From a139fcc3118d3ce02f1f0645ee9b2b3e67f9830d Mon Sep 17 00:00:00 2001
From: "ogueler@idiap.ch" <ogueler@vws110.idiap.ch>
Date: Mon, 3 Apr 2023 02:59:53 +0200
Subject: [PATCH] updated documentation with tbx11k

---
 doc/api.rst        |  2 ++
 doc/config.rst     |  3 +++
 doc/install.rst    | 37 +++++++++++++++++++++++++++++++++++++
 doc/links.rst      |  2 ++
 doc/references.rst | 10 ++++++++++
 5 files changed, 54 insertions(+)

diff --git a/doc/api.rst b/doc/api.rst
index 73143562..d73898d8 100644
--- a/doc/api.rst
+++ b/doc/api.rst
@@ -53,6 +53,8 @@ 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.api.models:
diff --git a/doc/config.rst b/doc/config.rst
index af8fa995..cd45c907 100644
--- a/doc/config.rst
+++ b/doc/config.rst
@@ -68,6 +68,9 @@ 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.folds:
diff --git a/doc/install.rst b/doc/install.rst
index 0ec7ad7d..f15aee34 100644
--- a/doc/install.rst
+++ b/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
@@ -143,6 +144,42 @@ In addition to the splits presented in the following table, 10 folds
      - 52
 
 
+.. _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.tb+signs:
 
 Tuberculosis + radiological findings dataset
diff --git a/doc/links.rst b/doc/links.rst
index df1ef5ea..92ecafd5 100644
--- a/doc/links.rst
+++ b/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
diff --git a/doc/references.rst b/doc/references.rst
index 4897ee5b..037aa8d8 100644
--- a/doc/references.rst
+++ b/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.
-- 
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