Ross
76 lines
2.3 KiB
Python
76 lines
2.3 KiB
Python
import re
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from django.conf import settings
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from django.core.management.base import BaseCommand, CommandError
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import pydicom
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import pydicom.errors
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from django_rich.management import RichCommand
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from rich.progress import track
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import six
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import os
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class Command(RichCommand):
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help = 'Checks dicom files for anonymisation'
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#def add_arguments(self, parser):
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# parser.add_argument('poll_ids', nargs='+', type=int)
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def handle(self, *args, **options):
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self.console.print("[bold blue]Finding files:[/bold blue]")
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files = get_all_media()
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self.console.print(f"[bold blue]Files to check: {len(files)}[/bold blue]")
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for file in track(files, description="Checking file..."):
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try:
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ds = pydicom.dcmread(file, force=False)
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except pydicom.errors.InvalidDicomError:
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continue
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site_codes = ("ref", "rk9", "ra9", "rh8", "rbz", "rba")
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for code in site_codes:
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# TODO rewrite
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try:
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if code in ds.PatientID.lower():
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self.stdout.write(self.style.WARNING(f"Identifiable dicom [{ds.PatientID.lower()}] {file}"))
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except AttributeError:
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self.stdout.write(self.style.WARNING(f"Error parsing {file}"))
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pass
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try:
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if code in ds.AccessionNumber.lower():
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self.stdout.write(self.style.WARNING(f"Error parsing [{ds.AccessionNumber.lower()}] {file}"))
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except AttributeError:
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pass
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if code in ds.to_json():
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self.stdout.write(self.style.WARNING(f"Error parsing [{code} in json dataset] {file}"))
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def get_all_media(exclude=None):
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"""
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Get all media from MEDIA_ROOT
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"""
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if not exclude:
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exclude = []
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media = set()
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for root, dirs, files in os.walk(six.text_type(settings.MEDIA_ROOT)):
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for name in files:
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path = os.path.abspath(os.path.join(root, name))
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relpath = os.path.relpath(path, settings.MEDIA_ROOT)
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for e in exclude:
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if re.match(r'^%s$' % re.escape(e).replace('\\*', '.*'), relpath):
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break
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else:
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media.add(path)
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return media |