Defines API for reading, writing, and appending data to a VAPOR Data Collection (Version 3) More...

#include <VDC.h>

Inheritance diagram for VAPoR::VDC:

Public Types
enum	AccessMode { R , W , A }

Public Types inherited from VAPoR::DC
enum	XType { INVALID = -1 , FLOAT , DOUBLE , UINT8 , INT8 , INT32 , INT64 , TEXT }
	External storage types for primitive data. More...

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

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

Public Member Functions
	VDC ()

virtual	~VDC ()

int	SetCompressionBlock (string wname, std::vector< size_t > cratios)

void	GetCompressionBlock (std::vector< size_t > &bs, string &wname, std::vector< size_t > &cratios) const

void	SetPeriodicBoundary (std::vector< bool > periodic)

std::vector< bool >	GetPeriodicBoundary () const

int	DefineDimension (string dimname, size_t length)

int	DefineDimension (string dimname, size_t length, int axis)

int	DefineCoordVar (string varname, std::vector< string > dimnames, string time_dim_name, string units, int axis, XType type, bool compressed)

int	DefineCoordVarUniform (string varname, std::vector< string > dimname, string time_dim_name, string units, int axis, XType type, bool compressed)

int	DefineDataVar (string varname, std::vector< string > dimnames, std::vector< string > coordvars, string units, XType type, bool compressed)

int	DefineDataVar (string varname, std::vector< string > dimnames, std::vector< string > coordvars, string units, XType type, double missing_value, string maskvar)

int	PutAtt (string varname, string attname, XType type, const vector< double > &values)

int	PutAtt (string varname, string attname, XType type, const vector< long > &values)

int	PutAtt (string varname, string attname, XType type, const string &values)

int	CopyAtt (const DC &src, string varname, string attname)

int	CopyAtt (const DC &src, string varname)

virtual int	SetMapProjection (string varname, string projstring)

virtual int	SetMapProjection (string projstring)

int	EndDefine ()

virtual int	GetPath (string varname, size_t ts, string &path, size_t &file_ts, size_t &max_ts) const =0

virtual int	OpenVariableWrite (size_t ts, string varname, int lod=-1)=0

virtual int	CloseVariableWrite (int fd)=0

virtual int	Write (int fd, const float *data)=0

virtual int	Write (int fd, const int *data)=0

virtual int	WriteSlice (int fd, const float *slice)=0

virtual int	WriteSlice (int fd, const int *slice)=0

virtual int	WriteSlice (int fd, const unsigned char *slice)=0

virtual int	PutVar (string varname, int lod, const float *data)=0

virtual int	PutVar (string varname, int lod, const int *data)=0

virtual int	PutVar (size_t ts, string varname, int lod, const float *data)=0

virtual int	PutVar (size_t ts, string varname, int lod, const int *data)=0

virtual int	CopyVar (DC &dc, string varname, int srclod, int dstlod)=0

virtual int	CopyVar (DC &dc, size_t ts, string varname, int srclod, int dstlod)=0

virtual bool	CompressionInfo (vector< size_t > bs, string wname, size_t &nlevels, size_t &maxcratio) const =0

virtual bool	variableExists (size_t ts, string varname, int reflevel=0, int lod=0) const =0

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

virtual	~DC ()

virtual int	Initialize (const std::vector< string > &paths, const std::vector< string > &options=std::vector< string >())

virtual bool	GetDimension (string dimname, DC::Dimension &dimension, long ts) const

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

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

virtual bool	GetMesh (string mesh_name, DC::Mesh &mesh) const

virtual bool	GetMeshDimLens (const string &mesh_name, std::vector< size_t > &dims, long ts=-1) const

virtual bool	GetMeshDimNames (const string &mesh_name, std::vector< string > &dimnames) const

virtual bool	GetCoordVarInfo (string varname, DC::CoordVar &cvar) const

virtual bool	GetDataVarInfo (string varname, DC::DataVar &datavar) const

virtual bool	GetAuxVarInfo (string varname, DC::AuxVar &var) const

virtual bool	GetBaseVarInfo (string varname, DC::BaseVar &var) const

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

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

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

virtual size_t	GetNumRefLevels (string varname) const

virtual bool	GetAtt (string varname, string attname, vector< double > &values) const

virtual bool	GetAtt (string varname, string attname, vector< long > &values) const

virtual bool	GetAtt (string varname, string attname, string &values) const

virtual std::vector< string >	GetAttNames (string varname) const

virtual XType	GetAttType (string varname, string attname) const

virtual int	GetDimLensAtLevel (string varname, int level, std::vector< size_t > &dims_at_level, std::vector< size_t > &bs_at_level, long ts=-1) const

virtual int	GetDimLens (string varname, std::vector< size_t > &dims, long ts=-1)

virtual string	GetMapProjection () const

virtual int	OpenVariableRead (size_t ts, string varname, int level=0, int lod=0)

virtual int	CloseVariable (int fd)

virtual int	Read (int fd, float *data)

virtual int	Read (int fd, double *data)

virtual int	Read (int fd, int *data)

virtual int	ReadSlice (int fd, float *slice)

virtual int	ReadSlice (int fd, double *slice)

virtual int	ReadSlice (int fd, int *slice)

virtual int	ReadRegion (int fd, const vector< size_t > &min, const vector< size_t > &max, float *region)

virtual int	ReadRegion (int fd, const vector< size_t > &min, const vector< size_t > &max, double *region)

virtual int	ReadRegion (int fd, const vector< size_t > &min, const vector< size_t > &max, int *region)

virtual int	GetVar (string varname, int level, int lod, float *data)

virtual int	GetVar (string varname, int level, int lod, double *data)

virtual int	GetVar (string varname, int level, int lod, int *data)

virtual int	GetVar (size_t ts, string varname, int level, int lod, float *data)

virtual int	GetVar (size_t ts, string varname, int level, int lod, double *data)

virtual int	GetVar (size_t ts, string varname, int level, int lod, int *data)

virtual bool	VariableExists (size_t ts, string varname, int reflevel=0, int lod=0) const

virtual int	GetHyperSliceInfo (string varname, int level, std::vector< size_t > &dims, size_t &nslice, long ts=-1)

virtual std::vector< string >	GetDataVarNames (int ndim) const

virtual bool	GetVarDimensions (string varname, bool spatial, vector< DC::Dimension > &dimensions, long ts) const

virtual bool	GetVarDimLens (string varname, bool spatial, vector< size_t > &dimlens, long ts=-1) const

virtual bool	GetVarDimLens (string varname, vector< size_t > &sdimlens, size_t &time_dimlen, long ts=-1) const

virtual bool	GetVarDimNames (string varname, bool spatial, vector< string > &dimnames) const

virtual bool	GetVarDimNames (string varname, vector< string > &sdimnames, string &time_dimname) const

virtual size_t	GetVarTopologyDim (string varname) const

virtual size_t	GetVarGeometryDim (string varname) const

virtual bool	IsTimeVarying (string varname) const

virtual bool	IsCompressed (string varname) const

virtual int	GetNumTimeSteps (string varname) const

virtual std::vector< size_t >	GetCRatios (string varname) const

virtual bool	IsDataVar (string varname) const

virtual bool	IsCoordVar (string varname) const

virtual bool	IsAuxVar (string varname) const

virtual bool	GetVarCoordVars (string varname, bool spatial, std::vector< string > &coord_vars) const

bool	GetVarConnVars (string varname, string &face_node_var, string &node_face_var, string &face_edge_var, string &face_face_var, string &edge_node_var, string &edge_face_var) const

virtual size_t	GetNumDimensions (string varname) const

std::vector< string >	GetTimeCoordVarNames () const

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

const string &	getClassName () const

Protected Member Functions
virtual int	initialize (const std::vector< string > &paths, const std::vector< string > &options, AccessMode mode, vector< size_t > bs)

virtual int	initialize (const std::vector< string > &paths, const std::vector< string > &options)

bool	getDimension (string dimname, DC::Dimension &dimension) const

std::vector< string >	getDimensionNames () const

std::vector< string >	getMeshNames () const

virtual bool	getMesh (string mesh_name, DC::Mesh &mesh) const

bool	getCoordVarInfo (string varname, DC::CoordVar &cvar) const

bool	getDataVarInfo (string varname, DC::DataVar &datavar) const

bool	getAuxVarInfo (string varname, DC::AuxVar &var) const

bool	getBaseVarInfo (string varname, DC::BaseVar &var) const

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

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

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

size_t	getNumRefLevels (string varname) const

bool	getAtt (string varname, string attname, vector< double > &values) const

bool	getAtt (string varname, string attname, vector< long > &values) const

bool	getAtt (string varname, string attname, string &values) const

std::vector< string >	getAttNames (string varname) const

XType	getAttType (string varname, string attname) const

virtual vector< size_t >	getBlockSize () const

virtual int	getDimLensAtLevel (string varname, int level, std::vector< size_t > &dims_at_level, std::vector< size_t > &bs_at_level) const =0

virtual string	getMapProjection (string varname) const

virtual string	getMapProjection () const

virtual string	getMapProjectionDefault () const

virtual int	openVariableRead (size_t ts, string varname, int level=0, int lod=0)=0

virtual int	closeVariable (int fd)=0

virtual int	readRegion (int fd, const vector< size_t > &min, const vector< size_t > &max, float *region)=0

virtual int	readRegion (int fd, const vector< size_t > &min, const vector< size_t > &max, double *region)=0

Protected Member Functions inherited from VAPoR::DC
virtual int	initialize (const std::vector< string > &paths, const std::vector< string > &options=std::vector< string >())=0

virtual bool	getDimension (string dimname, DC::Dimension &dimension) const =0

virtual bool	getDimension (string dimname, DC::Dimension &dimension, long ts) const

virtual std::vector< string >	getDimensionNames () const =0

virtual std::vector< string >	getMeshNames () const =0

virtual bool	getMesh (string mesh_name, DC::Mesh &mesh) const =0

virtual bool	getCoordVarInfo (string varname, DC::CoordVar &cvar) const =0

virtual bool	getDataVarInfo (string varname, DC::DataVar &datavar) const =0

virtual bool	getAuxVarInfo (string varname, DC::AuxVar &var) const =0

virtual bool	getBaseVarInfo (string varname, DC::BaseVar &var) const =0

virtual std::vector< string >	getDataVarNames () const =0

virtual std::vector< string >	getCoordVarNames () const =0

virtual std::vector< string >	getAuxVarNames () const =0

virtual size_t	getNumRefLevels (string varname) const =0

virtual bool	getAtt (string varname, string attname, vector< double > &values) const =0

virtual bool	getAtt (string varname, string attname, vector< long > &values) const =0

virtual bool	getAtt (string varname, string attname, string &values) const =0

virtual std::vector< string >	getAttNames (string varname) const =0

virtual XType	getAttType (string varname, string attname) const =0

virtual vector< size_t >	getBlockSize () const

virtual int	getDimLensAtLevel (string varname, int level, std::vector< size_t > &dims_at_level, std::vector< size_t > &bs_at_level) const =0

virtual int	getDimLensAtLevel (string varname, int level, std::vector< size_t > &dims_at_level, std::vector< size_t > &bs_at_level, long ts) const

virtual string	getMapProjection () const =0

virtual int	openVariableRead (size_t ts, string varname, int level=0, int lod=0)=0

virtual int	closeVariable (int fd)=0

virtual int	readRegion (int fd, const vector< size_t > &min, const vector< size_t > &max, float *region)=0

virtual int	readRegion (int fd, const vector< size_t > &min, const vector< size_t > &max, double *region)=0

virtual int	readRegion (int fd, const vector< size_t > &min, const vector< size_t > &max, int *region)=0

virtual bool	variableExists (size_t ts, string varname, int reflevel=0, int lod=0) const =0

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

Protected Attributes
string	_master_path

AccessMode	_mode

bool	_defineMode

std::vector< size_t >	_bs

string	_wname

std::vector< size_t >	_cratios

vector< bool >	_periodic

VAPoR::UDUnits	_udunits

std::map< string, Dimension >	_dimsMap

std::map< string, Attribute >	_atts

std::map< string, CoordVar >	_coordVars

std::map< string, DataVar >	_dataVars

std::map< string, Mesh >	_meshes

Protected Attributes inherited from VAPoR::DC
DC::FileTable	_fileTable

Friends
std::ostream &	operator<< (std::ostream &o, const VDC &vdc)

Additional Inherited Members
Static Public 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 Public 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

Defines API for reading, writing, and appending data to a VAPOR Data Collection (Version 3)

Author: John Clyne

Date: July, 2014

This abstract class efines API for reading, writing, and appending data to a VAPOR Data Collection (Version 3). The VDC class is an abstract virtual class, providing a public API, but performing no actual storage operations. Derived implementations of the VDC base class are required to support the API.

In version 3 of the VDC the metadata (.vdf) file found in VDC version 1 and 2 is replaced with a "master" file that describes the contents of the entire VDC. The master file imposes structure on the organization of the files containing data, determining, for example, which data files contain which variables and time steps.

Unlike the .vdf file, it is intended that the master file will be stored in the same scientific data file format as the data themselves (though this depends on the implementation of the derived class). Another important change in version 3 is that both the master file and the accompanying data files are intended to be accessible using the native file format API. I.e. users may operate on files in the VDC using, for example, the NetCDF API, or they may use the API provided by the VDC class object. The latter is only required when reading or writing compressed variables (not all variables in a VDC version 3 must be compressed). Thus if NetCDF is chosen as the underlying format the NetCDF API may be used directly to read and write NetCDF "attributes" and variables (provided the variables are not compressed).

Variables in a VDC may have 1, 2, or 3 spatial dimensions, and 0 or 1 temporal dimensions.

The VDC is structured in the spirit of the "NetCDF Climate and Forecast (CF) Metadata Conventions", version 1.6, 5, December 2011. It supports only a subset of the CF functionality (e.g. there is no support for "Discrete Sampling Geometries"). Moreover, it is more restrictive than the CF in a number of areas. Particular items of note include:

All dimensions defined in the VDC have a 1D coordinate variable associated with them with the same name as the dimension.

The API supports variables with 1 to 4 dimensions only.

Coordinate variables representing time must be 1D

All data variables have a "coordinate" attribute identifying the coordinate (or auxilliary coordinate) variables associated with each axis

To be consistent with VAPOR, when specified in vector form the ordering of dimension lengths and dimension names is from fastest varying dimension to slowest. For example, if 'dims' is a vector of dimensions, then dims[0] is the fastest varying dimension, dim[1] is the next fastest, and so on. This ordering is the opposite of the ordering used by NetCDF.

This class inherits from Wasp::MyBase. Unless otherwise documented any method that returns an integer value is returning status. A negative value indicates failure. Error messages are logged via Wasp::MyBase::SetErrMsg(). Methods that return a boolean do not, unless otherwise documented, log an error message upon failure (return of false).

Parameters

level	Grid refinement level for multiresolution variables. Compressed variables in the VDC have a multi-resolution representation: the sampling grid for multi-resolution variables is hierarchical, and the dimension lengths of adjacent levels in the hierarchy differ by a factor of two. The `level` parameter is used to select a particular depth of the hierarchy. To provide maximum flexibility as well as compatibility with previous versions of the VDC the interpretation of `level` is somewhat complex. Both positive and negative values may be used to specify the refinement level and have different interpretations. For positive values of `level`, a value of 0 indicates the coarsest member of the grid hierarchy. A value of 1 indicates the next grid refinement after the coarsest, and so on. Using postive values the finest level in the hierarchy is given by GetNumRefLevels() - 1. Values of `level` that are greater than GetNumRefLevels() - 1 are treated as if they were equal to GetNumRefLevels() - 1. For negative values of `level` a value of -1 indicates the variable's native grid resolution (the finest resolution available). A value of -2 indicates the next coarsest member in the hierarchy after the finest, and so on. Using negative values the coarsest available level in the hierarchy is given by negating the value returned by GetNumRefLevels(). Values of `level` that are less than the negation of GetNumRefLevels() are treated as if they were equal to the negation of the GetNumRefLevels() return value.
lod	The level-of-detail parameter, `lod`, selects the approximation level for a compressed variable. The `lod` parameter is similar to the `level` parameter in that it provides control over accuracy of a compressed variable. However, instead of selecting the grid resolution the `lod` parameter controls the compression factor by indexing into the `cratios` vector (see below). As with the `level` parameter, both positive and negative values may be used to index into `cratios` and different interpretations. For positive values of `lod`, a value of 0 indicates the the first element of `cratios`, a value of 1 indicates the second element, and so on up to the size of the `cratios` vector (See DC::GetCRatios()). For negative values of `lod` a value of -1 indexes the last element of `cratios`, a value of -2 indexes the second to last element, and so on. Using negative values the first element of `cratios` - the greatest compression rate - is indexed by negating the size of the `cratios` vector.
cratios	A monotonically decreasing vector of compression ratios. Compressed variables in the VDC are stored with a fixed, finite number of compression factors. The `cratios` vector is used to specify the available compression factors (ratios). A compression factor of 1 indicates no compression (1:1). A value of 2 indciates two to one compression (2:1), and so on. The minimum valid value of `cratios` is 1. The maximum value is determined by a number of factors and can be obtained using the CompressionInfo() method.
wname	Name of wavelet used for transforming compressed variables between wavelet and physical space. Valid values are "bior1.1", "bior1.3", "bior1.5", "bior2.2", "bior2.4", "bior2.6", "bior2.8", "bior3.1", "bior3.3", "bior3.5", "bior3.7", "bior3.9", "bior4.4"

Definition at line 165 of file VDC.h.

Member Enumeration Documentation

◆ AccessMode

enum VAPoR::VDC::AccessMode

Read, Write, Append access mode

Enumerator
R
W
A

Definition at line 169 of file VDC.h.

Constructor & Destructor Documentation

◆ VDC()

VAPoR::VDC::VDC ( )

Class constuctor

◆ ~VDC()

virtual VAPoR::VDC::~VDC ( )

inlinevirtual

Definition at line 175 of file VDC.h.

Member Function Documentation

◆ closeVariable()

virtual int VAPoR::VDC::closeVariable ( int fd )

protectedpure virtual

Close the currently opened variable

Close the handle for variable opened with OpenVariableRead()

Parameters

[in] fd A valid file descriptor returned by OpenVariableRead()

See also: OpenVariableRead()

Implements VAPoR::DC.

Implemented in VAPoR::VDCNetCDF.

◆ CloseVariableWrite()

virtual int VAPoR::VDC::CloseVariableWrite ( int fd )

pure virtual

Implemented in VAPoR::VDCNetCDF.

◆ CompressionInfo()

virtual bool VAPoR::VDC::CompressionInfo	(	vector< size_t >	bs,
		string	wname,
		size_t &	nlevels,
		size_t &	maxcratio
	)		const

pure virtual

This method computes and returns the depth (number of levels) in a a multi-resolution hierarch for a given wavelet, wname, and decomposition block, bs. It also computes the maximum compression ratio, cratio, possible for the the specified combination of block size, bs, and wavelet, wname. The maximum compression ratio is cratio:1.

Parameters

[in]	bs	Dimensions of native decomposition block. The rank of `bs` may be less than or equal to the rank of `dims`.
[in]	wname	wavelet name. Empty string if no compression is to be performed.
[out]	nlevels	Number of levels in hierarchy
[out]	maxcratio	Maximum compression ratio

Return values

bool	If `bs`, `wname`, or the combination there of is invalid false is returned and the values of `nlevels` and `maxcratio` are undefined. Upon success true is returned.

◆ CopyAtt() [1/2]

int VAPoR::VDC::CopyAtt	(	const DC &	src,
		string	varname
	)

Copy attributes

This method copies attributes from the src DC. The attributes can either be "global", if varname is the empty string, or bound to a variable if varname indentifies a variable in the src DC. All attributes associated with varname are copied.

Parameters

[in]	src	The source DC from which to copy.
[in]	varname	The name of the variable the attribute is bound to, or the empty string if the attribute is global

Return values

status A negative int is returned on failure. 0 returned on success.

See also: PutAtt()

◆ CopyAtt() [2/2]

int VAPoR::VDC::CopyAtt	(	const DC &	src,
		string	varname,
		string	attname
	)

Copy an attribute

This method copies an attribute from the src DC. The attribute can either be "global", if varname is the empty string, or bound to a variable if varname indentifies a variable in the src DC.

Parameters

[in]	src	The source DC from which to copy.
[in]	varname	The name of the variable the attribute is bound to, or the empty string if the attribute is global
[in]	attname	The attributes name

Return values

status A negative int is returned on failure. 0 returned on success.

See also: PutAtt()

◆ CopyVar() [1/2]

virtual int VAPoR::VDC::CopyVar	(	DC &	dc,
		size_t	ts,
		string	varname,
		int	srclod,
		int	dstlod
	)

pure virtual

Copy a variable from another data collection to this data collection at a single time step

Implemented in VAPoR::VDCNetCDF.

◆ CopyVar() [2/2]

virtual int VAPoR::VDC::CopyVar	(	DC &	dc,
		string	varname,
		int	srclod,
		int	dstlod
	)

pure virtual

Copy a variable from another data collection to this data collection

This method copies the variable named varname from the data collection specified by dc to this data collection. The variable must have previously been defined in this data collection.

Parameters

[in]	dc	A reference to a source data collection
[in]	varname	Name of variable to copy
[in]	srclod	The level-of-detail used to open `varname` in `dc`.
[in]	dstlod	The level-of-detail used to open `varname` in this data collection.

Implemented in VAPoR::VDCNetCDF.

◆ DefineCoordVar()

int VAPoR::VDC::DefineCoordVar	(	string	varname,
		std::vector< string >	dimnames,
		string	time_dim_name,
		string	units,
		int	axis,
		XType	type,
		bool	compressed
	)

Define a coordinate variable

This method provides the definition for a coordinate variable: a variable providing spatial or temporal coordinates for a subsequently defined data variable.

If the variable's name, varname, matches a dimension defined with DefineDimension(), only the units and external data type may differ from the 1D coordinate variable impliclity defined by DefineDimension()

Parameters

[in]	varname	The name of the coordinate variable.
[in]	dimnames	An ordered vector specifying the variable's spatial dimension names. The dimension names must have previously been defined with the DefineDimension() method.
[in]	time_dim_name	The name of the time varying dimension, if any.
[in]	units	This parameter specifies a string describing the units of measure for the variable. The string is compatible with the Unidata udunits2 conversion package. If the quantity is unitless an empty string may be specified.
[in]	axis	An integer indicating the spatial or temporal coordinate axis. Acceptable values are 0 (for X or longitude), 1 (for Y or latitude), 2 (for Z or vertical), and 3 (for time).
[in]	type	The primitive data type storage format. Currently supported values are FLOAT. This is the type that will be used to store the variable on disk
[in]	compressed	A boolean indicating whether the coordinate variable is to be wavelet transformed.

It is an error to call this method if the VDC master is not currently in define mode.

Note: Temporal coordinate variables (axis=3) must have exactly one dimension.; When in append (A) mode it is an error to redefine an existing variable.

Return values

status A negative int is returned on error

See also: DefineDimension(), DefineCoordVar(), SetCompressionBlock()

◆ DefineCoordVarUniform()

int VAPoR::VDC::DefineCoordVarUniform	(	string	varname,
		std::vector< string >	dimname,
		string	time_dim_name,
		string	units,
		int	axis,
		XType	type,
		bool	compressed
	)

Define a coordinate variable with uniform sampling

This method provides the definition for a uniform coordinate variable. A uniformly sampled coordinate variable is a variable for which the coordinates along the fastest varying axis may be given by i * dx , where i is an index starting from zero, and dx is a real number representing the spacing between points.

One-dimensional coordinate variables that have uniform sampling should be declared as such using this method rather than the more general DefineCoordVar().

Parameters

[in]	varname	The name of the coordinate variable.
[in]	dimnames	An ordered vector specifying the variable's spatial dimension names. The dimension names must have previously been defined with the DefineDimension() method.
[in]	time_dim_name	The name of the time varying dimension, if any.
[in]	units	This parameter specifies a string describing the units of measure for the variable. The string is compatible with the udunits2 conversion package. If the quantity is unitless an empty string may be specified.
[in]	axis	An integer indicating the spatial or temporal coordinate axis. Acceptable values are 0 (for X or longitude), 1 (for Y or latitude), 2 (for Z or vertical), and 3 (for time).
[in]	type	The primitive data type storage format. Currently supported values are FLOAT
[in]	compressed	A boolean indicating whether the coordinate variable is to be wavelet transformed.

It is an error to call this method if the VDC master is not currently in define mode.

Note: When in append (A) mode it is an error to redefine an existing variable.

Return values

status A negative int is returned on error

See also: DefineDimension(), DefineCoordVar(), SetCompressionBlock()

◆ DefineDataVar() [1/2]

int VAPoR::VDC::DefineDataVar	(	string	varname,
		std::vector< string >	dimnames,
		std::vector< string >	coordvars,
		string	units,
		XType	type,
		bool	compressed
	)

Define a data variable

This method defines a data variable in the VDC master file

Parameters

[in]	varname	The name of the data variable.
[in]	dimnames	An ordered vector specifying the variables dimension names. The dimension names must have previously be defined with the DefineDimension() method.
[in]	coordvars	An ordered vector specifying the coordinate variable names providing the coordinates for this variable. The coordinate variables must have previously been defined with the DefineCoordVar() method. Moreover, the dimension names of each coordinate variable must be a subset of those in `dimnames`.
[in]	units	This parameter specifies a string describing the units of measure for the variable. The string is compatible with the udunits2 conversion package. If the quantity is unitless an empty string may be specified.
[in]	type	The primitive data type storage format. Currently supported values are FLOAT
[in]	compressed	A boolean indicating whether the coordinate variable is to be wavelet transformed.

It is an error to call this method if the VDC master is not currently in define mode.

Note: When in append (A) mode it is an error to redefine an existing variable.

See also: DefineDimension(), DefineCoordVar(), SetCompressionBlock()

◆ DefineDataVar() [2/2]

int VAPoR::VDC::DefineDataVar	(	string	varname,
		std::vector< string >	dimnames,
		std::vector< string >	coordvars,
		string	units,
		XType	type,
		double	missing_value,
		string	maskvar
	)

Define a compressed or non-compressed data variable with missing data

Parameters

[in]	missing_value	Specifies a value that should be used for masked grid locations after a variable is reconstructed.
[in]	maskvar	Specifies the name of a variable whose contents indicate the presense or absense of invalid entries in the data variable. The contents of the mask array are treated as booleans, true values indicating valid data. The rank of of the variable may be less than or equal to that of `varname`. The dimensions of `maskvar` must match the fastest varying dimensions of `varname`. The `maskvar` variable must have been previously defined with DefineDataVar(). If `maskvar` is empty, the variable will not be compressed.

See also: DefineDimension(), DefineCoordVar(), SetCompressionBlock()

◆ DefineDimension() [1/2]

int VAPoR::VDC::DefineDimension	(	string	dimname,
		size_t	length
	)

Define a dimension in the VDC

This method specifies the name, and length of a dimension. A variable in the VDC may have one to four dimensions (one to three spatial, and zero or one temporal). Dimensions may be of any length greater than or equal to one.

This method must be called prior to defining any variables requring the defined dimensions.

There are no default dimensions defined.

It is an error to call this method if the VDC master is not currently in define mode.

Parameters

[in]	dimname	A string specifying the name of the dimension.
[in]	length	The dimension length, which must be greater than zero.

Note: When the VDC master file is initialized in append (mode = A) mode it is an error to redefine an existing dimension. New dimensions may, however, be defined.

Return values

status A negative int is returned on error

See also: DefineCoordVar(), DefineDataVar(), GetDimension()

◆ DefineDimension() [2/2]

int VAPoR::VDC::DefineDimension	(	string	dimname,
		size_t	length,
		int	axis
	)

Define a dimension in the VDC and an associated coordinate variable

This method defines a dimension and a 1D, unitless coordinate variable with the same name.

It is an error to call this method if the VDC master is not currently in define mode.

Parameters

[in]	name	A string specifying the name of the dimension, and the coordinate variable.
[in]	length	The dimension length, which must be greater than zero.
[in]	axis	An integer indicating the spatial or temporal coordinate axis. Acceptable values are 0 (for X or longitude), 1 (for Y or latitude), 2 (for Z or vertical), and 3 (for time).

Return values

status A negative int is returned on error

See also: DefineCoordVar(), DefineDataVar(), GetDimension()

◆ EndDefine()

int VAPoR::VDC::EndDefine ( )

When the open mode mode is A or W this method signals the class object that metadata defintions have been completed and it commits them to the master VDC file. This method also prepares the VDC for the reading or writing of variable or coordinate data.

Ignored if mode is R.

Return values

status A negative it is returned if the master file is not successfully written for any reason

Note: The master file should not be accessed with the native file format API (e.g. NetCDF) if the VDC is in define mode (e.g. until after EndDefine() is called).

See also: VDC()

◆ getAtt() [1/3]

bool VAPoR::VDC::getAtt	(	string	varname,
		string	attname,
		string &	values
	)		const

protectedvirtual

Implements VAPoR::DC.

◆ getAtt() [2/3]

bool VAPoR::VDC::getAtt	(	string	varname,
		string	attname,
		vector< double > &	values
	)		const

protectedvirtual

Implements VAPoR::DC.

◆ getAtt() [3/3]

bool VAPoR::VDC::getAtt	(	string	varname,
		string	attname,
		vector< long > &	values
	)		const

protectedvirtual

Implements VAPoR::DC.

◆ getAttNames()

std::vector< string > VAPoR::VDC::getAttNames ( string varname ) const

protectedvirtual

Return a list of available attribute's names

Returns a vector of all attribute names for the variable, varname. If varname is the empty string the names of all of the global attributes are returned. If varname is not defined an empty vector is returned.

Parameters

[in] varname The name of the variable to query, or the empty string if the names of global attributes are desired.

Return values

attnames A vector of returned attribute names

See also: GetAtt()

Implements VAPoR::DC.

◆ getAttType()

XType VAPoR::VDC::getAttType	(	string	varname,
		string	attname
	)		const

protectedvirtual

Return the external data type for an attribute

Returns the external storage type of the named variable attribute.

Parameters

[in]	varname	The name of the variable to query, or the empty string if the names of global attributes are desired.
[in]	name	Name of the attribute.

Return values

If	an attribute named by `name` does not exist, a negative value is returned.

Implements VAPoR::DC.

◆ getAuxVarInfo()

bool VAPoR::VDC::getAuxVarInfo	(	string	varname,
		DC::AuxVar &	var
	)		const

inlineprotectedvirtual

Return metadata about an auxiliary variable

If the variable varname is defined as an auxiliary variable its metadata will be returned in var.

Return values

bool	If the named variable cannot be found false is returned and the values of `var` are undefined.

See also: GetDataVarInfo(), GetCoordVarInfo()

Implements VAPoR::DC.

Definition at line 388 of file VDC.h.

◆ getAuxVarNames()

virtual std::vector< string > VAPoR::VDC::getAuxVarNames ( ) const

inlineprotectedvirtual

Return a list of names for all of the defined Auxiliary variables.

Returns a list of names for all Auxiliary variables defined

See also: DC::AuxVar

Implements VAPoR::DC.

Definition at line 396 of file VDC.h.

◆ getBaseVarInfo()

bool VAPoR::VDC::getBaseVarInfo	(	string	varname,
		DC::BaseVar &	var
	)		const

protectedvirtual

Return metadata about a data or coordinate variable

If the variable varname is defined as either a data or coordinate variable its metadata will be returned in var.

Return values

bool	If the named variable cannot be found false is returned and the values of `var` are undefined.

See also: GetDataVarInfo(), GetCoordVarInfo()

Implements VAPoR::DC.

◆ getBlockSize()

virtual vector< size_t > VAPoR::VDC::getBlockSize ( ) const

inlineprotectedvirtual

Reimplemented from VAPoR::DC.

Definition at line 412 of file VDC.h.

◆ GetCompressionBlock()

void VAPoR::VDC::GetCompressionBlock	(	std::vector< size_t > &	bs,
		string &	wname,
		std::vector< size_t > &	cratios
	)		const

Retrieve current compression block settings.

Parameters

[out]	bs	An ordered vector containing the current compression block dimensions.
[out]	wname	The wavelet family name.
[out]	cratios	A vector of compression of integer compression factors.

See also: SetCompressionBlock()

◆ getCoordVarInfo()

bool VAPoR::VDC::getCoordVarInfo	(	string	varname,
		DC::CoordVar &	cvar
	)		const

protectedvirtual

Return a coordinate variable's definition

Return a reference to a DC::CoordVar object describing the coordinate variable named by varname

Parameters

[in]	varname	A string specifying the name of the coordinate variable.
[out]	coordvar	A CoordVar object containing the definition of the named variable.

Return values

bool	False is returned if the named coordinate variable does not exist, and the contents of `cvar` will be undefined.

Implements VAPoR::DC.

◆ getCoordVarNames()

virtual std::vector< string > VAPoR::VDC::getCoordVarNames ( ) const

protectedvirtual

Return a list of names for all of the defined coordinate variables.

Returns a list of names for all coordinate variables defined

See also: DC::CoordVar

Implements VAPoR::DC.

◆ getDataVarInfo()

bool VAPoR::VDC::getDataVarInfo	(	string	varname,
		DC::DataVar &	datavar
	)		const

protectedvirtual

Return a data variable's definition

Return a reference to a DC::DataVar object describing the data variable named by varname

Parameters

[in]	varname	A string specifying the name of the variable.
[out]	datavar	A DataVar object containing the definition of the named Data variable.

Return values

bool	If the named data variable cannot be found false is returned and the values of `datavar` are undefined.

Implements VAPoR::DC.

◆ getDataVarNames()

virtual std::vector< string > VAPoR::VDC::getDataVarNames ( ) const

protectedvirtual

Return a list of names for all of the defined data variables.

Returns a list of names for all data variables defined

See also: DC::DataVar

Implements VAPoR::DC.

◆ getDimension()

bool VAPoR::VDC::getDimension	(	string	dimname,
		DC::Dimension &	dimension
	)		const

protectedvirtual

Implements VAPoR::DC.

◆ getDimensionNames()

std::vector< string > VAPoR::VDC::getDimensionNames ( ) const

protectedvirtual

Implements VAPoR::DC.

◆ getDimLensAtLevel()

virtual int VAPoR::VDC::getDimLensAtLevel	(	string	varname,
		int	level,
		std::vector< size_t > &	dims_at_level,
		std::vector< size_t > &	bs_at_level
	)		const

protectedpure virtual

Return a variable's array dimension lengths at a specified refinement level

Compressed variables may have a multi-resolution grid representation. This method returns the variable's ordered array dimension lengths, and block dimensions at the multiresolution refinement level specified by level.

If the variable named by varname is not compressed the variable's native dimensions are returned.

Note: The number of elements in dims_at_level will match that of bs_at_level. If the data are not blocked the value of each element of bs_at_level will be 1.

Parameters

[in]	varname	Data or coordinate variable name.
[in]	level	Specifies a member of a multi-resolution variable's grid hierarchy as described above.
[out]	dims_at_level	An ordered vector containing the variable's dimensions at the specified refinement level
[out]	bs_at_level	An ordered vector containing the variable's block dimensions at the specified refinement level

Return values

status Zero is returned upon success, otherwise -1.

Note: For unstructured grids the number of dimensions may be less than the topological dimension returned by DC::Mesh::GetTopologyDim().

See also: VAPoR::DC, DC::DataVar::GetBS(), DC::GetVarDimLens()

Implements VAPoR::DC.

◆ getMapProjection() [1/2]

virtual string VAPoR::VDC::getMapProjection ( ) const

protectedvirtual

Return default Proj4 map projection string.

For georeference data sets that have map projections this method returns the default properly formatted Proj4 projection string for mapping from geographic to cartographic coordinates. If no projection exists, an empty string is returned.

Return values

projstring An empty string if a Proj4 map projection is not available for the named variable, otherwise a properly formatted Proj4 projection string is returned.

Implements VAPoR::DC.

◆ getMapProjection() [2/2]

virtual string VAPoR::VDC::getMapProjection ( string varname ) const

protectedvirtual

◆ getMapProjectionDefault()

virtual string VAPoR::VDC::getMapProjectionDefault ( ) const

inlineprotectedvirtual

Definition at line 420 of file VDC.h.

◆ getMesh()

virtual bool VAPoR::VDC::getMesh	(	string	mesh_name,
		DC::Mesh &	mesh
	)		const

protectedvirtual

Return a Mesh's definition

This method returns the definition of the mesh named by mesh_name as a reference to a DC::Mesh object.

Parameters

[in]	mesh_name	A string specifying the name of the Mesh.
[out]	mesh	The returned Mesh object reference

Return values

bool	If the named mesh can not be found false is returned.

Implements VAPoR::DC.

◆ getMeshNames()

std::vector< string > VAPoR::VDC::getMeshNames ( ) const

protectedvirtual

Implements VAPoR::DC.

◆ getNumRefLevels()

size_t VAPoR::VDC::getNumRefLevels ( string varname ) const

protectedvirtual

Implements VAPoR::DC.

◆ GetPath()

virtual int VAPoR::VDC::GetPath	(	string	varname,
		size_t	ts,
		string &	path,
		size_t &	file_ts,
		size_t &	max_ts
	)		const

pure virtual

Return the path name and temporal offset for a variable

Data and coordinate variables in a VDC are in general distributed into multiple files. For example, for large variables only a single time step may be stored per file. This method returns the file path name, path, of the file containing varname at time step ts. Also returned is the integer time offset of the variable within path.

Parameters

[in]	varname	Data or coordinate variable name.
[in]	ts	Integer offset relative to a variable's temporal dimension
[out]	path	Path to file containing variable `varname` at time step `ts`.
[out]	file_ts	Temporal offset of variable `varname` in file `path`.
[out]	max_ts	Maximum number of time steps stored in `path`

Return values

status A negative int is returned if varname or ts are invalid, or if the class object is in define mode.

Implemented in VAPoR::VDCNetCDF.

◆ GetPeriodicBoundary()

std::vector< bool > VAPoR::VDC::GetPeriodicBoundary ( ) const

inline

Retrieve current boundary periodic settings

See also: SetPeriodicBoundary()

Definition at line 310 of file VDC.h.

◆ initialize() [1/2]

virtual int VAPoR::VDC::initialize	(	const std::vector< string > &	paths,
		const std::vector< string > &	options
	)

inlineprotectedvirtual

Initialize the DC class

Prepare a DC for reading. This method prepares the master DC file indicated by path for reading. The method should be called immediately after the constructor, before any other class methods. This method exists only because C++ constructors can not return error codes.

Parameters

[in]	path	Path name of file that contains, or will contain, the DC master file for this data collection
[in]	options	A vector of option pairs (name, value) that may be accepted by the derived class.

Return values

status A negative int is returned on failure

Implements VAPoR::DC.

Definition at line 230 of file VDC.h.

References initialize().

Referenced by initialize().

◆ initialize() [2/2]

virtual int VAPoR::VDC::initialize	(	const std::vector< string > &	paths,
		const std::vector< string > &	options,
		AccessMode	mode,
		vector< size_t >	bs
	)

protectedvirtual

Initialize the VDC class

Prepare a VDC for reading or writing/appending. This method prepares the master VDC file indicated by path for reading or writing. The method should be called immediately after the constructor, before any other class methods. This method exists only because C++ constructors can not return error codes.

Parameters

[in]	path	A single element vector that specifies the name of file that contains, or will contain, the VDC master file for this data collection
[in]	mode	One of R, W, or A, indicating whether `path` will be opened for reading, writing, or appending, respectively. When `mode` is A underlying NetCDF files will be opened opened with nc_open(path, NC_WRITE)). When `mode` is W NetCDF files will be created (opened with nc_create(path)). When `mode` is A additional time steps may be added to an existing file.

bs is a three-element array, with the first element specifying the length of the fastest varying spatial dimension (e.g. X) of the storage block, the second element specifies the length of the next fastest varying dimension, etc. If a variable definition defines a variable with n spatial , where n is less than three, only the first n elements of bs will be used. For example, if the rank of bs is greater than two a 2D variable will be stored in blocks having dimensions bs[0] x bs[1]. Time dimensions are never blocked. This parameter is ignored unless mode is W.

Note: The parameter mode controls the access to the master file indicated by path and the variable data files in a somewhat unintuitive manner. If mode is R or A the master file path must already exist. If mode is A or W the contents of the VDC master may be changed (written) and the VDC is put into define mode until EndDefine() is called. While in define mode metadata that will be contained in the VDC master file may be changed, but coordinate and data variables may not be accessed (read or written). Similarly, when not in define mode coordinate and data variables may be accessed (read or written), but metadata in the VDC master may not be changed. See OpenVariableRead() and OpenVariableWrite() for discussion on how mode effects reading and writing of coordinate and data variables.

Return values

status A negative int is returned on failure

See also: EndDefine();

◆ openVariableRead()

virtual int VAPoR::VDC::openVariableRead	(	size_t	ts,
		string	varname,
		int	level = `0`,
		int	lod = `0`
	)

protectedpure virtual

Open the named variable for reading

This method prepares a data or coordinate variable, indicated by a variable name and time step pair, for subsequent read operations by methods of this class. The value of the refinement levels parameter, level, indicates the resolution of the volume in the multiresolution hierarchy as described by GetDimLensAtLevel().

The level-of-detail parameter, lod, selects the approximation level. Valid values for lod are integers in the range 0..n-1, where n is returned by DC::BaseVar::GetCRatios().size(), or the value -1 may be used to select the best approximation available.

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

Parameters

[in]	ts	Time step of the variable to read. This is the integer offset into the variable's temporal dimension. If the variable does not have a temporal dimension `ts` is ignored.
[in]	varname	Name of the variable to read
[in]	level	Refinement level of the variable. Ignored if the variable is not compressed.
[in]	lod	Approximation level of the variable. A value of -1 indicates the maximum approximation level defined for the DC. Ignored if the variable is not compressed.

Return values

status Returns a non-negative file descriptor on success

See also: GetNumRefLevels(), DC::BaseVar::GetCRatios(), OpenVariableRead()

Implements VAPoR::DC.

Implemented in VAPoR::VDCNetCDF.

◆ OpenVariableWrite()

virtual int VAPoR::VDC::OpenVariableWrite	(	size_t	ts,
		string	varname,
		int	lod = `-1`
	)

pure virtual

Open the named variable for writing

This method prepares a data or coordinate variable, indicated by a variable name and time step pair, for subsequent write operations by methods of this class.

The behavior of this method is impacted somewhat by the setting of the Initialize() mode parameter. Coordinate or data variable files may be written regardless of the mode setting. However, if mode is W the first time a coordinate or data file is written it will be created (opened with nc_create(path), for example) regareless of whether the file previously existed. If mode is A or R existing coordinate or data files will be opened for appending (e.g. opened with nc_open(path, NC_WRITE)). New files will be created (opened with nc_create(path)).

An error occurs, indicated by a negative return value, if the varible identified by the {varname, timestep, lod} tupple is not defined.

Parameters

[in]	ts	Time step of the variable to read. This is the integer offset into the variable's temporal dimension. If the variable does not have a temporal dimension `ts` is ignored.
[in]	varname	Name of the variable to read
[in]	lod	Approximation level of the variable. A value of -1 indicates the maximum approximation level defined for the VDC. Ignored if the variable is not compressed.

Return values

status Returns a non-negative value on success

See also: GetNumRefLevels(), DC::BaseVar::GetCRatios(), OpenVariableRead()

Implemented in VAPoR::VDCNetCDF.

◆ PutAtt() [1/3]

int VAPoR::VDC::PutAtt	(	string	varname,
		string	attname,
		XType	type,
		const string &	values
	)

◆ PutAtt() [2/3]

int VAPoR::VDC::PutAtt	(	string	varname,
		string	attname,
		XType	type,
		const vector< double > &	values
	)

Write an attribute

This method write an attribute to the VDC. The attribute can either be "global", if varname is the empty string, or bound to a variable if varname indentifies a variable in the VDC.

Parameters

[in]	varname	The name of a variable already defined in the VDC, or the empty string if the attribute is to be global
[in]	attname	The attributes name
[in]	type	The primitive data type storage format. This is the type that will be used to store the attribute on disk
[in]	values	A vector of floating point attribute values

Return values

status A negative int is returned on failure

See also: GetAtt()

◆ PutAtt() [3/3]

int VAPoR::VDC::PutAtt	(	string	varname,
		string	attname,
		XType	type,
		const vector< long > &	values
	)

◆ PutVar() [1/4]

virtual int VAPoR::VDC::PutVar	(	size_t	ts,
		string	varname,
		int	lod,
		const float *	data
	)

pure virtual

Write a variable at single time step

This method writes a variable hyperslab consisting of the variable's entire spatial dimensions at the time step indicated by ts. Any variables currently opened with OpenVariableWrite() are first closed. Thus variables need not be opened with OpenVariableWrite() prior to calling PutVar();

It is an error to call this method in define mode

Parameters

[in]	ts	Time step of the variable to write. This is the integer offset into the variable's temporal dimension. If the variable does not have a temporal dimension `ts` is ignored.
[in]	varname	Name of the variable to write
[in]	lod	Approximation level of the variable. A value of -1 indicates the maximum approximation level defined for the VDC. Ignored if the variable is not compressed.
[in]	data	Pointer from where the data will be copied

Return values

status A negative int is returned on failure

See also: GetVar()

Implemented in VAPoR::VDCNetCDF.

◆ PutVar() [2/4]

virtual int VAPoR::VDC::PutVar	(	size_t	ts,
		string	varname,
		int	lod,
		const int *	data
	)

pure virtual

Implemented in VAPoR::VDCNetCDF.

◆ PutVar() [3/4]

virtual int VAPoR::VDC::PutVar	(	string	varname,
		int	lod,
		const float *	data
	)

pure virtual

Write an entire variable in one call

This method writes and entire variable (all time steps, all grid points) into a VDC. This is the simplest interface for writing data into a VDC. If the variable is split across multiple files PutVar() ensures that the data are correctly distributed. Any variables currently opened with OpenVariableWrite() are first closed. Thus variables need not be opened with OpenVariableWrite() prior to calling PutVar();

It is an error to call this method in define mode

Parameters

[in]	varname	Name of the variable to write
[in]	lod	Approximation level of the variable. A value of -1 indicates the maximum approximation level defined for the VDC. Ignored if the variable is not compressed.
[in]	data	Pointer from where the data will be copied

Return values

status A negative int is returned on failure

See also: GetVar()

Implemented in VAPoR::VDCNetCDF.

◆ PutVar() [4/4]

virtual int VAPoR::VDC::PutVar	(	string	varname,
		int	lod,
		const int *	data
	)

pure virtual

Implemented in VAPoR::VDCNetCDF.

◆ readRegion() [1/2]

virtual int VAPoR::VDC::readRegion	(	int	fd,
		const vector< size_t > &	min,
		const vector< size_t > &	max,
		double *	region
	)

protectedpure virtual

Implements VAPoR::DC.

◆ readRegion() [2/2]

virtual int VAPoR::VDC::readRegion	(	int	fd,
		const vector< size_t > &	min,
		const vector< size_t > &	max,
		float *	region
	)

protectedpure virtual

Read in and return a subregion from the currently opened variable

This method reads and returns a subset of variable data. The min and max vectors, whose dimensions must match the spatial rank of the currently opened variable, identify the minimum and maximum extents, in grid coordinates, of the subregion of interest. The minimum and maximum valid values of an element of min or max are 0 and n-1, respectively, where n is the length of the associated dimension at the opened refinement level.

The region 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]	fd	A valid file descriptor returned by OpenVariableRead()
[in]	min	Minimum region extents in grid coordinates
[in]	max	Maximum region extents in grid coordinates
[out]	region	The requested volume subregion

Return values

status Returns a non-negative value on success

See also: OpenVariableRead(), GetDimLensAtLevel(), GetDimensionNames()

Implements VAPoR::DC.

◆ SetCompressionBlock()

int VAPoR::VDC::SetCompressionBlock	(	string	wname,
		std::vector< size_t >	cratios
	)

Sets various parameters for storage blocks for subsequent variable definitions

This method sets the storage parameters for subsequent variable definitions for compressed variables.

Variables whose spatial dimension lengths are less than the coresponding dimension of bs will be padded to block boundaries.

wname set the wavelet family name and boundary handling mode for subsequent compressed variable definitions. Wider wavelets (those requiring more filter coefficients) will typically yield higher compression rates, but are more computationally expensive and will limit the depth of of the grid resolution refinement hierarchy.

Recommended values for wname are bior1.1, bior1.3, bior1.5 bior3.3, bior3.5, bior3.7, bior3.9, bior2.2, bior2.6, bior2.6, and bior2.8. For odd length filters (e.g. bior1.3)

Finally, cratios specifies a vector of compression factors for subsequent compressed variable definitions.

Note: For compressed variables compression is applied to individual blocks. Larger blocks permit deeper grid refinement hierarchies, but may result in poor cache performance and slowed disk storage access; The wavelet and compression ratio parameters are ignored by variable definitions for variables that are not compressed.

Parameters

[in]	wname	A wavelet family name. The default value is "bior4.4".
[in]	cratios	A vector of compression of integer compression factors. The default compression ratio vector is: (1, 10, 100, 500)

Return values

status A negative int is returned if an invalid parameter or parameter combination is specified.

See also: DefineDataVar(), DefineCoordVar(), VDC()

◆ SetMapProjection() [1/2]

virtual int VAPoR::VDC::SetMapProjection ( string projstring )

virtual

Set the default Proj4 map projection for georeferenced variables

This method sets the default Proj4 map projection string to be used for georeferenced variables. The string set by projstring is returned by VDC::GetMapProjection()

◆ SetMapProjection() [2/2]

virtual int VAPoR::VDC::SetMapProjection	(	string	varname,
		string	projstring
	)

virtual

Set a map projection string for a data variable

This method sets a properly formatted Proj4 map projection string for the data variable indicated by varname

See also: GetMapProjection()

◆ SetPeriodicBoundary()

void VAPoR::VDC::SetPeriodicBoundary ( std::vector< bool > periodic )

inline

Set the boundary periodic for subsequent variable definitions

This method specifies an ordered, three-element boolean vector indicating the boundary periodicty for a variable's spatial dimensions. The ordering is from fastest to slowest varying dimension.

Parameters

[in] periodic A three-element array of booleans. The default value of periodic is (false, false, false).

Return values

status A negative int is returned on error

Definition at line 300 of file VDC.h.

◆ variableExists()

virtual bool VAPoR::VDC::variableExists	(	size_t	ts,
		string	varname,
		int	reflevel = `0`,
		int	lod = `0`
	)		const

pure virtual

Returns true if indicated data volume is available

Returns true if the variable identified by the timestep, variable name, refinement level, and level-of-detail is present in the data set. Returns false if the variable is not available.

Parameters

[in]	ts	A valid time step between 0 and GetNumTimesteps()-1
[in]	varname	A valid variable name
[in]	reflevel	Refinement level requested.
[in]	lod	Compression level of detail requested. refinement level contained in the VDC.

Implements VAPoR::DC.

Implemented in VAPoR::VDCNetCDF.

◆ Write() [1/2]

virtual int VAPoR::VDC::Write	(	int	fd,
		const float *	data
	)

pure virtual

Write all spatial values to the currently opened variable

This method writes, and compresses as necessary, the contents of the array contained in data to the currently opened variable. The number of values written from data is given by the product of the spatial dimensions of the open variable.

Parameters

[in] data An array of data to be written

Return values

status Returns a non-negative value on success

See also: OpenVariableWrite()

Implemented in VAPoR::VDCNetCDF.

◆ Write() [2/2]

virtual int VAPoR::VDC::Write	(	int	fd,
		const int *	data
	)

pure virtual

Implemented in VAPoR::VDCNetCDF.

◆ WriteSlice() [1/3]

virtual int VAPoR::VDC::WriteSlice	(	int	fd,
		const float *	slice
	)

pure virtual

Write a single slice of data to the currently opened variable

Compress, and necessary, and write a single slice (2D array) of data to the variable indicated by the most recent call to OpenVariableWrite(). The dimensions of a slices are NX by NY, where NX is the dimension of the array along the fastest varying spatial dimension, specified in grid points, and NY is the length of the second fastest varying dimension at the currently opened refinement level. See OpenVariableWrite().

This method should be called exactly NZ times for each opened variable, where NZ is the dimension of third, and slowest varying dimension. In the case of a 2D variable, NZ is 1.

Parameters

[in] slice A 2D slice of data

Return values

status Returns a non-negative value on success

See also: OpenVariableWrite()

Implemented in VAPoR::VDCNetCDF.

◆ WriteSlice() [2/3]

virtual int VAPoR::VDC::WriteSlice	(	int	fd,
		const int *	slice
	)

pure virtual

Implemented in VAPoR::VDCNetCDF.

◆ WriteSlice() [3/3]

virtual int VAPoR::VDC::WriteSlice	(	int	fd,
		const unsigned char *	slice
	)

pure virtual

Implemented in VAPoR::VDCNetCDF.

Friends And Related Function Documentation

◆ operator<<

std::ostream & operator<<	(	std::ostream &	o,
		const VDC &	vdc
	)

friend

Member Data Documentation

◆ _atts

std::map<string, Attribute> VAPoR::VDC::_atts

protected

Definition at line 901 of file VDC.h.

◆ _bs

std::vector<size_t> VAPoR::VDC::_bs

protected

Definition at line 894 of file VDC.h.

◆ _coordVars

std::map<string, CoordVar> VAPoR::VDC::_coordVars

protected

Definition at line 902 of file VDC.h.

◆ _cratios

std::vector<size_t> VAPoR::VDC::_cratios

protected

Definition at line 896 of file VDC.h.

◆ _dataVars

std::map<string, DataVar> VAPoR::VDC::_dataVars

protected

Definition at line 903 of file VDC.h.

◆ _defineMode

bool VAPoR::VDC::_defineMode

protected

Definition at line 893 of file VDC.h.

◆ _dimsMap

std::map<string, Dimension> VAPoR::VDC::_dimsMap

protected

Definition at line 900 of file VDC.h.

◆ _master_path

string VAPoR::VDC::_master_path

protected

Definition at line 891 of file VDC.h.

◆ _meshes

std::map<string, Mesh> VAPoR::VDC::_meshes

protected

Definition at line 904 of file VDC.h.

◆ _mode

AccessMode VAPoR::VDC::_mode

protected

Definition at line 892 of file VDC.h.

◆ _periodic

vector<bool> VAPoR::VDC::_periodic

protected

Definition at line 897 of file VDC.h.

◆ _udunits

VAPoR::UDUnits VAPoR::VDC::_udunits

protected

Definition at line 898 of file VDC.h.

◆ _wname

string VAPoR::VDC::_wname

protected

Definition at line 895 of file VDC.h.

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

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

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ AccessMode

Constructor & Destructor Documentation

◆ VDC()

◆ ~VDC()

Member Function Documentation

◆ closeVariable()

◆ CloseVariableWrite()

◆ CompressionInfo()

◆ CopyAtt() [1/2]

◆ CopyAtt() [2/2]

◆ CopyVar() [1/2]

◆ CopyVar() [2/2]

◆ DefineCoordVar()

◆ DefineCoordVarUniform()

◆ DefineDataVar() [1/2]

◆ DefineDataVar() [2/2]

◆ DefineDimension() [1/2]

◆ DefineDimension() [2/2]

◆ EndDefine()

◆ getAtt() [1/3]

◆ getAtt() [2/3]

◆ getAtt() [3/3]

◆ getAttNames()

◆ getAttType()

◆ getAuxVarInfo()

◆ getAuxVarNames()

◆ getBaseVarInfo()

◆ getBlockSize()

◆ GetCompressionBlock()

◆ getCoordVarInfo()

◆ getCoordVarNames()

◆ getDataVarInfo()

◆ getDataVarNames()

◆ getDimension()

◆ getDimensionNames()

◆ getDimLensAtLevel()

◆ getMapProjection() [1/2]

◆ getMapProjection() [2/2]

◆ getMapProjectionDefault()

◆ getMesh()

◆ getMeshNames()

◆ getNumRefLevels()

◆ GetPath()

◆ GetPeriodicBoundary()

◆ initialize() [1/2]

◆ initialize() [2/2]

◆ openVariableRead()

◆ OpenVariableWrite()

◆ PutAtt() [1/3]

◆ PutAtt() [2/3]

◆ PutAtt() [3/3]

◆ PutVar() [1/4]

◆ PutVar() [2/4]

◆ PutVar() [3/4]

◆ PutVar() [4/4]

◆ readRegion() [1/2]

◆ readRegion() [2/2]

◆ SetCompressionBlock()

◆ SetMapProjection() [1/2]

◆ SetMapProjection() [2/2]

◆ SetPeriodicBoundary()

◆ variableExists()

◆ Write() [1/2]

◆ Write() [2/2]

◆ WriteSlice() [1/3]

◆ WriteSlice() [2/3]

◆ WriteSlice() [3/3]

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ _atts

◆ _bs