A sub-region reader for VDF files. More...

#include <WaveCodecIO.h>

Inheritance diagram for VAPoR::WaveCodecIO:

Public Member Functions
	WaveCodecIO (const MetadataVDC &metadata, int nthreads=0)

	WaveCodecIO (const string &metafile, int nthreads=0)

virtual	~WaveCodecIO ()

virtual int	OpenVariableRead (size_t timestep, const char *varname, int reflevel=0, int lod=0)

virtual int	OpenVariableWrite (size_t timestep, const char *varname, int reflevel=-1, int lod=-1)

virtual int	CloseVariable ()

virtual int	BlockReadRegion (const size_t bmin[3], const size_t bmax[3], float *region, bool unblock=true)

virtual int	ReadRegion (const size_t min[3], const size_t max[3], float *region)

virtual int	ReadRegion (float *region)

virtual int	ReadSlice (float *slice)

virtual int	BlockWriteRegion (const float *region, const size_t bmin[3], const size_t bmax[3], bool block=true)

virtual int	WriteRegion (const float *region, const size_t min[3], const size_t max[3])

virtual int	WriteRegion (const float *region)

virtual int	WriteSlice (const float *slice)

virtual void	SetBoundaryPadOnOff (bool pad)

const float *	GetDataRange () const

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

virtual int	VariableExists (size_t ts, const char *varname, int reflevel=0, int lod=0) const

virtual int	GetNumTransforms () const

virtual void	GetBlockSize (size_t bs[3], int reflevel) const

void	SetCollectiveIO (bool newCollectiveIO)

int	getNumThread ()

void	EnableBuffering (size_t count[3], size_t divisor, int rank)

Static Public Member Functions
static size_t	GetMaxCRatio (const size_t bs[3], string wavename, string wmode)

Public Attributes
int	_nthreads

Friends
void *	RunBlockReadRegionThread (void *object)

void *	RunBlockWriteRegionThread (void *object)

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

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

Protected Member Functions inherited from Wasp::EasyThreads
	EasyThreads (int nthreads)

	~EasyThreads ()

int	ParRun (void (start)(void ), std::vector< void > arg)

int	ParRun (void (start)(void ), void *arg)

int	Barrier ()

int	MutexLock ()

int	MutexUnlock ()

int	GetNumThreads () const

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

	MyBase ()

const string &	getClassName () const

Static Protected Member Functions inherited from Wasp::EasyThreads
static void	Decompose (int n, int size, int rank, int offset, int length)

static int	NProc ()

Static Protected Member Functions inherited from Wasp::MyBase
static void	SetErrMsg (const char *format,...)
	Record a formatted error message.

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

static const char *	GetErrMsg ()

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

static int	GetErrCode ()
	Retrieve the current error code.

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.

static const char *	GetDiagMsg ()

static void	SetDiagMsgCB (DiagMsgCB_T cb)

static DiagMsgCB_T	GetDiagMsgCB ()

static void	SetDiagMsgFilePtr (FILE *fp)

static bool	EnableErrMsg (bool enable)

static bool	GetEnableErrMsg ()

Static Protected Attributes inherited from Wasp::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

Detailed Description

A sub-region reader for VDF files.

Author: John Clyne

Version: $Revision$

Date: $Date$

This class provides an API for reading and writing VDC2 data. VDC2 data may be accessed with two forms of wavelet based progressive refinement, : hierarchical or level-of-detail. The former supports coarsening and refinement of the sampling grid resolution (the dimensions of the sampling grid) at varying powers-of-two, and is controled by the reflevel parameter. The latter allows for arbitrary approximations by restricting the number of wavelet basis coefficients used when reconstructing the data from their wavelet representation. The level-of-detail is controled with the lod parameter.

Definition at line 38 of file WaveCodecIO.h.

Constructor & Destructor Documentation

◆ WaveCodecIO() [1/2]

VAPoR::WaveCodecIO::WaveCodecIO	(	const MetadataVDC &	metadata,
		int	nthreads = `0`
	)

Parameters

[in] nthreads Number of execution threads that may be used by the class for parallel execution. If zero, the system hardware will be queried via sysconf to determine the number of processors available and this value will be used.

◆ WaveCodecIO() [2/2]

VAPoR::WaveCodecIO::WaveCodecIO	(	const string &	metafile,
		int	nthreads = `0`
	)

Parameters

[in] nthreads Number of execution threads that may be used by the class for parallel execution. If zero, the system hardware will be queried via sysconf to determine the number of processors available and this value will be used.

◆ ~WaveCodecIO()

virtual VAPoR::WaveCodecIO::~WaveCodecIO ( )

virtual

Member Function Documentation

◆ BlockReadRegion()

virtual int VAPoR::WaveCodecIO::BlockReadRegion	(	const size_t	bmin[3],
		const size_t	bmax[3],
		float *	region,
		bool	unblock = `true`
	)

virtual

Read in and return a subregion from the currently opened data volume.

The bmin and bmax vectors identify the minimum and maximum extents, in block coordinates, of the subregion of interest. The minimum valid value of 'bmin' is (0,0,0), the maximum valid value of bmax is (nbx-1,nby-1,nbz-1), where nx, ny, and nz are the block dimensions of the volume at the currently opened refinement level as retuned by GetDimBlk(). The volume returned is stored in the memory region pointed to by region. It is the caller's responsbility to ensure adequate space is available.

Parameters

[in]	bmin	Minimum region extents in block coordinates
[in]	bmax	Maximum region extents in block coordinates
[out]	region	The requested volume subregion
[in]	unblock	If true, unblock the data before copying to `region`

Return values

status Returns a non-negative value on success

See also: OpenVariableRead(), GetBlockSize(), MapVoxToBlk()

◆ BlockWriteRegion()

virtual int VAPoR::WaveCodecIO::BlockWriteRegion	(	const float *	region,
		const size_t	bmin[3],
		const size_t	bmax[3],
		bool	block = `true`
	)

virtual

Write a volume subregion to the currently opened progressive access data volume.

This method is identical to the WriteRegion() method with the exception that the region boundaries are defined in block, not voxel, coordinates. Secondly, unless the 'block' parameter is set, the internal blocking of the data will be preserved. I.e. the data are assumed to already be blocked.

The number of voxels contained in region must be the product over i :

(bmax[i] - bmin[i] + 1) * bs[i]

where bs[i] is the ith dimension of the block size.

Parameters

[in]	bmin	Minimum region extents in block coordinates
[in]	bmax	Maximum region extents in block coordinates
[in]	region	The volume subregion to write
[in]	block	If true, block the data before writing/transforming

Return values

status Returns a non-negative value on success

See also: OpenVariableWrite() SetBoundarPadOnOff()

◆ CloseVariable()

virtual int VAPoR::WaveCodecIO::CloseVariable ( )

virtual

Close the currently opened variable.

See also: OpenVariableWrite(), OpenVariableRead()

◆ EnableBuffering()

void VAPoR::WaveCodecIO::EnableBuffering	(	size_t	count[3],
		size_t	divisor,
		int	rank
	)

◆ GetBlockSize()

virtual void VAPoR::WaveCodecIO::GetBlockSize	(	size_t	bs[3],
		int	reflevel
	)		const

virtual

◆ GetDataRange()

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

inline

Return the data range of the currently opened volume as a two-element array

This method returns the minimum and maximum data values of the currently opened variable within the valid domain bounds. See GetValidRegion().

Note: The range values returned are valid for the native data only. Data approximations produced by level-of-detail or through multi-resolution may have values outside of this range.

Return values

[out] range A two-element vector containing the current minimum and maximum.

Definition at line 308 of file WaveCodecIO.h.

◆ GetMaxCRatio()

static size_t VAPoR::WaveCodecIO::GetMaxCRatio	(	const size_t	bs[3],
		string	wavename,
		string	wmode
	)

static

Return the maximimum compression ratio possible

This static methods returns the maximum possible compression ratio possible for a given combination of blocksize, ps, wavele name, wname, and wavelet boundary handling mode, wmode.

Parameters

[in]	bs	A three-element vector providing the dimensions of a block
[in]	wavename	The name of the wavelet
[in]	wmode	The wavelet boundary handling mode

Return values

ratio A value of zero is returned if the wavename or wmode are invalid, otherwise the maximum possible data compression ratio is returned.

See also: Metadata::GetCRatios()

◆ getNumThread()

int VAPoR::WaveCodecIO::getNumThread ( )

inline

Definition at line 416 of file WaveCodecIO.h.

◆ GetNumTransforms()

virtual int VAPoR::WaveCodecIO::GetNumTransforms ( ) const

virtual

◆ GetValidRegion()

void VAPoR::WaveCodecIO::GetValidRegion	(	size_t	min[3],
		size_t	max[3],
		int	reflevel
	)		const

Return the valid region bounds for the currently opened variable

This method returns the minimum and maximum valid coordinate bounds (in voxels) of the currently opened variable. In general, the minimum bounds are (0,0,0) and the maximum bounds are (nx-1, ny-1, nz-1), where nx, ny, and nz are the volume dimensions returned by GetDim(). However, partial regions (sub-volumes) may be written to the VDC as well.

Parameters

[in]	reflevel	Refinement level of the variable
[out]	min	Minimum coordinate bounds (in voxels) of volume
[out]	max	Maximum coordinate bounds (in voxels) of volume

Return values

status A non-negative int is returned on success

◆ OpenVariableRead()

virtual int VAPoR::WaveCodecIO::OpenVariableRead	(	size_t	timestep,
		const char *	varname,
		int	reflevel = `0`,
		int	lod = `0`
	)

virtual

Open the named variable for reading

This method prepares a data volume (slice), indicated by a variable name and time step pair, for subsequent read operations by methods of this class. The number of the refinement levels parameter, reflevel, indicates the resolution of the volume in the multiresolution hierarchy. The valid range of values for reflevel is [0..max_refinement], where max_refinement is the maximum refinement level of the data set: Metadata::GetNumTransforms(). A value of zero indicates the coarsest resolution data, a value of max_refinement (or -1) indicates the finest resolution data. The level-of-detail parameter, lod, selects the approximation level. Valid values for lod are integers in the range 0..GetCRatios().size()-1, or the value -1 may be used to select the best approximation available: GetCRatios().size()-1.

An error occurs, indicated by a negative return value, if the volume identified by the {varname, timestep, reflevel, lod} tupple is not available. Note the availability of a volume can be tested with the VariableExists() method.

Parameters

[in]	timestep	Time step of the variable to read
[in]	varname	Name of the variable to read
[in]	reflevel	Refinement level of the variable. A value of -1 indicates the maximum refinment level defined for the VDC
[in]	lod	Approximation level of the variable. A value of -1 indicates the maximum approximation level defined for the VDC

Return values

status Returns a non-negative value on success

See also: Metadata::GetVariableNames(), Metadata::GetNumTransforms(), GetNumTimeSteps(), GetCRatios()

◆ OpenVariableWrite()

virtual int VAPoR::WaveCodecIO::OpenVariableWrite	(	size_t	timestep,
		const char *	varname,
		int	reflevel = `-1`,
		int	lod = `-1`
	)

virtual

Open the named variable for writing

Prepare a VDC for writing a data volume (slice). The data volume is identified by the specfied time step and variable name. The number of resulting approximations for the data volume is determined by the Metadata object used to initialize the class. Moreover, the number of levels-of-detail actually saved to the data collection are determined by lod. If lod is maximum level of detail (or the special value -1, the default) all of the wavelet coefficients are saved, and it is possible to fully reconstruct the volume later without loss of information (beyond floating point round off).

Parameters

[in]	timestep	Time step of the variable to read
[in]	varname	Name of the variable to read
[in]	lod	Level of detail saved. A value of -1 indicates the maximum level of detail.

Return values

status Returns a non-negative value on success

See also: Metadata::GetVariableNames(), Metadata::GetNumTransforms()

◆ ReadRegion() [1/2]

virtual int VAPoR::WaveCodecIO::ReadRegion	(	const size_t	min[3],
		const size_t	max[3],
		float *	region
	)

virtual

Read in and return a subregion from the currently opened data volume.

This method is similar to BlockReadRegion() with the exception that the region bounds are specified in voxel coordinates. The min and max vectors identify the minimum and maximum extents, in voxel coordinates, of the subregion of interest. The minimum valid value of 'min' is (0,0,0), the maximum valid value of max is (nx-1,ny-1,nz-1), where nx, ny, and nz are the voxel dimensions of the volume at the currently opened refinement level as returned by GetDim().

The volume returned is stored in the memory region pointed to by region. It is the caller's responsbility to ensure adequate space is available.

Parameters

[in]	min	Minimum region extents in voxel coordinates
[in]	max	Maximum region extents in voxel coordinates
[out]	region	The requested volume subregion

Return values

status Returns a non-negative value on success

See also: OpenVariableRead(), GetDim(), MapVoxToBlk()

◆ ReadRegion() [2/2]

virtual int VAPoR::WaveCodecIO::ReadRegion ( float * region )

virtual

◆ ReadSlice()

virtual int VAPoR::WaveCodecIO::ReadSlice ( float * slice )

virtual

Read the next volume slice from the currently opened file

Read in and return a slice (2D array) of voxels from the currently opened data volume at the current refinement level. Subsequent calls will read successive slices until the entire volume has been read. It is the caller's responsibility to ensure that the array pointed to by slice contains enough space to accomodate an NX by NY dimensioned slice, where NX is the dimesion of the volume along the X axis, specified in voxels, and NY is the Y axis dimension, as returned by GetDim().

Note: ReadSlice returns 0 if the entire volume has been read.

Parameters

[out] slice The requested volume slice

Return values

status Returns a non-negative value on success

See also: OpenVariableRead(), Metadata::GetDim()

◆ SetBoundaryPadOnOff()

virtual void VAPoR::WaveCodecIO::SetBoundaryPadOnOff ( bool pad )

inlinevirtual

Toggle padding of data on writes

If true, incomplete data blocks will be padded prior to transformation and storage to disk. A block is incomplete iff it is a boundary block (a block that contains a volume region boundary) and the extents of the region do not coincide with block boundaries

Parameters

[in] pad Boolean indicating whether padding should (true) or should not (false) take place

See also: GetBoundaryMode()

Definition at line 292 of file WaveCodecIO.h.

◆ SetCollectiveIO()

void VAPoR::WaveCodecIO::SetCollectiveIO ( bool newCollectiveIO )

inline

Definition at line 373 of file WaveCodecIO.h.

◆ VariableExists()

virtual int VAPoR::WaveCodecIO::VariableExists	(	size_t	ts,
		const char *	varname,
		int	reflevel = `0`,
		int	lod = `0`
	)		const

virtual

Returns true if the indicated data volume exists on disk

Returns true if the variable identified by the timestep, variable name, refinement level, and level-of-detail is present on disk. Returns 0 if the variable is not present.

Parameters

[in]	ts	A valid time step from the Metadata object used to initialize the class
[in]	varname	A valid variable name
[in]	reflevel	Ignored
[in]	lod	Compression level of detail requested. The coarsest approximation level is 0 (zero). A value of -1 indicates the finest refinement level contained in the VDC.

◆ WriteRegion() [1/2]

virtual int VAPoR::WaveCodecIO::WriteRegion ( const float * region )

virtual

◆ WriteRegion() [2/2]

virtual int VAPoR::WaveCodecIO::WriteRegion	(	const float *	region,
		const size_t	min[3],
		const size_t	max[3]
	)

virtual

Write a volume subregion to the currently opened progressive access data volume.

This method is identical to the WriteRegion() method with the exception that the region boundaries are defined in block, not voxel, coordinates. Secondly, unless the 'block' parameter is set, the internal blocking of the data will be preserved. I.e. the data are assumed to already be blocked.

The number of voxels contained in region must be the product over i :

(max[i] - min[i] + 1)

Parameters

[in]	min	Minimum region extents in voxel coordinates
[in]	max	Maximum region extents in voxel coordinates
[in]	region	The volume subregion to write

Return values

status Returns a non-negative value on success

See also: OpenVariableWrite(), GetBlockSize(), MapVoxToBlk(); SetBoundarPadOnOff()

Note: Unexpected results may be obtained if this method is invoked multiple times for adjacent regions if the region boundaries do not coincide with block boundaries.

◆ WriteSlice()

virtual int VAPoR::WaveCodecIO::WriteSlice ( const float * slice )

virtual

Write a single slice of voxels to the currently opened variable

Transform and write a single slice (2D array) of voxels to the variable indicated by the most recent call to OpenVariableWrite(). The dimensions of a slices is NX by NY, where NX is the dimesion of the volume along the X axis, specified in voxels, and NY is the Y axis dimension.

This method should be called exactly NZ times for each opened variable, where NZ is the dimension of the volume in voxels along the Z axis. Each invocation should pass a successive slice of volume data.

Parameters

[in] slice A slices of volume data

Return values

status Returns a non-negative value on success

See also: OpenVariableRead()

Friends And Related Function Documentation

◆ RunBlockReadRegionThread

void * RunBlockReadRegionThread ( void * object )

friend

◆ RunBlockWriteRegionThread

void * RunBlockWriteRegionThread ( void * object )

friend

Member Data Documentation

◆ _nthreads

int VAPoR::WaveCodecIO::_nthreads

Definition at line 415 of file WaveCodecIO.h.

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

/Users/pearse/VAPOR/include/vapor/WaveCodecIO.h

Public Member Functions

Static Public Member Functions

Public Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ WaveCodecIO() [1/2]

◆ WaveCodecIO() [2/2]

◆ ~WaveCodecIO()

Member Function Documentation

◆ BlockReadRegion()

◆ BlockWriteRegion()

◆ CloseVariable()

◆ EnableBuffering()

◆ GetBlockSize()

◆ GetDataRange()

◆ GetMaxCRatio()

◆ getNumThread()

◆ GetNumTransforms()

◆ GetValidRegion()

◆ OpenVariableRead()

◆ OpenVariableWrite()

◆ ReadRegion() [1/2]

◆ ReadRegion() [2/2]

◆ ReadSlice()

◆ SetBoundaryPadOnOff()

◆ SetCollectiveIO()

◆ VariableExists()

◆ WriteRegion() [1/2]

◆ WriteRegion() [2/2]

◆ WriteSlice()

Friends And Related Function Documentation

◆ RunBlockReadRegionThread

◆ RunBlockWriteRegionThread

Member Data Documentation

◆ _nthreads