[data] Fixes #32 by reverting some of the changes from 05bbb35f

pyproject.toml

@@ -67,6 +67,7 @@ test = ["pytest", "pytest-cov", "coverage"]
 ptbench = "ptbench.scripts.cli:cli"
 
 [project.entry-points."ptbench.config"]
+
 # models
 pasa = "ptbench.configs.models.pasa"
 signs_to_tb = "ptbench.configs.models.signs_to_tb"
@@ -76,42 +77,46 @@ alexnet = "ptbench.configs.models.alexnet"
 alexnet_pre = "ptbench.configs.models.alexnet_pretrained"
 densenet = "ptbench.configs.models.densenet"
 densenet_pre = "ptbench.configs.models.densenet_pretrained"
+
 # montgomery dataset (and cross-validation folds)
-montgomery = "ptbench.data.montgomery.datamodules:default"
-montgomery_f0 = "ptbench.data.montgomery.datamodules:fold_0"
-montgomery_f1 = "ptbench.data.montgomery.datamodules:fold_1"
-montgomery_f2 = "ptbench.data.montgomery.datamodules:fold_2"
-montgomery_f3 = "ptbench.data.montgomery.datamodules:fold_3"
-montgomery_f4 = "ptbench.data.montgomery.datamodules:fold_4"
-montgomery_f5 = "ptbench.data.montgomery.datamodules:fold_5"
-montgomery_f6 = "ptbench.data.montgomery.datamodules:fold_6"
-montgomery_f7 = "ptbench.data.montgomery.datamodules:fold_7"
-montgomery_f8 = "ptbench.data.montgomery.datamodules:fold_8"
-montgomery_f9 = "ptbench.data.montgomery.datamodules:fold_9"
+montgomery = "ptbench.data.montgomery.default"
+montgomery_f0 = "ptbench.data.montgomery.fold_0"
+montgomery_f1 = "ptbench.data.montgomery.fold_1"
+montgomery_f2 = "ptbench.data.montgomery.fold_2"
+montgomery_f3 = "ptbench.data.montgomery.fold_3"
+montgomery_f4 = "ptbench.data.montgomery.fold_4"
+montgomery_f5 = "ptbench.data.montgomery.fold_5"
+montgomery_f6 = "ptbench.data.montgomery.fold_6"
+montgomery_f7 = "ptbench.data.montgomery.fold_7"
+montgomery_f8 = "ptbench.data.montgomery.fold_8"
+montgomery_f9 = "ptbench.data.montgomery.fold_9"
+
 # shenzhen dataset (and cross-validation folds)
-shenzhen = "ptbench.data.shenzhen.datamodules:default"
-shenzhen_f0 = "ptbench.data.shenzhen.datamodules:fold_0"
-shenzhen_f1 = "ptbench.data.shenzhen.datamodules:fold_1"
-shenzhen_f2 = "ptbench.data.shenzhen.datamodules:fold_2"
-shenzhen_f3 = "ptbench.data.shenzhen.datamodules:fold_3"
-shenzhen_f4 = "ptbench.data.shenzhen.datamodules:fold_4"
-shenzhen_f5 = "ptbench.data.shenzhen.datamodules:fold_5"
-shenzhen_f6 = "ptbench.data.shenzhen.datamodules:fold_6"
-shenzhen_f7 = "ptbench.data.shenzhen.datamodules:fold_7"
-shenzhen_f8 = "ptbench.data.shenzhen.datamodules:fold_8"
-shenzhen_f9 = "ptbench.data.shenzhen.datamodules:fold_9"
+shenzhen = "ptbench.data.shenzhen.default"
+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"
+
 # indian dataset (and cross-validation folds)
-indian = "ptbench.data.indian.datamodules:default"
-indian_f0 = "ptbench.data.indian.datamodules:fold_0"
-indian_f1 = "ptbench.data.indian.datamodules:fold_1"
-indian_f2 = "ptbench.data.indian.datamodules:fold_2"
-indian_f3 = "ptbench.data.indian.datamodules:fold_3"
-indian_f4 = "ptbench.data.indian.datamodules:fold_4"
-indian_f5 = "ptbench.data.indian.datamodules:fold_5"
-indian_f6 = "ptbench.data.indian.datamodules:fold_6"
-indian_f7 = "ptbench.data.indian.datamodules:fold_7"
-indian_f8 = "ptbench.data.indian.datamodules:fold_8"
-indian_f9 = "ptbench.data.indian.datamodules:fold_9"
+indian = "ptbench.data.indian.default"
+indian_f0 = "ptbench.data.indian.fold_0"
+indian_f1 = "ptbench.data.indian.fold_1"
+indian_f2 = "ptbench.data.indian.fold_2"
+indian_f3 = "ptbench.data.indian.fold_3"
+indian_f4 = "ptbench.data.indian.fold_4"
+indian_f5 = "ptbench.data.indian.fold_5"
+indian_f6 = "ptbench.data.indian.fold_6"
+indian_f7 = "ptbench.data.indian.fold_7"
+indian_f8 = "ptbench.data.indian.fold_8"
+indian_f9 = "ptbench.data.indian.fold_9"
+
 # TBX11K simplified dataset split 1 (and cross-validation folds)
 tbx11k_simplified = "ptbench.data.tbx11k_simplified.default"
 tbx11k_simplified_f0 = "ptbench.data.tbx11k_simplified.fold_0"
@@ -124,6 +129,7 @@ tbx11k_simplified_f6 = "ptbench.data.tbx11k_simplified.fold_6"
 tbx11k_simplified_f7 = "ptbench.data.tbx11k_simplified.fold_7"
 tbx11k_simplified_f8 = "ptbench.data.tbx11k_simplified.fold_8"
 tbx11k_simplified_f9 = "ptbench.data.tbx11k_simplified.fold_9"
+
 # TBX11K simplified dataset split 2 (and cross-validation folds)
 tbx11k_simplified_v2 = "ptbench.data.tbx11k_simplified_v2.default"
 tbx11k_simplified_v2_f0 = "ptbench.data.tbx11k_simplified_v2.fold_0"
@@ -136,6 +142,7 @@ tbx11k_simplified_v2_f6 = "ptbench.data.tbx11k_simplified_v2.fold_6"
 tbx11k_simplified_v2_f7 = "ptbench.data.tbx11k_simplified_v2.fold_7"
 tbx11k_simplified_v2_f8 = "ptbench.data.tbx11k_simplified_v2.fold_8"
 tbx11k_simplified_v2_f9 = "ptbench.data.tbx11k_simplified_v2.fold_9"
+
 # montgomery-shenzhen aggregated dataset
 mc_ch = "ptbench.data.mc_ch.default"
 mc_ch_f0 = "ptbench.data.mc_ch.fold_0"
@@ -148,6 +155,7 @@ mc_ch_f6 = "ptbench.data.mc_ch.fold_6"
 mc_ch_f7 = "ptbench.data.mc_ch.fold_7"
 mc_ch_f8 = "ptbench.data.mc_ch.fold_8"
 mc_ch_f9 = "ptbench.data.mc_ch.fold_9"
+
 # montgomery-shenzhen-indian aggregated dataset
 mc_ch_in = "ptbench.data.mc_ch_in.default"
 mc_ch_in_f0 = "ptbench.data.mc_ch_in.fold_0"
@@ -160,6 +168,7 @@ mc_ch_in_f6 = "ptbench.data.mc_ch_in.fold_6"
 mc_ch_in_f7 = "ptbench.data.mc_ch_in.fold_7"
 mc_ch_in_f8 = "ptbench.data.mc_ch_in.fold_8"
 mc_ch_in_f9 = "ptbench.data.mc_ch_in.fold_9"
+
 # montgomery-shenzhen-indian-tbx11k aggregated dataset
 mc_ch_in_11k = "ptbench.data.mc_ch_in_11k.default"
 mc_ch_in_11k_f0 = "ptbench.data.mc_ch_in_11k.fold_0"
@@ -172,6 +181,7 @@ mc_ch_in_11k_f6 = "ptbench.data.mc_ch_in_11k.fold_6"
 mc_ch_in_11k_f7 = "ptbench.data.mc_ch_in_11k.fold_7"
 mc_ch_in_11k_f8 = "ptbench.data.mc_ch_in_11k.fold_8"
 mc_ch_in_11k_f9 = "ptbench.data.mc_ch_in_11k.fold_9"
+
 # montgomery-shenzhen-indian-tbx11kv2 aggregated dataset
 mc_ch_in_11kv2 = "ptbench.data.mc_ch_in_11kv2.default"
 mc_ch_in_11kv2_f0 = "ptbench.data.mc_ch_in_11kv2.fold_0"
@@ -184,6 +194,7 @@ mc_ch_in_11kv2_f6 = "ptbench.data.mc_ch_in_11kv2.fold_6"
 mc_ch_in_11kv2_f7 = "ptbench.data.mc_ch_in_11kv2.fold_7"
 mc_ch_in_11kv2_f8 = "ptbench.data.mc_ch_in_11kv2.fold_8"
 mc_ch_in_11kv2_f9 = "ptbench.data.mc_ch_in_11kv2.fold_9"
+
 # tbpoc dataset (and cross-validation folds)
 tbpoc_f0 = "ptbench.data.tbpoc.fold_0"
 tbpoc_f1 = "ptbench.data.tbpoc.fold_1"
@@ -195,6 +206,7 @@ tbpoc_f6 = "ptbench.data.tbpoc.fold_6"
 tbpoc_f7 = "ptbench.data.tbpoc.fold_7"
 tbpoc_f8 = "ptbench.data.tbpoc.fold_8"
 tbpoc_f9 = "ptbench.data.tbpoc.fold_9"
+
 # hivtb dataset (and cross-validation folds)
 hivtb_f0 = "ptbench.data.hivtb.fold_0"
 hivtb_f1 = "ptbench.data.hivtb.fold_1"
@@ -206,13 +218,17 @@ 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"
+
 # montgomery-shenzhen-indian-padchest aggregated dataset
 mc_ch_in_pc = "ptbench.data.mc_ch_in_pc.default"
+
 # NIH CXR14 (relabeled)
 nih_cxr14 = "ptbench.data.nih_cxr14_re.default"
 nih_cxr14_cm = "ptbench.data.nih_cxr14_re.cardiomegaly"
+
 # NIH CXR14 / PadChest aggregated dataset
 nih_cxr14_pc_idiap = "ptbench.data.nih_cxr14_re_pc.idiap"
+
 # PadChest
 padchest_idiap = "ptbench.data.padchest.idiap"
 padchest_tb_idiap = "ptbench.data.padchest.tb_idiap"

src/ptbench/data/montgomery/datamodules.py → src/ptbench/data/montgomery/datamodule.py

@@ -134,16 +134,3 @@ class DataModule(CachingDataModule):
             ),
             raw_data_loader=RawDataLoader(),
         )
-
-
-default = DataModule("default.json.bz2")
-fold_0 = DataModule("fold_0.json.bz2")
-fold_1 = DataModule("fold_1.json.bz2")
-fold_2 = DataModule("fold_2.json.bz2")
-fold_3 = DataModule("fold_3.json.bz2")
-fold_4 = DataModule("fold_4.json.bz2")
-fold_5 = DataModule("fold_5.json.bz2")
-fold_6 = DataModule("fold_6.json.bz2")
-fold_7 = DataModule("fold_7.json.bz2")
-fold_8 = DataModule("fold_8.json.bz2")
-fold_9 = DataModule("fold_9.json.bz2")

src/ptbench/data/montgomery/default.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("default.json.bz2")

src/ptbench/data/montgomery/fold_0.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold_0.json.bz2")

src/ptbench/data/montgomery/fold_1.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold_1.json.bz2")

src/ptbench/data/montgomery/fold_2.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold_2.json.bz2")

src/ptbench/data/montgomery/fold_3.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold_3.json.bz2")

src/ptbench/data/montgomery/fold_4.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold_4.json.bz2")

src/ptbench/data/montgomery/fold_5.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold_5.json.bz2")

src/ptbench/data/montgomery/fold_6.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold_6.json.bz2")

src/ptbench/data/montgomery/fold_7.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold_7.json.bz2")

src/ptbench/data/montgomery/fold_8.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold_8.json.bz2")

src/ptbench/data/montgomery/fold_9.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold_9.json.bz2")

src/ptbench/data/shenzhen/datamodules.py → src/ptbench/data/shenzhen/datamodule.py

@@ -141,16 +141,3 @@ class DataModule(CachingDataModule):
             ),
             raw_data_loader=RawDataLoader(),
         )
-
-
-default = DataModule("default.json.bz2")
-fold_0 = DataModule("fold_0.json.bz2")
-fold_1 = DataModule("fold_1.json.bz2")
-fold_2 = DataModule("fold_2.json.bz2")
-fold_3 = DataModule("fold_3.json.bz2")
-fold_4 = DataModule("fold_4.json.bz2")
-fold_5 = DataModule("fold_5.json.bz2")
-fold_6 = DataModule("fold_6.json.bz2")
-fold_7 = DataModule("fold_7.json.bz2")
-fold_8 = DataModule("fold_8.json.bz2")
-fold_9 = DataModule("fold_9.json.bz2")

src/ptbench/data/shenzhen/default.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("default.json.bz2")

src/ptbench/data/shenzhen/fold_0.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold_0.json.bz2")

src/ptbench/data/shenzhen/fold_1.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold_1.json.bz2")

src/ptbench/data/shenzhen/fold_2.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold_2.json.bz2")

src/ptbench/data/shenzhen/fold_3.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold_3.json.bz2")

src/ptbench/data/shenzhen/fold_4.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .datamodule import DataModule
+
+datamodule = DataModule("fold_4.json.bz2")