diff --git a/src/mednet/libs/segmentation/config/data/refuge/__init__.py b/src/mednet/libs/segmentation/config/data/refuge/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/src/mednet/libs/segmentation/config/data/refuge/cup.py b/src/mednet/libs/segmentation/config/data/refuge/cup.py
new file mode 100644
index 0000000000000000000000000000000000000000..6b51b66c91cfcc77995bd8f3ae304a75ad2090a1
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/refuge/cup.py
@@ -0,0 +1,13 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""REFUGE dataset for Optic Cup Segmentation (default protocol).
+
+* 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
+
+datamodule = DataModule("default.json", target_type="cup")
diff --git a/src/mednet/libs/segmentation/config/data/refuge/datamodule.py b/src/mednet/libs/segmentation/config/data/refuge/datamodule.py
new file mode 100644
index 0000000000000000000000000000000000000000..665db0de8f06a1ceaee7f129ca8086f1219d43a3
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/refuge/datamodule.py
@@ -0,0 +1,143 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""DREFUGE for Optic Disc and Cup Segmentation."""
+
+import os
+import pathlib
+
+import PIL.Image
+import pkg_resources
+from mednet.libs.common.data.datamodule import CachingDataModule
+from mednet.libs.common.data.split import make_split
+from mednet.libs.common.data.typing import Sample
+from mednet.libs.segmentation.data.typing import (
+ SegmentationRawDataLoader as _SegmentationRawDataLoader,
+)
+from torchvision import tv_tensors
+from torchvision.transforms.functional import to_tensor
+
+from ....utils.rc import load_rc
+
+CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
+"""Key to search for in the configuration file for the root directory of this
+database."""
+
+
+class SegmentationRawDataLoader(_SegmentationRawDataLoader):
+ """A specialized raw-data-loader for the drishtigs1 dataset.
+
+ Parameters
+ ----------
+ target_type
+ Indicate whether to use the "cup" or "disc" target.
+ """
+
+ datadir: pathlib.Path
+ """This variable contains the base directory where the database raw data is
+ stored."""
+
+ def __init__(self, target_type: str):
+ self.datadir = pathlib.Path(
+ load_rc().get(CONFIGURATION_KEY_DATADIR, os.path.realpath(os.curdir))
+ )
+
+ self._pkg_path = pathlib.Path(
+ pkg_resources.resource_filename(__name__, "masks")
+ )
+
+ self.target_type = target_type
+
+ def sample(self, sample: tuple[str, str, str]) -> Sample:
+ """Load a single image sample from the disk.
+
+ Parameters
+ ----------
+ sample
+ A tuple containing path suffixes to the sample image, target, and mask
+ to be loaded, within the dataset root folder.
+
+ Returns
+ -------
+ The sample representation.
+ """
+
+ image = to_tensor(PIL.Image.open(self.datadir / sample[0]).convert(mode="RGB"))
+
+ if self.target_type == "disc":
+ target = to_tensor(
+ PIL.Image.open(self.datadir / sample[1])
+ .convert(mode="RGB", dither=None)
+ .convert("L")
+ .point(lambda p: p <= 150, mode="1")
+ )
+ elif self.target_type == "cup":
+ target = to_tensor(
+ PIL.Image.open(self.datadir / sample[1])
+ .convert(mode="RGB", dither=None)
+ .convert("L")
+ .point(lambda p: p <= 100, mode="1")
+ )
+ else:
+ raise ValueError(
+ f"Target type {self.target_type} is not an option. Available options are 'cup' and 'disc'."
+ )
+
+ mask = to_tensor(
+ PIL.Image.open(self._pkg_path / sample[2]).convert(mode="1", dither=None)
+ )
+
+ tensor = tv_tensors.Image(image)
+ target = tv_tensors.Image(target)
+ mask = tv_tensors.Mask(mask)
+
+ return tensor, dict(target=target, mask=mask, name=sample[0]) # type: ignore[arg-type]
+
+
+class DataModule(CachingDataModule):
+ """REFUGE for Optic Disc and Cup Segmentation.
+
+ The dataset consists of 1200 color fundus photographs, created for a MICCAI
+ challenge. The goal of the challenge is to evaluate and compare automated
+ algorithms for glaucoma detection and optic disc/cup segmentation on a common
+ dataset of retinal fundus images.
+
+ * Reference (including train/dev/test split): [REFUGE-2018]_
+ * Protocols ``optic-disc`` and ``cup``:
+
+ * Training samples:
+
+ * 400
+ * includes optic-disc and cup labels
+ * includes label: glaucomatous and non-glaucomatous
+ * original resolution: 2056 x 2124
+
+ * Validation samples:
+
+ * 400
+ * includes optic-disc and cup labels
+ * original resolution: 1634 x 1634
+
+ * Test samples:
+
+ * 400
+ * includes optic-disc and cup labels
+ * includes label: glaucomatous and non-glaucomatous
+ * original resolution:
+
+ Parameters
+ ----------
+ split_filename
+ Name of the .json file containing the split to load.
+ target_type
+ Indicate whether to use the "cup" or "disc" target.
+ """
+
+ def __init__(self, split_filename: str, target_type: str):
+ assert __package__ is not None
+ super().__init__(
+ database_split=make_split(__package__, split_filename),
+ raw_data_loader=SegmentationRawDataLoader(target_type),
+ database_name=__package__.rsplit(".", 1)[1],
+ split_name=pathlib.Path(split_filename).stem,
+ )
diff --git a/src/mednet/libs/segmentation/config/data/refuge/default.json b/src/mednet/libs/segmentation/config/data/refuge/default.json
new file mode 100644
index 0000000000000000000000000000000000000000..6e7e69b1cc86068afc860fa24c90ab5648242649
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/refuge/default.json
@@ -0,0 +1,6008 @@
+{
+ "train":[
+ [
+ "Training400/Glaucoma/g0001.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0001.bmp",
+ "Training400/Glaucoma/g0001.png"
+ ],
+ [
+ "Training400/Glaucoma/g0002.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0002.bmp",
+ "Training400/Glaucoma/g0002.png"
+ ],
+ [
+ "Training400/Glaucoma/g0003.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0003.bmp",
+ "Training400/Glaucoma/g0003.png"
+ ],
+ [
+ "Training400/Glaucoma/g0004.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0004.bmp",
+ "Training400/Glaucoma/g0004.png"
+ ],
+ [
+ "Training400/Glaucoma/g0005.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0005.bmp",
+ "Training400/Glaucoma/g0005.png"
+ ],
+ [
+ "Training400/Glaucoma/g0006.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0006.bmp",
+ "Training400/Glaucoma/g0006.png"
+ ],
+ [
+ "Training400/Glaucoma/g0007.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0007.bmp",
+ "Training400/Glaucoma/g0007.png"
+ ],
+ [
+ "Training400/Glaucoma/g0008.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0008.bmp",
+ "Training400/Glaucoma/g0008.png"
+ ],
+ [
+ "Training400/Glaucoma/g0009.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0009.bmp",
+ "Training400/Glaucoma/g0009.png"
+ ],
+ [
+ "Training400/Glaucoma/g0010.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0010.bmp",
+ "Training400/Glaucoma/g0010.png"
+ ],
+ [
+ "Training400/Glaucoma/g0011.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0011.bmp",
+ "Training400/Glaucoma/g0011.png"
+ ],
+ [
+ "Training400/Glaucoma/g0012.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0012.bmp",
+ "Training400/Glaucoma/g0012.png"
+ ],
+ [
+ "Training400/Glaucoma/g0013.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0013.bmp",
+ "Training400/Glaucoma/g0013.png"
+ ],
+ [
+ "Training400/Glaucoma/g0014.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0014.bmp",
+ "Training400/Glaucoma/g0014.png"
+ ],
+ [
+ "Training400/Glaucoma/g0015.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0015.bmp",
+ "Training400/Glaucoma/g0015.png"
+ ],
+ [
+ "Training400/Glaucoma/g0016.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0016.bmp",
+ "Training400/Glaucoma/g0016.png"
+ ],
+ [
+ "Training400/Glaucoma/g0017.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0017.bmp",
+ "Training400/Glaucoma/g0017.png"
+ ],
+ [
+ "Training400/Glaucoma/g0018.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0018.bmp",
+ "Training400/Glaucoma/g0018.png"
+ ],
+ [
+ "Training400/Glaucoma/g0019.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0019.bmp",
+ "Training400/Glaucoma/g0019.png"
+ ],
+ [
+ "Training400/Glaucoma/g0020.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0020.bmp",
+ "Training400/Glaucoma/g0020.png"
+ ],
+ [
+ "Training400/Glaucoma/g0021.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0021.bmp",
+ "Training400/Glaucoma/g0021.png"
+ ],
+ [
+ "Training400/Glaucoma/g0022.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0022.bmp",
+ "Training400/Glaucoma/g0022.png"
+ ],
+ [
+ "Training400/Glaucoma/g0023.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0023.bmp",
+ "Training400/Glaucoma/g0023.png"
+ ],
+ [
+ "Training400/Glaucoma/g0024.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0024.bmp",
+ "Training400/Glaucoma/g0024.png"
+ ],
+ [
+ "Training400/Glaucoma/g0025.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0025.bmp",
+ "Training400/Glaucoma/g0025.png"
+ ],
+ [
+ "Training400/Glaucoma/g0026.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0026.bmp",
+ "Training400/Glaucoma/g0026.png"
+ ],
+ [
+ "Training400/Glaucoma/g0027.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0027.bmp",
+ "Training400/Glaucoma/g0027.png"
+ ],
+ [
+ "Training400/Glaucoma/g0028.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0028.bmp",
+ "Training400/Glaucoma/g0028.png"
+ ],
+ [
+ "Training400/Glaucoma/g0029.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0029.bmp",
+ "Training400/Glaucoma/g0029.png"
+ ],
+ [
+ "Training400/Glaucoma/g0030.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0030.bmp",
+ "Training400/Glaucoma/g0030.png"
+ ],
+ [
+ "Training400/Glaucoma/g0031.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0031.bmp",
+ "Training400/Glaucoma/g0031.png"
+ ],
+ [
+ "Training400/Glaucoma/g0032.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0032.bmp",
+ "Training400/Glaucoma/g0032.png"
+ ],
+ [
+ "Training400/Glaucoma/g0033.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0033.bmp",
+ "Training400/Glaucoma/g0033.png"
+ ],
+ [
+ "Training400/Glaucoma/g0034.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0034.bmp",
+ "Training400/Glaucoma/g0034.png"
+ ],
+ [
+ "Training400/Glaucoma/g0035.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0035.bmp",
+ "Training400/Glaucoma/g0035.png"
+ ],
+ [
+ "Training400/Glaucoma/g0036.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0036.bmp",
+ "Training400/Glaucoma/g0036.png"
+ ],
+ [
+ "Training400/Glaucoma/g0037.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0037.bmp",
+ "Training400/Glaucoma/g0037.png"
+ ],
+ [
+ "Training400/Glaucoma/g0038.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0038.bmp",
+ "Training400/Glaucoma/g0038.png"
+ ],
+ [
+ "Training400/Glaucoma/g0039.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0039.bmp",
+ "Training400/Glaucoma/g0039.png"
+ ],
+ [
+ "Training400/Glaucoma/g0040.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0040.bmp",
+ "Training400/Glaucoma/g0040.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0001.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0001.bmp",
+ "Training400/Non-Glaucoma/n0001.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0002.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0002.bmp",
+ "Training400/Non-Glaucoma/n0002.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0003.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0003.bmp",
+ "Training400/Non-Glaucoma/n0003.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0004.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0004.bmp",
+ "Training400/Non-Glaucoma/n0004.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0005.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0005.bmp",
+ "Training400/Non-Glaucoma/n0005.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0006.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0006.bmp",
+ "Training400/Non-Glaucoma/n0006.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0007.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0007.bmp",
+ "Training400/Non-Glaucoma/n0007.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0008.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0008.bmp",
+ "Training400/Non-Glaucoma/n0008.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0009.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0009.bmp",
+ "Training400/Non-Glaucoma/n0009.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0010.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0010.bmp",
+ "Training400/Non-Glaucoma/n0010.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0011.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0011.bmp",
+ "Training400/Non-Glaucoma/n0011.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0012.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0012.bmp",
+ "Training400/Non-Glaucoma/n0012.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0013.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0013.bmp",
+ "Training400/Non-Glaucoma/n0013.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0014.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0014.bmp",
+ "Training400/Non-Glaucoma/n0014.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0015.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0015.bmp",
+ "Training400/Non-Glaucoma/n0015.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0016.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0016.bmp",
+ "Training400/Non-Glaucoma/n0016.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0017.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0017.bmp",
+ "Training400/Non-Glaucoma/n0017.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0018.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0018.bmp",
+ "Training400/Non-Glaucoma/n0018.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0019.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0019.bmp",
+ "Training400/Non-Glaucoma/n0019.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0020.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0020.bmp",
+ "Training400/Non-Glaucoma/n0020.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0021.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0021.bmp",
+ "Training400/Non-Glaucoma/n0021.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0022.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0022.bmp",
+ "Training400/Non-Glaucoma/n0022.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0023.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0023.bmp",
+ "Training400/Non-Glaucoma/n0023.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0024.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0024.bmp",
+ "Training400/Non-Glaucoma/n0024.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0025.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0025.bmp",
+ "Training400/Non-Glaucoma/n0025.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0026.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0026.bmp",
+ "Training400/Non-Glaucoma/n0026.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0027.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0027.bmp",
+ "Training400/Non-Glaucoma/n0027.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0028.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0028.bmp",
+ "Training400/Non-Glaucoma/n0028.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0029.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0029.bmp",
+ "Training400/Non-Glaucoma/n0029.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0030.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0030.bmp",
+ "Training400/Non-Glaucoma/n0030.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0031.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0031.bmp",
+ "Training400/Non-Glaucoma/n0031.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0032.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0032.bmp",
+ "Training400/Non-Glaucoma/n0032.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0033.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0033.bmp",
+ "Training400/Non-Glaucoma/n0033.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0034.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0034.bmp",
+ "Training400/Non-Glaucoma/n0034.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0035.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0035.bmp",
+ "Training400/Non-Glaucoma/n0035.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0036.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0036.bmp",
+ "Training400/Non-Glaucoma/n0036.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0037.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0037.bmp",
+ "Training400/Non-Glaucoma/n0037.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0038.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0038.bmp",
+ "Training400/Non-Glaucoma/n0038.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0039.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0039.bmp",
+ "Training400/Non-Glaucoma/n0039.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0040.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0040.bmp",
+ "Training400/Non-Glaucoma/n0040.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0041.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0041.bmp",
+ "Training400/Non-Glaucoma/n0041.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0042.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0042.bmp",
+ "Training400/Non-Glaucoma/n0042.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0043.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0043.bmp",
+ "Training400/Non-Glaucoma/n0043.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0044.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0044.bmp",
+ "Training400/Non-Glaucoma/n0044.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0045.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0045.bmp",
+ "Training400/Non-Glaucoma/n0045.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0046.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0046.bmp",
+ "Training400/Non-Glaucoma/n0046.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0047.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0047.bmp",
+ "Training400/Non-Glaucoma/n0047.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0048.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0048.bmp",
+ "Training400/Non-Glaucoma/n0048.png"
+ ],
+ [
+ "Training400/Non-Glaucoma/n0049.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Non-Glaucoma/n0049.bmp",
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+ ],
+ [
+ "Test400/T0368.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/G/T0368.bmp",
+ "Test400/T0368.png"
+ ],
+ [
+ "Test400/T0369.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0369.bmp",
+ "Test400/T0369.png"
+ ],
+ [
+ "Test400/T0370.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/G/T0370.bmp",
+ "Test400/T0370.png"
+ ],
+ [
+ "Test400/T0371.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/G/T0371.bmp",
+ "Test400/T0371.png"
+ ],
+ [
+ "Test400/T0372.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0372.bmp",
+ "Test400/T0372.png"
+ ],
+ [
+ "Test400/T0373.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0373.bmp",
+ "Test400/T0373.png"
+ ],
+ [
+ "Test400/T0374.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0374.bmp",
+ "Test400/T0374.png"
+ ],
+ [
+ "Test400/T0375.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0375.bmp",
+ "Test400/T0375.png"
+ ],
+ [
+ "Test400/T0376.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0376.bmp",
+ "Test400/T0376.png"
+ ],
+ [
+ "Test400/T0377.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0377.bmp",
+ "Test400/T0377.png"
+ ],
+ [
+ "Test400/T0378.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0378.bmp",
+ "Test400/T0378.png"
+ ],
+ [
+ "Test400/T0379.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0379.bmp",
+ "Test400/T0379.png"
+ ],
+ [
+ "Test400/T0380.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0380.bmp",
+ "Test400/T0380.png"
+ ],
+ [
+ "Test400/T0381.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0381.bmp",
+ "Test400/T0381.png"
+ ],
+ [
+ "Test400/T0382.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0382.bmp",
+ "Test400/T0382.png"
+ ],
+ [
+ "Test400/T0383.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0383.bmp",
+ "Test400/T0383.png"
+ ],
+ [
+ "Test400/T0384.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0384.bmp",
+ "Test400/T0384.png"
+ ],
+ [
+ "Test400/T0385.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0385.bmp",
+ "Test400/T0385.png"
+ ],
+ [
+ "Test400/T0386.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0386.bmp",
+ "Test400/T0386.png"
+ ],
+ [
+ "Test400/T0387.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0387.bmp",
+ "Test400/T0387.png"
+ ],
+ [
+ "Test400/T0388.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0388.bmp",
+ "Test400/T0388.png"
+ ],
+ [
+ "Test400/T0389.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0389.bmp",
+ "Test400/T0389.png"
+ ],
+ [
+ "Test400/T0390.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0390.bmp",
+ "Test400/T0390.png"
+ ],
+ [
+ "Test400/T0391.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0391.bmp",
+ "Test400/T0391.png"
+ ],
+ [
+ "Test400/T0392.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0392.bmp",
+ "Test400/T0392.png"
+ ],
+ [
+ "Test400/T0393.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0393.bmp",
+ "Test400/T0393.png"
+ ],
+ [
+ "Test400/T0394.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0394.bmp",
+ "Test400/T0394.png"
+ ],
+ [
+ "Test400/T0395.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0395.bmp",
+ "Test400/T0395.png"
+ ],
+ [
+ "Test400/T0396.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0396.bmp",
+ "Test400/T0396.png"
+ ],
+ [
+ "Test400/T0397.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/G/T0397.bmp",
+ "Test400/T0397.png"
+ ],
+ [
+ "Test400/T0398.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0398.bmp",
+ "Test400/T0398.png"
+ ],
+ [
+ "Test400/T0399.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0399.bmp",
+ "Test400/T0399.png"
+ ],
+ [
+ "Test400/T0400.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0400.bmp",
+ "Test400/T0400.png"
+ ]
+ ]
+}
diff --git a/src/mednet/libs/segmentation/config/data/refuge/disc.py b/src/mednet/libs/segmentation/config/data/refuge/disc.py
new file mode 100644
index 0000000000000000000000000000000000000000..54062406dd636989456bfcf6ede357c5c807eaab
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/refuge/disc.py
@@ -0,0 +1,13 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""REFUGE dataset for Optic Disc Segmentation (default protocol).
+
+* 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
+
+datamodule = DataModule("default.json", target_type="disc")
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+ ]
+}
diff --git a/src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_refuge_cup.json b/src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_refuge_cup.json
new file mode 100644
index 0000000000000000000000000000000000000000..64df6a37635c2b29fd86189047c2d64a01778dbe
--- /dev/null
+++ b/src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_refuge_cup.json
@@ -0,0 +1,23 @@
+{
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+ ]
+}
diff --git a/src/mednet/libs/segmentation/tests/test_refuge.py b/src/mednet/libs/segmentation/tests/test_refuge.py
new file mode 100644
index 0000000000000000000000000000000000000000..07dedfc2f1a1872752a0e09765508c19dd291f8b
--- /dev/null
+++ b/src/mednet/libs/segmentation/tests/test_refuge.py
@@ -0,0 +1,134 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""Tests for refuge dataset."""
+
+import importlib
+
+import pytest
+from click.testing import CliRunner
+
+
+def id_function(val):
+ if isinstance(val, dict):
+ return str(val)
+ return repr(val)
+
+
+@pytest.mark.parametrize(
+ "split,lengths",
+ [
+ ("default", dict(train=400, validation=400, test=400)),
+ ],
+ ids=id_function, # just changes how pytest prints it
+)
+def test_protocol_consistency(
+ database_checkers,
+ split: str,
+ lengths: dict[str, int],
+):
+ from mednet.libs.common.data.split import make_split
+
+ database_checkers.check_split(
+ make_split("mednet.libs.segmentation.config.data.refuge", f"{split}.json"),
+ lengths=lengths,
+ )
+
+
+@pytest.mark.skip_if_rc_var_not_set("datadir.refuge")
+def test_database_check():
+ from mednet.libs.segmentation.scripts.database import check
+
+ runner = CliRunner()
+ result = runner.invoke(check, ["--limit=10", "refuge-disc"])
+ assert (
+ result.exit_code == 0
+ ), f"Exit code {result.exit_code} != 0 -- Output:\n{result.output}"
+
+
+@pytest.mark.skip_if_rc_var_not_set("datadir.refuge")
+@pytest.mark.parametrize(
+ "dataset",
+ [
+ "train",
+ "validation",
+ "test",
+ ],
+)
+@pytest.mark.parametrize(
+ "name",
+ [
+ "cup",
+ "disc",
+ ],
+)
+def test_loading(database_checkers, name: str, dataset: str):
+ datamodule = importlib.import_module(
+ f".{name}",
+ "mednet.libs.segmentation.config.data.refuge",
+ ).datamodule
+
+ datamodule.model_transforms = [] # should be done before setup()
+ datamodule.setup("predict") # sets up all datasets
+
+ loader = datamodule.predict_dataloader()[dataset]
+
+ limit = 3 # limit load checking
+ for batch in loader:
+ if limit == 0:
+ break
+ database_checkers.check_loaded_batch(
+ batch,
+ batch_size=1,
+ color_planes=3,
+ expected_num_targets=1,
+ )
+ limit -= 1
+
+
+@pytest.mark.skip_if_rc_var_not_set("datadir.refuge")
+def test_raw_transforms_image_quality(database_checkers, datadir):
+ reference_histogram_file = str(
+ datadir / "histograms/raw_data/histograms_refuge_cup.json",
+ )
+
+ datamodule = importlib.import_module(
+ ".cup",
+ "mednet.libs.segmentation.config.data.refuge",
+ ).datamodule
+
+ datamodule.model_transforms = []
+ datamodule.setup("predict")
+
+ database_checkers.check_image_quality(datamodule, reference_histogram_file)
+
+
+@pytest.mark.skip_if_rc_var_not_set("datadir.refuge")
+@pytest.mark.parametrize(
+ "model_name",
+ ["lwnet"],
+)
+def test_model_transforms_image_quality(database_checkers, datadir, model_name):
+ reference_histogram_file = str(
+ datadir / f"histograms/models/histograms_{model_name}_refuge_cup.json",
+ )
+
+ datamodule = importlib.import_module(
+ ".cup",
+ "mednet.libs.segmentation.config.data.refuge",
+ ).datamodule
+
+ model = importlib.import_module(
+ f".{model_name}",
+ "mednet.libs.segmentation.config.models",
+ ).model
+
+ datamodule.model_transforms = model.model_transforms
+ datamodule.setup("predict")
+
+ database_checkers.check_image_quality(
+ datamodule,
+ reference_histogram_file,
+ compare_type="statistical",
+ pearson_coeff_threshold=0.005,
+ )