mednet.data.segment.jsrt¶
Japanese Society of Radiological Technology dataset for lung segmentation.
The database includes 154 nodule and 93 non-nodule images. It contains a total of 247 resolution of 2048 x 2048 pixels, issued from original digitized Radiographies (laser scanner). One set of ground-truth lung annotations is available.
Important
Raw data organization
The JSRT base datadir, which you should configure following the Setup instructions, must contain at least the following directories:
All247images/
(directory containing the CXR images, in raw format)scratch/
(must contain masks downloaded from JSRT-Annotations)
Data specifications:
Raw data input (on disk):
Original images encoded in proprietary 12-bit RAW format. A PNG-converted set of images is provided at JSRT-Kaggle for your reference. Input resolution is 2048 x 2048 pixels.
Masks: encoded as GIF files with separate portions for left and right lungs, with a resolution of 1024 x 1024 pixels
Total samples: 247
Output sample:
Image: Load raw image from folder
All247images/
usingnumpy.fromfile()
, then applies a simple histogram equalization to the 8-bit representation of the image, to obtain something along the lines of the PNG (unofficial) version distributed at JSRT-Kaggle. Output images have a size of 1024 x 1024 pixels, achieved by resizing the original input with bilinear interpolation.Labels for each of the lungs are read from the provided GIF files and merged into a single output image.
The default
split contains 172 samples for training, 25 for validation and
50 for test.
This module contains the base declaration of common data modules and raw-data loaders for this database. All configured splits inherit from this definition.
Module Attributes
Pythonic name to refer to this database. |
|
Key to search for in the configuration file for the root directory of this database. |
Classes
|
Japanese Society of Radiological Technology dataset for lung segmentation. |
A specialized raw-data-loader for the jsrt dataset. |
- mednet.data.segment.jsrt.DATABASE_SLUG = 'jsrt'¶
Pythonic name to refer to this database.
- mednet.data.segment.jsrt.CONFIGURATION_KEY_DATADIR = 'datadir.jsrt'¶
Key to search for in the configuration file for the root directory of this database.
- class mednet.data.segment.jsrt.RawDataLoader[source]¶
Bases:
RawDataLoader
A specialized raw-data-loader for the jsrt dataset.
- load_pil_raw_12bit_jsrt(path)[source]¶
Load a raw 16-bit sample data.
This method was designed to handle the raw images from the JSRT dataset. It reads the data file and applies a simple histogram equalization to the 8-bit representation of the image to obtain something along the lines of the PNG (unofficial) version distributed at JSRT-Kaggle.
- class mednet.data.segment.jsrt.DataModule(split_path)[source]¶
Bases:
CachingDataModule
Japanese Society of Radiological Technology dataset for lung segmentation.
- Parameters:
split_path (
Path
|Traversable
) – Path or traversable (resource) with the JSON split description to load.