{"action":"created","issue":{"url":"https://api.github.com/repos/pangeo-data/pangeo-example-notebooks/issues/11","repository_url":"https://api.github.com/repos/pangeo-data/pangeo-example-notebooks","labels_url":"https://api.github.com/repos/pangeo-data/pangeo-example-notebooks/issues/11/labels{/name}","comments_url":"https://api.github.com/repos/pangeo-data/pangeo-example-notebooks/issues/11/comments","events_url":"https://api.github.com/repos/pangeo-data/pangeo-example-notebooks/issues/11/events","html_url":"https://github.com/pangeo-data/pangeo-example-notebooks/issues/11","id":355406064,"node_id":"MDU6SXNzdWUzNTU0MDYwNjQ=","number":11,"title":"render MOM6 example with correct mesh geometry","user":{"login":"rabernat","id":1197350,"node_id":"MDQ6VXNlcjExOTczNTA=","avatar_url":"https://avatars1.githubusercontent.com/u/1197350?v=4","gravatar_id":"","url":"https://api.github.com/users/rabernat","html_url":"https://github.com/rabernat","followers_url":"https://api.github.com/users/rabernat/followers","following_url":"https://api.github.com/users/rabernat/following{/other_user}","gists_url":"https://api.github.com/users/rabernat/gists{/gist_id}","starred_url":"https://api.github.com/users/rabernat/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rabernat/subscriptions","organizations_url":"https://api.github.com/users/rabernat/orgs","repos_url":"https://api.github.com/users/rabernat/repos","events_url":"https://api.github.com/users/rabernat/events{/privacy}","received_events_url":"https://api.github.com/users/rabernat/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-08-30T03:02:28Z","updated_at":"2018-09-03T21:51:35Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"Currently the MOM6 example by @gustavo-marques shows maps like this\r\n\r\n![image](https://user-images.githubusercontent.com/1197350/44826994-139e5380-abdf-11e8-8371-52293004987c.png)\r\n\r\n@adcroft correctly pointed out that these are not the correct coordinates. We should be creating an irregular QuadMesh. This is apparently possible with holoviews / geoviews\r\n- http://holoviews.org/reference/elements/bokeh/QuadMesh.html\r\n- http://geo.holoviews.org/gallery/bokeh/xarray_quadmesh.html\r\n\r\nThis example from geoviews in particular looks like what we want.\r\n![image](https://user-images.githubusercontent.com/1197350/44827045-506a4a80-abdf-11e8-8b01-f1c85e7ce3ab.png)\r\n\r\nHowever, the current MOM6 zarr dataset doesn't even have the geographic coordinates in it.\r\n```\r\n<xarray.Dataset>\r\nDimensions:     (Time: 7300, nv: 2, xh: 540, xq: 540, yh: 458, yq: 458)\r\nCoordinates:\r\n  * Time        (Time) int64 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 ...\r\n  * nv          (nv) float64 1.0 2.0\r\n  * xh          (xh) float64 -286.7 -286.0 -285.3 -284.7 -284.0 -283.3 ...\r\n  * xq          (xq) float64 -286.3 -285.7 -285.0 -284.3 -283.7 -283.0 ...\r\n  * yh          (yh) float64 -79.2 -79.08 -78.95 -78.82 -78.69 -78.56 -78.43 ...\r\n  * yq          (yq) float64 -79.14 -79.01 -78.89 -78.76 -78.63 -78.49 ...\r\nData variables:\r\n    SSH         (Time, yh, xh) float32 dask.array<shape=(7300, 458, 540), chunksize=(365, 458, 540)>\r\n    SSS         (Time, yh, xh) float32 dask.array<shape=(7300, 458, 540), chunksize=(365, 458, 540)>\r\n    SST         (Time, yh, xh) float32 dask.array<shape=(7300, 458, 540), chunksize=(365, 458, 540)>\r\n    Time_bnds   (Time, nv) float64 dask.array<shape=(7300, 2), chunksize=(7300, 2)>\r\n    average_DT  (Time) float64 dask.array<shape=(7300,), chunksize=(7300,)>\r\n    average_T1  (Time) float64 dask.array<shape=(7300,), chunksize=(7300,)>\r\n    average_T2  (Time) float64 dask.array<shape=(7300,), chunksize=(7300,)>\r\n    ePBL_h_ML   (Time, yh, xh) float32 dask.array<shape=(7300, 458, 540), chunksize=(365, 458, 540)>\r\nAttributes:\r\n    associated_files:  area_t: g.c2b6.GNYF.T62_t061.control.004.mom6.static.nc\r\n    filename:          g.c2b6.GNYF.T62_t061.control.004.mom6.sfc.day._0001_00...\r\n    grid_tile:         N/A\r\n    grid_type:         regular\r\n    title:             MOM6 g.c2b6.GNYF.T62_t061.control.004 Experiment\r\n```\r\n\r\nSo before we can fix the plot, we need to fix the data. @gustavo-marques, could you add the lat / lon coordinates? You can just upload the directories to the existing zarr group and it should \"just work\". (A lot easier than adding a variable to a netCDF file!)\r\n"},"comment":{"url":"https://api.github.com/repos/pangeo-data/pangeo-example-notebooks/issues/comments/418197285","html_url":"https://github.com/pangeo-data/pangeo-example-notebooks/issues/11#issuecomment-418197285","issue_url":"https://api.github.com/repos/pangeo-data/pangeo-example-notebooks/issues/11","id":418197285,"node_id":"MDEyOklzc3VlQ29tbWVudDQxODE5NzI4NQ==","user":{"login":"gustavo-marques","id":11339137,"node_id":"MDQ6VXNlcjExMzM5MTM3","avatar_url":"https://avatars0.githubusercontent.com/u/11339137?v=4","gravatar_id":"","url":"https://api.github.com/users/gustavo-marques","html_url":"https://github.com/gustavo-marques","followers_url":"https://api.github.com/users/gustavo-marques/followers","following_url":"https://api.github.com/users/gustavo-marques/following{/other_user}","gists_url":"https://api.github.com/users/gustavo-marques/gists{/gist_id}","starred_url":"https://api.github.com/users/gustavo-marques/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gustavo-marques/subscriptions","organizations_url":"https://api.github.com/users/gustavo-marques/orgs","repos_url":"https://api.github.com/users/gustavo-marques/repos","events_url":"https://api.github.com/users/gustavo-marques/events{/privacy}","received_events_url":"https://api.github.com/users/gustavo-marques/received_events","type":"User","site_admin":false},"created_at":"2018-09-03T21:51:35Z","updated_at":"2018-09-03T21:51:35Z","author_association":"NONE","body":"I've 2D added lon/lat arrays, but open_zarr interprets them as variables:\r\n\r\n![image](https://user-images.githubusercontent.com/11339137/45002092-5621b080-af90-11e8-8b68-eb2f1fe91d96.png)\r\n\r\nI tried append/concat, but this is still an open [issue](https://github.com/pydata/xarray/issues/2022). @rabernat, any ideas?\r\n\r\nAnother approach is to follow @adcroft 's suggestion, but for that I will have to re-run the model since the original data has been purged.  "}}
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