mednet.data.segment.iostar

IOSTAR (training set) for vessel and optic-disc segmentation.

The IOSTAR vessel segmentation dataset includes 30 images with a resolution of 1024×1024 pixels. All the vessels in this dataset are annotated by a group of experts working in the field of retinal image analysis. Additionally the dataset includes annotations for the optic disc and the artery/vein ratio.

  • Reference: [ZDB+16]

  • Original resolution (height x width): 1024×1024

  • Split reference: [MCG+17]

  • Protocol vessel:

    • Training samples: 20 (including labels and masks)

    • Test samples: 10 (including labels and masks)

  • Protocol optic-disc:

    • Training samples: 20 (including labels and masks)

    • Test samples: 10 (including labels and masks)

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

DATABASE_SLUG

Pythonic name to refer to this database.

CONFIGURATION_KEY_DATADIR

Key to search for in the configuration file for the root directory of this database.

Classes

DataModule(split_path)

IOSTAR (training set) for vessel and optic-disc segmentation.

RawDataLoader()

A specialized raw-data-loader for the iostar dataset.
mednet.data.segment.iostar.DATABASE_SLUG = 'iostar'

Pythonic name to refer to this database.

mednet.data.segment.iostar.CONFIGURATION_KEY_DATADIR = 'datadir.iostar'

Key to search for in the configuration file for the root directory of this database.

class mednet.data.segment.iostar.RawDataLoader[source]

Bases: RawDataLoader

A specialized raw-data-loader for the iostar dataset.

datadir: Path

This variable contains the base directory where the database raw data is stored.

sample(sample)[source]

Load a single image sample from the disk.

Parameters:

sample (Any) – A tuple containing the path suffix, within the dataset root folder, where to find the image to be loaded, and an integer, representing the sample label.

Return type:

Mapping[str, Any]

Returns:

The sample representation.

target(sample)[source]

Load only sample target from its raw representation.

Parameters:

sample (Any) – A tuple containing the path suffix, within the dataset root folder, where to find the image to be loaded, and an integer, representing the sample target.

Return type:

Tensor

Returns:

The label corresponding to the specified sample, encapsulated as a torch float tensor.

class mednet.data.segment.iostar.DataModule(split_path)[source]

Bases: CachingDataModule

IOSTAR (training set) for vessel and optic-disc segmentation.

Parameters:

split_path (Path | Traversable) – Path or traversable (resource) with the JSON split description to load.