fix how spot_ids are handled by build_traces_sequential and Label._as…

…sign() (#1872) * Made build_traces_sequential reassign unique spot_ids to every feature after concatenating PerImageSliceResults. Also made Label._assign() explicitly label features by spot_id instead of row number, ensuring that labeling is accurate even when spot_ids do not match row_numbers in an IntensityTable. Spot_ids must still be unique for accurate labeling though.
spacetx · May 7, 2020 · 7f15413 · 7f15413
1 parent 0aafaaf
commit 7f15413
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/starfish/core/spots/AssignTargets/label.py b/starfish/core/spots/AssignTargets/label.py
@@ -61,7 +61,8 @@ def _assign(
                 selectors['z'] = in_bbox.z
             in_mask = mask.sel(**selectors)
             spot_ids = in_bbox[Features.SPOT_ID][in_mask.values]
-            decoded_intensities[Features.CELL_ID].loc[spot_ids] = mask.name
+            decoded_intensities[Features.CELL_ID].loc[
+                decoded_intensities[Features.SPOT_ID].isin(spot_ids)] = mask.name
 
         return decoded_intensities
 

diff --git a/starfish/core/spots/DecodeSpots/trace_builders.py b/starfish/core/spots/DecodeSpots/trace_builders.py
@@ -55,7 +55,10 @@ def build_traces_sequential(spot_results: SpotFindingResults, **kwargs) -> Inten
 
     """
 
-    all_spots = pd.concat([sa.spot_attrs.data for sa in spot_results.values()], sort=True)
+    all_spots = pd.concat([sa.spot_attrs.data for sa in spot_results.values()],
+                          ignore_index=True, sort=True)
+    # reassign spot_ids to index number so they are unique
+    all_spots['spot_id'] = all_spots.index
 
     intensity_table = IntensityTable.zeros(
         spot_attributes=SpotAttributes(all_spots),