src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py

 # 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

src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py

 # 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

src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py

 # 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

src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py

 # 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

src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py

 # 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

src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py

 # 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,

src/mednet/config/data/nih_cxr14/cardiomegaly.py

 # 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]_

src/mednet/config/data/nih_cxr14/datamodule.py

 # 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]_
 """
@@ -63,7 +63,7 @@ class RawDataLoader(_BaseRawDataLoader):
         )
 
     def sample(self, sample: tuple[str, list[int]]) -> Sample:
-        """Loads a single image sample from the disk.
+        """Load a single image sample from the disk.
 
         Parameters
         ----------
@@ -72,10 +72,9 @@ class RawDataLoader(_BaseRawDataLoader):
             where to find the image to be loaded, and an integer, representing the
             sample label.
 
-
         Returns
         -------
-            The sample representation
+            The sample representation.
         """
         file_path = sample[0]  # default
         if self.idiap_file_organisation:
@@ -103,7 +102,7 @@ class RawDataLoader(_BaseRawDataLoader):
         return tensor, dict(label=sample[1], name=sample[0])  # type: ignore[arg-type]
 
     def label(self, sample: tuple[str, list[int]]) -> list[int]:
-        """Loads a single image sample label from the disk.
+        """Load a single image sample label from the disk.
 
         Parameters
         ----------
@@ -112,16 +111,26 @@ class RawDataLoader(_BaseRawDataLoader):
             where to find the image to be loaded, and an integer, representing the
             sample label.
 
-
         Returns
         -------
-            The integer labels associated with the sample
+        list[int]
+            The integer labels associated with the sample.
         """
         return sample[1]
 
 
 def make_split(basename: str) -> DatabaseSplit:
-    """Returns a database split for the NIH CXR-14 database."""
+    """Return a database split for the NIH CXR-14 database.
+
+    Parameters
+    ----------
+    basename
+        Name of the .json file containing the split to load.
+
+    Returns
+    -------
+        An instance of DatabaseSplit.
+    """
 
     return JSONDatabaseSplit(
         importlib.resources.files(__name__.rsplit(".", 1)[0]).joinpath(basename)
@@ -129,7 +138,7 @@ 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
@@ -172,6 +181,11 @@ class DataModule(CachingDataModule):
               * fibrosis
               * edema
               * consolidation
+
+    Parameters
+    ----------
+    split_filename
+        Name of the .json file containing the split to load.
     """
 
     def __init__(self, split_filename: str):

src/mednet/config/data/nih_cxr14/default.py

 # 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

src/mednet/config/data/nih_cxr14_padchest/datamodule.py

@@ -11,7 +11,15 @@ from ..padchest.datamodule import make_split as make_padchest_split
 
 class DataModule(ConcatDataModule):
     """Aggregated dataset composed of NIH CXR14 relabeld and PadChest
-    (normalized) datasets."""
+    (normalized) datasets.
+
+    Parameters
+    ----------
+    cxr14_split_filename
+        Name of the .json file from crx14 containing the split to load.
+    padchest_split_filename
+        Name of the .json file from padchest containing the split to load.
+    """
 
     def __init__(self, cxr14_split_filename: str, padchest_split_filename):
         cxr14_loader = CXR14Loader()

src/mednet/config/data/nih_cxr14_padchest/idiap.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated dataset composed of NIH CXR14 relabeld and PadChest (normalized)
-datasets (no-tb-idiap split)."""
+"""Aggregated dataset composed of NIH CXR14 relabeld and PadChest (normalized) datasets (no-tb-idiap split)."""
 
 from mednet.config.data.nih_cxr14_padchest.datamodule import DataModule
 

src/mednet/config/data/padchest/datamodule.py

@@ -41,7 +41,7 @@ class RawDataLoader(_BaseRawDataLoader):
         )
 
     def sample(self, sample: tuple[str, int | list[int]]) -> Sample:
-        """Loads a single image sample from the disk.
+        """Load a single image sample from the disk.
 
         Parameters
         ----------
@@ -50,10 +50,9 @@ class RawDataLoader(_BaseRawDataLoader):
             where to find the image to be loaded, and an integer, representing the
             sample label.
 
-
         Returns
         -------
-            The sample representation
+            The sample representation.
         """
         # N.B.: PadChest images are encoded as 16-bit grayscale images
         image = PIL.Image.open(os.path.join(self.datadir, sample[0]))
@@ -70,7 +69,7 @@ class RawDataLoader(_BaseRawDataLoader):
         return tensor, dict(label=sample[1], name=sample[0])  # type: ignore[arg-type]
 
     def label(self, sample: tuple[str, int | list[int]]) -> int | list[int]:
-        """Loads a single image sample label from the disk.
+        """Load a single image sample label from the disk.
 
         Parameters
         ----------
@@ -79,16 +78,26 @@ class RawDataLoader(_BaseRawDataLoader):
             where to find the image to be loaded, and an integer, representing the
             sample label.
 
-
         Returns
         -------
-            The integer labels associated with the sample
+        list[int]
+            The integer labels associated with the sample.
         """
         return sample[1]
 
 
 def make_split(basename: str) -> DatabaseSplit:
-    """Returns a database split for the NIH CXR-14 database."""
+    """Return a database split for the NIH CXR-14 database.
+
+    Parameters
+    ----------
+    basename
+        Name of the .json file containing the split to load.
+
+    Returns
+    -------
+        An instance of DatabaseSplit.
+    """
 
     return JSONDatabaseSplit(
         importlib.resources.files(__name__.rsplit(".", 1)[0]).joinpath(basename)
@@ -322,6 +331,11 @@ class DataModule(CachingDataModule):
           * vertebral degenerative changes
           * vertebral fracture
           * volume loss
+
+    Parameters
+    ----------
+    split_filename
+        Name of the .json file containing the split to load.
     """
 
     def __init__(self, split_filename: str):

src/mednet/config/data/shenzhen/datamodule.py

 # 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]_
 """
@@ -27,7 +27,14 @@ database."""
 
 
 class RawDataLoader(_BaseRawDataLoader):
-    """A specialized raw-data-loader for the Shenzhen dataset."""
+    """A specialized raw-data-loader for the Shenzhen dataset.
+
+    Parameters
+    ----------
+    config_variable
+        Key to search for in the configuration file for the root directory of this
+        database.
+    """
 
     datadir: str
     """This variable contains the base directory where the database raw data is
@@ -41,7 +48,7 @@ class RawDataLoader(_BaseRawDataLoader):
         )
 
     def sample(self, sample: tuple[str, int]) -> Sample:
-        """Loads a single image sample from the disk.
+        """Load a single image sample from the disk.
 
         Parameters
         ----------
@@ -50,10 +57,9 @@ class RawDataLoader(_BaseRawDataLoader):
             where to find the image to be loaded, and an integer, representing the
             sample label.
 
-
         Returns
         -------
-            The sample representation
+            The sample representation.
         """
         # N.B.: Image.convert("L") is required to normalize grayscale back to
         # normal (instead of inverted).
@@ -72,7 +78,7 @@ class RawDataLoader(_BaseRawDataLoader):
         return tensor, dict(label=sample[1], name=sample[0])  # type: ignore[arg-type]
 
     def label(self, sample: tuple[str, int]) -> int:
-        """Loads a single image sample label from the disk.
+        """Load a single image sample label from the disk.
 
         Parameters
         ----------
@@ -81,16 +87,26 @@ class RawDataLoader(_BaseRawDataLoader):
             where to find the image to be loaded, and an integer, representing the
             sample label.
 
-
         Returns
         -------
-            The integer label associated with the sample
+        int
+            The integer label associated with the sample.
         """
         return sample[1]
 
 
 def make_split(basename: str) -> DatabaseSplit:
-    """Returns a database split for the Shenzhen database."""
+    """Return a database split for the Shenzhen database.
+
+    Parameters
+    ----------
+    basename
+        Name of the .json file containing the split to load.
+
+    Returns
+    -------
+        An instance of DatabaseSplit.
+    """
 
     return JSONDatabaseSplit(
         importlib.resources.files(__name__.rsplit(".", 1)[0]).joinpath(basename)
@@ -98,7 +114,7 @@ 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
@@ -129,6 +145,11 @@ class DataModule(CachingDataModule):
         * Grayscale, encoded as a single plane tensor, 32-bit floats,
           square with varying resolutions, depending on the input image
         * Labels: 0 (healthy), 1 (active tuberculosis)
+
+    Parameters
+    ----------
+    split_filename
+        Name of the .json file containing the split to load.
     """
 
     def __init__(self, split_filename: str):

src/mednet/config/data/shenzhen/fold_0.py

 # 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]_
 

src/mednet/config/data/shenzhen/fold_1.py

 # 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]_
 

src/mednet/config/data/shenzhen/fold_2.py

 # 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]_
 

src/mednet/config/data/shenzhen/fold_3.py

 # 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]_
 

src/mednet/config/data/shenzhen/fold_4.py

 # 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]_
 

src/mednet/config/data/shenzhen/fold_5.py

 # 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]_
 

src/mednet/config/data/shenzhen/fold_6.py

 # 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]_