Python for Earth Sciences

Instructor: Rebekah Esmaili

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A crash course in Python focusing on reading and visualizing data-sets used in Earth sciences.

This code is interactive! Click:

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Getting Started

This workshop will cover:

• Launching Jupyter Notebooks
• Working with arrays using the Numpy package
• Importing text datasets using the Pandas package
• Creating simple graphics with Matplotlib
• Importing scientific data formats, such as netCDF and GRIB2
• Creating maps from datasets

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Installation requirements

"I am really new to Python!"

• I recommend launching binder, which is a "cloud version" of this course. No installation required!

• Need help with Binder? Video tutorial on YouTube.

"I have used Python before!"

• If you wish to run the examples locally, I recommend installing Anaconda. If you are having trouble with your installation, contact the instructor before the course or use binder.

• Need help installing Anaconda? Video tutorial on YouTube.

• Download the contents of the GitHub repository to your computer.

• Launch Jupyter Notebooks from the Anaconda Navigator. This will open a window in your default browser. Navigate to the folder that contains the notebooks (*.ipynb) and click on the tutorial for the day.

• New to Jupyter? Here's a video tutorial on YouTube.

• Additional packages:

  • Launch the Anaconda Prompt (Windows) or Terminal (MacOS/Linux). Then copy/paste and hit enter:

    conda install -c conda-forge cartopy
    conda install -c conda-forge netCDF4
    conda install -c conda-forge xarray
    conda install -c conda-forge pygrib
    

  • If there are no errors, then you are set-up!
  • Alternatively, if you are familiar with environments, you can use the environments.yml to install the necessary packages. You can do this in the terminal using:

  conda env create -f environment.yml
  

  Then, switch to the new environment (conda activate python-workshop) once the installation is complete.

I do not recommend:

• Using Python on a remote server for this tutorial (I cannot help troubleshoot)
• Using your operating system's Python or a shared Python installations unless you are advanced!

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Course Philosophy

• Increase accessibility of satellite data and analysis
• Teach Python using practical examples and real-world datasets
• Promote reproducible and transparent scientific research

Resources

Packages and Tutorials

Pandas

• Short Introduction: https://pandas.pydata.org/pandas-docs/stable/getting_started/10min.html
• Cookbook for more details: https://pandas.pydata.org/pandas-docs/stable/user_guide/cookbook.html#cookbook

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Matplotlib

• Pyplot Tutorial: https://matplotlib.org/3.1.1/tutorials/introductory/pyplot.html

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Reading self describing file

• NETCDF
  • Detailed tutorial on the netCDF4 package: https://unidata.github.io/netcdf4-python.
  • Xarray tutorial: https://xarray-contrib.github.io/xarray-tutorial/
• HDF files
  • The package h5py is similar to netcdf4.
  • User manual at http://docs.h5py.org/en/stable/.
  • Xarray can also open HDF files!
• GRIB/GRIB2 files
  • World Meteorology Association standard format, e.g. commonly used with weather-related models like ECMWF and GFS.
  • Can be opened using pygrib.
  • Example usage at https://jswhit.github.io/pygrib/docs/.
• BUFR
  • Another common table-driven format.
  • Open with python-bufr, part of the pytroll project.

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General Python resources

Beginner Tutorials

* Youtube series for absolute beginners [CS Dojo](https://www.youtube.com/watch?v=Z1Yd7upQsXY&list=PLBZBJbE_rGRWeh5mIBhD-hhDwSEDxogDg)

* [Research Software Engineering with Python](https://merely-useful.tech/py-rse/) Free eBook to enhance your workflow.

Intermediate Tutorials

* Last year's workshop, [Python for Earth Science with Rebekah](https://youtube.com/playlist?list=PLlcgQ3Rl-9fR4oOmfeKPKHuk2Lj57bNJy), is available online. I'll upload this one once available.

* [Python for Climate and Meteorology](https://www.youtube.com/watch?v=uQZAEPnUZ5o) Another tutorial taught at AMS, a little more advanced.

* Learn more about [Python for Atmosphere and Ocean Scientists](https://carpentries-lab.github.io/python-aos-lesson/) using Software Carpentry lesson plans.

* [Earth Observation using Python](https://www.wiley.com/en-us/Earth+Observation+using+Python%3A+A+Practical+Programming+Guide-p-9781119606888) is a book I wrote that builds on the content of the workshop.

Acknowledgements

Special thanks to past contributors, Kriti Bhargava and Eviatar Bach!