One of my worries about leaving academia is to see the programmatic core of my work disappear in the vast graveyard of undocumented methodologies. This was one of my motivations to, earlier this year, publish the first versions of hyoga, a Python library to plot results from numerical ice sheet models.
Tip: Hyōga (氷河) is the Japanese word for glacier (lit. ice river).
A bit of history
My beginnings with Python
In the spring of 2011, I was at a turning point in my doctoral studies. I had been a Ph.D. student at Stockholm University for more than a year, yet I had achieved little besides taking some of the necessary courses for my diploma. My project was moving very much too slow and, even more importantly in hindsight, it was boring. I came to my advisors with a bold proposition, to essentially dump all the methodological work I’d done thus far, and to start over with a different code. For the second time.
My advisors gave me two weeks to attempt the ambitious move. Within the first week, I could compile the Parallel Ice Sheet Model (PISM, the code we had settled on) on my office workstation, and to make it run. PISM produced a netCDF file, a totally new format for me at the time. Since I had a vague notion that netCDF was somewhat standard in the climate sciences, I asked an oceanographer friend what to do. He recommended Python, pointed me to the beautiful example gallery on the matplotlib website (much smaller at that time), and gave me a fifty-line Python code he’d used on his files. Another week later, I had my first Python script, my first plots, and my first PhD results. They were faulty, and I was certainly not at the end of my pains. But without knowing it, I had built the foundations for a workflow I have used and improved continuously to this day.
Towards an object-oriented library
Two years later, I was working hard on my first scientific publications and found that I was often re-using the same pieces of code in my figure scripts. So came the idea for an object-oriented ice-sheet-model plotting library. I began developing an extension on the python-netcdf4 Dataset class in a little Python 2 package called iceplotlib, which has been used with more or less success by some of my co-workers. Soon, however, the little work I had done became very, very largely outpaced by the powerful new additions to the growing Python geoscience ecosystem such as cartopy, pandas, dask, and xarray. One day I made the move to xarray, and gave up developing iceplotlib.
Fast-forward to late 2019, as I was looking for a new academic position, a new library building upon these tools imposed itself as the evident technical ground for future research work. However, science proposals for that work were rejected, and I abandoned the idea again for several months. It is only in early 2021, as new openings fueled once more my hopes to get back to research, and to perhaps rejoin academia, that I decided to get going anyway, and to develop hyoga even without funding, as a hobby. Hyoga’s first version (v0.1) was finally released on March 1st, 2021, exactly a year after my last, pre-pandemic, position ended.
Passing the baton
Today, my motivations to continue development work on hyoga have changed. As I see my chance to remain in academia on the long run diminish, I have decided to face the underlying fear that all the methodological work that I’ve done may be lost. A fear which, paradoxically, also prevents me from fully leaving research work and moving on to new things. While my research results have been published in academic journals, I’ve arguably done comparatively little so far to ensure their reproducibility, and their applicability to other regions. Hyoga is thus my attempt to leave more than a few obscure articles (and undocumented code) to the younger generation of scientific programmers.
Warning: hyoga is being developed slowly, on an entirely voluntary basis, and comes with absolutely no warranty. As you could read above, so far all my attempts to get (research) funds have failed. It’s actually worse: I have not even received feedback on any of my proposals. Suggestions would be greatly appreciated.
Using hyoga
Installation
Hyoga works as a thin wrapper around the very powerful Python package xarray. So far, the library has only been tested on output files from the Parallel Ice Sheet Model (PISM). However, the code follows Climate and Forecast (CF) conventions, so that it should in principle work with any CF-compliant ice sheet models. Starting with the next version (v0.2), this functionality will be assured by the separate package cf_xarray.
While hyoga’s plotting capabilities are still limited, getting started with it should be relatively straightforward. Hyoga is on PyPI and I recommend to install it via:
pip install hyoga
The latest development source code is also available on Github, where I invite you to please report bugs and potentially missing dependencies.
Getting started
Given a two-dimensional netCDF filename following the CF conventions and containing, in this case, ice thickness and ice surface altitude variables, plotting model output data should be as as easy as:
import hyoga
import xarray as xr
# open data file
with xr.open_dataset('filename.nc') as ds:
ds = ds.hyoga.where_thicker(1)
# plot model output
ds.hyoga.plot.bedrock_altitude(vmin=0, vmax=4500)
ds.hyoga.plot.ice_margin(facecolor='tab:blue')
Many more plotting methods are available. To learn more about them, please take a look at the online documentation and particularly the matplotlib-style examples gallery.
Plotting interpolated results
One currently available functionality of hyoga is to interpolate two-dimensional ice-sheet model results onto a higher resolution topography. This follows the method I have used to produce detailed animations of Alpine paleoglaciers for museums and education, such as the one included above. Once again, I invite you to take a look at the relevant examples in the gallery if interested about this functionality.
Tip: assign bedrock uplift first so that it is corrected for during interpolation.
