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

#include <NetCDFCFCollection.h>

Inheritance diagram for VAPoR::NetCDFCFCollection:

Public Member Functions
	NetCDFCFCollection ()

virtual	~NetCDFCFCollection ()

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

virtual bool	IsCoordVarCF (string var) const

virtual bool	IsAuxCoordVarCF (string var) const

virtual bool	IsLatCoordVar (string var) const

virtual bool	IsLonCoordVar (string var) const

virtual bool	IsTimeCoordVar (string var) const

virtual bool	IsVertCoordVar (string var) const

virtual bool	IsVertCoordVarUp (string var) const

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

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

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

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

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

virtual int	GetVarCoordVarNames (string var, std::vector< string > &cvars) const

virtual int	GetVarUnits (string var, string &units) const

const UDUnits *	GetUDUnits () const

virtual int	Convert (const string from, const string to, const double src, double dst, size_t n) const

virtual int	Convert (const string from, const string to, const float src, float dst, size_t n) const

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

virtual int	OpenRead (size_t ts, string varname)

virtual bool	IsVertDimensionless (string cvar) const

virtual int	InstallStandardVerticalConverter (string cvar, string newvar, string units="meters")

virtual void	UninstallStandardVerticalConverter (string cvar)

virtual int	InstallStandardTimeConverter (string cvar, string newvar, string units="seconds")

virtual void	UninstallStandardTimeConverter (string cvar)

void	InstallDerivedCoordVar (string varname, DerivedVar *derivedVar, int axis)

void	RemoveDerivedVar (string varname)

bool	GetMapProjectionProj4 (string varname, string &proj4string) const

void	FormatTimeStr (double time, string &str) const

Public Member Functions inherited from VAPoR::NetCDFCollection
	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 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

Friends
std::ostream &	operator<< (std::ostream &o, const NetCDFCFCollection &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

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

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

Detailed Description

Wrapper for a collection of netCDF files.

Author: John Clyne

Version: $Revision$

Date: $Date$

This class provides access to CF-1 compliant collection of netCDF files. This work is based on the "NetCDF Climate and Forecast (CF) Metadata Conventions", version 1.6, 5, December 2011.

Definition at line 35 of file NetCDFCFCollection.h.

Constructor & Destructor Documentation

VAPoR::NetCDFCFCollection::NetCDFCFCollection ( )

virtual VAPoR::NetCDFCFCollection::~NetCDFCFCollection ( )

virtual

Member Function Documentation

virtual int VAPoR::NetCDFCFCollection::Convert	(	const string	from,
		const string	to,
		const double *	src,
		double *	dst,
		size_t	n
	)		const

virtual

Convert an array of floating point values from one unit to another

This method uses the UDUnits class to convert an array of floating point values from one unit measure to another as supported by Unidata's udunits2 library. See from A string containing the unit to convert from (e.g. "meters") to A string containing the unit to convert to (e.g. "feet") src An array of input values to be converted dst An output buffer large enough to contained the converted data n The number of elements in src status a non-negative int is returned on success

virtual int VAPoR::NetCDFCFCollection::Convert	(	const string	from,
		const string	to,
		const float *	src,
		float *	dst,
		size_t	n
	)		const

virtual

void VAPoR::NetCDFCFCollection::FormatTimeStr	(	double	time,
		string &	str
	)		const

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

virtual

Return a list of data variables with a given rank

Returns a list of data variables having a dimension rank of ndim. If spatial is true only the data 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.

Names of variables that are coordinate or auxiliary coordinate variables are not returned, nor are variables that are missing coordinate variables.

Parameters

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

See also: NetCDFCollection::GetVariableNames()

virtual std::vector<string> VAPoR::NetCDFCFCollection::GetLatCoordVars ( ) const

inlinevirtual

Return a vector of all latitude coordinate variables

Definition at line 161 of file NetCDFCFCollection.h.

virtual std::vector<string> VAPoR::NetCDFCFCollection::GetLonCoordVars ( ) const

inlinevirtual

Return a vector of all longitude coordinate variables

Definition at line 165 of file NetCDFCFCollection.h.

bool VAPoR::NetCDFCFCollection::GetMapProjectionProj4	(	string	varname,
		string &	proj4string
	)		const

Get a map projection as a proj4 string

If a variable has a map projection generate a proj4 transformation string for converting from geographic to Cartographic coordinates. Returns false if no proj4 string could be generated: either no map projection exists, or one exists but is not supported.

virtual bool VAPoR::NetCDFCFCollection::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.

Missing data values are indicated using the _FillValue, or missing_value attributes as defined in section 2.5.1 of the CF 1.6 spec.

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 from VAPoR::NetCDFCollection.

virtual std::vector<string> VAPoR::NetCDFCFCollection::GetTimeCoordVars ( ) const

inlinevirtual

Return a vector of all time coordinate variables

Definition at line 169 of file NetCDFCFCollection.h.

const UDUnits* VAPoR::NetCDFCFCollection::GetUDUnits ( ) const

inline

Return a pointer to the internal UDUnits object used to perform unit conversion.

Definition at line 254 of file NetCDFCFCollection.h.

virtual int VAPoR::NetCDFCFCollection::GetVarCoordVarNames	(	string	var,
		std::vector< string > &	cvars
	)		const

virtual

Return ordered list of coordinate or auxliary coordinate variables for the named variable.

This method returns in cvars an ordered list of all of the spatio-temporal coordinate or auxliary coordinate variables associated with the variable named by var. See Chapter 5 of the CF 1.X spec. for more detail, summarized here:

CF1.X Chap. 5 excerpt :

"The use of coordinate variables is required whenever they are applicable. That is, auxiliary coordinate variables may not be used as the only way to identify latitude and longitude coordinates that could be identified using coordinate variables. This is both to enhance conformance to COARDS and to facilitate the use of generic applications that recognize the NUG convention for coordinate variables. An application that is trying to find the latitude coordinate of a variable should always look first to see if any of the variable's dimensions correspond to a latitude coordinate variable. If the latitude coordinate is not found this way, then the auxiliary coordinate variables listed by the coordinates attribute should be checked. Note that it is permissible, but optional, to list coordinate variables as well as auxiliary coordinate variables in the coordinates attribute."

Parameters

[in]	varname	A variable name
[out]	cvars	A ordered vector of coordinate variable names

Return values

status a negative int is returned if the number of elements in cvars does not match the number of spatio-temporal dimensions of the variable named by var

virtual int VAPoR::NetCDFCFCollection::GetVarUnits	(	string	var,
		string &	units
	)		const

virtual

Return the value of the 'units' attribute for the named variable

This method fetches the value of the 'units' attribute, if present, for the variable named by var. If a units attribute is not present then units will contain an empty string.

Parameters

[in]	varname	A variable name
[out]	units	The value of the variable's 'units' attribute. If the 'units' attribute is not present the parameter will contain the empty string.

Return values

status a non-negative int is returned on success

virtual std::vector<string> VAPoR::NetCDFCFCollection::GetVertCoordVars ( ) const

inlinevirtual

Return a vector of all vertical coordinate variables

Definition at line 173 of file NetCDFCFCollection.h.

virtual int VAPoR::NetCDFCFCollection::Initialize ( const std::vector< string > & files )

virtual

void VAPoR::NetCDFCFCollection::InstallDerivedCoordVar	(	string	varname,
		DerivedVar *	derivedVar,
		int	axis
	)

Install a derived coordinate variable

This method can be used to create a derived coordinate variable.

Parameters

[in]	varname	A unique name for the new variable
[in]	derivedVar	A pointer to a NetCDFCollection::DerivedVar instance
[in]	axis	An integer indicating the coordinate axis that the coordinate variable coresponds to. 0 implies the X axis, 1 the Y axis 2 the Z axis, and 3 is time.

See also: NetCDFCollectin::InstallDerivedVar()

virtual int VAPoR::NetCDFCFCollection::InstallStandardTimeConverter	(	string	cvar,
		string	newvar,
		string	units = `"seconds"`
	)

virtual

This method defines a converter for time coordinates

This method can be used to create a derived time coordinate variable containing with units specified by units from a native time coordinate variable. The native coordinate variable must contain a units attribute that is recognized by UDUnits as a time specification.

Parameters

[in]	cvar	A dimensionless variable with a `units` attribute
[in]	newvar	The name of the new derived variable
[in]	units	The length units of the new variable

Return values

status a non-negative int is returned on success

See also: UninstallStandardTimeConverter()

virtual int VAPoR::NetCDFCFCollection::InstallStandardVerticalConverter	(	string	cvar,
		string	newvar,
		string	units = `"meters"`
	)

virtual

This method defines a converter from dimensionless vertical coordinates to dimensioned vertical coordinates

This method can be used to create a derived variable containing dimensioned vertical coordinates from a native variable containing dimensionless vertical coordinates. Once defined, the derived variable can be operated on like any other native variable contained in the data collection using methods such as OpenRead(), and ReadSlice(). The dimensionless vertical coordinate variable must contain a standard_name attribute containing a supported dimensionless coordinate. Currently supported standard names are:

ocean_s_coordinate_g1
ocean_s_coordinate_g2

See also: Appendix D of the CF 1.6 spec.

Parameters

[in]	cvar	A dimensionless variable with a `standard_name` attribute
[in]	newvar	The name of the new derived variable
[in]	units	The length units of the new variable

Return values

status a non-negative int is returned on success

See also: UninstallStandardVerticalConverter()

virtual bool VAPoR::NetCDFCFCollection::IsAuxCoordVarCF ( string var ) const

inlinevirtual

Return boolean indicating whether the named variable is a CF auxiliary coordinate variable

This method returns true if the variable named by var is a "auxiliary coordinate variable"

CF1.X Definition of auxiliary coordinate variable :

Any netCDF variable that contains coordinate data, but is not a coordinate variable (in the sense of that term defined by the NUG and used by this standard - see below). Unlike coordinate variables, there is no relationship between the name of an auxiliary coordinate variable and the name(s) of its dimension(s).

Return values

true	if `var` is an auxliary coordinate variable, false otherwise

Definition at line 81 of file NetCDFCFCollection.h.

virtual bool VAPoR::NetCDFCFCollection::IsCoordVarCF ( string var ) const

inlinevirtual

Return boolean indicating whether variable is a CF coordinate variable

This method returns true if the variable named by var is a "coordinate variable"

CF1.X Definition of coordinate variable :

"We use this term precisely as it is defined in section 2.3.1 of the NUG. It is a one- dimensional variable with the same name as its dimension [e.g., time(time)], and it is defined as a numeric data type with values that are ordered monotonically. Missing values are not allowed in coordinate variables."

Return values

true	if `var` is a coordinate variable, false otherwise

Definition at line 61 of file NetCDFCFCollection.h.

virtual bool VAPoR::NetCDFCFCollection::IsLatCoordVar ( string var ) const

inlinevirtual

Return boolean indicating whether the named variable represents latitude.

This method returns true if the variable named by var is a latitude coordinate variable. See section 4.1 of the CF spec.

Return values

true	if `var` is latitude coordinate variable, false otherwise

Definition at line 95 of file NetCDFCFCollection.h.

virtual bool VAPoR::NetCDFCFCollection::IsLonCoordVar ( string var ) const

inlinevirtual

Return boolean indicating whether the named variable represents longitude.

This method returns true if the variable named by var is a longitude coordinate variable. See section 4.2 of the CF spec.

Return values

true	if `var` is longitude coordinate variable, false otherwise

Definition at line 108 of file NetCDFCFCollection.h.

virtual bool VAPoR::NetCDFCFCollection::IsTimeCoordVar ( string var ) const

inlinevirtual

Return boolean indicating whether the named variable represents time.

This method returns true if the variable named by var is a time coordinate variable. See section 4.4 of the CF spec.

Return values

true	if `var` is a time coordinate variable, false otherwise

Definition at line 121 of file NetCDFCFCollection.h.

virtual bool VAPoR::NetCDFCFCollection::IsVertCoordVar ( string var ) const

inlinevirtual

Return boolean indicating whether the named variable represents a vertical coordinate.

This method returns true if the variable named by var is a dimesional or dimensionless vertical coordinate variable. See section 4.3 of the CF spec.

Return values

true	if `var` is a time coordinate variable, false otherwise

Definition at line 135 of file NetCDFCFCollection.h.

virtual bool VAPoR::NetCDFCFCollection::IsVertCoordVarUp ( string var ) const

virtual

Return true if the increasing direction of the named vertical coordinate variable is up

CF 1.x description of vertical coordinate direction:

The direction of positive (i.e., the direction in which the coordinate values are increasing), whether up or down, cannot in all cases be inferred from the units. The direction of positive is useful for applications displaying the data. For this reason the attribute positive as defined in the COARDS standard is required if the vertical axis units are not a valid unit of pressure (a determination which can be made using the udunits routine, utScan) – otherwise its inclusion is optional. The positive attribute may have the value up or down (case insensitive).

virtual bool VAPoR::NetCDFCFCollection::IsVertDimensionless ( string cvar ) const

virtual

Return true if the named variable is a dimensionless vertical coordinate variable.

This method returns true if the variable named by cvar is both a vertical coordinate variable and it is dimensionless. See section 4.3.2 of the CF 1.6 spec.

virtual int VAPoR::NetCDFCFCollection::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 from VAPoR::NetCDFCollection.

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

virtual void VAPoR::NetCDFCFCollection::UninstallStandardTimeConverter ( string cvar )

virtual

Remove the converter for a previously defined dimensionless time coordinate converter

Parameters

[in] cvar The name of a derived variable previousl defined with InstallStandardTimeConverter()

See also: InstallStandardTimeConverter()

virtual void VAPoR::NetCDFCFCollection::UninstallStandardVerticalConverter ( string cvar )

virtual

Remove the converter for a previously defined dimensionless vertical coordinate converter

Parameters

[in] cvar The name of a derived variable previousl defined with InstallStandardVerticalConverter()

See also: InstallStandardVerticalConverter()

Friends And Related Function Documentation

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

friend

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

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

Public Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation