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itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage > Class Template Reference

This class implements a finite difference partial differential equation solver for evolving surfaces embedded in volumes as level-sets. More...

#include <itkParallelSparseFieldLevelSetImageFilter.h>

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List of all members.

[NOHEADER]

void Iterate ()
ITK_THREAD_RETURN_TYPE IterateThreaderCallback (void *arg)

Public Types

typedef ParallelSparseFieldLevelSetImageFilter Self
typedef FiniteDifferenceImageFilter<
TInputImage, TOutputImage > 
Superclass
typedef SmartPointer< SelfPointer
typedef SmartPointer< const
Self
ConstPointer
typedef Superclass::TimeStepType TimeStepType
typedef Superclass::FiniteDifferenceFunctionType FiniteDifferenceFunctionType
typedef TInputImage InputImageType
typedef TOutputImage OutputImageType
typedef OutputImageType::IndexType IndexType
typedef OutputImageType::PixelType PixelType
typedef OutputImageType::RegionType ThreadRegionType
typedef OutputImageType::ValueType ValueType
typedef ParallelSparseFieldLevelSetNode<
IndexType
LayerNodeType
typedef SparseFieldLayer<
LayerNodeType
LayerType
typedef LayerType::Pointer LayerPointerType
typedef std::vector< LayerPointerTypeLayerListType
typedef signed char StatusType
typedef Image< StatusType,
itkGetStaticConstMacro(ImageDimension) 
StatusImageType )
typedef ObjectStore< LayerNodeTypeLayerNodeStorageType
typedef Offset< itkGetStaticConstMacro(ImageDimension) OffsetType )

Public Member Functions

virtual const char * GetClassName () const
 itkStaticConstMacro (ImageDimension, unsigned int, TOutputImage::ImageDimension)
LayerPointerType GetActiveListForIndex (const IndexType index)
virtual void SetNumberOfLayers (StatusType _arg)
virtual StatusType GetNumberOfLayers ()
virtual void SetIsoSurfaceValue (ValueType _arg)
virtual ValueType GetIsoSurfaceValue ()

Static Public Member Functions

Pointer New ()

Protected Member Functions

 ParallelSparseFieldLevelSetImageFilter ()
 ~ParallelSparseFieldLevelSetImageFilter ()
virtual void PrintSelf (std::ostream &os, Indent indent) const
virtual void GenerateData ()
void CopyInputToOutput ()
void AllocateUpdateBuffer ()
void Initialize ()
void ConstructActiveLayer ()
void InitializeActiveLayerValues ()
void ConstructLayer (StatusType from, StatusType to)
void ProcessStatusList (LayerType *InputList, StatusType ChangeToStatus, StatusType SearchForStatus, unsigned int ThreadId)
void PropagateAllLayerValues ()
void PropagateLayerValues (StatusType from, StatusType to, StatusType promote, unsigned int InOrOut)
virtual void InitializeBackgroundPixels ()
void ComputeInitialThreadBoundaries ()
unsigned int GetThreadNumber (unsigned int splitAxisValue)
void GetThreadRegionSplitByBoundary (unsigned int ThreadId, ThreadRegionType &ThreadRegion)
void DeallocateData ()
virtual ValueType ThreadedCalculateUpdateValue (const unsigned int, const IndexType, const TimeStepType &dt, const ValueType &value, const ValueType &change)
virtual void ThreadedProcessPixelEnteringActiveLayer (const IndexType, const ValueType, const unsigned int)
void ApplyUpdate (TimeStepType)
virtual void ThreadedApplyUpdate (TimeStepType dt, unsigned int ThreadId)
TimeStepType CalculateChange ()
virtual TimeStepType ThreadedCalculateChange (unsigned int ThreadId)
void ThreadedUpdateActiveLayerValues (TimeStepType dt, LayerType *StatusUpList, LayerType *StatusDownList, unsigned int ThreadId)
void CopyInsertList (unsigned int ThreadId, LayerPointerType FromListPtr, LayerPointerType ToListPtr)
void ClearList (unsigned int ThreadId, LayerPointerType ListPtr)
void CopyInsertInterNeighborNodeTransferBufferLayers (unsigned int ThreadId, LayerPointerType InputList, unsigned int InOrOut, unsigned int BufferLayerNumber)
void ClearInterNeighborNodeTransferBufferLayers (unsigned int ThreadId, unsigned int InOrOut, unsigned int BufferLayerNumber)
void ThreadedProcessFirstLayerStatusLists (unsigned int InputLayerNumber, unsigned int OutputLayerNumber, StatusType SearchForStatus, unsigned int InOrOut, unsigned int BufferLayerNumber, unsigned int ThreadId)
void ThreadedProcessStatusList (unsigned int InputLayerNumber, unsigned int OutputLayerNumber, StatusType ChangeToStatus, StatusType SearchForStatus, unsigned int InOrOut, unsigned int BufferLayerNumber, unsigned int ThreadId)
void ThreadedProcessOutsideList (unsigned int InputLayerNumber, StatusType ChangeToStatus, unsigned int InOrOut, unsigned int BufferLayerNumber, unsigned int ThreadId)
void ThreadedPropagateLayerValues (StatusType from, StatusType to, StatusType promote, unsigned int InorOut, unsigned int ThreadId)
void GetThreadRegionSplitUniformly (unsigned int ThreadId, ThreadRegionType &ThreadRegion)
void ThreadedPostProcessOutput (const ThreadRegionType &regionToProcess)
virtual void CheckLoadBalance ()
virtual void ThreadedLoadBalance (unsigned int ThreadId)
virtual void ThreadedInitializeIteration (unsigned int ThreadId)
void ThreadedAllocateData (unsigned int ThreadId)
void ThreadedInitializeData (unsigned int ThreadId, const ThreadRegionType &ThreadRegion)
void WaitForAll ()
void SignalNeighborsAndWait (unsigned int ThreadId)
void SignalNeighbor (unsigned int SemaphoreArrayNumber, unsigned int ThreadId)
void WaitForNeighbor (unsigned int SemaphoreArrayNumber, unsigned int ThreadId)

Protected Attributes

ParallelSparseFieldCityBlockNeighborList<
NeighborhoodIterator< OutputImageType > > 
m_NeighborList
OutputImageType::Pointer m_ShiftedImage
LayerListType m_Layers
StatusType m_NumberOfLayers
StatusImageType::Pointer m_StatusImage
OutputImageType::Pointer m_OutputImage
StatusImageType::Pointer m_StatusImageTemp
OutputImageType::Pointer m_OutputImageTemp
LayerNodeStorageType::Pointer m_LayerNodeStore
ValueType m_IsoSurfaceValue
unsigned int m_NumOfThreads
unsigned int m_SplitAxis
unsigned int m_ZSize
bool m_BoundaryChanged
unsigned int * m_Boundary
int * m_GlobalZHistogram
unsigned int * m_MapZToThreadNumber
int * m_ZCumulativeFrequency
Barrier::Pointer m_Barrier
ThreadDatam_Data
bool m_Stop
bool m_InterpolateSurfaceLocation

Static Protected Attributes

double m_ConstantGradientValue
ValueType m_ValueOne
ValueType m_ValueZero
StatusType m_StatusActiveChangingUp
StatusType m_StatusActiveChangingDown
StatusType m_StatusNull
StatusType m_StatusChanging
StatusType m_StatusBoundaryPixel

Detailed Description

template<class TInputImage, class TOutputImage>
class itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >

This class implements a finite difference partial differential equation solver for evolving surfaces embedded in volumes as level-sets.

The ``sparse field'' approach to the level-set model is a logical extension of the classical narrow band technique, which seeks to minimize computational effort by restricting calculations to those pixels in a region of interest around the moving surface (the $k$-level curve). The sparse field method uses a narrow band that is exactly the width needed to calculate changes on the level curve for the next time step. Because the band of grid points under consideration is so sparse, this approach has several advantages: the algorithm does exactly the number of calculations needed to determine the next position of the $k$-level curve, and the distance transform around the level curve can be recomputed at each iteration.
The sparse field algorithm works by constructing a linked list of indicies that are adjacent to the $k$-level set. These indicies are called the ``active set''. The values at these active set indicies define the position of the $k$-level curve. The active set indicies are shifted to follow the distance transform embedding of the $k$-level curve as their values move in and out of a fixed numerical range about $k$. In this way, the active set is maintained as only those pixels adjacent to the evolving surface. Calculations are then done only at indicies contained in the active set.
The city-block neighborhoods of the active set indicies are maintained as separate lists called ``layers''. At each iteration, the values at the layers are reinitialized as the distance transform from the active set. The number of layers can be adjusted according to the footprint needed for the calculations on the level curve.
Briefly, the sparse field solver algorithm is as follows:
1. For each active layer index $x_j$: Compute the change at $u_{x_j}$, the grid point in the embedding, based on local geometry and external forces and using a stable numerical scheme.
2. For each active layer index $x_j$, add the change to the grid point value and redefine the active set indicies and those of its layers based on any value changes which have moved outside of the numerical range allowed for the active set.

3. Starting with the first layers adjacent to the active set and moving outwards, reconstruct the distance transform by setting values in the layers according to their neighbors. At the very outer layers, add or remove indicies which have come into or moved out of the sparse field.

HOW TO USE THIS CLASS
Typically, this class should be subclassed with additional functionality for specific applications. It is possible, however to use this solver as a filter directly by instantiating it and supplying it with an appropriate LevelSetFunction object via the SetDifferenceFunction method. See the subclasses and their associated documentation for more information on using this class. Also see the FiniteDifferenceImageFilter documentation for a general overview of this class of solvers.
INPUTS
This filter takes an itk::Image as input. The appropriate type of input image is entirely determined by the application. As a rule, however, the input type is immediately converted to the output type before processing. This is because the input is not assumed to be a real value type and must be converted to signed, real values for the calculations. The input values will also be shifted by the $k$ isosurface value so that the algorithm only needs to consider the zero level set.
OUTPUTS
The output of the filter is the distance transform embedding of the isosurface as the zero level set. Values outside the surface will be negative and values inside the surface will be positive. The distance transform only holds for those indicies in layers around the active layer. Elsewhere, the values are a fixed positive or negative that is one greater than the layer of greatest magnitude. In other words, if there are three layers, then inside values increase only to 4.0 and outside values only to -4.0.
PARAMETERS
The NumberOfLayers parameter controls the number of layers inside and outside of the active set (see description above). The sparse field will contain 2*NumberOfLayers+1 lists of indices: the active set and city block neighbors inside and outside the active set. It is important to specify enough layers to cover the footprint of your calculations. Curvature calculations in three dimensions, for example, require 3 layers. In two dimensions, a minimum of 2 layers is probably required. Higher order derivatives and other geometrical measures may require more layers. If too few layers are specified, then the calculations will pull values from the background, which may consist of arbitrary or random values.
The IsoSurfaceValue indicates which value in the input represents the interface of interest. By default, this value is zero. When the solver initializes, it will subtract the IsoSurfaceValue from all values, in the input, shifting the isosurface of interest to zero in the output.
IMPORTANT!
Read the documentation for FiniteDifferenceImageFilter before attempting to use this filter. The solver requires that you specify a FiniteDifferenceFunction to use for calculations. This is set using the method SetDifferenceFunction in the parent class.
REFERENCES
Whitaker, Ross. A Level-Set Approach to 3D Reconstruction from Range Data. International Journal of Computer Vision. V. 29 No. 3, 203-231. 1998.
Sethian, J.A. Level Set Methods. Cambridge University Press. 1996.

Definition at line 247 of file itkParallelSparseFieldLevelSetImageFilter.h.


Member Typedef Documentation

template<class TInputImage, class TOutputImage>
typedef SmartPointer<const Self> itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ConstPointer
 

Reimplemented from itk::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

Definition at line 256 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef Superclass::FiniteDifferenceFunctionType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::FiniteDifferenceFunctionType
 

The value type of the time step. This is distinct from PixelType because PixelType may often be a vector value, while the TimeStep is a scalar value.

Reimplemented from itk::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

Definition at line 260 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef OutputImageType::IndexType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::IndexType
 

Definition at line 271 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef TInputImage itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::InputImageType
 

Information derived from the image types.

Reimplemented from itk::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

Definition at line 269 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef std::vector<LayerPointerType> itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::LayerListType
 

A type for a list of LayerPointerTypes Definition at line 291 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef ObjectStore<LayerNodeType> itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::LayerNodeStorageType
 

Memory pre-allocator used to manage layer nodes in a multithreaded environment. Definition at line 302 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef ParallelSparseFieldLevelSetNode<IndexType> itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::LayerNodeType
 

Node type used in parallel sparse field layer lists. Definition at line 284 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef LayerType::Pointer itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::LayerPointerType
 

Definition at line 288 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef SparseFieldLayer<LayerNodeType> itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::LayerType
 

A list type used in the algorithm. Definition at line 287 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef Offset<itkGetStaticConstMacro(ImageDimension) itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::OffsetType)
 

Definition at line 304 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef TOutputImage itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::OutputImageType
 

Some convenient typedefs.

Reimplemented from itk::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

Definition at line 270 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef OutputImageType::PixelType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::PixelType
 

The pixel type of the output image will be used in computations.

Reimplemented from itk::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

Definition at line 275 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef SmartPointer<Self> itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::Pointer
 

Reimplemented from itk::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

Definition at line 255 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef ParallelSparseFieldLevelSetImageFilter itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::Self
 

Standard class typedefs

Reimplemented from itk::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

Definition at line 253 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef Image<StatusType, itkGetStaticConstMacro(ImageDimension) itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::StatusImageType)
 

The type of the image used to index status information. Necessary for the internals of the algorithm. Definition at line 298 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef signed char itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::StatusType
 

Type used for storing status information Definition at line 294 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef FiniteDifferenceImageFilter<TInputImage, TOutputImage> itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::Superclass
 

Reimplemented from itk::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

Definition at line 254 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef OutputImageType::RegionType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ThreadRegionType
 

Definition at line 277 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
typedef Superclass::TimeStepType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::TimeStepType
 

Typedefs from the superclass

Reimplemented from itk::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

Definition at line 259 of file itkParallelSparseFieldLevelSetImageFilter.h.

Referenced by itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ApplyUpdate().

template<class TInputImage, class TOutputImage>
typedef OutputImageType::ValueType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ValueType
 

The data type used in numerical computations. Derived from the output image type. Definition at line 281 of file itkParallelSparseFieldLevelSetImageFilter.h.


Constructor & Destructor Documentation

template<class TInputImage, class TOutputImage>
itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ParallelSparseFieldLevelSetImageFilter  )  [protected]
 

template<class TInputImage, class TOutputImage>
itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::~ParallelSparseFieldLevelSetImageFilter  )  [inline, protected]
 

Definition at line 330 of file itkParallelSparseFieldLevelSetImageFilter.h.


Member Function Documentation

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::AllocateUpdateBuffer  )  [inline, protected, virtual]
 

Reserves memory in the update buffer

Implements itk::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

Definition at line 414 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ApplyUpdate TimeStepType   )  [inline, protected, virtual]
 

This method is not implemented or necessary for this solver

Implements itk::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

Definition at line 526 of file itkParallelSparseFieldLevelSetImageFilter.h.

References itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::TimeStepType.

template<class TInputImage, class TOutputImage>
TimeStepType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::CalculateChange  )  [inline, protected, virtual]
 

This method is not implemented or necessary for this solver

Implements itk::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

Definition at line 533 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
virtual void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::CheckLoadBalance  )  [protected, virtual]
 

Check if the load is fairly balanced among the threads. This is performed by just one thread while all other threads wait. This need NOT be performed every iteration because the level-set surface moves slowly and it is correct to believe that during an iteration the movement is small enough that the small gain obtained by load balancing (if any) does not warrant the overhead for calling this method. How often this is done is controlled by a parameter LOAD_BALANCE_ITERATION_FREQUENCY which is defined in the IterateThreaderCallback() function. A parameter that defines a degree of unbalancedness of the load among threads is MAX_PIXEL_DIFFERENCE_PERCENT which is defined in CheckLoadBalance().

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ClearInterNeighborNodeTransferBufferLayers unsigned int  ThreadId,
unsigned int  InOrOut,
unsigned int  BufferLayerNumber
[protected]
 

Delete all nodes in a thread's own lists which its used to transfer nodes to neighboring threads.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ClearList unsigned int  ThreadId,
LayerPointerType  ListPtr
[protected]
 

Delete all nodes in the List

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ComputeInitialThreadBoundaries  )  [protected]
 

This performs the initial load distribution among the threads. Every thread gets a slab of the data to work on. The slabs created along a specific dimension. Load balancing is performed along the greatest numbered dimension (i.e. the 3rd dimension in the 3D case and the 2nd dimension in the 2D case). During the initializing of the sparse field layer an histogram is computed that stores the number of nodes in the active set for each index along the chosen dimension. This histogram is used to divide the work "equally" among threads so that each thread approximately get the same number of nodes to process.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ConstructActiveLayer  )  [protected]
 

Constructs the active layer and initialize the first layers inside and outside of the active layer. The active layer defines the position of the zero level set by its values, which are constrained within a range around zero.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ConstructLayer StatusType  from,
StatusType  to
[protected]
 

Initializes a layer of the sparse field using a previously initialized layer. Builds the list of nodes in m_Layer[to] using m_Layer[from]. Marks values in the m_StatusImage.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::CopyInputToOutput  )  [protected, virtual]
 

Copies the input to the output image. Processing occurs on the output image, so the data type of the output image determines the precision of the calculations (i.e. double or float). This method overrides the parent class method to do some additional processing.

Implements itk::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::CopyInsertInterNeighborNodeTransferBufferLayers unsigned int  ThreadId,
LayerPointerType  InputList,
unsigned int  InOrOut,
unsigned int  BufferLayerNumber
[protected]
 

Make a copy of the nodes given to one thread by its neighbors to process and insert them into the thread's own list.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::CopyInsertList unsigned int  ThreadId,
LayerPointerType  FromListPtr,
LayerPointerType  ToListPtr
[protected]
 

Make a copy of the nodes in the FromList and insert them into the ToList.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::DeallocateData  )  [protected]
 

Delete the data and synchronization primitives used by the threads during iterations.

template<class TInputImage, class TOutputImage>
virtual void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::GenerateData  )  [protected, virtual]
 

Reimplement the GenerateData() function from FiniteDifferenceImageFilter for more effective multithreading

Reimplemented from itk::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

template<class TInputImage, class TOutputImage>
LayerPointerType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::GetActiveListForIndex const IndexType  index  )  [inline]
 

Definition at line 318 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
virtual const char* itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::GetClassName  )  const [virtual]
 

Run-time type information (and related methods).

Reimplemented from itk::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

template<class TInputImage, class TOutputImage>
virtual ValueType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::GetIsoSurfaceValue  )  [virtual]
 

Set/Get the value of the isosurface to use in the input image.

template<class TInputImage, class TOutputImage>
virtual StatusType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::GetNumberOfLayers  )  [virtual]
 

Set/Get the number of layers to use in the sparse field. Argument is the number of layers on ONE side of the active layer, so the total layers in the sparse field is 2 * NumberOfLayers + 1

template<class TInputImage, class TOutputImage>
unsigned int itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::GetThreadNumber unsigned int  splitAxisValue  )  [protected]
 

Find the thread to which a pixel belongs

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::GetThreadRegionSplitByBoundary unsigned int  ThreadId,
ThreadRegionType ThreadRegion
[protected]
 

Obtain a thread's region split as per the load balancing is done.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::GetThreadRegionSplitUniformly unsigned int  ThreadId,
ThreadRegionType ThreadRegion
[protected]
 

Split the volume uniformly along the chosen dimension for post processing the output.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::Initialize  )  [protected, virtual]
 

Constructs the sparse field layers and initializes their values. Also creates data structures that are NOT local to a thread.

Reimplemented from itk::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::InitializeActiveLayerValues  )  [protected]
 

Initializes the values of the active layer set.

template<class TInputImage, class TOutputImage>
virtual void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::InitializeBackgroundPixels  )  [protected, virtual]
 

This method pre-processes pixels inside and outside the sparse field layers. The default is to set them to positive and negative values, respectively. This is not necessary as part of the calculations, but produces a more intuitive output for the user.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::Iterate  )  [protected]
 

This method calculates the change and does the update, i.e. one iteration of this iterative solver. A barrier class is used to synchronize execution and keep the CalculateChange and ApplyUpdate sections from executing simultaneously.

template<class TInputImage, class TOutputImage>
ITK_THREAD_RETURN_TYPE itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::IterateThreaderCallback void *  arg  )  [static, protected]
 

This method calculates the change and does the update, i.e. one iteration of this iterative solver. A barrier class is used to synchronize execution and keep the CalculateChange and ApplyUpdate sections from executing simultaneously.

template<class TInputImage, class TOutputImage>
itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::itkStaticConstMacro ImageDimension  ,
unsigned  int,
TOutputImage::ImageDimension 
 

template<class TInputImage, class TOutputImage>
Pointer itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::New  )  [static]
 

Method for creation through the object factory.

Reimplemented from itk::Object.

template<class TInputImage, class TOutputImage>
virtual void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::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::FiniteDifferenceImageFilter< TInputImage, TOutputImage >.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ProcessStatusList LayerType InputList,
StatusType  ChangeToStatus,
StatusType  SearchForStatus,
unsigned int  ThreadId
[protected]
 

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::PropagateAllLayerValues  )  [protected]
 

Adjusts the values associated with all the index layers of the sparse field by propagating out one layer at a time from the active set. This method also takes care of deleting nodes from the layers which have been marked in the status image as having been moved to other layers.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::PropagateLayerValues StatusType  from,
StatusType  to,
StatusType  promote,
unsigned int  InOrOut
[protected]
 

Adjusts the values in a single layer "to" using values in a neighboring layer "from". The list of indicies in "to" are traversed and assigned new values appropriately. Any indicies in "to" without neighbors in "from" are moved into the "promote" layer (or deleted if "promote" is greater than the number of layers). "InOrOut" == 1 indicates this propagation is inwards (more negative). "InOrOut" == 0 indicates this propagation is outwards (more positive).

template<class TInputImage, class TOutputImage>
virtual void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::SetIsoSurfaceValue ValueType  _arg  )  [virtual]
 

Set/Get the value of the isosurface to use in the input image.

template<class TInputImage, class TOutputImage>
virtual void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::SetNumberOfLayers StatusType  _arg  )  [virtual]
 

Set/Get the number of layers to use in the sparse field. Argument is the number of layers on ONE side of the active layer, so the total layers in the sparse field is 2 * NumberOfLayers + 1

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::SignalNeighbor unsigned int  SemaphoreArrayNumber,
unsigned int  ThreadId
[protected]
 

Thread synchronization methods.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::SignalNeighborsAndWait unsigned int  ThreadId  )  [protected]
 

Thread synchronization methods.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ThreadedAllocateData unsigned int  ThreadId  )  [protected]
 

Each thread allocates and initializes the data it will use by itself. This maintains the memory locality of data w.r.t. the thread in a shared memory environment.

template<class TInputImage, class TOutputImage>
virtual void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ThreadedApplyUpdate TimeStepType  dt,
unsigned int  ThreadId
[protected, virtual]
 

Does the actual work of updating the output from the UpdateContainer over an output region supplied by the multithreading mechanism.

template<class TInputImage, class TOutputImage>
virtual TimeStepType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ThreadedCalculateChange unsigned int  ThreadId  )  [protected, virtual]
 

This method does the actual work of calculating change over a region supplied by the multithreading mechanism.

template<class TInputImage, class TOutputImage>
virtual ValueType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ThreadedCalculateUpdateValue const unsigned  int,
const  IndexType,
const TimeStepType dt,
const ValueType value,
const ValueType change
[inline, protected, virtual]
 

This method allows a subclass to override the way in which updates to output values are applied during each iteration. The default simply follows the standard finite difference scheme of scaling the change by the timestep and adding to the value of the previous iteration. Definition at line 509 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ThreadedInitializeData unsigned int  ThreadId,
const ThreadRegionType ThreadRegion
[protected]
 

Each thread allocates and initializes the data it will use by itself. This maintains the memory locality of data w.r.t. the thread in a shared memory environment.

template<class TInputImage, class TOutputImage>
virtual void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ThreadedInitializeIteration unsigned int  ThreadId  )  [protected, virtual]
 

If child classes need an entry point to the start of every iteration step they can override this method. This method is defined but empty in this class.

template<class TInputImage, class TOutputImage>
virtual void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ThreadedLoadBalance unsigned int  ThreadId  )  [protected, virtual]
 

Redistribute an load among the threads to obtain a more balanced load distribution. This is performed in parallel by all the threads.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ThreadedPostProcessOutput const ThreadRegionType regionToProcess  )  [protected]
 

Assign background pixels INSIDE the sparse field layers to a new level set with value less than the innermost layer. Assign background pixels OUTSIDE the sparse field layers to a new level set with value greater than the outermost layer.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ThreadedProcessFirstLayerStatusLists unsigned int  InputLayerNumber,
unsigned int  OutputLayerNumber,
StatusType  SearchForStatus,
unsigned int  InOrOut,
unsigned int  BufferLayerNumber,
unsigned int  ThreadId
[protected]
 

Performs two tasks. The situation here is that ThreadedProcessStatusList has been called just once after the active layer values have been updated and the UpLists and DownLists formed. Some nodes are now moving into the active layer. The two tasks performed are: 1. modify the status-image like it is performed by the ThreadedProcessStatusList. 2. Update the values in the output-image for those nodes that are moving IN the active layer.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ThreadedProcessOutsideList unsigned int  InputLayerNumber,
StatusType  ChangeToStatus,
unsigned int  InOrOut,
unsigned int  BufferLayerNumber,
unsigned int  ThreadId
[protected]
 

Push each index in the input list into its appropriate status layer (ChangeToStatus) and ... ... update the status image value at that index

template<class TInputImage, class TOutputImage>
virtual void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ThreadedProcessPixelEnteringActiveLayer const  IndexType,
const  ValueType,
const unsigned  int
[protected, virtual]
 

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ThreadedProcessStatusList unsigned int  InputLayerNumber,
unsigned int  OutputLayerNumber,
StatusType  ChangeToStatus,
StatusType  SearchForStatus,
unsigned int  InOrOut,
unsigned int  BufferLayerNumber,
unsigned int  ThreadId
[protected]
 

Push each index in the input list into its appropriate status layer (ChangeToStatus) and update the status image value at that index. Also examine the neighbors of the index, (with status SearchForStatus) to determine which need to go onto the output list.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ThreadedPropagateLayerValues StatusType  from,
StatusType  to,
StatusType  promote,
unsigned int  InorOut,
unsigned int  ThreadId
[protected]
 

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::ThreadedUpdateActiveLayerValues TimeStepType  dt,
LayerType StatusUpList,
LayerType StatusDownList,
unsigned int  ThreadId
[protected]
 

1. Updates the values (in the output-image) of the nodes in the active layer that are moving OUT of the active layer. These values are used in the ThreadedProcessFirstLayerStatusLists() method to assign values for new nodes that are moving IN the active layer. 2. This function also constructs the up/down lists for nodes that are moving out of the active layer.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::WaitForAll  )  [protected]
 

Thread synchronization methods.

template<class TInputImage, class TOutputImage>
void itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::WaitForNeighbor unsigned int  SemaphoreArrayNumber,
unsigned int  ThreadId
[protected]
 

Thread synchronization methods.


Member Data Documentation

template<class TInputImage, class TOutputImage>
Barrier::Pointer itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_Barrier [protected]
 

A global barrier used for synchronization between all threads. Definition at line 672 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
unsigned int* itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_Boundary [protected]
 

The boundaries defining thread regions Definition at line 659 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
bool itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_BoundaryChanged [protected]
 

A boolean variable stating if the boundaries had been changed during CheckLoadBalance() Definition at line 656 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
double itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_ConstantGradientValue [static, protected]
 

The constant gradient to maintain between isosurfaces in the spare-field of the level-set image. This value defaults to 1.0 Definition at line 339 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
ThreadData* itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_Data [protected]
 

An array storing the individual (local) data structures for each thread. Definition at line 719 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
int* itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_GlobalZHistogram [protected]
 

Histogram of number of pixels in each Z plane for the entire 3D volume Definition at line 662 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
bool itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_InterpolateSurfaceLocation [protected]
 

This flag tells the solver whether or not to interpolate for the actual surface location when calculating change at each active layer node. By default this is turned on. Subclasses which do not sample propagation (speed), advection, or curvature terms should turn this flag off. Definition at line 729 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
ValueType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_IsoSurfaceValue [protected]
 

The value in the input which represents the isosurface of interest. Definition at line 396 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
LayerNodeStorageType::Pointer itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_LayerNodeStore [protected]
 

Storage for layer node objects. Definition at line 393 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
LayerListType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_Layers [protected]
 

An array which contains all of the layers needed in the sparse field. Layers are organized as follows: m_Layer[0] = active layer, m_Layer[i:odd] = inside layer (i+1)/2, m_Layer[i:even] = outside layer i/2. This is used only during the initialization of the level set. Definition at line 377 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
unsigned int* itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_MapZToThreadNumber [protected]
 

The mapping from a z-value to the thread in whose region the z-value lies Definition at line 665 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
ParallelSparseFieldCityBlockNeighborList< NeighborhoodIterator<OutputImageType> > itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_NeighborList [protected]
 

Connectivity information for examining neighbor pixels. Definition at line 335 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
StatusType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_NumberOfLayers [protected]
 

The number of layers to use in the sparse field. Sparse field will consist of m_NumberOfLayers layers on both sides of a single active layer. This active layer is the interface of interest, i.e. the zero level set. Definition at line 382 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
unsigned int itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_NumOfThreads [protected]
 

The number of threads to use. Definition at line 646 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
OutputImageType::Pointer itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_OutputImage [protected]
 

Definition at line 386 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
OutputImageType::Pointer itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_OutputImageTemp [protected]
 

Definition at line 390 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
OutputImageType::Pointer itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_ShiftedImage [protected]
 

This image is a copy of the input with m_IsoSurfaceValue subtracted from each pixel. This way we only need to consider the zero level set in our calculations. Makes the implementation easier and more efficient. This is used only during the initialization of the level set. Definition at line 371 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
unsigned int itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_SplitAxis [protected]
 

The dimension along which to distribute the load. Definition at line 649 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
StatusType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_StatusActiveChangingDown [static, protected]
 

Special status value which indicates a pending change to a more negative sparse field. Definition at line 353 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
StatusType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_StatusActiveChangingUp [static, protected]
 

Special status value which indicates a pending change to a more positive sparse field. Definition at line 349 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
StatusType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_StatusBoundaryPixel [static, protected]
 

Special status value which indicates a pixel is on the boundary of the image Definition at line 365 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
StatusType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_StatusChanging [static, protected]
 

Special status value which indicates pending change to another sparse field layer. Definition at line 361 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
StatusImageType::Pointer itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_StatusImage [protected]
 

An image of status values used internally by the algorithm. Definition at line 385 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
StatusImageType::Pointer itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_StatusImageTemp [protected]
 

Images used temporarily during the initialization of the thread data structures. Definition at line 389 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
StatusType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_StatusNull [static, protected]
 

Special status value used as a default for indicies which have no meaningful status. Definition at line 357 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
bool itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_Stop [protected]
 

Used to check if there are too few pixels remaining. If yes, then we can stop iterating. Definition at line 723 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
ValueType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_ValueOne [static, protected]
 

Multiplicative identity of the ValueType. Definition at line 342 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
ValueType itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_ValueZero [static, protected]
 

Additive identity of the ValueType. Definition at line 345 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
int* itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_ZCumulativeFrequency [protected]
 

Cumulative frequency of number of pixels in each Z plane for the entire 3D volume Definition at line 669 of file itkParallelSparseFieldLevelSetImageFilter.h.

template<class TInputImage, class TOutputImage>
unsigned int itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::m_ZSize [protected]
 

The length of the dimension along which to distribute the load. Definition at line 652 of file itkParallelSparseFieldLevelSetImageFilter.h.


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