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[easy] adding spot ids to pixel results #1687

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merged 1 commit into from
Dec 6, 2019
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shanaxel42
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Fixes: #1273

Added small test

@shanaxel42 shanaxel42 requested a review from ttung December 5, 2019 22:50
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pls see comment.

@@ -342,6 +342,7 @@ def _create_spot_attributes(
passes_filter = np.array(passes_area_filter, dtype=np.bool)

spot_attributes = SpotAttributes(pd.DataFrame.from_records(spot_attrs))
spot_attributes.data[Features.SPOT_ID] = list(range(len(spot_attributes.data)))
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Suggested change
spot_attributes.data[Features.SPOT_ID] = list(range(len(spot_attributes.data)))
spot_attributes.data[Features.SPOT_ID] = np.arange(0, len(spot_attributes.data))

@shanaxel42 shanaxel42 force-pushed the saxelrod-spotid-pixel branch from 7ba15e3 to 8a8095b Compare December 6, 2019 17:48
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codecov-io commented Dec 6, 2019

Codecov Report

Merging #1687 into master will increase coverage by <.01%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1687      +/-   ##
==========================================
+ Coverage   89.85%   89.85%   +<.01%     
==========================================
  Files         239      239              
  Lines        8962     8964       +2     
==========================================
+ Hits         8053     8055       +2     
  Misses        909      909
Impacted Files Coverage Δ
starfish/test/full_pipelines/api/test_merfish.py 100% <100%> (ø) ⬆️
...re/spots/DetectPixels/combine_adjacent_features.py 98.18% <100%> (+0.01%) ⬆️

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@shanaxel42 shanaxel42 merged commit 56cfdbe into master Dec 6, 2019
@shanaxel42 shanaxel42 deleted the saxelrod-spotid-pixel branch December 6, 2019 18:36
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Successfully merging this pull request may close these issues.

PixelSpotDecoder does not add spot_id to IntensityTable
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