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[easy] adding spot ids to pixel results #1687

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Dec 6, 2019
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[easy] adding spot ids to pixel results #1687

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1 change: 1 addition & 0 deletions starfish/core/spots/DetectPixels/combine_adjacent_features.py
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Expand Up @@ -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] = np.arange(0, len(spot_attributes.data))
return spot_attributes, passes_filter

def run(
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3 changes: 3 additions & 0 deletions starfish/test/full_pipelines/api/test_merfish.py
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Expand Up @@ -215,6 +215,9 @@ def test_merfish_pipeline_cropped_data():

spot_intensities = merfish.initial_spot_intensities

# check that intensities were giving spot ids using PixelSpotDecoding
assert "spot_id" in spot_intensities.coords

# verify that the number of spots are correct
spots_passing_filters = spot_intensities[Features.PASSES_THRESHOLDS].sum()
assert spots_passing_filters == 1410
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