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1566 shape feature extract #381

Merged
merged 7 commits into from
Aug 24, 2023
Merged

1566 shape feature extract #381

merged 7 commits into from
Aug 24, 2023

Commits on Aug 24, 2023

  1. feat: dsa_viz extract joint object tile

    @raylim
    raylim committed Aug 24, 2023
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  2. build: update shapely

    @raylim
    raylim committed Aug 24, 2023
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  3. feat: extract tile shape features cli 

    chore: 377, 375, 374, 379, 382 package versions

feat: extract_tile_shape_features: add options for limiting variables in final output, clean up output a bit

feat: add extra features to extract_tile_shape_features
    @raylim
    raylim committed Aug 24, 2023
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  4. Added spatial analysis tutorial notebook 

    This is just Armaan's original notebook, updated for the current
state of luna.  It still uses the CLIs.
    @raylim
    Tom Pollard authored and raylim committed Aug 24, 2023
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  5. Rewrote spatial tutorial notebook as Python code, and removed UMAP calcs 

    1. Added function to pull output file names from metadata.yml files.
2. Cast Path objects to strings in a couple of places.
3. Check for both `aperio.MPP` and `openslide.mpp-x` in the slide
   image properties, and log a warning if neither is found.
4. Added new notebook to the tutorial docs
5. Renamed notebook to spatial_stats.ipynb
    @raylim
    Tom Pollard authored and raylim committed Aug 24, 2023
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  6. Allow non-local connections to the docs server 

    This lets us run a docs server on one of the compute servers and view
the docs site on our laptops.
    @raylim
    Tom Pollard authored and raylim committed Aug 24, 2023
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  7. tests: update test_extract_shape_features

    @raylim
    raylim committed Aug 24, 2023
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