Merge branch 'move-to-lightning' into 'main'

Moved code to lightning

See merge request biosignal/software/ptbench!4

conda/meta.yaml

@@ -36,7 +36,7 @@ requirements:
     - torchvision  {{ torchvision }}
     - tqdm {{ tqdm }}
     - tensorboard {{ tensorboard }}
-    - pytorch-lightning {{ pytorch_lightning }}
+    - lightning {{ lightning }}
     - clapper
   run:
     - python >=3.9
@@ -53,7 +53,7 @@ requirements:
     - {{ pin_compatible('torchvision') }}
     - {{ pin_compatible('tqdm') }}
     - {{ pin_compatible('tensorboard') }}
-    - {{ pin_compatible('pytorch-lightning') }}
+    - {{ pin_compatible('lightning') }}
     - clapper
 
 test:

doc/api.rst

@@ -53,6 +53,10 @@ Direct data-access through iterators.
    ptbench.data.indian
    ptbench.data.nih_cxr14_re
    ptbench.data.padchest_RS
+   ptbench.data.tbx11k_simplified
+   ptbench.data.tbx11k_simplified_RS
+   ptbench.data.tbx11k_simplified_v2
+   ptbench.data.tbx11k_simplified_v2_RS
 
 
 .. _ptbench.api.models:

doc/catalog.json

@@ -5,5 +5,13 @@
       "latest": "https://clapper.readthedocs.io/en/latest/"
     },
     "sources": {}
+  },
+  "lightning": {
+    "versions": {
+      "stable": "https://lightning.ai/docs/pytorch/stable/"
+    },
+    "sources": {
+      "environment": "lightning"
+    }
   }
 }

doc/conf.py

@@ -122,6 +122,7 @@ auto_intersphinx_packages = [
     "psutil",
     "torch",
     "torchvision",
+    "lightning",
     ("clapper", "latest"),
     ("python", "3"),
 ]

doc/config.rst

@@ -50,6 +50,12 @@ if applicable.  Use these datasets for training and evaluating your models.
    ptbench.configs.datasets.mc_ch_in.default
    ptbench.configs.datasets.mc_ch_in.rgb
    ptbench.configs.datasets.mc_ch_in_RS.default
+   ptbench.configs.datasets.mc_ch_in_11k.default
+   ptbench.configs.datasets.mc_ch_in_11k.rgb
+   ptbench.configs.datasets.mc_ch_in_11k_RS.default
+   ptbench.configs.datasets.mc_ch_in_11kv2.default
+   ptbench.configs.datasets.mc_ch_in_11kv2.rgb
+   ptbench.configs.datasets.mc_ch_in_11kv2_RS.default
    ptbench.configs.datasets.mc_ch_in_pc.default
    ptbench.configs.datasets.mc_ch_in_pc.rgb
    ptbench.configs.datasets.mc_ch_in_pc_RS.default
@@ -68,6 +74,12 @@ if applicable.  Use these datasets for training and evaluating your models.
    ptbench.configs.datasets.shenzhen.default
    ptbench.configs.datasets.shenzhen.rgb
    ptbench.configs.datasets.shenzhen_RS.default
+   ptbench.configs.datasets.tbx11k_simplified.default
+   ptbench.configs.datasets.tbx11k_simplified.rgb
+   ptbench.configs.datasets.tbx11k_simplified_RS.default
+   ptbench.configs.datasets.tbx11k_simplified_v2.default
+   ptbench.configs.datasets.tbx11k_simplified_v2.rgb
+   ptbench.configs.datasets.tbx11k_simplified_v2_RS.default
 
 
 .. _ptbench.configs.datasets.folds:
@@ -97,6 +109,12 @@ datasets.  Nine other folds are available for every configuration (from 1 to
    ptbench.configs.datasets.mc_ch_in.fold_0
    ptbench.configs.datasets.mc_ch_in.fold_0_rgb
    ptbench.configs.datasets.mc_ch_in_RS.fold_0
+   ptbench.configs.datasets.mc_ch_in_11k.fold_0
+   ptbench.configs.datasets.mc_ch_in_11k.fold_0_rgb
+   ptbench.configs.datasets.mc_ch_in_11k_RS.fold_0
+   ptbench.configs.datasets.mc_ch_in_11kv2.fold_0
+   ptbench.configs.datasets.mc_ch_in_11kv2.fold_0_rgb
+   ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_0
    ptbench.configs.datasets.montgomery.fold_0
    ptbench.configs.datasets.montgomery.fold_0_rgb
    ptbench.configs.datasets.montgomery_RS.fold_0
@@ -106,6 +124,12 @@ datasets.  Nine other folds are available for every configuration (from 1 to
    ptbench.configs.datasets.tbpoc.fold_0
    ptbench.configs.datasets.tbpoc.fold_0_rgb
    ptbench.configs.datasets.tbpoc_RS.fold_0
+   ptbench.configs.datasets.tbx11k_simplified.fold_0
+   ptbench.configs.datasets.tbx11k_simplified.fold_0_rgb
+   ptbench.configs.datasets.tbx11k_simplified_RS.fold_0
+   ptbench.configs.datasets.tbx11k_simplified_v2.fold_0
+   ptbench.configs.datasets.tbx11k_simplified_v2.fold_0_rgb
+   ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_0
 
 
 .. include:: links.rst

doc/extras.inv

@@ -2,5 +2,5 @@
 # Project: extras
 # Version: stable
 # The remainder of this file is compressed using zlib.
-xE
 лSt
i
*
-	P~M߃lYfh5Wٯit}No!%]B-4OΌ 
+xڭA
+1E[[R
MH2A\.{OItņTLR+.$Uns<lI	ԟ2hl1iB$`g/aG%<XU)ibłw/
\ No newline at end of file

doc/extras.txt

@@ -3,3 +3,6 @@
 # Version: stable
 # The remainder of this file is compressed using zlib.
 torchvision.transforms py:module 1 https://pytorch.org/vision/stable/transforms.html -
+lightning.pytorch.core.module.LightningModule.forward py:method 1 api/lightning.pytorch.core.LightningModule.html#$ -
+lightning.pytorch.core.module.LightningModule.predict_step py:method 1 api/lightning.pytorch.core.LightningModule.html#$ -
+optimizer_step py:method 1 api/lightning.pytorch.core.LightningModule.html#$ -

doc/install.rst

@@ -66,6 +66,7 @@ Here is an example configuration file that may be useful as a starting point:
    montgomery = "/Users/myself/dbs/montgomery-xrayset"
    shenzhen = "/Users/myself/dbs/shenzhen"
    nih_cxr14_re = "/Users/myself/dbs/nih-cxr14-re"
+   tbx11k_simplified = "/Users/myself/dbs/tbx11k-simplified"
 
    [nih_cxr14_re]
    idiap_folder_structure = false  # set to `true` if at Idiap
@@ -145,6 +146,42 @@ In addition to the splits presented in the following table, 10 folds
 
 .. _ptbench.setup.datasets.tb+signs:
 
+Tuberculosis multilabel dataset
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following dataset contains the labels healthy, sick & non-TB, active TB,
+and latent TB. The implemented tbx11k dataset in this package is based on
+the simplified version, which is just a more compact version of the original.
+In addition to the splits presented in the following table, 10 folds
+(for cross-validation) randomly generated are available for these datasets.
+
+.. list-table::
+
+   * - Dataset
+     - Reference
+     - H x W
+     - Samples
+     - Training
+     - Validation
+     - Test
+   * - TBX11K_
+     - [TBX11K-2020]_
+     - 512 x 512
+     - 11'200
+     - 6600
+     - 1800
+     - 2800
+   * - TBX11K_SIMPLIFIED_
+     - [TBX11K-SIMPLIFIED-2020]_
+     - 512 x 512
+     - 11'200
+     - 6600
+     - 1800
+     - 2800
+
+
+.. _ptbench.setup.datasets.tbmultilabel+signs:
+
 Tuberculosis + radiological findings dataset
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

doc/links.rst

@@ -18,3 +18,5 @@
 .. _indian: https://sourceforge.net/projects/tbxpredict/
 .. _NIH_CXR14_re: https://nihcc.app.box.com/v/ChestXray-NIHCC
 .. _PadChest: https://bimcv.cipf.es/bimcv-projects/padchest/
+.. _TBX11K: https://mmcheng.net/tb/
+.. _TBX11K_simplified: https://www.kaggle.com/datasets/vbookshelf/tbx11k-simplified

doc/references.rst

@@ -59,3 +59,13 @@
    performance and interobserver agreement of urine lipoarabinomannan in
    diagnosing HIV-Associated tuberculosis in an emergency center.**,
    J. Acquir. Immune Defic. Syndr. 1999 81, e10–e14 (2019).
+
+.. [TBX11K-2020] *Liu, Y., Wu, Y.-H., Ban, Y., Wang, H., and Cheng, M.-*,
+   **Rethinking computer-aided tuberculosis diagnosis.**,
+   In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern
+   Recognition, pages 2646–2655.
+
+.. [TBX11K-SIMPLIFIED-2020] *Liu, Y., Wu, Y.-H., Ban, Y., Wang, H., and Cheng, M.-*,
+   **Rethinking computer-aided tuberculosis diagnosis.**,
+   In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern
+   Recognition, pages 2646–2655.

pyproject.toml

@@ -41,7 +41,7 @@ dependencies = [
    "pillow",
    "torch>=1.8",
    "torchvision>=0.10",
-   "pytorch-lightning",
+   "lightning",
    "tensorboard",
 ]
 
@@ -186,6 +186,76 @@ indian_rs_f6 = "ptbench.configs.datasets.indian_RS.fold_6"
 indian_rs_f7 = "ptbench.configs.datasets.indian_RS.fold_7"
 indian_rs_f8 = "ptbench.configs.datasets.indian_RS.fold_8"
 indian_rs_f9 = "ptbench.configs.datasets.indian_RS.fold_9"
+# TBX11K simplified dataset split 1 (and cross-validation folds)
+tbx11k_simplified = "ptbench.configs.datasets.tbx11k_simplified.default"
+tbx11k_simplified_rgb = "ptbench.configs.datasets.tbx11k_simplified.rgb"
+tbx11k_simplified_f0 = "ptbench.configs.datasets.tbx11k_simplified.fold_0"
+tbx11k_simplified_f1 = "ptbench.configs.datasets.tbx11k_simplified.fold_1"
+tbx11k_simplified_f2 = "ptbench.configs.datasets.tbx11k_simplified.fold_2"
+tbx11k_simplified_f3 = "ptbench.configs.datasets.tbx11k_simplified.fold_3"
+tbx11k_simplified_f4 = "ptbench.configs.datasets.tbx11k_simplified.fold_4"
+tbx11k_simplified_f5 = "ptbench.configs.datasets.tbx11k_simplified.fold_5"
+tbx11k_simplified_f6 = "ptbench.configs.datasets.tbx11k_simplified.fold_6"
+tbx11k_simplified_f7 = "ptbench.configs.datasets.tbx11k_simplified.fold_7"
+tbx11k_simplified_f8 = "ptbench.configs.datasets.tbx11k_simplified.fold_8"
+tbx11k_simplified_f9 = "ptbench.configs.datasets.tbx11k_simplified.fold_9"
+tbx11k_simplified_f0_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_0_rgb"
+tbx11k_simplified_f1_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_1_rgb"
+tbx11k_simplified_f2_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_2_rgb"
+tbx11k_simplified_f3_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_3_rgb"
+tbx11k_simplified_f4_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_4_rgb"
+tbx11k_simplified_f5_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_5_rgb"
+tbx11k_simplified_f6_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_6_rgb"
+tbx11k_simplified_f7_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_7_rgb"
+tbx11k_simplified_f8_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_8_rgb"
+tbx11k_simplified_f9_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_9_rgb"
+# extended TBX11K simplified dataset split 1 (with radiological signs)
+tbx11k_simplified_rs = "ptbench.configs.datasets.tbx11k_simplified_RS.default"
+tbx11k_simplified_rs_f0 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_0"
+tbx11k_simplified_rs_f1 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_1"
+tbx11k_simplified_rs_f2 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_2"
+tbx11k_simplified_rs_f3 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_3"
+tbx11k_simplified_rs_f4 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_4"
+tbx11k_simplified_rs_f5 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_5"
+tbx11k_simplified_rs_f6 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_6"
+tbx11k_simplified_rs_f7 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_7"
+tbx11k_simplified_rs_f8 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_8"
+tbx11k_simplified_rs_f9 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_9"
+# TBX11K simplified dataset split 2 (and cross-validation folds)
+tbx11k_simplified_v2 = "ptbench.configs.datasets.tbx11k_simplified_v2.default"
+tbx11k_simplified_v2_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.rgb"
+tbx11k_simplified_v2_f0 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_0"
+tbx11k_simplified_v2_f1 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_1"
+tbx11k_simplified_v2_f2 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_2"
+tbx11k_simplified_v2_f3 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_3"
+tbx11k_simplified_v2_f4 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_4"
+tbx11k_simplified_v2_f5 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_5"
+tbx11k_simplified_v2_f6 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_6"
+tbx11k_simplified_v2_f7 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_7"
+tbx11k_simplified_v2_f8 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_8"
+tbx11k_simplified_v2_f9 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_9"
+tbx11k_simplified_v2_f0_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_0_rgb"
+tbx11k_simplified_v2_f1_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_1_rgb"
+tbx11k_simplified_v2_f2_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_2_rgb"
+tbx11k_simplified_v2_f3_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_3_rgb"
+tbx11k_simplified_v2_f4_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_4_rgb"
+tbx11k_simplified_v2_f5_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_5_rgb"
+tbx11k_simplified_v2_f6_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_6_rgb"
+tbx11k_simplified_v2_f7_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_7_rgb"
+tbx11k_simplified_v2_f8_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_8_rgb"
+tbx11k_simplified_v2_f9_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_9_rgb"
+# extended TBX11K simplified dataset split 2 (with radiological signs)
+tbx11k_simplified_v2_rs = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.default"
+tbx11k_simplified_v2_rs_f0 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_0"
+tbx11k_simplified_v2_rs_f1 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_1"
+tbx11k_simplified_v2_rs_f2 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_2"
+tbx11k_simplified_v2_rs_f3 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_3"
+tbx11k_simplified_v2_rs_f4 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_4"
+tbx11k_simplified_v2_rs_f5 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_5"
+tbx11k_simplified_v2_rs_f6 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_6"
+tbx11k_simplified_v2_rs_f7 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_7"
+tbx11k_simplified_v2_rs_f8 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_8"
+tbx11k_simplified_v2_rs_f9 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_9"
 # montgomery-shenzhen aggregated dataset
 mc_ch = "ptbench.configs.datasets.mc_ch.default"
 mc_ch_rgb = "ptbench.configs.datasets.mc_ch.rgb"
@@ -258,6 +328,78 @@ mc_ch_in_rs_f6 = "ptbench.configs.datasets.mc_ch_in_RS.fold_6"
 mc_ch_in_rs_f7 = "ptbench.configs.datasets.mc_ch_in_RS.fold_7"
 mc_ch_in_rs_f8 = "ptbench.configs.datasets.mc_ch_in_RS.fold_8"
 mc_ch_in_rs_f9 = "ptbench.configs.datasets.mc_ch_in_RS.fold_9"
+# montgomery-shenzhen-indian-tbx11k aggregated dataset
+mc_ch_in_11k = "ptbench.configs.datasets.mc_ch_in_11k.default"
+mc_ch_in_11k_rgb = "ptbench.configs.datasets.mc_ch_in_11k.rgb"
+mc_ch_in_11k_f0 = "ptbench.configs.datasets.mc_ch_in_11k.fold_0"
+mc_ch_in_11k_f1 = "ptbench.configs.datasets.mc_ch_in_11k.fold_1"
+mc_ch_in_11k_f2 = "ptbench.configs.datasets.mc_ch_in_11k.fold_2"
+mc_ch_in_11k_f3 = "ptbench.configs.datasets.mc_ch_in_11k.fold_3"
+mc_ch_in_11k_f4 = "ptbench.configs.datasets.mc_ch_in_11k.fold_4"
+mc_ch_in_11k_f5 = "ptbench.configs.datasets.mc_ch_in_11k.fold_5"
+mc_ch_in_11k_f6 = "ptbench.configs.datasets.mc_ch_in_11k.fold_6"
+mc_ch_in_11k_f7 = "ptbench.configs.datasets.mc_ch_in_11k.fold_7"
+mc_ch_in_11k_f8 = "ptbench.configs.datasets.mc_ch_in_11k.fold_8"
+mc_ch_in_11k_f9 = "ptbench.configs.datasets.mc_ch_in_11k.fold_9"
+mc_ch_in_11k_f0_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_0_rgb"
+mc_ch_in_11k_f1_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_1_rgb"
+mc_ch_in_11k_f2_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_2_rgb"
+mc_ch_in_11k_f3_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_3_rgb"
+mc_ch_in_11k_f4_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_4_rgb"
+mc_ch_in_11k_f5_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_5_rgb"
+mc_ch_in_11k_f6_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_6_rgb"
+mc_ch_in_11k_f7_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_7_rgb"
+mc_ch_in_11k_f8_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_8_rgb"
+mc_ch_in_11k_f9_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_9_rgb"
+# extended montgomery-shenzhen-indian-tbx11k aggregated dataset
+# (with radiological signs)
+mc_ch_in_11k_rs = "ptbench.configs.datasets.mc_ch_in_11k_RS.default"
+mc_ch_in_11k_rs_f0 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_0"
+mc_ch_in_11k_rs_f1 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_1"
+mc_ch_in_11k_rs_f2 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_2"
+mc_ch_in_11k_rs_f3 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_3"
+mc_ch_in_11k_rs_f4 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_4"
+mc_ch_in_11k_rs_f5 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_5"
+mc_ch_in_11k_rs_f6 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_6"
+mc_ch_in_11k_rs_f7 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_7"
+mc_ch_in_11k_rs_f8 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_8"
+mc_ch_in_11k_rs_f9 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_9"
+# montgomery-shenzhen-indian-tbx11kv2 aggregated dataset
+mc_ch_in_11kv2 = "ptbench.configs.datasets.mc_ch_in_11kv2.default"
+mc_ch_in_11kv2_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.rgb"
+mc_ch_in_11kv2_f0 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_0"
+mc_ch_in_11kv2_f1 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_1"
+mc_ch_in_11kv2_f2 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_2"
+mc_ch_in_11kv2_f3 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_3"
+mc_ch_in_11kv2_f4 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_4"
+mc_ch_in_11kv2_f5 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_5"
+mc_ch_in_11kv2_f6 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_6"
+mc_ch_in_11kv2_f7 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_7"
+mc_ch_in_11kv2_f8 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_8"
+mc_ch_in_11kv2_f9 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_9"
+mc_ch_in_11kv2_f0_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_0_rgb"
+mc_ch_in_11kv2_f1_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_1_rgb"
+mc_ch_in_11kv2_f2_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_2_rgb"
+mc_ch_in_11kv2_f3_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_3_rgb"
+mc_ch_in_11kv2_f4_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_4_rgb"
+mc_ch_in_11kv2_f5_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_5_rgb"
+mc_ch_in_11kv2_f6_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_6_rgb"
+mc_ch_in_11kv2_f7_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_7_rgb"
+mc_ch_in_11kv2_f8_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_8_rgb"
+mc_ch_in_11kv2_f9_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_9_rgb"
+# extended montgomery-shenzhen-indian-tbx11kv2 aggregated dataset
+# (with radiological signs)
+mc_ch_in_11kv2_rs = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.default"
+mc_ch_in_11kv2_rs_f0 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_0"
+mc_ch_in_11kv2_rs_f1 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_1"
+mc_ch_in_11kv2_rs_f2 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_2"
+mc_ch_in_11kv2_rs_f3 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_3"
+mc_ch_in_11kv2_rs_f4 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_4"
+mc_ch_in_11kv2_rs_f5 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_5"
+mc_ch_in_11kv2_rs_f6 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_6"
+mc_ch_in_11kv2_rs_f7 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_7"
+mc_ch_in_11kv2_rs_f8 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_8"
+mc_ch_in_11kv2_rs_f9 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_9"
 # tbpoc dataset (and cross-validation folds)
 tbpoc_f0 = "ptbench.configs.datasets.tbpoc.fold_0"
 tbpoc_f1 = "ptbench.configs.datasets.tbpoc.fold_1"

src/ptbench/configs/datasets/mc_ch_in_11k/__init__.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from torch.utils.data.dataset import ConcatDataset
+
+
+def _maker(protocol):
+    if protocol == "default":
+        from ..indian import default as indian
+        from ..montgomery import default as mc
+        from ..shenzhen import default as ch
+        from ..tbx11k_simplified import default as tbx11k
+    elif protocol == "rgb":
+        from ..indian import rgb as indian
+        from ..montgomery import rgb as mc
+        from ..shenzhen import rgb as ch
+        from ..tbx11k_simplified import rgb as tbx11k
+    elif protocol == "fold_0":
+        from ..indian import fold_0 as indian
+        from ..montgomery import fold_0 as mc
+        from ..shenzhen import fold_0 as ch
+        from ..tbx11k_simplified import fold_0 as tbx11k
+    elif protocol == "fold_1":
+        from ..indian import fold_1 as indian
+        from ..montgomery import fold_1 as mc
+        from ..shenzhen import fold_1 as ch
+        from ..tbx11k_simplified import fold_1 as tbx11k
+    elif protocol == "fold_2":
+        from ..indian import fold_2 as indian
+        from ..montgomery import fold_2 as mc
+        from ..shenzhen import fold_2 as ch
+        from ..tbx11k_simplified import fold_2 as tbx11k
+    elif protocol == "fold_3":
+        from ..indian import fold_3 as indian
+        from ..montgomery import fold_3 as mc
+        from ..shenzhen import fold_3 as ch
+        from ..tbx11k_simplified import fold_3 as tbx11k
+    elif protocol == "fold_4":
+        from ..indian import fold_4 as indian
+        from ..montgomery import fold_4 as mc
+        from ..shenzhen import fold_4 as ch
+        from ..tbx11k_simplified import fold_4 as tbx11k
+    elif protocol == "fold_5":
+        from ..indian import fold_5 as indian
+        from ..montgomery import fold_5 as mc
+        from ..shenzhen import fold_5 as ch
+        from ..tbx11k_simplified import fold_5 as tbx11k
+    elif protocol == "fold_6":
+        from ..indian import fold_6 as indian
+        from ..montgomery import fold_6 as mc
+        from ..shenzhen import fold_6 as ch
+        from ..tbx11k_simplified import fold_6 as tbx11k
+    elif protocol == "fold_7":
+        from ..indian import fold_7 as indian
+        from ..montgomery import fold_7 as mc
+        from ..shenzhen import fold_7 as ch
+        from ..tbx11k_simplified import fold_7 as tbx11k
+    elif protocol == "fold_8":
+        from ..indian import fold_8 as indian
+        from ..montgomery import fold_8 as mc
+        from ..shenzhen import fold_8 as ch
+        from ..tbx11k_simplified import fold_8 as tbx11k
+    elif protocol == "fold_9":
+        from ..indian import fold_9 as indian
+        from ..montgomery import fold_9 as mc
+        from ..shenzhen import fold_9 as ch
+        from ..tbx11k_simplified import fold_9 as tbx11k
+    elif protocol == "fold_0_rgb":
+        from ..indian import fold_0_rgb as indian
+        from ..montgomery import fold_0_rgb as mc
+        from ..shenzhen import fold_0_rgb as ch
+        from ..tbx11k_simplified import fold_0_rgb as tbx11k
+    elif protocol == "fold_1_rgb":
+        from ..indian import fold_1_rgb as indian
+        from ..montgomery import fold_1_rgb as mc
+        from ..shenzhen import fold_1_rgb as ch
+        from ..tbx11k_simplified import fold_1_rgb as tbx11k
+    elif protocol == "fold_2_rgb":
+        from ..indian import fold_2_rgb as indian
+        from ..montgomery import fold_2_rgb as mc
+        from ..shenzhen import fold_2_rgb as ch
+        from ..tbx11k_simplified import fold_2_rgb as tbx11k
+    elif protocol == "fold_3_rgb":
+        from ..indian import fold_3_rgb as indian
+        from ..montgomery import fold_3_rgb as mc
+        from ..shenzhen import fold_3_rgb as ch
+        from ..tbx11k_simplified import fold_3_rgb as tbx11k
+    elif protocol == "fold_4_rgb":
+        from ..indian import fold_4_rgb as indian
+        from ..montgomery import fold_4_rgb as mc
+        from ..shenzhen import fold_4_rgb as ch
+        from ..tbx11k_simplified import fold_4_rgb as tbx11k
+    elif protocol == "fold_5_rgb":
+        from ..indian import fold_5_rgb as indian
+        from ..montgomery import fold_5_rgb as mc
+        from ..shenzhen import fold_5_rgb as ch
+        from ..tbx11k_simplified import fold_5_rgb as tbx11k
+    elif protocol == "fold_6_rgb":
+        from ..indian import fold_6_rgb as indian
+        from ..montgomery import fold_6_rgb as mc
+        from ..shenzhen import fold_6_rgb as ch
+        from ..tbx11k_simplified import fold_6_rgb as tbx11k
+    elif protocol == "fold_7_rgb":
+        from ..indian import fold_7_rgb as indian
+        from ..montgomery import fold_7_rgb as mc
+        from ..shenzhen import fold_7_rgb as ch
+        from ..tbx11k_simplified import fold_7_rgb as tbx11k
+    elif protocol == "fold_8_rgb":
+        from ..indian import fold_8_rgb as indian
+        from ..montgomery import fold_8_rgb as mc
+        from ..shenzhen import fold_8_rgb as ch
+        from ..tbx11k_simplified import fold_8_rgb as tbx11k
+    elif protocol == "fold_9_rgb":
+        from ..indian import fold_9_rgb as indian
+        from ..montgomery import fold_9_rgb as mc
+        from ..shenzhen import fold_9_rgb as ch
+        from ..tbx11k_simplified import fold_9_rgb as tbx11k
+
+    mc = mc.dataset
+    ch = ch.dataset
+    indian = indian.dataset
+    tbx11k = tbx11k.dataset
+
+    dataset = {}
+    dataset["__train__"] = ConcatDataset(
+        [
+            mc["__train__"],
+            ch["__train__"],
+            indian["__train__"],
+            tbx11k["__train__"],
+        ]
+    )
+    dataset["train"] = ConcatDataset(
+        [mc["train"], ch["train"], indian["train"], tbx11k["train"]]
+    )
+    dataset["__valid__"] = ConcatDataset(
+        [
+            mc["__valid__"],
+            ch["__valid__"],
+            indian["__valid__"],
+            tbx11k["__valid__"],
+        ]
+    )
+    dataset["validation"] = ConcatDataset(
+        [
+            mc["validation"],
+            ch["validation"],
+            indian["validation"],
+            tbx11k["validation"],
+        ]
+    )
+    dataset["test"] = ConcatDataset(
+        [mc["test"], ch["test"], indian["test"], tbx11k["test"]]
+    )
+
+    return dataset

src/ptbench/configs/datasets/mc_ch_in_11k/default.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""Aggregated dataset composed of Montgomery, Shenzhen, Indian and the default
+TBX11K-simplified datasets."""
+
+from . import _maker
+
+dataset = _maker("default")

src/ptbench/configs/datasets/mc_ch_in_11k/fold_0.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""Aggregated dataset composed of Montgomery, Shenzhen, Indian and the default
+TBX11K-simplified datasets (cross validation fold 0)"""
+
+from . import _maker
+
+dataset = _maker("fold_0")

src/ptbench/configs/datasets/mc_ch_in_11k/fold_0_rgb.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""Aggregated dataset composed of Montgomery, Shenzhen, Indian and the default
+TBX11K-simplified datasets (cross validation fold 0, RGB)"""
+
+from . import _maker
+
+dataset = _maker("fold_0_rgb")

src/ptbench/configs/datasets/mc_ch_in_11k/fold_1.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""Aggregated dataset composed of Montgomery, Shenzhen, Indian and the default
+TBX11K-simplified datasets (cross validation fold 1)"""
+
+from . import _maker
+
+dataset = _maker("fold_1")

src/ptbench/configs/datasets/mc_ch_in_11k/fold_1_rgb.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""Aggregated dataset composed of Montgomery, Shenzhen, Indian and the default
+TBX11K-simplified datasets (cross validation fold 1, RGB)"""
+
+from . import _maker
+
+dataset = _maker("fold_1_rgb")

src/ptbench/configs/datasets/mc_ch_in_11k/fold_2.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""Aggregated dataset composed of Montgomery, Shenzhen, Indian and the default
+TBX11K-simplified datasets (cross validation fold 2)"""
+
+from . import _maker
+
+dataset = _maker("fold_2")

src/ptbench/configs/datasets/mc_ch_in_11k/fold_2_rgb.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""Aggregated dataset composed of Montgomery, Shenzhen, Indian and the default
+TBX11K-simplified datasets (cross validation fold 2, RGB)"""
+
+from . import _maker
+
+dataset = _maker("fold_2_rgb")

src/ptbench/configs/datasets/mc_ch_in_11k/fold_3.py

+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""Aggregated dataset composed of Montgomery, Shenzhen, Indian and the default
+TBX11K-simplified datasets (cross validation fold 3)"""
+
+from . import _maker
+
+dataset = _maker("fold_3")