[segmetnation] Add hrf database

pyproject.toml

@@ -446,6 +446,9 @@ drishtigs1-disc-any = "mednet.libs.segmentation.config.data.drishtigs1.optic_dis
 drishtigs1-cup-all = "mednet.libs.segmentation.config.data.drishtigs1.optic_cup_all"
 drishtigs1-cup-any = "mednet.libs.segmentation.config.data.drishtigs1.optic_cup_any"
 
+# hrf - retinography
+hrf = "mednet.libs.segmentation.config.data.hrf.default"
+
 # iostar - retinography
 iostar-vessel = "mednet.libs.segmentation.config.data.iostar.vessel"
 iostar-disc = "mednet.libs.segmentation.config.data.iostar.optic_disc"

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

+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""HRF dataset for Vessel Segmentation."""
+
+import os
+import pathlib
+
+import PIL.Image
+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 drishtigs1hrf dataset."""
+
+    datadir: pathlib.Path
+    """This variable contains the base directory where the database raw data is
+    stored."""
+
+    def __init__(self):
+        self.datadir = pathlib.Path(
+            load_rc().get(CONFIGURATION_KEY_DATADIR, os.path.realpath(os.curdir))
+        )
+
+    def sample(self, sample: tuple[str, str, str]) -> Sample:
+        """Load a single image sample from the disk.
+
+        Parameters
+        ----------
+        sample
+            A tuple containing the path suffix, within the dataset root folder,
+            where to find the image to be loaded, and an integer, representing the
+            sample label.
+
+        Returns
+        -------
+            The sample representation.
+        """
+
+        image = to_tensor(PIL.Image.open(self.datadir / sample[0]).convert(mode="RGB"))
+
+        target = to_tensor(
+            PIL.Image.open(self.datadir / sample[1]).convert(mode="1", dither=None)
+        )
+
+        mask = to_tensor(
+            PIL.Image.open(self.datadir / 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):
+    """HRF dataset for Vessel Segmentation.
+
+    The database includes 15 images of each healthy, diabetic retinopathy (DR), and
+    glaucomatous eyes.  It contains a total  of 45 eye fundus images with a
+    resolution of 3304 x 2336. One set of ground-truth vessel annotations is
+    available.
+
+    * Reference: [HRF-2013]_
+    * Original resolution (height x width): 2336 x 3504
+    * Configuration resolution: 1168 x 1648 (after specific cropping and rescaling)
+    * Split reference: [ORLANDO-2017]_
+    * Protocol ``default``:
+
+    * Training samples: 15 (including labels)
+    * Test samples: 30 (including labels)
+
+    Parameters
+    ----------
+    split_filename
+        Name of the .json file containing the split to load.
+    """
+
+    def __init__(self, split_filename: str):
+        assert __package__ is not None
+        super().__init__(
+            database_split=make_split(__package__, split_filename),
+            raw_data_loader=SegmentationRawDataLoader(),
+            database_name=__package__.rsplit(".", 1)[1],
+            split_name=pathlib.Path(split_filename).stem,
+        )

src/mednet/libs/segmentation/config/data/hrf/default.json

+{
+ "train": [
+  [
+   "images/01_dr.JPG",
+   "manual1/01_dr.tif",
+   "mask/01_dr_mask.tif"
+  ],
+  [
+   "images/02_dr.JPG",
+   "manual1/02_dr.tif",
+   "mask/02_dr_mask.tif"
+  ],
+  [
+   "images/03_dr.JPG",
+   "manual1/03_dr.tif",
+   "mask/03_dr_mask.tif"
+  ],
+  [
+   "images/04_dr.JPG",
+   "manual1/04_dr.tif",
+   "mask/04_dr_mask.tif"
+  ],
+  [
+   "images/05_dr.JPG",
+   "manual1/05_dr.tif",
+   "mask/05_dr_mask.tif"
+  ],
+  [
+   "images/01_g.jpg",
+   "manual1/01_g.tif",
+   "mask/01_g_mask.tif"
+  ],
+  [
+   "images/02_g.jpg",
+   "manual1/02_g.tif",
+   "mask/02_g_mask.tif"
+  ],
+  [
+   "images/03_g.jpg",
+   "manual1/03_g.tif",
+   "mask/03_g_mask.tif"
+  ],
+  [
+   "images/04_g.jpg",
+   "manual1/04_g.tif",
+   "mask/04_g_mask.tif"
+  ],
+  [
+   "images/05_g.jpg",
+   "manual1/05_g.tif",
+   "mask/05_g_mask.tif"
+  ],
+  [
+   "images/01_h.jpg",
+   "manual1/01_h.tif",
+   "mask/01_h_mask.tif"
+  ],
+  [
+   "images/02_h.jpg",
+   "manual1/02_h.tif",
+   "mask/02_h_mask.tif"
+  ],
+  [
+   "images/03_h.jpg",
+   "manual1/03_h.tif",
+   "mask/03_h_mask.tif"
+  ],
+  [
+   "images/04_h.jpg",
+   "manual1/04_h.tif",
+   "mask/04_h_mask.tif"
+  ],
+  [
+   "images/05_h.jpg",
+   "manual1/05_h.tif",
+   "mask/05_h_mask.tif"
+  ]
+ ],
+ "test": [
+  [
+   "images/06_dr.JPG",
+   "manual1/06_dr.tif",
+   "mask/06_dr_mask.tif"
+  ],
+  [
+   "images/07_dr.JPG",
+   "manual1/07_dr.tif",
+   "mask/07_dr_mask.tif"
+  ],
+  [
+   "images/08_dr.JPG",
+   "manual1/08_dr.tif",
+   "mask/08_dr_mask.tif"
+  ],
+  [
+   "images/09_dr.JPG",
+   "manual1/09_dr.tif",
+   "mask/09_dr_mask.tif"
+  ],
+  [
+   "images/10_dr.JPG",
+   "manual1/10_dr.tif",
+   "mask/10_dr_mask.tif"
+  ],
+  [
+   "images/11_dr.JPG",
+   "manual1/11_dr.tif",
+   "mask/11_dr_mask.tif"
+  ],
+  [
+   "images/12_dr.JPG",
+   "manual1/12_dr.tif",
+   "mask/12_dr_mask.tif"
+  ],
+  [
+   "images/13_dr.JPG",
+   "manual1/13_dr.tif",
+   "mask/13_dr_mask.tif"
+  ],
+  [
+   "images/14_dr.JPG",
+   "manual1/14_dr.tif",
+   "mask/14_dr_mask.tif"
+  ],
+  [
+   "images/15_dr.JPG",
+   "manual1/15_dr.tif",
+   "mask/15_dr_mask.tif"
+  ],
+  [
+   "images/06_g.jpg",
+   "manual1/06_g.tif",
+   "mask/06_g_mask.tif"
+  ],
+  [
+   "images/07_g.jpg",
+   "manual1/07_g.tif",
+   "mask/07_g_mask.tif"
+  ],
+  [
+   "images/08_g.jpg",
+   "manual1/08_g.tif",
+   "mask/08_g_mask.tif"
+  ],
+  [
+   "images/09_g.jpg",
+   "manual1/09_g.tif",
+   "mask/09_g_mask.tif"
+  ],
+  [
+   "images/10_g.jpg",
+   "manual1/10_g.tif",
+   "mask/10_g_mask.tif"
+  ],
+  [
+   "images/11_g.jpg",
+   "manual1/11_g.tif",
+   "mask/11_g_mask.tif"
+  ],
+  [
+   "images/12_g.jpg",
+   "manual1/12_g.tif",
+   "mask/12_g_mask.tif"
+  ],
+  [
+   "images/13_g.jpg",
+   "manual1/13_g.tif",
+   "mask/13_g_mask.tif"
+  ],
+  [
+   "images/14_g.jpg",
+   "manual1/14_g.tif",
+   "mask/14_g_mask.tif"
+  ],
+  [
+   "images/15_g.jpg",
+   "manual1/15_g.tif",
+   "mask/15_g_mask.tif"
+  ],
+  [
+   "images/06_h.jpg",
+   "manual1/06_h.tif",
+   "mask/06_h_mask.tif"
+  ],
+  [
+   "images/07_h.jpg",
+   "manual1/07_h.tif",
+   "mask/07_h_mask.tif"
+  ],
+  [
+   "images/08_h.jpg",
+   "manual1/08_h.tif",
+   "mask/08_h_mask.tif"
+  ],
+  [
+   "images/09_h.jpg",
+   "manual1/09_h.tif",
+   "mask/09_h_mask.tif"
+  ],
+  [
+   "images/10_h.jpg",
+   "manual1/10_h.tif",
+   "mask/10_h_mask.tif"
+  ],
+  [
+   "images/11_h.jpg",
+   "manual1/11_h.tif",
+   "mask/11_h_mask.tif"
+  ],
+  [
+   "images/12_h.jpg",
+   "manual1/12_h.tif",
+   "mask/12_h_mask.tif"
+  ],
+  [
+   "images/13_h.jpg",
+   "manual1/13_h.tif",
+   "mask/13_h_mask.tif"
+  ],
+  [
+   "images/14_h.jpg",
+   "manual1/14_h.tif",
+   "mask/14_h_mask.tif"
+  ],
+  [
+   "images/15_h.jpg",
+   "manual1/15_h.tif",
+   "mask/15_h_mask.tif"
+  ]
+ ]
+}

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

+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""HRF dataset for Vessel Segmentation (default protocol).
+
+* Split reference: [ORLANDO-2017]_
+* Configuration resolution: 1168 x 1648 (about half full HRF resolution)
+* See :py:mod:`deepdraw.data.hrf` for dataset details
+"""
+
+from mednet.libs.segmentation.config.data.hrf.datamodule import (
+    DataModule,
+)
+
+datamodule = DataModule("default.json")

src/mednet/libs/segmentation/tests/test_hrf.py

+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""Tests for hrf 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=15, test=30)),
+    ],
+    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.hrf", f"{split}.json"),
+        lengths=lengths,
+    )
+
+
+@pytest.mark.skip_if_rc_var_not_set("datadir.hrf")
+def test_database_check():
+    from mednet.libs.segmentation.scripts.database import check
+
+    runner = CliRunner()
+    result = runner.invoke(check, ["hrf"])
+    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.hrf")
+@pytest.mark.parametrize(
+    "dataset",
+    [
+        "train",
+        "test",
+    ],
+)
+@pytest.mark.parametrize(
+    "name",
+    [
+        "default",
+    ],
+)
+def test_loading(database_checkers, name: str, dataset: str):
+    datamodule = importlib.import_module(
+        f".{name}",
+        "mednet.libs.segmentation.config.data.hrf",
+    ).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.hrf")
+def test_raw_transforms_image_quality(database_checkers, datadir):
+    reference_histogram_file = str(
+        datadir / "histograms/raw_data/histograms_hrf_default.json",
+    )
+
+    datamodule = importlib.import_module(
+        ".default",
+        "mednet.libs.segmentation.config.data.hrf",
+    ).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.hrf")
+@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}_hrf_default.json",
+    )
+
+    datamodule = importlib.import_module(
+        ".default",
+        "mednet.libs.segmentation.config.data.hrf",
+    ).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,
+    )