This class manages an AMR tree data structure. More...

#include <AMRTree.h>

Inheritance diagram for VAPoR::AMRTree:

Public Types
typedef AMRTreeBranch::cid_t	cid_t

Public Types inherited from VetsUtil::MyBase
typedef void(*	ErrMsgCB_T )(const char *msg, int err_code)

typedef void(*	DiagMsgCB_T )(const char *msg)

Public Member Functions
	AMRTree (const size_t basedim[3], const double min[3], const double max[3])

	AMRTree (const string &path)

	AMRTree (const size_t basedim[3], const int paramesh_gids[][15], const float paramesh_bboxs[][3][2], const int paramesh_refine_levels[], int paramesh_total_blocks)

	AMRTree ()

virtual	~AMRTree ()

void	DecodeCellID (AMRTree::cid_t cellid, AMRTree::cid_t baseblockidx, AMRTree::cid_t nodeidx) const

int	DeleteCell (AMRTree::cid_t cellid)

AMRTree::cid_t	FindCell (const double ucoord[3], int reflevel=-1) const

int	GetCellLocation (AMRTree::cid_t cellid, size_t xyz[3], int *reflevel) const

AMRTree::cid_t	GetCellID (const size_t xyz[3], int reflevel) const

const size_t *	GetBaseDim () const

const AMRTreeBranch *	GetBranch (const size_t xyz[3]) const

const AMRTreeBranch *	GetBranch (cid_t baseblockidx) const

int	GetCellBounds (cid_t cellid, double minu[3], double maxu[3]) const

AMRTree::cid_t	GetCellChildren (AMRTree::cid_t cellid) const

int	GetCellLevel (AMRTree::cid_t cellid) const

AMRTree::cid_t	GetCellNeighbor (AMRTree::cid_t cellid, int face) const

AMRTree::cid_t	GetCellParent (AMRTree::cid_t cellid) const

int	GetRefinementLevel (const size_t min[3], const size_t max[3]) const

int	GetRefinementLevel () const
	Returns the maximum refinement of the entire tree. More...

AMRTree::cid_t	GetNumCells (const size_t min[3], const size_t max[3], int reflevel=-1) const

AMRTree::cid_t	GetNumCells (int reflevel=-1) const

AMRTree::cid_t	RefineCell (AMRTree::cid_t cellid)

void	EndRefinement ()

AMRTree::cid_t	GetNextCell (bool restart)

int	MapUserToVoxel (int reflevel, const double ucoord[3], size_t vcoord[3])

int	Write (const string &path) const

int	Read (const string &path)

int	_parameshGetBaseBlocks (vector< int > &baseblocks, const size_t basedim[3], const int gids[][15], const float bboxs[][3][2], int totalblocks) const

Public Member Functions inherited from VetsUtil::MyBase
	MyBase ()

const string &	getClassName () const

Public Member Functions inherited from VAPoR::ParsedXml
virtual	~ParsedXml ()

virtual bool	charHandler (ExpatParseMgr , const XML_Char , int)

Additional Inherited Members
Static Public Member Functions inherited from VetsUtil::MyBase
static void	SetErrMsg (const char *format,...)
	Record a formatted error message. More...

static void	SetErrMsg (int errcode, const char *format,...)
	Record a formatted error message and an error code. More...

static const char *	GetErrMsg ()

static void	SetErrCode (int err_code)
	Record an error code. More...

static int	GetErrCode ()
	Retrieve the current error code. More...

static void	SetErrMsgCB (ErrMsgCB_T cb)

static ErrMsgCB_T	GetErrMsgCB ()

static void	SetErrMsgFilePtr (FILE *fp)

static const FILE *	SetErrMsgFilePtr ()

static void	SetDiagMsg (const char *format,...)
	Record a formatted diagnostic message. More...

static const char *	GetDiagMsg ()

static void	SetDiagMsgCB (DiagMsgCB_T cb)

static DiagMsgCB_T	GetDiagMsgCB ()

static void	SetDiagMsgFilePtr (FILE *fp)

static bool	EnableErrMsg (bool enable)

Public Attributes inherited from VAPoR::ParsedXml
ParsedXml *	previousClass

Static Public Attributes inherited from VetsUtil::MyBase
static char *	ErrMsg

static int	ErrCode

static int	ErrMsgSize

static FILE *	ErrMsgFilePtr

static ErrMsgCB_T	ErrMsgCB

static char *	DiagMsg

static int	DiagMsgSize

static FILE *	DiagMsgFilePtr

static DiagMsgCB_T	DiagMsgCB

static bool	Enabled

Protected Member Functions inherited from VetsUtil::MyBase
void	SetClassName (const string &name)

Static Protected Attributes inherited from VAPoR::ParsedXml
static const string	_stringType

static const string	_longType

static const string	_doubleType

static const string	_typeAttr

Detailed Description

This class manages an AMR tree data structure.

Author: John Clyne

Version: $Revision$

Date: $Date$

This class manages an Adaptive Mesh Refinement tree data object for a block structured AMR grid. The AMR grid is composed of a Cartesian base grid of cells (blocks) that are recursively refined into octants. Each base block is represented by a AMRTreeBranch object class.

This class is derived from the MyBase base class. Hence all of the methods make use of MyBase's error reporting capability - the success of any method (including constructors) can (and should) be tested with the GetErrCode() method. If non-zero, an error message can be retrieved with GetErrMsg().

No field data is stored with the AMRTreeBranch class.

See also: AMRTreeBranch

Definition at line 62 of file AMRTree.h.

Member Typedef Documentation

typedef AMRTreeBranch::cid_t VAPoR::AMRTree::cid_t

Definition at line 69 of file AMRTree.h.

Constructor & Destructor Documentation

VAPoR::AMRTree::AMRTree	(	const size_t	basedim[3],
		const double	min[3],
		const double	max[3]
	)

Constructor for the AMRTree class.

Parameters

[in]	basedim	A three element array specifying the topological dimensions of the tree in base blocks
[in]	min	A tree element array specifying the minimum XYZ extents of the tree in user-defined coordinates.
[in]	max	A tree element array specifying the maximum XYZ extents of the tree in user-defined coordinates.

Return values

status A non-negative value is returned on success

VAPoR::AMRTree::AMRTree ( const string & path )

Construct a tree from a file

This constructor initializes an AMRTree object class from a file previously written by AMRTree::Write()

Parameters

[in] path Path name to file

See also: Write()

VAPoR::AMRTree::AMRTree	(	const size_t	basedim[3],
		const int	paramesh_gids[][15],
		const float	paramesh_bboxs[][3][2],
		const int	paramesh_refine_levels[],
		int	paramesh_total_blocks
	)

Constructor an AMRTree from a Paramesh AMR grid

This constructor initializes and fully populates an AMR tree from a Paramesh block structured AMR grid stored in an HDF5 file. The arguments to this constructor are read directly from HDF5

Parameters

[in]	basedim	A three element array specifying the topological dimensions of the tree in base blocks
[in]	paramesh_gids	An array of Paramesh global identifiers
[in]	paramesh_bboxs	An array of Paramesh bounding boxes
[in]	paramesh_refine_levels	An array of Paramesh refinement levels
[in]	paramesh_total_blocks	Total number of nodes (both leaf and non-leaf) stored in the Paramesh AMR tree.

See also: http://ct.gsfc.nasa.gov/paramesh/Users_manual/amr.html; http://flash.uchicago.edu/website/home/

VAPoR::AMRTree::AMRTree ( )

Construct a simple tree

Construct a tree with base dimensions 1x1x1 and min and max user extents set to (0.0, 0.0, 0.0) and (1.0, 1.0, 1.0), respectively

virtual VAPoR::AMRTree::~AMRTree ( )

virtual

Member Function Documentation

int VAPoR::AMRTree::_parameshGetBaseBlocks	(	vector< int > &	baseblocks,
		const size_t	basedim[3],
		const int	gids[][15],
		const float	bboxs[][3][2],
		int	totalblocks
	)		const

void VAPoR::AMRTree::DecodeCellID	(	AMRTree::cid_t	cellid,
		AMRTree::cid_t *	baseblockidx,
		AMRTree::cid_t *	nodeidx
	)		const

Decode an AMRTree cell id

Decode an AMRTree cell indentifier into a AMRTreeBranch cell id and a base block index (branch index). Branch indecies are numbered from 0 to (basedim[0]*basedim[1]*basedim[2])-1, with the X base blocks varying fastest, followed by Y, than Z.

Parameters

[in]	cellid	The AMRTree cell id to decode
[out]	baseblockidx	The decoded branch index
[out]	nodeidx	The decoded AMRTreeBranch cell id

See also: AMRTreeBranch

int VAPoR::AMRTree::DeleteCell ( AMRTree::cid_t cellid )

Delete a node from the tree

Deletes the indicated node from the tree

Parameters

[in] cellid Cell id of node to delete

Return values

status Returns a non-negative value on success

void VAPoR::AMRTree::EndRefinement ( )

End cell refinement

This method informs the class that cell refinement is complete, allowing the class to build data structures that may speed subsequent class methods. Calling this method is optional. The results of calling this method before cell refinement is complete are undefined.

See also: RefineCell()

AMRTree::cid_t VAPoR::AMRTree::FindCell	(	const double	ucoord[3],
		int	reflevel = `-1`
	)		const

Find a cell containing a point.

This method returns the cell id of the node containing a point. The coordinates of the point are specfied in the user coordinates defined by the during the tree's construction (it is assumed that the tree occupies Cartesian space and that all nodes are rectangular. By default, the leaf node containing the point is returned. However, an ancestor node may be returned by limiting the refinement level.

Parameters

[in]	ucoord	A three element array containing the coordintes of the point to be found.
[in]	reflevel	The refinement level of the cell to be returned. If -1, a leaf node is returned.

Return values

cellid A valid cell id is returned if the tree contains the indicated point. Otherwise a negative integer is returned

const size_t* VAPoR::AMRTree::GetBaseDim ( ) const

inline

Get the dimensions of the base grid

This method returns the XYZ dimensions of the tree's base grid

Return values

dim	A three element array containing the tree's base grid dimensions.

Definition at line 228 of file AMRTree.h.

const AMRTreeBranch* VAPoR::AMRTree::GetBranch ( const size_t xyz[3] ) const

Return the AMRTreeBranch associated with a base block

This method returns a pointer to the AMRTreeBranch object for the block with topological coordinates given by xyz.

Parameters

[in]	xyz	The toplogical (i-j-k) coordinates of the base block tree branch to return
[in]	baseblockidx	The serialized offset of `xyz`

Return values

treebranch A pointer to a AMRTreeBranch object

const AMRTreeBranch* VAPoR::AMRTree::GetBranch ( cid_t baseblockidx ) const

Return the AMRTreeBranch associated with a base block

This method returns a pointer to the AMRTreeBranch object for the block with topological coordinates given by xyz.

Parameters

[in]	xyz	The toplogical (i-j-k) coordinates of the base block tree branch to return
[in]	baseblockidx	The serialized offset of `xyz`

Return values

treebranch A pointer to a AMRTreeBranch object

int VAPoR::AMRTree::GetCellBounds	(	cid_t	cellid,
		double	minu[3],
		double	maxu[3]
	)		const

Return the user coordinate bounds of a cell

This method returns the minimum and maximum extents of the indicated cell. The extents are in user coordinates as defined by the constructor for the class.

Parameters

[in]	cellid	The cell id of the cell whose bounds are to be returned
[out]	minu	A three element array to which the minimum cell extents will be copied.
[out]	maxu	A three element array to which the maximum cell extents will be copied.

Return values

status Returns a non-negative value on success

AMRTree::cid_t VAPoR::AMRTree::GetCellChildren ( AMRTree::cid_t cellid ) const

Returns the cell id of the first child of a node

This method returns the cell id of the first of the eight children of the cell indicated by cellid. The remaining seven children's ids may be calulated by incrementing the first child's id successively. I.e. the children have contiguous integer ids. Octants are ordered with the X axis varying fastest, followed by Y, then Z.

Parameters

[in] cellid The cell id of the cell whose first child is to be returned.

Return values

cellid A valid cell id is returned if the branch contains the indicated point. Otherwise a negative value is returned.

AMRTree::cid_t VAPoR::AMRTree::GetCellID	(	const size_t	xyz[3],
		int	reflevel
	)		const

Return the cellid for a cell with the given i-j-k coordinates

This method returns the cellid for the cell indicated by the i-j-k coordinates at a given refinement level.

Parameters

[in]	xyz	The cell's location
[in]	reflevel	The refinement level of the cell
[out]	cellid	The cell id of the cell at the specified location

Return values

status Returns a non-negative value on success. A negative int is returned xyz are invalid for refinement level.

See also: GetCellLocation()

int VAPoR::AMRTree::GetCellLevel ( AMRTree::cid_t cellid ) const

Return the refinement level of a cell

Returns the refinement level of the cell indicated by cellid. The base (coarsest) refinement level is zero (0).

Parameters

[in] cellid The cell id of the cell whose refinement level is to be returned.

Return values

status Returns a non-negative value on success

int VAPoR::AMRTree::GetCellLocation	(	AMRTree::cid_t	cellid,
		size_t	xyz[3],
		int *	reflevel
	)		const

Return the topological coordinates of a cell within the tree.

This method returns topological coordinates of a cell within the tree, relative to the cell's refinement level. Each cell in a tree has an i-j-k location for it's refinement level. The range of i-j-k values runs from 0 to basedim * 2^j - 1, where basedim is the base dimension for the respective i-j-k axis specified in the AMRTree() constructor, and j is the refinement level. The base refinement level is zer0. is relative to the branch's location.

Parameters

[in]	cellid	The cell id of the cell whose bounds are to be returned
[out]	xyz	The cell's location
[out]	cellid	The refinement level of the cell

Return values

status Returns a non-negative value on success. A negative int is returned if cellid does not exist in the tree.

AMRTree::cid_t VAPoR::AMRTree::GetCellNeighbor	(	AMRTree::cid_t	cellid,
		int	face
	)		const

Return the cell id of a cell's neighbor.

Returns the cell id of the cell adjacent to the indicated face of the cell with id cellid. The face parameter is an integer in the range [0..5], where 0 coresponds to the face on the XY plane with Z = 0; 1 is the YZ plane with X = 1; 2 is the XY plane, Z = 1; 3 is the YZ plane; Z = 0, 4 is the XZ plane, Y = 0; and 5 is the XZ plane, Z = 1.

Parameters

[in]	cellid	The cell id of the cell whose neighbor is to be returned.
[in]	face	Indicates the cell's face adjacent to the desired neighbor.

Return values

cellid A valid cell id is returned if the branch contains the indicated point. Otherwise a negative value is returned

AMRTree::cid_t VAPoR::AMRTree::GetCellParent ( AMRTree::cid_t cellid ) const

Returns the cell id of the parent of a child node

This method returns the cell id of the parent of the cell indicated by cellid.

Parameters

[in] cellid The cell id of the cell whose parent is to be returned.

Return values

cellid A valid cell id is returned if the branch contains the indicated point. Otherwise a negative int is returned.

AMRTree::cid_t VAPoR::AMRTree::GetNextCell ( bool restart )

Return next node in a tree treversal

Each time this method is called it returns the cellid for the next node in a complete treversal of the tree. If restart is true the first node in the tree is returned: the node with topological coordinates (0,0,0), and refinement level zero. The order of the treversal is as follows: branches are treversed, one at a time in a top-to-bottom, breadth first manner. The branch with branch id zero is treversed first, followed by branch id 1, and so on. When the entire tree has been completely treversed a negative cell id is returned.

Parameters

[in] restart If true, the treversal is restarted from the first cell in the tree.

AMRTree::cid_t VAPoR::AMRTree::GetNumCells	(	const size_t	min[3],
		const size_t	max[3],
		int	reflevel = `-1`
	)		const

Return number of nodes in the indicated subtree

The number of leaf and non-leaf nodes in a subtree indicated by min and max is returned. If the parameter is non-negative, the number of nodes in the tree up to the refinement level indicated by reflevel are returned.

Parameters

[in]	min	Minumum topological (i-j-k) coordinates, specified in base blocks, of the region of interest
[in]	max	Maximum topological (i-j-k) coordinates, specified in base blocks, of the region of interest
[in]	reflevel	Requested refinment level. The maximum refinement level is used if the argument is negative

AMRTree::cid_t VAPoR::AMRTree::GetNumCells ( int reflevel = -1 ) const

Return number of nodes in the tree

The number of leaf and non-leaf nodes is returned. If the parameter is non-negative, the number of nodes in the tree up to the refinement level indicated by reflevel are returned.

Parameters

[in] reflevel Requested refinment level. The maximum refinement level is used if the argument is negative

Return values

numnodes The number of nodes

int VAPoR::AMRTree::GetRefinementLevel	(	const size_t	min[3],
		const size_t	max[3]
	)		const

Returns the maximum refinement of the indicated subregion

int VAPoR::AMRTree::GetRefinementLevel ( ) const

Returns the maximum refinement of the entire tree.

int VAPoR::AMRTree::MapUserToVoxel	(	int	reflevel,
		const double	ucoord[3],
		size_t	vcoord[3]
	)

int VAPoR::AMRTree::Read ( const string & path )

Read the AMR tree from a file as XML data

Parameters

[in] path Name of the file to write to

Return values

status Returns a non-negative integer on success

AMRTree::cid_t VAPoR::AMRTree::RefineCell ( AMRTree::cid_t cellid )

Refine a cell

This method refines a cell, creating eight new child octants. Upon success the cell id of the first child is returned.

Parameters

[in] cellid The cell id of the cell to be refined

Return values

cellid A valid cell id is returned if the branch contains the indicated point. Otherwise a negative value is returned

int VAPoR::AMRTree::Write ( const string & path ) const

Write the AMR tree to a file as XML data

Parameters

[in] path Name of the file to write to

Return values

status Returns a non-negative integer on success

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

/Users/clyne/src/vapor/lib/vdf/AMRTree.h

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation