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- Loading from NetCDF creates unnecessary numpy.ndarray-views that clears the OWNDATA-flag · 4 ✖
id | html_url | issue_url | node_id | user | created_at | updated_at ▲ | author_association | body | reactions | performed_via_github_app | issue |
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1116397246 | https://github.com/pydata/xarray/issues/6517#issuecomment-1116397246 | https://api.github.com/repos/pydata/xarray/issues/6517 | IC_kwDOAMm_X85Cit6- | shoyer 1217238 | 2022-05-03T18:09:42Z | 2022-05-03T18:09:42Z | MEMBER | I'm a little skeptical that it makes sense to add special case logic into Xarray in an attempt to keep NumPy's "OWNDATA" flag up to date. There are lots of places where we create views of data from existing arrays inside Xarray operations. There are definitely cases where Xarray's internal operations do memory copies followed by views, which would also result in datasets with misleading "OWNDATA" flags if you look only at resulting datasets, e.g.,
Overall, I just don't think this is a reliable way to trace memory allocation with NumPy. Maybe you could do better by also tracing back to source arrays with |
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Loading from NetCDF creates unnecessary numpy.ndarray-views that clears the OWNDATA-flag 1216517115 | |
1110703065 | https://github.com/pydata/xarray/issues/6517#issuecomment-1110703065 | https://api.github.com/repos/pydata/xarray/issues/6517 | IC_kwDOAMm_X85CM_vZ | kmuehlbauer 5821660 | 2022-04-27T08:24:56Z | 2022-04-27T08:24:56Z | MEMBER | FYI: Since h5netcdf recently moved to version 1.0, I've checked with latest xarray (2022.3.0) and latest h5netcdf (1.0.0). The OP example with the OP fix reproduces nicely as well with the updated fix. |
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Loading from NetCDF creates unnecessary numpy.ndarray-views that clears the OWNDATA-flag 1216517115 | |
1110354387 | https://github.com/pydata/xarray/issues/6517#issuecomment-1110354387 | https://api.github.com/repos/pydata/xarray/issues/6517 | IC_kwDOAMm_X85CLqnT | max-sixty 5635139 | 2022-04-26T23:48:44Z | 2022-04-26T23:48:44Z | MEMBER | I don't know this well — maybe others can comment — but the example checks out. Would we take this as a PR? Is there a simpler way to express that logic? |
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Loading from NetCDF creates unnecessary numpy.ndarray-views that clears the OWNDATA-flag 1216517115 | |
1110353767 | https://github.com/pydata/xarray/issues/6517#issuecomment-1110353767 | https://api.github.com/repos/pydata/xarray/issues/6517 | IC_kwDOAMm_X85CLqdn | max-sixty 5635139 | 2022-04-26T23:47:14Z | 2022-04-26T23:47:14Z | MEMBER | For others, here's the diff: ```diff diff --git "indexing.original.py" "indexing.patched.py" --- "indexing.original.py" +++ "indexing.patched.py" @@ -709,8 +709,12 @@ def explicit_indexing_adapter( """ raw_key, numpy_indices = decompose_indexer(key, shape, indexing_support) result = raw_indexing_method(raw_key.tuple) - if numpy_indices.tuple: - result = NumpyIndexingAdapter(np.asarray(result))[numpy_indices] + if numpy_indices.tuple and (not isinstance(result, np.ndarray) + or not all(i == slice(None, None, None) for i in numpy_indices.tuple)): + # The conditions within parentehses are to avoid unnecessary array slice/view-creation + # that would set flags['OWNDATA'] to False for no reason. + # Index the loaded np.ndarray. + result = NumpyIndexingAdapter(np.asarray(result))[numpy_indices] return result @@ -1156,6 +1160,11 @@ class NumpyIndexingAdapter(ExplicitlyIndexedNDArrayMixin):
``` |
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Loading from NetCDF creates unnecessary numpy.ndarray-views that clears the OWNDATA-flag 1216517115 |
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