Format complete ISS experiment and expose in starfish.data #1316
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… experiment, update TileFetcher
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@@ Coverage Diff @@
## master #1316 +/- ##
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- Coverage 88.96% 69.05% -19.92%
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Files 146 148 +2
Lines 5258 5377 +119
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- Hits 4678 3713 -965
- Misses 580 1664 +1084
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docs/source/_static/data_formatting_examples/format_iss_breast_data.py
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| self.coordinates_df.loc[fov, "y_min"], | ||
| self.coordinates_df.loc[fov, "y_max"] | ||
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| Coordinates.Z: 0 |
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Does this experiment have multiple Z layers? If not, I think you can just omit this.
| self.coordinates_df.loc[fov, "y_min"], | ||
| self.coordinates_df.loc[fov, "y_max"] | ||
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| Coordinates.Z: 0 |
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| if __name__ == "__main__": | ||
| """ | ||
| This TileFetcher should be run on data found at: | ||
| s3://spacetx.starfish.data/mignardi_breast_1/raw/ |
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do we want to move this sucker?
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Yes, we should move this in #1314
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| if __name__ == "__main__": | ||
| """ |
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consider moving this to be the description argument passed to argparse.ArgumentParser()
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If we want these scripts to be user-facing and user-friendly there's a lot of work to be done across them; right now we have a mixture of click and argparse scripts. If we think it's worth cleaning these up I'd suggest we do them all in a separate PR.
…_data.py Co-Authored-By: Tony Tung <tonytung@merly.org>
Testing strategy:
fov_000in new experiment (is namedfov_001in master)