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ENH: Remove deepcopies when slicing cubes and copying coords
- When indexing a cube when the data is reaslised (not lazy), a view of the original array is returned where possible (subject to the rules when slicing in numpy). - When indexing a cube when the data is not reaslised (lazy), realising the data on one will still not realise the data on the other. - Existing behaviour is that slicing coordinates returns views of the original points and bounds (where possible). This was likely chosen behaviour on the basis that DimCoords at least are not writeable. This is not the same however for Auxiliary coordinates and likely raises the likely case for this being a bug (i.e. one can modify AuxCoord object points and bounds). - DimCoord slicing will now return views of its data like AuxCoords. DimCoords will continue to realise data unlike AuxCoords due to the validation necessary for being monotonically increasing.
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Carwyn Pelley
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Jan 10, 2017
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docs/iris/src/whatsnew/contributions_1.12/deprecate_2016-Dec-08_share_data.txt
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,3 @@ | ||
| * Deprecated the data-copying behaviour of Cube indexing. | ||
| The `share_data` attribute of `iris.FUTURE` can be used to switch to | ||
| the new data-sharing behaviour See :class:`iris.Future`. |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,120 @@ | ||
| # (C) British Crown Copyright 2017, Met Office | ||
| # | ||
| # This file is part of Iris. | ||
| # | ||
| # Iris is free software: you can redistribute it and/or modify it under | ||
| # the terms of the GNU Lesser General Public License as published by the | ||
| # Free Software Foundation, either version 3 of the License, or | ||
| # (at your option) any later version. | ||
| # | ||
| # Iris is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU Lesser General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU Lesser General Public License | ||
| # along with Iris. If not, see <http://www.gnu.org/licenses/>. | ||
| """Unit tests for :class:`iris.coords.AuxCoord`.""" | ||
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| from __future__ import (absolute_import, division, print_function) | ||
| from six.moves import (filter, input, map, range, zip) # noqa | ||
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| # Import iris.tests first so that some things can be initialised before | ||
| # importing anything else. | ||
| import iris.tests as tests | ||
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| import numpy as np | ||
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| import biggus | ||
| from iris.coords import AuxCoord | ||
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| class Test___init__(tests.IrisTest): | ||
| def test_writeable(self): | ||
| coord = AuxCoord([1, 2], bounds=[[1, 2], [2, 3]]) | ||
| self.assertTrue(coord.points.flags.writeable) | ||
| self.assertTrue(coord.bounds.flags.writeable) | ||
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| def fetch_base(ndarray): | ||
| if ndarray.base is not None: | ||
| return fetch_base(ndarray.base) | ||
| return ndarray | ||
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| class Test___getitem__(tests.IrisTest): | ||
| def test_share_data(self): | ||
| # Ensure that slicing a coordinate behaves like slicing a numpy array | ||
| # i.e. that the points and bounds are views of the original. | ||
| original = AuxCoord([1, 2], bounds=[[1, 2], [2, 3]], | ||
| attributes={'dummy1': None}, | ||
| coord_system=tests.mock.sentinel.coord_system) | ||
| sliced_coord = original[:] | ||
| self.assertIs(fetch_base(sliced_coord._points), | ||
| fetch_base(original._points)) | ||
| self.assertIs(fetch_base(sliced_coord._bounds), | ||
| fetch_base(original._bounds)) | ||
| self.assertIsNot(sliced_coord.coord_system, original.coord_system) | ||
| self.assertIsNot(sliced_coord.attributes, original.attributes) | ||
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| def test_lazy_data_realisation(self): | ||
| # Capture the fact that we realise the data when slicing. | ||
| points = np.array([1, 2]) | ||
| points = biggus.NumpyArrayAdapter(points) | ||
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| bounds = np.array([[1, 2], [2, 3]]) | ||
| bounds = biggus.NumpyArrayAdapter(bounds) | ||
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| original = AuxCoord(points, bounds=bounds, | ||
| attributes={'dummy1': None}, | ||
| coord_system=tests.mock.sentinel.coord_system) | ||
| sliced_coord = original[:] | ||
| # Returned coord is realised. | ||
| self.assertIsInstance(sliced_coord._points, biggus.NumpyArrayAdapter) | ||
| self.assertIsInstance(sliced_coord._bounds, biggus.NumpyArrayAdapter) | ||
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| # Original coord remains unrealised. | ||
| self.assertIsInstance(points, biggus.NumpyArrayAdapter) | ||
| self.assertIsInstance(bounds, biggus.NumpyArrayAdapter) | ||
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| class Test_copy(tests.IrisTest): | ||
| def setUp(self): | ||
| self.original = AuxCoord([1, 2], bounds=[[1, 2], [2, 3]], | ||
| attributes={'dummy1': None}, | ||
| coord_system=tests.mock.sentinel.coord_system) | ||
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| def assert_data_no_share(self, coord_copy): | ||
| self.assertIsNot(fetch_base(coord_copy._points), | ||
| fetch_base(self.original._points)) | ||
| self.assertIsNot(fetch_base(coord_copy._bounds), | ||
| fetch_base(self.original._bounds)) | ||
| self.assertIsNot(coord_copy.coord_system, self.original.coord_system) | ||
| self.assertIsNot(coord_copy.attributes, self.original.attributes) | ||
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| def test_existing_points(self): | ||
| # Ensure that copying a coordinate does not return a view of its | ||
| # points or bounds. | ||
| coord_copy = self.original.copy() | ||
| self.assert_data_no_share(coord_copy) | ||
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| def test_existing_points_deepcopy_call(self): | ||
| # Ensure that the coordinate object itself is deepcopied called. | ||
| with tests.mock.patch('copy.deepcopy') as mock_copy: | ||
| self.original.copy() | ||
| mock_copy.assert_called_once_with(self.original) | ||
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| def test_new_points(self): | ||
| coord_copy = self.original.copy([1, 2], bounds=[[1, 2], [2, 3]]) | ||
| self.assert_data_no_share(coord_copy) | ||
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| def test_new_points_shallowcopy_call(self): | ||
| # Ensure that the coordinate object itself is shallow copied so that | ||
| # the points and bounds are not unnecessarily copied. | ||
| with tests.mock.patch('copy.copy') as mock_copy: | ||
| self.original.copy([1, 2], bounds=[[1, 2], [2, 3]]) | ||
| mock_copy.assert_called_once_with(self.original) | ||
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| if __name__ == '__main__': | ||
| tests.main() |
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