Wrapper for a collection of netCDF files. More...

#include <NetCDFCollection.h>

Inheritance diagram for VAPoR::NetCDFCollection:

Classes
class	DerivedVar

class	TimeVaryingVar

Public Member Functions
	NetCDFCollection ()

virtual	~NetCDFCollection ()

virtual int	Initialize (const std::vector< string > &files, const std::vector< string > &time_dimnames, const std::vector< string > &time_coordvar)

virtual bool	VariableExists (string varname) const

virtual bool	VariableExists (size_t ts, string varname) const

virtual bool	IsDerivedVar (string varname) const

virtual bool	IsStaggeredVar (string varname) const

virtual bool	IsStaggeredDim (string dimname) const

virtual std::vector< string >	GetVariableNames (int ndim, bool spatial) const

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

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

virtual size_t	GetTimeDim (string varname) const

virtual string	GetTimeDimName (string varname) const

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

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

virtual bool	IsTimeVarying (string varname) const

int	GetXType (string varname) const

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

int	GetAttType (string varname, string attname) const

void	GetAtt (string varname, string attname, std::vector< double > &values) const

void	GetAtt (string varname, string attname, std::vector< long > &values) const

void	GetAtt (string varname, string attname, string &values) const

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

virtual std::vector< size_t >	GetDims () const

virtual size_t	GetNumTimeSteps () const

virtual size_t	GetNumTimeSteps (string varname) const

virtual int	GetTime (size_t ts, double &time) const

virtual int	GetTimes (string varname, std::vector< double > &times) const

virtual std::vector< double >	GetTimes () const

virtual int	GetFile (size_t ts, string varname, string &file, size_t &local_ts) const

virtual int	GetVariableInfo (string varname, NetCDFSimple::Variable &varinfo) const

virtual bool	GetMissingValue (string varname, double &mv) const

virtual int	OpenRead (size_t ts, string varname)

virtual int	Read (size_t start[], size_t count[], float *data, int fd=0)

virtual int	Read (size_t start[], size_t count[], int *data, int fd=0)

virtual int	Read (std::vector< size_t > start, std::vector< size_t > count, float *data, int fd=0)

virtual int	Read (std::vector< size_t > start, std::vector< size_t > count, int *data, int fd=0)

virtual int	Read (float *data, int fd=0)

virtual int	Read (char *data, int fd=0)

virtual int	ReadNative (size_t start[], size_t count[], float *data, int fd=0)

virtual int	ReadNative (size_t start[], size_t count[], int *data, int fd=0)

virtual int	ReadNative (size_t start[], size_t count[], char *data, int fd=0)

virtual int	ReadNative (float *data, int fd=0)

virtual int	ReadNative (int *data, int fd=0)

virtual int	ReadSlice (float *data, int fd=0)

virtual int	ReadSliceNative (float *data, int fd=0)

virtual int	SeekSlice (int offset, int whence, int fd=0)

virtual int	Close (int fd=0)

virtual void	SetStaggeredDims (const std::vector< string > dimnames)

virtual void	SetMissingValueAttName (string attname)

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

void	InstallDerivedVar (string varname, DerivedVar *derivedVar)

void	RemoveDerivedVar (string varname)

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

const string &	getClassName () const

Protected Member Functions
bool	_GetVariableInfo (string varname, NetCDFSimple::Variable &variable) const

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

Friends
std::ostream &	operator<< (std::ostream &o, const NetCDFCollection &ncdfc)

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

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

Static Public 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)

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

Detailed Description

Wrapper for a collection of netCDF files.

Author: John Clyne

Version

Revision: 1.7

Date

Date: 2013/05/16 21:39:38

This class treats a collection of netCDF files as a single, time-varying data set, providing a unified interface for accessing named 0D, 1D, 2D, and 3D spatial variables at a specified timestep, independent of which netCDF file contains the data.

The netCDF variables may be "explicitly" time-varying: the slowest varying dimension may correspond to time, while the remaining dimensions correspond to space. Or the variables may be implicitly time-varying, possessing no explicit time dimension, in which case the time index of a variable is determined by file ordering. For example, if the variable "v" is found in the files "a.nc" and "b.nc" and nowhere else, and "a.nc" preceeds "b.nc" in the list of files provided to the class constructor, then a.nc is assumed to contain "v" at time step 0, and "b.nc" contains "v" at time step 1.

The class understands the Arakawa C-Grid ("staggered" variables), and can interpolate them onto a common (unstaggered) grid.

Note: The specification of dimensions and coordinates in this class follows the netCDF API convention of ordering from slowest varying dimension to fastest varying dimension. For example, if 'dims' is a vector of dimensions, then dims[0] is the slowest varying dimension, dim[1] is the next slowest, and so on. This ordering is the opposite of the ordering used by most of the VAPoR API.

Several file organizations are supported and discussed below. To ease discussion we introduce the terminology:

define TD : Time Dimension
define TCV : Time Coordinate Variable
define TVV : an explicitly Time Varying Variable (it has a time dimension)
define ITVV : an Implicit Time Varying Variable (has no time dimension, but has multiple occurences => order determines time)
define CV: Constant Variable (has no TD, occurs only once). CV variables are define for all time steps

Four file organizations are supported as described below:

case 1: No TD specified (therefore no TCV):

All variables are ITVV
synthesize TCV by order of appearance of variables (file order only)
ITVV time derived by order of appearance (file order only).
only one time step per variable per file

case 2: TD specified, but no TCV:

All variables are TVV or CV
synthesize TCV by order of appearance (file order, then TD).
multiple time steps per variable per file
variables with TD are TVV
variables with no TD are CV (available for all time)
A CV that occurs multiple times overwrites prior occurence (there can be no ITVV variables).

case 3a: TD & TCV specified, TCV appears in only file:

All variables are TVV or CV
TVVs indexed to time in TCV by order of appearance (file order, TD within file)
A CV that occurs multiple times overwrites prior occurence
Require TCV to appear in first file

case 3b: TD & TCV specified, TCV appears in every file with TVV:

Only have TVV and CV variables
TVVs indexed to time by TD offset within a file
A CV that occurs multiple times overwrites prior occurence
Order of file specification is irrelevant (except for multiple occurences of CVs of same name)

Definition at line 96 of file NetCDFCollection.h.

Constructor & Destructor Documentation

VAPoR::NetCDFCollection::NetCDFCollection ( )

virtual VAPoR::NetCDFCollection::~NetCDFCollection ( )

virtual

Member Function Documentation

bool VAPoR::NetCDFCollection::_GetVariableInfo	(	string	varname,
		NetCDFSimple::Variable &	variable
	)		const

protected

virtual int VAPoR::NetCDFCollection::Close ( int fd = 0 )

virtual

Close the currently opened variable

Parameters

[in] fd A currently opened file descriptor returned by OpenRead().

See also: OpenRead()

void VAPoR::NetCDFCollection::GetAtt	(	string	varname,
		string	attname,
		std::vector< double > &	values
	)		const

Return attribute values for attribute of type float

Return the values of the named attribute converted to type float.

Note: Attributes of type int are cast to float; All attributes with floating point representation of any precision are returned by this method. Attributes that do not have floating point internal representations can not be returned.

Parameters

[in]	attname	Name of the attribute
[out]	values	A vector of attribute values

void VAPoR::NetCDFCollection::GetAtt	(	string	varname,
		string	attname,
		std::vector< long > &	values
	)		const

void VAPoR::NetCDFCollection::GetAtt	(	string	varname,
		string	attname,
		string &	values
	)		const

std::vector<string> VAPoR::NetCDFCollection::GetAttNames ( string varname ) const

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

int VAPoR::NetCDFCollection::GetAttType	(	string	varname,
		string	attname
	)		const

Return the netCDF external data type for an attribute

Returns the nc_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.

virtual std::vector<string> VAPoR::NetCDFCollection::GetDimNames ( string varname ) const

virtual

Return a variable's temporal and spatial dimension names

Returns the ordered list of temporal and spatial dimension names of the named variable.

Note: The order follows the netCDF convention (slowest varying dimension is the first vector element returned), not the VDC convention.

Parameters

[in] varname Name of variable

Return values

dimnames An ordered vector containing the variable's temporal and spatial dimension names. If varname is not defined an empty list is returned.

virtual std::vector<string> VAPoR::NetCDFCollection::GetDimNames ( ) const

inlinevirtual

Return the names of all the dimensions.

Returns a list of all dimension names defined by all netCDF files in the entire collection. The ordering of the returned list coresponds to the ordering of the list of dimenension lengths returned by GetDims(). I.e. the length of the dimension with name GetDimNames()[i] is GetDims[i].

Return values

dimnames A vector containing all dimension names.

See also: GetDims()

Definition at line 394 of file NetCDFCollection.h.

virtual std::vector<size_t> VAPoR::NetCDFCollection::GetDims ( string varname ) const

virtual

Return a variable's temporal and spatial dimensions

Returns the ordered list of temporal and spatial dimensions of the named variable.

Note: The order follows the netCDF convention (slowest varying dimension is the first vector element returned), not the VDC convention.

Parameters

[in] varname Name of variable

Return values

dims	An ordered vector containing the variables temporal and spatial dimensions. If `varname` is not defined a zero length vector is returned

virtual std::vector<size_t> VAPoR::NetCDFCollection::GetDims ( ) const

inlinevirtual

Return the lengths of all the dimensions.

Returns a list of all dimension lengths defined by all netCDF files in the entire collection. The ordering of the returned list coresponds to the ordering of the list of dimenension names returned by GetDimNames(). I.e. the length of the dimension with name GetDimNames()[i] is GetDims[i].

Return values

dimlens A vector containing all dimension lengths.

See also: GetDimNames()

Definition at line 409 of file NetCDFCollection.h.

virtual std::vector<string> VAPoR::NetCDFCollection::GetFailedVars ( ) const

inlinevirtual

Return a list of variables that are not available for access

This method returns a list of variables that were detected in the collection of netCDF files but are not accessible from the NetCDFCollection class.

Definition at line 714 of file NetCDFCollection.h.

virtual int VAPoR::NetCDFCollection::GetFile	(	size_t	ts,
		string	varname,
		string &	file,
		size_t &	local_ts
	)		const

virtual

Return the path to the netCDF file containing a variable

This method returns the path to the netCDF file containing the variable varname, at the time step ts.

Parameters

[in]	ts	time step of variable
[in]	varname	Name of variable
[out]	file	The netCDF file path
[out]	local_ts	local time index of variable within `file`

Return values

retval A negative int is returned on failure.

virtual bool VAPoR::NetCDFCollection::GetMissingValue	(	string	varname,
		double &	mv
	)		const

virtual

Return the missing value, if any, for a variable

This method returns the value of the missing data value marker, if defined, for the variable named by varname.

Parameters

[in]	varname	The variable name
[out]	mv	The missing value for the variabled name by `varname`

Return values

bool	The boolean true is returned if a missing value is defined. If no missing variable is defined the return value is false and the value of `mv` is not defined.

Reimplemented in VAPoR::NetCDFCFCollection.

virtual size_t VAPoR::NetCDFCollection::GetNumTimeSteps ( ) const

inlinevirtual

Return the number of time steps in the data collection all variables

Return the number of time steps present. The number of time steps returned is the number of unique times present, and

Note: Not all variables in a collection need have the same number of time steps

Parameters

[in] varname Name of variable

Return values

value The number of time steps

Definition at line 424 of file NetCDFCollection.h.

virtual size_t VAPoR::NetCDFCollection::GetNumTimeSteps ( string varname ) const

inlinevirtual

Return the number of time available for the named variable

Return the number of time steps present for the variable named by varname.

Note: Not all variables in a collection need have the same number of time steps

Parameters

[in] varname Name of variable

Return values

value The number of time steps. If varname is either not defined, or is defined but not time varying, 0 is returned.

Definition at line 439 of file NetCDFCollection.h.

References GetTimeDim().

virtual std::vector<string> VAPoR::NetCDFCollection::GetSpatialDimNames ( string varname ) const

virtual

Return a variable's spatial dimension names

Returns the ordered list of spatial dimension names of the named variable.

Note: The order follows the netCDF convention (slowest varying dimension is the first vector element returned), not the VDC convention.

Parameters

[in] varname Name of variable

Return values

dimnames An ordered vector containing the variable's spatial dimension names. If varname is not defined an empty list is returned.

virtual std::vector<size_t> VAPoR::NetCDFCollection::GetSpatialDims ( string varname ) const

virtual

Return a variable's spatial dimensions

Returns the ordered list of spatial dimensions of the named variable.

Note: The order follows the netCDF convention (slowest varying dimension is the first vector element returned), not the VDC convention.

Parameters

[in] varname Name of variable

Return values

dims	An ordered vector containing the variables spatial dimensions. If `varname` is not defined a zero length vector is returned

virtual int VAPoR::NetCDFCollection::GetTime	(	size_t	ts,
		double &	time
	)		const

virtual

Return the user time associated with a time step

This method returns the time, in user-defined coordinates, associated with the time step, ts. If no time coordinate variable was specified the user time is equivalent to the time step, ts.

Parameters

[in]	ts	A valid data set time step in the range from zero to GetNumTimeSteps() - 1.
[out]	time	The user time

Return values

retval A negative int is returned on failure.

virtual size_t VAPoR::NetCDFCollection::GetTimeDim ( string varname ) const

virtual

Return a variable's time dimension

Returns time dimension of the named variable.

Parameters

[in] varname Name of variable

Return values

dim	Number of time steps (time dimension) If `varname` is invalid or `varname` is not time varying 0 is returned.

Referenced by GetNumTimeSteps().

virtual string VAPoR::NetCDFCollection::GetTimeDimName ( string varname ) const

virtual

Return a variable's time dimension name

Returns the time dimension name of the named variable.

Parameters

[in] varname Name of variable

Return values

name	A string containing the variable's time dimension name. If `varname` is invalid or `varname` is not time varying the empty string is returned.

virtual int VAPoR::NetCDFCollection::GetTimes	(	string	varname,
		std::vector< double > &	times
	)		const

virtual

Return all the user times associated with a variable

This method returns the times, in user-defined coordinates, associated with the the variable, varname.

Parameters

[in]	varname	Name of variable

virtual std::vector<double> VAPoR::NetCDFCollection::GetTimes ( ) const

inlinevirtual

Return all the user times for this collection

This method returns the times, in user-defined coordinates, for this data collection.

Return values

retval times A vector of user times.

See also: Initialize()

Definition at line 485 of file NetCDFCollection.h.

virtual int VAPoR::NetCDFCollection::GetVariableInfo	(	string	varname,
		NetCDFSimple::Variable &	varinfo
	)		const

virtual

Return the NetCDFSimple::Variable for the named variable

This method copies the contents of the NetCDFSimple::Variable class for the named variable into varinfo

Parameters

[in] varname Name of variable

Return values

retval A negative int is returned on failure.

virtual std::vector<string> VAPoR::NetCDFCollection::GetVariableNames	(	int	ndim,
		bool	spatial
	)		const

virtual

Return a list of variables with a given rank

Returns a list of variables having a dimension rank of ndim. If spatial is true only the variable's spatial dimension rank is examined. Thus if spatial is true, and the named variable is explicitly time varying, the time-varying dimension is not counted. For example, if a variable named 'v' is defined with 4 dimensions in the netCDF file, and the slowest varying dimension name matches a named dimension specified in Initialize() by time_dimnames, then the variable 'v' would be returned by a query with ndim==3 and spatial==true.

Parameters

[in]	ndim	Rank of dimensions
[in]	spatial	Only compare spatial dimensions against `ndim`

int VAPoR::NetCDFCollection::GetXType ( string varname ) const

Return the netCDF external data type a variable

Returns the nc_type of the named variable

Parameters

[in] varname The name of the variable to query.

Return values

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

virtual int VAPoR::NetCDFCollection::Initialize	(	const std::vector< string > &	files,
		const std::vector< string > &	time_dimnames,
		const std::vector< string > &	time_coordvar
	)

virtual

Initialze a new collection

Variables contained in the netCDF files may be explicitly time-varying (i.e. have a time dimension defined), or their time step may be determined implicitly by which file they are contained in.

The time ordering of time-varying variables is determined by:

A 1D time coordinate variable, if it exists
A time dimension, if it exists
The ordering of the files in files in which the variable occurs

Parameters

[in]	files	A list of file containing time-varying 1D, 2D, and 3D variables. In the absense of an explicit time dimension, or time coordinate variable, the ordering of the files determines the the time steps of the variables contained therein.
[in]	time_dimnames	A list of netCDF time dimensions. A variable whose slowest varying dimension name matches a name in `time_dimnames` is an explict time-varying variable with a time dimension.
[in]	time_coordvar	The name of a coordinate variable containing time data. If a 1D variable with a name given by `time_coordvar` exists, this variable will be used to determine the time associated with each time step of a variable.

void VAPoR::NetCDFCollection::InstallDerivedVar	(	string	varname,
		DerivedVar *	derivedVar
	)

inline

Definition at line 795 of file NetCDFCollection.h.

virtual bool VAPoR::NetCDFCollection::IsDerivedVar ( string varname ) const

inlinevirtual

Returns true if the named variable is a derived variable.

This method returns true if the variable named by varname is derived from other variables in the data collection.

Parameters

[in] varname A variable name

Return values

bool	Returns true if `varname` is a derived variable.

Definition at line 184 of file NetCDFCollection.h.

virtual bool VAPoR::NetCDFCollection::IsStaggeredDim ( string dimname ) const

virtual

Returns true if the specified dimension is staggered

If the dimension named by dimname is a staggered dimension, true is returned

Parameters

[in] dimname Name of dimension

See also: SetStaggeredDims()

virtual bool VAPoR::NetCDFCollection::IsStaggeredVar ( string varname ) const

virtual

Returns true if the specified variable has any staggered dimensions

If the variabled named by varname has any staggered dimensions, true is returned

Parameters

[in] varname Name of variable

Return values

boolean indicating where variable varname has any staggered dimensions.

See also: SetStaggeredDims()

virtual bool VAPoR::NetCDFCollection::IsTimeVarying ( string varname ) const

virtual

Return true if variable is time varying

Returns true if the variable named by varname has a time varying coordinate

Parameters

[in] varname Name of variable

virtual int VAPoR::NetCDFCollection::OpenRead	(	size_t	ts,
		string	varname
	)

virtual

Open the named variable for reading

This method prepares a netCDF variable, indicated by a variable name and time step pair, for subsequent read operations by methods of this class. A small, non-negative integer for use in subsequent read operations is returned. The file descriptor returned by a successful call will be the lowest-numbered file descriptor not currently open for the process, starting with zero.

Parameters

[in]	ts	Time step of the variable to read
[in]	varname	Name of the variable to read

Return values

status Returns a non-negative file descriptor on success

See also: Read(), ReadNative(), ReadSliceNative() ReadSlice()

Reimplemented in VAPoR::NetCDFCFCollection.

virtual int VAPoR::NetCDFCollection::Read	(	size_t	start[],
		size_t	count[],
		float *	data,
		int	fd = `0`
	)

virtual

Read data from the currently opened variable on an unstaggered grid

Read the hyperslice defined by start and count from the currently opened variable into the buffer pointed to by data.

This method is identical in functionality to the netCDF function, nc_get_var_float, with the following two exceptions:

If the opened variable has staggered dimensions, the data are resampled onto the non-staggered grid. Moreover, the region coordinates (start and count) should be specified in the non-staggered coordinates.
If the currently opened variable is explicitly time-varying (has a time-varying dimension), only the spatial dimensions should be provied by start and count. I.e. if the variable contains n dimensions in the netCDF file, only the n-1 fastest-varying (spatial) dimensions should be specified.

Parameters

[in]	start	Start vector with one element for each dimension
[in]	count	Count vector with one element for each dimension
[in]	fd	A currently opened file descriptor returned by OpenRead().

Return values

retval A negative int is returned on failure.

See also: SetStaggeredDims(), ReadNative(), NetCDFSimple::Read(), SetMissingValueAttName(), SetMissingValueAttName()

virtual int VAPoR::NetCDFCollection::Read	(	size_t	start[],
		size_t	count[],
		int *	data,
		int	fd = `0`
	)

virtual

virtual int VAPoR::NetCDFCollection::Read	(	std::vector< size_t >	start,
		std::vector< size_t >	count,
		float *	data,
		int	fd = `0`
	)

virtual

virtual int VAPoR::NetCDFCollection::Read	(	std::vector< size_t >	start,
		std::vector< size_t >	count,
		int *	data,
		int	fd = `0`
	)

virtual

virtual int VAPoR::NetCDFCollection::Read	(	float *	data,
		int	fd = `0`
	)

virtual

virtual int VAPoR::NetCDFCollection::Read	(	char *	data,
		int	fd = `0`
	)

virtual

virtual int VAPoR::NetCDFCollection::ReadNative	(	size_t	start[],
		size_t	count[],
		float *	data,
		int	fd = `0`
	)

virtual

Read data from the currently opened variable on the native grid

This method is identical to the Read() method except that staggered variables are not interpolated to the non-staggered grid. Hence, start and count should be specified in staggered coordinates if the variable is staggered, and non-staggerd coordinates if the variable is not staggered.

Parameters

[in]	start	Start vector with one element for each dimension
[in]	count	Count vector with one element for each dimension
[in]	fd	A currently opened file descriptor returned by OpenRead().

Return values

retval A negative int is returned on failure.

See also: SetStaggeredDims(), NetCDFSimple::Read()

virtual int VAPoR::NetCDFCollection::ReadNative	(	size_t	start[],
		size_t	count[],
		int *	data,
		int	fd = `0`
	)

virtual

virtual int VAPoR::NetCDFCollection::ReadNative	(	size_t	start[],
		size_t	count[],
		char *	data,
		int	fd = `0`
	)

virtual

virtual int VAPoR::NetCDFCollection::ReadNative	(	float *	data,
		int	fd = `0`
	)

virtual

virtual int VAPoR::NetCDFCollection::ReadNative	(	int *	data,
		int	fd = `0`
	)

virtual

virtual int VAPoR::NetCDFCollection::ReadSlice	(	float *	data,
		int	fd = `0`
	)

virtual

Read a 2D slice from a 2D or 3D variable

The method will read 2D slices from a 2D or 3D variable until all slices have been processed. If the variable is staggered the slices will be interpolated onto the non-staggered grid for the currently opened variable. For 3D data each call to ReadSlice() will return a subsequent slice until all slices have been processed. The total number of slices is the value of the slowest varying dimension.

Parameters

[in]	fd	A currently opened file descriptor returned by OpenRead().
[out]	data	The possibly resampled 2D data slice. It is the caller's responsibility to ensure that `data` points to sufficient space.

Return values

status Returns 1 if successful, 0 if there are no more slices to read, and a negative integer on error.

See also: OpenRead(), Read(), SetStaggeredDims(), SetMissingValueAttName(), SetMissingValueAttName()

virtual int VAPoR::NetCDFCollection::ReadSliceNative	(	float *	data,
		int	fd = `0`
	)

virtual

Read a 2D slice from a 2D or 3D variable on the native grid

This method is identical to ReadSlice() with the exception that if the currently opened variable is staggered, the variable will not be resampled to a non-staggered grid.

Parameters

[in]	fd	A currently opened file descriptor returned by OpenRead().
[out]	data	The possibly resampled 2D data slice. It is the caller's responsibility to ensure that `data` points to sufficient space.

Return values

status Returns 1 if successful, 0 if there are no more slices to read, and a negative integer on error.

See also: OpenRead(), Read(), SetStaggeredDims()

void VAPoR::NetCDFCollection::RemoveDerivedVar ( string varname )

inline

Definition at line 799 of file NetCDFCollection.h.

virtual int VAPoR::NetCDFCollection::SeekSlice	(	int	offset,
		int	whence,
		int	fd = `0`
	)

virtual

Set the variable slice position indicator

This method changes the position of the slice indicator for an open variable. Subsequent reads with ReadSlice() or ReadSliceNative() will position the slice offset based on offset. If whence is 0 then offset is added to the first variable slice. If whence is one then offset is added to the current slice position. If whence is 2 then offset is added to the last slice. If the resulting slice position, after adding offset, lies outside of the variable the offset will be mapped to the closest valid value (i.e. the first or last slice).

Parameters

[in]	offset	integer slice offset
[in]	whence	one of 0, 1, 2
[in]	fd	A currently opened file descriptor returned by OpenRead().

Return values

A	negative int is returned if `fd` is not valid (an open file descriptor) or if `whence` is not one of 0, 1, or 2.

virtual void VAPoR::NetCDFCollection::SetMissingValueAttName ( string attname )

inlinevirtual

Identify missing value variable attribute name

This method informs the class instance of the name of a netCDF variable attribute, if one exists, that contains the missing value for the variable. During interpolation of staggered variables the missing value is needed for correct processing

Parameters

attname Name of netCDF variable attribute specifying the missing value

Definition at line 704 of file NetCDFCollection.h.

virtual void VAPoR::NetCDFCollection::SetStaggeredDims ( const std::vector< string > dimnames )

inlinevirtual

Identify staggered dimensions

This method informs the class instance of any staggered dimensions. Class methods that read variable data will use the staggered dimension list to identify staggered variables and may interpolate the data to a non staggered grid

Parameters

dimnames A list of staggered netCDF dimension names

Definition at line 690 of file NetCDFCollection.h.

virtual bool VAPoR::NetCDFCollection::VariableExists ( string varname ) const

virtual

Return a boolean indicating whether a variable exists in the data collection.

This method returns true if the variable named by varname is contained in the data collection. The variable may be present inside of a netCDF file, or may be a variable derived the the NetCDFCFCollection class. In the latter case all native variables used to construct varname must also be present.

Parameters

[in] varname A netCDF variable name

Return values

bool	Returns true if `varname` is contained any one of the netCDF files used to instantiate the class, or if `varname` is a derived variable.

See also: GetTimes(), GetVariables()

virtual bool VAPoR::NetCDFCollection::VariableExists	(	size_t	ts,
		string	varname
	)		const

virtual

Return a boolean indicating whether a variable is defined for a particular time step.

This method returns true if the variable named by varname is contained in the data collection and defined for time step ts. The variable may be present inside of a netCDF file, or may be a variable derived the the NetCDFCFCollection class. In the latter case all native variables used to construct varname must also be present.

Parameters

[in]	ts	A valid data set time step in the range from zero to GetNumTimeSteps() - 1.
[in]	varname	A netCDF variable name

Return values

bool	Returns true if `varname` is contained any one of the netCDF files used to instantiate the class, or if `varname` is a derived variable.

See also: GetTimes(), GetNumTimeSteps(), GetVariables()

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	o,
		const NetCDFCollection &	ncdfc
	)

friend

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

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

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