adding spot ids to pixel results

spacetx · Dec 6, 2019 · 8a8095b · 8a8095b
1 parent 339eaa9
commit 8a8095b
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diff --git a/starfish/core/spots/DetectPixels/combine_adjacent_features.py b/starfish/core/spots/DetectPixels/combine_adjacent_features.py
@@ -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(

diff --git a/starfish/test/full_pipelines/api/test_merfish.py b/starfish/test/full_pipelines/api/test_merfish.py
@@ -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