assign_fix_coords.md

I was delighted to learn that flexible coordinates in xarray are fully operational.

Following on from this (unfinished) blog post on unnecessary netcdf longlat coordinates, I now have a neat xarray/netcdf native fix for the problem I was discussing, it is a direct match to the "parse_coordinates": False example in the xarray indexes gallery.

This only a few weeks ago was challenging for me to present to non-R audiences, so I'm very excited that we can now fix these broken grids in a way more accessible to Python communities. Degenerate coordinates represent a huge entropy problem in array metadata, and (I think) we need a coordinated effort to be able to easily assign a fix

(like in GDAL with vrt://{dsn}?a_gt=c,a,b,f,d,e) and have that knowledge also feed back up to the providers to stem the flow of problematic coordinates.

from affine import Affine
from rasterix import RasterIndex
import xarray

## this dataset has poorly formed coordinates, unnecessary and messily generate lonlat arrays
ds = xarray.open_dataset("https://zenodo.org/records/7327711/files/CS2WFA_25km_201007.nc?download=1", engine = "h5netcdf")

## so let's fix them
transform = Affine.from_gdal(-3950000, 25000, 0, 4350000, 0, -25000)
shape = ds.sea_ice_concentration.shape
ds = ds.assign_coords(xarray.Coordinates.from_xindex(RasterIndex.from_transform(transform, width=shape[2], height=shape[1])))
ds["lon"] = None
ds["lat"] = None

ds

<xarray.Dataset> Size: 3MB
Dimensions:                (time: 1, y: 332, x: 316)
Coordinates:
  * time                   (time) object 8B 2010-07-01 00:00:00
  * x                      (x) float64 3kB -3.938e+06 -3.912e+06 ... 3.938e+06
  * y                      (y) float64 3kB 4.338e+06 4.312e+06 ... -3.938e+06
Data variables:
    lat                    object 8B None
    lon                    object 8B None
    snow_freeboard         (time, y, x) float64 839kB ...
    ice_freeboard          (time, y, x) float64 839kB ...
    snow_depth             (time, y, x) float64 839kB ...
    sea_ice_concentration  (time, y, x) float64 839kB ...
Indexes:
  ┌ x        RasterIndex (crs=None)
  └ y
Attributes:
    title:        Antarctic sea ice physical properties obtained from CryoSat...
    institution:  NASA GSFC Cryospheric Sciences Laboratory and University of...
    history:      File created on November 15, 2022, 12:09:06

I'm not yet able to set the crs above yet, but I'm sure that's as easy to do.

mdsumner/assign_fix_coords.md