accessing MPEG4 - H.264 video

[armenabnousi]

I'm running into the following error. I understand this specific format is not supported yet. Could you suggest any workarounds? Is there a way to extract the bytes for the video and pass it to another library to run (or save it to the disk as an mp4)? thanks!

Unable to decode pixel data with a transfer syntax UID of '1.2.840.10008.1.2.4.102' (MPEG-4 AVC/H.264 High Profile / Level 4.1) as there are no pixel data handlers available that support it. Please see the pydicom documentation for information on supported transfer syntaxes

[scaramallion]

I've never had any opportunities to check, but looking at what the DICOM Standard says:

One fragment shall contain the whole MPEG-4 AVC/H.264 bit stream

I would try:

from pydicom.encaps import generate_pixel_data_frame

with open('test.mp4', 'wb') as f:
    f.write(next(generate_pixel_data_frame(ds.PixelData)))

Also this might be relevant:

The container format for the video bit stream shall be MPEG-2 Transport Stream, a.k.a. MPEG-TS (see [ISO/IEC 13818-1]) or MPEG-4, a.k.a. MP4 container (see [ISO/IEC 14496-12] and [ISO/IEC 14496-14]). The PTS/DTS of the transport stream shall be used in the MPEG coding.

And

If a video stream exceeds the maximum length of one fragment (approximately 4 GB), it may be sent as multiple SOP Instances, but each SOP Instance will contain an independent and playable bit stream, and not depend on the encoded bit stream in other (previous) instances. The manner in which such separate instances are related is not specified in the Standard, but mechanisms such as grouping into the same Series, and references to earlier instances using Referenced Image Sequence may be used.

If you had a (small) anonymised dataset we could probably add a guide to our documentation for dealing with MPEG transfer syntaxes and/or a pixel data handler.

[scaramallion]

@armenabnousi did you figure it out?

[NodOzz]

Hi,
since I am also interested in DICOM and H.264 videos I tried it out.
I found a sample DICOM-File to download with an encoded MP4-Video in this GoogleGroup (the respective Stackoverflow for DCMTK can be found here )

Your suggested method from above works like a charm.

Now I would be interested in the reverse method: how to encapsulate a h.264-ByteStream into PixelData ?

I played around with encapsulation:

with open('video.mp4', 'rb') as f:
    ds.PixelData = encapsulate(f.read())

But since this function expects a List of bytes, this throws an error `TypeError: object of type 'int' has no len()´

The following technically "works" and would produce an readable DICOM, however the encoded video seems to be wrong; since I can't play it in any DICOM-Viewer or also the initial video extraction does not produce a valid video file:

with open('video.mp4', 'rb') as f:
    ds.PixelData = encapsulate(f.readlines())

The rest of the relevant tags should be correct: among others

ds.file_meta.TransferSyntaxUID = pydicom.uid.MPEG4HP41 
ds.PhotometricInterpretation = 'YBR_PARTIAL_420'
ds.LossyImageCompressionMethod = 'ISO_14496_10'
...

Do you have advice on how to encapsulate the raw mp4-ByteStream into PixelData?

Thanks!

[scaramallion]

Maybe pass the expected list of bytes?

encapsulate([f.read()])  # List[bytes]

[NodOzz]

Perfect! that did the trick. Thank you!