diff --git a/pyproject.toml b/pyproject.toml
index 14e273f73ce1f0785f6f33ffeddde67e669d651c..7faa0e98e296fcfdaa211da6a57def2687308cf9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -440,6 +440,12 @@ drionsdb-2nd = "mednet.libs.segmentation.config.data.drionsdb.expert2"
# drive dataset - retinography
drive = "mednet.libs.segmentation.config.data.drive.default"
+# drishti-gs1 - retinography
+drishtigs1-disc-all = "mednet.libs.segmentation.config.data.drishtigs1.optic_disc_all"
+drishtigs1-disc-any = "mednet.libs.segmentation.config.data.drishtigs1.optic_disc_any"
+drishtigs1-cup-all = "mednet.libs.segmentation.config.data.drishtigs1.optic_cup_all"
+drishtigs1-cup-any = "mednet.libs.segmentation.config.data.drishtigs1.optic_cup_any"
+
# iostar - retinography
iostar-vessel = "mednet.libs.segmentation.config.data.iostar.vessel"
iostar-disc = "mednet.libs.segmentation.config.data.iostar.optic_disc"
diff --git a/src/mednet/libs/segmentation/config/data/drishtigs1/__init__.py b/src/mednet/libs/segmentation/config/data/drishtigs1/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/src/mednet/libs/segmentation/config/data/drishtigs1/datamodule.py b/src/mednet/libs/segmentation/config/data/drishtigs1/datamodule.py
new file mode 100644
index 0000000000000000000000000000000000000000..bf73162c1d009d500e04482f8312511a56745d04
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/drishtigs1/datamodule.py
@@ -0,0 +1,130 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""Drishti-GS1 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.common.models.transforms import crop_image_to_mask
+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_all
+ Indicate whether to use the "all" or "any" target.
+ """
+
+ datadir: pathlib.Path
+ """This variable contains the base directory where the database raw data is
+ stored."""
+
+ def __init__(self, target_all: bool):
+ 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_all = target_all
+
+ 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_all:
+ target = to_tensor(
+ PIL.Image.open(self.datadir / sample[1])
+ .convert(mode="RGB", dither=None)
+ .convert("L")
+ .point(lambda p: p > 254, mode="1")
+ )
+ else:
+ target = to_tensor(
+ PIL.Image.open(self.datadir / sample[1])
+ .convert(mode="RGB", dither=None)
+ .convert("L")
+ .point(lambda p: p > 0, mode="1")
+ )
+
+ mask = to_tensor(
+ PIL.Image.open(self._pkg_path / sample[2]).convert(mode="1", dither=None)
+ )
+
+ tensor = tv_tensors.Image(crop_image_to_mask(image, mask))
+ target = tv_tensors.Image(crop_image_to_mask(target, mask))
+ mask = tv_tensors.Mask(crop_image_to_mask(mask, mask))
+
+ return tensor, dict(target=target, mask=mask, name=sample[0]) # type: ignore[arg-type]
+
+
+class DataModule(CachingDataModule):
+ """Drishti-GS1 for Optic Disc and Cup Segmentation.
+
+ Drishti-GS is a dataset meant for validation of segmenting OD, cup and
+ detecting notching. The images in the Drishti-GS dataset have been collected
+ and annotated by Aravind Eye hospital, Madurai, India. This dataset is of a
+ single population as all subjects whose eye images are part of this dataset are
+ Indians.
+
+ The dataset is divided into two: a training set and a testing set of images.
+ Training images (50) are provided with groundtruths for OD and Cup segmentation
+ and notching information.
+
+ * Reference (including train/test split): [DRISHTIGS1-2014]_
+ * Original resolution (height x width): varying (min: 1749 x 2045, max: 1845 x
+ 2468)
+ * Configuration resolution: 1760 x 2048 (after center cropping)
+ * Protocols ``optic-disc`` and ``optic-cup``:
+ * Training: 50
+ * Test: 51
+
+ Parameters
+ ----------
+ split_filename
+ Name of the .json file containing the split to load.
+ target_all
+ Indicate whether to use the "all" or "any" target.
+ """
+
+ def __init__(self, split_filename: str, target_all: bool):
+ assert __package__ is not None
+ super().__init__(
+ database_split=make_split(__package__, split_filename),
+ raw_data_loader=SegmentationRawDataLoader(target_all),
+ database_name=__package__.rsplit(".", 1)[1],
+ split_name=pathlib.Path(split_filename).stem,
+ )
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index 0000000000000000000000000000000000000000..b0f9b156378d77cd5d012cb316fb941bac66cb1b
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+ "Drishti-GS1_files/Test/Test_GT/drishtiGS_074/SoftMap/drishtiGS_074_ODsegSoftmap.png",
+ "Drishti-GS1_files/Test/Images/drishtiGS_074.png"
+ ],
+ [
+ "Drishti-GS1_files/Test/Images/drishtiGS_077.png",
+ "Drishti-GS1_files/Test/Test_GT/drishtiGS_077/SoftMap/drishtiGS_077_ODsegSoftmap.png",
+ "Drishti-GS1_files/Test/Images/drishtiGS_077.png"
+ ],
+ [
+ "Drishti-GS1_files/Test/Images/drishtiGS_078.png",
+ "Drishti-GS1_files/Test/Test_GT/drishtiGS_078/SoftMap/drishtiGS_078_ODsegSoftmap.png",
+ "Drishti-GS1_files/Test/Images/drishtiGS_078.png"
+ ],
+ [
+ "Drishti-GS1_files/Test/Images/drishtiGS_079.png",
+ "Drishti-GS1_files/Test/Test_GT/drishtiGS_079/SoftMap/drishtiGS_079_ODsegSoftmap.png",
+ "Drishti-GS1_files/Test/Images/drishtiGS_079.png"
+ ],
+ [
+ "Drishti-GS1_files/Test/Images/drishtiGS_082.png",
+ "Drishti-GS1_files/Test/Test_GT/drishtiGS_082/SoftMap/drishtiGS_082_ODsegSoftmap.png",
+ "Drishti-GS1_files/Test/Images/drishtiGS_082.png"
+ ],
+ [
+ "Drishti-GS1_files/Test/Images/drishtiGS_083.png",
+ "Drishti-GS1_files/Test/Test_GT/drishtiGS_083/SoftMap/drishtiGS_083_ODsegSoftmap.png",
+ "Drishti-GS1_files/Test/Images/drishtiGS_083.png"
+ ],
+ [
+ "Drishti-GS1_files/Test/Images/drishtiGS_085.png",
+ "Drishti-GS1_files/Test/Test_GT/drishtiGS_085/SoftMap/drishtiGS_085_ODsegSoftmap.png",
+ "Drishti-GS1_files/Test/Images/drishtiGS_085.png"
+ ],
+ [
+ "Drishti-GS1_files/Test/Images/drishtiGS_086.png",
+ "Drishti-GS1_files/Test/Test_GT/drishtiGS_086/SoftMap/drishtiGS_086_ODsegSoftmap.png",
+ "Drishti-GS1_files/Test/Images/drishtiGS_086.png"
+ ],
+ [
+ "Drishti-GS1_files/Test/Images/drishtiGS_087.png",
+ "Drishti-GS1_files/Test/Test_GT/drishtiGS_087/SoftMap/drishtiGS_087_ODsegSoftmap.png",
+ "Drishti-GS1_files/Test/Images/drishtiGS_087.png"
+ ],
+ [
+ "Drishti-GS1_files/Test/Images/drishtiGS_091.png",
+ "Drishti-GS1_files/Test/Test_GT/drishtiGS_091/SoftMap/drishtiGS_091_ODsegSoftmap.png",
+ "Drishti-GS1_files/Test/Images/drishtiGS_091.png"
+ ],
+ [
+ "Drishti-GS1_files/Test/Images/drishtiGS_093.png",
+ "Drishti-GS1_files/Test/Test_GT/drishtiGS_093/SoftMap/drishtiGS_093_ODsegSoftmap.png",
+ "Drishti-GS1_files/Test/Images/drishtiGS_093.png"
+ ],
+ [
+ "Drishti-GS1_files/Test/Images/drishtiGS_095.png",
+ "Drishti-GS1_files/Test/Test_GT/drishtiGS_095/SoftMap/drishtiGS_095_ODsegSoftmap.png",
+ "Drishti-GS1_files/Test/Images/drishtiGS_095.png"
+ ],
+ [
+ "Drishti-GS1_files/Test/Images/drishtiGS_096.png",
+ "Drishti-GS1_files/Test/Test_GT/drishtiGS_096/SoftMap/drishtiGS_096_ODsegSoftmap.png",
+ "Drishti-GS1_files/Test/Images/drishtiGS_096.png"
+ ],
+ [
+ "Drishti-GS1_files/Test/Images/drishtiGS_097.png",
+ "Drishti-GS1_files/Test/Test_GT/drishtiGS_097/SoftMap/drishtiGS_097_ODsegSoftmap.png",
+ "Drishti-GS1_files/Test/Images/drishtiGS_097.png"
+ ],
+ [
+ "Drishti-GS1_files/Test/Images/drishtiGS_099.png",
+ "Drishti-GS1_files/Test/Test_GT/drishtiGS_099/SoftMap/drishtiGS_099_ODsegSoftmap.png",
+ "Drishti-GS1_files/Test/Images/drishtiGS_099.png"
+ ],
+ [
+ "Drishti-GS1_files/Test/Images/drishtiGS_100.png",
+ "Drishti-GS1_files/Test/Test_GT/drishtiGS_100/SoftMap/drishtiGS_100_ODsegSoftmap.png",
+ "Drishti-GS1_files/Test/Images/drishtiGS_100.png"
+ ]
+ ]
+ }
diff --git a/src/mednet/libs/segmentation/config/data/drishtigs1/optic_cup_all.py b/src/mednet/libs/segmentation/config/data/drishtigs1/optic_cup_all.py
new file mode 100644
index 0000000000000000000000000000000000000000..5dd8ca224ec5c841b4128d94772de4399d16cea8
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/drishtigs1/optic_cup_all.py
@@ -0,0 +1,13 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""DRISHTI-GS1 dataset for Cup Segmentation (agreed by all annotators).
+
+* Configuration resolution: 1760 x 2048 (after center cropping)
+* Reference (includes split): [DRISHTIGS1-2014]_
+* See :py:mod:`deepdraw.data.drishtigs1` for dataset details
+"""
+
+from mednet.libs.segmentation.config.data.drishtigs1.datamodule import DataModule
+
+datamodule = DataModule("optic-cup.json", target_all=True)
diff --git a/src/mednet/libs/segmentation/config/data/drishtigs1/optic_cup_any.py b/src/mednet/libs/segmentation/config/data/drishtigs1/optic_cup_any.py
new file mode 100644
index 0000000000000000000000000000000000000000..47c56927e0cc5b6dd784fa67bf7f81b3bd88d6fa
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/drishtigs1/optic_cup_any.py
@@ -0,0 +1,13 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""DRISHTI-GS1 dataset for Cup Segmentation (agreed by all annotators).
+
+* Configuration resolution: 1760 x 2048 (after center cropping)
+* Reference (includes split): [DRISHTIGS1-2014]_
+* See :py:mod:`deepdraw.data.drishtigs1` for dataset details
+"""
+
+from mednet.libs.segmentation.config.data.drishtigs1.datamodule import DataModule
+
+datamodule = DataModule("optic-cup.json", target_all=False)
diff --git a/src/mednet/libs/segmentation/config/data/drishtigs1/optic_disc_all.py b/src/mednet/libs/segmentation/config/data/drishtigs1/optic_disc_all.py
new file mode 100644
index 0000000000000000000000000000000000000000..6a592c62d9c9c5642709adc42c5aa1ae9477fd51
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/drishtigs1/optic_disc_all.py
@@ -0,0 +1,13 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""DRISHTI-GS1 dataset for Cup Segmentation (agreed by all annotators).
+
+* Configuration resolution: 1760 x 2048 (after center cropping)
+* Reference (includes split): [DRISHTIGS1-2014]_
+* See :py:mod:`deepdraw.data.drishtigs1` for dataset details
+"""
+
+from mednet.libs.segmentation.config.data.drishtigs1.datamodule import DataModule
+
+datamodule = DataModule("optic-disc.json", target_all=True)
diff --git a/src/mednet/libs/segmentation/config/data/drishtigs1/optic_disc_any.py b/src/mednet/libs/segmentation/config/data/drishtigs1/optic_disc_any.py
new file mode 100644
index 0000000000000000000000000000000000000000..5c8e840e0eb3df234fb99e539cf3621e00e67f86
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/drishtigs1/optic_disc_any.py
@@ -0,0 +1,13 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""DRISHTI-GS1 dataset for Cup Segmentation (agreed by all annotators).
+
+* Configuration resolution: 1760 x 2048 (after center cropping)
+* Reference (includes split): [DRISHTIGS1-2014]_
+* See :py:mod:`deepdraw.data.drishtigs1` for dataset details
+"""
+
+from mednet.libs.segmentation.config.data.drishtigs1.datamodule import DataModule
+
+datamodule = DataModule("optic-disc.json", target_all=False)
diff --git a/src/mednet/libs/segmentation/tests/data/histograms/models/histograms_lwnet_drishtigs1_optic_cup_all.json b/src/mednet/libs/segmentation/tests/data/histograms/models/histograms_lwnet_drishtigs1_optic_cup_all.json
new file mode 100644
index 0000000000000000000000000000000000000000..4582f7cab131b1c0472d97d2027d6a1fdcb7cdab
--- /dev/null
+++ b/src/mednet/libs/segmentation/tests/data/histograms/models/histograms_lwnet_drishtigs1_optic_cup_all.json
@@ -0,0 +1,16 @@
+{
+ "train": [
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+}
diff --git a/src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_drishtigs1_optic_cup_all.json b/src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_drishtigs1_optic_cup_all.json
new file mode 100644
index 0000000000000000000000000000000000000000..c62c780ff1ee32098be92e7092c2278c0a4ad3a9
--- /dev/null
+++ b/src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_drishtigs1_optic_cup_all.json
@@ -0,0 +1,16 @@
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+ ]
+}
diff --git a/src/mednet/libs/segmentation/tests/test_drishtigs1.py b/src/mednet/libs/segmentation/tests/test_drishtigs1.py
new file mode 100644
index 0000000000000000000000000000000000000000..0c099b556a7f23a96b7de53861bf2b8bdcd878fa
--- /dev/null
+++ b/src/mednet/libs/segmentation/tests/test_drishtigs1.py
@@ -0,0 +1,137 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""Tests for drishtigs1 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",
+ [
+ ("optic-cup", dict(train=50, test=51)),
+ ("optic-disc", dict(train=50, test=51)),
+ ],
+ 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.drishtigs1", f"{split}.json"),
+ lengths=lengths,
+ )
+
+
+@pytest.mark.skip_if_rc_var_not_set("datadir.drishtigs1")
+def test_database_check():
+ from mednet.libs.segmentation.scripts.database import check
+
+ runner = CliRunner()
+ result = runner.invoke(check, ["drishtigs1-disc-all"])
+ 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.drishtigs1")
+@pytest.mark.parametrize(
+ "dataset",
+ [
+ "train",
+ "test",
+ ],
+)
+@pytest.mark.parametrize(
+ "name",
+ [
+ "optic_cup_all",
+ "optic_cup_any",
+ "optic_disc_all",
+ "optic_disc_any",
+ ],
+)
+def test_loading(database_checkers, name: str, dataset: str):
+ datamodule = importlib.import_module(
+ f".{name}",
+ "mednet.libs.segmentation.config.data.drishtigs1",
+ ).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.drishtigs1")
+def test_raw_transforms_image_quality(database_checkers, datadir):
+ reference_histogram_file = str(
+ datadir / "histograms/raw_data/histograms_drishtigs1_optic_cup_all.json",
+ )
+
+ datamodule = importlib.import_module(
+ ".optic_cup_all",
+ "mednet.libs.segmentation.config.data.drishtigs1",
+ ).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.drishtigs1")
+@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}_drishtigs1_optic_cup_all.json",
+ )
+
+ datamodule = importlib.import_module(
+ ".optic_cup_all",
+ "mednet.libs.segmentation.config.data.drishtigs1",
+ ).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,
+ )