Range of Pixel Data for a Dicom File

[PONY1ST]

I am trying to combine several dicom files in a larger one using python3 with pydicom library and encounters an error message I do not understand.

Let several dicom files be given. We assume that each dicom file contains a video. That is, after calling pydicom.dcmread and calling the pixel_array, I get a numpy array in shape (number_of_frames, rows, columns, 3), with number_of_frames > 0. We will also assume that each dicom only differs in number of frames.

So I read their pixel_array, use numpy to concatenate them, and gets a bigger video with more frames. I would like to save this bigger video as another dicom. So I write the new video into a filedataset and call save_as in pydicom library. It turns out that:

1. If my concatenated video is small, then my code runs without problem.
2. If my concatenated video is sufficiently large (one example would be (6000,500,500,3)), then I get the following error:

Traceback (most recent call last):
  File "...\Lib\site-packages\pydicom\tag.py", line 28, in tag_in_exception
    yield
  File "...\Lib\site-packages\pydicom\filewriter.py", line 662, in write_dataset
    write_data_element(fp, dataset.get_item(tag), dataset_encoding)
  File "...\Lib\site-packages\pydicom\filewriter.py", line 620, in write_data_element
    fp.write_UL(0xFFFFFFFF if is_undefined_length else value_length)
  File "...\Lib\site-packages\pydicom\filebase.py", line 119, in write_leUL
    self.write(pack(b"<L", val))
               ^^^^^^^^^^^^^^^^
struct.error: argument out of range

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "...\dicom_concatenate.py", line 56, in work
    first_dicom.save_as(absolute_save_path)
  File "...\Lib\site-packages\pydicom\dataset.py", line 2061, in save_as
    pydicom.dcmwrite(filename, self, write_like_original)
  File "...\Lib\site-packages\pydicom\filewriter.py", line 1153, in dcmwrite
    _write_dataset(fp, dataset, write_like_original)
  File "...\Lib\site-packages\pydicom\filewriter.py", line 889, in _write_dataset
    write_dataset(fp, get_item(dataset, slice(0x00010000, None)))
  File "...\Lib\site-packages\pydicom\filewriter.py", line 661, in write_dataset
    with tag_in_exception(tag):
  File "...\Lib\contextlib.py", line 155, in __exit__
    self.gen.throw(typ, value, traceback)
  File "...\Lib\site-packages\pydicom\tag.py", line 32, in tag_in_exception
    raise type(exc)(msg) from exc
struct.error: With tag (7fe0, 0010) got exception: argument out of range
Traceback (most recent call last):
  File "...\Lib\site-packages\pydicom\tag.py", line 28, in tag_in_exception
    yield
  File "...\Lib\site-packages\pydicom\filewriter.py", line 662, in write_dataset
    write_data_element(fp, dataset.get_item(tag), dataset_encoding)
  File "...\Lib\site-packages\pydicom\filewriter.py", line 620, in write_data_element
    fp.write_UL(0xFFFFFFFF if is_undefined_length else value_length)
  File "...\Lib\site-packages\pydicom\filebase.py", line 119, in write_leUL
    self.write(pack(b"<L", val))
               ^^^^^^^^^^^^^^^^
struct.error: argument out of range

I do not understand this error message. What exactly goes wrong? It seems my video is too large (?). Is there any way to help me save my concatenated video?

(StackExchange version of this post: https://stackoverflow.com/questions/76799001/range-of-pixel-data-for-a-dicom-file)

[mrbean-bremen]

Yes, there is a size limit of 2GB in the content of a DICOM tag, which you see to exceed. It is possible to save data that is larger than that using a compressed transfer syntax, if the compressed size is not smaller than 2 GB, or you just have to split up the video.

[PONY1ST]

Thank you for the quick response! Do you mean that I have to compress if the data exceeds 2GB? If so, do you know how should I compress my video? I am open to any method as long as my video can be saved as dicom and can be read using pydicom as usual.

[mrbean-bremen]

Unfortunately, I have no experience at all with videos in DICOM. There are several MPEG4 based transfer syntaxes in DICOM, but to my knowledge pydicom itself is not able to read them, as it has the focus on image data and uses thirdparty libraries for decompression that do not support video as far as I know. Maybe @darcymason can say more...

[darcymason]

I can't add anything to what @mrbean-bremen has said. I don't know of anyone manipulating dicom files with video using pydicom.