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bugfix/incorrect-ome-tiff-dim-order#24
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@@ Coverage Diff @@
## master #24 +/- ##
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+ Coverage 86.96% 87.23% +0.26%
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Files 27 27
Lines 1036 1042 +6
==========================================
+ Hits 901 909 +8
+ Misses 135 133 -2
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AetherUnbound
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Oct 11, 2019
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A couple minor logic things, but looks good! 👍
| """ | ||
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| # Hold onto known dims until data is requested | ||
| if known_dims: |
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Since known_dims is None by default anyway, can't this just be self._known_dims?
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| if self._known_dims: | ||
| pass_dims = self._known_dims | ||
| else: | ||
| pass_dims = self.reader.dims |
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Optionally: (this could also be done below on L139)
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| if self._known_dims: | |
| pass_dims = self._known_dims | |
| else: | |
| pass_dims = self.reader.dims | |
| pass_dims = self._known_dims or self.reader.dims |
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It's enough to make me think it should be named override_dims instead of known_dims :)
| dimension_order = dimension_order.replace("Z", "") | ||
| if self.size_z() < 2: | ||
| dimension_order = dimension_order.replace("Z", "") | ||
| if self.size_c() < 2: |
| (np.zeros((10, 20)), "XY", (1, 1, 1, 1, 20, 10)), | ||
| pytest.param(np.zeros((2, 2, 2)), "ABI", None, marks=pytest.mark.raises(exception=TypeError)) | ||
| ]) | ||
| def test_known_dims(data, dims, expected_shape): |
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Freaking love pytest.mark.parametrize
toloudis
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Oct 11, 2019
| if self.size_c() < 2: | ||
| dimension_order = dimension_order.replace("Z", "") | ||
| if self.size_z() < 2: | ||
| dimension_order = dimension_order.replace("Z", "") |
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toloudis
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Pull request recommendations:
known_dimskwarg to theAICSImageobject to allow explicit override of dimension ordering. The data is still reshaped to the standardSTCZYX.Thanks for contributing!