Codes dealing with NetCDF I/O calls. More...

Classes
class	netcdf_tt
	A traits class mapping to netcdf from C++. More...

class	cpp_tt
	A traits class mapping to C++ from netcdf. More...

class	netcdf_tt< char >

class	netcdf_tt< unsigned char >

class	netcdf_tt< short int >

class	netcdf_tt< unsigned short int >

class	netcdf_tt< int >

class	netcdf_tt< long >

class	netcdf_tt< unsigned long >

class	netcdf_tt< unsigned int >

class	netcdf_tt< long long >

class	netcdf_tt< unsigned long long >

class	netcdf_tt< float >

class	netcdf_tt< double >

class	cpp_tt< NC_BYTE >

class	cpp_tt< NC_UBYTE >

class	cpp_tt< NC_SHORT >

class	cpp_tt< NC_USHORT >

class	cpp_tt< NC_INT >

class	cpp_tt< NC_UINT >

class	cpp_tt< NC_INT64 >

class	cpp_tt< NC_UINT64 >

class	cpp_tt< NC_FLOAT >

class	cpp_tt< NC_DOUBLE >

class	netcdf_handle
	A RAII class for managing NETCDF files. The file is kept open while the object exists. More...

class	read_variable_and_attributes
	Functional that reads and returns a variable from the named file. More...

class	read_variable
	Function that reads and returns a variable from the named file. More...

Functions
void	crtrim (char *s, long n)

std::mutex &	get_netcdf_mutex ()

TECA_EXPORT int	read_attribute (int parent_id, int var_id, const std::string &att_name, teca_metadata &atts)

TECA_EXPORT int	read_attribute (int parent_id, int var_id, int att_id, teca_metadata &atts)

TECA_EXPORT int	read_variable_attributes (netcdf_handle &fh, const std::string &parent_group, int var_id, const std::string &x_variable, const std::string &y_variable, const std::string &z_variable, const std::string &t_variable, const std::string &ensemble_dimension_name, int clamp_dimensions_of_one, std::string &name, teca_metadata &atts)

TECA_EXPORT int	read_variable_attributes (netcdf_handle &fh, const std::string &parent_group, int var_id, std::string &name, teca_metadata &atts)

TECA_EXPORT int	get_varid (netcdf_handle &fh, const std::string &var_name, int parent_id, int var_id)

TECA_EXPORT int	read_variable_attributes (netcdf_handle &fh, const std::string &name, const std::string &x_variable, const std::string &y_variable, const std::string &z_variable, const std::string &t_variable, const std::string &ensemble_dim_name, int clamp_dimensions_of_one, teca_metadata &atts)

TECA_EXPORT int	read_variable_attributes (netcdf_handle &fh, const std::string &var_name, teca_metadata &atts)

TECA_EXPORT int	write_variable_attributes (int parent_id, int var_id, teca_metadata &array_atts)

Detailed Description

Codes dealing with NetCDF I/O calls.

Function Documentation

◆ crtrim()

void teca_netcdf_util::crtrim	(	char *	s,
		long	n
	)

To deal with fortran fixed length strings which are not properly nulll terminated.

◆ get_netcdf_mutex()

std::mutex& teca_netcdf_util::get_netcdf_mutex ( )

NetCDF 3 is not threadsafe. The HDF5 C-API can be compiled to be threadsafe, but it is usually not. NetCDF uses HDF5-HL API to access HDF5, but HDF5-HL API is not threadsafe without the –enable-unsupported flag. For all those reasons it's best for the time being to protect all NetCDF I/O.

◆ get_varid()

TECA_EXPORT int teca_netcdf_util::get_varid	(	netcdf_handle &	fh,
		const std::string &	var_name,
		int *	parent_id,
		int *	var_id
	)

Get the variable ID in a NetCDF file where var_name can be a fully qualified path including group names, such as "global/lat"

◆ read_attribute() [1/2]

TECA_EXPORT int teca_netcdf_util::read_attribute	(	int	parent_id,
		int	var_id,
		const std::string &	att_name,
		teca_metadata &	atts
	)

Read the specified variable attribute by name. Its value is stored in the metadata object return is non-zero if an error occurred.

◆ read_attribute() [2/2]

TECA_EXPORT int teca_netcdf_util::read_attribute	(	int	parent_id,
		int	var_id,
		int	att_id,
		teca_metadata &	atts
	)

Read the specified variable attribute by id. Its value is stored in the metadata object return is non-zero if an error occurred.

◆ read_variable_attributes() [1/4]

TECA_EXPORT int teca_netcdf_util::read_variable_attributes	(	netcdf_handle &	fh,
		const std::string &	name,
		const std::string &	x_variable,
		const std::string &	y_variable,
		const std::string &	z_variable,
		const std::string &	t_variable,
		const std::string &	ensemble_dim_name,
		int	clamp_dimensions_of_one,
		teca_metadata &	atts
	)

Read the specified variable's dimensions, and it's associated NetCDF attributes into the metadata object. See CF Attributes for details of attributes returned. returns non-zero if an error occurred.

◆ read_variable_attributes() [2/4]

TECA_EXPORT int teca_netcdf_util::read_variable_attributes	(	netcdf_handle &	fh,
		const std::string &	parent_group,
		int	var_id,
		const std::string &	x_variable,
		const std::string &	y_variable,
		const std::string &	z_variable,
		const std::string &	t_variable,
		const std::string &	ensemble_dimension_name,
		int	clamp_dimensions_of_one,
		std::string &	name,
		teca_metadata &	atts
	)

Read the specified variable's name, dimensions, and it's associated NetCDF attributes into the metadata object. Additionally the following key/value pairs are added and useful for subsequent I/O and processing

CF Attributes

Key	Description
cf_parent_group	The name of the group containing the NetCF variable
	id or an empty string if variable is in the root
	group (likely the most common case)
cf_id	The NetCDF variable id that can be used to read the
	variable.
cf_dims	A vector of the NetCDF dimension lengths (i.e. the
	variable's shape).
cf_dim_names	A vector of the names of the NetCDF dimensions.
cf_type_code	The NetCDF type code.
type_code	The teca_variant_array::code type code.
centering	The mesh centering, point_centering or no_centering
have_mesh_dim	Flags indicating the presence of the x,y,z, and t
	mesh dimensions
mesh_dim_active	Flags indicating if the x,y,z, and t dimension is
	active.

In order for centering and have_mesh_dim flags to be set, the x_variable, y_variable, z_variable, and t_variable must be specified.

If dimension is 1 and clamp_dimensions_of_one is set then the dimension is marked as inactive.

returns non-zero if an error occurred.

◆ read_variable_attributes() [3/4]

TECA_EXPORT int teca_netcdf_util::read_variable_attributes	(	netcdf_handle &	fh,
		const std::string &	parent_group,
		int	var_id,
		std::string &	name,
		teca_metadata &	atts
	)

Read the specified variable's name, dimensions, and it's associated NetCDF attributes into the metadata object. See CF Attributes for details of attributes returned. returns non-zero if an error occurred.

◆ read_variable_attributes() [4/4]

TECA_EXPORT int teca_netcdf_util::read_variable_attributes	(	netcdf_handle &	fh,
		const std::string &	var_name,
		teca_metadata &	atts
	)