From d0e03dfeb2284e6f7f37bb6da8bc22d5aa77492b Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Mon, 5 Jun 2023 13:05:20 +0200
Subject: [PATCH] Moved tbx11k_simplified configs to data
---
.../datasets/tbx11k_simplified/__init__.py | 25 ----------
.../datasets/tbx11k_simplified/default.py | 17 -------
.../datasets/tbx11k_simplified/fold_0.py | 17 -------
.../datasets/tbx11k_simplified/fold_0_rgb.py | 17 -------
.../datasets/tbx11k_simplified/fold_1.py | 17 -------
.../datasets/tbx11k_simplified/fold_1_rgb.py | 17 -------
.../datasets/tbx11k_simplified/fold_2.py | 17 -------
.../datasets/tbx11k_simplified/fold_2_rgb.py | 17 -------
.../datasets/tbx11k_simplified/fold_3.py | 17 -------
.../datasets/tbx11k_simplified/fold_3_rgb.py | 17 -------
.../datasets/tbx11k_simplified/fold_4.py | 17 -------
.../datasets/tbx11k_simplified/fold_4_rgb.py | 17 -------
.../datasets/tbx11k_simplified/fold_5.py | 17 -------
.../datasets/tbx11k_simplified/fold_5_rgb.py | 17 -------
.../datasets/tbx11k_simplified/fold_6.py | 17 -------
.../datasets/tbx11k_simplified/fold_6_rgb.py | 17 -------
.../datasets/tbx11k_simplified/fold_7.py | 17 -------
.../datasets/tbx11k_simplified/fold_7_rgb.py | 17 -------
.../datasets/tbx11k_simplified/fold_8.py | 17 -------
.../datasets/tbx11k_simplified/fold_8_rgb.py | 17 -------
.../datasets/tbx11k_simplified/fold_9.py | 17 -------
.../datasets/tbx11k_simplified/fold_9_rgb.py | 17 -------
.../configs/datasets/tbx11k_simplified/rgb.py | 17 -------
.../data/tbx11k_simplified/__init__.py | 25 +++++++++-
src/ptbench/data/tbx11k_simplified/default.py | 49 ++++++++++++++++++
src/ptbench/data/tbx11k_simplified/fold_0.py | 49 ++++++++++++++++++
.../data/tbx11k_simplified/fold_0_rgb.py | 49 ++++++++++++++++++
src/ptbench/data/tbx11k_simplified/fold_1.py | 49 ++++++++++++++++++
.../data/tbx11k_simplified/fold_1_rgb.py | 50 +++++++++++++++++++
src/ptbench/data/tbx11k_simplified/fold_2.py | 49 ++++++++++++++++++
.../data/tbx11k_simplified/fold_2_rgb.py | 49 ++++++++++++++++++
src/ptbench/data/tbx11k_simplified/fold_3.py | 49 ++++++++++++++++++
.../data/tbx11k_simplified/fold_3_rgb.py | 49 ++++++++++++++++++
src/ptbench/data/tbx11k_simplified/fold_4.py | 49 ++++++++++++++++++
.../data/tbx11k_simplified/fold_4_rgb.py | 49 ++++++++++++++++++
src/ptbench/data/tbx11k_simplified/fold_5.py | 49 ++++++++++++++++++
.../data/tbx11k_simplified/fold_5_rgb.py | 49 ++++++++++++++++++
src/ptbench/data/tbx11k_simplified/fold_6.py | 49 ++++++++++++++++++
.../data/tbx11k_simplified/fold_6_rgb.py | 49 ++++++++++++++++++
src/ptbench/data/tbx11k_simplified/fold_7.py | 49 ++++++++++++++++++
.../data/tbx11k_simplified/fold_7_rgb.py | 49 ++++++++++++++++++
src/ptbench/data/tbx11k_simplified/fold_8.py | 49 ++++++++++++++++++
.../data/tbx11k_simplified/fold_8_rgb.py | 49 ++++++++++++++++++
src/ptbench/data/tbx11k_simplified/fold_9.py | 49 ++++++++++++++++++
.../data/tbx11k_simplified/fold_9_rgb.py | 49 ++++++++++++++++++
src/ptbench/data/tbx11k_simplified/rgb.py | 49 ++++++++++++++++++
46 files changed, 1102 insertions(+), 401 deletions(-)
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/__init__.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/default.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_0.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_0_rgb.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_1.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_1_rgb.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_2.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_2_rgb.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_3.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_3_rgb.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_4.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_4_rgb.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_5.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_5_rgb.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_6.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_6_rgb.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_7.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_7_rgb.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_8.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_8_rgb.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_9.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/fold_9_rgb.py
delete mode 100644 src/ptbench/configs/datasets/tbx11k_simplified/rgb.py
create mode 100644 src/ptbench/data/tbx11k_simplified/default.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_0.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_0_rgb.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_1.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_1_rgb.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_2.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_2_rgb.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_3.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_3_rgb.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_4.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_4_rgb.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_5.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_5_rgb.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_6.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_6_rgb.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_7.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_7_rgb.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_8.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_8_rgb.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_9.py
create mode 100644 src/ptbench/data/tbx11k_simplified/fold_9_rgb.py
create mode 100644 src/ptbench/data/tbx11k_simplified/rgb.py
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/__init__.py b/src/ptbench/configs/datasets/tbx11k_simplified/__init__.py
deleted file mode 100644
index 595c3231..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/__init__.py
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-
-def _maker(protocol, RGB=False):
- from torchvision import transforms
-
- from ....data.tbx11k_simplified import dataset as raw
- from ....data.transforms import ElasticDeformation
- 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)],
- [],
- [ElasticDeformation(p=0.8)],
- post_transforms,
- )
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/default.py b/src/ptbench/configs/datasets/tbx11k_simplified/default.py
deleted file mode 100644
index cb23f352..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/default.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("default")
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_0.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_0.py
deleted file mode 100644
index 8f907af7..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_0.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_0")
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_0_rgb.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_0_rgb.py
deleted file mode 100644
index 141a3e95..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_0_rgb.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_0", RGB=True)
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_1.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_1.py
deleted file mode 100644
index cb7e2360..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_1.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_1")
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_1_rgb.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_1_rgb.py
deleted file mode 100644
index a9cecd0b..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_1_rgb.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_1", RGB=True)
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_2.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_2.py
deleted file mode 100644
index 1cffe2fb..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_2.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_2")
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_2_rgb.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_2_rgb.py
deleted file mode 100644
index fadd67cc..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_2_rgb.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_2", RGB=True)
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_3.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_3.py
deleted file mode 100644
index 64743fbd..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_3.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_3")
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_3_rgb.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_3_rgb.py
deleted file mode 100644
index d17f3e6a..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_3_rgb.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_3", RGB=True)
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_4.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_4.py
deleted file mode 100644
index 0739b98b..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_4.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_4")
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_4_rgb.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_4_rgb.py
deleted file mode 100644
index 83a560c4..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_4_rgb.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_4", RGB=True)
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_5.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_5.py
deleted file mode 100644
index dc200e16..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_5.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_5")
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_5_rgb.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_5_rgb.py
deleted file mode 100644
index e7471a1f..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_5_rgb.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_5", RGB=True)
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_6.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_6.py
deleted file mode 100644
index 6bfb172b..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_6.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_6")
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_6_rgb.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_6_rgb.py
deleted file mode 100644
index 89987781..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_6_rgb.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_6", RGB=True)
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_7.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_7.py
deleted file mode 100644
index 55350496..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_7.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_7")
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_7_rgb.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_7_rgb.py
deleted file mode 100644
index 82b419f0..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_7_rgb.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_7", RGB=True)
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_8.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_8.py
deleted file mode 100644
index d4cdc774..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_8.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_8")
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_8_rgb.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_8_rgb.py
deleted file mode 100644
index 8d008ce3..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_8_rgb.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_8", RGB=True)
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_9.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_9.py
deleted file mode 100644
index f46b3549..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_9.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_9")
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/fold_9_rgb.py b/src/ptbench/configs/datasets/tbx11k_simplified/fold_9_rgb.py
deleted file mode 100644
index 73507723..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/fold_9_rgb.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("fold_9", RGB=True)
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/rgb.py b/src/ptbench/configs/datasets/tbx11k_simplified/rgb.py
deleted file mode 100644
index e22dff69..00000000
--- a/src/ptbench/configs/datasets/tbx11k_simplified/rgb.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-"""TBX11k simplified dataset for TB detection (default protocol)
-
-* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
-* "validation", 21.6% for "test"
-* This split only consists of healthy and active TB samples
-* "Latent TB" or "sick & non-TB" samples are not included in this configuration
-* This configuration resolution: 512 x 512 (default)
-* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
-"""
-
-from . import _maker
-
-dataset = _maker("default", RGB=True)
diff --git a/src/ptbench/data/tbx11k_simplified/__init__.py b/src/ptbench/data/tbx11k_simplified/__init__.py
index dd2be35d..3080b63a 100644
--- a/src/ptbench/data/tbx11k_simplified/__init__.py
+++ b/src/ptbench/data/tbx11k_simplified/__init__.py
@@ -76,15 +76,36 @@ def _loader_bbox(context, sample):
return make_delayed_bbox(sample, _raw_data_loader_bbox)
-dataset = JSONDataset(
+json_dataset = JSONDataset(
protocols=_protocols,
fieldnames=("data", "label"),
loader=_loader,
)
-dataset_with_bboxes = JSONDataset(
+json_dataset_with_bboxes = JSONDataset(
protocols=_protocols,
fieldnames=("data", "label", "bboxes"),
loader=_loader_bbox,
)
"""TBX11K simplified dataset object."""
+
+
+def _maker(protocol, RGB=False):
+ from torchvision import transforms
+
+ from .. import make_dataset
+ from ..transforms import ElasticDeformation
+
+ post_transforms = []
+ if RGB:
+ post_transforms = [
+ transforms.Lambda(lambda x: x.convert("RGB")),
+ transforms.ToTensor(),
+ ]
+
+ return make_dataset(
+ [json_dataset.subsets(protocol)],
+ [],
+ [ElasticDeformation(p=0.8)],
+ post_transforms,
+ )
diff --git a/src/ptbench/data/tbx11k_simplified/default.py b/src/ptbench/data/tbx11k_simplified/default.py
new file mode 100644
index 00000000..945449b3
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/default.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class DefaultModule(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("default")
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = DefaultModule
diff --git a/src/ptbench/data/tbx11k_simplified/fold_0.py b/src/ptbench/data/tbx11k_simplified/fold_0.py
new file mode 100644
index 00000000..84fa352c
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_0.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_0")
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_0_rgb.py b/src/ptbench/data/tbx11k_simplified/fold_0_rgb.py
new file mode 100644
index 00000000..349b226e
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_0_rgb.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_0", RGB=True)
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_1.py b/src/ptbench/data/tbx11k_simplified/fold_1.py
new file mode 100644
index 00000000..8356e523
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_1.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_1")
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_1_rgb.py b/src/ptbench/data/tbx11k_simplified/fold_1_rgb.py
new file mode 100644
index 00000000..439dff09
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_1_rgb.py
@@ -0,0 +1,50 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_1", RGB=True)
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_2.py b/src/ptbench/data/tbx11k_simplified/fold_2.py
new file mode 100644
index 00000000..9231a256
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_2.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_2")
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_2_rgb.py b/src/ptbench/data/tbx11k_simplified/fold_2_rgb.py
new file mode 100644
index 00000000..60a6322f
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_2_rgb.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_2", RGB=True)
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_3.py b/src/ptbench/data/tbx11k_simplified/fold_3.py
new file mode 100644
index 00000000..13817463
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_3.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_3")
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_3_rgb.py b/src/ptbench/data/tbx11k_simplified/fold_3_rgb.py
new file mode 100644
index 00000000..3a2975ed
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_3_rgb.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_3", RGB=True)
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_4.py b/src/ptbench/data/tbx11k_simplified/fold_4.py
new file mode 100644
index 00000000..15825b31
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_4.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_4")
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_4_rgb.py b/src/ptbench/data/tbx11k_simplified/fold_4_rgb.py
new file mode 100644
index 00000000..021aa7a7
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_4_rgb.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_4", RGB=True)
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_5.py b/src/ptbench/data/tbx11k_simplified/fold_5.py
new file mode 100644
index 00000000..a090f398
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_5.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_5")
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_5_rgb.py b/src/ptbench/data/tbx11k_simplified/fold_5_rgb.py
new file mode 100644
index 00000000..07e4209e
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_5_rgb.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_5", RGB=True)
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_6.py b/src/ptbench/data/tbx11k_simplified/fold_6.py
new file mode 100644
index 00000000..edfc4004
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_6.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_6")
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_6_rgb.py b/src/ptbench/data/tbx11k_simplified/fold_6_rgb.py
new file mode 100644
index 00000000..e4e2b1fc
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_6_rgb.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_6", RGB=True)
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_7.py b/src/ptbench/data/tbx11k_simplified/fold_7.py
new file mode 100644
index 00000000..08997127
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_7.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_7")
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_7_rgb.py b/src/ptbench/data/tbx11k_simplified/fold_7_rgb.py
new file mode 100644
index 00000000..0412530e
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_7_rgb.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_7", RGB=True)
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_8.py b/src/ptbench/data/tbx11k_simplified/fold_8.py
new file mode 100644
index 00000000..9bb46f96
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_8.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_8")
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_8_rgb.py b/src/ptbench/data/tbx11k_simplified/fold_8_rgb.py
new file mode 100644
index 00000000..c88b51d9
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_8_rgb.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_8", RGB=True)
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_9.py b/src/ptbench/data/tbx11k_simplified/fold_9.py
new file mode 100644
index 00000000..db5abd74
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_9.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_9")
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/fold_9_rgb.py b/src/ptbench/data/tbx11k_simplified/fold_9_rgb.py
new file mode 100644
index 00000000..20cb6d49
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/fold_9_rgb.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class Fold0Module(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("fold_9", RGB=True)
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = Fold0Module
diff --git a/src/ptbench/data/tbx11k_simplified/rgb.py b/src/ptbench/data/tbx11k_simplified/rgb.py
new file mode 100644
index 00000000..4a0b72fb
--- /dev/null
+++ b/src/ptbench/data/tbx11k_simplified/rgb.py
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""TBX11k simplified dataset for TB detection (default protocol)
+
+* Split reference: first 62.5% of TB and healthy CXR for "train" 15.9% for
+* "validation", 21.6% for "test"
+* This split only consists of healthy and active TB samples
+* "Latent TB" or "sick & non-TB" samples are not included in this configuration
+* This configuration resolution: 512 x 512 (default)
+* See :py:mod:`ptbench.data.tbx11k_simplified` for dataset details
+"""
+
+from clapper.logging import setup
+
+from .. import return_subsets
+from ..base_datamodule import BaseDataModule
+from . import _maker
+
+logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+
+
+class DefaultModule(BaseDataModule):
+ def __init__(
+ self,
+ train_batch_size=1,
+ predict_batch_size=1,
+ drop_incomplete_batch=False,
+ multiproc_kwargs=None,
+ ):
+ super().__init__(
+ train_batch_size=train_batch_size,
+ predict_batch_size=predict_batch_size,
+ drop_incomplete_batch=drop_incomplete_batch,
+ multiproc_kwargs=multiproc_kwargs,
+ )
+
+ def setup(self, stage: str):
+ self.dataset = _maker("default", RGB=True)
+ (
+ self.train_dataset,
+ self.validation_dataset,
+ self.extra_validation_datasets,
+ self.predict_dataset,
+ ) = return_subsets(self.dataset)
+
+
+datamodule = DefaultModule
--
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