diff --git a/src/ptbench/data/hivtb/datamodule.py b/src/ptbench/data/hivtb/datamodule.py index 63075c61720e393edd2953a29af67336be954952..b5b84ec434ea4ce4145119bf565d0d8ee8a091d9 100644 --- a/src/ptbench/data/hivtb/datamodule.py +++ b/src/ptbench/data/hivtb/datamodule.py @@ -11,7 +11,7 @@ from torchvision.transforms.functional import center_crop, to_tensor from ...utils.rc import load_rc from ..datamodule import CachingDataModule -from ..image_utils import load_pil_grayscale, remove_black_borders +from ..image_utils import remove_black_borders from ..split import JSONDatabaseSplit from ..typing import DatabaseSplit from ..typing import RawDataLoader as _BaseRawDataLoader @@ -54,7 +54,9 @@ class RawDataLoader(_BaseRawDataLoader): sample The sample representation """ - image = load_pil_grayscale(os.path.join(self.datadir, sample[0])) + image = PIL.Image.open(os.path.join(self.datadir, sample[0])).convert( + "L" + ) image = remove_black_borders(image) tensor = to_tensor(image) tensor = center_crop(tensor, min(*tensor.shape[1:])) @@ -99,21 +101,21 @@ class DataModule(CachingDataModule): """HIV-TB dataset for computer-aided diagnosis (only BMP files) * Database reference: [HIV-TB-2019]_ - * Original resolution (height x width or width x height): 2048 x 2500 pixels - or 2500 x 2048 pixels - + * Original resolution, varying with most images being 2048 x 2500 pixels + or 2500 x 2048 pixels, but not all. + Data specifications: * Raw data input (on disk): - * BMP images 8 bit grayscale - * resolution fixed to one of the cases above + * BMP (BMP3) and JPEG grayscale images encoded as 8-bit RGB, with + varying resolution * Output image: * Transforms: - * Load raw BMP with :py:mod:`PIL` + * Load raw BMP or JPEG with :py:mod:`PIL` * Remove black borders * Convert to torch tensor * Torch center cropping to get square image diff --git a/src/ptbench/data/hivtb/fold_0.py b/src/ptbench/data/hivtb/fold_0.py index ba9e9150efd11f36b0b846b894e318200f7a2957..57d77952ad0f012f4c7224f38dc293aa58d72dcd 100644 --- a/src/ptbench/data/hivtb/fold_0.py +++ b/src/ptbench/data/hivtb/fold_0.py @@ -2,20 +2,10 @@ # # SPDX-License-Identifier: GPL-3.0-or-later -"""HIV-TB dataset for TB detection (cross validation fold 0) - -* Split reference: none (stratified kfolding) - -* Stratified kfold protocol: - * Training samples: 72% of TB and healthy CXR (including labels) - * Validation samples: 18% of TB and healthy CXR (including labels) - * Test samples: 10% of TB and healthy CXR (including labels) - -* This configuration resolution: 2048 x 2048 (default) -* See :py:mod:`ptbench.data.hivtb` for dataset details -""" - from .datamodule import DataModule datamodule = DataModule("fold-0.json") +"""HIV-TB dataset for TB detection (cross validation fold 0). +See :py:class:`DataModule` for technical details. +""" diff --git a/src/ptbench/data/hivtb/fold_1.py b/src/ptbench/data/hivtb/fold_1.py index 84fb758134f62c4d496aedd35377c17f90876389..c91a968f500204bd1fa30e43e168dbf3e7f0edab 100644 --- a/src/ptbench/data/hivtb/fold_1.py +++ b/src/ptbench/data/hivtb/fold_1.py @@ -2,20 +2,10 @@ # # SPDX-License-Identifier: GPL-3.0-or-later -"""HIV-TB dataset for TB detection (cross validation fold 1) - -* Split reference: none (stratified kfolding) - -* Stratified kfold protocol: - * Training samples: 72% of TB and healthy CXR (including labels) - * Validation samples: 18% of TB and healthy CXR (including labels) - * Test samples: 10% of TB and healthy CXR (including labels) - -* This configuration resolution: 2048 x 2048 (default) -* See :py:mod:`ptbench.data.hivtb` for dataset details -""" - from .datamodule import DataModule datamodule = DataModule("fold-1.json") +"""HIV-TB dataset for TB detection (cross validation fold 1). +See :py:class:`DataModule` for technical details. +""" diff --git a/src/ptbench/data/hivtb/fold_2.py b/src/ptbench/data/hivtb/fold_2.py index a5f5e97a6d66d0938ba26a357786d03efb1716a5..323e80a02a0b44b5691d13abc971679182e2d97f 100644 --- a/src/ptbench/data/hivtb/fold_2.py +++ b/src/ptbench/data/hivtb/fold_2.py @@ -2,20 +2,10 @@ # # SPDX-License-Identifier: GPL-3.0-or-later -"""HIV-TB dataset for TB detection (cross validation fold 2) - -* Split reference: none (stratified kfolding) - -* Stratified kfold protocol: - * Training samples: 72% of TB and healthy CXR (including labels) - * Validation samples: 18% of TB and healthy CXR (including labels) - * Test samples: 10% of TB and healthy CXR (including labels) - -* This configuration resolution: 2048 x 2048 (default) -* See :py:mod:`ptbench.data.hivtb` for dataset details -""" - from .datamodule import DataModule datamodule = DataModule("fold-2.json") +"""HIV-TB dataset for TB detection (cross validation fold 2). +See :py:class:`DataModule` for technical details. +""" diff --git a/src/ptbench/data/hivtb/fold_3.py b/src/ptbench/data/hivtb/fold_3.py index 1b643ae4cf515f3b9219fa75a950bca77297eaa4..1eed4c056648bce88f174ccbce8a71efe69fc136 100644 --- a/src/ptbench/data/hivtb/fold_3.py +++ b/src/ptbench/data/hivtb/fold_3.py @@ -2,20 +2,10 @@ # # SPDX-License-Identifier: GPL-3.0-or-later -"""HIV-TB dataset for TB detection (cross validation fold 3) - -* Split reference: none (stratified kfolding) - -* Stratified kfold protocol: - * Training samples: 72% of TB and healthy CXR (including labels) - * Validation samples: 18% of TB and healthy CXR (including labels) - * Test samples: 10% of TB and healthy CXR (including labels) - -* This configuration resolution: 2048 x 2048 (default) -* See :py:mod:`ptbench.data.hivtb` for dataset details -""" - from .datamodule import DataModule datamodule = DataModule("fold-3.json") +"""HIV-TB dataset for TB detection (cross validation fold 3). +See :py:class:`DataModule` for technical details. +""" diff --git a/src/ptbench/data/hivtb/fold_4.py b/src/ptbench/data/hivtb/fold_4.py index 581eb85ce1023410e2a1cf31128f3b8effa183ed..9cfa6186d6dc7d44f8bcfa56d7c978e7bf346c54 100644 --- a/src/ptbench/data/hivtb/fold_4.py +++ b/src/ptbench/data/hivtb/fold_4.py @@ -2,20 +2,10 @@ # # SPDX-License-Identifier: GPL-3.0-or-later -"""HIV-TB dataset for TB detection (cross validation fold 4) - -* Split reference: none (stratified kfolding) - -* Stratified kfold protocol: - * Training samples: 72% of TB and healthy CXR (including labels) - * Validation samples: 18% of TB and healthy CXR (including labels) - * Test samples: 10% of TB and healthy CXR (including labels) - -* This configuration resolution: 2048 x 2048 (default) -* See :py:mod:`ptbench.data.hivtb` for dataset details -""" - from .datamodule import DataModule datamodule = DataModule("fold-4.json") +"""HIV-TB dataset for TB detection (cross validation fold 4). +See :py:class:`DataModule` for technical details. +""" diff --git a/src/ptbench/data/hivtb/fold_5.py b/src/ptbench/data/hivtb/fold_5.py index 47ae66d13f22764f73ee83c8605f1f57686448b5..591fef3732b522569a92082cb7e3c208c16bf2da 100644 --- a/src/ptbench/data/hivtb/fold_5.py +++ b/src/ptbench/data/hivtb/fold_5.py @@ -2,20 +2,10 @@ # # SPDX-License-Identifier: GPL-3.0-or-later -"""HIV-TB dataset for TB detection (cross validation fold 5) - -* Split reference: none (stratified kfolding) - -* Stratified kfold protocol: - * Training samples: 72% of TB and healthy CXR (including labels) - * Validation samples: 18% of TB and healthy CXR (including labels) - * Test samples: 10% of TB and healthy CXR (including labels) - -* This configuration resolution: 2048 x 2048 (default) -* See :py:mod:`ptbench.data.hivtb` for dataset details -""" - from .datamodule import DataModule datamodule = DataModule("fold-5.json") +"""HIV-TB dataset for TB detection (cross validation fold 5). +See :py:class:`DataModule` for technical details. +""" diff --git a/src/ptbench/data/hivtb/fold_6.py b/src/ptbench/data/hivtb/fold_6.py index c93232f4ef9dd80009541414de1881573b7c88cd..fb5e1614b349779d42771bd165a9a1d96c6cb83d 100644 --- a/src/ptbench/data/hivtb/fold_6.py +++ b/src/ptbench/data/hivtb/fold_6.py @@ -2,20 +2,10 @@ # # SPDX-License-Identifier: GPL-3.0-or-later -"""HIV-TB dataset for TB detection (cross validation fold 6) - -* Split reference: none (stratified kfolding) - -* Stratified kfold protocol: - * Training samples: 72% of TB and healthy CXR (including labels) - * Validation samples: 18% of TB and healthy CXR (including labels) - * Test samples: 10% of TB and healthy CXR (including labels) - -* This configuration resolution: 2048 x 2048 (default) -* See :py:mod:`ptbench.data.hivtb` for dataset details -""" - from .datamodule import DataModule datamodule = DataModule("fold-6.json") +"""HIV-TB dataset for TB detection (cross validation fold 6). +See :py:class:`DataModule` for technical details. +""" diff --git a/src/ptbench/data/hivtb/fold_7.py b/src/ptbench/data/hivtb/fold_7.py index 33d5cc83de84c41d30ed490650eb0ca077be05b8..d64db4837f24058d34b2daf4c8383595aee7be21 100644 --- a/src/ptbench/data/hivtb/fold_7.py +++ b/src/ptbench/data/hivtb/fold_7.py @@ -2,20 +2,10 @@ # # SPDX-License-Identifier: GPL-3.0-or-later -"""HIV-TB dataset for TB detection (cross validation fold 7) - -* Split reference: none (stratified kfolding) - -* Stratified kfold protocol: - * Training samples: 72% of TB and healthy CXR (including labels) - * Validation samples: 18% of TB and healthy CXR (including labels) - * Test samples: 10% of TB and healthy CXR (including labels) - -* This configuration resolution: 2048 x 2048 (default) -* See :py:mod:`ptbench.data.hivtb` for dataset details -""" - from .datamodule import DataModule datamodule = DataModule("fold-7.json") +"""HIV-TB dataset for TB detection (cross validation fold 7). +See :py:class:`DataModule` for technical details. +""" diff --git a/src/ptbench/data/hivtb/fold_8.py b/src/ptbench/data/hivtb/fold_8.py index 91d89557ef60cc116cf6d4f4f8c216fac1b797a5..8a0f87d10c934f08249ed4f0206c09b5bbc6a7a9 100644 --- a/src/ptbench/data/hivtb/fold_8.py +++ b/src/ptbench/data/hivtb/fold_8.py @@ -2,20 +2,10 @@ # # SPDX-License-Identifier: GPL-3.0-or-later -"""HIV-TB dataset for TB detection (cross validation fold 8) - -* Split reference: none (stratified kfolding) - -* Stratified kfold protocol: - * Training samples: 72% of TB and healthy CXR (including labels) - * Validation samples: 18% of TB and healthy CXR (including labels) - * Test samples: 10% of TB and healthy CXR (including labels) - -* This configuration resolution: 2048 x 2048 (default) -* See :py:mod:`ptbench.data.hivtb` for dataset details -""" - from .datamodule import DataModule datamodule = DataModule("fold-8.json") +"""HIV-TB dataset for TB detection (cross validation fold 8). +See :py:class:`DataModule` for technical details. +""" diff --git a/src/ptbench/data/hivtb/fold_9.py b/src/ptbench/data/hivtb/fold_9.py index 0e0063e8b13a997ce6670714836610260aff1952..d92de50e75cd18ea9b99d1bdb010f6f88872b9cc 100644 --- a/src/ptbench/data/hivtb/fold_9.py +++ b/src/ptbench/data/hivtb/fold_9.py @@ -2,20 +2,10 @@ # # SPDX-License-Identifier: GPL-3.0-or-later -"""HIV-TB dataset for TB detection (cross validation fold 9) - -* Split reference: none (stratified kfolding) - -* Stratified kfold protocol: - * Training samples: 72% of TB and healthy CXR (including labels) - * Validation samples: 18% of TB and healthy CXR (including labels) - * Test samples: 10% of TB and healthy CXR (including labels) - -* This configuration resolution: 2048 x 2048 (default) -* See :py:mod:`ptbench.data.hivtb` for dataset details -""" - from .datamodule import DataModule datamodule = DataModule("fold-9.json") +"""HIV-TB dataset for TB detection (cross validation fold 9). +See :py:class:`DataModule` for technical details. +"""