Add threshold as option

nerval/evaluate.py

@@ -9,9 +9,10 @@ import editdistance
 import edlib
 import termtables as tt
 
-THRESHOLD = 0.30
 NOT_ENTITY_TAG = "O"
 
+THRESHOLD = 0.30
+
 
 def get_type_label(label: str) -> str:
     """Return the type (tag) of a label
@@ -189,7 +190,11 @@ def look_for_further_entity_part(index, tag, characters, labels):
 
 
 def compute_matches(
-    annotation: str, prediction: str, labels_annot: list, labels_predict: list
+    annotation: str,
+    prediction: str,
+    labels_annot: list,
+    labels_predict: list,
+    threshold: int,
 ) -> dict:
     """Compute prediction score from annotation string to prediction string.
 
@@ -274,7+279,7 @@
                     ):
                         j -= 1
 
                     if (
                         "B" in labels_predict[j]
                         and get_type_label(labels_predict[j]) == tag_ref
                         and j not in visited_predict
@@ -324,7+329,7 @@
                 score = (
                     1
                     if editdistance.eval(entity_ref, entity_compar) / len_entity
-                    < THRESHOLD
+                    <= threshold
                     else 0
                 )
                 entity_count[last_tag] = entity_count.get(last_tag, 0) + score
@@ -454,7 +459,7 @@ def print_results(scores: dict):
     tt.print(results, header, style=tt.styles.markdown)
 
 
-def run(annotation: str, prediction: str) -> dict:
+def run(annotation: str, prediction: str, threshold: int) -> dict:
     """Compute recall and precision for each entity type found in annotation and/or prediction.
 
     Each measure is given at document level, global score is a micro-average across entity types.
@@ -486,7 +491,11 @@ def run(annotation: str, prediction: str) -> dict:
 
     # Get nb match
     matches = compute_matches(
-        annot_aligned, predict_aligned, labels_annot_aligned, labels_predict_aligned
+        annot_aligned,
+        predict_aligned,
+        labels_annot_aligned,
+        labels_predict_aligned,
+        threshold,
     )
 
     # Compute scores
@@ -498,6 +507,17 @@ def run(annotation: str, prediction: str) -> dict:
     return scores
 
 
+def threshold_float_type(arg):
+    """Type function for argparse."""
+    try:
+        f = float(arg)
+    except ValueError:
+        raise argparse.ArgumentTypeError("Must be a floating point number.")
+    if f < 0 or f > 1:
+        raise argparse.ArgumentTypeError("Must be between 0 and 1.")
+    return f
+
+
 def main():
     """Get arguments and run."""
 
@@ -510,9 +530,17 @@ def main():
     parser.add_argument(
         "-p", "--predict", help="Prediction in BIO format.", required=True
     )
+    parser.add_argument(
+        "-t",
+        "--threshold",
+        help="Set a distance threshold for the match between gold and predicted entity.",
+        required=False,
+        default=THRESHOLD,
+        type=threshold_float_type,
+    )
     args = parser.parse_args()
 
-    run(args.annot, args.predict)
+    run(args.annot, args.predict, args.threshold)
 
 
 if __name__ == "__main__":