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- Multidimensional groupby · 27 ✖
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230796165 | https://github.com/pydata/xarray/pull/818#issuecomment-230796165 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIzMDc5NjE2NQ== | rabernat 1197350 | 2016-07-06T14:50:42Z | 2016-07-06T14:50:42Z | MEMBER | I just rebased and updated this PR. I have not resolved all of the edge cases, such as what to do about non-reducing groupby_bins operations that don't span the entire coordinate. Unfortunately merging @shoyer's fix from #875 did not resolve this problem, at least not in a way that was obvious to me. My feeling is that this PR in its current form introduces some very useful new features. For my part, I am eager to start using it for actual science projects. Multidimensional grouping is unfamiliar territory. I don't think every potential issue can be resolved by me right now via this PR--I don't have the necessary skills, nor can I anticipate every use case. I think that getting this merged and out in the wild will give us some valuable user feedback which will help figure out where to go next. Plus it would get exposed to developers with the skills to resolve some of the issues. By waiting much longer, we risk it going stale, since lots of other xarray elements are also in flux. Please let me know what you think. |
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224691235 | https://github.com/pydata/xarray/pull/818#issuecomment-224691235 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIyNDY5MTIzNQ== | rabernat 1197350 | 2016-06-08T18:51:37Z | 2016-06-08T18:51:37Z | MEMBER |
Should I try to merge your branch with my branch...or wait for your branch to get merged into master? |
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223934668 | https://github.com/pydata/xarray/pull/818#issuecomment-223934668 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIyMzkzNDY2OA== | rabernat 1197350 | 2016-06-06T11:36:02Z | 2016-06-06T11:36:02Z | MEMBER | @shoyer: I'm not sure this is as simple as a technical fix. It is a design question. With regular With In both cases, it is not obvious to me what should happen when calling |
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223817102 | https://github.com/pydata/xarray/pull/818#issuecomment-223817102 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIyMzgxNzEwMg== | rabernat 1197350 | 2016-06-05T14:47:12Z | 2016-06-05T14:47:12Z | MEMBER | @shoyer, @jhamman, could you give me some feedback on one outstanding issue with this PR? I am stuck on a kind of obscure edge case, but I really want to get this finished. Consider the following groupby operation, which creates bins which are finer than the original coordinate. In other words, some bins are empty because there are too many bins.
gives
If I try a reducing apply operation, e.g.
I get an error on the concat step
I'm really not sure what the "correct behavior" should even be in this case. It is not even possible to reconstitute the original data array by doing Do you have any thoughts / suggestions? I'm not sure I can solve this issue right now, but I would at least like to have a more useful error message. |
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221859813 | https://github.com/pydata/xarray/pull/818#issuecomment-221859813 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIyMTg1OTgxMw== | rabernat 1197350 | 2016-05-26T12:42:20Z | 2016-05-26T12:42:20Z | MEMBER | Just a little update--I realized that calling apply on multidimensional binned groups fails when the group is not reduced. For example
raises errors because of conflicting coordinates when trying to concat the results. I only discovered this when making my tutorial notebook. I think I know how to fix it, but I haven't had time yet. So it is moving along... I am excited about this feature and am confident it can make it into the next release. |
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220859076 | https://github.com/pydata/xarray/pull/818#issuecomment-220859076 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIyMDg1OTA3Ng== | rabernat 1197350 | 2016-05-22T21:59:05Z | 2016-05-22T21:59:05Z | MEMBER |
I disagree. I don't want to use the default dimensions as the x and y coords for the plot. I want to use the true lat / lon coords, which are
This would fail of course if you could only use 1d coords for plotting, so I definitely think we should keep the plot code as is for now (not raise an error). I am happy with this example for now. |
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220833788 | https://github.com/pydata/xarray/pull/818#issuecomment-220833788 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIyMDgzMzc4OA== | rabernat 1197350 | 2016-05-22T13:55:51Z | 2016-05-22T13:55:51Z | MEMBER | @jhamman, @clarkfitzg: I am working on an example notebook for multidimensional coordinates. In addition to the new groupby features, I wanted to include an example of a 2D pcolormesh using the Just doing the simplest possible thing, i.e.
gives me a slightly mangled plot:
Am I missing something obvious here? Seems somehow related to #781, #792. |
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220065292 | https://github.com/pydata/xarray/pull/818#issuecomment-220065292 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIyMDA2NTI5Mg== | rabernat 1197350 | 2016-05-18T15:33:45Z | 2016-05-18T15:33:45Z | MEMBER |
There is indeed basic documentation, but not a detailed tutorial of what these features are good for. For this, this dataset from @jhamman with a non-uniform grid would actually be ideal. The monthly-means example I think contains a reference to a similar dataset. How were the files in the doc/examples directory generated? |
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220029256 | https://github.com/pydata/xarray/pull/818#issuecomment-220029256 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIyMDAyOTI1Ng== | rabernat 1197350 | 2016-05-18T13:41:47Z | 2016-05-18T13:41:47Z | MEMBER |
I think this should wait for a future PR. It is pretty complicated. I think it would be better to get the current features out in the wild first and play with it a bit before moving forward.
It is resolved, but not tested. I'll add a test. |
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219847587 | https://github.com/pydata/xarray/pull/818#issuecomment-219847587 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIxOTg0NzU4Nw== | rabernat 1197350 | 2016-05-17T20:43:31Z | 2016-05-17T20:43:31Z | MEMBER | @shoyer, @jhamman: I'm pretty happy with where this is at. It's quite useful for a lots of things I want to do with xarray. Any more feedback? One outstanding issue involves some buggy behavior with |
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219262958 | https://github.com/pydata/xarray/pull/818#issuecomment-219262958 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIxOTI2Mjk1OA== | rabernat 1197350 | 2016-05-15T02:44:19Z | 2016-05-15T02:44:19Z | MEMBER | Just updated this to use the |
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219231243 | https://github.com/pydata/xarray/pull/818#issuecomment-219231243 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIxOTIzMTI0Mw== | rabernat 1197350 | 2016-05-14T17:00:33Z | 2016-05-14T17:00:33Z | MEMBER | This is a good question, with a simple answer (stack), but it doesn't belong on the the discussion for this PR. Open a new issue or email your question to the mailing list.
|
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219063079 | https://github.com/pydata/xarray/pull/818#issuecomment-219063079 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIxOTA2MzA3OQ== | rabernat 1197350 | 2016-05-13T14:41:43Z | 2016-05-13T14:41:43Z | MEMBER |
Why? This was in fact my original idea, but you encouraged me to use What about
|
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218756580 | https://github.com/pydata/xarray/pull/818#issuecomment-218756580 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIxODc1NjU4MA== | rabernat 1197350 | 2016-05-12T13:27:38Z | 2016-05-12T13:27:38Z | MEMBER | I suppose I should also add a test for non-monotonic multidimensional binning. |
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218756391 | https://github.com/pydata/xarray/pull/818#issuecomment-218756391 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIxODc1NjM5MQ== | rabernat 1197350 | 2016-05-12T13:26:58Z | 2016-05-12T13:26:58Z | MEMBER | @jhamman: My latest commit followed @shoyer's suggestion to fix the "non-monotonic" error. I successfully loaded your data and took a zonal average in 10-degree bins with the following code: ``` python
The only big remaining issue is the values of the new coordinate. Currently it is just using the labels output by We could either allow the user to specify labels by adding a
Please weigh in if you have an opinion about that. |
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218450849 | https://github.com/pydata/xarray/pull/818#issuecomment-218450849 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIxODQ1MDg0OQ== | rabernat 1197350 | 2016-05-11T12:56:47Z | 2016-05-11T12:56:47Z | MEMBER | @jhamman: Could you post [a slice of] your dataset for me to try?
The TODO comment was there when I started working on this. The error is raised by these lines
I'm not sure this check is necessary for binning. |
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208092684 | https://github.com/pydata/xarray/pull/818#issuecomment-208092684 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIwODA5MjY4NA== | rabernat 1197350 | 2016-04-10T23:39:29Z | 2016-04-10T23:39:29Z | MEMBER | @shoyer, @jhamman I think this is ready for a review There are two distinct features added here:
1. ``` python
I'm not sure this is the ideal behavior, since the categories are hard to slice. For my purposes, I would rather assign an integer or float index to each bin using e.g. the central value of the bin. note: Both of these features have problems when used with |
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207983237 | https://github.com/pydata/xarray/pull/818#issuecomment-207983237 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIwNzk4MzIzNw== | rabernat 1197350 | 2016-04-10T13:15:49Z | 2016-04-10T13:15:49Z | MEMBER | So I tracked down the cause of the original array dimensions being overwritten. It happens within
At this point, @shoyer should I just focus on the case where |
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207531654 | https://github.com/pydata/xarray/pull/818#issuecomment-207531654 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIwNzUzMTY1NA== | rabernat 1197350 | 2016-04-08T17:39:10Z | 2016-04-08T18:07:11Z | MEMBER | I have tried adding a new keyword The way it works is like this: ``` python
The only problem is that it seems to overwrite the original dimension of the array! After calling groupby ``` python
I think that I guess something similar should be possible here... |
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207417668 | https://github.com/pydata/xarray/pull/818#issuecomment-207417668 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIwNzQxNzY2OA== | rabernat 1197350 | 2016-04-08T12:41:00Z | 2016-04-08T12:41:00Z | MEMBER | @shoyer regarding the binning, should I modify |
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207077942 | https://github.com/pydata/xarray/pull/818#issuecomment-207077942 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIwNzA3Nzk0Mg== | rabernat 1197350 | 2016-04-07T20:34:53Z | 2016-04-07T20:34:53Z | MEMBER | The travis build failure is a conda problem, not my commit. |
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207068032 | https://github.com/pydata/xarray/pull/818#issuecomment-207068032 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIwNzA2ODAzMg== | rabernat 1197350 | 2016-04-07T20:03:48Z | 2016-04-07T20:03:48Z | MEMBER | I think I got it working. |
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207000636 | https://github.com/pydata/xarray/pull/818#issuecomment-207000636 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIwNzAwMDYzNg== | rabernat 1197350 | 2016-04-07T17:14:55Z | 2016-04-07T17:14:55Z | MEMBER | My new commit supports unstacking in apply with Consider the behavior of the text case: ``` python
Coordinates: * ny (ny) int64 0 1 * nx (nx) int64 0 1 lat (lon_groups, ny, nx) float64 10.0 nan nan nan nan 10.0 20.0 ... lon (lon_groups, ny, nx) float64 30.0 nan nan nan nan 40.0 40.0 ... * lon_groups (lon_groups) int64 30 40 50 ``` When unstacking, the indices that are not part of the group get filled with nans. We are not able to put these arrays back together into a single array. Note that if we do not rename the group name here: https://github.com/pydata/xarray/pull/818/files#diff-96b65e0bfec9fd2b9d562483f53661f5R121 Then we get an error here: https://github.com/pydata/xarray/pull/818/files#diff-96b65e0bfec9fd2b9d562483f53661f5R407
|
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206628737 | https://github.com/pydata/xarray/pull/818#issuecomment-206628737 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIwNjYyODczNw== | rabernat 1197350 | 2016-04-07T00:14:17Z | 2016-04-07T00:14:17Z | MEMBER | @shoyer I'm having a tough time figuring out where to put the unstacking logic...maybe you can give me some advice. My first idea was to add a method to the GroupBy class called If you think that is the right approach, I will forge ahead. But maybe, as the author of both the groupby and stack / unstack logic, you can see an easier way. |
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206418244 | https://github.com/pydata/xarray/pull/818#issuecomment-206418244 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIwNjQxODI0NA== | rabernat 1197350 | 2016-04-06T15:05:54Z | 2016-04-06T15:05:54Z | MEMBER | Let me try to clarify what I mean in item 2:
Say you have the following dataset ``` python
Now imagine you want to average humidity in temperature coordinates. (This might sound like a bizarre operation, but it is actually the foundation of a sophisticated sort of thermodynamic analysis.) Currently this works as follows ``` python
However, this sums over all time. What if you wanted to preserve the time dependence, but replace the
and get back a DataArray with dimensions Maybe this is already possible with a sophisticated use of |
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206389664 | https://github.com/pydata/xarray/pull/818#issuecomment-206389664 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIwNjM4OTY2NA== | rabernat 1197350 | 2016-04-06T14:09:43Z | 2016-04-06T14:09:43Z | MEMBER |
I normally used Should this go into a separate PR? |
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206386864 | https://github.com/pydata/xarray/pull/818#issuecomment-206386864 | https://api.github.com/repos/pydata/xarray/issues/818 | MDEyOklzc3VlQ29tbWVudDIwNjM4Njg2NA== | rabernat 1197350 | 2016-04-06T14:04:20Z | 2016-04-06T14:04:20Z | MEMBER |
Can you clarify what you mean by this? At what point should the unstack happen? With the current code, apply seems to work ok: ``` python
But perhaps I am missing a certain use case you have in mind? |
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