Abstract base class for performing data IO to a VDC. More...

#include <VDFIOBase.h>

Inheritance diagram for VAPoR::VDFIOBase:

Classes
class	BitMask

Public Member Functions
	VDFIOBase (const MetadataVDC &metadata)

	VDFIOBase (const string &metafile)

virtual	~VDFIOBase ()

double	GetReadTimer () const

double	GetSeekTimer () const

void	SeekTimerReset ()

void	SeekTimerStart ()

void	SeekTimerStop ()

double	GetWriteTimer () const

double	GetXFormTimer () const

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

virtual int	BlockReadRegion (const size_t bmin[3], const size_t bmax[3], float *region, bool unblock=true)=0

virtual int	ReadRegion (const size_t min[3], const size_t max[3], float *region)=0

virtual int	ReadRegion (float *region)=0

virtual int	ReadSlice (float *slice)=0

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

virtual int	BlockWriteRegion (const float *region, const size_t bmin[3], const size_t bmax[3], bool block=true)=0

virtual int	WriteRegion (const float *region, const size_t min[3], const size_t max[3])=0

virtual int	WriteRegion (const float *region)=0

virtual int	WriteSlice (const float *slice)=0

virtual int	CloseVariable ()

virtual const float *	GetDataRange () const =0

Public Member Functions inherited from VAPoR::MetadataVDC
	MetadataVDC (const size_t dim[3], size_t numTransforms, const size_t bs[3], int nFilterCoef=1, int nLiftingCoef=1, int msbFirst=1, int vdfVersion=VDF_VERSION)

	MetadataVDC (const size_t dim[3], const size_t bs[3], const vector< size_t > &cratios, string wname, string wmode)

	MetadataVDC (const string &metafile)

	MetadataVDC (const MetadataVDC &node)

virtual	~MetadataVDC ()

int	Merge (const MetadataVDC &metadata, size_t ts=0)

int	Merge (const string &path, size_t ts=0)

int	MakeCurrent () const

const string &	GetParentDir () const

const string &	GetMetafileName () const

const string &	GetDataDirName () const

int	ConstructFullVBase (size_t ts, const string &var, string *path) const

int	ConstructFullAuxBase (size_t ts, string *path) const

int	Write (const string &path, int relative_path=1)

virtual const size_t *	GetBlockSize () const

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

virtual void	GetGridDim (size_t dim[3]) const

const size_t *	GetDimension () const

int	GetFilterCoef () const

int	GetLiftingCoef () const

virtual int	GetNumTransforms () const

int	GetMSBFirst () const

int	GetVDFVersion () const

string	GetWaveName () const

string	GetBoundaryMode () const

virtual vector< size_t >	GetCRatios () const

int	GetVDCType () const

int	SetGridType (const string &value)

string	GetGridType () const

int	IsValidGridType (const string &value) const

int	SetCoordSystemType (const string &value)

string	GetCoordSystemType () const

int	IsValidCoordSystemType (const string &value) const

int	SetExtents (const vector< double > &value)

vector< double >	GetExtents (size_t ts=0) const

int	IsValidExtents (const vector< double > &value) const

int	SetNumTimeSteps (long value)

long	GetNumTimeSteps () const

int	IsValidTimeStep (long value) const

int	SetVariableNames (const vector< string > &value)

int	SetVariables3D (const vector< string > &value)

vector< string >	GetVariables3D () const

vector< string >	GetCoordinateVariables () const

int	SetCoordinateVariables (const vector< string > &value)

int	SetVariables2DXY (const vector< string > &value)

int	SetVariables2DXZ (const vector< string > &value)

int	SetVariables2DYZ (const vector< string > &value)

vector< string >	GetVariables2DXY () const

vector< string >	GetVariables2DXZ () const

vector< string >	GetVariables2DYZ () const

int	SetComment (const string &value)

string	GetComment () const

int	SetPeriodicBoundary (const vector< long > &value)

vector< long >	GetPeriodicBoundary () const

int	SetGridPermutation (const vector< long > &value)

int	SetMissingValue (double value)

int	SetMissingValue ()

vector< double >	GetMissingValue () const

vector< long >	GetGridPermutation () const

int	SetMapProjection (const string &value)

virtual string	GetMapProjection () const

int	SetTSUserTime (size_t ts, const vector< double > &value)

double	GetTSUserTime (size_t ts) const

int	SetTSUserTimeStamp (size_t ts, const string &s)

void	GetTSUserTimeStamp (size_t ts, string &s) const

string	GetTSAuxBasePath (size_t ts) const

int	HasTSUserTime (size_t ts) const

int	IsValidUserTime (const vector< double > &value) const

int	SetTSXCoords (size_t ts, const vector< double > &value)

vector< double >	GetTSXCoords (size_t ts) const

int	SetTSYCoords (size_t ts, const vector< double > &value)

vector< double >	GetTSYCoords (size_t ts) const

int	SetTSZCoords (size_t ts, const vector< double > &value)

vector< double >	GetTSZCoords (size_t ts) const

int	SetTSComment (size_t ts, const string &value)
	Set a comment for the time step indicated by `ts`. More...

string	GetTSComment (size_t ts) const
	Return the comment for the indicated time step, `ts`, if it exists. More...

int	SetTSExtents (size_t ts, const vector< double > &value)

vector< double >	GetTSExtents (size_t ts) const

int	SetTSMissingValue (size_t ts, double v)

vector< double >	GetTSMissingValue (size_t ts) const
	Returns the time-varying missing value, if any. More...

int	SetVComment (size_t ts, const string &var, const string &value)

string	GetVComment (size_t ts, const string &var) const

string	GetVBasePath (size_t ts, const string &var) const

int	SetVBasePath (size_t ts, const string &var, const string &value)

int	SetVDataRange (size_t ts, const string &var, const vector< double > &value)

vector< double >	GetVDataRange (size_t ts, const string &var) const

int	IsValidVDataRange (const vector< double > &value) const

int	SetVMissingValue (size_t ts, const string &var, double v)

vector< double >	GetVMissingValue (size_t ts, const string &var) const

vector< string >	GetUserDataLongTags () const

int	SetUserDataLong (const string &tag, const vector< long > &value)

vector< long >	GetUserDataLong (const string &tag) const

vector< string >	GetUserDataDoubleTags () const

int	SetUserDataDouble (const string &tag, const vector< double > &value)

vector< double >	GetUserDataDouble (const string &tag) const

vector< string >	GetUserDataStringTags () const

int	SetUserDataString (const string &tag, const string &value)

string	GetUserDataString (const string &tag) const

int	SetUserDataStringVec (const string &tag, const vector< string > &value)

vector< string >	GetUserDataStringVec (const string &tag) const

vector< string >	GetTSUserDataLongTags () const

int	SetTSUserDataLong (size_t ts, const string &tag, const vector< long > &value)

vector< long >	GetTSUserDataLong (size_t ts, const string &tag) const

int	SetTSUserDataDouble (size_t ts, const string &tag, const vector< double > &value)

vector< double >	GetTSUserDataDouble (size_t ts, const string &tag) const

vector< string >	GetTSUserDataDoubleTags () const

int	SetTSUserDataString (size_t ts, const string &tag, const string &value)

string	GetTSUserDataString (size_t ts, const string &tag) const

vector< string >	GetTSUserDataStringTags () const

vector< string >	GetVUserDataLongTags () const

int	SetVUserDataLong (size_t ts, const string &var, const string &tag, const vector< long > &value)

vector< long >	GetVUserDataLong (size_t ts, const string &var, const string &tag) const

vector< string >	GetVUserDataDoubleTags () const

int	SetVUserDataDouble (size_t ts, const string &var, const string &tag, const vector< double > &value)

vector< double >	GetVUserDataDouble (size_t ts, const string &var, const string &tag) const

int	SetVUserDataString (size_t ts, const string &var, const string &tag, const string &value)

string	GetVUserDataString (size_t ts, const string &var, const string &tag) const

vector< string >	GetVUserDataStringTags () const

Public Member Functions inherited from VAPoR::Metadata
	Metadata ()

virtual	~Metadata ()

virtual std::vector< std::string >	GetVariableNames () const

virtual void	GetTSUserTimeStamp (size_t ts, std::string &s) const =0

virtual void	GetDim (size_t dim[3], int reflevel=0) const

virtual void	GetDimBlk (size_t bdim[3], int reflevel=0) const

virtual bool	GetMissingValue (std::string varname, float &value) const

virtual void	MapVoxToBlk (const size_t vcoord[3], size_t bcoord[3], int reflevel=-1) const

virtual void	MapVoxToUser (size_t timestep, const size_t vcoord0[3], double vcoord1[3], int ref_level=0) const

void	MapUserToVox (size_t timestep, const double vcoord0[3], size_t vcoord1[3], int reflevel) const

virtual VarType_T	GetVarType (const std::string &varname) const

virtual int	IsValidRegion (const size_t min[3], const size_t max[3], int reflevel=0) const

virtual int	IsValidRegionBlk (const size_t min[3], const size_t max[3], int reflevel=0) const

virtual bool	IsCoordinateVariable (std::string varname) 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)

Protected Member Functions
void	_ReadTimerReset ()

void	_ReadTimerStart ()

void	_ReadTimerStop ()

void	_WriteTimerReset ()

void	_WriteTimerStart ()

void	_WriteTimerStop ()

void	_XFormTimerReset ()

void	_XFormTimerStart ()

void	_XFormTimerStop ()

int	_MaskOpenWrite (size_t timestep, string varname, int reflevel)

int	_MaskOpenRead (size_t timestep, string varname, int reflevel)

int	_MaskClose ()

int	_MaskWrite (const float *srcblk, const size_t bmin_p[3], const size_t bmax_p[3], bool block)

int	_MaskRead (const size_t bmin_p[3], const size_t bmax_p[3])

void	_MaskRemove (float *blk, bool &valid_data) const

void	_MaskReplace (size_t bx, size_t by, size_t bz, float *blk) const

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

Static Protected Member Functions
static void	_UnpackCoord (VarType_T vtype, const size_t src[3], size_t dst[3], size_t fill)

static void	_PackCoord (VarType_T vtype, const size_t src[3], size_t dst[3], size_t fill)

static void	_FillPackedCoord (VarType_T vtype, const size_t src[3], size_t dst[3], size_t fill)

Additional Inherited Members
Public Types inherited from VAPoR::Metadata
enum	VarType_T { VARUNKNOWN = -1, VAR3D, VAR2D_XY, VAR2D_XZ, VAR2D_YZ }

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 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 Attributes inherited from VAPoR::Metadata
bool	_deprecated_get_dim

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

Abstract base class for performing data IO to a VDC.

Author: John Clyne

Version: $Revision$

Date: $Date$

This class provides an API for performing low-level IO to/from a Vapor Data Collection (VDC)

Definition at line 27 of file VDFIOBase.h.

Constructor & Destructor Documentation

VAPoR::VDFIOBase::VDFIOBase ( const MetadataVDC & metadata )

Constructor for the VDFIOBase class.

Parameters

[in] metadata Pointer to a metadata class object for which all future class operations will apply

Note: The success or failure of this constructor can be checked with the GetErrCode() method.

See also: Metadata, GetErrCode(),

VAPoR::VDFIOBase::VDFIOBase ( const string & metafile )

Constructor for the VDFIOBase class.

Parameters

[in] metafile Path to a metadata file for which all future class operations will apply

Note: The success or failure of this constructor can be checked with the GetErrCode() method.

See also: Metadata, GetErrCode(),

virtual VAPoR::VDFIOBase::~VDFIOBase ( )

virtual

Member Function Documentation

static void VAPoR::VDFIOBase::_FillPackedCoord	(	VarType_T	vtype,
		const size_t	src[3],
		size_t	dst[3],
		size_t	fill
	)

staticprotected

int VAPoR::VDFIOBase::_MaskClose ( )

protected

int VAPoR::VDFIOBase::_MaskOpenRead	(	size_t	timestep,
		string	varname,
		int	reflevel
	)

protected

int VAPoR::VDFIOBase::_MaskOpenWrite	(	size_t	timestep,
		string	varname,
		int	reflevel
	)

protected

int VAPoR::VDFIOBase::_MaskRead	(	const size_t	bmin_p[3],
		const size_t	bmax_p[3]
	)

protected

void VAPoR::VDFIOBase::_MaskRemove	(	float *	blk,
		bool &	valid_data
	)		const

protected

void VAPoR::VDFIOBase::_MaskReplace	(	size_t	bx,
		size_t	by,
		size_t	bz,
		float *	blk
	)		const

protected

int VAPoR::VDFIOBase::_MaskWrite	(	const float *	srcblk,
		const size_t	bmin_p[3],
		const size_t	bmax_p[3],
		bool	block
	)

protected

static void VAPoR::VDFIOBase::_PackCoord	(	VarType_T	vtype,
		const size_t	src[3],
		size_t	dst[3],
		size_t	fill
	)

staticprotected

void VAPoR::VDFIOBase::_ReadTimerReset ( )

inlineprotected

Definition at line 186 of file VDFIOBase.h.

void VAPoR::VDFIOBase::_ReadTimerStart ( )

inlineprotected

Definition at line 187 of file VDFIOBase.h.

References VetsUtil::GetTime().

void VAPoR::VDFIOBase::_ReadTimerStop ( )

inlineprotected

Definition at line 188 of file VDFIOBase.h.

References VetsUtil::GetTime().

static void VAPoR::VDFIOBase::_UnpackCoord	(	VarType_T	vtype,
		const size_t	src[3],
		size_t	dst[3],
		size_t	fill
	)

staticprotected

void VAPoR::VDFIOBase::_WriteTimerReset ( )

inlineprotected

Definition at line 190 of file VDFIOBase.h.

void VAPoR::VDFIOBase::_WriteTimerStart ( )

inlineprotected

Definition at line 191 of file VDFIOBase.h.

References VetsUtil::GetTime().

void VAPoR::VDFIOBase::_WriteTimerStop ( )

inlineprotected

Definition at line 192 of file VDFIOBase.h.

References VetsUtil::GetTime().

void VAPoR::VDFIOBase::_XFormTimerReset ( )

inlineprotected

Definition at line 194 of file VDFIOBase.h.

void VAPoR::VDFIOBase::_XFormTimerStart ( )

inlineprotected

Definition at line 195 of file VDFIOBase.h.

References VetsUtil::GetTime().

void VAPoR::VDFIOBase::_XFormTimerStop ( )

inlineprotected

Definition at line 196 of file VDFIOBase.h.

References VetsUtil::GetTime().

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

pure virtual

Implemented in VAPoR::AMRIO, VAPoR::WaveCodecIO, VAPoR::WaveletBlockIOBase, and VAPoR::WaveletBlock3DRegionReader.

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

pure virtual

Implemented in VAPoR::WaveCodecIO, VAPoR::AMRIO, and VAPoR::WaveletBlockIOBase.

virtual int VAPoR::VDFIOBase::CloseVariable ( )

inlinevirtual

Reimplemented in VAPoR::AMRIO, VAPoR::WaveletBlockIOBase, VAPoR::WaveCodecIO, VAPoR::WaveletBlock3DRegionWriter, VAPoR::WaveletBlock3DRegionReader, VAPoR::WaveletBlock3DReader, VAPoR::WaveletBlock3DWriter, VAPoR::WaveletBlock3DBufReader, and VAPoR::WaveletBlock3DBufWriter.

Definition at line 121 of file VDFIOBase.h.

virtual const float* VAPoR::VDFIOBase::GetDataRange ( ) const

pure virtual

Implemented in VAPoR::WaveCodecIO, VAPoR::AMRIO, VAPoR::WaveletBlockIOBase, and VAPoR::WaveletBlock3DBufWriter.

double VAPoR::VDFIOBase::GetReadTimer ( ) const

inline

Return the read timer

This method returns the accumulated clock time, in seconds, spent reading data from files.

Definition at line 62 of file VDFIOBase.h.

double VAPoR::VDFIOBase::GetSeekTimer ( ) const

inline

Return the seek timer

This method returns the accumulated clock time, in seconds, spent performing file seeks (in general this is zero)

Definition at line 69 of file VDFIOBase.h.

double VAPoR::VDFIOBase::GetWriteTimer ( ) const

inline

Return the write timer

This method returns the accumulated clock time, in seconds, spent writing data to files.

Definition at line 79 of file VDFIOBase.h.

double VAPoR::VDFIOBase::GetXFormTimer ( ) const

inline

Return the transform timer

This method returns the accumulated clock time, in seconds, spent transforming data.

Definition at line 86 of file VDFIOBase.h.

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

inlinevirtual

Reimplemented in VAPoR::AMRIO, VAPoR::WaveletBlockIOBase, VAPoR::WaveCodecIO, VAPoR::WaveletBlock3DRegionWriter, VAPoR::WaveletBlock3DWriter, VAPoR::WaveletBlock3DReader, VAPoR::WaveletBlock3DRegionReader, and VAPoR::WaveletBlock3DBufReader.

Definition at line 88 of file VDFIOBase.h.

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

inlinevirtual

Reimplemented in VAPoR::AMRIO, VAPoR::WaveCodecIO, VAPoR::WaveletBlockIOBase, VAPoR::WaveletBlock3DReader, VAPoR::WaveletBlock3DRegionReader, VAPoR::WaveletBlock3DRegionWriter, VAPoR::WaveletBlock3DBufWriter, and VAPoR::WaveletBlock3DWriter.

Definition at line 104 of file VDFIOBase.h.

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

pure virtual

Implemented in VAPoR::AMRIO, VAPoR::WaveCodecIO, VAPoR::WaveletBlockIOBase, and VAPoR::WaveletBlock3DRegionReader.

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

pure virtual

Implemented in VAPoR::AMRIO, VAPoR::WaveCodecIO, VAPoR::WaveletBlockIOBase, and VAPoR::WaveletBlock3DRegionReader.

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

pure virtual

Implemented in VAPoR::AMRIO, VAPoR::WaveCodecIO, VAPoR::WaveletBlockIOBase, and VAPoR::WaveletBlock3DBufReader.

void VAPoR::VDFIOBase::SeekTimerReset ( )

inline

Definition at line 70 of file VDFIOBase.h.

void VAPoR::VDFIOBase::SeekTimerStart ( )

inline

Definition at line 71 of file VDFIOBase.h.

References VetsUtil::GetTime().

void VAPoR::VDFIOBase::SeekTimerStop ( )

inline

Definition at line 72 of file VDFIOBase.h.

References VetsUtil::GetTime().

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

pure virtual

Implemented in VAPoR::WaveCodecIO, VAPoR::AMRIO, VAPoR::WaveletBlock3DRegionWriter, and VAPoR::WaveletBlockIOBase.

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

pure virtual

Implemented in VAPoR::WaveCodecIO, VAPoR::AMRIO, VAPoR::WaveletBlock3DRegionWriter, and VAPoR::WaveletBlockIOBase.

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

pure virtual

Implemented in VAPoR::WaveCodecIO, VAPoR::AMRIO, VAPoR::WaveletBlockIOBase, and VAPoR::WaveletBlock3DBufWriter.

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

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

Classes

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation