From 17cb2882a16a96c4d0544bedec00ea5ed5672aa0 Mon Sep 17 00:00:00 2001
From: Andre Anjos <andre.dos.anjos@gmail.com>
Date: Wed, 2 Aug 2023 10:21:29 +0200
Subject: [PATCH] [data] Improve datamodule documentation across different
databases
---
src/ptbench/data/indian/datamodule.py | 10 +++++---
src/ptbench/data/montgomery/datamodule.py | 6 +++--
src/ptbench/data/nih_cxr14/datamodule.py | 31 ++++++++++++++++++-----
src/ptbench/data/shenzhen/datamodule.py | 11 ++++----
src/ptbench/data/tbx11k/datamodule.py | 15 ++++++-----
5 files changed, 49 insertions(+), 24 deletions(-)
diff --git a/src/ptbench/data/indian/datamodule.py b/src/ptbench/data/indian/datamodule.py
index 34fb4b5a..6316f264 100644
--- a/src/ptbench/data/indian/datamodule.py
+++ b/src/ptbench/data/indian/datamodule.py
@@ -25,14 +25,14 @@ class DataModule(CachingDataModule):
in computer-aided diagnosis of pulmonary diseases with a special
focus on pulmonary tuberculosis (TB).
- * Original resolution (height x width or width x height): more than 1024 x 1024
+ * Original images PNG, 8-bit grayscale, 1024 x 1024 pixels
* Split reference: [INDIAN-2013]_ with 20% of train set for the validation set
Data specifications:
* Raw data input (on disk):
- * PNG images (grayscale, encoded as RGB images with "inverted" grayscale scale)
+ * PNG RGB 8-bit depth images with "inverted" grayscale scale
* Variable width and height
* Output image:
@@ -41,12 +41,14 @@ class DataModule(CachingDataModule):
* Load raw PNG with :py:mod:`PIL`
* Remove black borders
+ * Convert to torch tensor
* Torch center cropping to get square image
* Final specifications:
- * Grayscale, encoded as a single plane image, 8 bits
- * Square, with varying resolutions, depending on the input image
+ * Grayscale, encoded as a single plane tensor, 32-bit floats,
+ square, with varying resolutions, depending on the input raw image
+ * Labels: 0 (healthy), 1 (active tuberculosis)
"""
def __init__(self, split_filename: str):
diff --git a/src/ptbench/data/montgomery/datamodule.py b/src/ptbench/data/montgomery/datamodule.py
index e04efebd..12ead6e8 100644
--- a/src/ptbench/data/montgomery/datamodule.py
+++ b/src/ptbench/data/montgomery/datamodule.py
@@ -120,12 +120,14 @@ class DataModule(CachingDataModule):
* Load raw PNG with :py:mod:`PIL`
* Remove black borders
+ * Convert to torch tensor
* Torch center cropping to get square image
* Final specifications
- * Grayscale, encoded as a single plane image, 8 bits
- * Square (4020x4020 px)
+ * Grayscale, encoded as a single plane tensor, 32-bit floats,
+ square at 4020 x 4020 pixels
+ * Labels: 0 (healthy), 1 (active tuberculosis)
"""
def __init__(self, split_filename: str):
diff --git a/src/ptbench/data/nih_cxr14/datamodule.py b/src/ptbench/data/nih_cxr14/datamodule.py
index 54526409..b5bf77a2 100644
--- a/src/ptbench/data/nih_cxr14/datamodule.py
+++ b/src/ptbench/data/nih_cxr14/datamodule.py
@@ -127,7 +127,11 @@ class DataModule(CachingDataModule):
CheXNeXt study.
* Reference: [NIH-CXR14-2017]_
- * Original resolution (height x width): 1024 x 1024
+ * Raw data input (on disk):
+
+ * PNG RGB 8-bit depth images
+ * Resolution: 1024 x 1024 pixels
+
* Labels: [CHEXNEXT-2018]_
* Split reference: [CHEXNEXT-2018]_
* Protocol ``default``:
@@ -141,11 +145,26 @@ class DataModule(CachingDataModule):
* Transforms:
* Load raw PNG with :py:mod:`PIL`
-
- * Final specifications
-
- * RGB, encoded as a 3-plane image, 8 bits
- * Square (1024x1024 px)
+ * Convert to torch tensor
+
+ * Final specifications:
+
+ * RGB, encoded as a 3-plane tensor, 32-bit floats, square (1024x1024 px)
+ * Labels in order:
+ * cardiomegaly
+ * emphysema
+ * effusion
+ * hernia
+ * infiltration
+ * mass
+ * nodule
+ * atelectasis
+ * pneumothorax
+ * pleural thickening
+ * pneumonia
+ * fibrosis
+ * edema
+ * consolidation
"""
def __init__(self, split_filename: str):
diff --git a/src/ptbench/data/shenzhen/datamodule.py b/src/ptbench/data/shenzhen/datamodule.py
index 8307396d..7cf1833b 100644
--- a/src/ptbench/data/shenzhen/datamodule.py
+++ b/src/ptbench/data/shenzhen/datamodule.py
@@ -112,14 +112,14 @@ class DataModule(CachingDataModule):
Philips DR Digital Diagnose systems.
* Database reference: [MONTGOMERY-SHENZHEN-2014]_
- * Original resolution (height x width or width x height): 3000 x 3000 or less
Data specifications:
* Raw data input (on disk):
- * PNG images (grayscale, encoded as RGB images with "inverted" grayscale scale)
- * Variable width and height
+ * PNG 8-bit RGB images (grayscale, but encoded as RGB images with
+ "inverted" grayscale scale requiring special treatment).
+ * Variable width and height of 3000 x 3000 pixels or less
* Output image:
@@ -131,8 +131,9 @@ class DataModule(CachingDataModule):
* Final specifications:
- * Grayscale, encoded as a single plane image, 8 bits
- * Square, with varying resolutions, depending on the input image
+ * Grayscale, encoded as a single plane tensor, 32-bit floats,
+ square with varying resolutions, depending on the input image
+ * Labels: 0 (healthy), 1 (active tuberculosis)
"""
def __init__(self, split_filename: str):
diff --git a/src/ptbench/data/tbx11k/datamodule.py b/src/ptbench/data/tbx11k/datamodule.py
index 3420b6de..45785ddb 100644
--- a/src/ptbench/data/tbx11k/datamodule.py
+++ b/src/ptbench/data/tbx11k/datamodule.py
@@ -246,17 +246,17 @@ class DataModule(CachingDataModule):
active TB cases (total samples = 8369):
- ``train`` dataset samples:
- - Healthy: 4864
+ - Healthy, Sick or Latent TB: 4864
- Active TB only: 377
- Total: 5241
- ``validation`` dataset samples:
+ - Healthy, Sick or Latent TB: 1239
- Active TB only: 96
- - Healthy: 1239
- Total: 1335
- ``test`` dataset samples:
- - Healthy: 1636
+ - Healthy, Sick or Latent TB: 1636
- Active TB only: 157
- Total: 1793
@@ -265,8 +265,7 @@ class DataModule(CachingDataModule):
* Raw data input (on disk):
- * PNG images 8 bits RGB
- * Resolution: 512x512 pixels
+ * PNG images 8 bits RGB, 512 x 512 pixels
* Output image:
@@ -276,8 +275,10 @@ class DataModule(CachingDataModule):
* Final specifications:
- * RGB, encoded as a 3-plane image, 8 bits
- * Square (512x512 px)
+ * RGB, encoded as a 3-plane tensor using 32-bit floats, square
+ (512x512 pixels)
+ * Labels: 0 (healthy, latent tb or sick but no tb depending on the
+ protocol), 1 (active tuberculosis)
"""
def __init__(self, split_filename: str):
--
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