Difference between revisions of "Python tools for use with GEOS-Chem"

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__FORCETOC__
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'''''[[GEOS-Chem_diagnostic_output_files|Previous]] | [[GEOS-Chem_coding_and_debugging|Next]] | [[Getting Started with GEOS-Chem]]'''''
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#[[Minimum system requirements for GEOS-Chem|Minimum system requirements]]
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#[[Installing required software]]
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#[[Configuring your computational environment]]
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#[[Downloading GEOS-Chem source code|Downloading source code]]
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#[[Downloading GEOS-Chem data directories|Downloading data directories]]
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#[[Creating GEOS-Chem run directories|Creating run directories]]
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#[[GEOS-Chem input files|Configuring runs]]
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#[[Compiling GEOS-Chem|Compiling]]
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#[[Running GEOS-Chem|Running]]
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#[[GEOS-Chem output files|Output files]]
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#<span style="color:blue">'''Python tools for use with GEOS-Chem'''</span>
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#[[GEOS-Chem_coding_and_debugging|Coding and debugging]]
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#[[GEOS-Chem_overview#Further_reading|Further reading]]
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On this page, we provide information about free and open-source Python-language tools for visualizing or analyzing GEOS-Chem data.
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== GCPy ==
 
== GCPy ==
  
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The GEOS-Chem Support Team is currently developing [https://github.com/geoschem/gcpy GCPy], which is used to create the evaluation plots from GEOS-Chem benchmark simulations.  While GCPy is still in development, we encourage interested users to start using GCPy and to report any issues.
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The GEOS-Chem Support Team develops [https://github.com/geoschem/gcpy '''GCPy'''], which is a Python-based toolkit containing useful functions and routines for working with GEOS-Chem.  GCPy builds upon the well-established scientific python technical stack, leveraging tools like cartopy and xarray to simplify the task of working with model output and performing atmospheric chemistry analyses. GCPy features several plotting and tabling functions, and also supports regridding GEOS-Chem NetCDF files between the grid formats used in GEOS-Chem Classic and GCHP.
  
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Also, if you have your own Python plotting or analysis code, and would like to make it a part of GCPy, please contact the [[GEOS-Chem Support Team]].
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Full GCPy documentation is available at [https://gcpy.readthedocs.io/en/latest/ '''gcpy.readthedocs.io'''].
  
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== Third-party packages ==
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== Third-party Python tools ==
  
 
Several third-party Python packages have been developed for GEOS-Chem.  If you are interested in using any of these, we recommend that you follow up with the developers directly.  The [[GEOS-Chem Support Team]] is not responsible for maintaining these tools.
 
Several third-party Python packages have been developed for GEOS-Chem.  If you are interested in using any of these, we recommend that you follow up with the developers directly.  The [[GEOS-Chem Support Team]] is not responsible for maintaining these tools.
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|Jiawei Zhuang
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|Jiawei Zhuang<br>(since taken over by Pangeo)
 
|[https://xesmf.readthedocs.io/en/latest/why.html xESMF]: A universal regridder.  Leverages ESMF's regridding capabilities to easily regrid data between lon-lat and cubed-sphere grids.  Other grids are supported as well.
 
|[https://xesmf.readthedocs.io/en/latest/why.html xESMF]: A universal regridder.  Leverages ESMF's regridding capabilities to easily regrid data between lon-lat and cubed-sphere grids.  Other grids are supported as well.
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|[https://github.com/JiaweiZhuang/xESMF Available on github]
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|[https://github.com/JiaweiZhuang/xESMF Available on Github]
  
 
|-valign="top"
 
|-valign="top"
 
|[[User:darothen|Daniel Rothenberg]]
 
|[[User:darothen|Daniel Rothenberg]]
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|[[#xbpch|xbpch]]: Backend for reading bpch output into [http://xarray.pydata.org xarray]/[http://dask.pydata.org dask]
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|[https://xbpch.readthedocs.io/en/latest/ xbpch]: Backend for reading bpch output into [http://xarray.pydata.org xarray]/[http://dask.pydata.org dask]
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|[https://github.com/darothen/xbpch Available on github]
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|[https://github.com/darothen/xbpch Available on Github]
  
 
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#[[#PseudoNetCDF|PseudoNetCDF]]: a NetCDF like system including visualization (maps, profiles, timeseries, etc)
 
#[[#PseudoNetCDF|PseudoNetCDF]]: a NetCDF like system including visualization (maps, profiles, timeseries, etc)
 
#[[#Process analysis diagnostics|Process analysis diagnostics]]: A tool for examining the change in each species due to each process and reaction.  
 
#[[#Process analysis diagnostics|Process analysis diagnostics]]: A tool for examining the change in each species due to each process and reaction.  
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|[https://github.com/barronh/pseudonetcdf Available on github]
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|[https://github.com/barronh/pseudonetcdf Available on Github]
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|[https://github.com/frodre Andre Perkins]
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|[https://github.com/frodre/pyEnsemble pyEnsemble]: This code is useful for running ensembles of GEOS-Chem adjoint model simulations within an MPI environment.
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|[https://github.com/frodre/pyEnsemble Available on Github]
  
 
|}
 
|}
  
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== Tutorials ==
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== Core Python packages for Earth Science data ==
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For the most part, you don't need to use a lot of Python packages to read and plot GEOS-Chem data.  For example, the [[#GCPy|GCPy]] package mostly relies on the following packages, which can be downloaded with either PyPI and/or Conda.
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*[http://xarray.pydata.org/en/stable/ xarray]: For reading netCDF, HDF5, GRIB, etc. data into a common data structure for later manipulation
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*[https://matplotlib.org/ matplotlib]: For general plotting operations
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*[https://scitools.org.uk/cartopy/docs/latest/ cartopy]: For plotting data on world maps
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*[http://www.numpy.org/ numpy]: For math operations
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*[https://xesmf.readthedocs.io/en/latest/ xESMF]: For regrididdng between cubed-sphere to lat-lon grids
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*[https://pandas.pydata.org/ pandas]: For spreadsheet-like data analysis
  
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If you are new to Python, we strongly recommend that you take our GEOS-Chem Python tutorial.  It will walk you though the steps of creating sample plots from GEOS-Chem output:
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== Python tutorials and resources ==
  
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*[https://github.com/geoschem/GEOSChem-python-tutorial]
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If you are new to Python, we strongly recommend that you take our [https://github.com/geoschem/GEOSChem-python-tutorial '''GEOS-Chem Python Tutorial'''].  It will walk you though the steps of creating sample plots from GEOS-Chem output:
  
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You may also find these tutorials useful:
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You may also find these resources useful:
  
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*[http://www.python.org Python.org]: Main site for all things Python
 
*[https://developers.google.com/edu/python/ Google's Python course]
 
*[https://developers.google.com/edu/python/ Google's Python course]
 
*[http://docs.python.org/3/tutorial/ Python 3 tutorial]
 
*[http://docs.python.org/3/tutorial/ Python 3 tutorial]
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*[http://learnpythonthehardway.org/book/ ''Learn Python the hard way'' book]
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*[https://www.geeksforgeeks.org/python-programming-language/ GeeksForGeeks Python page]
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*[http://wiki.python.org/moin/BeginnersGuide/Programmers PythonWiki.org: List of tutorials and resources]
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*[https://developers.google.com/edu/python/ Google's Python tutorial]
  
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For the most part, you don't need to use a lot of Python packages to read and plot GEOS-Chem data.  For example, GCPy package mostly relies on [http://xarray.pydata.org/en/stable/ xarray] (to read netCDF data), [https://matplotlib.org/ matplotlib] and [https://scitools.org.uk/cartopy/docs/latest/ cartopy] (to plot data), [http://www.numpy.org/ numpy] (for math operations) and [https://xesmf.readthedocs.io/en/latest/ xESMF] (to regrid between cubed-sphere to lat-lon grids).
 
  
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:15, 14 June 2019 (UTC)
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----
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'''''[[GEOS-Chem_diagnostic_output_files|Previous]] | [[GEOS-Chem_coding_and_debugging|Next]] | [[Getting Started with GEOS-Chem]]'''''

Latest revision as of 17:00, 31 August 2021

Previous | Next | Getting Started with GEOS-Chem

  1. Minimum system requirements
  2. Installing required software
  3. Configuring your computational environment
  4. Downloading source code
  5. Downloading data directories
  6. Creating run directories
  7. Configuring runs
  8. Compiling
  9. Running
  10. Output files
  11. Python tools for use with GEOS-Chem
  12. Coding and debugging
  13. Further reading


On this page, we provide information about free and open-source Python-language tools for visualizing or analyzing GEOS-Chem data.

GCPy

The GEOS-Chem Support Team develops GCPy, which is a Python-based toolkit containing useful functions and routines for working with GEOS-Chem. GCPy builds upon the well-established scientific python technical stack, leveraging tools like cartopy and xarray to simplify the task of working with model output and performing atmospheric chemistry analyses. GCPy features several plotting and tabling functions, and also supports regridding GEOS-Chem NetCDF files between the grid formats used in GEOS-Chem Classic and GCHP.

Full GCPy documentation is available at gcpy.readthedocs.io.

Third-party Python tools

Several third-party Python packages have been developed for GEOS-Chem. If you are interested in using any of these, we recommend that you follow up with the developers directly. The GEOS-Chem Support Team is not responsible for maintaining these tools.

Developer Packages/Description Status
Jiawei Zhuang
(since taken over by Pangeo) 		xESMF: A universal regridder. Leverages ESMF's regridding capabilities to easily regrid data between lon-lat and cubed-sphere grids. Other grids are supported as well. Available on Github
Daniel Rothenberg xbpch: Backend for reading bpch output into xarray/dask Available on Github
Barron Henderson Several software packages, including:
  1. PseudoNetCDF: a NetCDF like system including visualization (maps, profiles, timeseries, etc)
  2. Process analysis diagnostics: A tool for examining the change in each species due to each process and reaction.
Available on Github
Andre Perkins pyEnsemble: This code is useful for running ensembles of GEOS-Chem adjoint model simulations within an MPI environment. Available on Github

Core Python packages for Earth Science data

For the most part, you don't need to use a lot of Python packages to read and plot GEOS-Chem data. For example, the GCPy package mostly relies on the following packages, which can be downloaded with either PyPI and/or Conda.

  • xarray: For reading netCDF, HDF5, GRIB, etc. data into a common data structure for later manipulation
  • matplotlib: For general plotting operations
  • cartopy: For plotting data on world maps
  • numpy: For math operations
  • xESMF: For regrididdng between cubed-sphere to lat-lon grids
  • pandas: For spreadsheet-like data analysis

Python tutorials and resources

If you are new to Python, we strongly recommend that you take our GEOS-Chem Python Tutorial. It will walk you though the steps of creating sample plots from GEOS-Chem output:

You may also find these resources useful:


Previous | Next | Getting Started with GEOS-Chem

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