Record the tile shape in our data structures if it's not provided. #73
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If the tile_shape is not provided by the json file, we should infer it from the actual data. This is a suboptimal data path since it requires a decoding step just to get the shape of the tile, so we warn about it. Previously, this field was set by `_load()`, but that was removed in #72. Test plan: Generate a tileset document, and then strip the shape data from the tiles. Then read it back. The correct tile shapes should be provided, but getting them should trigger a warning.
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@@ Coverage Diff @@
## master #73 +/- ##
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+ Coverage 82.49% 82.72% +0.23%
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Files 18 18
Lines 514 521 +7
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+ Hits 424 431 +7
Misses 90 90
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ambrosejcarr
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Oct 10, 2018
| def tile_shape(self): | ||
| if self._tile_shape is None: | ||
| warnings.warn( | ||
| "Decoding tile just to obtain shape. It is recommended to include the tile shape " |
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I think this is a FieldOfView.json, right? Does it make more sense to call it by name?
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FieldOfView is a specific subset of TileSet in my mind.
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Both notebooks had datasets where the tile shapes were not consistently provided. spacetx/slicedimage#72 broke the recording of the tile shape, and spacetx/slicedimage#73 fixes it. Test plan: `make -j run__notebooks/py/ISS_Pipeline_-_Breast_-_1_FOV.py run__notebooks/py/assay_comparison.py`
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Both notebooks had datasets where the tile shapes were not consistently provided. spacetx/slicedimage#72 broke the recording of the tile shape, and spacetx/slicedimage#73 fixes it. Test plan: `make -j run__notebooks/py/ISS_Pipeline_-_Breast_-_1_FOV.py run__notebooks/py/assay_comparison.py`
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If the tile_shape is not provided by the json file, we should infer it from the actual data. This is a suboptimal data path since it requires a decoding step just to get the shape of the tile, so we warn about it.
Previously, this field was set by
_load(), but that was removed in #72.Test plan: Generate a tileset document, and then strip the shape data from the tiles. Then read it back. The correct tile shapes should be provided, but getting them should trigger a warning.