Difference between revisions of "Python code for GEOS-Chem"

Revision as of 16:09, 16 May 2016

On this page, we list information about Python software packages that are being created for use with GEOS-Chem.

Overview

Traditionally, GEOS-chem users have relied on IDL-based software, such as GAMAP, for data analysis and visualization. But to many GEOS-Chem user groups, the IDL software has become prohibitively expensive. Several members of the GEOS-Chem community have begun to develop file software programs in the Python language for reading, visualizing, and processing GEOS-Chem data. Python is a free and open-source computer language that comes with several pre-packaged libraries for numerical computation and visualization.

On this page we provide a list of Python software that is being developed for use with GEOS-Chem. For more information, please contact the individual authors listed below.

--Bob Y. 13:51, 28 May 2013 (EDT)

Development Teams

--Bob Y. 11:40, 28 May 2013 (EDT)

Information about existing Python packages

bpchdump

Author: Liang Feng (U. Edinburgh, UK)

Here are some screenshots of our bpchdump.py package, which allow you to browse the contents of a bpch file and plot them:

bpchdump.py GUI interface:

Sample plot generated with bpchdump.py:

--Bob Y. 11:40, 28 May 2013 (EDT)

bpch to netCDF converter

Author: Barron Henderson (U. Florida)

Barron Henderson wrote:

I wanted to clarify a little bit about my own project, which I have named simply bpch. bpch is registered with pypi (and installable with the command `pip install bpch`).

bpch is netcdf-like reader for bpch files returns a netcdf-like object with CF-1.6 compliant meta-data. The interface for bpch mimics the netcdf4-python interface (the successor to SciPy.io.netcdf.netcdffile).

If the bpch module is called from the command line (see below), it creates a netcdf file. If the module is used in a python program, then no netcdf file is created. At the command line, it also supports nco-like dimension and variable subsetting. Optionally, it can output figures and animations as well.

Example command line:

   $ python -m bpch ctm.bpch -o ctm.bpch.nc

would create ctm.bpch.nc that is readable by Panoply. The output is not currently readable by IDV because of some dimension naming assumptions for vertical dimensions.

In script form, the bpch module is simple a reader. The script below would simply print out some statistics twice. The first time demonstrates the netcdf3-classic style and the second demonstrates the netcdf4 style. The module uses numpy array structures, so it is fully compatible with matplotlib plotting functions.

   #!/usr/bin/env python
   #--Begin Script--
   from bpch import bpch
   import numpy as np

   f = bpch('ctm.bpch')
   key = 'IJ-AVG-$_Ox'
   v = f.variables[key]
   print key
   print v.units, v.dimensions
   print 'Min, Median, Max, Mean, Std:', v[:].min(), np.median(v[:]), v[:].max(), v[:].mean(), v[:].std()

   group = 'IJ-AVG-$'
   key = 'Ox'
   v = f.groups[group].variables[key]
   print key
   print v.units, v.dimensions
   print 'Min, Median, Max, Mean, Std:', v[:].min(), np.median(v[:]), v[:].max(), v[:].mean(), v[:].std()

   #--End Script--

--Bob Y. 11:40, 28 May 2013 (EDT)

PseudoNetCDF

PseudoNetCDF supersedes the python bpch library. It has all the same functionality and much much more.

• Converts bpch to CF compliant NetCDF pncgen -f bpch inpath outpath
• View a lon/lat point pncdump -f bpch --extract=-74,25 inpath
• Make maps - pncmap.py -f bpch -r time,mean -s layer47,0 inpath outpath
• Make profiles - pncvertprofile.py -f bpch -r time,mean -r latitude,mean -r longitude,mean inpath outpath

   $ pncmap.py -f "bpch,vertgrid='GEOS-5-NATIVE'" --norm="Normalize()" -v IJ-AVG-\$_O3 -r time,mean -s layer72,0 trac_avg.geosfp_4x5_benchmark.201307010000 pnc_trac_avg.geosfp_4x5_benchmark.20130701000_
   IJ-AVG-$_O3
   Saved fig pnc_trac_avg.geosfp_4x5_benchmark.20130701000_IJ-AVG-$_O3.png

pncvertprofile.py has options to add tes and omi to the plot (not shown here)

   $ pncvertprofile.py -f "bpch,vertgrid='GEOS-5-NATIVE'" -v IJ-AVG-\$_O3 -r time,mean trac_avg.geosfp_4x5_benchmark.201307010000 pnc_trac_avg.geosfp_4x5_benchmark.20130701000_pncprofile 

Latest code at github.com/barronh/pseudonetcdf Details for basic operation: https://github.com/barronh/pseudonetcdf/wiki/GC-Tutorials

-- Barron H. Henderson 11:49pm, April 20 2016

Process analysis diagnostics

Author: Barron Henderson (U. Florida)

Barron Henderson wrote:

Process-based Analysis examines the change in each species due to each process and reaction. Models predict atmospheric state, which in a time-series can be used to create net-change of each species. What this cannot tell us, is which processes led to that change. To supplement state (or concentration, GEOS-Chem has long archived emissions and employed advanced diagnostics to predict gross chemical production or loss. Process Analysis goes a step further archiving grid-cell budgets for each species, and decomposing gross production/loss into individual reaction contributions. Process Analysis extensions are currently available in CAMx, WRF-Chem, CMAQ, and now GEOS-Chem. This allows for direct comparisons of models at a fundamental, process level.

For more information, or to download the code, please see our Process Analysis Diagnostics page on the GEOS-Chem wiki.

Gchem

Author: Gerrit Kuhlmann (City University of Hong Kong)

My package Gchem is mainly a reader/writer for bpch files. To visualize data I use available libraries (Matplotlib and basemap).

PyGChem

Authors: Benoit Bovy and Emanuel Mahieu (U. Liege, Belgium)

Benoit Bovy wrote:

The PyGChem Python package aims to connect GEOS-Chem to the Python Scientific (SciPy) Stack, which consists of several core packages and many specialized packages for scientific computing. PyGChem is under active development. Currently, it allows reading GEOS-Chem datasets from both bpch and netCDF formats and handling it as Iris's cubes. Other dataset handling backends such as xray will be added soon. An API for HEMCO is also under development ; it will allow users to dynamically read/write, create, edit, test, and visualize HEMCO configurations.

Preliminary documentation is available as IPython notebooks.

--Benoit B. 10:45, 7 May 2015 (EDT)

Python Ensemble Manager

Author: Andre Perkins (U. Wisconsin-Madison, USA)

This code is useful for running ensembles of GEOS-Chem adjoint model simulations within an MPI environment. For more information about our Python Ensemble Manager, please see the source code on github.

--Daven 14:46, 8 May 2015 (EDT)

Python resources

• Python.org: Main site for all things Python
• Python.org Tutorial
• PythonWiki.org: List of tutorials and resources
• Google's Python tutorial