From 32440226c37aef3fb76d6e7d97cbb2be574cb01c Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Tue, 28 May 2024 10:05:50 +0200
Subject: [PATCH] [segmentation] Add stare database
---
helpers/extract_hdf5_images.py | 12 +-
pyproject.toml | 2 +
.../config/data/stare/__init__.py | 0
.../segmentation/config/data/stare/ah.json | 106 +++++++++++++
.../libs/segmentation/config/data/stare/ah.py | 6 +
.../config/data/stare/datamodule.py | 128 ++++++++++++++++
.../data/stare/masks/stare-images/im0001.png | Bin 0 -> 10107 bytes
.../data/stare/masks/stare-images/im0002.png | Bin 0 -> 1659 bytes
.../data/stare/masks/stare-images/im0003.png | Bin 0 -> 1639 bytes
.../data/stare/masks/stare-images/im0004.png | Bin 0 -> 1622 bytes
.../data/stare/masks/stare-images/im0005.png | Bin 0 -> 1608 bytes
.../data/stare/masks/stare-images/im0044.png | Bin 0 -> 1560 bytes
.../data/stare/masks/stare-images/im0077.png | Bin 0 -> 1596 bytes
.../data/stare/masks/stare-images/im0081.png | Bin 0 -> 1595 bytes
.../data/stare/masks/stare-images/im0082.png | Bin 0 -> 1571 bytes
.../data/stare/masks/stare-images/im0139.png | Bin 0 -> 1711 bytes
.../data/stare/masks/stare-images/im0162.png | Bin 0 -> 1596 bytes
.../data/stare/masks/stare-images/im0163.png | Bin 0 -> 1568 bytes
.../data/stare/masks/stare-images/im0235.png | Bin 0 -> 1573 bytes
.../data/stare/masks/stare-images/im0236.png | Bin 0 -> 1567 bytes
.../data/stare/masks/stare-images/im0239.png | Bin 0 -> 1608 bytes
.../data/stare/masks/stare-images/im0240.png | Bin 0 -> 1546 bytes
.../data/stare/masks/stare-images/im0255.png | Bin 0 -> 1596 bytes
.../data/stare/masks/stare-images/im0291.png | Bin 0 -> 1561 bytes
.../data/stare/masks/stare-images/im0319.png | Bin 0 -> 1618 bytes
.../data/stare/masks/stare-images/im0324.png | Bin 0 -> 1593 bytes
.../segmentation/config/data/stare/vk.json | 106 +++++++++++++
.../libs/segmentation/config/data/stare/vk.py | 6 +
.../models/histograms_lwnet_stare_ah.json | 16 ++
.../raw_data/histograms_stare_ah.json | 16 ++
.../libs/segmentation/tests/test_stare.py | 143 ++++++++++++++++++
31 files changed, 532 insertions(+), 9 deletions(-)
create mode 100644 src/mednet/libs/segmentation/config/data/stare/__init__.py
create mode 100644 src/mednet/libs/segmentation/config/data/stare/ah.json
create mode 100644 src/mednet/libs/segmentation/config/data/stare/ah.py
create mode 100644 src/mednet/libs/segmentation/config/data/stare/datamodule.py
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0001.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0002.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0003.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0004.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0005.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0044.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0077.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0081.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0082.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0139.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0162.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0163.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0235.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0236.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0239.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0240.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0255.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0291.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0319.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0324.png
create mode 100644 src/mednet/libs/segmentation/config/data/stare/vk.json
create mode 100644 src/mednet/libs/segmentation/config/data/stare/vk.py
create mode 100644 src/mednet/libs/segmentation/tests/data/histograms/models/histograms_lwnet_stare_ah.json
create mode 100644 src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_stare_ah.json
create mode 100644 src/mednet/libs/segmentation/tests/test_stare.py
diff --git a/helpers/extract_hdf5_images.py b/helpers/extract_hdf5_images.py
index a093412d..61c79c91 100644
--- a/helpers/extract_hdf5_images.py
+++ b/helpers/extract_hdf5_images.py
@@ -23,8 +23,8 @@ def extract_images_from_hdf5(hdf5_file):
return tensors_dict
-def get_hdf5_files(directory, recursive=False) -> list[pathlib.Path]:
- return directory.glob("**/*.hdf5", recursive=recursive)
+def get_hdf5_files(directory) -> list[pathlib.Path]:
+ return directory.glob("**/*.hdf5")
def main():
@@ -34,16 +34,10 @@ def main():
type=pathlib.Path,
help="Directory in which hdf5 files are located.",
)
- parser.add_argument(
- "--recursive",
- "-r",
- action="store_true",
- help="Set to true to search recursively in the input directory.",
- )
args = parser.parse_args()
- hdf5_files = get_hdf5_files(args.input_dir, recursive=args.recursive)
+ hdf5_files = get_hdf5_files(args.input_dir)
for hdf5_file in hdf5_files:
tensors_dict = extract_images_from_hdf5(hdf5_file)
diff --git a/pyproject.toml b/pyproject.toml
index 5d2bcc64..0be3495e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -425,6 +425,8 @@ lwnet = "mednet.libs.segmentation.config.models.lwnet"
# drive dataset - retinal vessel segmentation
drive = "mednet.libs.segmentation.config.data.drive.default"
+stare = "mednet.libs.segmentation.config.data.stare.ah"
+stare-2nd = "mednet.libs.segmentation.config.data.stare.vk"
[tool.ruff]
line-length = 88
diff --git a/src/mednet/libs/segmentation/config/data/stare/__init__.py b/src/mednet/libs/segmentation/config/data/stare/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/mednet/libs/segmentation/config/data/stare/ah.json b/src/mednet/libs/segmentation/config/data/stare/ah.json
new file mode 100644
index 00000000..1192d3fe
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/stare/ah.json
@@ -0,0 +1,106 @@
+{
+ "train": [
+ [
+ "stare-images/im0001.ppm",
+ "labels-ah/im0001.ah.ppm",
+ "stare-images/im0001.png"
+ ],
+ [
+ "stare-images/im0002.ppm",
+ "labels-ah/im0002.ah.ppm",
+ "stare-images/im0002.png"
+ ],
+ [
+ "stare-images/im0003.ppm",
+ "labels-ah/im0003.ah.ppm",
+ "stare-images/im0003.png"
+ ],
+ [
+ "stare-images/im0004.ppm",
+ "labels-ah/im0004.ah.ppm",
+ "stare-images/im0004.png"
+ ],
+ [
+ "stare-images/im0005.ppm",
+ "labels-ah/im0005.ah.ppm",
+ "stare-images/im0005.png"
+ ],
+ [
+ "stare-images/im0044.ppm",
+ "labels-ah/im0044.ah.ppm",
+ "stare-images/im0044.png"
+ ],
+ [
+ "stare-images/im0077.ppm",
+ "labels-ah/im0077.ah.ppm",
+ "stare-images/im0077.png"
+ ],
+ [
+ "stare-images/im0081.ppm",
+ "labels-ah/im0081.ah.ppm",
+ "stare-images/im0081.png"
+ ],
+ [
+ "stare-images/im0082.ppm",
+ "labels-ah/im0082.ah.ppm",
+ "stare-images/im0082.png"
+ ],
+ [
+ "stare-images/im0139.ppm",
+ "labels-ah/im0139.ah.ppm",
+ "stare-images/im0139.png"
+ ]
+ ],
+ "test": [
+ [
+ "stare-images/im0162.ppm",
+ "labels-ah/im0162.ah.ppm",
+ "stare-images/im0162.png"
+ ],
+ [
+ "stare-images/im0163.ppm",
+ "labels-ah/im0163.ah.ppm",
+ "stare-images/im0163.png"
+ ],
+ [
+ "stare-images/im0235.ppm",
+ "labels-ah/im0235.ah.ppm",
+ "stare-images/im0235.png"
+ ],
+ [
+ "stare-images/im0236.ppm",
+ "labels-ah/im0236.ah.ppm",
+ "stare-images/im0236.png"
+ ],
+ [
+ "stare-images/im0239.ppm",
+ "labels-ah/im0239.ah.ppm",
+ "stare-images/im0239.png"
+ ],
+ [
+ "stare-images/im0240.ppm",
+ "labels-ah/im0240.ah.ppm",
+ "stare-images/im0240.png"
+ ],
+ [
+ "stare-images/im0255.ppm",
+ "labels-ah/im0255.ah.ppm",
+ "stare-images/im0255.png"
+ ],
+ [
+ "stare-images/im0291.ppm",
+ "labels-ah/im0291.ah.ppm",
+ "stare-images/im0291.png"
+ ],
+ [
+ "stare-images/im0319.ppm",
+ "labels-ah/im0319.ah.ppm",
+ "stare-images/im0319.png"
+ ],
+ [
+ "stare-images/im0324.ppm",
+ "labels-ah/im0324.ah.ppm",
+ "stare-images/im0324.png"
+ ]
+ ]
+}
diff --git a/src/mednet/libs/segmentation/config/data/stare/ah.py b/src/mednet/libs/segmentation/config/data/stare/ah.py
new file mode 100644
index 00000000..cf6051a1
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/stare/ah.py
@@ -0,0 +1,6 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+from mednet.libs.segmentation.config.data.stare.datamodule import DataModule
+
+datamodule = DataModule("ah.json")
diff --git a/src/mednet/libs/segmentation/config/data/stare/datamodule.py b/src/mednet/libs/segmentation/config/data/stare/datamodule.py
new file mode 100644
index 00000000..5fc90042
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/stare/datamodule.py
@@ -0,0 +1,128 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""STARE dataset for Vessel Segmentation."""
+
+import importlib.resources
+import os
+from pathlib import Path
+
+import PIL.Image
+import pkg_resources
+from mednet.libs.common.data.datamodule import CachingDataModule
+from mednet.libs.common.data.split import JSONDatabaseSplit
+from mednet.libs.common.data.typing import DatabaseSplit, 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 Stare dataset."""
+
+ datadir: str
+ """This variable contains the base directory where the database raw data is
+ stored."""
+
+ def __init__(self):
+ self.datadir = load_rc().get(
+ CONFIGURATION_KEY_DATADIR, os.path.realpath(os.curdir)
+ )
+ self._pkg_path = pkg_resources.resource_filename(__name__, "masks")
+
+ 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 = PIL.Image.open(Path(self.datadir) / str(sample[0])).convert(
+ mode="RGB"
+ )
+ tensor = tv_tensors.Image(to_tensor(image))
+ target = tv_tensors.Image(
+ to_tensor(
+ PIL.Image.open(Path(self.datadir) / str(sample[1])).convert(
+ mode="1", dither=None
+ )
+ )
+ )
+ mask = tv_tensors.Mask(
+ to_tensor(
+ PIL.Image.open(Path(self._pkg_path) / str(sample[2])).convert(
+ mode="1", dither=None
+ )
+ )
+ )
+
+ return tensor, dict(target=target, mask=mask, name=sample[0]) # type: ignore[arg-type]
+
+
+def make_split(basename: str) -> DatabaseSplit:
+ """Return a database split for the Stare database.
+
+ Parameters
+ ----------
+ basename
+ Name of the .json file containing the split to load.
+
+ Returns
+ -------
+ An instance of DatabaseSplit.
+ """
+
+ return JSONDatabaseSplit(
+ importlib.resources.files(__name__.rsplit(".", 1)[0]).joinpath(basename)
+ )
+
+
+class DataModule(CachingDataModule):
+ """STARE dataset for Vessel Segmentation.
+
+ A subset of the original STARE dataset contains 20 annotated eye fundus images
+ with a resolution of 700 x 605 (width x height). Two sets of ground-truth
+ vessel annotations are available. The first set by Adam Hoover ("ah") is
+ commonly used for training and testing. The second set by Valentina Kouznetsova
+ ("vk") is typically used as a “human†baseline.
+
+ * Reference: [STARE-2000]_
+ * Original resolution (width x height): 700 x 605
+ * Split reference: [MANINIS-2016]_
+ * Protocol ``ah`` (default baseline):
+
+ * Training samples: 10 (including labels from annotator "ah")
+ * Test samples: 10 (including labels from annotator "ah")
+
+ * Protocol ``vk`` (normally used as human comparison):
+
+ * Training samples: 10 (including labels from annotator "vk")
+ * Test samples: 10 (including labels from annotator "vk")
+
+ Parameters
+ ----------
+ split_filename
+ Name of the .json file containing the split to load.
+ """
+
+ def __init__(self, split_filename: str):
+ super().__init__(
+ database_split=make_split(split_filename),
+ raw_data_loader=SegmentationRawDataLoader(),
+ )
diff --git a/src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0001.png b/src/mednet/libs/segmentation/config/data/stare/masks/stare-images/im0001.png
new file mode 100644
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diff --git a/src/mednet/libs/segmentation/config/data/stare/vk.json b/src/mednet/libs/segmentation/config/data/stare/vk.json
new file mode 100644
index 00000000..3af0c783
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/stare/vk.json
@@ -0,0 +1,106 @@
+{
+ "train": [
+ [
+ "stare-images/im0001.ppm",
+ "labels-vk/im0001.vk.ppm",
+ "stare-images/im0001.png"
+ ],
+ [
+ "stare-images/im0002.ppm",
+ "labels-vk/im0002.vk.ppm",
+ "stare-images/im0002.png"
+ ],
+ [
+ "stare-images/im0003.ppm",
+ "labels-vk/im0003.vk.ppm",
+ "stare-images/im0003.png"
+ ],
+ [
+ "stare-images/im0004.ppm",
+ "labels-vk/im0004.vk.ppm",
+ "stare-images/im0004.png"
+ ],
+ [
+ "stare-images/im0005.ppm",
+ "labels-vk/im0005.vk.ppm",
+ "stare-images/im0005.png"
+ ],
+ [
+ "stare-images/im0044.ppm",
+ "labels-vk/im0044.vk.ppm",
+ "stare-images/im0044.png"
+ ],
+ [
+ "stare-images/im0077.ppm",
+ "labels-vk/im0077.vk.ppm",
+ "stare-images/im0077.png"
+ ],
+ [
+ "stare-images/im0081.ppm",
+ "labels-vk/im0081.vk.ppm",
+ "stare-images/im0081.png"
+ ],
+ [
+ "stare-images/im0082.ppm",
+ "labels-vk/im0082.vk.ppm",
+ "stare-images/im0082.png"
+ ],
+ [
+ "stare-images/im0139.ppm",
+ "labels-vk/im0139.vk.ppm",
+ "stare-images/im0139.png"
+ ]
+ ],
+ "test": [
+ [
+ "stare-images/im0162.ppm",
+ "labels-vk/im0162.vk.ppm",
+ "stare-images/im0162.png"
+ ],
+ [
+ "stare-images/im0163.ppm",
+ "labels-vk/im0163.vk.ppm",
+ "stare-images/im0163.png"
+ ],
+ [
+ "stare-images/im0235.ppm",
+ "labels-vk/im0235.vk.ppm",
+ "stare-images/im0235.png"
+ ],
+ [
+ "stare-images/im0236.ppm",
+ "labels-vk/im0236.vk.ppm",
+ "stare-images/im0236.png"
+ ],
+ [
+ "stare-images/im0239.ppm",
+ "labels-vk/im0239.vk.ppm",
+ "stare-images/im0239.png"
+ ],
+ [
+ "stare-images/im0240.ppm",
+ "labels-vk/im0240.vk.ppm",
+ "stare-images/im0240.png"
+ ],
+ [
+ "stare-images/im0255.ppm",
+ "labels-vk/im0255.vk.ppm",
+ "stare-images/im0255.png"
+ ],
+ [
+ "stare-images/im0291.ppm",
+ "labels-vk/im0291.vk.ppm",
+ "stare-images/im0291.png"
+ ],
+ [
+ "stare-images/im0319.ppm",
+ "labels-vk/im0319.vk.ppm",
+ "stare-images/im0319.png"
+ ],
+ [
+ "stare-images/im0324.ppm",
+ "labels-vk/im0324.vk.ppm",
+ "stare-images/im0324.png"
+ ]
+ ]
+}
diff --git a/src/mednet/libs/segmentation/config/data/stare/vk.py b/src/mednet/libs/segmentation/config/data/stare/vk.py
new file mode 100644
index 00000000..f4c88abc
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/stare/vk.py
@@ -0,0 +1,6 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+from mednet.libs.segmentation.config.data.stare.datamodule import DataModule
+
+datamodule = DataModule("vk.json")
diff --git a/src/mednet/libs/segmentation/tests/data/histograms/models/histograms_lwnet_stare_ah.json b/src/mednet/libs/segmentation/tests/data/histograms/models/histograms_lwnet_stare_ah.json
new file mode 100644
index 00000000..aa9585ed
--- /dev/null
+++ b/src/mednet/libs/segmentation/tests/data/histograms/models/histograms_lwnet_stare_ah.json
@@ -0,0 +1,16 @@
+{
+ "train": [
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+}
diff --git a/src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_stare_ah.json b/src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_stare_ah.json
new file mode 100644
index 00000000..901cb9ae
--- /dev/null
+++ b/src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_stare_ah.json
@@ -0,0 +1,16 @@
+{
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+ ["stare-images/im0324.ppm", [143, 282, 513, 721, 1000, 1061, 1379, 1760, 4375, 8532, 11395, 12048, 11722, 9618, 7073, 5597, 4596, 3939, 3279, 2603, 1717, 1242, 1013, 874, 945, 1135, 1236, 1196, 1312, 1254, 1188, 905, 814, 732, 660, 620, 614, 553, 583, 490, 402, 315, 250, 162, 171, 135, 87, 77, 73, 67, 54, 58, 51, 37, 33, 32, 28, 36, 23, 29, 43, 29, 31, 33, 25, 28, 33, 35, 32, 27, 30, 31, 31, 31, 24, 21, 15, 25, 20, 30, 29, 21, 29, 19, 21, 29, 30, 33, 27, 17, 29, 17, 16, 20, 23, 14, 13, 8, 17, 13, 16, 7, 13, 13, 16, 13, 10, 13, 21, 9, 16, 13, 7, 10, 15, 13, 13, 10, 9, 6, 15, 13, 18, 14, 14, 12, 10, 11, 12, 10, 14, 17, 7, 13, 10, 11, 17, 7, 12, 13, 15, 18, 11, 16, 13, 5, 15, 12, 8, 13, 11, 11, 16, 13, 20, 12, 22, 17, 20, 17, 13, 14, 23, 18, 16, 22, 18, 25, 17, 22, 16, 24, 19, 14, 10, 17, 15, 16, 16, 19, 22, 25, 23, 40, 45, 70, 77, 97, 128, 111, 164, 190, 202, 270, 293, 391, 454, 564, 674, 768, 850, 876, 970, 903, 969, 1089, 1152, 1228, 1173, 1171, 1152, 1160, 1187, 1206, 1310, 1269, 1453, 1421, 1549, 1632, 1751, 1886, 1991, 2050, 2254, 2366, 2634, 2853, 3035, 3282, 3536, 3716, 3892, 4010, 4102, 4327, 4620, 4886, 5021, 5076, 5077, 4960, 4924, 4968, 5328, 5595, 6124, 6763, 7386, 8335, 9451, 10239, 11157, 13162, 19392, 90053, 15198, 2090, 1513, 820, 770, 332, 407, 598, 996, 1648, 2370, 3305, 4146, 4762, 5007, 5182, 5083, 5072, 4694, 4518, 4264, 3949, 3726, 3325, 3029, 2692, 2452, 2068, 1986, 1895, 1804, 1883, 1843, 1629, 1486, 1266, 1028, 921, 763, 583, 466, 395, 342, 256, 142, 91, 96, 74, 80, 80, 89, 71, 70, 54, 61, 48, 64, 46, 49, 50, 43, 37, 32, 36, 33, 27, 30, 30, 23, 29, 18, 22, 34, 19, 18, 32, 21, 24, 20, 33, 27, 22, 17, 14, 20, 17, 24, 27, 30, 38, 61, 105, 119, 165, 222, 221, 212, 208, 204, 218, 281, 292, 390, 515, 668, 867, 1193, 1720, 2630, 4116, 5295, 6032, 5279, 4737, 4436, 4296, 4428, 4563, 4751, 5352, 5965, 5886, 5635, 5541, 5121, 4717, 4547, 4304, 4314, 4337, 4526, 4725, 4933, 5023, 5131, 5276, 5289, 4868, 4822, 4516, 4548, 4387, 4562, 4508, 4674, 4627, 4397, 4399, 4747, 5164, 5549, 5583, 5587, 5313, 5004, 4958, 4662, 4457, 4208, 3728, 3387, 3069, 2878, 2625, 2490, 2349, 2233, 2245, 2117, 2011, 1864, 1762, 1542, 1552, 1331, 1259, 1246, 1107, 1112, 1114, 963, 985, 986, 1074, 1030, 887, 847, 772, 713, 620, 494, 407, 314, 277, 254, 193, 183, 123, 80, 81, 70, 49, 46, 38, 37, 18, 13, 10, 4, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 280294, 2594, 2171, 1736, 1499, 1424, 1528, 1820, 2196, 2746, 3658, 4913, 7604, 11056, 13988, 15004, 14431, 13139, 10443, 7835, 5551, 4159, 3557, 2651, 1928, 1325, 892, 704, 588, 494, 385, 318, 260, 187, 162, 99, 70, 38, 30, 11, 6, 2, 3, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]
+ ]
+}
diff --git a/src/mednet/libs/segmentation/tests/test_stare.py b/src/mednet/libs/segmentation/tests/test_stare.py
new file mode 100644
index 00000000..99b36913
--- /dev/null
+++ b/src/mednet/libs/segmentation/tests/test_stare.py
@@ -0,0 +1,143 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""Tests for stare 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",
+ [
+ ("ah", dict(train=10, test=10)),
+ ("vk", dict(train=10, test=10)),
+ ],
+ ids=id_function, # just changes how pytest prints it
+)
+def test_protocol_consistency(
+ database_checkers,
+ split: str,
+ lengths: dict[str, int],
+):
+ from mednet.libs.segmentation.config.data.stare.datamodule import (
+ make_split,
+ )
+
+ database_checkers.check_split(
+ make_split(f"{split}.json"),
+ lengths=lengths,
+ )
+
+
+@pytest.mark.skip_if_rc_var_not_set("datadir.stare")
+def test_database_check():
+ from mednet.libs.segmentation.scripts.database import check
+
+ runner = CliRunner()
+ result = runner.invoke(check, ["stare"])
+ 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.stare")
+@pytest.mark.parametrize(
+ "dataset",
+ [
+ "train",
+ "test",
+ ],
+)
+@pytest.mark.parametrize(
+ "name",
+ [
+ "ah",
+ "vk",
+ ],
+)
+def test_loading(database_checkers, name: str, dataset: str):
+ datamodule = importlib.import_module(
+ f".{name}",
+ "mednet.libs.segmentation.config.data.stare",
+ ).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.stare")
+def test_raw_transforms_image_quality(database_checkers, datadir):
+ reference_histogram_file = str(
+ datadir / "histograms/raw_data/histograms_stare_ah.json",
+ )
+
+ datamodule = importlib.import_module(
+ ".ah",
+ "mednet.libs.segmentation.config.data.stare",
+ ).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.stare")
+@pytest.mark.parametrize(
+ "model_name",
+ ["lwnet"],
+)
+def test_model_transforms_image_quality(database_checkers, datadir, model_name):
+ # Densenet's model.name is "densenet-212" and does not correspond to its module name.
+ if model_name == "densenet":
+ reference_histogram_file = str(
+ datadir / "histograms/models/histograms_densenet-121_stare_ah.json",
+ )
+ else:
+ reference_histogram_file = str(
+ datadir
+ / f"histograms/models/histograms_{model_name}_stare_ah.json",
+ )
+
+ datamodule = importlib.import_module(
+ ".ah",
+ "mednet.libs.segmentation.config.data.stare",
+ ).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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