From c844e0240956215180dffdc7a1f457c83f119959 Mon Sep 17 00:00:00 2001
From: EvaBardou <bardou@teklia.com>
Date: Wed, 3 Jan 2024 17:11:34 +0100
Subject: [PATCH] Utils method to print a Markdown table
---
nerval/evaluate.py | 22 +++++++---------------
nerval/utils.py | 45 +++++++++++++++++++++++----------------------
2 files changed, 30 insertions(+), 37 deletions(-)
diff --git a/nerval/evaluate.py b/nerval/evaluate.py
index d25903f..62e6b88 100644
--- a/nerval/evaluate.py
+++ b/nerval/evaluate.py
@@ -5,7 +5,6 @@ from typing import List
import editdistance
import edlib
-from prettytable import MARKDOWN, PrettyTable
from nerval.parse import (
BEGINNING_POS,
@@ -15,7 +14,7 @@ from nerval.parse import (
look_for_further_entity_part,
parse_bio,
)
-from nerval.utils import print_result_compact, print_results
+from nerval.utils import print_mardown_table, print_result_compact, print_results
logger = logging.getLogger(__name__)
@@ -391,16 +390,9 @@ def run_multiple(file_csv: Path, folder: Path, threshold: int, verbose: bool):
raise Exception("No file were counted")
logger.info("Average score on all corpus")
- table = PrettyTable()
- table.field_names = ["Precision", "Recall", "F1"]
- table.set_style(MARKDOWN)
- table.add_rows(
- [
- [
- round(precision / count, 3),
- round(recall / count, 3),
- round(f1 / count, 3),
- ],
- ],
- )
- print(table)
+ result = [
+ round(precision / count, 3),
+ round(recall / count, 3),
+ round(f1 / count, 3),
+ ]
+ print_mardown_table(["Precision", "Recall", "F1"], [result])
diff --git a/nerval/utils.py b/nerval/utils.py
index 01d4f83..253c14d 100644
--- a/nerval/utils.py
+++ b/nerval/utils.py
@@ -1,12 +1,19 @@
from prettytable import MARKDOWN, PrettyTable
+def print_mardown_table(header: list[str], rows: list[list]):
+ table = PrettyTable()
+ table.field_names = header
+ table.set_style(MARKDOWN)
+ table.add_rows(rows)
+ print(table)
+
+
def print_results(scores: dict):
"""Display final results.
None values are kept to indicate the absence of a certain tag in either annotation or prediction.
"""
- header = ["tag", "predicted", "matched", "Precision", "Recall", "F1", "Support"]
results = []
for tag in sorted(scores, reverse=True):
prec = None if scores[tag]["P"] is None else round(scores[tag]["P"], 3)
@@ -25,29 +32,23 @@ def print_results(scores: dict):
],
)
- table = PrettyTable()
- table.field_names = header
- table.set_style(MARKDOWN)
- table.add_rows(results)
- print(table)
+ print_mardown_table(
+ ["tag", "predicted", "matched", "Precision", "Recall", "F1", "Support"],
+ results,
+ )
def print_result_compact(scores: dict):
- header = ["tag", "predicted", "matched", "Precision", "Recall", "F1", "Support"]
result = [
- [
- "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"],
- ],
+ "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"],
]
-
- table = PrettyTable()
- table.field_names = header
- table.set_style(MARKDOWN)
- table.add_rows(result)
- print(table)
+ print_mardown_table(
+ ["tag", "predicted", "matched", "Precision", "Recall", "F1", "Support"],
+ [result],
+ )
--
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