combine_by_coords could use allclose instead of equal to compare coordinates
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 4.2k
- Forks
- 1.4k
- Avg merge
- 2d 15h
- Merged PRs (30d)
- 14
Description
Is your feature request related to a problem? Please describe.
When a coordinate in different dataset / netcdf files has slightly different values, combine_by_coords considers the coordinate are different and attempts a concatenation of the coordinates.
Concretely, I produce netcdf with (lat, lon, time) coordinates, annually. Apparently the lat is not the same in all the files (difference is 1e-14), which I suspect is due to different pyproj version used to produce the lon,lat grid. Reprocessing all the annual netcdf is not an option. When using open_mfdataset on these netcdf, the lat coordinate is concatenated which leads to a MemoryError in my case.
Describe the solution you'd like
Two options:
-
add a coord_tolerance argument to xr.combine_by_coords and use np.allclose to compare the coordinates. In line 69 combine.py the comparison uses strict equality "if not all(index.equals(indexes[0]) for index in indexes[1:]):". This does not break the compatibility because coord_tolerance=0 should be the default.
-
add an argument to explicity list the coordinates to NOT concatenate. I tried to play with the coords argument to solve my problem, but was not succesfull.
Describe alternatives you've considered
- I certainly could find a workaround for this specific case, but I often had issue with the magic in combine_by_coords, and imho adding more control by the user would be useful in general.
Additional context
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start in combine.py at the comparison around line 69 and trace how combine_by_coords decides whether coordinates can be concatenated. Reproduce the near-equal-coordinate case described for open_mfdataset, then compare the two proposed API approaches and their default behavior. Done means the chosen option handles tiny coordinate differences without changing strict-comparison behavior by default.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- numpy, python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100