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Adding verbose option lunched by adding -v

Merged Adding verbose option lunched by adding -v
feature_verbose into master
2 unresolved threads
Merged Thibault Lavigne requested to merge feature_verbose into master
2 unresolved threads
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2 files
+ 34
− 8
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2
nerval/evaluate.py
+ 32
− 6
@@ -492,7 +492,24 @@ def print_results(scores: dict):
tt.print(results, header, style=tt.styles.markdown)
def run(annotation: str, prediction: str, threshold: int) -> dict:
def print_result_compact(scores: dict):
result = []
header = ["tag", "predicted", "matched", "Precision", "Recall", "F1", "Support"]
result.append(
[
"ALl",
scores["All"]["predicted"],
scores["All"]["matched"],
round(scores["All"]["P"], 3),
round(scores["All"]["R"], 3),
round(scores["All"]["F1"], 3),
scores["All"]["Support"],
]
)
tt.print(result, header, style=tt.styles.markdown)
def run(annotation: str, prediction: str, threshold: int, verbose: bool) -> 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.
@@ -535,12 +552,15 @@ def run(annotation: str, prediction: str, threshold: int) -> dict:
scores = compute_scores(annot["entity_count"], predict["entity_count"], matches)
# Print results
print_results(scores)
if verbose:
print_results(scores)
else:
print_result_compact(scores)
return scores
def run_multiple(file_csv, folder, threshold):
def run_multiple(file_csv, folder, threshold, verbose):
"""Run the program for multiple files (correlation indicated in the csv file)"""
# Read the csv in a list
with open(file_csv, "r") as read_obj:
@@ -563,7 +583,7 @@ def run_multiple(file_csv, folder, threshold):
if annot and predict:
print(os.path.basename(predict))
run(annot, predict, threshold)
run(annot, predict, threshold, verbose)
print()
else:
raise f"No file found for files {annot}, {predict}"
@@ -624,6 +644,12 @@ def main():
help="Folder containing the bio files referred to in the csv file",
type=Path,
)
parser.add_argument(
"-v",
"--verbose",
help="Print only the recap if False",
action="store_false",
)
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args = parser.parse_args()
if args.multiple == 1 or args.multiple == 2:
@@ -633,14 +659,14 @@ def main():
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)
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)
run(args.annot, args.predict, args.threshold, args.verbose)
else:
raise argparse.ArgumentTypeError("Value has to be 1 or 2")