Permission denied error when reading files in zip folder using python in Django

Question

I'm trying to read dicom files in a zip folder but when I run this code it gives me this error:

[Errno 13] Permission denied: 'PATIENT_DICOM/'

file = patient.PATIENT_DICOM

with zipfile.ZipFile(file,'r') as zip:
    zip.extractall()
    ls= zip.infolist()
    slices = [pydicom.read_file(s.filename) for s in ls]

I don't think you can directly work on a zipfile this way - you probably have to extract the zip first. — MrBean Bremen, Feb 12 '20 at 14:35
At what point do you get the exception? Can you add the stacktrace? — MrBean Bremen, Feb 12 '20 at 15:09

MrBean Bremen · Answer 1 · 2020-02-12T19:45:35.203

0

Basically, you have to read the extracted DICOM files:

zip_path = patient.PATIENT_DICOM
with zipfile.ZipFile(zip_path, 'r') as zip:
    path = tempfile.mkdtemp()
    zip.extractall(path)
    slices = []
    for root, _, filenames in os.walk(path):
        for filename in filenames:
            filepath = os.path.join(root, filename)
            slices.append(pydicom.dcmread(filepath))
    shutil.rmtree(path)

Note that this first extracts all files into a temp dir, which is probably faster than accessing them one by one. This assumes, that all files in the zip belong to the same volume or series. If you want to work with the slices further, you have to sort them properly first, for example by InstanceNumber.

edited Feb 12 '20 at 19:45

answered Feb 12 '20 at 15:08

MrBean Bremen

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i did it and i got another error [WinError 3] The system cannot find the path specified: 'C:\\Users\\Dell_5G\\AppData\\Local\\Temp\\tmpotwe933h\\PATIENT_DICOM' – Abdullah Shaker Feb 12 '20 at 15:22
At what line does this happen? In `zip.extract`? – MrBean Bremen Feb 12 '20 at 16:10
Ok, I changed the code by just extracting all files first - see above. – MrBean Bremen Feb 12 '20 at 19:46

score 0 · Answer 2 · edited Feb 12 '20 at 16:30

0

I think you have to try this:

data = pydicom.dcmread(filename)

edited Feb 12 '20 at 16:30

Eliahu Aaron

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answered Feb 12 '20 at 15:27

PRANEETH ALURU

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`dcmread` is an alias for `read_file`, and while it is correct that it shall be used, it does not change the semantics. – MrBean Bremen Feb 12 '20 at 16:12

Permission denied error when reading files in zip folder using python in Django

2 Answers2