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ogueler@idiap.ch authoredogueler@idiap.ch authored
Installation
We support two installation modes, through pip_, or mamba_ (conda).
Setup
A configuration file may be useful to setup global options that should be often
reused. The location of the configuration file depends on the value of the
environment variable $XDG_CONFIG_HOME
, but defaults to
~/.config/ptbench.toml
. You may edit this file using your preferred
editor.
Here is an example configuration file that may be useful as a starting point:
[datadir]
indian = "/Users/myself/dbs/tbxpredict"
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
Tip
To get a list of valid data directories that can be configured, execute:
ptbench dataset list
You must procure and download datasets by yourself. The raw data is not included in this package as we are not authorised to redistribute it.
To check whether the downloaded version is consistent with the structure that is expected by this package, run:
ptbench dataset check montgomery
Supported Datasets
Here is a list of currently supported datasets in this package, alongside notable properties. Each dataset name is linked to the location where raw data can be downloaded. The list of images in each split is available in the source code.
Tuberculosis datasets
The following datasets contain only the tuberculosis final diagnosis (0 or 1). In addition to the splits presented in the following table, 10 folds (for cross-validation) randomly generated are available for these datasets.
Dataset | Reference | H x W | Samples | Training | Validation | Test |
Montgomery_ | [MONTGOMERY-SHENZHEN-2014]_ | 4020 x 4892 | 138 | 88 | 22 | 28 |
Shenzhen_ | [MONTGOMERY-SHENZHEN-2014]_ | Varying | 662 | 422 | 107 | 133 |
Indian_ | [INDIAN-2013]_ | Varying | 155 | 83 | 20 | 52 |
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.
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 |
Tuberculosis + radiological findings dataset
The following dataset contains both the tuberculosis final diagnosis (0 or 1) and radiological findings.
Dataset | Reference | H x W | Samples | Train | Test |
PadChest_ | [PADCHEST-2019]_ | Varying | 160'861 | 160'861 | 0 |
Radiological findings datasets
The following dataset contains only the radiological findings without any information about tuberculosis.
Note
NIH CXR14 labels for training and validation sets are the relabeled versions done by the author of the CheXNeXt study [CHEXNEXT-2018]_.
Dataset | Reference | H x W | Samples | Training | Validation | Test |
NIH_CXR14_re_ | [NIH-CXR14-2017]_ | 1024 x 1024 | 109'041 | 98'637 | 6'350 | 4'054 |
HIV-Tuberculosis datasets
The following datasets contain only the tuberculosis final diagnosis (0 or 1) and come from HIV infected patients. 10 folds (for cross-validation) randomly generated are available for these datasets.
Please contact the authors of these datasets to have access to the data.
Dataset | Reference | H x W | Samples |
TB POC | [TB-POC-2018]_ | 2048 x 2500 | 407 |
HIV TB | [HIV-TB-2019]_ | 2048 x 2500 | 243 |