Moved hivtb configs to data

pyproject.toml

@@ -152,7 +152,7 @@ shenzhen_rs_f7 = "ptbench.configs.datasets.shenzhen_RS.fold_7"
 shenzhen_rs_f8 = "ptbench.configs.datasets.shenzhen_RS.fold_8"
 shenzhen_rs_f9 = "ptbench.configs.datasets.shenzhen_RS.fold_9"
 # indian dataset (and cross-validation folds)
-indian = "ptbench.configs.datasets.indian.default"
+indian = "ptbench.data.indian.default"
 indian_rgb = "ptbench.configs.datasets.indian.rgb"
 indian_f0 = "ptbench.configs.datasets.indian.fold_0"
 indian_f1 = "ptbench.configs.datasets.indian.fold_1"
@@ -433,26 +433,26 @@ tbpoc_rs_f7 = "ptbench.configs.datasets.tbpoc_RS.fold_7"
 tbpoc_rs_f8 = "ptbench.configs.datasets.tbpoc_RS.fold_8"
 tbpoc_rs_f9 = "ptbench.configs.datasets.tbpoc_RS.fold_9"
 # hivtb dataset (and cross-validation folds)
-hivtb_f0 = "ptbench.configs.datasets.hivtb.fold_0"
-hivtb_f1 = "ptbench.configs.datasets.hivtb.fold_1"
-hivtb_f2 = "ptbench.configs.datasets.hivtb.fold_2"
-hivtb_f3 = "ptbench.configs.datasets.hivtb.fold_3"
-hivtb_f4 = "ptbench.configs.datasets.hivtb.fold_4"
-hivtb_f5 = "ptbench.configs.datasets.hivtb.fold_5"
-hivtb_f6 = "ptbench.configs.datasets.hivtb.fold_6"
-hivtb_f7 = "ptbench.configs.datasets.hivtb.fold_7"
-hivtb_f8 = "ptbench.configs.datasets.hivtb.fold_8"
-hivtb_f9 = "ptbench.configs.datasets.hivtb.fold_9"
-hivtb_f0_rgb = "ptbench.configs.datasets.hivtb.fold_0_rgb"
-hivtb_f1_rgb = "ptbench.configs.datasets.hivtb.fold_1_rgb"
-hivtb_f2_rgb = "ptbench.configs.datasets.hivtb.fold_2_rgb"
-hivtb_f3_rgb = "ptbench.configs.datasets.hivtb.fold_3_rgb"
-hivtb_f4_rgb = "ptbench.configs.datasets.hivtb.fold_4_rgb"
-hivtb_f5_rgb = "ptbench.configs.datasets.hivtb.fold_5_rgb"
-hivtb_f6_rgb = "ptbench.configs.datasets.hivtb.fold_6_rgb"
-hivtb_f7_rgb = "ptbench.configs.datasets.hivtb.fold_7_rgb"
-hivtb_f8_rgb = "ptbench.configs.datasets.hivtb.fold_8_rgb"
-hivtb_f9_rgb = "ptbench.configs.datasets.hivtb.fold_9_rgb"
+hivtb_f0 = "ptbench.data.hivtb.fold_0"
+hivtb_f1 = "ptbench.data.hivtb.fold_1"
+hivtb_f2 = "ptbench.data.hivtb.fold_2"
+hivtb_f3 = "ptbench.data.hivtb.fold_3"
+hivtb_f4 = "ptbench.data.hivtb.fold_4"
+hivtb_f5 = "ptbench.data.hivtb.fold_5"
+hivtb_f6 = "ptbench.data.hivtb.fold_6"
+hivtb_f7 = "ptbench.data.hivtb.fold_7"
+hivtb_f8 = "ptbench.data.hivtb.fold_8"
+hivtb_f9 = "ptbench.data.hivtb.fold_9"
+hivtb_f0_rgb = "ptbench.data.hivtb.fold_0_rgb"
+hivtb_f1_rgb = "ptbench.data.hivtb.fold_1_rgb"
+hivtb_f2_rgb = "ptbench.data.hivtb.fold_2_rgb"
+hivtb_f3_rgb = "ptbench.data.hivtb.fold_3_rgb"
+hivtb_f4_rgb = "ptbench.data.hivtb.fold_4_rgb"
+hivtb_f5_rgb = "ptbench.data.hivtb.fold_5_rgb"
+hivtb_f6_rgb = "ptbench.data.hivtb.fold_6_rgb"
+hivtb_f7_rgb = "ptbench.data.hivtb.fold_7_rgb"
+hivtb_f8_rgb = "ptbench.data.hivtb.fold_8_rgb"
+hivtb_f9_rgb = "ptbench.data.hivtb.fold_9_rgb"
 # extended hivtb dataset (with radiological signs)
 hivtb_rs_f0 = "ptbench.configs.datasets.hivtb_RS.fold_0"
 hivtb_rs_f1 = "ptbench.configs.datasets.hivtb_RS.fold_1"

src/ptbench/configs/datasets/hivtb/__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.hivtb 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/hivtb/fold_0.py

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 0)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_0")

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 0)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_0", RGB=True)

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 1)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_1")

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 1)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_1", RGB=True)

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 2)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_2")

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 2)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_2", RGB=True)

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 3)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_3")

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 3)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_3", RGB=True)

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 4)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_4")

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 4)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_4", RGB=True)

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 5)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_5")

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 5)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_5", RGB=True)

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 6)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_6")

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 6)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_6", RGB=True)

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 7)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_7")

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 7)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_7", RGB=True)

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 8)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_8")

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

-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""HIV-TB dataset for TB detection (cross validation fold 8)
-
-* Split reference: none (stratified kfolding)
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.hivtb` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_8", RGB=True)