diff --git a/src/ptbench/configs/models/alexnet.py b/src/ptbench/configs/models/alexnet.py
index 0028e810ed34658b754ea0fe89b75bf64faae4a0..8de265c568da58295a1de7e89c9205a20e90f9e0 100644
--- a/src/ptbench/configs/models/alexnet.py
+++ b/src/ptbench/configs/models/alexnet.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""AlexNet."""
from torch.nn import BCEWithLogitsLoss
diff --git a/src/ptbench/configs/models/alexnet_pretrained.py b/src/ptbench/configs/models/alexnet_pretrained.py
index 9c772f42e935b2b995030e6d73fcc044fdcbcc76..b6db6c5941aa2d50baf90dc414ea93042c570307 100644
--- a/src/ptbench/configs/models/alexnet_pretrained.py
+++ b/src/ptbench/configs/models/alexnet_pretrained.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""AlexNet."""
from torch.nn import BCEWithLogitsLoss
diff --git a/src/ptbench/configs/models/densenet.py b/src/ptbench/configs/models/densenet.py
index 5d453a6d4ff75514c0e7669a01b43be3e1aa3473..cce44a25b4a42b35d9998eb0ef156ce0160c5dc3 100644
--- a/src/ptbench/configs/models/densenet.py
+++ b/src/ptbench/configs/models/densenet.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""DenseNet."""
from torch.nn import BCEWithLogitsLoss
diff --git a/src/ptbench/configs/models/densenet_pretrained.py b/src/ptbench/configs/models/densenet_pretrained.py
index 49b0162f5fb1defd3bfc7b64bcc390c9e2bd0c27..9e32807e5edb9ed4c7637928192bed58231f7848 100644
--- a/src/ptbench/configs/models/densenet_pretrained.py
+++ b/src/ptbench/configs/models/densenet_pretrained.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""DenseNet."""
from torch.nn import BCEWithLogitsLoss
diff --git a/src/ptbench/configs/models/logistic_regression.py b/src/ptbench/configs/models/logistic_regression.py
index 145dddd7a3a9c6e0b0574f3c6358f6f9f51056a0..dab855aaee6fa478a2e1210d559a26242ba6cfe7 100644
--- a/src/ptbench/configs/models/logistic_regression.py
+++ b/src/ptbench/configs/models/logistic_regression.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Feedforward network for Tuberculosis Detection.
Simple feedforward network taking radiological signs in output and
diff --git a/src/ptbench/configs/models/pasa.py b/src/ptbench/configs/models/pasa.py
index b1a201e5b2d1f5a1b22135ee46ea148d8f655536..22e664a214bdf563a1d92657c0c52add875c56c1 100644
--- a/src/ptbench/configs/models/pasa.py
+++ b/src/ptbench/configs/models/pasa.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""CNN for Tuberculosis Detection.
Implementation of the model architecture proposed by F. Pasa in the article
diff --git a/src/ptbench/configs/models/signs_to_tb.py b/src/ptbench/configs/models/signs_to_tb.py
index 1ce89b1299764463f3f7f9e54e2ad2172acfea6f..acec64f3115d27dc129b3a79a6e59b1d2567e15f 100644
--- a/src/ptbench/configs/models/signs_to_tb.py
+++ b/src/ptbench/configs/models/signs_to_tb.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Feedforward network for Tuberculosis Detection.
Simple feedforward network taking radiological signs in output and
diff --git a/src/ptbench/configs/models_datasets/densenet_rs.py b/src/ptbench/configs/models_datasets/densenet_rs.py
index 714404bf173c8868e4c67e49f257a1b221e540d7..b1ba206b54d9918747c29de54d9215b707b66f93 100644
--- a/src/ptbench/configs/models_datasets/densenet_rs.py
+++ b/src/ptbench/configs/models_datasets/densenet_rs.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""CNN for radiological findings detection.
A Densenet121 model for radiological extraction
diff --git a/src/ptbench/data/hivtb/__init__.py b/src/ptbench/data/hivtb/__init__.py
index e004c1dcdaa983aea81d2c2afd67b7dbce25165d..0fca31ae5ad1553328baa81b59282fb1c8622391 100644
--- a/src/ptbench/data/hivtb/__init__.py
+++ b/src/ptbench/data/hivtb/__init__.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""HIV-TB dataset for computer-aided diagnosis (only BMP files)
* Reference: [HIV-TB-2019]_
diff --git a/src/ptbench/data/hivtb/fold_0.py b/src/ptbench/data/hivtb/fold_0.py
index af3be161a75f76c8287168fdca0e4cac2c5b43d3..dae7f3dc6080845c4c4e4992d44a064a435ff595 100644
--- a/src/ptbench/data/hivtb/fold_0.py
+++ b/src/ptbench/data/hivtb/fold_0.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""HIV-TB dataset for TB detection (cross validation fold 0)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/hivtb/fold_1.py b/src/ptbench/data/hivtb/fold_1.py
index ec86cab362f9b4f298f3b92f7e62893d2f83d16b..e2f31bb958ed13bb993788a90968f1cdc9e32e08 100644
--- a/src/ptbench/data/hivtb/fold_1.py
+++ b/src/ptbench/data/hivtb/fold_1.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""HIV-TB dataset for TB detection (cross validation fold 1)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/hivtb/fold_2.py b/src/ptbench/data/hivtb/fold_2.py
index 56ae69fee9fe57a2a9d2042f0b20e984832334ac..2bb387e746654fc830f1d57de9016ce3beede077 100644
--- a/src/ptbench/data/hivtb/fold_2.py
+++ b/src/ptbench/data/hivtb/fold_2.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""HIV-TB dataset for TB detection (cross validation fold 2)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/hivtb/fold_3.py b/src/ptbench/data/hivtb/fold_3.py
index 5dbddeda83eda1b46e485a7cbed619a3f8ff1714..ff3ca7e6b0de4ff5e9fcb17c94ab6d71908e25a9 100644
--- a/src/ptbench/data/hivtb/fold_3.py
+++ b/src/ptbench/data/hivtb/fold_3.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""HIV-TB dataset for TB detection (cross validation fold 3)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/hivtb/fold_4.py b/src/ptbench/data/hivtb/fold_4.py
index 9ab5a79fe3642254302388e0e054f6753cc8e3f5..1111102586d102e6eca83f278500acb8ff4e6aed 100644
--- a/src/ptbench/data/hivtb/fold_4.py
+++ b/src/ptbench/data/hivtb/fold_4.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""HIV-TB dataset for TB detection (cross validation fold 4)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/hivtb/fold_5.py b/src/ptbench/data/hivtb/fold_5.py
index 445ce4589a85bf6323de19f654e93bbd5d766e4b..b27e34df371e39cfb812fcf713fe583039b00268 100644
--- a/src/ptbench/data/hivtb/fold_5.py
+++ b/src/ptbench/data/hivtb/fold_5.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""HIV-TB dataset for TB detection (cross validation fold 5)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/hivtb/fold_6.py b/src/ptbench/data/hivtb/fold_6.py
index fbbea2ad903d704787d106077fdfc60cc35b2988..f6cd1cf5b522c7df91faa725084bdfe53a6609f4 100644
--- a/src/ptbench/data/hivtb/fold_6.py
+++ b/src/ptbench/data/hivtb/fold_6.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""HIV-TB dataset for TB detection (cross validation fold 6)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/hivtb/fold_7.py b/src/ptbench/data/hivtb/fold_7.py
index dcce836d87ff865a88f5f22c8a98bea7f2ded780..7fabae5c6ef0bd316c8d2b6ad21dbf9fabdc596e 100644
--- a/src/ptbench/data/hivtb/fold_7.py
+++ b/src/ptbench/data/hivtb/fold_7.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""HIV-TB dataset for TB detection (cross validation fold 7)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/hivtb/fold_8.py b/src/ptbench/data/hivtb/fold_8.py
index 7ba95a1e1cb501b408d409ce04cd2f466bdd55c3..53a0e1a71b1f857b7d2ccfe937cd94bffe5fa737 100644
--- a/src/ptbench/data/hivtb/fold_8.py
+++ b/src/ptbench/data/hivtb/fold_8.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""HIV-TB dataset for TB detection (cross validation fold 8)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/hivtb/fold_9.py b/src/ptbench/data/hivtb/fold_9.py
index 4a244adfd3807f1abfb46b5b7f55dcedf6dc0292..dcac4d53dfcc4a075673768a1a953ededa258011 100644
--- a/src/ptbench/data/hivtb/fold_9.py
+++ b/src/ptbench/data/hivtb/fold_9.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""HIV-TB dataset for TB detection (cross validation fold 9)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/image_utils.py b/src/ptbench/data/image_utils.py
index 9103126f4179c552d7107471cc373a510500e2c0..b9f8c8108dd0db18a0cd796b968d26f82da49906 100644
--- a/src/ptbench/data/image_utils.py
+++ b/src/ptbench/data/image_utils.py
@@ -1,8 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
-
"""Data loading code."""
import pathlib
@@ -16,9 +14,9 @@ class SingleAutoLevel16to8:
This transform assumes that the input image is gray-scaled.
- To auto-level, we calculate the maximum and the minimum of the image, and
- consider such a range should be mapped to the [0,255] range of the
- destination image.
+ To auto-level, we calculate the maximum and the minimum of the
+ image, and consider such a range should be mapped to the [0,255]
+ range of the destination image.
"""
def __call__(self, img):
diff --git a/src/ptbench/data/mc_ch_in_pc/default.py b/src/ptbench/data/mc_ch_in_pc/default.py
index 0b8be8f44d10fb859dcb7c044a6646c1375fda5a..4715b13d2b50893ab9de25c779b54507df2ff564 100644
--- a/src/ptbench/data/mc_ch_in_pc/default.py
+++ b/src/ptbench/data/mc_ch_in_pc/default.py
@@ -1,7 +1,6 @@
# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Aggregated dataset composed of Montgomery, Shenzhen, Indian and Padchest
datasets."""
diff --git a/src/ptbench/data/padchest/__init__.py b/src/ptbench/data/padchest/__init__.py
index f6f39a9ebe98eb68a88374b8d83a70447a4ad995..1151b55f28eb1a6e90310e0abc5c544991b314bb 100644
--- a/src/ptbench/data/padchest/__init__.py
+++ b/src/ptbench/data/padchest/__init__.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Padchest dataset for computer-aided diagnosis.
A large chest x-ray image dataset with multi-label annotated reports.
diff --git a/src/ptbench/data/padchest/cardiomegaly_idiap.py b/src/ptbench/data/padchest/cardiomegaly_idiap.py
index 25eaa6e8fd0ba15db3a46f4d14366bcf5bc91667..d25387388d1540e706876eef2e15543b293113e0 100644
--- a/src/ptbench/data/padchest/cardiomegaly_idiap.py
+++ b/src/ptbench/data/padchest/cardiomegaly_idiap.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Padchest cardiomegaly (idiap protocol) dataset for computer-aided diagnosis.
The first 40 images with cardiomegaly.
diff --git a/src/ptbench/data/padchest/idiap.py b/src/ptbench/data/padchest/idiap.py
index d91b552f39123cfc6e808dfe3bc8bab097448497..284a944d0d83bd933123d63732f4f045549084d3 100644
--- a/src/ptbench/data/padchest/idiap.py
+++ b/src/ptbench/data/padchest/idiap.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Padchest (idiap protocol) dataset for computer-aided diagnosis.
* See :py:mod:`ptbench.data.padchest` for dataset details
diff --git a/src/ptbench/data/padchest/no_tb_idiap.py b/src/ptbench/data/padchest/no_tb_idiap.py
index 78155abf3c5a44de88920da1833ddfa09b6bb244..a424e0fe46890b899804aeac954cb3bd710429ae 100644
--- a/src/ptbench/data/padchest/no_tb_idiap.py
+++ b/src/ptbench/data/padchest/no_tb_idiap.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Padchest tuberculosis (no TB idiap protocol) dataset for computer-aided
diagnosis.
diff --git a/src/ptbench/data/padchest/tb_idiap.py b/src/ptbench/data/padchest/tb_idiap.py
index 51428935d728d243b34eec4e54c2d1fcc911224b..1a2516202e676386d149fbfc684e3b93e805978e 100644
--- a/src/ptbench/data/padchest/tb_idiap.py
+++ b/src/ptbench/data/padchest/tb_idiap.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Padchest tuberculosis (idiap protocol) dataset for computer-aided diagnosis.
The 125 healthy images are the first 125 padchest images with the following
diff --git a/src/ptbench/data/tbpoc/__init__.py b/src/ptbench/data/tbpoc/__init__.py
index 4d9f455055203710549e879d5091078ade40f97e..00f5f42c7f81b93c5ab4c037d289275e3477b00b 100644
--- a/src/ptbench/data/tbpoc/__init__.py
+++ b/src/ptbench/data/tbpoc/__init__.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""TB-POC dataset for computer-aided diagnosis.
* Reference: [TB-POC-2018]_
diff --git a/src/ptbench/data/tbpoc/fold_0.py b/src/ptbench/data/tbpoc/fold_0.py
index a440117f88e8009fc0fa20716ab84b4cbb573977..332347a9434978f415d472c240e92a155e7f2e2b 100644
--- a/src/ptbench/data/tbpoc/fold_0.py
+++ b/src/ptbench/data/tbpoc/fold_0.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""TB-POC dataset for TB detection (cross validation fold 0)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/tbpoc/fold_1.py b/src/ptbench/data/tbpoc/fold_1.py
index 95a54ee3b7b347c53dc351430a90cb0d394b4f42..c8b055f356ee40e56bbfc8dc5b397f055aae3b29 100644
--- a/src/ptbench/data/tbpoc/fold_1.py
+++ b/src/ptbench/data/tbpoc/fold_1.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""TB-POC dataset for TB detection (cross validation fold 1)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/tbpoc/fold_2.py b/src/ptbench/data/tbpoc/fold_2.py
index 508c54a83114a1803cec97bbb885ba437e8a0105..33a2329aadf93377d0d86763575c28c360d0f1a0 100644
--- a/src/ptbench/data/tbpoc/fold_2.py
+++ b/src/ptbench/data/tbpoc/fold_2.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""TB-POC dataset for TB detection (cross validation fold 2)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/tbpoc/fold_3.py b/src/ptbench/data/tbpoc/fold_3.py
index 28d34553422830e45b9b2893edfa8722c504924a..ac418f20eddc49e7fcefa35de5bf3745b93c80ad 100644
--- a/src/ptbench/data/tbpoc/fold_3.py
+++ b/src/ptbench/data/tbpoc/fold_3.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""TB-POC dataset for TB detection (cross validation fold 3)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/tbpoc/fold_4.py b/src/ptbench/data/tbpoc/fold_4.py
index 90bff0b284f91e94ce660f60d95f67049f402a77..da21a88287d0f646778823da6353a370502b6862 100644
--- a/src/ptbench/data/tbpoc/fold_4.py
+++ b/src/ptbench/data/tbpoc/fold_4.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""TB-POC dataset for TB detection (cross validation fold 4)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/tbpoc/fold_5.py b/src/ptbench/data/tbpoc/fold_5.py
index cbe4ff6e06e4dbe1c1617a298f943904334da88d..323996c710e291456a29ec2ae6d7aaf4af677361 100644
--- a/src/ptbench/data/tbpoc/fold_5.py
+++ b/src/ptbench/data/tbpoc/fold_5.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""TB-POC dataset for TB detection (cross validation fold 5)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/tbpoc/fold_6.py b/src/ptbench/data/tbpoc/fold_6.py
index 3edeb7273bac27f5fe3249bbcd6aa5e1fb2840f5..7be3befa3d6d57dd831f34f210c69708c61cac66 100644
--- a/src/ptbench/data/tbpoc/fold_6.py
+++ b/src/ptbench/data/tbpoc/fold_6.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""TB-POC dataset for TB detection (cross validation fold 6)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/tbpoc/fold_7.py b/src/ptbench/data/tbpoc/fold_7.py
index 3ef4fe0be368435272a611c319a8497183edfd82..9c84b929938106d54e141edcdcc17ea55e12863a 100644
--- a/src/ptbench/data/tbpoc/fold_7.py
+++ b/src/ptbench/data/tbpoc/fold_7.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""TB-POC dataset for TB detection (cross validation fold 7)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/tbpoc/fold_8.py b/src/ptbench/data/tbpoc/fold_8.py
index 6b68c0c3dae48e3b95af34acbce4c868de7b2c46..c647f6f6486e5e4d624ca44a889d2a26bf761824 100644
--- a/src/ptbench/data/tbpoc/fold_8.py
+++ b/src/ptbench/data/tbpoc/fold_8.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""TB-POC dataset for TB detection (cross validation fold 8)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/data/tbpoc/fold_9.py b/src/ptbench/data/tbpoc/fold_9.py
index 0f2565a449450cfa6685bbf4546e7abe4d7999ab..aad4c14eddd46075c5c97e13238bcd741a4322b2 100644
--- a/src/ptbench/data/tbpoc/fold_9.py
+++ b/src/ptbench/data/tbpoc/fold_9.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""TB-POC dataset for TB detection (cross validation fold 9)
* Split reference: none (stratified kfolding)
diff --git a/src/ptbench/engine/evaluator.py b/src/ptbench/engine/evaluator.py
index a551dba65f4ed0deaab1b4a5ef541accaf79d454..9d14f79078dc255ac2dec738584675331c74111f 100644
--- a/src/ptbench/engine/evaluator.py
+++ b/src/ptbench/engine/evaluator.py
@@ -1,14 +1,14 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Defines functionality for the evaluation of predictions."""
import logging
import os
import re
-from typing import Iterable, Optional
+from collections.abc import Iterable
+from typing import Optional
import matplotlib.pyplot as plt
import numpy
@@ -292,7 +292,6 @@ def run(
),
)
data_df = data_df.set_index("index")
-
"""# Save evaluation csv
if output_folder is not None:
fullpath = os.path.join(output_folder, f"{name}.csv")
@@ -353,7 +352,6 @@ def run(
axes.spines["right"].set_visible(False)
axes.spines["top"].set_visible(False)
axes.spines["left"].set_position(("data", -0.015))
-
"""if f1_thresh is not None and eer_thresh is not None:
# get the closest possible threshold we have
index = int(round(steps * f1_thresh))
diff --git a/src/ptbench/models/normalizer.py b/src/ptbench/models/normalizer.py
index ce68f4b558b2812d17a8f54954e197a086233a52..147efc7e02beac30bab6f79678b6860c3b42c810 100644
--- a/src/ptbench/models/normalizer.py
+++ b/src/ptbench/models/normalizer.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""A network model that prefixes a subtract/divide step to any other module."""
import torch
diff --git a/src/ptbench/models/transforms.py b/src/ptbench/models/transforms.py
index 585b5846151292c69c8bb3411f68e28dc5eb97e2..8ff0af726aada9256603882dd8a6c0aeb6d34cad 100644
--- a/src/ptbench/models/transforms.py
+++ b/src/ptbench/models/transforms.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""A transform that turns grayscale images to RGB."""
import torch
diff --git a/src/ptbench/scripts/relevance_analysis.py b/src/ptbench/scripts/relevance_analysis.py
index 1771c107f1317ad181838cf408a76d2c955ad30c..6be7abd5bdf49995a3910404d971f523893537a7 100644
--- a/src/ptbench/scripts/relevance_analysis.py
+++ b/src/ptbench/scripts/relevance_analysis.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Import copy import os import shutil.
import numpy as np
diff --git a/src/ptbench/utils/resources.py b/src/ptbench/utils/resources.py
index d6ed02196ca73286ac19520e6f327b8d4ebf8021..ca0f5efa3727e5cc53ac6c722f2371e0ccc4d00d 100644
--- a/src/ptbench/utils/resources.py
+++ b/src/ptbench/utils/resources.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tools for interacting with the running computer or GPU."""
import logging
diff --git a/tests/data/iris.json b/tests/data/iris.json
index 1777efc361562880096b9a21b2011218c152ecac..4bbc1d841f4ba9052fa7eecdd751e1582510acc1 100644
--- a/tests/data/iris.json
+++ b/tests/data/iris.json
@@ -1,156 +1,156 @@
-{
- "train": [
- [5.1,3.5,1.4,0.2,"Iris-setosa"],
- [4.9,3,1.4,0.2,"Iris-setosa"],
- [4.7,3.2,1.3,0.2,"Iris-setosa"],
- [4.6,3.1,1.5,0.2,"Iris-setosa"],
- [5,3.6,1.4,0.2,"Iris-setosa"],
- [5.4,3.9,1.7,0.4,"Iris-setosa"],
- [4.6,3.4,1.4,0.3,"Iris-setosa"],
- [5,3.4,1.5,0.2,"Iris-setosa"],
- [4.4,2.9,1.4,0.2,"Iris-setosa"],
- [4.9,3.1,1.5,0.1,"Iris-setosa"],
- [5.4,3.7,1.5,0.2,"Iris-setosa"],
- [4.8,3.4,1.6,0.2,"Iris-setosa"],
- [4.8,3,1.4,0.1,"Iris-setosa"],
- [4.3,3,1.1,0.1,"Iris-setosa"],
- [5.8,4,1.2,0.2,"Iris-setosa"],
- [5.7,4.4,1.5,0.4,"Iris-setosa"],
- [5.4,3.9,1.3,0.4,"Iris-setosa"],
- [5.1,3.5,1.4,0.3,"Iris-setosa"],
- [5.7,3.8,1.7,0.3,"Iris-setosa"],
- [5.1,3.8,1.5,0.3,"Iris-setosa"],
- [5.4,3.4,1.7,0.2,"Iris-setosa"],
- [5.1,3.7,1.5,0.4,"Iris-setosa"],
- [4.6,3.6,1,0.2,"Iris-setosa"],
- [5.1,3.3,1.7,0.5,"Iris-setosa"],
- [4.8,3.4,1.9,0.2,"Iris-setosa"],
- [7,3.2,4.7,1.4,"Iris-versicolor"],
- [6.4,3.2,4.5,1.5,"Iris-versicolor"],
- [6.9,3.1,4.9,1.5,"Iris-versicolor"],
- [5.5,2.3,4,1.3,"Iris-versicolor"],
- [6.5,2.8,4.6,1.5,"Iris-versicolor"],
- [5.7,2.8,4.5,1.3,"Iris-versicolor"],
- [6.3,3.3,4.7,1.6,"Iris-versicolor"],
- [4.9,2.4,3.3,1,"Iris-versicolor"],
- [6.6,2.9,4.6,1.3,"Iris-versicolor"],
- [5.2,2.7,3.9,1.4,"Iris-versicolor"],
- [5,2,3.5,1,"Iris-versicolor"],
- [5.9,3,4.2,1.5,"Iris-versicolor"],
- [6,2.2,4,1,"Iris-versicolor"],
- [6.1,2.9,4.7,1.4,"Iris-versicolor"],
- [5.6,2.9,3.6,1.3,"Iris-versicolor"],
- [6.7,3.1,4.4,1.4,"Iris-versicolor"],
- [5.6,3,4.5,1.5,"Iris-versicolor"],
- [5.8,2.7,4.1,1,"Iris-versicolor"],
- [6.2,2.2,4.5,1.5,"Iris-versicolor"],
- [5.6,2.5,3.9,1.1,"Iris-versicolor"],
- [5.9,3.2,4.8,1.8,"Iris-versicolor"],
- [6.1,2.8,4,1.3,"Iris-versicolor"],
- [6.3,2.5,4.9,1.5,"Iris-versicolor"],
- [6.1,2.8,4.7,1.2,"Iris-versicolor"],
- [6.4,2.9,4.3,1.3,"Iris-versicolor"],
- [6.3,3.3,6,2.5,"Iris-virginica"],
- [5.8,2.7,5.1,1.9,"Iris-virginica"],
- [7.1,3,5.9,2.1,"Iris-virginica"],
- [6.3,2.9,5.6,1.8,"Iris-virginica"],
- [6.5,3,5.8,2.2,"Iris-virginica"],
- [7.6,3,6.6,2.1,"Iris-virginica"],
- [4.9,2.5,4.5,1.7,"Iris-virginica"],
- [7.3,2.9,6.3,1.8,"Iris-virginica"],
- [6.7,2.5,5.8,1.8,"Iris-virginica"],
- [7.2,3.6,6.1,2.5,"Iris-virginica"],
- [6.5,3.2,5.1,2,"Iris-virginica"],
- [6.4,2.7,5.3,1.9,"Iris-virginica"],
- [6.8,3,5.5,2.1,"Iris-virginica"],
- [5.7,2.5,5,2,"Iris-virginica"],
- [5.8,2.8,5.1,2.4,"Iris-virginica"],
- [6.4,3.2,5.3,2.3,"Iris-virginica"],
- [6.5,3,5.5,1.8,"Iris-virginica"],
- [7.7,3.8,6.7,2.2,"Iris-virginica"],
- [7.7,2.6,6.9,2.3,"Iris-virginica"],
- [6,2.2,5,1.5,"Iris-virginica"],
- [6.9,3.2,5.7,2.3,"Iris-virginica"],
- [5.6,2.8,4.9,2,"Iris-virginica"],
- [7.7,2.8,6.7,2,"Iris-virginica"],
- [6.3,2.7,4.9,1.8,"Iris-virginica"],
- [6.7,3.3,5.7,2.1,"Iris-virginica"]
- ],
- "test": [
- [5,3,1.6,0.2,"Iris-setosa"],
- [5,3.4,1.6,0.4,"Iris-setosa"],
- [5.2,3.5,1.5,0.2,"Iris-setosa"],
- [5.2,3.4,1.4,0.2,"Iris-setosa"],
- [4.7,3.2,1.6,0.2,"Iris-setosa"],
- [4.8,3.1,1.6,0.2,"Iris-setosa"],
- [5.4,3.4,1.5,0.4,"Iris-setosa"],
- [5.2,4.1,1.5,0.1,"Iris-setosa"],
- [5.5,4.2,1.4,0.2,"Iris-setosa"],
- [4.9,3.1,1.5,0.1,"Iris-setosa"],
- [5,3.2,1.2,0.2,"Iris-setosa"],
- [5.5,3.5,1.3,0.2,"Iris-setosa"],
- [4.9,3.1,1.5,0.1,"Iris-setosa"],
- [4.4,3,1.3,0.2,"Iris-setosa"],
- [5.1,3.4,1.5,0.2,"Iris-setosa"],
- [5,3.5,1.3,0.3,"Iris-setosa"],
- [4.5,2.3,1.3,0.3,"Iris-setosa"],
- [4.4,3.2,1.3,0.2,"Iris-setosa"],
- [5,3.5,1.6,0.6,"Iris-setosa"],
- [5.1,3.8,1.9,0.4,"Iris-setosa"],
- [4.8,3,1.4,0.3,"Iris-setosa"],
- [5.1,3.8,1.6,0.2,"Iris-setosa"],
- [4.6,3.2,1.4,0.2,"Iris-setosa"],
- [5.3,3.7,1.5,0.2,"Iris-setosa"],
- [5,3.3,1.4,0.2,"Iris-setosa"],
- [6.6,3,4.4,1.4,"Iris-versicolor"],
- [6.8,2.8,4.8,1.4,"Iris-versicolor"],
- [6.7,3,5,1.7,"Iris-versicolor"],
- [6,2.9,4.5,1.5,"Iris-versicolor"],
- [5.7,2.6,3.5,1,"Iris-versicolor"],
- [5.5,2.4,3.8,1.1,"Iris-versicolor"],
- [5.5,2.4,3.7,1,"Iris-versicolor"],
- [5.8,2.7,3.9,1.2,"Iris-versicolor"],
- [6,2.7,5.1,1.6,"Iris-versicolor"],
- [5.4,3,4.5,1.5,"Iris-versicolor"],
- [6,3.4,4.5,1.6,"Iris-versicolor"],
- [6.7,3.1,4.7,1.5,"Iris-versicolor"],
- [6.3,2.3,4.4,1.3,"Iris-versicolor"],
- [5.6,3,4.1,1.3,"Iris-versicolor"],
- [5.5,2.5,4,1.3,"Iris-versicolor"],
- [5.5,2.6,4.4,1.2,"Iris-versicolor"],
- [6.1,3,4.6,1.4,"Iris-versicolor"],
- [5.8,2.6,4,1.2,"Iris-versicolor"],
- [5,2.3,3.3,1,"Iris-versicolor"],
- [5.6,2.7,4.2,1.3,"Iris-versicolor"],
- [5.7,3,4.2,1.2,"Iris-versicolor"],
- [5.7,2.9,4.2,1.3,"Iris-versicolor"],
- [6.2,2.9,4.3,1.3,"Iris-versicolor"],
- [5.1,2.5,3,1.1,"Iris-versicolor"],
- [5.7,2.8,4.1,1.3,"Iris-versicolor"],
- [7.2,3.2,6,1.8,"Iris-virginica"],
- [6.2,2.8,4.8,1.8,"Iris-virginica"],
- [6.1,3,4.9,1.8,"Iris-virginica"],
- [6.4,2.8,5.6,2.1,"Iris-virginica"],
- [7.2,3,5.8,1.6,"Iris-virginica"],
- [7.4,2.8,6.1,1.9,"Iris-virginica"],
- [7.9,3.8,6.4,2,"Iris-virginica"],
- [6.4,2.8,5.6,2.2,"Iris-virginica"],
- [6.3,2.8,5.1,1.5,"Iris-virginica"],
- [6.1,2.6,5.6,1.4,"Iris-virginica"],
- [7.7,3,6.1,2.3,"Iris-virginica"],
- [6.3,3.4,5.6,2.4,"Iris-virginica"],
- [6.4,3.1,5.5,1.8,"Iris-virginica"],
- [6,3,4.8,1.8,"Iris-virginica"],
- [6.9,3.1,5.4,2.1,"Iris-virginica"],
- [6.7,3.1,5.6,2.4,"Iris-virginica"],
- [6.9,3.1,5.1,2.3,"Iris-virginica"],
- [5.8,2.7,5.1,1.9,"Iris-virginica"],
- [6.8,3.2,5.9,2.3,"Iris-virginica"],
- [6.7,3.3,5.7,2.5,"Iris-virginica"],
- [6.7,3,5.2,2.3,"Iris-virginica"],
- [6.3,2.5,5,1.9,"Iris-virginica"],
- [6.5,3,5.2,2,"Iris-virginica"],
- [6.2,3.4,5.4,2.3,"Iris-virginica"],
- [5.9,3,5.1,1.8,"Iris-virginica"]
- ]
-}
+{
+ "train": [
+ [5.1, 3.5, 1.4, 0.2, "Iris-setosa"],
+ [4.9, 3, 1.4, 0.2, "Iris-setosa"],
+ [4.7, 3.2, 1.3, 0.2, "Iris-setosa"],
+ [4.6, 3.1, 1.5, 0.2, "Iris-setosa"],
+ [5, 3.6, 1.4, 0.2, "Iris-setosa"],
+ [5.4, 3.9, 1.7, 0.4, "Iris-setosa"],
+ [4.6, 3.4, 1.4, 0.3, "Iris-setosa"],
+ [5, 3.4, 1.5, 0.2, "Iris-setosa"],
+ [4.4, 2.9, 1.4, 0.2, "Iris-setosa"],
+ [4.9, 3.1, 1.5, 0.1, "Iris-setosa"],
+ [5.4, 3.7, 1.5, 0.2, "Iris-setosa"],
+ [4.8, 3.4, 1.6, 0.2, "Iris-setosa"],
+ [4.8, 3, 1.4, 0.1, "Iris-setosa"],
+ [4.3, 3, 1.1, 0.1, "Iris-setosa"],
+ [5.8, 4, 1.2, 0.2, "Iris-setosa"],
+ [5.7, 4.4, 1.5, 0.4, "Iris-setosa"],
+ [5.4, 3.9, 1.3, 0.4, "Iris-setosa"],
+ [5.1, 3.5, 1.4, 0.3, "Iris-setosa"],
+ [5.7, 3.8, 1.7, 0.3, "Iris-setosa"],
+ [5.1, 3.8, 1.5, 0.3, "Iris-setosa"],
+ [5.4, 3.4, 1.7, 0.2, "Iris-setosa"],
+ [5.1, 3.7, 1.5, 0.4, "Iris-setosa"],
+ [4.6, 3.6, 1, 0.2, "Iris-setosa"],
+ [5.1, 3.3, 1.7, 0.5, "Iris-setosa"],
+ [4.8, 3.4, 1.9, 0.2, "Iris-setosa"],
+ [7, 3.2, 4.7, 1.4, "Iris-versicolor"],
+ [6.4, 3.2, 4.5, 1.5, "Iris-versicolor"],
+ [6.9, 3.1, 4.9, 1.5, "Iris-versicolor"],
+ [5.5, 2.3, 4, 1.3, "Iris-versicolor"],
+ [6.5, 2.8, 4.6, 1.5, "Iris-versicolor"],
+ [5.7, 2.8, 4.5, 1.3, "Iris-versicolor"],
+ [6.3, 3.3, 4.7, 1.6, "Iris-versicolor"],
+ [4.9, 2.4, 3.3, 1, "Iris-versicolor"],
+ [6.6, 2.9, 4.6, 1.3, "Iris-versicolor"],
+ [5.2, 2.7, 3.9, 1.4, "Iris-versicolor"],
+ [5, 2, 3.5, 1, "Iris-versicolor"],
+ [5.9, 3, 4.2, 1.5, "Iris-versicolor"],
+ [6, 2.2, 4, 1, "Iris-versicolor"],
+ [6.1, 2.9, 4.7, 1.4, "Iris-versicolor"],
+ [5.6, 2.9, 3.6, 1.3, "Iris-versicolor"],
+ [6.7, 3.1, 4.4, 1.4, "Iris-versicolor"],
+ [5.6, 3, 4.5, 1.5, "Iris-versicolor"],
+ [5.8, 2.7, 4.1, 1, "Iris-versicolor"],
+ [6.2, 2.2, 4.5, 1.5, "Iris-versicolor"],
+ [5.6, 2.5, 3.9, 1.1, "Iris-versicolor"],
+ [5.9, 3.2, 4.8, 1.8, "Iris-versicolor"],
+ [6.1, 2.8, 4, 1.3, "Iris-versicolor"],
+ [6.3, 2.5, 4.9, 1.5, "Iris-versicolor"],
+ [6.1, 2.8, 4.7, 1.2, "Iris-versicolor"],
+ [6.4, 2.9, 4.3, 1.3, "Iris-versicolor"],
+ [6.3, 3.3, 6, 2.5, "Iris-virginica"],
+ [5.8, 2.7, 5.1, 1.9, "Iris-virginica"],
+ [7.1, 3, 5.9, 2.1, "Iris-virginica"],
+ [6.3, 2.9, 5.6, 1.8, "Iris-virginica"],
+ [6.5, 3, 5.8, 2.2, "Iris-virginica"],
+ [7.6, 3, 6.6, 2.1, "Iris-virginica"],
+ [4.9, 2.5, 4.5, 1.7, "Iris-virginica"],
+ [7.3, 2.9, 6.3, 1.8, "Iris-virginica"],
+ [6.7, 2.5, 5.8, 1.8, "Iris-virginica"],
+ [7.2, 3.6, 6.1, 2.5, "Iris-virginica"],
+ [6.5, 3.2, 5.1, 2, "Iris-virginica"],
+ [6.4, 2.7, 5.3, 1.9, "Iris-virginica"],
+ [6.8, 3, 5.5, 2.1, "Iris-virginica"],
+ [5.7, 2.5, 5, 2, "Iris-virginica"],
+ [5.8, 2.8, 5.1, 2.4, "Iris-virginica"],
+ [6.4, 3.2, 5.3, 2.3, "Iris-virginica"],
+ [6.5, 3, 5.5, 1.8, "Iris-virginica"],
+ [7.7, 3.8, 6.7, 2.2, "Iris-virginica"],
+ [7.7, 2.6, 6.9, 2.3, "Iris-virginica"],
+ [6, 2.2, 5, 1.5, "Iris-virginica"],
+ [6.9, 3.2, 5.7, 2.3, "Iris-virginica"],
+ [5.6, 2.8, 4.9, 2, "Iris-virginica"],
+ [7.7, 2.8, 6.7, 2, "Iris-virginica"],
+ [6.3, 2.7, 4.9, 1.8, "Iris-virginica"],
+ [6.7, 3.3, 5.7, 2.1, "Iris-virginica"]
+ ],
+ "test": [
+ [5, 3, 1.6, 0.2, "Iris-setosa"],
+ [5, 3.4, 1.6, 0.4, "Iris-setosa"],
+ [5.2, 3.5, 1.5, 0.2, "Iris-setosa"],
+ [5.2, 3.4, 1.4, 0.2, "Iris-setosa"],
+ [4.7, 3.2, 1.6, 0.2, "Iris-setosa"],
+ [4.8, 3.1, 1.6, 0.2, "Iris-setosa"],
+ [5.4, 3.4, 1.5, 0.4, "Iris-setosa"],
+ [5.2, 4.1, 1.5, 0.1, "Iris-setosa"],
+ [5.5, 4.2, 1.4, 0.2, "Iris-setosa"],
+ [4.9, 3.1, 1.5, 0.1, "Iris-setosa"],
+ [5, 3.2, 1.2, 0.2, "Iris-setosa"],
+ [5.5, 3.5, 1.3, 0.2, "Iris-setosa"],
+ [4.9, 3.1, 1.5, 0.1, "Iris-setosa"],
+ [4.4, 3, 1.3, 0.2, "Iris-setosa"],
+ [5.1, 3.4, 1.5, 0.2, "Iris-setosa"],
+ [5, 3.5, 1.3, 0.3, "Iris-setosa"],
+ [4.5, 2.3, 1.3, 0.3, "Iris-setosa"],
+ [4.4, 3.2, 1.3, 0.2, "Iris-setosa"],
+ [5, 3.5, 1.6, 0.6, "Iris-setosa"],
+ [5.1, 3.8, 1.9, 0.4, "Iris-setosa"],
+ [4.8, 3, 1.4, 0.3, "Iris-setosa"],
+ [5.1, 3.8, 1.6, 0.2, "Iris-setosa"],
+ [4.6, 3.2, 1.4, 0.2, "Iris-setosa"],
+ [5.3, 3.7, 1.5, 0.2, "Iris-setosa"],
+ [5, 3.3, 1.4, 0.2, "Iris-setosa"],
+ [6.6, 3, 4.4, 1.4, "Iris-versicolor"],
+ [6.8, 2.8, 4.8, 1.4, "Iris-versicolor"],
+ [6.7, 3, 5, 1.7, "Iris-versicolor"],
+ [6, 2.9, 4.5, 1.5, "Iris-versicolor"],
+ [5.7, 2.6, 3.5, 1, "Iris-versicolor"],
+ [5.5, 2.4, 3.8, 1.1, "Iris-versicolor"],
+ [5.5, 2.4, 3.7, 1, "Iris-versicolor"],
+ [5.8, 2.7, 3.9, 1.2, "Iris-versicolor"],
+ [6, 2.7, 5.1, 1.6, "Iris-versicolor"],
+ [5.4, 3, 4.5, 1.5, "Iris-versicolor"],
+ [6, 3.4, 4.5, 1.6, "Iris-versicolor"],
+ [6.7, 3.1, 4.7, 1.5, "Iris-versicolor"],
+ [6.3, 2.3, 4.4, 1.3, "Iris-versicolor"],
+ [5.6, 3, 4.1, 1.3, "Iris-versicolor"],
+ [5.5, 2.5, 4, 1.3, "Iris-versicolor"],
+ [5.5, 2.6, 4.4, 1.2, "Iris-versicolor"],
+ [6.1, 3, 4.6, 1.4, "Iris-versicolor"],
+ [5.8, 2.6, 4, 1.2, "Iris-versicolor"],
+ [5, 2.3, 3.3, 1, "Iris-versicolor"],
+ [5.6, 2.7, 4.2, 1.3, "Iris-versicolor"],
+ [5.7, 3, 4.2, 1.2, "Iris-versicolor"],
+ [5.7, 2.9, 4.2, 1.3, "Iris-versicolor"],
+ [6.2, 2.9, 4.3, 1.3, "Iris-versicolor"],
+ [5.1, 2.5, 3, 1.1, "Iris-versicolor"],
+ [5.7, 2.8, 4.1, 1.3, "Iris-versicolor"],
+ [7.2, 3.2, 6, 1.8, "Iris-virginica"],
+ [6.2, 2.8, 4.8, 1.8, "Iris-virginica"],
+ [6.1, 3, 4.9, 1.8, "Iris-virginica"],
+ [6.4, 2.8, 5.6, 2.1, "Iris-virginica"],
+ [7.2, 3, 5.8, 1.6, "Iris-virginica"],
+ [7.4, 2.8, 6.1, 1.9, "Iris-virginica"],
+ [7.9, 3.8, 6.4, 2, "Iris-virginica"],
+ [6.4, 2.8, 5.6, 2.2, "Iris-virginica"],
+ [6.3, 2.8, 5.1, 1.5, "Iris-virginica"],
+ [6.1, 2.6, 5.6, 1.4, "Iris-virginica"],
+ [7.7, 3, 6.1, 2.3, "Iris-virginica"],
+ [6.3, 3.4, 5.6, 2.4, "Iris-virginica"],
+ [6.4, 3.1, 5.5, 1.8, "Iris-virginica"],
+ [6, 3, 4.8, 1.8, "Iris-virginica"],
+ [6.9, 3.1, 5.4, 2.1, "Iris-virginica"],
+ [6.7, 3.1, 5.6, 2.4, "Iris-virginica"],
+ [6.9, 3.1, 5.1, 2.3, "Iris-virginica"],
+ [5.8, 2.7, 5.1, 1.9, "Iris-virginica"],
+ [6.8, 3.2, 5.9, 2.3, "Iris-virginica"],
+ [6.7, 3.3, 5.7, 2.5, "Iris-virginica"],
+ [6.7, 3, 5.2, 2.3, "Iris-virginica"],
+ [6.3, 2.5, 5, 1.9, "Iris-virginica"],
+ [6.5, 3, 5.2, 2, "Iris-virginica"],
+ [6.2, 3.4, 5.4, 2.3, "Iris-virginica"],
+ [5.9, 3, 5.1, 1.8, "Iris-virginica"]
+ ]
+}
diff --git a/tests/test_11k.py b/tests/test_11k.py
index 2a82b459b6f4dab5002723e51e3907667ad9c8ee..b08a249ca592334fef3816171fbcc11aa60ad19a 100644
--- a/tests/test_11k.py
+++ b/tests/test_11k.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for TBX11K simplified dataset split 1."""
import pytest
diff --git a/tests/test_11k_RS.py b/tests/test_11k_RS.py
index 9cbcee2046841bb402929158d55b0a92100e49e5..1f9d975d95e50c1166dff3d5f8fad939948956bd 100644
--- a/tests/test_11k_RS.py
+++ b/tests/test_11k_RS.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for Extended TBX11K simplified dataset split 1."""
import pytest
diff --git a/tests/test_11k_v2.py b/tests/test_11k_v2.py
index 8751a9b8a136d37261966b962152a03c3a81b1e3..9feab3ce74ffe53d414771908ce3ba63a8db74de 100644
--- a/tests/test_11k_v2.py
+++ b/tests/test_11k_v2.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for TBX11K simplified dataset split 2."""
import pytest
diff --git a/tests/test_11k_v2_RS.py b/tests/test_11k_v2_RS.py
index 4b1c7a4c3f8bb28d830d34f767cf5ac964075414..590d2872ac915ef9f61eaea91d45dd2e9d911f4c 100644
--- a/tests/test_11k_v2_RS.py
+++ b/tests/test_11k_v2_RS.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for Extended TBX11K simplified dataset split 2."""
import pytest
diff --git a/tests/test_ch_RS.py b/tests/test_ch_RS.py
index fbe1c3b6cabcfd2a25aa2bedf22bdd379a0626d7..0f1fa60252a21f5658729d27dcb1cf82e8c81fe3 100644
--- a/tests/test_ch_RS.py
+++ b/tests/test_ch_RS.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for Extended Shenzhen dataset."""
import pytest
diff --git a/tests/test_cli.py b/tests/test_cli.py
index dd6e34459b383a575d9a0eaac610f500168d5326..67b39bd742d34ea8f30fa8555a003f1c68fbe3cf 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for our CLI applications."""
import contextlib
diff --git a/tests/test_database_split.py b/tests/test_database_split.py
index 851a10975d14900de91f007abbfb575754bff9de..aa360e2c889952d976252aac68725dbc6ced1095 100644
--- a/tests/test_database_split.py
+++ b/tests/test_database_split.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Test code for datasets."""
from ptbench.data.split import CSVDatabaseSplit, JSONDatabaseSplit
@@ -14,14 +13,14 @@ def test_csv_loading(datadir):
assert len(database_split["iris-train"]) == 75
for k in database_split["iris-train"]:
for f in range(4):
- assert type(k[f]) == str # csv only loads stringd
- assert type(k[4]) == str
+ assert isinstance(k[f], str) # csv only loads stringd
+ assert isinstance(k[4], str)
assert len(database_split["iris-test"]) == 75
for k in database_split["iris-test"]:
for f in range(4):
- assert type(k[f]) == str # csv only loads stringd
- assert type(k[4]) == str
+ assert isinstance(k[f], str) # csv only loads stringd
+ assert isinstance(k[4], str)
assert k[4] in ("Iris-setosa", "Iris-versicolor", "Iris-virginica")
@@ -33,11 +32,11 @@ def test_json_loading(datadir):
assert len(database_split["train"]) == 75
for k in database_split["train"]:
for f in range(4):
- assert type(k[f]) in [int, float]
- assert type(k[4]) == str
+ assert isinstance(k[f], (int, float))
+ assert isinstance(k[4], str)
assert len(database_split["test"]) == 75
for k in database_split["test"]:
for f in range(4):
- assert type(k[f]) in [int, float]
- assert type(k[4]) == str
+ assert isinstance(k[f], (int, float))
+ assert isinstance(k[4], str)
diff --git a/tests/test_hivtb.py b/tests/test_hivtb.py
index 0398085a1ae401ea854e9386a6014d501e187a2d..37876051415f25dcc7d43072af08c27c9f8ff0a9 100644
--- a/tests/test_hivtb.py
+++ b/tests/test_hivtb.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for HIV-TB dataset."""
import pytest
diff --git a/tests/test_hivtb_RS.py b/tests/test_hivtb_RS.py
index fb9732b4ced25e396e7f6f131a487b7152adc5dd..9a440598c9316e3fc6bab487f2f2d6123c1b666c 100644
--- a/tests/test_hivtb_RS.py
+++ b/tests/test_hivtb_RS.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for HIV-TB_RS dataset."""
import pytest
diff --git a/tests/test_image_utils.py b/tests/test_image_utils.py
index 3b56fad9238808d96a8ec0cb24108a0b95dc0b1d..e6da9ceed2abcd7442a144324b298ef232340982 100644
--- a/tests/test_image_utils.py
+++ b/tests/test_image_utils.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for image utilities."""
import numpy
diff --git a/tests/test_in_RS.py b/tests/test_in_RS.py
index b4215593909cc99de4fa5ab1b8b25cea1e371198..551265ad9546bff576c46f8fcb167585cacf7892 100644
--- a/tests/test_in_RS.py
+++ b/tests/test_in_RS.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for Extended Indian dataset."""
import pytest
diff --git a/tests/test_indian.py b/tests/test_indian.py
index f7d16ff8e56ab3475d1dbc5b4808c1c6c2e13a9a..87660c1af4073fde09cc13d5a6f616d9180a3e4e 100644
--- a/tests/test_indian.py
+++ b/tests/test_indian.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for Indian dataset."""
import pytest
diff --git a/tests/test_mc_RS.py b/tests/test_mc_RS.py
index 4f7b4e6e0491c65b72f1509174898e1eb0bad0fc..a0175c23f8d00556b041792b378001eec1430962 100644
--- a/tests/test_mc_RS.py
+++ b/tests/test_mc_RS.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for Extended Montgomery dataset."""
import pytest
diff --git a/tests/test_mc_ch.py b/tests/test_mc_ch.py
index 885576334e31401a494d4de9775a667a160fdae9..17c1fb4c49ee6f0e88e6468f459109643a9bf71a 100644
--- a/tests/test_mc_ch.py
+++ b/tests/test_mc_ch.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for the aggregated Montgomery-Shenzhen dataset."""
import pytest
diff --git a/tests/test_mc_ch_RS.py b/tests/test_mc_ch_RS.py
index 327998b179fea0471fb06482dafdf8e3cd10ef29..7e91622906cf9b6497e6d73ee3b29d0e9cf0b42b 100644
--- a/tests/test_mc_ch_RS.py
+++ b/tests/test_mc_ch_RS.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for the aggregated Montgomery-Shenzhen dataset."""
import pytest
diff --git a/tests/test_mc_ch_in.py b/tests/test_mc_ch_in.py
index a3ae89318c31993326dda913453c21bf64d2c4f6..7305b66b7777f390c23a77a758f3dc5371fdb1bc 100644
--- a/tests/test_mc_ch_in.py
+++ b/tests/test_mc_ch_in.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for the aggregated Montgomery-Shenzhen-Indian dataset."""
import pytest
diff --git a/tests/test_mc_ch_in_11k.py b/tests/test_mc_ch_in_11k.py
index f7be318e2d014ac44544cad267feed1569170982..964faf06ec8feba1fb8b7f50d38cbd6c225e061b 100644
--- a/tests/test_mc_ch_in_11k.py
+++ b/tests/test_mc_ch_in_11k.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for the aggregated Montgomery-Shenzhen-Indian dataset."""
import pytest
diff --git a/tests/test_mc_ch_in_11k_RS.py b/tests/test_mc_ch_in_11k_RS.py
index bc3fcfb541ccd133c8523facc8c4f15812658de6..f8843befc928558ae9917eed3f41549dfd798e31 100644
--- a/tests/test_mc_ch_in_11k_RS.py
+++ b/tests/test_mc_ch_in_11k_RS.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for the aggregated Montgomery-Shenzhen-Indian-tbx11k_simplified
dataset."""
diff --git a/tests/test_mc_ch_in_11kv2.py b/tests/test_mc_ch_in_11kv2.py
index 1c514fd61f81705a254093cc9bbf29594df4d188..a4d801d6cc7f61a0ced15b0dfa9c6de52f573986 100644
--- a/tests/test_mc_ch_in_11kv2.py
+++ b/tests/test_mc_ch_in_11kv2.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for the aggregated Montgomery-Shenzhen-Indian dataset."""
import pytest
diff --git a/tests/test_mc_ch_in_11kv2_RS.py b/tests/test_mc_ch_in_11kv2_RS.py
index d8143a4b848debc0af0016d2c09ee0723f4c90ba..3c128968613ebc33198643407283bb5810b2725f 100644
--- a/tests/test_mc_ch_in_11kv2_RS.py
+++ b/tests/test_mc_ch_in_11kv2_RS.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for the aggregated Montgomery-Shenzhen-Indian-tbx11k_simplified_v2
dataset."""
diff --git a/tests/test_mc_ch_in_RS.py b/tests/test_mc_ch_in_RS.py
index 14283d893cb411420dd935a5d2fc29198b08b6ba..1600f60ba45e0f503f34224b144d0ed84259d361 100644
--- a/tests/test_mc_ch_in_RS.py
+++ b/tests/test_mc_ch_in_RS.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for the aggregated Montgomery-Shenzhen-Indian dataset."""
import pytest
diff --git a/tests/test_mc_ch_in_pc.py b/tests/test_mc_ch_in_pc.py
index 1680fdedaada7653b35c457ccc464db8395d1055..8aa38bef456e8f153ab596f09f26baa4a2c42788 100644
--- a/tests/test_mc_ch_in_pc.py
+++ b/tests/test_mc_ch_in_pc.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for the aggregated Montgomery-Shenzhen-Indian-Padchest dataset."""
import pytest
diff --git a/tests/test_mc_ch_in_pc_RS.py b/tests/test_mc_ch_in_pc_RS.py
index 21c568569c81e18ba1e6339bf67a89aa6ff65715..1014fb1df1c3d606ea1abe69693e7244c06d667f 100644
--- a/tests/test_mc_ch_in_pc_RS.py
+++ b/tests/test_mc_ch_in_pc_RS.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for the aggregated Montgomery-Shenzhen-Indian-Padchest(TB) dataset."""
import pytest
diff --git a/tests/test_measures.py b/tests/test_measures.py
index 181ea8a596c0e3a3a6090a8c06d75b80ff109b01..69bcdc3c0d6c748f75897fd2b7942497a8fd7f19 100644
--- a/tests/test_measures.py
+++ b/tests/test_measures.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for measure functions."""
import random
diff --git a/tests/test_nih_cxr14.py b/tests/test_nih_cxr14.py
index 78f0ce097bd4c5b9bc2901f7251078aab090438f..d7cc149a788072db3a3f2a5c48b2fb788f620951 100644
--- a/tests/test_nih_cxr14.py
+++ b/tests/test_nih_cxr14.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for NIH CXR14 dataset."""
import pytest
diff --git a/tests/test_nih_cxr14_pc.py b/tests/test_nih_cxr14_pc.py
index 3b951f2f11897e8789ec1676c57cf98018b5e56a..05ae5a13ec648b75e566646330a9803fda22b453 100644
--- a/tests/test_nih_cxr14_pc.py
+++ b/tests/test_nih_cxr14_pc.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for the aggregated NIH CXR14-PadChest dataset."""
import pytest
diff --git a/tests/test_pc.py b/tests/test_pc.py
index 6f013cdeadc7ac8925ba32bae7eef87412f34bf3..1ac31cbd3a0febd2201f04f42d4c1840b11db8bc 100644
--- a/tests/test_pc.py
+++ b/tests/test_pc.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for Padchest dataset."""
import pytest
diff --git a/tests/test_pc_RS.py b/tests/test_pc_RS.py
index e895dbea21e164be53f9adc23c3d8175b27878de..c62ef78001634cd04ecc93eaf0c7dc4fb0d22ffd 100644
--- a/tests/test_pc_RS.py
+++ b/tests/test_pc_RS.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for Extended Padchest dataset."""
import pytest
diff --git a/tests/test_shenzhen.py b/tests/test_shenzhen.py
index 1452a232b87ea64958acef5be85b522da3e0f64a..6e577081a83a075c92a4808bbfb1c876d247fdde 100644
--- a/tests/test_shenzhen.py
+++ b/tests/test_shenzhen.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for Shenzhen dataset."""
import importlib
diff --git a/tests/test_tbpoc.py b/tests/test_tbpoc.py
index b7be97d96fb1f00a1f17293e98fc3090fd8b1d62..9609ea66be7f59a655f744cba8b7f94e8cafb382 100644
--- a/tests/test_tbpoc.py
+++ b/tests/test_tbpoc.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for TB-POC dataset."""
import pytest
diff --git a/tests/test_tbpoc_RS.py b/tests/test_tbpoc_RS.py
index 175bb5fbf9f6e70287285a4c4723488e705d1e3a..72f3e5968ba755319c9c36b3b206e342639b7152 100644
--- a/tests/test_tbpoc_RS.py
+++ b/tests/test_tbpoc_RS.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for TB-POC_RS dataset."""
import pytest
diff --git a/tests/test_tranforms.py b/tests/test_tranforms.py
index c02c80d077e1e43f73451b01d32a9e9066067934..2c324aa1691d897c6acb0f9c71e7bd4f9d2cb089 100644
--- a/tests/test_tranforms.py
+++ b/tests/test_tranforms.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for transforms."""
import numpy