Add Decoded Spot Table #1087
Add Decoded Spot Table #1087
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@@ Coverage Diff @@
## master #1087 +/- ##
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+ Coverage 88.8% 88.89% +0.08%
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Files 165 167 +2
Lines 6433 6481 +48
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+ Hits 5713 5761 +48
Misses 720 720
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this looks good. Thanks!
Let's run with this and discuss with WG5 users about how to organize multi-cell assignment with probabilities within this framework. My suggestion would be further optional columns in pairs, i.e. cell_0, probability_0, cell_1, probability_1,... . And yes, we should really be able to stop at 10!
Sounds good. I'd also be fine adding a sparse matrix and saving both tables in an archive. What would be your preferred way to proceed with WG5? CC then on this PR? email them? post this in slack? |
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| Implementation | ||
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| Starfish Implements the :py:class:`DecodedSpots` as a wrapper for the :code:`pd.DataFrame` object |
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| Starfish Implements the :py:class:`DecodedSpots` as a wrapper for the :code:`pd.DataFrame` object | |
| Starfish implements the :py:class:`DecodedSpots` as a wrapper for the :code:`pd.DataFrame` object |
| spot coordinates (z, y, x) and gene target. Does not contain pixel coordinates. | ||
| """ | ||
| if Features.TARGET not in self.coords.keys(): | ||
| raise RuntimeError( |
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| raise RuntimeError( | |
| raise ValueError( |
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| # test serialization | ||
| tempdir = tempfile.mkdtemp() | ||
| filename = os.path.join(tempdir, 'spots.csv') |
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You should probably just use: with tempfile.NamedTemporaryFile(...)
| required_fields = { | ||
| Coordinates.X.value, # spot x-coordinate | ||
| Coordinates.Y.value, # spot y-coordinate | ||
| Features.TARGET, # spot gene target |
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some wonky alignment going on.
Adds a
DecodedSpotTableand some basic serialization tooling to address #1076. Users who want the underlying dataframe can get it withDecodedSpotTable.data.See documentation included in PR for more details.
closes #1076