Moved shenzhen configs to data

pyproject.toml

@@ -118,27 +118,27 @@ montgomery_rs_f8 = "ptbench.configs.datasets.montgomery_RS.fold_8"
 montgomery_rs_f9 = "ptbench.configs.datasets.montgomery_RS.fold_9"
 # shenzhen dataset (and cross-validation folds)
 shenzhen = "ptbench.data.shenzhen.default"
-shenzhen_rgb = "ptbench.configs.datasets.shenzhen.rgb"
-shenzhen_f0 = "ptbench.configs.datasets.shenzhen.fold_0"
-shenzhen_f1 = "ptbench.configs.datasets.shenzhen.fold_1"
-shenzhen_f2 = "ptbench.configs.datasets.shenzhen.fold_2"
-shenzhen_f3 = "ptbench.configs.datasets.shenzhen.fold_3"
-shenzhen_f4 = "ptbench.configs.datasets.shenzhen.fold_4"
-shenzhen_f5 = "ptbench.configs.datasets.shenzhen.fold_5"
-shenzhen_f6 = "ptbench.configs.datasets.shenzhen.fold_6"
-shenzhen_f7 = "ptbench.configs.datasets.shenzhen.fold_7"
-shenzhen_f8 = "ptbench.configs.datasets.shenzhen.fold_8"
-shenzhen_f9 = "ptbench.configs.datasets.shenzhen.fold_9"
-shenzhen_f0_rgb = "ptbench.configs.datasets.shenzhen.fold_0_rgb"
-shenzhen_f1_rgb = "ptbench.configs.datasets.shenzhen.fold_1_rgb"
-shenzhen_f2_rgb = "ptbench.configs.datasets.shenzhen.fold_2_rgb"
-shenzhen_f3_rgb = "ptbench.configs.datasets.shenzhen.fold_3_rgb"
-shenzhen_f4_rgb = "ptbench.configs.datasets.shenzhen.fold_4_rgb"
-shenzhen_f5_rgb = "ptbench.configs.datasets.shenzhen.fold_5_rgb"
-shenzhen_f6_rgb = "ptbench.configs.datasets.shenzhen.fold_6_rgb"
-shenzhen_f7_rgb = "ptbench.configs.datasets.shenzhen.fold_7_rgb"
-shenzhen_f8_rgb = "ptbench.configs.datasets.shenzhen.fold_8_rgb"
-shenzhen_f9_rgb = "ptbench.configs.datasets.shenzhen.fold_9_rgb"
+shenzhen_rgb = "ptbench.data.shenzhen.rgb"
+shenzhen_f0 = "ptbench.data.shenzhen.fold_0"
+shenzhen_f1 = "ptbench.data.shenzhen.fold_1"
+shenzhen_f2 = "ptbench.data.shenzhen.fold_2"
+shenzhen_f3 = "ptbench.data.shenzhen.fold_3"
+shenzhen_f4 = "ptbench.data.shenzhen.fold_4"
+shenzhen_f5 = "ptbench.data.shenzhen.fold_5"
+shenzhen_f6 = "ptbench.data.shenzhen.fold_6"
+shenzhen_f7 = "ptbench.data.shenzhen.fold_7"
+shenzhen_f8 = "ptbench.data.shenzhen.fold_8"
+shenzhen_f9 = "ptbench.data.shenzhen.fold_9"
+shenzhen_f0_rgb = "ptbench.data.shenzhen.fold_0_rgb"
+shenzhen_f1_rgb = "ptbench.data.shenzhen.fold_1_rgb"
+shenzhen_f2_rgb = "ptbench.data.shenzhen.fold_2_rgb"
+shenzhen_f3_rgb = "ptbench.data.shenzhen.fold_3_rgb"
+shenzhen_f4_rgb = "ptbench.data.shenzhen.fold_4_rgb"
+shenzhen_f5_rgb = "ptbench.data.shenzhen.fold_5_rgb"
+shenzhen_f6_rgb = "ptbench.data.shenzhen.fold_6_rgb"
+shenzhen_f7_rgb = "ptbench.data.shenzhen.fold_7_rgb"
+shenzhen_f8_rgb = "ptbench.data.shenzhen.fold_8_rgb"
+shenzhen_f9_rgb = "ptbench.data.shenzhen.fold_9_rgb"
 # extended shenzhen dataset (with radiological signs)
 shenzhen_rs = "ptbench.configs.datasets.shenzhen_RS.default"
 shenzhen_rs_f0 = "ptbench.configs.datasets.shenzhen_RS.fold_0"

src/ptbench/configs/datasets/shenzhen/__init__.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-
-def _maker(protocol, resize_size=512, cc_size=512, RGB=False):
-    from torchvision import transforms
-
-    from ....data.shenzhen import dataset as raw
-    from ....data.transforms import ElasticDeformation, RemoveBlackBorders
-    from .. import make_dataset as mk
-
-    post_transforms = []
-    if RGB:
-        post_transforms = [
-            transforms.Lambda(lambda x: x.convert("RGB")),
-            transforms.ToTensor(),
-        ]
-
-    return mk(
-        [raw.subsets(protocol)],
-        [
-            RemoveBlackBorders(),
-            transforms.Resize(resize_size),
-            transforms.CenterCrop(cc_size),
-        ],
-        [ElasticDeformation(p=0.8)],
-        post_transforms,
-    )

src/ptbench/configs/datasets/shenzhen/fold_0.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 0)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_0")

src/ptbench/configs/datasets/shenzhen/fold_0_rgb.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 0, RGB)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_0", RGB=True)

src/ptbench/configs/datasets/shenzhen/fold_1.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 1)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_1")

src/ptbench/configs/datasets/shenzhen/fold_1_rgb.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 1, RGB)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_1", RGB=True)

src/ptbench/configs/datasets/shenzhen/fold_2.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 2)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_2")

src/ptbench/configs/datasets/shenzhen/fold_2_rgb.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 2, RGB)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_2", RGB=True)

src/ptbench/configs/datasets/shenzhen/fold_3.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 3)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_3")

src/ptbench/configs/datasets/shenzhen/fold_3_rgb.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 3, RGB)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_3", RGB=True)

src/ptbench/configs/datasets/shenzhen/fold_4.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 4)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_4")

src/ptbench/configs/datasets/shenzhen/fold_4_rgb.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 4, RGB)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_4", RGB=True)

src/ptbench/configs/datasets/shenzhen/fold_5.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 5)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_5")

src/ptbench/configs/datasets/shenzhen/fold_5_rgb.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 5, RGB)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_5", RGB=True)

src/ptbench/configs/datasets/shenzhen/fold_6.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 6)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_6")

src/ptbench/configs/datasets/shenzhen/fold_6_rgb.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 6, RGB)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_6", RGB=True)

src/ptbench/configs/datasets/shenzhen/fold_7.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 7)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_7")

src/ptbench/configs/datasets/shenzhen/fold_7_rgb.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 7, RGB)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_7", RGB=True)

src/ptbench/configs/datasets/shenzhen/fold_8.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 8)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_8")

src/ptbench/configs/datasets/shenzhen/fold_8_rgb.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""Shenzhen dataset for TB detection (cross validation fold 8, RGB)
-
-* Split reference: first 80% of TB and healthy CXR for "train", rest for "test"
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.shenzhen` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_8", RGB=True)