[models] Improve documentation of config files; Make ptbench config work again

doc/links.rst

@@ -21,3 +21,10 @@
 .. _PadChest: https://bimcv.cipf.es/bimcv-projects/padchest/
 .. _TBX11K: https://mmcheng.net/tb/
 .. _TBX11K_simplified: https://www.kaggle.com/datasets/vbookshelf/tbx11k-simplified
+
+.. models
+.. _imagenet: https://www.image-net.org
+.. _alexnet: https://en.wikipedia.org/wiki/AlexNet
+.. _alexnet_pytorch: https://pytorch.org/hub/pytorch_vision_alexnet/
+.. _densenet: https://arxiv.org/abs/1608.06993
+.. _densenet_pytorch: https://pytorch.org/hub/pytorch_vision_densenet/

pyproject.toml

@@ -71,7 +71,7 @@ ptbench = "ptbench.scripts.cli:cli"
 
 # models
 pasa = "ptbench.models.config.pasa"
-signs-to-tb = "ptbench.models.config.signs_to_tb"
+mlp = "ptbench.models.config.mlp"
 logistic-regression = "ptbench.models.config.logistic_regression"
 alexnet = "ptbench.models.config.alexnet"
 alexnet-pretrained = "ptbench.models.config.alexnet_pretrained"

src/ptbench/data/hivtb/datamodule.py

 # 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)
+
+Database reference: [HIV-TB-2019]_
+"""
+
 
 import importlib.resources
 import os

src/ptbench/data/hivtb/fold_0.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
-from .datamodule import DataModule
-
-datamodule = DataModule("fold-0.json")
 """HIV-TB dataset for TB detection (cross validation fold 0).
 
+Database reference: [HIV-TB-2019]_
+
 See :py:class:`.hivtb.datamodule.DataModule` for technical details.
 """
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold-0.json")

src/ptbench/data/hivtb/fold_1.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
-from .datamodule import DataModule
-
-datamodule = DataModule("fold-1.json")
 """HIV-TB dataset for TB detection (cross validation fold 1).
 
+Database reference: [HIV-TB-2019]_
+
 See :py:class:`.hivtb.datamodule.DataModule` for technical details.
 """
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold-1.json")

src/ptbench/data/hivtb/fold_2.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
-from .datamodule import DataModule
-
-datamodule = DataModule("fold-2.json")
 """HIV-TB dataset for TB detection (cross validation fold 2).
 
+Database reference: [HIV-TB-2019]_
+
 See :py:class:`.hivtb.datamodule.DataModule` for technical details.
 """
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold-2.json")

src/ptbench/data/hivtb/fold_3.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
-from .datamodule import DataModule
-
-datamodule = DataModule("fold-3.json")
 """HIV-TB dataset for TB detection (cross validation fold 3).
 
+Database reference: [HIV-TB-2019]_
+
 See :py:class:`.hivtb.datamodule.DataModule` for technical details.
 """
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold-3.json")

src/ptbench/data/hivtb/fold_4.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
-from .datamodule import DataModule
-
-datamodule = DataModule("fold-4.json")
 """HIV-TB dataset for TB detection (cross validation fold 4).
 
+Database reference: [HIV-TB-2019]_
+
 See :py:class:`.hivtb.datamodule.DataModule` for technical details.
 """
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold-4.json")

src/ptbench/data/hivtb/fold_5.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
-from .datamodule import DataModule
-
-datamodule = DataModule("fold-5.json")
 """HIV-TB dataset for TB detection (cross validation fold 5).
 
+Database reference: [HIV-TB-2019]_
+
 See :py:class:`.hivtb.datamodule.DataModule` for technical details.
 """
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold-5.json")

src/ptbench/data/hivtb/fold_6.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
-from .datamodule import DataModule
-
-datamodule = DataModule("fold-6.json")
 """HIV-TB dataset for TB detection (cross validation fold 6).
 
+Database reference: [HIV-TB-2019]_
+
 See :py:class:`.hivtb.datamodule.DataModule` for technical details.
 """
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold-6.json")

src/ptbench/data/hivtb/fold_7.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
-from .datamodule import DataModule
-
-datamodule = DataModule("fold-7.json")
 """HIV-TB dataset for TB detection (cross validation fold 7).
 
+Database reference: [HIV-TB-2019]_
+
 See :py:class:`.hivtb.datamodule.DataModule` for technical details.
 """
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold-7.json")

src/ptbench/data/hivtb/fold_8.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
-from .datamodule import DataModule
-
-datamodule = DataModule("fold-8.json")
 """HIV-TB dataset for TB detection (cross validation fold 8).
 
+Database reference: [HIV-TB-2019]_
+
 See :py:class:`.hivtb.datamodule.DataModule` for technical details.
 """
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold-8.json")

src/ptbench/data/hivtb/fold_9.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
-from .datamodule import DataModule
-
-datamodule = DataModule("fold-9.json")
 """HIV-TB dataset for TB detection (cross validation fold 9).
 
+Database reference: [HIV-TB-2019]_
+
 See :py:class:`.hivtb.datamodule.DataModule` for technical details.
 """
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold-9.json")

src/ptbench/data/indian/datamodule.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
+"""Indian database for TB detection (a.k.a. Dataset A/Dataset B).
+
+Database reference: [INDIAN-2013]_
+"""
 
 import importlib.resources
 
@@ -19,13 +23,14 @@ def make_split(basename: str) -> DatabaseSplit:
 
 
 class DataModule(CachingDataModule):
-    """Indian collection dataset for computer-aided diagnosis.
+    """Indian database for TB detection (a.k.a. Dataset A/Dataset B).
 
     The Indian collection database has been established to foster research in
     computer-aided diagnosis of pulmonary diseases with a special focus on
     pulmonary tuberculosis (TB).  This database is also known as the "Database
     A/Database B" database.
 
+    * Database reference: [INDIAN-2013]_
     * Original images PNG, 8-bit grayscale, 1024 x 1024 pixels
     * Split reference: [INDIAN-2013]_ with 20% of train set for the validation set
 

src/ptbench/data/indian/default.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
+"""Indian database for TB detection (a.k.a. Dataset A/Dataset B).
+
+Database reference: [INDIAN-2013]_
+
+See :py:class:`.indian.datamodule.DataModule` for technical details.
+"""
 
 from .datamodule import DataModule
 

src/ptbench/data/indian/fold_0.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
-from .datamodule import DataModule
-
-datamodule = DataModule("fold-0.json")
 """Indian collection dataset for computer-aided diagnosis (cross validation
 fold 0).
 
+Database reference: [INDIAN-2013]_
+
 See :py:class:`.indian.datamodule.DataModule` for technical details.
 """
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold-0.json")

src/ptbench/data/indian/fold_1.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
-from .datamodule import DataModule
-
-datamodule = DataModule("fold-1.json")
 """Indian collection dataset for computer-aided diagnosis (cross validation
 fold 1).
 
+Database reference: [INDIAN-2013]_
+
 See :py:class:`.indian.datamodule.DataModule` for technical details.
 """
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold-1.json")

src/ptbench/data/indian/fold_2.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
-from .datamodule import DataModule
-
-datamodule = DataModule("fold-2.json")
 """Indian collection dataset for computer-aided diagnosis (cross validation
 fold 2).
 
+Database reference: [INDIAN-2013]_
+
 See :py:class:`.indian.datamodule.DataModule` for technical details.
 """
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold-2.json")

src/ptbench/data/indian/fold_3.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
-from .datamodule import DataModule
-
-datamodule = DataModule("fold-3.json")
 """Indian collection dataset for computer-aided diagnosis (cross validation
 fold 3).
 
+Database reference: [INDIAN-2013]_
+
 See :py:class:`.indian.datamodule.DataModule` for technical details.
 """
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold-3.json")

src/ptbench/data/indian/fold_4.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
-from .datamodule import DataModule
-
-datamodule = DataModule("fold-4.json")
 """Indian collection dataset for computer-aided diagnosis (cross validation
 fold 4).
 
+Database reference: [INDIAN-2013]_
+
 See :py:class:`.indian.datamodule.DataModule` for technical details.
 """
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold-4.json")