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  • Bug when accessing sorted dataset before loading · 6 ✖

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id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
144274152 https://github.com/pydata/xarray/issues/593#issuecomment-144274152 https://api.github.com/repos/pydata/xarray/issues/593 MDEyOklzc3VlQ29tbWVudDE0NDI3NDE1Mg== jhamman 2443309 2015-09-30T03:46:24Z 2015-09-30T03:46:24Z MEMBER

Okay then, I think it makes sense to re-raise as you originally suggested. I'll put together a PR tomorrow.

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  Bug when accessing sorted dataset before loading 108769226
144270497 https://github.com/pydata/xarray/issues/593#issuecomment-144270497 https://api.github.com/repos/pydata/xarray/issues/593 MDEyOklzc3VlQ29tbWVudDE0NDI3MDQ5Nw== shoyer 1217238 2015-09-30T03:18:15Z 2015-09-30T03:18:15Z MEMBER

I'm all behind that error message in principle, but it needs to be specific to the netcdf4 backend. For example, this works perfectly fine with scipy. Given these constraints, especially given that either of these arrays may be triggered lazily by a dask.array, I think this will be difficult to solve at all times when the expression is written.

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  Bug when accessing sorted dataset before loading 108769226
144214269 https://github.com/pydata/xarray/issues/593#issuecomment-144214269 https://api.github.com/repos/pydata/xarray/issues/593 MDEyOklzc3VlQ29tbWVudDE0NDIxNDI2OQ== jhamman 2443309 2015-09-29T22:54:13Z 2015-09-30T00:07:14Z MEMBER

I'm going to argue that it is better to raise an error at the time of offense. Currently we are failing silently, and yielding objects that are unusable. The logic I'm envisioning is like this:

Python if not issorted(indexer) and not self.loaded: raise IndexError('...')

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  Bug when accessing sorted dataset before loading 108769226
144133156 https://github.com/pydata/xarray/issues/593#issuecomment-144133156 https://api.github.com/repos/pydata/xarray/issues/593 MDEyOklzc3VlQ29tbWVudDE0NDEzMzE1Ng== shoyer 1217238 2015-09-29T17:46:04Z 2015-09-29T17:46:04Z MEMBER

My vote would be for catching and re-raising the error with a more informative message. Something like:

``` IndexError: the indexing operation you are attempting to perform is not valid on netCDF4.Variable object. Try loading your data into memory first by calling .load().

Original traceback: ... ```

This is automatic when you re-raise on Python 3. On Python 2, you'll have to use traceback.format_exc() to capture the traceback.

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  Bug when accessing sorted dataset before loading 108769226
144098447 https://github.com/pydata/xarray/issues/593#issuecomment-144098447 https://api.github.com/repos/pydata/xarray/issues/593 MDEyOklzc3VlQ29tbWVudDE0NDA5ODQ0Nw== jhamman 2443309 2015-09-29T15:43:36Z 2015-09-29T15:43:36Z MEMBER

That makes sense. I agree that this is ultimately a netCDF4 limitation.

So moving forward, we could one or more of the following: 1. Fix this in netCDF4, allowing unsorted integer arrays as indexers. 2. Check in isel that the indexer is valid when the data is still sitting on disk. Raise an IndexError in the cases that will fail later on. 3. Ugly: In cases where isel is provided with unsorted integer arrays, we could force the data to be loaded. 4. Uglier: Somehow store the integer array mapping in xray, using netCDF4 as is, and returning a view after the data has been loaded.

In my view, the current behavior of isel is failing silently and this is not what we want.

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  Bug when accessing sorted dataset before loading 108769226
143914481 https://github.com/pydata/xarray/issues/593#issuecomment-143914481 https://api.github.com/repos/pydata/xarray/issues/593 MDEyOklzc3VlQ29tbWVudDE0MzkxNDQ4MQ== shoyer 1217238 2015-09-29T01:01:39Z 2015-09-29T01:01:39Z MEMBER

We could work around this, but this is arguably a bug/limitation of netCDF4 Python, which no longer allows indexing with unsorted integer sequences. See https://github.com/Unidata/netcdf4-python/issues/300 and https://github.com/Unidata/netcdf4-python/pull/308.

I think this could probably be fixed upstream somewhat straightforwardly by canonicalizing indexers as integer arrays instead of as boolean arrays. I'm not sure what we can do about it here.

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  Bug when accessing sorted dataset before loading 108769226

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