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Commit 9b297231 authored by ogueler@idiap.ch's avatar ogueler@idiap.ch
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removed unusable tbx11k custom split 3

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2 merge requests!5Tbx11k,!4Moved code to lightning
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# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
"""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
focus on tuberculosis (aTB). The dataset was specifically
designed to be used with CNNs. It contains 11,000 chest X-ray
images, each of a unique patient. They were labeled by expert
radiologists with 5 - 10+ years of experience. Possible labels
are: "healthy", "active TB", "latent TB", and "sick & non-tb".
The version of the dataset used in this benchmark is a simplified.
* Reference: [TBX11K-SIMPLIFIED-2020]_
* Original (released) resolution (height x width or width x height): 512 x 512
* Split reference: none
* Protocol ``default``:
* Training samples: 62.6% of CXR (including labels)
* Validation samples: 16% of CXR (including labels)
* Test samples: 21.4% of CXR (including labels)
"""
import importlib.resources
from ..dataset import JSONDataset
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"),
]
def _raw_data_loader(sample):
return dict(data=sample["data"], label=sample["label"])
def _loader(context, sample):
# "context" is ignored in this case - database is homogeneous
# we returned delayed samples to avoid loading all images at once
return make_delayed(sample, _raw_data_loader, key=sample["filename"])
dataset = JSONDataset(
protocols=_protocols,
fieldnames=("filename", "label", "data"),
loader=_loader,
)
"""Extended TBX11K simplified dataset object."""
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