From 871b2ddc6faf4e53205be9cdbe73c3131c8185ef Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Tue, 23 Jan 2024 16:56:57 +0100
Subject: [PATCH] [doc] Fix typos and clarify docstrings
---
src/mednet/engine/evaluator.py | 2 +-
src/mednet/engine/saliency/evaluator.py | 8 ++++----
src/mednet/engine/saliency/interpretability.py | 6 +++---
src/mednet/scripts/evaluate.py | 2 +-
src/mednet/scripts/saliency/completeness.py | 2 +-
5 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/src/mednet/engine/evaluator.py b/src/mednet/engine/evaluator.py
index 829b9a6b..1add3edb 100644
--- a/src/mednet/engine/evaluator.py
+++ b/src/mednet/engine/evaluator.py
@@ -202,7 +202,7 @@ def run_binary(
A list of predictions to consider for measurement
threshold_a_priori
A threshold to use, evaluated *a priori*, if must report single values.
- If this value is not provided, a *a posteriori* threshold is calculated
+ If this value is not provided, an *a posteriori* threshold is calculated
on the input scores. This is a biased estimator.
diff --git a/src/mednet/engine/saliency/evaluator.py b/src/mednet/engine/saliency/evaluator.py
index f8a9c04e..aae1acca 100644
--- a/src/mednet/engine/saliency/evaluator.py
+++ b/src/mednet/engine/saliency/evaluator.py
@@ -16,9 +16,10 @@ def _reconcile_metrics(
completeness: list,
interpretability: list,
) -> list[tuple[str, int, float, float, float]]:
- """Summarizes samples into a new table containing most important scores.
+ """Summarizes samples into a new table containing the most important
+ scores.
- It returns a list containing a table with completeness and road scorse per
+ It returns a list containing a table with completeness and ROAD scores per
sample, for the selected dataset. Only samples for which a completness and
interpretability scores are availble are returned in the reconciled list.
@@ -198,8 +199,7 @@ def _extract_statistics(
name
The name of the variable being analysed
index
- Which of the indexes on the tuples containing in ``data`` that should
- be extracted.
+ The index of the tuple contained in ``data`` that should be extracted.
dataset
The name of the dataset being analysed
xlim
diff --git a/src/mednet/engine/saliency/interpretability.py b/src/mednet/engine/saliency/interpretability.py
index 89873d0e..95e184f4 100644
--- a/src/mednet/engine/saliency/interpretability.py
+++ b/src/mednet/engine/saliency/interpretability.py
@@ -382,8 +382,8 @@ def run(
target_label: int,
datamodule: lightning.pytorch.LightningDataModule,
) -> dict[str, list[typing.Any]]:
- """Applies visualization techniques on input CXR, outputs images with
- overlaid heatmaps and csv files with measurements.
+ """Computes the proportional energy and average saliency focus for a given
+ target label in a datamodule.
Parameters
---------
@@ -399,7 +399,7 @@ def run(
Returns
-------
- A dictionary where keys are dataset names in the provide datamodule,
+ A dictionary where keys are dataset names in the provided datamodule,
and values are lists containing sample information alongside metrics
calculated:
diff --git a/src/mednet/scripts/evaluate.py b/src/mednet/scripts/evaluate.py
index 2a5a85cb..ec8365b9 100644
--- a/src/mednet/scripts/evaluate.py
+++ b/src/mednet/scripts/evaluate.py
@@ -114,7 +114,7 @@ def evaluate(
raise click.BadParameter(
f"""The value of --threshold=`{threshold}` does not match one
of the database split names ({', '.join(predict_data.keys())})
- or can be converted to float. Check your input."""
+ or can not be converted to a float. Check your input."""
)
results: dict[
diff --git a/src/mednet/scripts/saliency/completeness.py b/src/mednet/scripts/saliency/completeness.py
index 41b877d4..16d9c8df 100644
--- a/src/mednet/scripts/saliency/completeness.py
+++ b/src/mednet/scripts/saliency/completeness.py
@@ -21,7 +21,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
cls=ConfigCommand,
epilog="""Examples:
-1. Calculates the ROAD scores for an existing dataset configuration and stores them in .csv files:
+1. Calculates the ROAD scores for an existing dataset configuration and stores them in .json files:
.. code:: sh
--
GitLab