Source code for torchio.datasets.bite

import abc
from pathlib import Path
from typing import Dict
from typing import Optional

from .. import Image
from .. import LabelMap
from .. import ScalarImage
from .. import Subject
from .. import SubjectsDataset
from ..download import download_and_extract_archive
from ..transforms import Transform
from ..typing import TypePath


class BITE(SubjectsDataset, abc.ABC):
    base_url = 'http://www.bic.mni.mcgill.ca/uploads/Services/'

    def __init__(
        self,
        root: TypePath,
        transform: Optional[Transform] = None,
        download: bool = False,
        **kwargs,
    ):
        root = Path(root).expanduser().absolute()
        if download:
            self._download(root)
        subjects_list = self._get_subjects_list(root)
        self.kwargs = kwargs
        super().__init__(subjects_list, transform=transform, **kwargs)

    @abc.abstractmethod
    def _download(self, root: Path):
        raise NotImplementedError

    @abc.abstractmethod
    def _get_subjects_list(self, root: Path):
        raise NotImplementedError




class BITE3(BITE):
    """Pre- and post-resection MR images in BITE.

    *The goal of BITE is to share in vivo medical images of patients wtith
    brain tumors to facilitate the development and validation of new image
    processing algorithms.*

    Please check the `BITE website`_ for more information and
    acknowledgments instructions.

    .. _BITE website: http://nist.mni.mcgill.ca/bite-brain-images-of-tumors-for-evaluation-database/

    Args:
        root: Root directory to which the dataset will be downloaded.
        transform: An instance of
            :class:`~torchio.transforms.transform.Transform`.
        download: If set to ``True``, will download the data into :attr:`root`.
    """  # noqa: B950

    dirname = 'group3'

    def _download(self, root: Path):
        if (root / self.dirname).is_dir():
            return
        root.mkdir(exist_ok=True, parents=True)
        filename = f'{self.dirname}.tar.gz'
        url = self.base_url + filename
        download_and_extract_archive(
            url,
            download_root=root,
            md5='e415b63887c40b727c45552614b44634',
        )
        (root / filename).unlink()  # cleanup

    def _get_subjects_list(self, root: Path):
        subjects_dir = root / self.dirname
        subjects = []
        for i in range(1, 15):
            if i == 13:
                continue  # no MRI for this subject
            subject_id = f'{i:02d}'
            subject_dir = subjects_dir / subject_id
            preop_path = subject_dir / f'{subject_id}_preop_mri.mnc'
            postop_path = subject_dir / f'{subject_id}_postop_mri.mnc'
            images_dict: Dict[str, Image] = {}
            images_dict['preop'] = ScalarImage(preop_path)
            images_dict['postop'] = ScalarImage(postop_path)
            for fp in subject_dir.glob('*tumor*'):
                images_dict[fp.stem[3:]] = LabelMap(fp)
            subject = Subject(images_dict)
            subjects.append(subject)
        return subjects