diff --git a/README.md b/README.md
index 2a3848e0020239c8cdd0f1e81fcc90fd91b7c5b8..4a4f41c19308acd4ea9b35bc35e80fb69b632327 100644
--- a/README.md
+++ b/README.md
@@ -50,7 +50,7 @@ Counting the spaces, 7 characters differ over 24 characters in the reference ent
### Demo
```
-$ nerval -a demo/demo_annot.bio -p demo/demo_predict.bio
+$ nerval -a demo/bio_folder/demo_annot.bio -p demo/bio_folder/demo_predict.bio
```
We also provide two annotation and prediction toy files, which are identical for now and produce perfect scores. Feel free to play with the the text and entity tags in the prediction file to see the impact on the score.
@@ -65,6 +65,12 @@ You can also indicate a folder and a csv file to have multiple evaluation at onc
$ nerval -c demo/mapping_file.csv -f demo/bio_folder
```
+And with the verbose option that's triggered by -v
+
+```
+$ nerval -a demo/bio_folder/demo_annot.bio -p demo/bio_folder/demo_predict.bio -v
+```
+
## Metric
This metric uses string alignment at character level.
diff --git a/demo/bio_folder/demo_annot.bio b/demo/bio_folder/demo_annot.bio
deleted file mode 100644
index cf16200fcd0436d943f71127f63894e428fafea7..0000000000000000000000000000000000000000
--- a/demo/bio_folder/demo_annot.bio
+++ /dev/null
@@ -1,82 +0,0 @@
-Césaire B-PER
-Alphonse I-PER
-Garon I-PER
-marraine O
-Adeline B-PER
-Dionne I-PER
-, O
-soussignés O
-Lecture O
-faite O
-Adéline O
-Dionne O
-Arsène O
-Côté O
-Arpin O
-R O
-Le O
-onze B-DAT
-aout I-DAT
-mil I-DAT
-neuf I-DAT
-cent I-DAT
-un I-DAT
-nous O
-prêtre O
-soussigné O
-avons O
-baptisé O
-Marie B-PER
-Luce I-PER
-Louise I-PER
-, O
-née O
-la B-DAT
-veille I-DAT
-, O
-fille O
-légitime O
-de O
-Carmel B-PER
-Côté I-PER
-, O
-cordonnier B-OCC
-, O
-pré O
-- O
-sent O
-, O
-déclarant O
-ne O
-savoir O
-signer O
-, O
-et O
-de O
-Eugé B-PER
-nie I-PER
-Fréchette I-PER
-, O
-de O
-cette B-LOC
-paroisse I-LOC
-. O
-Parrain O
-Napoléon B-PER
-Fréchette I-PER
-, O
-marraine O
-Adeline B-PER
-Tremblay I-PER
-, O
-soussignés O
-, O
-de O
-Ste B-LOC
-Luce I-LOC
-, O
-Lec O
-- O
-ture O
-faite O
-. O
diff --git a/demo/bio_folder/demo_predict.bio b/demo/bio_folder/demo_predict.bio
deleted file mode 100644
index 7e01c2d127aa47c95c49ab87a06e06d86f9af9b0..0000000000000000000000000000000000000000
--- a/demo/bio_folder/demo_predict.bio
+++ /dev/null
@@ -1,81 +0,0 @@
-Césaire B-PER
-Alphonse O
-Garon B-PER
-marraine O
-Adeline B-PER
-Dionne I-PER
-, O
-soussignés O
-Lecture O
-faite O
-Adéline O
-Dionne O
-Arsène O
-Côté O
-Arpin O
-R O
-Le O
-onze B-DAT
-aout I-DAT
-mil I-DAT
-neuf I-DAT
-cent I-DAT
-un O
-nous O
-pretre O
-soussigné O
-avons O
-baptisé O
-Marie B-PER
-Luce I-PER
-Louise I-PER
-, O
-née O
-la B-DAT
-veille I-DAT
-, O
-fille O
-légitime O
-de O
-Carmel B-PER
-Côté I-PER
-, O
-cordonnier B-OCC
-, O
-pré O
-- O
-sent O
-, O
-déclarant O
-ne O
-savoir O
-signer O
-, O
-et O
-de O
-Eugé B-PER
-nie I-PER
-Fréchette I-PER
-, O
-de O
-cette B-LOC
-paroisse I-LOC
-. O
-Parrain O
-Napoléon B-PER
-Fréchette I-PER
-, O
-marraine O
-Adéline B-PER
-Tremblay I-PER
-, O
-sousignés O
-, O
-de O
-St B-LOC
-. I-LOC
-Luce O
-, O
-Lec O
-ture O
-faite O
diff --git a/demo/bio_folder/toy_test_annot.bio b/demo/bio_folder/toy_test_annot.bio
deleted file mode 100644
index 5a941ee8ce361e67dbd213b2b2cd5d6a6a53e4ef..0000000000000000000000000000000000000000
--- a/demo/bio_folder/toy_test_annot.bio
+++ /dev/null
@@ -1,39 +0,0 @@
-John B-PER
-Ronald I-PER
-Reuel I-PER
-Tolkien I-PER
-was O
-born O
-on O
-three B-DAT
-January I-DAT
-eighteen I-DAT
-ninety I-DAT
-- I-DAT
-two I-DAT
-in O
-Bloemfontein B-LOC
-in O
-the O
-Orange B-LOC
-Free I-LOC
-State I-LOC
-, O
-to O
-Arthur B-PER
-Reuel I-PER
-Tolkien I-PER
-, O
-an O
-English O
-bank B-OCC
-manager I-OCC
-, O
-and O
-his O
-wife O
-Mabel B-PER
-, O
-née O
-Suffield B-PER
-. O
diff --git a/demo/bio_folder/toy_test_predict.bio b/demo/bio_folder/toy_test_predict.bio
deleted file mode 100644
index 5a941ee8ce361e67dbd213b2b2cd5d6a6a53e4ef..0000000000000000000000000000000000000000
--- a/demo/bio_folder/toy_test_predict.bio
+++ /dev/null
@@ -1,39 +0,0 @@
-John B-PER
-Ronald I-PER
-Reuel I-PER
-Tolkien I-PER
-was O
-born O
-on O
-three B-DAT
-January I-DAT
-eighteen I-DAT
-ninety I-DAT
-- I-DAT
-two I-DAT
-in O
-Bloemfontein B-LOC
-in O
-the O
-Orange B-LOC
-Free I-LOC
-State I-LOC
-, O
-to O
-Arthur B-PER
-Reuel I-PER
-Tolkien I-PER
-, O
-an O
-English O
-bank B-OCC
-manager I-OCC
-, O
-and O
-his O
-wife O
-Mabel B-PER
-, O
-née O
-Suffield B-PER
-. O
diff --git a/nerval/evaluate.py b/nerval/evaluate.py
index 2f0070d218c9985ac0ba336e5af4bc33143dd245..80335e94fcff6d8c992fc1fa961639458ed7d812 100644
--- a/nerval/evaluate.py
+++ b/nerval/evaluate.py
@@ -595,11 +595,17 @@ def run_multiple(file_csv, folder, threshold, verbose):
else:
raise Exception(f"No file found for files {annot}, {predict}")
if count:
- print(
- "Average scores in all corpus (mean of final files scores)\n"
- f" * Precision: {round(precision/count, 3)}\n"
- f" * Recall: {round(recall/count, 3)}\n"
- f" * F1: {round(f1/count, 3)}\n"
+ print("Average score on all corpus")
+ tt.print(
+ [
+ [
+ round(precision / count, 3),
+ round(recall / count, 3),
+ round(f1 / count, 3),
+ ]
+ ],
+ ["Precision", "Recall", "F1"],
+ style=tt.styles.markdown,
)
else:
raise Exception("No file were counted")
@@ -624,36 +630,24 @@ def main():
logging.basicConfig(level=logging.INFO)
parser = argparse.ArgumentParser(description="Compute score of NER on predict.")
- parser.add_argument(
- "-m",
- "--multiple",
- help="Single if 1, multiple 2",
- type=int,
- required=True,
- )
- parser.add_argument(
+
+ group = parser.add_mutually_exclusive_group()
+ group.add_argument(
"-a",
"--annot",
help="Annotation in BIO format.",
)
- parser.add_argument(
- "-p",
- "--predict",
- help="Prediction in BIO format.",
- )
- parser.add_argument(
- "-t",
- "--threshold",
- help="Set a distance threshold for the match between gold and predicted entity.",
- default=THRESHOLD,
- type=threshold_float_type,
- )
- parser.add_argument(
+ group.add_argument(
"-c",
"--csv",
help="Csv with the correlation between the annotation bio files and the predict bio files",
type=Path,
)
+ parser.add_argument(
+ "-p",
+ "--predict",
+ help="Prediction in BIO format.",
+ )
parser.add_argument(
"-f",
"--folder",
@@ -666,25 +660,30 @@ def main():
help="Print only the recap if False",
action="store_false",
)
+ parser.add_argument(
+ "-t",
+ "--threshold",
+ help="Set a distance threshold for the match between gold and predicted entity.",
+ default=THRESHOLD,
+ type=threshold_float_type,
+ )
+
args = parser.parse_args()
- if args.multiple == 1 or args.multiple == 2:
- if args.multiple == 2:
- if not args.folder:
- raise argparse.ArgumentError(args.folder, "-f must be given if -m is 2")
- if not args.csv:
- raise argparse.ArgumentError(args.folder, "-c must be given if -m is 2")
- if args.folder and args.csv:
- run_multiple(args.csv, args.folder, args.threshold, args.verbose)
- if args.multiple == 1:
- if not args.annot:
- raise argparse.ArgumentError(args.folder, "-a must be given if -m is 1")
- if not args.predict:
- raise argparse.ArgumentError(args.folder, "-p must be given if -m is 1")
- if args.annot and args.predict:
- run(args.annot, args.predict, args.threshold, args.verbose)
+ if args.annot:
+ if not args.predict:
+ raise parser.error("You need to specify the path to a predict file with -p")
+ if args.annot and args.predict:
+ run(args.annot, args.predict, args.threshold, args.verbose)
+ elif args.csv:
+ if not args.folder:
+ raise parser.error(
+ "You need to specify the path to a folder of bio files with -f"
+ )
+ if args.folder and args.csv:
+ run_multiple(args.csv, args.folder, args.threshold, args.verbose)
else:
- raise argparse.ArgumentTypeError("Value has to be 1 or 2")
+ raise parser.error("You need to specify the argument of input file")
if __name__ == "__main__":