Allow for intensity tables with labeled axes #1181
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@@ Coverage Diff @@
## master #1181 +/- ##
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- Coverage 88.52% 88.29% -0.23%
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Files 133 134 +1
Lines 4976 5008 +32
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+ Hits 4405 4422 +17
- Misses 571 586 +15
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ambrosejcarr
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Apr 14, 2019
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shanaxel42
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| ymin = crop_y | ||
| xmin = crop_x | ||
| zmax = image_stack.shape['z'] - crop_z | ||
| zmax = image_stack.axis_labels(Axes.ZPLANE)[-crop_z - 1] |
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-crop_z - 1 this is weird, what value is this?
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So this is to allow for cropping from the maximum zlayer. crop_z=0 => zmax=-1 (i.e., last plane). crop_z=1 => zmax=-2 (i.e., second to last plane).
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Currently, we use the offset of r/c/z to label the axes on the intensity table. We should instead be using the axes labels from the ImageStack. This PR makes that change in three key areas: 1. `IntensityTable.empty_intensity_table` now accepts the labels for the axes. 2. `IntensityTable.from_spot_data` now accepts the labels for the axes and verifies that the number of labels matches the intensity data. 3. `IntensityTable.from_image_stack` reads the labels for the zplane axes and assigns them correctly. Test plan: Add a test that instantiates a labeled ImageStack and derives an IntensityTable from it. Also ran `make test && make -j run-notebooks`. Depends on #1178 Fixes #1168
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Currently, we use the offset of r/c/z to label the axes on the intensity table. We should instead be using the axes labels from the ImageStack. This PR makes that change in three key areas:
IntensityTable.empty_intensity_tablenow accepts the labels for the axes.IntensityTable.from_spot_datanow accepts the labels for the axes and verifies that the number of labels matches the intensity data.IntensityTable.from_image_stackreads the labels for the zplane axes and assigns them correctly.Test plan: Add a test that instantiates a labeled ImageStack and derives an IntensityTable from it. Also ran
make test && make -j run-notebooks.Depends on #1178
Fixes #1168