Source code for torchio.datasets.mni.pediatric

import urllib.parse

from ...utils import compress
from ... import ScalarImage, LabelMap
from ...download import download_and_extract_archive
from .mni import SubjectMNI


SUPPORTED_YEARS = (
    (4.5, 18.5),
    (4.5, 8.5),
    (7, 11),
    (7.5, 13.5),
    (10, 14),
    (13, 18.5),
)


def format_age(n):
    integer = int(n)
    decimal = int(10 * (n - integer))
    return f'{integer:02d}.{decimal}'


[docs]class Pediatric(SubjectMNI): """MNI pediatric atlases. See `the MNI website <http://nist.mni.mcgill.ca/?p=974>`_ for more information. .. image:: http://nist.mni.mcgill.ca/wp-content/uploads/2016/04/nihpd_asym_all_sm.jpg :alt: Pediatric MNI template Arguments: years: Tuple of 2 ages. Possible values are: ``(4.5, 18.5)``, ``(4.5, 8.5)``, ``(7, 11)``, ``(7.5, 13.5)``, ``(10, 14)`` and ``(13, 18.5)``. symmetric: If ``True``, the left-right symmetric templates will be used. Else, the asymmetric (natural) templates will be used. """ # noqa: E501 def __init__(self, years, symmetric=False): self.url_dir = 'http://www.bic.mni.mcgill.ca/~vfonov/nihpd/obj1/' sym_string = 'sym' if symmetric else 'asym' if not isinstance(years, tuple) or years not in SUPPORTED_YEARS: message = f'Years must be a tuple in {SUPPORTED_YEARS}' raise ValueError(message) a, b = years self.file_id = f'{sym_string}_{format_age(a)}-{format_age(b)}' self.name = f'nihpd_{self.file_id}_nifti' self.filename = f'{self.name}.zip' self.url = urllib.parse.urljoin(self.url_dir, self.filename) if not self.download_root.is_dir(): download_and_extract_archive( self.url, download_root=self.download_root, filename=self.filename, ) (self.download_root / self.filename).unlink() for path in self.download_root.glob('*.nii'): compress(path) path.unlink() try: subject_dict = self.get_subject_dict('.nii.gz') except FileNotFoundError: # for backward compatibility subject_dict = self.get_subject_dict('.nii') super().__init__(subject_dict) def get_subject_dict(self, extension): root = self.download_root subject_dict = { 't1': ScalarImage(root / f'nihpd_{self.file_id}_t1w{extension}'), 't2': ScalarImage(root / f'nihpd_{self.file_id}_t2w{extension}'), 'pd': ScalarImage(root / f'nihpd_{self.file_id}_pdw{extension}'), 'mask': LabelMap(root / f'nihpd_{self.file_id}_mask{extension}'), } return subject_dict