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import urllib.parse |
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from ...utils import compress |
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from ... import ScalarImage, LabelMap |
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from ...download import download_and_extract_archive |
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from .mni import SubjectMNI |
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SUPPORTED_YEARS = ( |
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(4.5, 18.5), |
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(4.5, 8.5), |
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(7, 11), |
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(7.5, 13.5), |
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(10, 14), |
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(13, 18.5), |
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) |
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def format_age(n): |
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integer = int(n) |
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decimal = int(10 * (n - integer)) |
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return f'{integer:02d}.{decimal}' |
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class Pediatric(SubjectMNI): |
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"""MNI pediatric atlases. |
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See `the MNI website <http://nist.mni.mcgill.ca/?p=974>`_ for more |
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information. |
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.. image:: http://nist.mni.mcgill.ca/wp-content/uploads/2016/04/nihpd_asym_all_sm.jpg |
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:alt: Pediatric MNI template |
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Arguments: |
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years: Tuple of 2 ages. Possible values are: ``(4.5, 18.5)``, |
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``(4.5, 8.5)``, |
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``(7, 11)``, |
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``(7.5, 13.5)``, |
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``(10, 14)`` and |
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``(13, 18.5)``. |
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symmetric: If ``True``, the left-right symmetric templates will be |
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used. Else, the asymmetric (natural) templates will be used. |
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""" # noqa: E501 |
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def __init__(self, years, symmetric=False): |
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self.url_dir = 'http://www.bic.mni.mcgill.ca/~vfonov/nihpd/obj1/' |
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sym_string = 'sym' if symmetric else 'asym' |
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if not isinstance(years, tuple) or years not in SUPPORTED_YEARS: |
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message = f'Years must be a tuple in {SUPPORTED_YEARS}' |
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raise ValueError(message) |
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a, b = years |
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self.file_id = f'{sym_string}_{format_age(a)}-{format_age(b)}' |
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self.name = f'nihpd_{self.file_id}_nifti' |
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self.filename = f'{self.name}.zip' |
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self.url = urllib.parse.urljoin(self.url_dir, self.filename) |
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if not self.download_root.is_dir(): |
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download_and_extract_archive( |
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self.url, |
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download_root=self.download_root, |
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filename=self.filename, |
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) |
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(self.download_root / self.filename).unlink() |
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for path in self.download_root.glob('*.nii'): |
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compress(path) |
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path.unlink() |
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try: |
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subject_dict = self.get_subject_dict('.nii.gz') |
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except FileNotFoundError: # for backward compatibility |
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subject_dict = self.get_subject_dict('.nii') |
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super().__init__(subject_dict) |
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def get_subject_dict(self, extension): |
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root = self.download_root |
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subject_dict = { |
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't1': ScalarImage(root / f'nihpd_{self.file_id}_t1w{extension}'), |
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't2': ScalarImage(root / f'nihpd_{self.file_id}_t2w{extension}'), |
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'pd': ScalarImage(root / f'nihpd_{self.file_id}_pdw{extension}'), |
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'mask': LabelMap(root / f'nihpd_{self.file_id}_mask{extension}'), |
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} |
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return subject_dict |
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fepegar /
torchio
