Fix Jaccard Calculation (#165)

tansey-lab · Dec 2, 2024 · a13a7d2 · a13a7d2
1 parent 54e433c
commit a13a7d2
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Showing 2 changed files with 5 additions and 12 deletions.
diff --git a/src/nuc2seg/cli/calculate_benchmarks.py b/src/nuc2seg/cli/calculate_benchmarks.py
@@ -1,19 +1,13 @@
 import argparse
 import logging
-
-import numpy as np
-import torch
-import tqdm
 import os
 
 from nuc2seg import log_config
-from nuc2seg.data import Nuc2SegDataset, TiledDataset
-from nuc2seg.segment import stitch_predictions
-from nuc2seg.xenium import load_vertex_file, load_and_filter_transcripts_as_points
 from nuc2seg.postprocess import (
     calculate_average_intersection_over_union,
     calculate_segmentation_jaccard_index,
 )
+from nuc2seg.xenium import load_vertex_file, load_and_filter_transcripts_as_points
 
 logger = logging.getLogger(__name__)
 

diff --git a/src/nuc2seg/postprocess.py b/src/nuc2seg/postprocess.py
@@ -252,20 +252,19 @@ def calculate_segmentation_jaccard_index(
     sjoined_gdf.reset_index(inplace=True, drop=False, names="index")
 
     segment_id_to_transcripts_a = (
-        sjoined_gdf[["index", "index_right"]]
-        .groupby("index")
+        sjoined_gdf[["segment_id_a", "index_right"]]
+        .groupby("segment_id_a")
         .agg({"index_right": set})["index_right"]
         .to_dict()
     )
 
     sjoined_gdf = spatial_join_polygons_and_transcripts(
         boundaries=segmentation_b, transcripts=transcripts
     )
-    sjoined_gdf.reset_index(inplace=True, drop=False, names="index")
 
     segment_id_to_transcripts_b = (
-        sjoined_gdf[["index", "index_right"]]
-        .groupby("index")
+        sjoined_gdf[["segment_id_b", "index_right"]]
+        .groupby("segment_id_b")
         .agg({"index_right": set})["index_right"]
         .to_dict()
     )