I know I can view a dicom file using following code:

import dicom

from dicom.contrib.pydicom_PIL import show_PIL

f = "CT-MONO2-8-abdo.dcm"

ds = dicom.read_file(f, force=True)

show_PIL(ds)

However, how can I extract and view all frames from a multi-frame DICOM file? I tried using above code but got following error:

File "/home/auser/.local/lib/python3.5/site-packages/dicom/dataset.py", line 399, in _get_pixel_array

raise NotImplementedError("Pixel Data is compressed in a format pydicom does not yet handle. Cannot return array")

NotImplementedError: Pixel Data is compressed in a format pydicom does not yet handle. Cannot return array

I had tried with some multi-frame files located at http://www.barre.nom.fr/medical/samples/. The pixel size etc are available for these files.

How can I extract and/or view different frames of a multi-frame DICOM file?

Edit: Following command using gdcm works on Linux to convert these to uncompressed file:

$ gdcmconv --raw compressed.dcm uncompressed.dcm

This is then read by python code above but that shows only first frame. How can I extract and view other frames?

解决方案

pydicom supports reading pixel data. Refer this documentation.

pydicom tends to be “lazy” in interpreting DICOM data. For example, by

default it doesn’t do anything with pixel data except read in the raw

bytes:

import dicom

ds=dicom.read_file("MR_small.dcm")

ds.PixelData

'\x89\x03\xfb\x03\xcb\x04\xeb\x04\xf9\x02\x94\x01\x7f ...

...

About pixel_array

A property of Dataset called pixel_array provides more useful pixel

data for uncompressed images. The NumPy numerical package must be

installed on your system to use this property, because pixel_array

returns a NumPy array:

import dicom

ds=dicom.read_file("MR_small.dcm")

ds.pixel_array

array([[ 905, 1019, 1227, ..., 302, 304, 328],

[ 628, 770, 907, ..., 298, 331, 355],

[ 498, 566, 706, ..., 280, 285, 320],

...,

[ 334, 400, 431, ..., 1094, 1068, 1083],

[ 339, 377, 413, ..., 1318, 1346, 1336],

[ 378, 374, 422, ..., 1369, 1129, 862]], dtype=int16)

ds.pixel_array.shape

(64, 64)

As explained in error message (and by @kritzel_sw in comment) the pydicom does not support the Transfer Syntax of source image yet. Change the Transfer Syntax using some other tool before attempting to extract the frames.

Also check this Stack Overflow question; it is about old version but may be helpful.