cf.write

cf.write(fields, filename, fmt='NETCDF4', overwrite=True, verbose=False, cfa_options=None, mode='w', least_significant_digit=None, endian='native', compress=0, fletcher32=False, no_shuffle=False, datatype=None, single=False, double=False, reference_datetime=None, variable_attributes=None, HDF_chunksizes=None, unlimited=None, _debug=False)

Write fields to a netCDF file.

NetCDF dimension and variable names will be taken, if present, from variables’ ncvar attributes and the domain axis ncdim attributes, otherwise they are inferred from standard names or set to defaults. NetCDF names may be automatically given a numerical suffix to avoid duplication.

Output netCDF file global properties are those which occur in the set of CF global properties and non-standard data variable properties and which have equal values across all input fields.

See also

cf.read

Examples 1:

>>> cf.write(f, new_file.nc')

Parameters:

fields: (arbitrarily nested sequence of) cf.Field or cf.FieldList

The field or fields to write to the file.

filename: str

The output netCDF file. Various type of expansion are applied to the file names:

Expansion	Description
Tilde	An initial component of ~ or ~user is replaced by that user’s home directory.
Environment variable	Substrings of the form $name or ${name} are replaced by the value of environment variable name.

Where more than one type of expansion is used in the same string, they are applied in the order given in the above table.

Example:

If the environment variable MYSELF has been set to the 'david', then '~$MYSELF/out.nc' is equivalent to '~david/out.nc'.

fmt: str, optional

The format of the output file. One of:

fmt	Output file type
'NETCDF4'	NetCDF4 format file. This is the default.
'NETCDF4_CLASSIC'	NetCDF4 classic format file (see below)
'NETCDF3_CLASSIC'	NetCDF3 classic format file (limited to file sizes less than 2 Gb).
'NETCDF3_64BIT_OFFSET'	NetCDF3 64-bit offset format file
'NETCDF3_64BIT_DATA'	NetCDF3 64-bit offset format file with extensions (see below)
'NETCDF3_64BIT'	An alias for 'NETCDF3_64BIT_OFFSET'
'CFA3'	CFA-netCDF3 classic format file
'CFA4'	CFA-netCDF4 format file

By default the format is 'NETCDF4'.

Note that the netCDF3 formats may be considerably slower than any of the other options.

All formats support large files (i.e. those greater than 2 Gb) except 'NETCDF3_CLASSIC'.

'NETCDF3_64BIT_DATA' is a format that requires version 4.4.0 or newer of the C library (use cf.environment to see which version if the netCDF-C library is in use). It extends the 'NETCDF3_64BIT_OFFSET' binary format to allow for unsigned/64 bit integer data types and 64-bit dimension sizes.

'NETCDF4_CLASSIC' files use the version 4 disk format (HDF5), but omits features not found in the version 3 API. They can be read by HDF5 clients. They can also be read by netCDF 3 clients only if they have been relinked against the netCDF4 library.

'NETCDF4' files use the version 4 disk format (HDF5) and use the new features of the version 4 API.

overwrite: bool, optional

If False then raise an exception if the output file pre-exists. By default a pre-existing output file is over written.

verbose : bool, optional

If True then print one-line summaries of each field written.

cfa_options: dict, optional

A dictionary giving parameters for configuring the output CFA-netCDF file:

Key

Value

'base'

If None (the default) then file names within CFA-netCDF files are stored with absolute paths. If set to an empty string then file names within CFA-netCDF files are given relative to the directory or URL base containing the output CFA-netCDF file. If set to a string then file names within CFA-netCDF files are given relative to the directory or URL base described by the value. For example: '../archive'.

By default no parameters are specified.

mode: str, optional

Specify the mode of write access for the output file. One of:

mode	Description
'w'	Open a new file for writing to. If it exists and overwrite is True then the file is deleted prior to being recreated.

By default the file is opened with write access mode 'w'.

endian: str, optional

The endian-ness of the output file. Valid values are 'little', 'big' or 'native'. By default the output is native endian.

compress: int, optional

Regulate the speed and efficiency of compression. Must be an integer between 0 and 9. 0 means no compression; 1 is the fastest, but has the lowest compression ratio; 9 is the slowest but best compression ratio. The default value is 0. An exception is raised if compression is requested for a netCDF3 output file format.

least_significant_digit: int, optional

Truncate the input field data arrays. For a positive integer, N the precision that is retained in the compressed data is ‘10 to the power -N’. For example, a value of 2 will retain a precision of 0.01. In conjunction with the compress parameter this produces ‘lossy’, but significantly more efficient compression.

fletcher32: bool, optional

If True then the Fletcher-32 HDF5 checksum algorithm is activated to detect compression errors. Ignored if compress is 0.

no_shuffle: bool, optional

If True then the HDF5 shuffle filter (which de-interlaces a block of data before compression by reordering the bytes by storing the first byte of all of a variable’s values in the chunk contiguously, followed by all the second bytes, and so on) is turned off. By default the filter is applied because if the data array values are not all wildly different, using the filter can make the data more easily compressible. Ignored if compress is 0.

datatype: dict, optional

Specify data type conversions to be applied prior to writing data to disk. Arrays with data types which are not specified remain unchanged. By default, input data types are preserved. Data types defined by numpy.dtype objects in a dictionary whose are input data types with values of output data types.

Example:

To convert 64-bit floats and 64-bit integers to their 32-bit counterparts: datatype={numpy.dtype('float64'): numpy.dtype('float32'), numpy.dtype('int64'): numpy.dtype('int32')}.

single: bool, optional

Write 64-bit floats as 32-bit floats and 64-bit integers as 32-bit integers. By default, input data types are preserved. Note that single=True is exactly equivalent to datatype={numpy.dtype('float64'): numpy.dtype('float32'), numpy.dtype('int64'): numpy.dtype('int32')}.

double: bool, optional

Write 32-bit floats as 64-bit floats and 32-bit integers as 64-bit integers. By default, input data types are preserved. Note that double=True is exactly equivalent to datatype={numpy.dtype('float32'): numpy.dtype('float64'), numpy.dtype('int32'): numpy.dtype('int64')}.

HDF_chunksizes: dict, optional

Manually specify HDF5 chunks for the field data arrays.

Chunking refers to a storage layout where a data array is partitioned into fixed-size multi-dimensional chunks when written to a netCDF4 file on disk. Chunking is ignored if the field is written to a netCDF3 format file.

A chunk has the same rank as the data array, but with fewer (or no more) elements along each axes. The chunk is defined by a dictionary whose keys identify axes with values of the chunks size for those axes.

If a given chunk size for an axis is larger than the axis size for any field, then the size of the axis at the time of writing to disk will be used instead.

If chunk sizes have been specified for some but not all axes, then the each unset chunk size is assumed to be the full size of the axis for each field.

If no chunk sizes have been set for any axes then the netCDF default chunk is used (http://www.unidata.ucar.edu/software/netcdf/docs/netcdf_perf_chunking.html).

If any chunk sizes have already been set on a field with the cf.Field.HDF_chunks method then these are used in instead.

A detailed discussion of HDF chunking and I/O performance is available at https://www.hdfgroup.org/HDF5/doc/H5.user/Chunking.html and http://www.unidata.ucar.edu/software/netcdf/workshops/2011/nc4chunking. Basically, you want the chunks for each dimension to match as closely as possible the size and shape of the data block that users will read from the file.

unlimited: sequence of str, optional

Create unlimited dimensions (dimensions that can be appended to). A dimension is identified by either a standard name; one of T, Z, Y, X denoting time, height or horixontal axes repsectively (as defined by the CF conventions); or the value of an arbitrary CF property preceeded by the property name and a colon.

Returns:

None

Examples 2:

>>> f
[<CF Field: air_pressure(30, 24)>,
 <CF Field: u_compnt_of_wind(19, 29, 24)>,
 <CF Field: v_compnt_of_wind(19, 29, 24)>,
 <CF Field: potential_temperature(19, 30, 24)>]
>>> write(f, 'file')

>>> cf.write([f, g], 'file.nc', verbose=True)
[<CF Field: air_pressure(30, 24)>,
 <CF Field: u_compnt_of_wind(19, 29, 24)>,
 <CF Field: v_compnt_of_wind(19, 29, 24)>,
 <CF Field: potential_temperature(19, 30, 24)>]