__init__.py

#!/usr/bin/env python
# coding=utf-8

"""REFUGE (training set) for Optic Disc Segmentation

The dataset consists of 1200 color fundus photographs, created for a MICCAI
challenge. The goal of the challenge is to evaluate and compare automated
algorithms for glaucoma detection and optic disc/cup segmentation on a common
dataset of retinal fundus images.

* Reference (including train/dev/test split): [REFUGE-2018]_
* Protocols ``optic-disc`` and ``cup``:

  * Training samples:

    * 400
    * includes optic-disc and cup labels
    * includes label: glaucomatous and non-glaucomatous
    * original resolution: 2056 x 2124

  * Validation samples:

    * 400
    * includes optic-disc and cup labels
    * original resolution: 1634 x 1634

  * Test samples:

    * 400
    * includes optic-disc and cup labels
    * includes label: glaucomatous and non-glaucomatous
    * original resolution:
"""

import os
import pkg_resources

import bob.extension

from ..jsondataset import JSONDataset
from ..loader import load_pil_rgb

_protocols = [
        pkg_resources.resource_filename(__name__, "optic-disc.json"),
        pkg_resources.resource_filename(__name__, "optic-cup.json"),
        ]

_root_path = bob.extension.rc.get('bob.ip.binseg.refuge.datadir',
        os.path.realpath(os.curdir))

def _loader(context, sample):
    retval = dict(
            data=load_pil_rgb(sample["data"]),
            label=load_pil_rgb(sample["label"]),
            )

    if context["subset"] == "train":
        # adds binary metadata for glaucoma/non-glaucoma patients
        retval["glaucoma"] = os.path.basename(sample["label"]).startswith("g")
    elif context["subset"] == "test":
        retval["glaucoma"] = sample["label"].split(os.sep)[-2] == "G"
    elif context["subset"] == "validation":
        pass
    else:
        raise RuntimeError(f"Unknown subset {context['subset']}")

    # optic disc is drawn with gray == 128 and includes the cup, drawn with
    # black == 0.  The rest is white == 255.
    if context["protocol"] == "optic-disc":
        retval["label"] = retval["label"].convert("L")
        retval["label"] = retval["label"].point(lambda p: p<=150, mode="1")
    elif context["protocol"] == "optic-cup":
        retval["label"] = retval["label"].convert("L")
        retval["label"] = retval["label"].point(lambda p: p<=100, mode="1")
    else:
        raise RuntimeError(f"Unknown protocol {context['protocol']}")

    return retval

dataset = JSONDataset(protocols=_protocols, root_path=_root_path, loader=_loader)
"""REFUGE dataset object"""