From fe2424b7ae887b0f5a41f6a085b91b3b793d0a6f Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Mon, 29 Jan 2024 09:35:38 +0100
Subject: [PATCH] [doc] Various docstring improvements
---
doc/config.rst | 12 ++++++------
doc/data_model.rst | 2 +-
doc/usage/evaluation.rst | 2 +-
doc/usage/saliency.rst | 10 +++++-----
doc/usage/training.rst | 4 ++--
src/mednet/config/data/montgomery/datamodule.py | 4 ++--
src/mednet/config/data/montgomery/default.py | 2 +-
src/mednet/config/data/montgomery/fold_0.py | 2 +-
src/mednet/config/data/montgomery/fold_1.py | 2 +-
src/mednet/config/data/montgomery/fold_2.py | 2 +-
src/mednet/config/data/montgomery/fold_3.py | 2 +-
src/mednet/config/data/montgomery/fold_4.py | 2 +-
src/mednet/config/data/montgomery/fold_5.py | 2 +-
src/mednet/config/data/montgomery/fold_6.py | 2 +-
src/mednet/config/data/montgomery/fold_7.py | 2 +-
src/mednet/config/data/montgomery/fold_8.py | 2 +-
src/mednet/config/data/montgomery/fold_9.py | 2 +-
.../data/montgomery_shenzhen/datamodule.py | 2 +-
.../config/data/montgomery_shenzhen/default.py | 2 +-
.../config/data/montgomery_shenzhen/fold_0.py | 2 +-
.../config/data/montgomery_shenzhen/fold_1.py | 2 +-
.../config/data/montgomery_shenzhen/fold_2.py | 2 +-
.../config/data/montgomery_shenzhen/fold_3.py | 2 +-
.../config/data/montgomery_shenzhen/fold_4.py | 2 +-
.../config/data/montgomery_shenzhen/fold_5.py | 2 +-
.../config/data/montgomery_shenzhen/fold_6.py | 2 +-
.../config/data/montgomery_shenzhen/fold_7.py | 2 +-
.../config/data/montgomery_shenzhen/fold_8.py | 2 +-
.../config/data/montgomery_shenzhen/fold_9.py | 2 +-
.../montgomery_shenzhen_indian/datamodule.py | 4 ++--
.../data/montgomery_shenzhen_indian/default.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_0.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_1.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_2.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_3.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_4.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_5.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_6.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_7.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_8.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_9.py | 2 +-
.../datamodule.py | 4 ++--
.../datamodule.py | 4 ++--
.../v1_fold_0.py | 2 +-
.../v1_fold_1.py | 2 +-
.../v1_fold_2.py | 2 +-
.../v1_fold_3.py | 2 +-
.../v1_fold_4.py | 2 +-
.../v1_fold_5.py | 2 +-
.../v1_fold_6.py | 2 +-
.../v1_fold_7.py | 2 +-
.../v1_fold_8.py | 2 +-
.../v1_fold_9.py | 2 +-
.../v1_healthy_vs_atb.py | 2 +-
.../v2_fold_0.py | 2 +-
.../v2_fold_1.py | 2 +-
.../v2_fold_2.py | 2 +-
.../v2_fold_3.py | 2 +-
.../v2_fold_4.py | 2 +-
.../v2_fold_5.py | 2 +-
.../v2_fold_6.py | 2 +-
.../v2_fold_7.py | 2 +-
.../v2_fold_8.py | 2 +-
.../v2_fold_9.py | 2 +-
.../v2_others_vs_atb.py | 2 +-
src/mednet/config/data/nih_cxr14/cardiomegaly.py | 2 +-
src/mednet/config/data/nih_cxr14/datamodule.py | 4 ++--
src/mednet/config/data/nih_cxr14/default.py | 2 +-
src/mednet/config/data/shenzhen/datamodule.py | 4 ++--
src/mednet/config/data/shenzhen/fold_0.py | 2 +-
src/mednet/config/data/shenzhen/fold_1.py | 2 +-
src/mednet/config/data/shenzhen/fold_2.py | 2 +-
src/mednet/config/data/shenzhen/fold_3.py | 2 +-
src/mednet/config/data/shenzhen/fold_4.py | 2 +-
src/mednet/config/data/shenzhen/fold_5.py | 2 +-
src/mednet/config/data/shenzhen/fold_6.py | 2 +-
src/mednet/config/data/shenzhen/fold_7.py | 2 +-
src/mednet/config/data/shenzhen/fold_8.py | 2 +-
src/mednet/config/data/shenzhen/fold_9.py | 2 +-
src/mednet/data/datamodule.py | 12 ++++++------
src/mednet/data/split.py | 4 ++--
src/mednet/engine/predictor.py | 6 +++---
src/mednet/engine/saliency/completeness.py | 6 +++---
src/mednet/engine/saliency/generator.py | 2 +-
src/mednet/engine/saliency/interpretability.py | 6 +++---
src/mednet/engine/saliency/viewer.py | 2 +-
src/mednet/engine/trainer.py | 2 +-
src/mednet/scripts/database.py | 4 ++--
src/mednet/scripts/evaluate.py | 4 ++--
src/mednet/scripts/predict.py | 12 ++++++------
src/mednet/scripts/saliency/completeness.py | 16 ++++++++--------
src/mednet/scripts/saliency/evaluate.py | 2 +-
src/mednet/scripts/saliency/generate.py | 10 +++++-----
src/mednet/scripts/saliency/interpretability.py | 13 ++++++-------
src/mednet/scripts/saliency/view.py | 6 +++---
src/mednet/scripts/train.py | 8 ++++----
src/mednet/scripts/train_analysis.py | 4 ++--
tests/test_cli.py | 2 +-
98 files changed, 155 insertions(+), 156 deletions(-)
diff --git a/doc/config.rst b/doc/config.rst
index 1d6c5af9..307e5d3e 100644
--- a/doc/config.rst
+++ b/doc/config.rst
@@ -8,7 +8,7 @@ Preset Configurations
---------------------
This module contains preset configurations for baseline CNN architectures and
-datamodules.
+DataModules.
.. _mednet.config.models:
@@ -38,9 +38,9 @@ DataModule support
==================
Base DataModules and raw data loaders for the various databases currently
-supported in this package, for your reference. Each pre-configured data module
+supported in this package, for your reference. Each pre-configured DataModule
can receive the name of one or more splits as argument to build a fully
-functional data module that can be used in training, prediction or testing.
+functional DataModule that can be used in training, prediction or testing.
.. autosummary::
:toctree: api/config.datamodules
@@ -67,7 +67,7 @@ Pre-configured DataModules
DataModules provide access to preset pytorch dataloaders for training,
validating, testing and running prediction tasks. Each of the pre-configured
-DataModule is based on one (or more) of the :ref:`supported base data modules
+DataModule is based on one (or more) of the :ref:`supported base DataModules
<mednet.config.datamodules>`.
.. autosummary::
@@ -97,8 +97,8 @@ Cross-validation DataModules
We support cross-validation with precise preset folds. In this section, you
will find the configuration for the first fold (fold-0) for all supported
-datamodules. Nine other folds are available for every configuration (from 1 to
-9), making up 10 folds per supported datamodule.
+DataModules. Nine other folds are available for every configuration (from 1 to
+9), making up 10 folds per supported DataModule.
.. autosummary::
diff --git a/doc/data_model.rst b/doc/data_model.rst
index 1d698abd..d0284195 100644
--- a/doc/data_model.rst
+++ b/doc/data_model.rst
@@ -64,6 +64,6 @@ before optionally caching in-memory Sample representations. The "raw" representa
DataModule
----------
-A datamodule aggregates Splits and RawDataLoaders to provide lightning a known-interface to the complete evaluation protocol (train, validation, prediction and testing)
+A DataModule aggregates Splits and RawDataLoaders to provide lightning a known-interface to the complete evaluation protocol (train, validation, prediction and testing)
required for a full experiment to take place. It automates control over data loading parallelisation and caching inside our framework,
providing final access to readily-usable pytorch DataLoaders.
diff --git a/doc/usage/evaluation.rst b/doc/usage/evaluation.rst
index cee0eb45..4bdd7e84 100644
--- a/doc/usage/evaluation.rst
+++ b/doc/usage/evaluation.rst
@@ -39,7 +39,7 @@ Evaluation
----------
In evaluation, we input predictions to generate performance summaries that help analysis of a trained model.
-The generated files are a pdf containing various plots and a table of metrics for each dataset split.
+The generated files are a .pdf containing various plots and a table of metrics for each dataset split.
Evaluation is done using the :ref:`evaluate command <mednet.cli>` followed by the json file generated during
the inference step and a threshold.
diff --git a/doc/usage/saliency.rst b/doc/usage/saliency.rst
index 8eb3723c..65074ae5 100644
--- a/doc/usage/saliency.rst
+++ b/doc/usage/saliency.rst
@@ -25,7 +25,7 @@ Several mapping algorithms are available to choose from, which can be specified
Examples
========
-Generates saliency maps for all prediction dataloaders on a datamodule,
+Generates saliency maps for all prediction dataloaders on a DataModule,
using a pre-trained pasa model, and saves them as numpy-pickeled
objects on the output directory:
@@ -53,12 +53,12 @@ Generates visualizations in form of heatmaps from existing saliency maps for a d
Interpretability
----------------
-Given a target label, the interpretability step computes the proportional energy and average saliency focus in a datamodule.
+Given a target label, the interpretability step computes the proportional energy and average saliency focus in a DataModule.
The proportional energy is defined as the quantity of activation that lies within the ground truth boxes compared to the total sum of the activations.
The average saliency focus is the sum of the values of the saliency map over the ground-truth bounding boxes, normalized by the total area covered by all ground-truth bounding boxes.
-This requires a datamodule containing human-annotated bounding boxes.
+This requires a DataModule containing human-annotated bounding boxes.
Examples
========
@@ -72,7 +72,7 @@ Evaluate the generated saliency maps for their localization performance:
Completeness
------------
-The saliency completeness script computes ROAD scores of saliency maps and saves them in a JSON file.
+The saliency completeness script computes ROAD scores of saliency maps and saves them in a .json file.
The ROAD algorithm estimates the explainability (in the completeness sense) of saliency maps by substituting
relevant pixels in the input image by a local average, re-running prediction on the altered image,
@@ -82,7 +82,7 @@ the importance of such elements in the produced saliency map.
More information can be found in [ROAD-2022]_.
-This requires a datamodule containing human-annotated bounding boxes.
+This requires a DataModule containing human-annotated bounding boxes.
Examples
========
diff --git a/doc/usage/training.rst b/doc/usage/training.rst
index f071febe..7cd58605 100644
--- a/doc/usage/training.rst
+++ b/doc/usage/training.rst
@@ -71,12 +71,12 @@ Plotting training metrics
Various metrics are recorded at each epoch during training, such as the execution time, loss and resource usage.
These are saved in a Tensorboard file, located in a `logs` subdirectory of the training output folder.
-Mednet provides a :ref:`train-analysis <mednet.cli>` convenience script that graphs the scalars stored in these files and saves them in a pdf file.
+Mednet provides a :ref:`train-analysis <mednet.cli>` convenience script that graphs the scalars stored in these files and saves them in a .pdf file.
Examples
========
-Generates a pdf file with plots showing the evolution of logged metrics in time:
+Generates a .pdf file with plots showing the evolution of logged metrics in time:
.. code:: sh
diff --git a/src/mednet/config/data/montgomery/datamodule.py b/src/mednet/config/data/montgomery/datamodule.py
index dbe43cc6..c7aac4c8 100644
--- a/src/mednet/config/data/montgomery/datamodule.py
+++ b/src/mednet/config/data/montgomery/datamodule.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Montgomery datamodule for TB detection.
+"""Montgomery DataModule for TB detection.
Database reference: [MONTGOMERY-SHENZHEN-2014]_
"""
@@ -95,7 +95,7 @@ def make_split(basename: str) -> DatabaseSplit:
class DataModule(CachingDataModule):
- """Montgomery datamodule for TB detection.
+ """Montgomery DataModule for TB detection.
The standard digital image database for Tuberculosis was created by the National
Library of Medicine, Maryland, USA in collaboration with Shenzhen No.3 People’s
diff --git a/src/mednet/config/data/montgomery/default.py b/src/mednet/config/data/montgomery/default.py
index edd014e8..afb62d5d 100644
--- a/src/mednet/config/data/montgomery/default.py
+++ b/src/mednet/config/data/montgomery/default.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Montgomery datamodule for TB detection.
+"""Montgomery DataModule for TB detection.
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/montgomery/fold_0.py b/src/mednet/config/data/montgomery/fold_0.py
index 6d623303..02597fad 100644
--- a/src/mednet/config/data/montgomery/fold_0.py
+++ b/src/mednet/config/data/montgomery/fold_0.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Montgomery datamodule for TB detection (cross validation fold 0).
+"""Montgomery DataModule for TB detection (cross validation fold 0).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/montgomery/fold_1.py b/src/mednet/config/data/montgomery/fold_1.py
index 649f625f..5aff117f 100644
--- a/src/mednet/config/data/montgomery/fold_1.py
+++ b/src/mednet/config/data/montgomery/fold_1.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Montgomery datamodule for TB detection (cross validation fold 1).
+"""Montgomery DataModule for TB detection (cross validation fold 1).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/montgomery/fold_2.py b/src/mednet/config/data/montgomery/fold_2.py
index 28f55b90..879562db 100644
--- a/src/mednet/config/data/montgomery/fold_2.py
+++ b/src/mednet/config/data/montgomery/fold_2.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Montgomery datamodule for TB detection (cross validation fold 2).
+"""Montgomery DataModule for TB detection (cross validation fold 2).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/montgomery/fold_3.py b/src/mednet/config/data/montgomery/fold_3.py
index e357f27e..1e8a31e0 100644
--- a/src/mednet/config/data/montgomery/fold_3.py
+++ b/src/mednet/config/data/montgomery/fold_3.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Montgomery datamodule for TB detection (cross validation fold 3).
+"""Montgomery DataModule for TB detection (cross validation fold 3).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/montgomery/fold_4.py b/src/mednet/config/data/montgomery/fold_4.py
index 57402c01..eb396a7a 100644
--- a/src/mednet/config/data/montgomery/fold_4.py
+++ b/src/mednet/config/data/montgomery/fold_4.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Montgomery datamodule for TB detection (cross validation fold 4).
+"""Montgomery DataModule for TB detection (cross validation fold 4).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/montgomery/fold_5.py b/src/mednet/config/data/montgomery/fold_5.py
index 30b17241..b3620674 100644
--- a/src/mednet/config/data/montgomery/fold_5.py
+++ b/src/mednet/config/data/montgomery/fold_5.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Montgomery datamodule for TB detection (cross validation fold 5).
+"""Montgomery DataModule for TB detection (cross validation fold 5).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/montgomery/fold_6.py b/src/mednet/config/data/montgomery/fold_6.py
index d8a2a8e2..298fc9c5 100644
--- a/src/mednet/config/data/montgomery/fold_6.py
+++ b/src/mednet/config/data/montgomery/fold_6.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Montgomery datamodule for TB detection (cross validation fold 6).
+"""Montgomery DataModule for TB detection (cross validation fold 6).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/montgomery/fold_7.py b/src/mednet/config/data/montgomery/fold_7.py
index 86d16e0c..93ca3c00 100644
--- a/src/mednet/config/data/montgomery/fold_7.py
+++ b/src/mednet/config/data/montgomery/fold_7.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Montgomery datamodule for TB detection (cross validation fold 7).
+"""Montgomery DataModule for TB detection (cross validation fold 7).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/montgomery/fold_8.py b/src/mednet/config/data/montgomery/fold_8.py
index 67a337d2..05b2b1d1 100644
--- a/src/mednet/config/data/montgomery/fold_8.py
+++ b/src/mednet/config/data/montgomery/fold_8.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Montgomery datamodule for TB detection (cross validation fold 8).
+"""Montgomery DataModule for TB detection (cross validation fold 8).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/montgomery/fold_9.py b/src/mednet/config/data/montgomery/fold_9.py
index 032cdbfe..ac6539d9 100644
--- a/src/mednet/config/data/montgomery/fold_9.py
+++ b/src/mednet/config/data/montgomery/fold_9.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Montgomery datamodule for TB detection (cross validation fold 9).
+"""Montgomery DataModule for TB detection (cross validation fold 9).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/montgomery_shenzhen/datamodule.py b/src/mednet/config/data/montgomery_shenzhen/datamodule.py
index 9699f19d..06100561 100644
--- a/src/mednet/config/data/montgomery_shenzhen/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen/datamodule.py
@@ -10,7 +10,7 @@ from ..shenzhen.datamodule import make_split as make_shenzhen_split
class DataModule(ConcatDataModule):
- """Aggregated datamodule composed of Montgomery and Shenzhen datasets."""
+ """Aggregated DataModule composed of Montgomery and Shenzhen datasets."""
def __init__(self, split_filename: str):
montgomery_loader = MontgomeryLoader()
diff --git a/src/mednet/config/data/montgomery_shenzhen/default.py b/src/mednet/config/data/montgomery_shenzhen/default.py
index 106bb415..24dcc4b3 100644
--- a/src/mednet/config/data/montgomery_shenzhen/default.py
+++ b/src/mednet/config/data/montgomery_shenzhen/default.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery and Shenzhen datasets (default
+"""Aggregated DataModule composed of Montgomery and Shenzhen datasets (default
split).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
diff --git a/src/mednet/config/data/montgomery_shenzhen/fold_0.py b/src/mednet/config/data/montgomery_shenzhen/fold_0.py
index d03c9c54..8d319156 100644
--- a/src/mednet/config/data/montgomery_shenzhen/fold_0.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_0.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery and Shenzhen datasets (cross
+"""Aggregated DataModule composed of Montgomery and Shenzhen datasets (cross
validation fold 0).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
diff --git a/src/mednet/config/data/montgomery_shenzhen/fold_1.py b/src/mednet/config/data/montgomery_shenzhen/fold_1.py
index 948a75b0..a9095a0d 100644
--- a/src/mednet/config/data/montgomery_shenzhen/fold_1.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_1.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery and Shenzhen datasets (cross
+"""Aggregated DataModule composed of Montgomery and Shenzhen datasets (cross
validation fold 1).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
diff --git a/src/mednet/config/data/montgomery_shenzhen/fold_2.py b/src/mednet/config/data/montgomery_shenzhen/fold_2.py
index c627fa22..79203be4 100644
--- a/src/mednet/config/data/montgomery_shenzhen/fold_2.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_2.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery and Shenzhen datasets (cross
+"""Aggregated DataModule composed of Montgomery and Shenzhen datasets (cross
validation fold 2).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
diff --git a/src/mednet/config/data/montgomery_shenzhen/fold_3.py b/src/mednet/config/data/montgomery_shenzhen/fold_3.py
index 9ba252f3..fb3114fd 100644
--- a/src/mednet/config/data/montgomery_shenzhen/fold_3.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_3.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery and Shenzhen datasets (cross
+"""Aggregated DataModule composed of Montgomery and Shenzhen datasets (cross
validation fold 3).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
diff --git a/src/mednet/config/data/montgomery_shenzhen/fold_4.py b/src/mednet/config/data/montgomery_shenzhen/fold_4.py
index 720a3adc..24cbc745 100644
--- a/src/mednet/config/data/montgomery_shenzhen/fold_4.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_4.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery and Shenzhen datasets (cross
+"""Aggregated DataModule composed of Montgomery and Shenzhen datasets (cross
validation fold 4).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
diff --git a/src/mednet/config/data/montgomery_shenzhen/fold_5.py b/src/mednet/config/data/montgomery_shenzhen/fold_5.py
index c784a4ea..887cc682 100644
--- a/src/mednet/config/data/montgomery_shenzhen/fold_5.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_5.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery and Shenzhen datasets (cross
+"""Aggregated DataModule composed of Montgomery and Shenzhen datasets (cross
validation fold 5).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
diff --git a/src/mednet/config/data/montgomery_shenzhen/fold_6.py b/src/mednet/config/data/montgomery_shenzhen/fold_6.py
index eaa46472..81a8a906 100644
--- a/src/mednet/config/data/montgomery_shenzhen/fold_6.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_6.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery and Shenzhen datasets (cross
+"""Aggregated DataModule composed of Montgomery and Shenzhen datasets (cross
validation fold 6).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
diff --git a/src/mednet/config/data/montgomery_shenzhen/fold_7.py b/src/mednet/config/data/montgomery_shenzhen/fold_7.py
index 7a6dd33b..298f1961 100644
--- a/src/mednet/config/data/montgomery_shenzhen/fold_7.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_7.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery and Shenzhen datasets (cross
+"""Aggregated DataModule composed of Montgomery and Shenzhen datasets (cross
validation fold 7).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
diff --git a/src/mednet/config/data/montgomery_shenzhen/fold_8.py b/src/mednet/config/data/montgomery_shenzhen/fold_8.py
index 8f295426..b8c2ff10 100644
--- a/src/mednet/config/data/montgomery_shenzhen/fold_8.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_8.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery and Shenzhen datasets (cross
+"""Aggregated DataModule composed of Montgomery and Shenzhen datasets (cross
validation fold 8).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
diff --git a/src/mednet/config/data/montgomery_shenzhen/fold_9.py b/src/mednet/config/data/montgomery_shenzhen/fold_9.py
index 1ec041b8..30528cae 100644
--- a/src/mednet/config/data/montgomery_shenzhen/fold_9.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_9.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery and Shenzhen datasets (cross
+"""Aggregated DataModule composed of Montgomery and Shenzhen datasets (cross
validation fold 9).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py b/src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py
index 20018573..303bf5e7 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py
@@ -1,7 +1,7 @@
# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen and Indian
+"""Aggregated DataModule composed of Montgomery, Shenzhen and Indian
datasets."""
from ....data.datamodule import ConcatDataModule
@@ -14,7 +14,7 @@ from ..shenzhen.datamodule import make_split as make_shenzhen_split
class DataModule(ConcatDataModule):
- """Aggregated datamodule composed of Montgomery, Shenzhen and Indian
+ """Aggregated DataModule composed of Montgomery, Shenzhen and Indian
datasets."""
def __init__(self, split_filename: str):
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian/default.py b/src/mednet/config/data/montgomery_shenzhen_indian/default.py
index a1ac8047..38fca2a9 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian/default.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/default.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen and Indian datasets.
+"""Aggregated DataModule composed of Montgomery, Shenzhen and Indian datasets.
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian/fold_0.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_0.py
index aecbbd10..83d67fe3 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian/fold_0.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_0.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen and Indian datasets
+"""Aggregated DataModule composed of Montgomery, Shenzhen and Indian datasets
(cross validation fold 0).
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian/fold_1.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_1.py
index bef0e4ae..a44b6a68 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian/fold_1.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_1.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen and Indian datasets
+"""Aggregated DataModule composed of Montgomery, Shenzhen and Indian datasets
(cross validation fold 1).
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical details.
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian/fold_2.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_2.py
index 4a75d332..5dac88e8 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian/fold_2.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_2.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen and Indian datasets
+"""Aggregated DataModule composed of Montgomery, Shenzhen and Indian datasets
(cross validation fold 2).
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian/fold_3.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_3.py
index a85428cb..8fe095a3 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian/fold_3.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_3.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen and Indian datasets
+"""Aggregated DataModule composed of Montgomery, Shenzhen and Indian datasets
(cross validation fold 3).
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian/fold_4.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_4.py
index 857a5b62..6524f589 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian/fold_4.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_4.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen and Indian datasets
+"""Aggregated DataModule composed of Montgomery, Shenzhen and Indian datasets
(cross validation fold 4).
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian/fold_5.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_5.py
index 58ac206c..8b0acbe6 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian/fold_5.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_5.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen and Indian datasets
+"""Aggregated DataModule composed of Montgomery, Shenzhen and Indian datasets
(cross validation fold 5).
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian/fold_6.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_6.py
index db77fcc0..d8b565ad 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian/fold_6.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_6.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen and Indian datasets
+"""Aggregated DataModule composed of Montgomery, Shenzhen and Indian datasets
(cross validation fold 6).
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian/fold_7.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_7.py
index aa7f79e5..248f6621 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian/fold_7.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_7.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen and Indian datasets
+"""Aggregated DataModule composed of Montgomery, Shenzhen and Indian datasets
(cross validation fold 7).
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical details.
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian/fold_8.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_8.py
index 31fca750..41c5e5ca 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian/fold_8.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_8.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen and Indian datasets
+"""Aggregated DataModule composed of Montgomery, Shenzhen and Indian datasets
(cross validation fold 8).
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian/fold_9.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_9.py
index 54c9a07e..f658cf37 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian/fold_9.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_9.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen and Indian datasets
+"""Aggregated DataModule composed of Montgomery, Shenzhen and Indian datasets
(cross validation fold 9).
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical details.
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
index 8414ad94..ee111c03 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
@@ -1,7 +1,7 @@
# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and PadChest
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and PadChest
datasets."""
from ....data.datamodule import ConcatDataModule
@@ -16,7 +16,7 @@ from ..shenzhen.datamodule import make_split as make_shenzhen_split
class DataModule(ConcatDataModule):
- """Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and
+ """Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and
PadChest datasets."""
def __init__(self, split_filename: str, padchest_split_filename: str):
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
index 783f7251..f83e4404 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
@@ -1,7 +1,7 @@
# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets."""
from ....data.datamodule import ConcatDataModule
@@ -16,7 +16,7 @@ from ..tbx11k.datamodule import make_split as make_tbx11k_split
class DataModule(ConcatDataModule):
- """Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and
+ """Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and
TBX11k datasets."""
def __init__(self, split_filename: str, tbx11_split_filename: str):
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py
index 88cd03e2..a866e229 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 0).
This remix dataset combines ``fold-0`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py
index 10f57c42..cc9d26ce 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 1).
This remix dataset combines ``fold-1`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py
index 6ec20140..c9f77703 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 2).
This remix dataset combines ``fold-2`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py
index 569ed801..639ac053 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 3).
This remix dataset combines ``fold-3`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py
index 04a74cd3..b08f0588 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 4).
This remix dataset combines ``fold-4`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py
index b528a7b6..7cfd7725 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 5).
This remix dataset combines ``fold-5`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py
index fdf55b42..c8341e7e 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 6).
This remix dataset combines ``fold-6`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py
index 833d2c04..9f9b19d5 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 7).
This remix dataset combines ``fold-7`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py
index a0dd7e82..a2124793 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 8).
This remix dataset combines ``fold-8`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py
index ea00d8ec..b2dff65b 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 9).
This remix dataset combines ``fold-9`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py
index 278ac64e..0f4d1393 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (v1-healthy-vs-atb).
This remix dataset combines the ``default`` split from Montgomery, Shenzhen,
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py
index 022824a1..93fe390d 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 0).
This remix dataset combines ``fold-0`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py
index e48e83e7..0ed16e70 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 1).
This remix dataset combines ``fold-1`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py
index 1e8f38fb..2ff42bcd 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 2).
This remix dataset combines ``fold-2`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py
index 553ea547..dc4b1a4c 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 3).
This remix dataset combines ``fold-3`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py
index 672c9bbe..55113094 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 4).
This remix dataset combines ``fold-4`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py
index b7b3c5ed..0bffb95e 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 5).
This remix dataset combines ``fold-5`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py
index e3001737..a5507999 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 6).
This remix dataset combines ``fold-6`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py
index 4f3b3e91..944c1eb9 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 7).
This remix dataset combines ``fold-7`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py
index afdb0f75..db5331c6 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 8).
This remix dataset combines ``fold-8`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py
index 31b1e440..898a46ae 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (cross-validation fold 9).
This remix dataset combines ``fold-9`` from Montgomery, Shenzhen, and Indian
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py
index 9dca2606..b0bce0ae 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets (v2-others-vs-atb).
This remix dataset combines the ``default`` split from Montgomery, Shenzhen,
diff --git a/src/mednet/config/data/nih_cxr14/cardiomegaly.py b/src/mednet/config/data/nih_cxr14/cardiomegaly.py
index 8be9fde0..255be72e 100644
--- a/src/mednet/config/data/nih_cxr14/cardiomegaly.py
+++ b/src/mednet/config/data/nih_cxr14/cardiomegaly.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""NIH CXR14 (relabeled) datamodule for computer-aided diagnosis (cardiomegaly
+"""NIH CXR14 (relabeled) DataModule for computer-aided diagnosis (cardiomegaly
split).
Database reference: [NIH-CXR14-2017]_
diff --git a/src/mednet/config/data/nih_cxr14/datamodule.py b/src/mednet/config/data/nih_cxr14/datamodule.py
index 4971814c..7c3edcef 100644
--- a/src/mednet/config/data/nih_cxr14/datamodule.py
+++ b/src/mednet/config/data/nih_cxr14/datamodule.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""NIH CXR14 (relabeled) datamodule for computer-aided diagnosis.
+"""NIH CXR14 (relabeled) DataModule for computer-aided diagnosis.
Database reference: [NIH-CXR14-2017]_
"""
@@ -129,7 +129,7 @@ def make_split(basename: str) -> DatabaseSplit:
class DataModule(CachingDataModule):
- """NIH CXR14 (relabeled) datamodule for computer-aided diagnosis.
+ """NIH CXR14 (relabeled) DataModule for computer-aided diagnosis.
This dataset was extracted from the clinical PACS database at the National
Institutes of Health Clinical Center (USA) and represents 60% of all their
diff --git a/src/mednet/config/data/nih_cxr14/default.py b/src/mednet/config/data/nih_cxr14/default.py
index 2fa797be..8c15cd71 100644
--- a/src/mednet/config/data/nih_cxr14/default.py
+++ b/src/mednet/config/data/nih_cxr14/default.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""NIH CXR14 (relabeled) datamodule (``default`` protocol).
+"""NIH CXR14 (relabeled) DataModule (``default`` protocol).
* Training samples: 98637
* Validation samples: 6350
diff --git a/src/mednet/config/data/shenzhen/datamodule.py b/src/mednet/config/data/shenzhen/datamodule.py
index 4a210cfe..15102202 100644
--- a/src/mednet/config/data/shenzhen/datamodule.py
+++ b/src/mednet/config/data/shenzhen/datamodule.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Shenzhen datamodule for computer-aided diagnosis.
+"""Shenzhen DataModule for computer-aided diagnosis.
Database reference: [MONTGOMERY-SHENZHEN-2014]_
"""
@@ -98,7 +98,7 @@ def make_split(basename: str) -> DatabaseSplit:
class DataModule(CachingDataModule):
- """Shenzhen datamodule for computer-aided diagnosis.
+ """Shenzhen DataModule for computer-aided diagnosis.
The standard digital image database for Tuberculosis was created by the National
Library of Medicine, Maryland, USA in collaboration with Shenzhen No.3 People’s
diff --git a/src/mednet/config/data/shenzhen/fold_0.py b/src/mednet/config/data/shenzhen/fold_0.py
index 17ab27e5..218211fa 100644
--- a/src/mednet/config/data/shenzhen/fold_0.py
+++ b/src/mednet/config/data/shenzhen/fold_0.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Shenzhen datamodule for computer-aided diagnosis (cross validation fold 0).
+"""Shenzhen DataModule for computer-aided diagnosis (cross validation fold 0).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/shenzhen/fold_1.py b/src/mednet/config/data/shenzhen/fold_1.py
index 61ea13aa..cee2fd62 100644
--- a/src/mednet/config/data/shenzhen/fold_1.py
+++ b/src/mednet/config/data/shenzhen/fold_1.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Shenzhen datamodule for computer-aided diagnosis (cross validation fold 1).
+"""Shenzhen DataModule for computer-aided diagnosis (cross validation fold 1).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/shenzhen/fold_2.py b/src/mednet/config/data/shenzhen/fold_2.py
index edb92477..1373a64c 100644
--- a/src/mednet/config/data/shenzhen/fold_2.py
+++ b/src/mednet/config/data/shenzhen/fold_2.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Shenzhen datamodule for computer-aided diagnosis (cross validation fold 2).
+"""Shenzhen DataModule for computer-aided diagnosis (cross validation fold 2).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/shenzhen/fold_3.py b/src/mednet/config/data/shenzhen/fold_3.py
index 61800848..8fa1c4c2 100644
--- a/src/mednet/config/data/shenzhen/fold_3.py
+++ b/src/mednet/config/data/shenzhen/fold_3.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Shenzhen datamodule for computer-aided diagnosis (cross validation fold 3).
+"""Shenzhen DataModule for computer-aided diagnosis (cross validation fold 3).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/shenzhen/fold_4.py b/src/mednet/config/data/shenzhen/fold_4.py
index 478af2ee..3998c2d2 100644
--- a/src/mednet/config/data/shenzhen/fold_4.py
+++ b/src/mednet/config/data/shenzhen/fold_4.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Shenzhen datamodule for computer-aided diagnosis (cross validation fold 4).
+"""Shenzhen DataModule for computer-aided diagnosis (cross validation fold 4).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/shenzhen/fold_5.py b/src/mednet/config/data/shenzhen/fold_5.py
index 21dcf8ff..71452ef2 100644
--- a/src/mednet/config/data/shenzhen/fold_5.py
+++ b/src/mednet/config/data/shenzhen/fold_5.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Shenzhen datamodule for computer-aided diagnosis (cross validation fold 5).
+"""Shenzhen DataModule for computer-aided diagnosis (cross validation fold 5).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/shenzhen/fold_6.py b/src/mednet/config/data/shenzhen/fold_6.py
index fbc6aac8..69a51cce 100644
--- a/src/mednet/config/data/shenzhen/fold_6.py
+++ b/src/mednet/config/data/shenzhen/fold_6.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Shenzhen datamodule for computer-aided diagnosis (cross validation fold 6).
+"""Shenzhen DataModule for computer-aided diagnosis (cross validation fold 6).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/shenzhen/fold_7.py b/src/mednet/config/data/shenzhen/fold_7.py
index 204f7b0b..619a28d0 100644
--- a/src/mednet/config/data/shenzhen/fold_7.py
+++ b/src/mednet/config/data/shenzhen/fold_7.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Shenzhen datamodule for computer-aided diagnosis (cross validation fold 7).
+"""Shenzhen DataModule for computer-aided diagnosis (cross validation fold 7).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/shenzhen/fold_8.py b/src/mednet/config/data/shenzhen/fold_8.py
index 3679fa18..1eb4278a 100644
--- a/src/mednet/config/data/shenzhen/fold_8.py
+++ b/src/mednet/config/data/shenzhen/fold_8.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Shenzhen datamodule for computer-aided diagnosis (cross validation fold 8).
+"""Shenzhen DataModule for computer-aided diagnosis (cross validation fold 8).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/config/data/shenzhen/fold_9.py b/src/mednet/config/data/shenzhen/fold_9.py
index 32afdbd8..c112edf9 100644
--- a/src/mednet/config/data/shenzhen/fold_9.py
+++ b/src/mednet/config/data/shenzhen/fold_9.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Shenzhen datamodule for computer-aided diagnosis (cross validation fold 9).
+"""Shenzhen DataModule for computer-aided diagnosis (cross validation fold 9).
Database reference: [MONTGOMERY-SHENZHEN-2014]_
diff --git a/src/mednet/data/datamodule.py b/src/mednet/data/datamodule.py
index 758f0ef0..539bd621 100644
--- a/src/mednet/data/datamodule.py
+++ b/src/mednet/data/datamodule.py
@@ -390,7 +390,7 @@ def _make_balanced_random_sampler(
class ConcatDataModule(lightning.LightningDataModule):
- """A conveninent data module with dictionary split loading, mini- batching,
+ """A conveninent DataModule with dictionary split loading, mini- batching,
parallelisation and caching, all in one.
Instances of this class can load and concatenate an arbitrary number of
@@ -399,7 +399,7 @@ class ConcatDataModule(lightning.LightningDataModule):
stores the data in associated CPU memory, which can improve data serving
while training and evaluating models.
- This datamodule defines basic operations to handle data loading and
+ This DataModule defines basic operations to handle data loading and
mini-batch handling within this package's framework. It can return
:py:class:`torch.utils.data.DataLoader` objects for training, validation,
prediction and testing conditions. Parallelisation is handled by a simple
@@ -582,8 +582,8 @@ class ConcatDataModule(lightning.LightningDataModule):
A list of transforms (torch modules) that will be applied after
raw-data-loading. and just before data is fed into the model or
eventual data-augmentation transformations for all data loaders
- produced by this data module. This part of the pipeline
- receives data as output by the raw-data-loader, or model-related
+ produced by this DataModule. This part of the pipeline receives
+ data as output by the raw-data-loader, or model-related
transforms (e.g. resize adaptions), if any is specified. If
data is cached, it is cached **after** model-transforms are
applied, as that is a potential memory saver (e.g., if it
@@ -873,9 +873,9 @@ class ConcatDataModule(lightning.LightningDataModule):
class CachingDataModule(ConcatDataModule):
- """A simplified version of our data module for a single split.
+ """A simplified version of our DataModule for a single split.
- Apart from construction, the behaviour of this data module is very similar
+ Apart from construction, the behaviour of this DataModule is very similar
to its simpler counterpart, serving training, validation and test sets.
Parameters
diff --git a/src/mednet/data/split.py b/src/mednet/data/split.py
index 634c1b65..7dc61f22 100644
--- a/src/mednet/data/split.py
+++ b/src/mednet/data/split.py
@@ -62,7 +62,7 @@ class JSONDatabaseSplit(DatabaseSplit):
Parameters
----------
path
- Absolute path to a JSON formatted file containing the database split to be
+ Absolute path to a .json formatted file containing the database split to be
recognized by this object.
"""
@@ -75,7 +75,7 @@ class JSONDatabaseSplit(DatabaseSplit):
def _datasets(self) -> DatabaseSplit:
"""Datasets in a split.
- The first call to this (cached) property will trigger full JSON file
+ The first call to this (cached) property will trigger full .json file
loading from disk. Subsequent calls will be cached.
Returns
diff --git a/src/mednet/engine/predictor.py b/src/mednet/engine/predictor.py
index e4d625fb..db7b6ac1 100644
--- a/src/mednet/engine/predictor.py
+++ b/src/mednet/engine/predictor.py
@@ -38,7 +38,7 @@ def run(
model
Neural network model (e.g. pasa).
datamodule
- The lightning datamodule to use for training **and** validation
+ The lightning DataModule to use for training **and** validation
device_manager
An internal device representation, to be used for training and
validation. This representation can be converted into a pytorch device
@@ -55,7 +55,7 @@ def run(
| MultiClassPredictionSplit
| None
)
- Depending on the return type of the datamodule's
+ Depending on the return type of the DataModule's
``predict_dataloader()`` method:
* if :py:class:`torch.utils.data.DataLoader`, then returns a
@@ -71,7 +71,7 @@ def run(
Raises
------
TypeError
- If the datamodule's ``predict_dataloader()`` method does not return any
+ If the DataModule's ``predict_dataloader()`` method does not return any
of the types described above.
"""
diff --git a/src/mednet/engine/saliency/completeness.py b/src/mednet/engine/saliency/completeness.py
index 655cdedc..c9a961f7 100644
--- a/src/mednet/engine/saliency/completeness.py
+++ b/src/mednet/engine/saliency/completeness.py
@@ -203,7 +203,7 @@ def run(
percentiles: typing.Sequence[int],
parallel: int,
) -> dict[str, list[typing.Any]]:
- """Evaluates ROAD scores for all samples in a datamodule.
+ """Evaluates ROAD scores for all samples in a DataModule.
The ROAD algorithm was first described in [ROAD-2022]_. It estimates
explainability (in the completeness sense) of saliency maps by substituting
@@ -225,7 +225,7 @@ def run(
model
Neural network model (e.g. pasa).
datamodule
- The lightning datamodule to iterate on.
+ The lightning DataModule to iterate on.
device_manager
An internal device representation, to be used for training and
validation. This representation can be converted into a pytorch device
@@ -254,7 +254,7 @@ def run(
Returns
-------
dict[str, list[typing.Any]]
- A dictionary where keys are dataset names in the provide datamodule,
+ A dictionary where keys are dataset names in the provide DataModule,
and values are lists containing sample information alongside metrics
calculated:
diff --git a/src/mednet/engine/saliency/generator.py b/src/mednet/engine/saliency/generator.py
index 2096adc1..72b53d51 100644
--- a/src/mednet/engine/saliency/generator.py
+++ b/src/mednet/engine/saliency/generator.py
@@ -125,7 +125,7 @@ def run(
model
Neural network model (e.g. pasa).
datamodule
- The lightning datamodule to iterate on.
+ The lightning DataModule to iterate on.
device_manager
An internal device representation, to be used for training and
validation. This representation can be converted into a pytorch device
diff --git a/src/mednet/engine/saliency/interpretability.py b/src/mednet/engine/saliency/interpretability.py
index b18cfe95..6611d157 100644
--- a/src/mednet/engine/saliency/interpretability.py
+++ b/src/mednet/engine/saliency/interpretability.py
@@ -388,7 +388,7 @@ def run(
datamodule: lightning.pytorch.LightningDataModule,
) -> dict[str, list[typing.Any]]:
"""Computes the proportional energy and average saliency focus for a given
- target label in a datamodule.
+ target label in a DataModule.
Parameters
---------
@@ -399,12 +399,12 @@ def run(
The label to target for evaluating interpretability metrics. Samples
contining any other label are ignored.
datamodule
- The lightning datamodule to iterate on.
+ The lightning DataModule to iterate on.
Returns
-------
dict[str, list[typing.Any]]
- A dictionary where keys are dataset names in the provided 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/engine/saliency/viewer.py b/src/mednet/engine/saliency/viewer.py
index 184a586d..4e4c6890 100644
--- a/src/mednet/engine/saliency/viewer.py
+++ b/src/mednet/engine/saliency/viewer.py
@@ -200,7 +200,7 @@ def run(
Parameters
----------
datamodule
- The lightning datamodule to iterate on.
+ The Lightning DataModule to iterate on.
input_folder
Directory in which the saliency maps are stored for a specific
visualization type.
diff --git a/src/mednet/engine/trainer.py b/src/mednet/engine/trainer.py
index 3c3deeee..c338d7f4 100644
--- a/src/mednet/engine/trainer.py
+++ b/src/mednet/engine/trainer.py
@@ -125,7 +125,7 @@ def run(
model
Neural network model (e.g. pasa).
datamodule
- The lightning datamodule to use for training **and** validation.
+ The lightning DataModule to use for training **and** validation.
validation_period
Number of epochs after which validation happens. By default, we run
validation after every training epoch (period=1). You can change this
diff --git a/src/mednet/scripts/database.py b/src/mednet/scripts/database.py
index 8bd43ff2..f58a2746 100644
--- a/src/mednet/scripts/database.py
+++ b/src/mednet/scripts/database.py
@@ -132,7 +132,7 @@ def list():
)
@verbosity_option(logger=logger, expose_value=False)
def check(split, limit):
- """Checks file access on one or more datamodules."""
+ """Checks file access on one or more DataModules."""
import importlib.metadata
import sys
@@ -189,5 +189,5 @@ def check(split, limit):
)
else:
click.secho(
- f"Found {errors} errors loading datamodule `{split}`.", fg="red"
+ f"Found {errors} errors loading DataModule `{split}`.", fg="red"
)
diff --git a/src/mednet/scripts/evaluate.py b/src/mednet/scripts/evaluate.py
index ec8365b9..25976eef 100644
--- a/src/mednet/scripts/evaluate.py
+++ b/src/mednet/scripts/evaluate.py
@@ -38,7 +38,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.option(
"--predictions",
"-p",
- help="Path where predictions are currently stored",
+ help="Directory in which predictions are currently stored",
required=True,
type=click.Path(
file_okay=True, dir_okay=False, writable=True, path_type=pathlib.Path
@@ -48,7 +48,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.option(
"--output-folder",
"-o",
- help="Path where to store the analysis result (created if does not exist)",
+ help="Directory in which to store the analysis result (created if does not exist)",
required=False,
default="results",
type=click.Path(file_okay=False, dir_okay=True, path_type=pathlib.Path),
diff --git a/src/mednet/scripts/predict.py b/src/mednet/scripts/predict.py
index c684ed95..34cf93aa 100644
--- a/src/mednet/scripts/predict.py
+++ b/src/mednet/scripts/predict.py
@@ -19,7 +19,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
cls=ConfigCommand,
epilog="""Examples:
-1. Runs prediction on an existing datamodule configuration:
+1. Runs prediction on an existing DataModule configuration:
.. code:: sh
@@ -36,8 +36,8 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.option(
"--output",
"-o",
- help="""Path where to store the JSON predictions for all samples in the
- input datamodule (leading directories are created if they do not
+ help="""Path to a .json file in which to save predictions for all samples in the
+ input DataModule (leading directories are created if they do not
exist).""",
required=True,
default="results",
@@ -57,9 +57,9 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.option(
"--datamodule",
"-d",
- help="""A lightning data module that will be asked for prediction data
- loaders. Typically, this includes all configured splits in a datamodule,
- however this is not a requirement. A datamodule that returns a single
+ help="""A lightning DataModule that will be asked for prediction data
+ loaders. Typically, this includes all configured splits in a DataModule,
+ however this is not a requirement. A DataModule that returns a single
dataloader for prediction (wrapped in a dictionary) is acceptable.""",
required=True,
cls=ResourceOption,
diff --git a/src/mednet/scripts/saliency/completeness.py b/src/mednet/scripts/saliency/completeness.py
index 62072612..1d9d7172 100644
--- a/src/mednet/scripts/saliency/completeness.py
+++ b/src/mednet/scripts/saliency/completeness.py
@@ -41,17 +41,17 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.option(
"--datamodule",
"-d",
- help="""A lightning data module that will be asked for prediction data
- loaders. Typically, this includes all configured splits in a datamodule,
- however this is not a requirement. A datamodule that returns a single
- dataloader for prediction (wrapped in a dictionary) is acceptable.""",
+ help="""A lightning DataModule that will be asked for prediction DataLoaders.
+ Typically, this includes all configured splits in a DataModule,
+ however this is not a requirement. A DataModule that returns a single
+ DataLoader for prediction (wrapped in a dictionary) is acceptable.""",
required=True,
cls=ResourceOption,
)
@click.option(
"--output-json",
"-o",
- help="""Path where to store the output JSON file containing all
+ help="""Directory in which to store the output .json file containing all
measures.""",
required=True,
type=click.Path(
@@ -188,15 +188,15 @@ def completeness(
2023, this measurement technique is considered to be one of the
state-of-the-art metrics of explainability.
- This program outputs a JSON file containing the ROAD evaluations (using
+ This program outputs a .json file containing the ROAD evaluations (using
most-relevant-first, or MoRF, and least-relevant-first, or LeRF for each
- sample in the datamodule. Values for MoRF and LeRF represent averages by
+ sample in the DataModule. Values for MoRF and LeRF represent averages by
removing 20, 40, 60 and 80% of most or least relevant pixels respectively
from the image, and averaging results for all these percentiles.
.. note::
- This application is relatively slow when processing a large datamodule
+ This application is relatively slow when processing a large DataModule
with many (positive) samples.
"""
import json
diff --git a/src/mednet/scripts/saliency/evaluate.py b/src/mednet/scripts/saliency/evaluate.py
index f84ee73e..4b00cc50 100644
--- a/src/mednet/scripts/saliency/evaluate.py
+++ b/src/mednet/scripts/saliency/evaluate.py
@@ -65,7 +65,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.option(
"--output-folder",
"-o",
- help="Path where to store the analysis result (created if does not exist)",
+ help="Directory in which to store the analysis result (created if does not exist)",
required=False,
default="results",
type=click.Path(file_okay=False, dir_okay=True, path_type=pathlib.Path),
diff --git a/src/mednet/scripts/saliency/generate.py b/src/mednet/scripts/saliency/generate.py
index 34e54fd4..c2ae4501 100644
--- a/src/mednet/scripts/saliency/generate.py
+++ b/src/mednet/scripts/saliency/generate.py
@@ -21,7 +21,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
cls=ConfigCommand,
epilog="""Examples:
-1. Generates saliency maps for all prediction dataloaders on a datamodule,
+1. Generates saliency maps for all prediction dataloaders on a DataModule,
using a pre-trained DenseNet model, and saves them as numpy-pickeled
objects on the output directory:
@@ -43,9 +43,9 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.option(
"--datamodule",
"-d",
- help="""A lightning data module that will be asked for prediction data
- loaders. Typically, this includes all configured splits in a datamodule,
- however this is not a requirement. A datamodule that returns a single
+ help="""A lightning DataModule that will be asked for prediction data
+ loaders. Typically, this includes all configured splits in a DataModule,
+ however this is not a requirement. A DataModule that returns a single
dataloader for prediction (wrapped in a dictionary) is acceptable.""",
required=True,
cls=ResourceOption,
@@ -53,7 +53,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.option(
"--output-folder",
"-o",
- help="Path where to store saliency maps (created if does not exist)",
+ help="Directory in which to store saliency maps (created if does not exist)",
required=True,
type=click.Path(
exists=False,
diff --git a/src/mednet/scripts/saliency/interpretability.py b/src/mednet/scripts/saliency/interpretability.py
index 321bb18f..e5fa9556 100644
--- a/src/mednet/scripts/saliency/interpretability.py
+++ b/src/mednet/scripts/saliency/interpretability.py
@@ -30,9 +30,9 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.option(
"--datamodule",
"-d",
- help="""A lightning data module that will be asked for prediction data
- loaders. Typically, this includes all configured splits in a datamodule,
- however this is not a requirement. A datamodule that returns a single
+ help="""A lightning DataModule that will be asked for prediction data
+ loaders. Typically, this includes all configured splits in a DataModule,
+ however this is not a requirement. A DataModule that returns a single
dataloader for prediction (wrapped in a dictionary) is acceptable.""",
required=True,
cls=ResourceOption,
@@ -66,8 +66,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.option(
"--output-json",
"-o",
- help="""Path where to store the output JSON file containing all
- measures.""",
+ help="""Path to the .json file in which all measures will be saved.""",
required=True,
type=click.Path(
file_okay=True,
@@ -98,8 +97,8 @@ def interpretability(
contain built-in annotations which corroborate classification.
- As a result of the evaluation, this application creates a single JSON file
- that resembles the original datamodule, with added information containing
+ As a result of the evaluation, this application creates a single .json file
+ that resembles the original DataModule, with added information containing
the following measures, for each sample:
* Proportional Energy: A measure that compares (UNthresholed) saliency maps
diff --git a/src/mednet/scripts/saliency/view.py b/src/mednet/scripts/saliency/view.py
index b61df6e2..928cac6b 100644
--- a/src/mednet/scripts/saliency/view.py
+++ b/src/mednet/scripts/saliency/view.py
@@ -35,14 +35,14 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.option(
"--datamodule",
"-d",
- help="A lightning data module containing the training, validation and test sets.",
+ help="A lightning DataModule containing the training, validation and test sets.",
required=True,
cls=ResourceOption,
)
@click.option(
"--input-folder",
"-i",
- help="Path to the folder containing the saliency maps for a specific visualization type.",
+ help="Path to the directory containing the saliency maps for a specific visualization type.",
required=True,
type=click.Path(
file_okay=False,
@@ -56,7 +56,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.option(
"--output-folder",
"-o",
- help="Path where to store the visualizations (created if does not exist)",
+ help="Directory in which to store the visualizations (created if does not exist)",
required=True,
type=click.Path(
file_okay=False,
diff --git a/src/mednet/scripts/train.py b/src/mednet/scripts/train.py
index de8801af..cc974870 100644
--- a/src/mednet/scripts/train.py
+++ b/src/mednet/scripts/train.py
@@ -35,7 +35,7 @@ def reusable_options(f):
@click.option(
"--output-folder",
"-o",
- help="Path where to store results (created if does not exist)",
+ help="Directory in which to store results (created if does not exist)",
required=True,
type=click.Path(
file_okay=False,
@@ -56,7 +56,7 @@ def reusable_options(f):
@click.option(
"--datamodule",
"-d",
- help="A lightning data module containing the training and validation sets.",
+ help="A lightning DataModule containing the training and validation sets.",
required=True,
cls=ResourceOption,
)
@@ -293,9 +293,9 @@ def train(
# If asked, rebalances the loss criterion based on the relative proportion
# of class examples available in the training set. Also affects the
- # validation loss if a validation set is available on the data module.
+ # validation loss if a validation set is available on the DataModule.
if balance_classes:
- logger.info("Applying datamodule train sampler balancing...")
+ logger.info("Applying DataModule train sampler balancing...")
datamodule.balance_sampler_by_class = True
# logger.info("Applying train/valid loss balancing...")
# model.balance_losses_by_class(datamodule)
diff --git a/src/mednet/scripts/train_analysis.py b/src/mednet/scripts/train_analysis.py
index 88a6bcb2..d3c979e0 100644
--- a/src/mednet/scripts/train_analysis.py
+++ b/src/mednet/scripts/train_analysis.py
@@ -123,7 +123,7 @@ def create_figures(
@click.option(
"--output",
"-o",
- help="Name of the output file to create (multi-page PDF)",
+ help="Name of the output file to create (multi-page .pdf)",
required=True,
show_default=True,
default="trainlog.pdf",
@@ -135,7 +135,7 @@ def train_analysis(
output: pathlib.Path,
) -> None:
"""Creates a plot for each metric in the training logs and saves them in a
- PDF file."""
+ .pdf file."""
import matplotlib.pyplot as plt
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 6648d135..64a9e2d5 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -87,7 +87,7 @@ def test_config_describe_montgomery():
runner = CliRunner()
result = runner.invoke(describe, ["montgomery"])
_assert_exit_0(result)
- assert "Montgomery datamodule for TB detection." in result.output
+ assert "Montgomery DataModule for TB detection." in result.output
def test_database_help():
--
GitLab