From 1ff2ec4c8386afca3bc771d759db678e9ceddc42 Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Tue, 11 Jun 2024 13:31:01 +0200
Subject: [PATCH] [segmentation.drive] Add missing config
---
pyproject.toml | 2 +
.../config/data/drive/drive_2nd.py | 14 +++
.../config/data/drive/second-annotator.json | 104 ++++++++++++++++++
.../libs/segmentation/tests/test_drive.py | 1 +
4 files changed, 121 insertions(+)
create mode 100644 src/mednet/libs/segmentation/config/data/drive/drive_2nd.py
create mode 100644 src/mednet/libs/segmentation/config/data/drive/second-annotator.json
diff --git a/pyproject.toml b/pyproject.toml
index fa28c5ab..581a89d1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -429,6 +429,7 @@ driu-pix = "mednet.libs.segmentation.config.models.driu_pix"
hed = "mednet.libs.segmentation.config.models.hed"
lwnet = "mednet.libs.segmentation.config.models.lwnet"
m2unet = "mednet.libs.segmentation.config.models.m2unet"
+resunet = "mednet.libs.segmentation.config.models.resunet"
unet = "mednet.libs.segmentation.config.models.unet"
# chase-db1 - retinography
@@ -447,6 +448,7 @@ drionsdb-2nd = "mednet.libs.segmentation.config.data.drionsdb.expert2"
# drive dataset - retinography
drive = "mednet.libs.segmentation.config.data.drive.default"
+drive-2nd = "mednet.libs.segmentation.config.data.drive.second_annotator"
# drishti-gs1 - retinography
drishtigs1-disc-all = "mednet.libs.segmentation.config.data.drishtigs1.optic_disc_all"
diff --git a/src/mednet/libs/segmentation/config/data/drive/drive_2nd.py b/src/mednet/libs/segmentation/config/data/drive/drive_2nd.py
new file mode 100644
index 00000000..3c0ac007
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/drive/drive_2nd.py
@@ -0,0 +1,14 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""DRIVE dataset for Vessel Segmentation (default protocol).
+
+* Split reference: [DRIVE-2004]_
+* This configuration resolution: 544 x 544 (center-crop)
+* See :py:mod:`deepdraw.data.drive` for dataset details
+* This dataset offers a second-annotator comparison for the test set only
+"""
+
+from mednet.libs.segmentation.config.data.drive.datamodule import DataModule
+
+datamodule = DataModule("second-annotator.json")
diff --git a/src/mednet/libs/segmentation/config/data/drive/second-annotator.json b/src/mednet/libs/segmentation/config/data/drive/second-annotator.json
new file mode 100644
index 00000000..fee520de
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/drive/second-annotator.json
@@ -0,0 +1,104 @@
+{
+ "test": [
+ [
+ "test/images/01_test.tif",
+ "test/2nd_manual/01_manual2.gif",
+ "test/mask/01_test_mask.gif"
+ ],
+ [
+ "test/images/02_test.tif",
+ "test/2nd_manual/02_manual2.gif",
+ "test/mask/02_test_mask.gif"
+ ],
+ [
+ "test/images/03_test.tif",
+ "test/2nd_manual/03_manual2.gif",
+ "test/mask/03_test_mask.gif"
+ ],
+ [
+ "test/images/04_test.tif",
+ "test/2nd_manual/04_manual2.gif",
+ "test/mask/04_test_mask.gif"
+ ],
+ [
+ "test/images/05_test.tif",
+ "test/2nd_manual/05_manual2.gif",
+ "test/mask/05_test_mask.gif"
+ ],
+ [
+ "test/images/06_test.tif",
+ "test/2nd_manual/06_manual2.gif",
+ "test/mask/06_test_mask.gif"
+ ],
+ [
+ "test/images/07_test.tif",
+ "test/2nd_manual/07_manual2.gif",
+ "test/mask/07_test_mask.gif"
+ ],
+ [
+ "test/images/08_test.tif",
+ "test/2nd_manual/08_manual2.gif",
+ "test/mask/08_test_mask.gif"
+ ],
+ [
+ "test/images/09_test.tif",
+ "test/2nd_manual/09_manual2.gif",
+ "test/mask/09_test_mask.gif"
+ ],
+ [
+ "test/images/10_test.tif",
+ "test/2nd_manual/10_manual2.gif",
+ "test/mask/10_test_mask.gif"
+ ],
+ [
+ "test/images/11_test.tif",
+ "test/2nd_manual/11_manual2.gif",
+ "test/mask/11_test_mask.gif"
+ ],
+ [
+ "test/images/12_test.tif",
+ "test/2nd_manual/12_manual2.gif",
+ "test/mask/12_test_mask.gif"
+ ],
+ [
+ "test/images/13_test.tif",
+ "test/2nd_manual/13_manual2.gif",
+ "test/mask/13_test_mask.gif"
+ ],
+ [
+ "test/images/14_test.tif",
+ "test/2nd_manual/14_manual2.gif",
+ "test/mask/14_test_mask.gif"
+ ],
+ [
+ "test/images/15_test.tif",
+ "test/2nd_manual/15_manual2.gif",
+ "test/mask/15_test_mask.gif"
+ ],
+ [
+ "test/images/16_test.tif",
+ "test/2nd_manual/16_manual2.gif",
+ "test/mask/16_test_mask.gif"
+ ],
+ [
+ "test/images/17_test.tif",
+ "test/2nd_manual/17_manual2.gif",
+ "test/mask/17_test_mask.gif"
+ ],
+ [
+ "test/images/18_test.tif",
+ "test/2nd_manual/18_manual2.gif",
+ "test/mask/18_test_mask.gif"
+ ],
+ [
+ "test/images/19_test.tif",
+ "test/2nd_manual/19_manual2.gif",
+ "test/mask/19_test_mask.gif"
+ ],
+ [
+ "test/images/20_test.tif",
+ "test/2nd_manual/20_manual2.gif",
+ "test/mask/20_test_mask.gif"
+ ]
+ ]
+}
diff --git a/src/mednet/libs/segmentation/tests/test_drive.py b/src/mednet/libs/segmentation/tests/test_drive.py
index 060d1132..9d356596 100644
--- a/src/mednet/libs/segmentation/tests/test_drive.py
+++ b/src/mednet/libs/segmentation/tests/test_drive.py
@@ -19,6 +19,7 @@ def id_function(val):
"split,lengths",
[
("default", dict(train=20, test=20)),
+ ("second-annotator", dict(test=20)),
],
ids=id_function, # just changes how pytest prints it
)
--
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