This class manages an Adaptive Mesh Refinement grid. More...

#include <AMRData.h>

Inheritance diagram for VAPoR::AMRData:

Public Member Functions
	AMRData (const AMRTree *tree, const size_t cell_dim[3], const size_t bmin[3], const size_t bmax[3], int reflevel=-1)

	AMRData (const AMRTree *tree, const size_t cell_dim[3], int reflevel=-1)

	AMRData (const AMRTree *tree)

	AMRData (const AMRTree *tree, const size_t cell_dim[3], const int paramesh_gids[][15], const float paramesh_bboxs[][3][2], const float paramesh_unk[], int total_blocks, int reflevel=-1)

virtual	~AMRData ()

int	SetRegion (const size_t min[3], const size_t max[3], int reflevel)

void	GetRegion (const size_t min, const size_t max, int *reflevel) const

void	Update ()

int	WriteNCDF (const string &path, int reflevel=-1)

int	ReadNCDF (const string &path, const size_t bmin[3], const size_t bmax[3], int reflevel=-1)

int	ReadNCDF (const string &path, int reflevel=-1)

float *	GetBlock (AMRTree::cid_t cellid) const

int	ReGrid (const size_t bmin[3], const size_t bmax[3], int reflevel, float *grid, const size_t dim[3]) const

const float *	GetDataRange () const

const AMRTree *	GetTree () const

void	GetBounds (size_t bmin[3], size_t bmax[3]) const

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

const string &	getClassName () const

Static Public Member Functions
static int	ReadAttributesNCDF (const string &path, size_t cell_dim[3], size_t bmin[3], size_t bmax[3], float data_range[2], int &reflevel, size_t &num_nodes)

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)

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

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

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)

Detailed Description

This class manages an Adaptive Mesh Refinement grid.

Author: John Clyne

Version: $Revision$

Date: $Date$

This class manages block-structured Adaptive Mesh Refinement grids. The AMR grid is composed of a Cartesian base grid of cells (blocks) that are recursively refined into octants. The representation of the tree data structure is managed by a AMRTree object.

Note: All blocks in the AMR grid, whether leaf or non-leaf nodes, contain data.

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().

See also: AMRTree

Definition at line 62 of file AMRData.h.

Constructor & Destructor Documentation

VAPoR::AMRData::AMRData	(	const AMRTree *	tree,
		const size_t	cell_dim[3],
		const size_t	bmin[3],
		const size_t	bmax[3],
		int	reflevel = `-1`
	)

Constructor for the AMRData class.

Construct block structured AMR grid data object. The

Parameters

	tree	parameter defines the octree hierarchy for the grid. The AMR grid defined by this object may be a subdomain of the tree pointed to by `tree`. The `bmin` and `bmax` parameters may be used to restrict the spatial domain to a subset of base blocks. Similarly, the `reflevel` parameter may be used to restrict the refinement level
[in]	tree	A pointer to an initialized AMRTree
[in]	cell_dim	A three-element array specifying the topological dimensions, in voxels, of all blocks in the grid
[in]	bmin	A three-element array specifying the coordinates, in base blocks, of the minimum extents of the subgrid. The default is (0,0,0).
[in]	bmax	A three-element array specifying the coordinates, in base blocks, of the maximum extents of the subgrid. The default is is AMRTree::GetBaseDim()[i] - 1
[in]	reflevel	The maximum refinement level of the grid. If a negative value is specified, the refinement level of the tree pointed to by the `tree` parameter is used.

Note: The AMRTree object is shallow copied - it's contents may not be changed by application until after this object is destroyed.

VAPoR::AMRData::AMRData	(	const AMRTree *	tree,
		const size_t	cell_dim[3],
		int	reflevel = `-1`
	)

Constructor for the AMRData class.

Construct block structured AMR grid data object. The

Parameters

	tree	parameter defines the octree hierarchy for the grid. The AMR grid defined by this object may be a subdomain of the tree pointed to by `tree`. The `bmin` and `bmax` parameters may be used to restrict the spatial domain to a subset of base blocks. Similarly, the `reflevel` parameter may be used to restrict the refinement level
[in]	tree	A pointer to an initialized AMRTree
[in]	cell_dim	A three-element array specifying the topological dimensions, in voxels, of all blocks in the grid
[in]	bmin	A three-element array specifying the coordinates, in base blocks, of the minimum extents of the subgrid. The default is (0,0,0).
[in]	bmax	A three-element array specifying the coordinates, in base blocks, of the maximum extents of the subgrid. The default is is AMRTree::GetBaseDim()[i] - 1
[in]	reflevel	The maximum refinement level of the grid. If a negative value is specified, the refinement level of the tree pointed to by the `tree` parameter is used.

Note: The AMRTree object is shallow copied - it's contents may not be changed by application until after this object is destroyed.

VAPoR::AMRData::AMRData ( const AMRTree * tree )

Constructor for the AMRData class.

Construct block structured AMR grid data object. The

Parameters

	tree	parameter defines the octree hierarchy for the grid. The AMR grid defined by this object may be a subdomain of the tree pointed to by `tree`. The `bmin` and `bmax` parameters may be used to restrict the spatial domain to a subset of base blocks. Similarly, the `reflevel` parameter may be used to restrict the refinement level
[in]	tree	A pointer to an initialized AMRTree
[in]	cell_dim	A three-element array specifying the topological dimensions, in voxels, of all blocks in the grid
[in]	bmin	A three-element array specifying the coordinates, in base blocks, of the minimum extents of the subgrid. The default is (0,0,0).
[in]	bmax	A three-element array specifying the coordinates, in base blocks, of the maximum extents of the subgrid. The default is is AMRTree::GetBaseDim()[i] - 1
[in]	reflevel	The maximum refinement level of the grid. If a negative value is specified, the refinement level of the tree pointed to by the `tree` parameter is used.

Note: The AMRTree object is shallow copied - it's contents may not be changed by application until after this object is destroyed.

VAPoR::AMRData::AMRData	(	const AMRTree *	tree,
		const size_t	cell_dim[3],
		const int	paramesh_gids[][15],
		const float	paramesh_bboxs[][3][2],
		const float	paramesh_unk[],
		int	total_blocks,
		int	reflevel = `-1`
	)

Constructor an AMRData object from a Paramesh (FLASH) AMR data set.

Construct block structured AMR grid data object using a Paramesh (FLASH) AMR data set to populate the grid's data elements. The reflevel parameter may be used to restrict the refinement level

Parameters

[in]	tree	A pointer to an initialized AMRTree
[in]	cell_dim	A three-element array specifying the topological dimensions, in voxels, of all blocks in the grid
[in]	paramesh_gids	A paramesh global identifier array
[in]	paramesh_bboxs	An array of Paramesh bounding boxes
[in]	paramesh_unk	A paramesh dependent data array
[in]	paramesh_total_blocks	Total number of nodes (both leaf and
[in]	reflevel	The maximum refinement level of the grid. If a negative value is specified, the refinement level of the tree pointed to by the `tree` parameter is used.

Note: The AMRTree object is shallow copied - it's contents may not be changed by application until after this object is destroyed.

virtual VAPoR::AMRData::~AMRData ( )

inlinevirtual

Definition at line 148 of file AMRData.h.

Member Function Documentation

float* VAPoR::AMRData::GetBlock ( AMRTree::cid_t cellid ) const

Get a block of data from the AMR grid

This method returns a pointer to the block of field data associated with the cell id indicated by the cellid parameter

Parameters

[in] cellid The cell identifier of the block to be returned.

Return values

data	A pointer to a block of field values

void VAPoR::AMRData::GetBounds	(	size_t	bmin[3],
		size_t	bmax[3]
	)		const

inline

Definition at line 320 of file AMRData.h.

const float* VAPoR::AMRData::GetDataRange ( ) const

inline

Return the data range for the grid

The method returns the minimum and maximum data values, respectively, for the current AMR grid.

Parameters

[out] range Min and Max data values, respectively

Return values

status A negative integer is returned on failure, otherwise the method has succeeded.

Definition at line 315 of file AMRData.h.

void VAPoR::AMRData::GetRegion	(	const size_t **	min,
		const size_t **	max,
		int *	reflevel
	)		const

Retrieve the current defined region of interest

This method returns the parameters defining the AMR data objects region of interest

See also: SetRegion()

const AMRTree* VAPoR::AMRData::GetTree ( ) const

inline

Definition at line 318 of file AMRData.h.

static int VAPoR::AMRData::ReadAttributesNCDF	(	const string &	path,
		size_t	cell_dim[3],
		size_t	bmin[3],
		size_t	bmax[3],
		float	data_range[2],
		int &	reflevel,
		size_t &	num_nodes
	)

static

Read AMRData attributes from a netCDF file

This static method can be used to return attribute data from a netCDF file generated by WriteNCDF().

Parameters

[in]	path	String containing path to input file
[out]	cell_dim	Three element array containing the the dimensions of each cell in the AMR data structure
[out]	bmin	Minimum bounds of AMR mesh in block coordinates
[out]	bmax	Maximum bounds of AMR mesh in block coordinates
[out]	data_range	Minimum and maximum values of floating point data stored in the mesh.
[out]	num_nodes	Total number of nodes (blocks) in AMR mesh

Return values

status A negative int is returned on failure.

int VAPoR::AMRData::ReadNCDF	(	const string &	path,
		const size_t	bmin[3],
		const size_t	bmax[3],
		int	reflevel = `-1`
	)

Read an AMR data object from a file

Read an ARM data object from a file. The subregion of the data read is determined by the objects currently defined extents and the refinement level specified by the reflevel parameter

Parameters

[in]	path	Path name of the file to be read
[in]	reflevel	The maximum refinement level to write. If negative, the maximum current refinement level defined by the object is read
[in]	bmin	Minimum bounds of data subregion expressed in block coordinates. The default is the minimum bounds the object was constructed with.
[in]	bmax	Maximum bounds of data subregion expressed in block coordinates. The default is the maximum bounds the object was constructed with.

See also: GetRegion(), SetRegion()

int VAPoR::AMRData::ReadNCDF	(	const string &	path,
		int	reflevel = `-1`
	)

Read an AMR data object from a file

Read an ARM data object from a file. The subregion of the data read is determined by the objects currently defined extents and the refinement level specified by the reflevel parameter

Parameters

[in]	path	Path name of the file to be read
[in]	reflevel	The maximum refinement level to write. If negative, the maximum current refinement level defined by the object is read
[in]	bmin	Minimum bounds of data subregion expressed in block coordinates. The default is the minimum bounds the object was constructed with.
[in]	bmax	Maximum bounds of data subregion expressed in block coordinates. The default is the maximum bounds the object was constructed with.

See also: GetRegion(), SetRegion()

int VAPoR::AMRData::ReGrid	(	const size_t	bmin[3],
		const size_t	bmax[3],
		int	reflevel,
		float *	grid,
		const size_t	dim[3]
	)		const

Resample an AMR grid to a Cartesian grid

This method permits the resampling of the AMR grid represented by this object to a regular, Cartesian grid. The refinemenlevel parameter indicates the refinement level of the AMR grid to use in the resampling. AMR blocks, intersecting the domain of interest that are coarser than the indicated refinement level, are interpolated to match the desired refinement level. The default interpolation method is linear.

Parameters

[in]	bmin	A three-element array specifying, in blocks, the minimum extents of the region of interest. The coordinate system employed is relative to the refinement level. I.e. with each successive refinement level the coordinate of a voxel is given by xyz = xyz' * 2, where xyz' is the coordinate a the preceeding level.
[in]	bmax	A three-element array specifying, in blocks, the maximum extents of the region of interest.
[in]	reflevel	The maximum refinement level of the grid. If a negative value is specified, the refinement level of the tree pointed to by the `tree` parameter is used.
[out]	grid	A pointer to floating point array large enough to to contain the resampled data (bmax[i] - bmin[i] + 1);

Return values

status A non-negative value is returned upon success

int VAPoR::AMRData::SetRegion	(	const size_t	min[3],
		const size_t	max[3],
		int	reflevel
	)

Change the spatial region of interest

This method redefines the spatial region of interest (spatial extents and the refinement level) of the AMR data object. Any field data contained in the object are lost.

Parameters

[in]	min	A three-element array specifying the coordinates, in base blocks, of the minimum extents of the subgrid.
[in]	max	A three-element array specifying the coordinates, in base blocks, of the maximum extents of the subgrid.
[in]	reflevel	The maximum refinement level of the grid. If a negative value is specified, the refinement level of the tree pointed to by the `tree` parameter is used.

void VAPoR::AMRData::Update ( )

Update the data range

This method updates the data range and should be called prior to calling GetDataRange() if the field values have been changed.

See also: GetDataRange();

int VAPoR::AMRData::WriteNCDF	(	const string &	path,
		int	reflevel = `-1`
	)

Save the object to a netCDF file

This method writes the entire AMR data object to the file specified by the path paramter. The refiment levels stored may be limited with the reflevel parameter.

Parameters

[in]	path	Path name of the file to be written
[in]	reflevel	The maximum refinement level to write. If negative, the maximum refinement level present is written

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

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

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation