[doc] Add segmentation configs in documentation

src/mednet/libs/segmentation/config/data/montgomery/default.py

 # SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-"""Montgomery County dataset for Lung Segmentation.
 
-The database includes 58 cases with manifestation of tuberculosis, and 80
-normal cases.  It contains a total of 138 resolution of 4020 x 4892, or
-4892 x 4020. One set of ground-truth lung annotations is available.
+"""Montgomery County dataset for Lung Segmentation (default protocol).
 
-* Reference: [MC-2014]_
-* Original resolution (height x width): 4020 x 4892, or 4892 x 4020
-* Configuration resolution: 512 x 512 (after rescaling)
 * Split reference: [GAAL-2020]_
-* Protocol ``default``:
-
-  * Training samples: 96 (including labels)
-  * Validation samples: 14 (including labels)
-  * Test samples: 28 (including labels)
+* Configuration resolution: 256 x 256
 """
 
 from mednet.libs.segmentation.config.data.montgomery.datamodule import (

src/mednet/libs/segmentation/config/data/refuge/cup.py

@@ -5,7 +5,6 @@
 
 * Configuration resolution: 1632 x 1632 (after resizing and padding)
 * Reference (including split): [REFUGE-2018]_
-* See :py:mod:`deepdraw.data.refuge` for dataset details
 """
 
 from mednet.libs.segmentation.config.data.refuge.datamodule import DataModule

src/mednet/libs/segmentation/config/data/refuge/disc.py

@@ -5,7 +5,6 @@
 
 * Configuration resolution: 1632 x 1632 (after resizing and padding)
 * Reference (including split): [REFUGE-2018]_
-* See :py:mod:`deepdraw.data.refuge` for dataset details
 """
 
 from mednet.libs.segmentation.config.data.refuge.datamodule import DataModule

src/mednet/libs/segmentation/config/data/rimoner3/cup_exp1.py

@@ -5,7 +5,6 @@
 
 * Configuration resolution: 1440 x 1088 (after padding)
 * Split reference: [MANINIS-2016]_
-* See :py:mod:`deepdraw.data.rimoner3` for dataset details
 """
 
 from mednet.libs.segmentation.config.data.rimoner3.datamodule import DataModule

src/mednet/libs/segmentation/config/data/rimoner3/cup_exp2.py

@@ -5,7 +5,6 @@
 
 * Configuration resolution: 1440 x 1088 (after padding)
 * Split reference: [MANINIS-2016]_
-* See :py:mod:`deepdraw.data.rimoner3` for dataset details
 """
 
 from mednet.libs.segmentation.config.data.rimoner3.datamodule import DataModule

src/mednet/libs/segmentation/config/data/rimoner3/datamodule.py

@@ -96,8 +96,7 @@ class DataModule(CachingDataModule):
     * Reference: [RIMONER3-2015]_
     * Original resolution (height x width): 1424 x 1072
     * Split reference: [MANINIS-2016]_
-    * Protocols ``optic-disc-exp1``, ``optic-cup-exp1``, ``optic-disc-exp2``,
-    ``optic-cup-exp2``, ``optic-disc-avg`` and ``optic-cup-avg``:
+    * Protocols ``optic-disc-exp1``, ``optic-cup-exp1``, ``optic-disc-exp2``, ``optic-cup-exp2``, ``optic-disc-avg`` and ``optic-cup-avg``:
 
     * Training: 99
     * Test: 60

src/mednet/libs/segmentation/config/data/rimoner3/disc_exp1.py

@@ -5,7 +5,6 @@
 
 * Configuration resolution: 1440 x 1088 (after padding)
 * Split reference: [MANINIS-2016]_
-* See :py:mod:`deepdraw.data.rimoner3` for dataset details
 """
 
 from mednet.libs.segmentation.config.data.rimoner3.datamodule import DataModule

src/mednet/libs/segmentation/config/data/rimoner3/disc_exp2.py

@@ -5,7 +5,6 @@
 
 * Configuration resolution: 1440 x 1088 (after padding)
 * Split reference: [MANINIS-2016]_
-* See :py:mod:`deepdraw.data.rimoner3` for dataset details
 """
 
 from mednet.libs.segmentation.config.data.rimoner3.datamodule import DataModule

src/mednet/libs/segmentation/config/data/shenzhen/default.py

@@ -5,7 +5,6 @@
 
 * Split reference: [GAAL-2020]_
 * Configuration resolution: 256 x 256
-* See :py:mod:`deepdraw.data.shenzhen` for dataset details
 """
 
 from mednet.libs.segmentation.config.data.shenzhen.datamodule import DataModule

src/mednet/libs/segmentation/config/data/stare/ah.py

 # SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
+
+"""STARE dataset for Vessel Segmentation (annotator AH).
+
+* Configuration resolution: 704 x 608 (after padding)
+* Split reference: [MANINIS-2016]_
+* This dataset offers a second-annotator comparison (using protocol "vk")
+"""
+
 from mednet.libs.segmentation.config.data.stare.datamodule import DataModule
 
 datamodule = DataModule("ah.json")

src/mednet/libs/segmentation/config/data/stare/vk.py

 # SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
+
+"""STARE dataset for Vessel Segmentation (annotator VK).
+
+* Configuration resolution: 704 x 608 (after padding)
+* Split reference: [MANINIS-2016]_
+* This dataset offers a second-annotator comparison (using protocol "ah")
+"""
+
 from mednet.libs.segmentation.config.data.stare.datamodule import DataModule
 
 datamodule = DataModule("vk.json")

src/mednet/libs/segmentation/scripts/evaluate.py

@@ -28,7 +28,7 @@ from mednet.libs.segmentation.engine.evaluator import run
 
      .. code:: sh
 
-        $ deepdraw evaluate -vv drive --predictions-folder=path/to/predictions --output-folder=path/to/results
+        $ mednet segmentation evaluate -vv drive --predictions-folder=path/to/predictions --output-folder=path/to/results
 
 \b
   2. To run evaluation on a folder with your own images and annotations, you
@@ -40,9 +40,9 @@ from mednet.libs.segmentation.engine.evaluator import run
 
      .. code:: sh
 
-        $ deepdraw config copy csv-dataset-example mydataset.py
+        $ mednet segmentation config copy csv-dataset-example mydataset.py
         # modify "mydataset.py" to your liking
-        $ deepdraw evaluate -vv mydataset.py --predictions-folder=path/to/predictions --output-folder=path/to/results
+        $ mednet segmentation evaluate -vv mydataset.py --predictions-folder=path/to/predictions --output-folder=path/to/results
 """,
 )
 @click.option(