From 5c6f8df2b095d9d475513d11cd6e99a85a391730 Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Thu, 6 Jun 2024 12:32:43 +0200
Subject: [PATCH] [segmentation] Add drionsdb database
---
pyproject.toml | 4 +
.../config/data/drionsdb/__init__.py | 0
.../config/data/drionsdb/datamodule.py | 129 ++++
.../config/data/drionsdb/expert1.json | 556 ++++++++++++++++++
.../config/data/drionsdb/expert1.py | 13 +
.../config/data/drionsdb/expert2.json | 556 ++++++++++++++++++
.../config/data/drionsdb/expert2.py | 13 +
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.../histograms_lwnet_drionsdb_expert1.json | 16 +
.../raw_data/histograms_drionsdb_expert1.json | 16 +
.../libs/segmentation/tests/test_drionsdb.py | 134 +++++
120 files changed, 1437 insertions(+)
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/__init__.py
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/datamodule.py
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/expert1.json
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/expert1.py
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/expert2.json
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/expert2.py
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_001.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_002.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_003.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_004.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_005.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_006.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_007.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_008.png
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create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_012.png
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create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_046.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_047.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_048.png
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create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_053.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_054.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_055.png
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create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_068.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_069.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_070.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_071.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_072.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_073.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_074.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_075.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_076.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_077.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_078.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_079.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_080.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_081.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_082.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_083.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_084.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_085.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_086.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_087.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_088.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_089.png
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create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_093.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_094.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_095.png
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create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_100.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_101.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_102.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_103.png
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create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_106.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_107.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_108.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_109.png
create mode 100644 src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_110.png
create mode 100644 src/mednet/libs/segmentation/tests/data/histograms/models/histograms_lwnet_drionsdb_expert1.json
create mode 100644 src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_drionsdb_expert1.json
create mode 100644 src/mednet/libs/segmentation/tests/test_drionsdb.py
diff --git a/pyproject.toml b/pyproject.toml
index 73ae90e9..14e273f7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -433,6 +433,10 @@ cxr8 = "mednet.libs.segmentation.config.data.cxr8.default"
# drhagis dataset - retinography
drhagis = "mednet.libs.segmentation.config.data.drhagis.default"
+# drionsdb - retinography
+drionsdb = "mednet.libs.segmentation.config.data.drionsdb.expert1"
+drionsdb-2nd = "mednet.libs.segmentation.config.data.drionsdb.expert2"
+
# drive dataset - retinography
drive = "mednet.libs.segmentation.config.data.drive.default"
diff --git a/src/mednet/libs/segmentation/config/data/drionsdb/__init__.py b/src/mednet/libs/segmentation/config/data/drionsdb/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/mednet/libs/segmentation/config/data/drionsdb/datamodule.py b/src/mednet/libs/segmentation/config/data/drionsdb/datamodule.py
new file mode 100644
index 00000000..554a44b9
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/drionsdb/datamodule.py
@@ -0,0 +1,129 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""DRIONS-DB (training set) for Optic Disc Segmentation."""
+
+import csv
+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 drionsdb 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))
+ )
+
+ self._pkg_path = pathlib.Path(
+ pkg_resources.resource_filename(__name__, "masks")
+ )
+
+ def _txt_to_pil_1(self, fname: pathlib.Path, size: tuple[int, int]) -> PIL.Image:
+ """Convert DRIONS-DB annotations to image format.
+
+ Parameters
+ ----------
+ fname
+ Path to a file containing annotations.
+ size
+ The size of the mask (width, height).
+
+ Returns
+ -------
+ The binary mask.
+ """
+ with fname.open("r") as f:
+ rows = csv.reader(f, delimiter=",", quoting=csv.QUOTE_NONNUMERIC)
+ data = list(map(tuple, rows))
+
+ retval = PIL.Image.new("1", size)
+ draw = PIL.ImageDraw.ImageDraw(retval)
+ draw.polygon(data, fill="white")
+ del draw
+ return retval
+
+ 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 = PIL.Image.open(self.datadir / sample[0]).convert(mode="RGB")
+ target = to_tensor(self._txt_to_pil_1(self.datadir / sample[1], image.size))
+ image = to_tensor(image)
+ 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):
+ """DRIONS-DB (training set) for Optic Disc Segmentation.
+
+ The dataset originates from data collected from 55 patients with glaucoma
+ (23.1%) and eye hypertension (76.9%), and random selected from an eye fundus
+ image base belonging to the Ophthalmology Service at Miguel Servet Hospital,
+ Saragossa (Spain). It contains 110 eye fundus images with a resolution of 600
+ x 400. Two sets of ground-truth optic disc annotations are available. The first
+ set is commonly used for training and testing. The second set acts as a "human"
+ baseline.
+
+ * Reference: [DRIONSDB-2008]_
+ * Original resolution (height x width): 400 x 600
+ * Configuration resolution: 416 x 608 (after padding)
+ * Split reference: [MANINIS-2016]_
+ * Protocols ``expert1`` (baseline) and ``expert2`` (human comparison):
+
+ * Training samples: 60
+ * Test samples: 50
+
+ 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,
+ )
diff --git a/src/mednet/libs/segmentation/config/data/drionsdb/expert1.json b/src/mednet/libs/segmentation/config/data/drionsdb/expert1.json
new file mode 100644
index 00000000..fae03329
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/drionsdb/expert1.json
@@ -0,0 +1,556 @@
+{
+ "train":[
+ [
+ "images/image_001.jpg",
+ "experts_anotation/anotExpert1_001.txt",
+ "images/image_001.png"
+ ],
+ [
+ "images/image_002.jpg",
+ "experts_anotation/anotExpert1_002.txt",
+ "images/image_002.png"
+ ],
+ [
+ "images/image_003.jpg",
+ "experts_anotation/anotExpert1_003.txt",
+ "images/image_003.png"
+ ],
+ [
+ "images/image_004.jpg",
+ "experts_anotation/anotExpert1_004.txt",
+ "images/image_004.png"
+ ],
+ [
+ "images/image_005.jpg",
+ "experts_anotation/anotExpert1_005.txt",
+ "images/image_005.png"
+ ],
+ [
+ "images/image_006.jpg",
+ "experts_anotation/anotExpert1_006.txt",
+ "images/image_006.png"
+ ],
+ [
+ "images/image_007.jpg",
+ "experts_anotation/anotExpert1_007.txt",
+ "images/image_007.png"
+ ],
+ [
+ "images/image_008.jpg",
+ "experts_anotation/anotExpert1_008.txt",
+ "images/image_008.png"
+ ],
+ [
+ "images/image_009.jpg",
+ "experts_anotation/anotExpert1_009.txt",
+ "images/image_009.png"
+ ],
+ [
+ "images/image_010.jpg",
+ "experts_anotation/anotExpert1_010.txt",
+ "images/image_010.png"
+ ],
+ [
+ "images/image_011.jpg",
+ "experts_anotation/anotExpert1_011.txt",
+ "images/image_011.png"
+ ],
+ [
+ "images/image_012.jpg",
+ "experts_anotation/anotExpert1_012.txt",
+ "images/image_012.png"
+ ],
+ [
+ "images/image_013.jpg",
+ "experts_anotation/anotExpert1_013.txt",
+ "images/image_013.png"
+ ],
+ [
+ "images/image_014.jpg",
+ "experts_anotation/anotExpert1_014.txt",
+ "images/image_014.png"
+ ],
+ [
+ "images/image_015.jpg",
+ "experts_anotation/anotExpert1_015.txt",
+ "images/image_015.png"
+ ],
+ [
+ "images/image_016.jpg",
+ "experts_anotation/anotExpert1_016.txt",
+ "images/image_016.png"
+ ],
+ [
+ "images/image_017.jpg",
+ "experts_anotation/anotExpert1_017.txt",
+ "images/image_017.png"
+ ],
+ [
+ "images/image_018.jpg",
+ "experts_anotation/anotExpert1_018.txt",
+ "images/image_018.png"
+ ],
+ [
+ "images/image_019.jpg",
+ "experts_anotation/anotExpert1_019.txt",
+ "images/image_019.png"
+ ],
+ [
+ "images/image_020.jpg",
+ "experts_anotation/anotExpert1_020.txt",
+ "images/image_020.png"
+ ],
+ [
+ "images/image_021.jpg",
+ "experts_anotation/anotExpert1_021.txt",
+ "images/image_021.png"
+ ],
+ [
+ "images/image_022.jpg",
+ "experts_anotation/anotExpert1_022.txt",
+ "images/image_022.png"
+ ],
+ [
+ "images/image_023.jpg",
+ "experts_anotation/anotExpert1_023.txt",
+ "images/image_023.png"
+ ],
+ [
+ "images/image_024.jpg",
+ "experts_anotation/anotExpert1_024.txt",
+ "images/image_024.png"
+ ],
+ [
+ "images/image_025.jpg",
+ "experts_anotation/anotExpert1_025.txt",
+ "images/image_025.png"
+ ],
+ [
+ "images/image_026.jpg",
+ "experts_anotation/anotExpert1_026.txt",
+ "images/image_026.png"
+ ],
+ [
+ "images/image_027.jpg",
+ "experts_anotation/anotExpert1_027.txt",
+ "images/image_027.png"
+ ],
+ [
+ "images/image_028.jpg",
+ "experts_anotation/anotExpert1_028.txt",
+ "images/image_028.png"
+ ],
+ [
+ "images/image_029.jpg",
+ "experts_anotation/anotExpert1_029.txt",
+ "images/image_029.png"
+ ],
+ [
+ "images/image_030.jpg",
+ "experts_anotation/anotExpert1_030.txt",
+ "images/image_030.png"
+ ],
+ [
+ "images/image_031.jpg",
+ "experts_anotation/anotExpert1_031.txt",
+ "images/image_031.png"
+ ],
+ [
+ "images/image_032.jpg",
+ "experts_anotation/anotExpert1_032.txt",
+ "images/image_032.png"
+ ],
+ [
+ "images/image_033.jpg",
+ "experts_anotation/anotExpert1_033.txt",
+ "images/image_033.png"
+ ],
+ [
+ "images/image_034.jpg",
+ "experts_anotation/anotExpert1_034.txt",
+ "images/image_034.png"
+ ],
+ [
+ "images/image_035.jpg",
+ "experts_anotation/anotExpert1_035.txt",
+ "images/image_035.png"
+ ],
+ [
+ "images/image_036.jpg",
+ "experts_anotation/anotExpert1_036.txt",
+ "images/image_036.png"
+ ],
+ [
+ "images/image_037.jpg",
+ "experts_anotation/anotExpert1_037.txt",
+ "images/image_037.png"
+ ],
+ [
+ "images/image_038.jpg",
+ "experts_anotation/anotExpert1_038.txt",
+ "images/image_038.png"
+ ],
+ [
+ "images/image_039.jpg",
+ "experts_anotation/anotExpert1_039.txt",
+ "images/image_039.png"
+ ],
+ [
+ "images/image_040.jpg",
+ "experts_anotation/anotExpert1_040.txt",
+ "images/image_040.png"
+ ],
+ [
+ "images/image_041.jpg",
+ "experts_anotation/anotExpert1_041.txt",
+ "images/image_041.png"
+ ],
+ [
+ "images/image_042.jpg",
+ "experts_anotation/anotExpert1_042.txt",
+ "images/image_042.png"
+ ],
+ [
+ "images/image_043.jpg",
+ "experts_anotation/anotExpert1_043.txt",
+ "images/image_043.png"
+ ],
+ [
+ "images/image_044.jpg",
+ "experts_anotation/anotExpert1_044.txt",
+ "images/image_044.png"
+ ],
+ [
+ "images/image_045.jpg",
+ "experts_anotation/anotExpert1_045.txt",
+ "images/image_045.png"
+ ],
+ [
+ "images/image_046.jpg",
+ "experts_anotation/anotExpert1_046.txt",
+ "images/image_046.png"
+ ],
+ [
+ "images/image_047.jpg",
+ "experts_anotation/anotExpert1_047.txt",
+ "images/image_047.png"
+ ],
+ [
+ "images/image_048.jpg",
+ "experts_anotation/anotExpert1_048.txt",
+ "images/image_048.png"
+ ],
+ [
+ "images/image_049.jpg",
+ "experts_anotation/anotExpert1_049.txt",
+ "images/image_049.png"
+ ],
+ [
+ "images/image_050.jpg",
+ "experts_anotation/anotExpert1_050.txt",
+ "images/image_050.png"
+ ],
+ [
+ "images/image_051.jpg",
+ "experts_anotation/anotExpert1_051.txt",
+ "images/image_051.png"
+ ],
+ [
+ "images/image_052.jpg",
+ "experts_anotation/anotExpert1_052.txt",
+ "images/image_052.png"
+ ],
+ [
+ "images/image_053.jpg",
+ "experts_anotation/anotExpert1_053.txt",
+ "images/image_053.png"
+ ],
+ [
+ "images/image_054.jpg",
+ "experts_anotation/anotExpert1_054.txt",
+ "images/image_054.png"
+ ],
+ [
+ "images/image_055.jpg",
+ "experts_anotation/anotExpert1_055.txt",
+ "images/image_055.png"
+ ],
+ [
+ "images/image_056.jpg",
+ "experts_anotation/anotExpert1_056.txt",
+ "images/image_056.png"
+ ],
+ [
+ "images/image_057.jpg",
+ "experts_anotation/anotExpert1_057.txt",
+ "images/image_057.png"
+ ],
+ [
+ "images/image_058.jpg",
+ "experts_anotation/anotExpert1_058.txt",
+ "images/image_058.png"
+ ],
+ [
+ "images/image_059.jpg",
+ "experts_anotation/anotExpert1_059.txt",
+ "images/image_059.png"
+ ],
+ [
+ "images/image_060.jpg",
+ "experts_anotation/anotExpert1_060.txt",
+ "images/image_060.png"
+ ]
+ ],
+ "test":[
+ [
+ "images/image_061.jpg",
+ "experts_anotation/anotExpert1_061.txt",
+ "images/image_061.png"
+ ],
+ [
+ "images/image_062.jpg",
+ "experts_anotation/anotExpert1_062.txt",
+ "images/image_062.png"
+ ],
+ [
+ "images/image_063.jpg",
+ "experts_anotation/anotExpert1_063.txt",
+ "images/image_063.png"
+ ],
+ [
+ "images/image_064.jpg",
+ "experts_anotation/anotExpert1_064.txt",
+ "images/image_064.png"
+ ],
+ [
+ "images/image_065.jpg",
+ "experts_anotation/anotExpert1_065.txt",
+ "images/image_065.png"
+ ],
+ [
+ "images/image_066.jpg",
+ "experts_anotation/anotExpert1_066.txt",
+ "images/image_066.png"
+ ],
+ [
+ "images/image_067.jpg",
+ "experts_anotation/anotExpert1_067.txt",
+ "images/image_067.png"
+ ],
+ [
+ "images/image_068.jpg",
+ "experts_anotation/anotExpert1_068.txt",
+ "images/image_068.png"
+ ],
+ [
+ "images/image_069.jpg",
+ "experts_anotation/anotExpert1_069.txt",
+ "images/image_069.png"
+ ],
+ [
+ "images/image_070.jpg",
+ "experts_anotation/anotExpert1_070.txt",
+ "images/image_070.png"
+ ],
+ [
+ "images/image_071.jpg",
+ "experts_anotation/anotExpert1_071.txt",
+ "images/image_071.png"
+ ],
+ [
+ "images/image_072.jpg",
+ "experts_anotation/anotExpert1_072.txt",
+ "images/image_072.png"
+ ],
+ [
+ "images/image_073.jpg",
+ "experts_anotation/anotExpert1_073.txt",
+ "images/image_073.png"
+ ],
+ [
+ "images/image_074.jpg",
+ "experts_anotation/anotExpert1_074.txt",
+ "images/image_074.png"
+ ],
+ [
+ "images/image_075.jpg",
+ "experts_anotation/anotExpert1_075.txt",
+ "images/image_075.png"
+ ],
+ [
+ "images/image_076.jpg",
+ "experts_anotation/anotExpert1_076.txt",
+ "images/image_076.png"
+ ],
+ [
+ "images/image_077.jpg",
+ "experts_anotation/anotExpert1_077.txt",
+ "images/image_077.png"
+ ],
+ [
+ "images/image_078.jpg",
+ "experts_anotation/anotExpert1_078.txt",
+ "images/image_078.png"
+ ],
+ [
+ "images/image_079.jpg",
+ "experts_anotation/anotExpert1_079.txt",
+ "images/image_079.png"
+ ],
+ [
+ "images/image_080.jpg",
+ "experts_anotation/anotExpert1_080.txt",
+ "images/image_080.png"
+ ],
+ [
+ "images/image_081.jpg",
+ "experts_anotation/anotExpert1_081.txt",
+ "images/image_081.png"
+ ],
+ [
+ "images/image_082.jpg",
+ "experts_anotation/anotExpert1_082.txt",
+ "images/image_082.png"
+ ],
+ [
+ "images/image_083.jpg",
+ "experts_anotation/anotExpert1_083.txt",
+ "images/image_083.png"
+ ],
+ [
+ "images/image_084.jpg",
+ "experts_anotation/anotExpert1_084.txt",
+ "images/image_084.png"
+ ],
+ [
+ "images/image_085.jpg",
+ "experts_anotation/anotExpert1_085.txt",
+ "images/image_085.png"
+ ],
+ [
+ "images/image_086.jpg",
+ "experts_anotation/anotExpert1_086.txt",
+ "images/image_086.png"
+ ],
+ [
+ "images/image_087.jpg",
+ "experts_anotation/anotExpert1_087.txt",
+ "images/image_087.png"
+ ],
+ [
+ "images/image_088.jpg",
+ "experts_anotation/anotExpert1_088.txt",
+ "images/image_088.png"
+ ],
+ [
+ "images/image_089.jpg",
+ "experts_anotation/anotExpert1_089.txt",
+ "images/image_089.png"
+ ],
+ [
+ "images/image_090.jpg",
+ "experts_anotation/anotExpert1_090.txt",
+ "images/image_090.png"
+ ],
+ [
+ "images/image_091.jpg",
+ "experts_anotation/anotExpert1_091.txt",
+ "images/image_091.png"
+ ],
+ [
+ "images/image_092.jpg",
+ "experts_anotation/anotExpert1_092.txt",
+ "images/image_092.png"
+ ],
+ [
+ "images/image_093.jpg",
+ "experts_anotation/anotExpert1_093.txt",
+ "images/image_093.png"
+ ],
+ [
+ "images/image_094.jpg",
+ "experts_anotation/anotExpert1_094.txt",
+ "images/image_094.png"
+ ],
+ [
+ "images/image_095.jpg",
+ "experts_anotation/anotExpert1_095.txt",
+ "images/image_095.png"
+ ],
+ [
+ "images/image_096.jpg",
+ "experts_anotation/anotExpert1_096.txt",
+ "images/image_096.png"
+ ],
+ [
+ "images/image_097.jpg",
+ "experts_anotation/anotExpert1_097.txt",
+ "images/image_097.png"
+ ],
+ [
+ "images/image_098.jpg",
+ "experts_anotation/anotExpert1_098.txt",
+ "images/image_098.png"
+ ],
+ [
+ "images/image_099.jpg",
+ "experts_anotation/anotExpert1_099.txt",
+ "images/image_099.png"
+ ],
+ [
+ "images/image_100.jpg",
+ "experts_anotation/anotExpert1_100.txt",
+ "images/image_100.png"
+ ],
+ [
+ "images/image_101.jpg",
+ "experts_anotation/anotExpert1_101.txt",
+ "images/image_101.png"
+ ],
+ [
+ "images/image_102.jpg",
+ "experts_anotation/anotExpert1_102.txt",
+ "images/image_102.png"
+ ],
+ [
+ "images/image_103.jpg",
+ "experts_anotation/anotExpert1_103.txt",
+ "images/image_103.png"
+ ],
+ [
+ "images/image_104.jpg",
+ "experts_anotation/anotExpert1_104.txt",
+ "images/image_104.png"
+ ],
+ [
+ "images/image_105.jpg",
+ "experts_anotation/anotExpert1_105.txt",
+ "images/image_105.png"
+ ],
+ [
+ "images/image_106.jpg",
+ "experts_anotation/anotExpert1_106.txt",
+ "images/image_106.png"
+ ],
+ [
+ "images/image_107.jpg",
+ "experts_anotation/anotExpert1_107.txt",
+ "images/image_107.png"
+ ],
+ [
+ "images/image_108.jpg",
+ "experts_anotation/anotExpert1_108.txt",
+ "images/image_108.png"
+ ],
+ [
+ "images/image_109.jpg",
+ "experts_anotation/anotExpert1_109.txt",
+ "images/image_109.png"
+ ],
+ [
+ "images/image_110.jpg",
+ "experts_anotation/anotExpert1_110.txt",
+ "images/image_110.png"
+ ]
+ ]
+ }
diff --git a/src/mednet/libs/segmentation/config/data/drionsdb/expert1.py b/src/mednet/libs/segmentation/config/data/drionsdb/expert1.py
new file mode 100644
index 00000000..40ac9797
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/drionsdb/expert1.py
@@ -0,0 +1,13 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""DRIONS-DB for Optic Disc Segmentation (expert #1 annotations).
+
+* Configuration resolution: 416 x 608 (after padding)
+* Split reference: [MANINIS-2016]_
+* See :py:mod:`deepdraw.data.drionsdb` for dataset details
+"""
+
+from mednet.libs.segmentation.config.data.drionsdb.datamodule import DataModule
+
+datamodule = DataModule("expert1.json")
diff --git a/src/mednet/libs/segmentation/config/data/drionsdb/expert2.json b/src/mednet/libs/segmentation/config/data/drionsdb/expert2.json
new file mode 100644
index 00000000..1668d540
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/drionsdb/expert2.json
@@ -0,0 +1,556 @@
+{
+ "train":[
+ [
+ "images/image_001.jpg",
+ "experts_anotation/anotExpert2_001.txt",
+ "images/image_001.png"
+ ],
+ [
+ "images/image_002.jpg",
+ "experts_anotation/anotExpert2_002.txt",
+ "images/image_002.png"
+ ],
+ [
+ "images/image_003.jpg",
+ "experts_anotation/anotExpert2_003.txt",
+ "images/image_003.png"
+ ],
+ [
+ "images/image_004.jpg",
+ "experts_anotation/anotExpert2_004.txt",
+ "images/image_004.png"
+ ],
+ [
+ "images/image_005.jpg",
+ "experts_anotation/anotExpert2_005.txt",
+ "images/image_005.png"
+ ],
+ [
+ "images/image_006.jpg",
+ "experts_anotation/anotExpert2_006.txt",
+ "images/image_006.png"
+ ],
+ [
+ "images/image_007.jpg",
+ "experts_anotation/anotExpert2_007.txt",
+ "images/image_007.png"
+ ],
+ [
+ "images/image_008.jpg",
+ "experts_anotation/anotExpert2_008.txt",
+ "images/image_008.png"
+ ],
+ [
+ "images/image_009.jpg",
+ "experts_anotation/anotExpert2_009.txt",
+ "images/image_009.png"
+ ],
+ [
+ "images/image_010.jpg",
+ "experts_anotation/anotExpert2_010.txt",
+ "images/image_010.png"
+ ],
+ [
+ "images/image_011.jpg",
+ "experts_anotation/anotExpert2_011.txt",
+ "images/image_011.png"
+ ],
+ [
+ "images/image_012.jpg",
+ "experts_anotation/anotExpert2_012.txt",
+ "images/image_012.png"
+ ],
+ [
+ "images/image_013.jpg",
+ "experts_anotation/anotExpert2_013.txt",
+ "images/image_013.png"
+ ],
+ [
+ "images/image_014.jpg",
+ "experts_anotation/anotExpert2_014.txt",
+ "images/image_014.png"
+ ],
+ [
+ "images/image_015.jpg",
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diff --git a/src/mednet/libs/segmentation/config/data/drionsdb/expert2.py b/src/mednet/libs/segmentation/config/data/drionsdb/expert2.py
new file mode 100644
index 00000000..9ee9733c
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/drionsdb/expert2.py
@@ -0,0 +1,13 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""DRIONS-DB for Optic Disc Segmentation (expert #2 annotations).
+
+* Configuration resolution: 416 x 608 (after padding)
+* Split reference: [MANINIS-2016]_
+* See :py:mod:`deepdraw.data.drionsdb` for dataset details
+"""
+
+from mednet.libs.segmentation.config.data.drionsdb.datamodule import DataModule
+
+datamodule = DataModule("expert2.json")
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diff --git a/src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_045.png b/src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_045.png
new file mode 100644
index 0000000000000000000000000000000000000000..22615b20de12d50090e895c6244220ae220b2f56
GIT binary patch
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HcmV?d00001
diff --git a/src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_046.png b/src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_046.png
new file mode 100644
index 0000000000000000000000000000000000000000..7e7645e6c3ef6b18a336b71a458b410c5d794363
GIT binary patch
literal 1523
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HcmV?d00001
diff --git a/src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_047.png b/src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_047.png
new file mode 100644
index 0000000000000000000000000000000000000000..c379f88e4960447bc004d2647656a8eff67becbf
GIT binary patch
literal 1534
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HcmV?d00001
diff --git a/src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_048.png b/src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_048.png
new file mode 100644
index 0000000000000000000000000000000000000000..e60d60c8cb103c7dc87a9f4ba6c2e900f582ac52
GIT binary patch
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HcmV?d00001
diff --git a/src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_049.png b/src/mednet/libs/segmentation/config/data/drionsdb/masks/images/image_049.png
new file mode 100644
index 0000000000000000000000000000000000000000..df664d5fc7dc9c826516cd45cd21b6c1dc2af5d6
GIT binary patch
literal 1549
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/src/mednet/libs/segmentation/tests/data/histograms/models/histograms_lwnet_drionsdb_expert1.json b/src/mednet/libs/segmentation/tests/data/histograms/models/histograms_lwnet_drionsdb_expert1.json
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--- /dev/null
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+ ]
+}
diff --git a/src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_drionsdb_expert1.json b/src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_drionsdb_expert1.json
new file mode 100644
index 00000000..48c5e7ed
--- /dev/null
+++ b/src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_drionsdb_expert1.json
@@ -0,0 +1,16 @@
+{
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+ ]
+}
diff --git a/src/mednet/libs/segmentation/tests/test_drionsdb.py b/src/mednet/libs/segmentation/tests/test_drionsdb.py
new file mode 100644
index 00000000..7d4e14f8
--- /dev/null
+++ b/src/mednet/libs/segmentation/tests/test_drionsdb.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 drionsdb 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",
+ [
+ ("expert1", dict(train=60, test=50)),
+ ("expert2", dict(train=60, test=50)),
+ ],
+ 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.drionsdb", f"{split}.json"),
+ lengths=lengths,
+ )
+
+
+@pytest.mark.skip_if_rc_var_not_set("datadir.drionsdb")
+def test_database_check():
+ from mednet.libs.segmentation.scripts.database import check
+
+ runner = CliRunner()
+ result = runner.invoke(check, ["drionsdb"])
+ 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.drionsdb")
+@pytest.mark.parametrize(
+ "dataset",
+ [
+ "train",
+ "test",
+ ],
+)
+@pytest.mark.parametrize(
+ "name",
+ [
+ "expert1",
+ "expert2",
+ ],
+)
+def test_loading(database_checkers, name: str, dataset: str):
+ datamodule = importlib.import_module(
+ f".{name}",
+ "mednet.libs.segmentation.config.data.drionsdb",
+ ).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.drionsdb")
+def test_raw_transforms_image_quality(database_checkers, datadir):
+ reference_histogram_file = str(
+ datadir / "histograms/raw_data/histograms_drionsdb_expert1.json",
+ )
+
+ datamodule = importlib.import_module(
+ ".expert1",
+ "mednet.libs.segmentation.config.data.drionsdb",
+ ).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.drionsdb")
+@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}_drionsdb_expert1.json",
+ )
+
+ datamodule = importlib.import_module(
+ ".expert1",
+ "mednet.libs.segmentation.config.data.drionsdb",
+ ).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,
+ )
--
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