cf python package

Introduction

Version 3.15.2 for version 1.10 of the CF conventions.

The Python cf package is an Earth Science data analysis library that is built on a complete implementation of the CF data model.

Functionality

The cf package implements the CF data model for its internal data structures and so is able to process any CF-compliant dataset. It is not strict about CF-compliance, however, so that partially conformant datasets may be ingested from existing datasets and written to new datasets.This is so that datasets that are partially conformant may nonetheless be modified in memory.

A basic example of reading a field construct from a file and inspecting it.
>>> import cf
>>> f = cf.read('file.nc')
>>> f
[<CF Field: air_temperature(time(12), latitude(64), longitude(128)) K>]
>>> print(f[0])
Field: air_temperature (ncvar%tas)
----------------------------------
Data            : air_temperature(time(12), latitude(64), longitude(128)) K
Cell methods    : time(12): mean (interval: 1.0 month)
Dimension coords: time(12) = [1991-11-16 00:00:00, ..., 1991-10-16 12:00:00] noleap
                : latitude(64) = [-87.8638, ..., 87.8638] degrees_north
                : longitude(128) = [0.0, ..., 357.1875] degrees_east
                : height(1) = [2.0] m

The cf package uses Dask for all of its array manipulation and can:

  • read field constructs and domain constructs from netCDF, CDL, PP and UM datasets,

  • create new field constructs in memory,

  • write and append field constructs to netCDF datasets on disk,

  • read, write, and create coordinates defined by geometry cells,

  • read netCDF and CDL datasets containing hierarchical groups,

  • inspect field constructs,

  • test whether two field constructs are the same,

  • modify field construct metadata and data,

  • create subspaces of field constructs,

  • write field constructs to netCDF datasets on disk,

  • incorporate, and create, metadata stored in external files,

  • read, write, and create data that have been compressed by convention (i.e. ragged or gathered arrays, or coordinate arrays compressed by subsampling), whilst presenting a view of the data in its uncompressed form,

  • combine field constructs arithmetically,

  • manipulate field construct data by arithmetical and trigonometrical operations,

  • perform statistical collapses on field constructs,

  • perform histogram, percentile and binning operations on field constructs,

  • regrid field constructs with (multi-)linear, nearest neighbour, first- and second-order conservative and higher order patch recovery methods,

  • apply convolution filters to field constructs,

  • create running means from field constructs,

  • apply differential operators to field constructs,

  • create derived quantities (such as relative vorticity).

Visualisation

Powerful, flexible, and user-friendly visualisations of field constructs are available with the cf-plot package that is installed separately to cf (see http://ajheaps.github.io/cf-plot for details).

See the cf-plot gallery for the wide range of plotting possibilities with example code.

_images/cfplot_example.png

Example output of cf-plot displaying a cf field construct.

Performance

As of version 3.14.0 (released 2023-01-31), cf uses Dask for all of its data manipulations, which provides lazy, parallelised, and out-of-core computations of array operations.

Command line utilities

During installation the cfa command line utility is also installed, which

  • generates text descriptions of field constructs contained in files, and

  • creates new datasets aggregated from existing files.

References

Eaton, B., Gregory, J., Drach, B., Taylor, K., Hankin, S., Caron, J.,

Signell, R., et al. NetCDF Climate and Forecast (CF) Metadata Conventions. CF Conventions Committee. https://cfconventions.org/cf-conventions/cf-conventions.html

Hassell, D., and Bartholomew, S. L. (2020). cfdm: A Python reference

implementation of the CF data model. Journal of Open Source Software, 5(54), 2717, https://doi.org/10.21105/joss.02717

Hassell, D., Gregory, J., Blower, J., Lawrence, B. N., and

Taylor, K. E. (2017). A data model of the Climate and Forecast metadata conventions (CF-1.6) with a software implementation (cf-python v2.1), Geosci. Model Dev., 10, 4619-4646, https://doi.org/10.5194/gmd-10-4619-2017

Rew, R., and Davis, G. (1990). NetCDF: An Interface for Scientific

Data Access. IEEE Computer Graphics and Applications, 10(4), 76–82. https://doi.org/10.1109/38.56302

Rew, R., Hartnett, E., and Caron, J. (2006). NetCDF-4: Software

Implementing an Enhanced Data Model for the Geosciences. In 22nd International Conference on Interactive Information Processing Systems for Meteorology, Oceanography, and Hydrology. AMS. Retrieved from https://www.unidata.ucar.edu/software/netcdf/papers/2006-ams.pdf

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