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import urllib.parse |
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from torchvision.datasets.utils import download_and_extract_archive |
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from ...utils import get_torchio_cache_dir |
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from ... import Subject, Image, LABEL |
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class SubjectITKSNAP(Subject): |
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"""ITK-SNAP Image Data Downloads. |
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See `the itk-SNAP website <http://www.itksnap.org/pmwiki/pmwiki.php?n=Downloads.Data>`_ |
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for more information. |
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""" |
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url_base = 'https://www.nitrc.org/frs/download.php/' |
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def __init__(self, name, code): |
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self.name = name |
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self.url_dir = urllib.parse.urljoin(self.url_base, f'{code}/') |
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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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self.download_root = get_torchio_cache_dir() / self.name |
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if self.download_root.is_dir(): |
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print(f'Using cache found in {self.download_root}') |
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else: |
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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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super().__init__(**self.get_kwargs()) |
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def get_kwargs(self): |
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raise NotImplementedError |
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class BrainTumor(SubjectITKSNAP): |
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def __init__(self): |
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super().__init__('braintumor', '6161') |
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def get_kwargs(self): |
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t1, t1c, t2, flair, seg = [ |
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self.download_root / self.name / f'BRATS_HG0015_{name}.mha' |
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for name in ('T1', 'T1C', 'T2', 'FLAIR', 'truth') |
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] |
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return dict( |
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t1=Image(t1), |
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t1c=Image(t1c), |
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t2=Image(t2), |
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flair=Image(flair), |
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seg=Image(seg, type=LABEL), |
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) |
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class T1T2(SubjectITKSNAP): |
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def __init__(self): |
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super().__init__('ashs_test', '10983') |
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def get_kwargs(self): |
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mprage = self.download_root / self.name / 'mprage_3T_bet_dr.nii' |
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tse = self.download_root / self.name / 'tse_3t_dr.nii' |
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return dict( |
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mprage=Image(mprage), |
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tse=Image(tse), |
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) |
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class AorticValve(SubjectITKSNAP): |
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def __init__(self): |
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super().__init__('bav_example', '11021') |
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def get_kwargs(self): |
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b14, b14_seg, b25, b25_seg = [ |
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self.download_root / self.name / f'bav_frame_{name}.nii.gz' |
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for name in ('14', '14_manseg', '25', '25_manseg') |
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] |
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return dict( |
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b14=Image(b14), |
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b14_seg=Image(b14_seg, type=LABEL), |
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b25=Image(b25), |
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b25_seg=Image(b25_seg, type=LABEL), |
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) |
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fepegar /
torchio
