Model agnostic tutorial #226

aidanheerdegen · 2023-01-24T04:44:40Z

Model agnostic tutorial using x-array and pint closes #211

…example

review-notebook-app · 2023-01-24T04:44:45Z

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Tutorials/Model_Agnostic_Analysis.ipynb

angus-g

Don't need explorer tools changes? Plus we can be a tidier with operations rather than going all the way through dimension names.

aidanheerdegen · 2023-01-24T05:52:40Z

Don't need explorer tools changes? Plus we can be a tidier with operations rather than going all the way through dimension names.

I don't think I understand.

angus-g · 2023-01-24T06:30:00Z

Just that you've also modified the explorer tools notebook in this PR! Not sure if that was intentional?

aidanheerdegen · 2023-01-24T06:56:44Z

Just that you've also modified the explorer tools notebook in this PR! Not sure if that was intentional?

Ah no. I did see that, but just assumed it was the change from the other PR. Will fix.

Plus we can be a tidier with operations rather than going all the way through dimension names.

In this notebook? If so, I don't understand.

angus-g · 2023-01-24T06:58:05Z

In this notebook? If so, I don't understand.

Was referring to the cf accessor, couldn't think of what to call it! You got what I meant anyway 😁 All good

aidanheerdegen · 2023-01-24T07:00:33Z

You got what I meant anyway 😁 All good

Ahh .. yeah, once you pointed it out I took a look, very neat!

Do you know off hand the limits of the method wrapping/translation? I think it is probably noting that it is worth using, but maybe won't work for more exotic functions .. or maybe it does work with everything?

angus-g · 2023-01-24T07:03:59Z

Do you know off hand the limits of the method wrapping/translation?

Not sure how it works actually, I think the intention is for it to work everywhere in xarray at least, and if something doesn't work it's a bug on their end. I'd say it's a safe bet to drop in to any method requiring a dimension argument.

aidanheerdegen · 2023-01-24T07:04:37Z

I initially tried also with some ice data, but the multiple grids are a bit annoying. I've realised I can fix that pretty easily, so I think I'll add an ice example as well, just to show it is possible and quite flexible.

navidcy · 2023-01-24T22:39:46Z

okie! some sea ice vars would be great to have here also!
happy to have a look at the notebook! @aidanheerdegen ping me when you are happy for me to do that.

edoddridge · 2023-01-24T23:00:14Z

This looks great! Can't wait to see the ice addition.

aidanheerdegen · 2023-01-25T04:21:16Z

Okey done. I've added an ice example. It is ugly because the coordinates etc in the ice files are terrible. I don't really like the "now do some barely explained magic" but this isn't a tutorial about fixing ice coordinate data so I haven't dwelt on it. Didn't want to take away from the message.

I kept all the errors in to hopefully show how problems like that can be understood and overcome. Hope you like it @edoddridge

navidcy · 2023-01-25T04:28:09Z

The coordinates in ice files are terrible. I am voicing this also. I'm glad somebody finally had the courage to admit this in public!

angus-g · 2023-01-25T04:58:17Z

That ice business seems like a bug, cf_xarray only forgets about the specific coordinates after the mean:

In [21]: d.Tair_m.cf
Out[21]: 
Coordinates:
- CF Axes:   X, Y, Z, T: n/a

- CF Coordinates:   longitude: ['TLON']
                    latitude: ['TLAT']
                    vertical, time: n/a

- Cell Measures:   area, volume: n/a

- Standard Names:   n/a

- Bounds:   n/a

In [22]: d.Tair_m.mean("time").cf
Out[22]: 
Coordinates:
- CF Axes:   X, Y, Z, T: n/a

- CF Coordinates:   longitude: ['TLON', 'ULON']
                    latitude: ['TLAT', 'ULAT']
                    vertical, time: n/a

- Cell Measures:   area, volume: n/a

- Standard Names:   n/a

- Bounds:   n/a

I've raised this as a bug xarray-contrib/cf-xarray#396

aidanheerdegen · 2023-01-25T05:06:54Z

That ice business seems like a bug, cf_xarray only forgets about the specific coordinates after the mean

Nice pick-up Angus. I'll change the wording.

dcherian · 2023-01-25T19:28:58Z

Hi 👋

I came over from the cf-xarray bug report and just wanted to say this is very cool to see.

When this notebook goes live, we'd appreciate a PR linking to it from our docs.

Our current ocean model demo really emphasizes the vertical aspect, so this would be a nice complement

navidcy · 2023-01-25T20:02:16Z

Hi @dcherian! That’s great to hear! :)

review-notebook-app · 2023-01-25T21:06:22Z

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navidcy commented on 2023-01-25T21:06:22Z
----------------------------------------------------------------

SST_time_mean.cf.plot(ax=ax,
                      x='longitude', y='latitude', 
                      transform=ccrs.PlateCarree(),
                      vmin=-2, vmax=30, extend='both',
                      cmap=cm.cm.thermal)

aidanheerdegen commented on 2023-01-26T01:57:17Z
----------------------------------------------------------------

This is to align indentation?

review-notebook-app · 2023-01-25T21:06:23Z

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navidcy commented on 2023-01-25T21:06:23Z
----------------------------------------------------------------

    da_time_mean.cf.plot(ax=ax,
                         x='longitude', y='latitude', 
                         transform=ccrs.PlateCarree(),
                         vmin=-2, vmax=30, extend='both',
                         cmap=cm.cm.thermal)

aidanheerdegen commented on 2023-01-26T01:57:30Z
----------------------------------------------------------------

And this too I guess?

review-notebook-app · 2023-01-25T21:06:24Z

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navidcy commented on 2023-01-25T21:06:23Z
----------------------------------------------------------------

Line #1.    ice_air_temp = ice_air_temp.drop_vars(['ULON', 'ULAT'])

review-notebook-app · 2023-01-25T21:06:25Z

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navidcy commented on 2023-01-25T21:06:24Z
----------------------------------------------------------------

Line #1.    ice_grid = xr.open_dataset('/g/data/ik11/inputs/access-om2/input_eee21b65/cice_025deg/grid.nc').rename({'ny': 'nj', 'nx': 'ni'})

review-notebook-app · 2023-01-25T21:06:26Z

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navidcy commented on 2023-01-25T21:06:25Z
----------------------------------------------------------------

    da_time_mean.cf.plot(ax=ax,
                         x='longitude', y='latitude', 
                         transform=ccrs.PlateCarree(),
                         vmin=vmin, vmax=vmax, extend='both',
                         cmap=cm.cm.thermal)

navidcy

@aidanheerdegen this is great! Two comments, don't feel that you need to act on them:

The notebook demonstrates also things that won't work so some cells fail on purpose. This, I presume, will make this tutorial not a good candidate for the automatic testing workflow.
I'm not sure if defining functions that plot is a good strategy as they are not so re-usable. I generally prefer to define a function that will do the conversions/transformations on the data array and then have another one that plots. But I feel that's a personal preference...

aidanheerdegen · 2023-01-26T00:16:51Z

Hi @dcherian,

Thanks for stopping by, but even more thanks for the great work you've done developing this and other tools. Much appreciated.

When this notebook goes live, we'd appreciate a PR linking to it from our docs.

Our current ocean model demo really emphasizes the vertical aspect, so this would be a nice complement

Sure thing. I'll make a PR to add it to your examples.

TBH I'd been telling people to use cf-xarray for ages, but hadn't had an opportunity to use it properly until now, and it is even more transformative than I had realised. It is a great tool.

navidcy · 2023-01-26T00:18:40Z

I admit, I've been hearing @aidanheerdegen saying this for ages but when I saw the tutorial it was when I really listened.

aidanheerdegen · 2023-01-26T01:57:19Z

This is to align indentation?

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aidanheerdegen · 2023-01-26T01:57:31Z

And this too I guess?

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aidanheerdegen · 2023-01-26T04:44:18Z

Ok, fixed all those formatting suggestions, and found a couple of other typos. I don't have merge permissions @navidcy. Can you do it. Squash the whole thing into a single commit.

dcherian · 2023-01-26T04:55:42Z

Thanks for the kind words!

Please open issues for any features you might find useful.

navidcy · 2023-01-26T04:58:40Z

And this too I guess?

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Yeap, it was to align the indentation so my OCD eyes are not triggered.

navidcy · 2023-01-26T04:59:39Z

@angus-g the PR needs your approval? are you happy?

aidanheerdegen · 2023-01-26T05:53:12Z

@angus-g the PR needs your approval? are you happy?

I'm pretty sure he was ok with it, should be fine to merge

#226 (comment)

navidcy · 2023-01-26T05:56:52Z

Done! :) Open the PR at cf-xarray?

aidanheerdegen · 2023-01-26T06:02:01Z

Done! :) Open the PR at cf-xarray?

In hand

access-hive-bot · 2023-01-27T03:26:52Z

This pull request has been mentioned on ACCESS Hive Community Forum. There might be relevant details there:

https://forum.access-hive.org.au/t/cosima-hackathon-v2-0-tuesday-january-24th-2023/307/46

aidanheerdegen added 3 commits January 23, 2023 16:28

Explorer tools: Update with latest kernel and save widget state

d2b4b6f

Initial commit of model agnostic notebook. Including non-working ice …

1bbdd83

…example

Added function and MOM6 example

fd53401

angus-g reviewed Jan 24, 2023

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Change to wrapped functions

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Revert Explorer Tools changes

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navidcy added the 📔 tutorial label Jan 24, 2023

navidcy assigned aidanheerdegen Jan 24, 2023

navidcy added MOM5+MOM6 ❤️ 💻 hackathon 2.0 like the 1.0 but better labels Jan 24, 2023

Add ice data example

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aidanheerdegen requested a review from angus-g January 25, 2023 04:36

Add comments about cf_xarray bug

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navidcy approved these changes Jan 25, 2023

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aidanheerdegen added 4 commits January 26, 2023 15:21

Fix code formatting

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More fixing code formatting

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Fix typo

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Fix typo

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navidcy self-requested a review January 26, 2023 04:57

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navidcy merged commit b855641 into master Jan 26, 2023

navidcy deleted the aidanheerdegen/issue-211 branch January 26, 2023 05:55

aidanheerdegen mentioned this pull request Jan 26, 2023

Add link to COSIMA Recipes model agnostic tutorial xarray-contrib/cf-xarray#397

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aidanheerdegen mentioned this pull request Jan 27, 2023

Update model agnostic tutorial when cf_xarray issue is resolved #237

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Model agnostic tutorial #226

Model agnostic tutorial #226

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