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I have data stored in the NumPy array in .pkl file format. I only had an idea that data consists of low-dose CT DICOM images. But as the data is in array format I don't know what the original images look like. I am stuck at this point may be my question is also not valid but still, does anybody have knowledge about it. I don't know whether my question is valid but I I am confused here and I want to get images from it

This is the .pkl format file lowDose_CT.pkl and when I read this file I got the following output

output

[[array([[[-1000, -1000, -1000, ..., -1000, -1000, -1000], [-1000, -1000, -1000, ..., -1000, -1000, -1000], [-1000, -1000, -1000, ..., -1000, -1000, -1000], ..., [-1000, -1000, -1000, ..., -1000, -1000, -1000], [-1000, -1000, -1000, ..., -1000, -1000, -1000], [-1000, -1000, -1000, ..., -1000, -1000, -1000]],

   [[-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    ...,
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000]],

   [[-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    ...,
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000]],

   ...,

   [[-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    ...,
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000]],

   [[-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    ...,
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000]],

   [[-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    ...,
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000]]], dtype=int16), array([[[-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    [-1000, -1000, -1000, ..., -1000, -1000, -1000],
    ...,........
Amit Joshi
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Farah Jabeen
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1 Answers1

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You should maybe consider using a program that can display this format. As far as I know, getting -1000 HU in some places is normal, as this represents the radiodensity of air.

Lucas Meier
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  • But what about images that I want from it. Like you are saying I can implement preprocessing, adding thresholding, implementing cropping, on this NumPy array that is stored in .pkl format? – Farah Jabeen Jul 07 '22 at 11:24
  • I mean you should maybe change the array to a format that is readable by the program I mentionned. I think each row in each array is a pixel, and each array in the total list is a row or a column. I would convert it to the standard from https://www.dicomstandard.org/current – Lucas Meier Jul 07 '22 at 11:58