Using Python with Climate Data

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At the Melbourne Uni follow-up meeting for the 2013 Software Carpentry workshop Damien Irving showed off several Python libraries for working with climate data. Damien's notes are given below, he also has material available on | his blog.

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Hi all,

Thanks for coming to the Software Carpentry boot camp follow up session this afternoon. Below is a summary of the text that I showed at the end, including the various links that I promised. If you're struggling with Python at all, feel free to look through my bitbucket repository for useful examples (https://bitbucket.org/DBrent/phd/src). At the 'cdat_tutorial' directory in that repository, you'll see the example code that I used today.

netCDF

• be CF compliant
• use attributes: data should be self-describing
• more details: http://drclimate.wordpress.com/2013/02/25/are-you-cf-compliant/

ipython

• excellent interactive development environment (IDE)
• use dir() and ? to explore objects
• use pdb for debugging
• use ! to run any command at the system shell
• on abyss: /usr/local/uvcdat/1.2.0rc1/bin/ipython

uvcdat

• for quickly viewing your data
• overview: http://drclimate.wordpress.com/2012/12/19/getting-started-with-python/
• youtube: http://www.youtube.com/watch?v=Nuer6B21NA0
• general cdat documentation: http://www2-pcmdi.llnl.gov/cdat
• on abyss: /usr/local/uvcdat/1.2.0rc1/bin/uvcdat

import cdms2

• for netCDF input and output
• documentation: http://esg.llnl.gov/cdat/cdms_html/cdms.htm

import cdutil

• climate relevant utilities (climatologies, regions, calendars etc)
• documentation: http://esg.llnl.gov/cdat/cdat_utilities/cdat_utilities.htm

import genutil

• climate relevant statistics (correlation, percentiles, etc)
• documentation: http://esg.llnl.gov/cdat/cdat_utilities/cdat_utilities.htm

import regrid2

• for regirdding

import MV2

• for masked arrays
• it's a copy of numpy.ma, but the data keep their attributes

import matplotlib

• for all plotting (timeseries, spatial maps, etc)
• from mpl_toolkits.basemap import Basemap, for spatial maps
• from mpl_toolkits.basemap import shiftgrid, for longitude axis fiddling
• documentation: http://matplotlib.org/

programming tips

• use the argparse module for parsing the command line
• create your own modules to avoid duplication of code
• use docstrings as your primary documentation method
• use pylint to test the quality of your code