From dd6c081c0e07ab5799e860e9450b8baf0debd5a4 Mon Sep 17 00:00:00 2001
From: "ogueler@idiap.ch" <ogueler@vws110.idiap.ch>
Date: Mon, 3 Apr 2023 03:09:41 +0200
Subject: [PATCH] cleanup and formatting fix
---
doc/install.rst | 2 +-
doc/references.rst | 4 ++--
.../datasets/tbx11k_simplified/__init__.py | 6 ++---
.../data/tbx11k_simplified/__init__.py | 24 ++++++++++---------
.../data/tbx11k_simplified_RS/__init__.py | 24 +++++++++----------
src/ptbench/data/transforms.py | 22 ++++++++++++-----
6 files changed, 46 insertions(+), 36 deletions(-)
diff --git a/doc/install.rst b/doc/install.rst
index f15aee34..940f103a 100644
--- a/doc/install.rst
+++ b/doc/install.rst
@@ -150,7 +150,7 @@ 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
+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.
diff --git a/doc/references.rst b/doc/references.rst
index 037aa8d8..5a349fa9 100644
--- a/doc/references.rst
+++ b/doc/references.rst
@@ -60,12 +60,12 @@
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.-*,
+.. [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.-*,
+.. [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.
diff --git a/src/ptbench/configs/datasets/tbx11k_simplified/__init__.py b/src/ptbench/configs/datasets/tbx11k_simplified/__init__.py
index 643625e0..277fd087 100644
--- a/src/ptbench/configs/datasets/tbx11k_simplified/__init__.py
+++ b/src/ptbench/configs/datasets/tbx11k_simplified/__init__.py
@@ -7,7 +7,7 @@ def _maker(protocol, RGB=False):
from torchvision import transforms
from ....data.tbx11k_simplified import dataset as raw
- from ....data.transforms import ElasticDeformation, RemoveBlackBorders, RGBtoGreyscale8bit
+ from ....data.transforms import ElasticDeformation, RGBtoGreyscale8bit
from .. import make_dataset as mk
post_transforms = []
@@ -19,9 +19,7 @@ def _maker(protocol, RGB=False):
return mk(
[raw.subsets(protocol)],
- [
- RGBtoGreyscale8bit()
- ],
+ [RGBtoGreyscale8bit()],
[ElasticDeformation(p=0.8)],
post_transforms,
)
diff --git a/src/ptbench/data/tbx11k_simplified/__init__.py b/src/ptbench/data/tbx11k_simplified/__init__.py
index e21d67fc..aa5abf05 100644
--- a/src/ptbench/data/tbx11k_simplified/__init__.py
+++ b/src/ptbench/data/tbx11k_simplified/__init__.py
@@ -32,19 +32,21 @@ from ..loader import load_pil_baw, make_delayed
_protocols = [
importlib.resources.files(__name__).joinpath("default.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_0.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_1.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_2.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_3.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_4.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_5.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_6.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_7.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_8.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_9.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_0.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_1.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_2.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_3.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_4.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_5.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_6.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_7.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_8.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_9.json.bz2"),
]
-_datadir = load_rc().get("datadir.tbx11k_simplified", os.path.realpath(os.curdir))
+_datadir = load_rc().get(
+ "datadir.tbx11k_simplified", os.path.realpath(os.curdir)
+)
def _raw_data_loader(sample):
diff --git a/src/ptbench/data/tbx11k_simplified_RS/__init__.py b/src/ptbench/data/tbx11k_simplified_RS/__init__.py
index 956ac0a4..8e782d45 100644
--- a/src/ptbench/data/tbx11k_simplified_RS/__init__.py
+++ b/src/ptbench/data/tbx11k_simplified_RS/__init__.py
@@ -2,8 +2,8 @@
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Extended TBX11K simplified dataset for computer-aided diagnosis
-(extended with DensenetRS predictions)
+"""Extended TBX11K simplified dataset for computer-aided diagnosis (extended
+with DensenetRS predictions)
The TBX11K database has been established to foster research
in computer-aided diagnosis of pulmonary diseases with a special
@@ -31,16 +31,16 @@ from ..loader import make_delayed
_protocols = [
importlib.resources.files(__name__).joinpath("default.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_0.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_1.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_2.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_3.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_4.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_5.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_6.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_7.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_8.json.bz2"),
- #importlib.resources.files(__name__).joinpath("fold_9.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_0.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_1.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_2.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_3.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_4.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_5.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_6.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_7.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_8.json.bz2"),
+ # importlib.resources.files(__name__).joinpath("fold_9.json.bz2"),
]
diff --git a/src/ptbench/data/transforms.py b/src/ptbench/data/transforms.py
index 993839df..031bde89 100644
--- a/src/ptbench/data/transforms.py
+++ b/src/ptbench/data/transforms.py
@@ -41,15 +41,16 @@ class SingleAutoLevel16to8:
).astype("uint8"),
).convert("L")
+
class RGBtoGreyscale8bit:
"""Converts a 24-bit RGB image to an 8-bit greyscale representation.
-
+
This transform assumes that the input image is RGB with 24 bits.
Converts the RGB image to a greyscale image using the well-known formula:
Y = 0.299 * R + 0.587 * G + 0.114 * B
This formula is based on the relative luminance of the RGB channels in the sRGB color space
-
+
consider such a range should be mapped to the [0,255] range of the
destination image.
"""
@@ -57,14 +58,23 @@ class RGBtoGreyscale8bit:
def __call__(self, img):
# Use the formula to convert the RGB image to a greyscale image
img_array = numpy.array(img).astype(float)
- grey_array = 0.299 * img_array[:, :, 0] + 0.587 * img_array[:, :, 1] + 0.114 * img_array[:, :, 2]
-
+ grey_array = (
+ 0.299 * img_array[:, :, 0]
+ + 0.587 * img_array[:, :, 1]
+ + 0.114 * img_array[:, :, 2]
+ )
+
# Normalize the greyscale image to the range [0, 255] and convert it to uint8
- grey_array = numpy.round(255.0 * (grey_array - grey_array.min()) / (grey_array.max() - grey_array.min())).astype('uint8')
-
+ grey_array = numpy.round(
+ 255.0
+ * (grey_array - grey_array.min())
+ / (grey_array.max() - grey_array.min())
+ ).astype("uint8")
+
# Create a new greyscale PIL image from the normalized array
return PIL.Image.fromarray(grey_array).convert("L")
+
class RemoveBlackBorders:
"""Remove black borders of CXR."""
--
GitLab