*=========================================================================
*
* Copyright Insight Software Consortium
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
#ifndef itkLabelOverlapMeasuresImageFilter_h
#define itkLabelOverlapMeasuresImageFilter_h
#include "itkImageToImageFilter.h"
#include "itkNumericTraits.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.
*
* This code was contributed in the Insight Journal paper:
* "Introducing Dice, Jaccard, and Other Label Overlap Measures To ITK"
* by Nicholas J. Tustison, James C. Gee
* https://hdl.handle.net/10380/3141
* http://www.insight-journal.org/browse/publication/707
*
* \author Nicholas J. Tustison
* \sa LabelOverlapMeasuresImageFilter
*
* \ingroup ITKImageStatistics
* \ingroup MultiThreaded
*/
template<typename TLabelImage>
class 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 );
/** 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 for computations. */
typedef typename NumericTraits<LabelType>::RealType RealType;
/** \class LabelSetMeasures
* \brief Metrics stored per label
* \ingroup ITKImageStatistics
*/
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 )
{
if(this != &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;
}
return *this;
}
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() const;
RealType GetUnionOverlap() const;
RealType GetMeanOverlap() const;
RealType GetVolumeSimilarity() const;
RealType GetFalseNegativeError() const;
RealType GetFalsePositiveError() const;
/** measures over individual labels */
RealType GetTargetOverlap( LabelType ) const;
RealType GetUnionOverlap( LabelType ) const;
RealType GetMeanOverlap( LabelType ) const;
RealType GetVolumeSimilarity( LabelType ) const;
RealType GetFalseNegativeError( LabelType ) const;
RealType GetFalsePositiveError( LabelType ) const;
/** alternative names */
RealType GetJaccardCoefficient() const
{ return this->GetUnionOverlap(); }
RealType GetJaccardCoefficient( LabelType label ) const
{ return this->GetUnionOverlap( label ); }
RealType GetDiceCoefficient() const
{ return this->GetMeanOverlap(); }
RealType GetDiceCoefficient( LabelType label ) const
{ 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 ITK_OVERRIDE;
/**
* 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() ITK_OVERRIDE;
void BeforeThreadedGenerateData() ITK_OVERRIDE;
void AfterThreadedGenerateData() ITK_OVERRIDE;
/** Multi-thread version GenerateData. */
void ThreadedGenerateData( const RegionType&, ThreadIdType ) ITK_OVERRIDE;
// Override since the filter produces all of its output
void EnlargeOutputRequestedRegion( DataObject *data ) ITK_OVERRIDE;
private:
LabelOverlapMeasuresImageFilter( const Self& ) ITK_DELETE_FUNCTION;
void operator=( const Self& ) ITK_DELETE_FUNCTION;
std::vector<MapType> m_LabelSetMeasuresPerThread;
MapType m_LabelSetMeasures;
}; // end of class
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
#include "itkLabelOverlapMeasuresImageFilter.hxx"
#endif
#endif
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