itk::watershed::Segmenter< TInputImage > Class Template Reference

#include <itkWatershedSegmenter.h>

Inheritance diagram for itk::watershed::Segmenter< TInputImage >:

[legend]Collaboration diagram for itk::watershed::Segmenter< TInputImage >:

[legend]List of all members.

[NOHEADER]
typedef TInputImage	InputImageType
typedef Image< unsigned long, itkGetStaticConstMacro(ImageDimension)	OutputImageType )
typedef InputImageType::RegionType	ImageRegionType
typedef InputImageType::PixelType	InputPixelType
typedef Boundary< InputPixelType, itkGetStaticConstMacro(ImageDimension)	BoundaryType )
typedef BoundaryType::IndexType	BoundaryIndexType
typedef BoundaryType::FlatHashValueType	BoundaryFlatHashValueType
typedef SegmentTable< InputPixelType >	SegmentTableType
typedef DataObject::Pointer	DataObjectPointer
	itkStaticConstMacro (ImageDimension, unsigned int, TInputImage::ImageDimension)
[NOHEADER]
typedef ProcessObject	Superclass
typedef SmartPointer< Self >	Pointer
typedef SmartPointer< const Self >	ConstPointer
virtual const char *	GetClassName () const
Pointer	New ()
Public Types
typedef Segmenter	Self
typedef InputImageType::Pointer	InputImageTypePointer
typedef OutputImageType::Pointer	OutputImageTypePointer
typedef SegmentTableType::Pointer	SegmentTableTypePointer
typedef BoundaryType::Pointer	BoundaryTypePointer
Public Member Functions
void	GenerateData ()
virtual DataObjectPointer	MakeOutput (unsigned int idx)
InputImageType *	GetInputImage (void)
void	SetInputImage (InputImageType *img)
OutputImageType *	GetOutputImage (void)
void	SetOutputImage (OutputImageType *img)
SegmentTableType *	GetSegmentTable (void)
void	SetSegmentTable (SegmentTableType *s)
BoundaryType *	GetBoundary (void)
void	SetBoundary (BoundaryType *b)
void	SetLargestPossibleRegion (ImageRegionType reg)
ImageRegionType	GetLargestPossibleRegion () const
virtual void	SetCurrentLabel (unsigned long _arg)
virtual unsigned long	GetCurrentLabel ()
virtual void	SetThreshold (double _arg)
virtual double	GetThreshold ()
virtual void	SetDoBoundaryAnalysis (bool _arg)
virtual bool	GetDoBoundaryAnalysis ()
virtual InputPixelType	GetMinimum ()
virtual void	SetMinimum (InputPixelType _arg)
virtual InputPixelType	GetMaximum ()
virtual void	SetMaximum (InputPixelType _arg)
virtual bool	GetSortEdgeLists ()
virtual void	SetSortEdgeLists (bool _arg)
Static Public Member Functions
void	RelabelImage (OutputImageTypePointer, ImageRegionType, EquivalencyTable::Pointer)
Static Public Attributes
unsigned long	NULL_LABEL
short	NULL_FLOW
Protected Types
typedef itk::hash_map< unsigned long, flat_region_t, itk::hash< unsigned long > >	flat_region_table_t
typedef itk::hash_map< unsigned long, InputPixelType, itk::hash< unsigned long > >	edge_table_t
typedef itk::hash_map< unsigned long, edge_table_t, itk::hash< unsigned long > >	edge_table_hash_t
Protected Member Functions
	Segmenter ()
	Segmenter (const Self &)
virtual	~Segmenter ()
void	PrintSelf (std::ostream &os, Indent indent) const
void	operator= (const Self &)
virtual void	GenerateConnectivity ()
void	InitializeBoundary ()
void	AnalyzeBoundaryFlow (InputImageTypePointer, flat_region_table_t &, InputPixelType)
void	BuildRetainingWall (InputImageTypePointer, ImageRegionType, InputPixelType)
void	LabelMinima (InputImageTypePointer, ImageRegionType, flat_region_table_t &, InputPixelType)
void	GradientDescent (InputImageTypePointer, ImageRegionType)
void	DescendFlatRegions (flat_region_table_t &, ImageRegionType)
void	UpdateSegmentTable (InputImageTypePointer, ImageRegionType)
void	CollectBoundaryInformation (flat_region_table_t &)
void	GenerateInputRequestedRegion ()
void	GenerateOutputRequestedRegion (DataObject *output)
void	UpdateOutputInformation ()
Static Protected Member Functions
void	Threshold (InputImageTypePointer destination, InputImageTypePointer source, const ImageRegionType source_region, const ImageRegionType destination_region, InputPixelType threshold)
void	MinMax (InputImageTypePointer img, ImageRegionType region, InputPixelType &min, InputPixelType &max)
void	MergeFlatRegions (flat_region_table_t &, EquivalencyTable::Pointer)
void	SetImageValues (InputImageTypePointer img, const ImageRegionType region, InputPixelType value)
void	SetImageValues (OutputImageTypePointer img, const ImageRegionType region, unsigned long value)
Protected Attributes
connectivity_t	m_Connectivity

template<class TInputImage>
class itk::watershed::Segmenter< TInputImage >

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Member Typedef Documentation

template<class TInputImage> typedef BoundaryType::FlatHashValueType itk::watershed::Segmenter< TInputImage >::BoundaryFlatHashValueType

Define image types and dimensionality Definition at line 106 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef BoundaryType::IndexType itk::watershed::Segmenter< TInputImage >::BoundaryIndexType

Define image types and dimensionality Definition at line 105 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef Boundary<InputPixelType, itkGetStaticConstMacro(ImageDimension) itk::watershed::Segmenter< TInputImage >::BoundaryType)

Define image types and dimensionality Definition at line 104 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef BoundaryType::Pointer itk::watershed::Segmenter< TInputImage >::BoundaryTypePointer

Definition at line 124 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef SmartPointer<const Self> itk::watershed::Segmenter< TInputImage >::ConstPointer

Methods to implement smart pointers and work with the itk object factory Reimplemented from itk::ProcessObject. Definition at line 115 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef DataObject::Pointer itk::watershed::Segmenter< TInputImage >::DataObjectPointer

Define image types and dimensionality Reimplemented from itk::ProcessObject. Definition at line 108 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef itk::hash_map<unsigned long, edge_table_t, itk::hash<unsigned long> > itk::watershed::Segmenter< TInputImage >::edge_table_hash_t [protected]

Definition at line 270 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef itk::hash_map<unsigned long, InputPixelType, itk::hash<unsigned long> > itk::watershed::Segmenter< TInputImage >::edge_table_t [protected]

Table for storing tables of edges. This is convenient in generating the segment table, even though the edge tables are stored as ordered lists. An ``edge'' in this context is synonymous with a segment ``adjacency''. Definition at line 267 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef itk::hash_map<unsigned long, flat_region_t, itk::hash<unsigned long> > itk::watershed::Segmenter< TInputImage >::flat_region_table_t [protected]

Table for storing flat region information. Definition at line 253 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef InputImageType::RegionType itk::watershed::Segmenter< TInputImage >::ImageRegionType

Define image types and dimensionality Definition at line 102 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef TInputImage itk::watershed::Segmenter< TInputImage >::InputImageType

Define image types and dimensionality Definition at line 98 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef InputImageType::Pointer itk::watershed::Segmenter< TInputImage >::InputImageTypePointer

Typedefs necessary on microsoft VC++ to avoid internal compiler errors Definition at line 121 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef InputImageType::PixelType itk::watershed::Segmenter< TInputImage >::InputPixelType

Define image types and dimensionality Definition at line 103 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef Image<unsigned long, itkGetStaticConstMacro(ImageDimension) itk::watershed::Segmenter< TInputImage >::OutputImageType)

Define image types and dimensionality Definition at line 101 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef OutputImageType::Pointer itk::watershed::Segmenter< TInputImage >::OutputImageTypePointer

Definition at line 122 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef SmartPointer<Self> itk::watershed::Segmenter< TInputImage >::Pointer

Methods to implement smart pointers and work with the itk object factory Reimplemented from itk::ProcessObject. Definition at line 114 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef SegmentTable<InputPixelType> itk::watershed::Segmenter< TInputImage >::SegmentTableType

Define image types and dimensionality Definition at line 107 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef SegmentTableType::Pointer itk::watershed::Segmenter< TInputImage >::SegmentTableTypePointer

Definition at line 123 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef Segmenter itk::watershed::Segmenter< TInputImage >::Self

Standard self typedefs Reimplemented from itk::ProcessObject. Definition at line 95 of file itkWatershedSegmenter.h.

template<class TInputImage> typedef ProcessObject itk::watershed::Segmenter< TInputImage >::Superclass

Methods to implement smart pointers and work with the itk object factory Reimplemented from itk::ProcessObject. Definition at line 113 of file itkWatershedSegmenter.h.

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Constructor & Destructor Documentation

template<class TInputImage> itk::watershed::Segmenter< TInputImage >::Segmenter (   )  [protected]

template<class TInputImage> itk::watershed::Segmenter< TInputImage >::Segmenter (  const Self &   )  [inline, protected]

Definition at line 273 of file itkWatershedSegmenter.h.

template<class TInputImage> virtual itk::watershed::Segmenter< TInputImage >::~Segmenter (   )  [inline, protected, virtual]

Definition at line 274 of file itkWatershedSegmenter.h.

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Member Function Documentation

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::AnalyzeBoundaryFlow (  InputImageTypePointer  , flat_region_table_t &  , InputPixelType  )  [protected]

Performs a gradient descent connected component analysis at the boundaries of the images that border other image chunks. Useful only in data streaming applications.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::BuildRetainingWall (  InputImageTypePointer  , ImageRegionType  , InputPixelType  )  [protected]

Fills boundary pixels with a specified value. Used by labeling methods to build a very high ``wall'' around the image so that gradient descent does not need to watch boundaries.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::CollectBoundaryInformation (  flat_region_table_t &   )  [protected]

Traverses each boundary and fills in the data needed for joining streamed chunks of an image volume. Only necessary for streaming applications.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::DescendFlatRegions (  flat_region_table_t &  , ImageRegionType  )  [protected]

Associates each flat region with a local minimum and relabels accordingly.

template<class TInputImage> virtual void itk::watershed::Segmenter< TInputImage >::GenerateConnectivity (   )  [protected, virtual]

Constructs the connectivity list and the corresponding set of directional Offset indicies.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::GenerateData (   )  [virtual]

Standard non-threaded pipeline execution method. Reimplemented from itk::ProcessObject.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::GenerateInputRequestedRegion (   )  [protected, virtual]

This method asks for an image region that is one pixel larger at each boundary than the region being processed. This single pixel expansion represents an overlap with adjacent image chunks Reimplemented from itk::ProcessObject.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::GenerateOutputRequestedRegion (  DataObject *  output  )  [protected, virtual]

This method asks for an image region that is one pixel larger at each boundary than the region being processed. This single pixel expansion represents an overlap with adjacent image chunks Reimplemented from itk::ProcessObject.

template<class TInputImage> BoundaryType* itk::watershed::Segmenter< TInputImage >::GetBoundary (  void   )  [inline]

Returns the boundary information data necessary only for data streaming applications. Definition at line 160 of file itkWatershedSegmenter.h.

template<class TInputImage> virtual const char* itk::watershed::Segmenter< TInputImage >::GetClassName (   )  const [virtual]

Methods to implement smart pointers and work with the itk object factory Reimplemented from itk::ProcessObject.

template<class TInputImage> virtual unsigned long itk::watershed::Segmenter< TInputImage >::GetCurrentLabel (   )  [virtual]

Gets/Sets the initial label (unsigned long integer value) used by the labeling algorithm. Only necessary for streaming applications.

template<class TInputImage> virtual bool itk::watershed::Segmenter< TInputImage >::GetDoBoundaryAnalysis (   )  [virtual]

Turns on special labeling of the boundaries for streaming applications. The default value is FALSE, meaning that boundary analysis is turned off.

template<class TInputImage> InputImageType* itk::watershed::Segmenter< TInputImage >::GetInputImage (  void   )  [inline]

Get/Set the input image. Definition at line 133 of file itkWatershedSegmenter.h.

template<class TInputImage> ImageRegionType itk::watershed::Segmenter< TInputImage >::GetLargestPossibleRegion (   )  const [inline]

This method is necessary until the streaming mechanisms of the Itk pipeline are full fleshed out. It is only used for streaming applications. Calling this method gets/sets the image size of the complete volume being streamed. The member variables controlled by this method will not be modified by the Itk pipeline and are necessary for analysis of boundaries. Definition at line 182 of file itkWatershedSegmenter.h.

template<class TInputImage> virtual InputPixelType itk::watershed::Segmenter< TInputImage >::GetMaximum (   )  [virtual]

Prior to thresholding the input image, the filter calculates minimum and maximum values for the image. These values are stored as member variables.

template<class TInputImage> virtual InputPixelType itk::watershed::Segmenter< TInputImage >::GetMinimum (   )  [virtual]

Prior to thresholding the input image, the filter calculates minimum and maximum values for the image. These values are stored as member variables.

template<class TInputImage> OutputImageType* itk::watershed::Segmenter< TInputImage >::GetOutputImage (  void   )  [inline]

Get/Set the labeled output image. The output image is always of unsigned long integers. Definition at line 142 of file itkWatershedSegmenter.h.

template<class TInputImage> SegmentTableType* itk::watershed::Segmenter< TInputImage >::GetSegmentTable (  void   )  [inline]

Get/Set the segment table. The segment table is a table of segmentation information identifying each region produced by the labeling algorithm. Definition at line 151 of file itkWatershedSegmenter.h.

template<class TInputImage> virtual bool itk::watershed::Segmenter< TInputImage >::GetSortEdgeLists (   )  [virtual]

Determines whether the algorithm will sort the adjacencies in its SegmentTable before returning. Default is true. This is an option only useful for streaming applications where the sorting only needs to be done after all iterations have taken place.

template<class TInputImage> virtual double itk::watershed::Segmenter< TInputImage >::GetThreshold (   )  [virtual]

Gets/Sets the input threshold. Threshold is specified as a percentage (0.0 - 1.0) of the maximum height of the image. This filter thresholds the input image to remove all values below /f$ L = min + T * (max - min) /f$, where /f$ max, min /f$ are the maximum, minimum values in the image and /f$ T /f$ is the threshold parameter value. Values in the image less than /f$ L /f$ are raised to /f$ L /f$. Thresholding minimum values in the image decreases the number of local minima in the image and produces an initial segmentation with fewer segments. The assumption is that the ``shallow'' regions that this thresholding eliminates are generally not of interest.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::GradientDescent (  InputImageTypePointer  , ImageRegionType  )  [protected]

Follows each unlabeled pixel in the image down its path of steepest descent. Each pixel along that path is identified with the local minima already labeled at the end of the path.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::InitializeBoundary (   )  [protected]

Allocates boundary structure information and sets the boundary data to null values.

template<class TInputImage> itk::watershed::Segmenter< TInputImage >::itkStaticConstMacro (  ImageDimension  , unsigned  int, TInputImage::ImageDimension  )

Define image types and dimensionality

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::LabelMinima (  InputImageTypePointer  , ImageRegionType  , flat_region_table_t &  , InputPixelType  )  [protected]

Labels all the local minima in the image. Also identifies and labels connected ``flat'' regions.

template<class TInputImage> virtual DataObjectPointer itk::watershed::Segmenter< TInputImage >::MakeOutput (  unsigned int  idx  )  [virtual]

Standard itk::ProcessObject subclass method. Reimplemented from itk::ProcessObject.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::MergeFlatRegions (  flat_region_table_t &  , EquivalencyTable::Pointer  )  [static, protected]

Helper function. Finds the minimum and maximum values in an image.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::MinMax (  InputImageTypePointer  img, ImageRegionType  region, InputPixelType &  min, InputPixelType &  max )  [static, protected]

Helper function. Finds the minimum and maximum values in an image.

template<class TInputImage> Pointer itk::watershed::Segmenter< TInputImage >::New (   )  [static]

Methods to implement smart pointers and work with the itk object factory Reimplemented from itk::Object.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::operator= (  const Self &   )  [inline, protected]

Reimplemented from itk::ProcessObject. Definition at line 280 of file itkWatershedSegmenter.h.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::PrintSelf (  std::ostream &  os, Indent  indent )  const [protected, virtual]

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes. Reimplemented from itk::ProcessObject.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::RelabelImage (  OutputImageTypePointer  , ImageRegionType  , EquivalencyTable::Pointer  )  [static]

Helper function. Other classes may have occasion to use this. Relabels an image according to a table of equivalencies.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::SetBoundary (  BoundaryType *  b  )  [inline]

Returns the boundary information data necessary only for data streaming applications. Definition at line 163 of file itkWatershedSegmenter.h.

template<class TInputImage> virtual void itk::watershed::Segmenter< TInputImage >::SetCurrentLabel (  unsigned long  _arg  )  [virtual]

Gets/Sets the initial label (unsigned long integer value) used by the labeling algorithm. Only necessary for streaming applications.

template<class TInputImage> virtual void itk::watershed::Segmenter< TInputImage >::SetDoBoundaryAnalysis (  bool  _arg  )  [virtual]

Turns on special labeling of the boundaries for streaming applications. The default value is FALSE, meaning that boundary analysis is turned off.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::SetImageValues (  OutputImageTypePointer  img, const ImageRegionType  region, unsigned long  value )  [static, protected]

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::SetImageValues (  InputImageTypePointer  img, const ImageRegionType  region, InputPixelType  value )  [static, protected]

Helper functions for filling in regions with values

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::SetInputImage (  InputImageType *  img  )  [inline]

Get/Set the input image. Definition at line 136 of file itkWatershedSegmenter.h.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::SetLargestPossibleRegion (  ImageRegionType  reg  )  [inline]

This method is necessary until the streaming mechanisms of the Itk pipeline are full fleshed out. It is only used for streaming applications. Calling this method gets/sets the image size of the complete volume being streamed. The member variables controlled by this method will not be modified by the Itk pipeline and are necessary for analysis of boundaries. Definition at line 176 of file itkWatershedSegmenter.h.

template<class TInputImage> virtual void itk::watershed::Segmenter< TInputImage >::SetMaximum (  InputPixelType  _arg  )  [virtual]

Prior to thresholding the input image, the filter calculates minimum and maximum values for the image. These values are stored as member variables.

template<class TInputImage> virtual void itk::watershed::Segmenter< TInputImage >::SetMinimum (  InputPixelType  _arg  )  [virtual]

Prior to thresholding the input image, the filter calculates minimum and maximum values for the image. These values are stored as member variables.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::SetOutputImage (  OutputImageType *  img  )  [inline]

Get/Set the labeled output image. The output image is always of unsigned long integers. Definition at line 145 of file itkWatershedSegmenter.h.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::SetSegmentTable (  SegmentTableType *  s  )  [inline]

Get/Set the segment table. The segment table is a table of segmentation information identifying each region produced by the labeling algorithm. Definition at line 154 of file itkWatershedSegmenter.h.

template<class TInputImage> virtual void itk::watershed::Segmenter< TInputImage >::SetSortEdgeLists (  bool  _arg  )  [virtual]

Determines whether the algorithm will sort the adjacencies in its SegmentTable before returning. Default is true. This is an option only useful for streaming applications where the sorting only needs to be done after all iterations have taken place.

template<class TInputImage> virtual void itk::watershed::Segmenter< TInputImage >::SetThreshold (  double  _arg  )  [virtual]

Gets/Sets the input threshold. Threshold is specified as a percentage (0.0 - 1.0) of the maximum height of the image. This filter thresholds the input image to remove all values below /f$ L = min + T * (max - min) /f$, where /f$ max, min /f$ are the maximum, minimum values in the image and /f$ T /f$ is the threshold parameter value. Values in the image less than /f$ L /f$ are raised to /f$ L /f$. Thresholding minimum values in the image decreases the number of local minima in the image and produces an initial segmentation with fewer segments. The assumption is that the ``shallow'' regions that this thresholding eliminates are generally not of interest.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::Threshold (  InputImageTypePointer  destination, InputImageTypePointer  source, const ImageRegionType  source_region, const ImageRegionType  destination_region, InputPixelType  threshold )  [static, protected]

Helper function. Thresholds low values and copies values from one image into another. The source and destination regions must match in size (not enforced).

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::UpdateOutputInformation (   )  [protected, virtual]

This method asks for an image region that is one pixel larger at each boundary than the region being processed. This single pixel expansion represents an overlap with adjacent image chunks Reimplemented from itk::ProcessObject.

template<class TInputImage> void itk::watershed::Segmenter< TInputImage >::UpdateSegmentTable (  InputImageTypePointer  , ImageRegionType  )  [protected]

Adds entries to the output segment table for all labeled segments in the image.

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Member Data Documentation

template<class TInputImage> connectivity_t itk::watershed::Segmenter< TInputImage >::m_Connectivity [protected]

Holds generalized connectivity information for connected component labeling and gradient descent analysis in pixel neighborhoods. Definition at line 367 of file itkWatershedSegmenter.h.

template<class TInputImage> short itk::watershed::Segmenter< TInputImage >::NULL_FLOW [static]

A constant used in the labeling algorithm. Definition at line 130 of file itkWatershedSegmenter.h.

template<class TInputImage> unsigned long itk::watershed::Segmenter< TInputImage >::NULL_LABEL [static]

A constant used in the labeling algorithm. Definition at line 127 of file itkWatershedSegmenter.h.

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The documentation for this class was generated from the following file:

• itkWatershedSegmenter.h

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