Via pyinstaller (exe): Unable to convert the Pixel Data as the 'pylibjpeg-libjpeg' plugin is not installed

[BJladika]

Hello, I've encountered a weird issue, with getting pixel_array via dataset.pixel_array from exactly one set of datasets (other datasets works correctly). If I use it via code (aka like python code.py) then it works without issues, but if I use it via built (with pyinstaller) exe code, then it starts to work incorrectly.

I tried to include hidden imports, but I don't get why exactly this dataset is not working.

I tried only with Windows 11 (but it also doesn't work on Windows 10, didn't try with alternate OS like Linux or MacOS)

# -*- mode: python ; coding: utf-8 -*-


block_cipher = None


a = Analysis(
    ['xdataset.py'],
    pathex=[],
    binaries=[],
    datas=[],
    hiddenimports=['pydicom.encoders.gdcm', 'pydicom.encoders.pylibjpeg'],
    hookspath=[],
    hooksconfig={},
    runtime_hooks=[],
    excludes=[],
    win_no_prefer_redirects=False,
    win_private_assemblies=False,
    cipher=block_cipher,
    noarchive=False,
)
pyz = PYZ(a.pure, a.zipped_data, cipher=block_cipher)

exe = EXE(
    pyz,
    a.scripts,
    [],
    exclude_binaries=True,
    name='xdataset',
    debug=False,
    bootloader_ignore_signals=False,
    strip=False,
    upx=True,
    console=True,
    disable_windowed_traceback=False,
    argv_emulation=False,
    target_arch=None,
    codesign_identity=None,
    entitlements_file=None,
)
coll = COLLECT(
    exe,
    a.binaries,
    a.zipfiles,
    a.datas,
    strip=False,
    upx=True,
    upx_exclude=[],
    name='xdataset',
)

Steps to reproduce

1. Build code, using dataset.pixel_array via pyinstaller
2. Use exactly this dataset
3. Run exe (of built code)

from pydicom import dcmread

x = dcmread("test_1.dcm")
y = x.pixel_array

Tried to use on both pydicom 2.3.0 and pydicom 2.1.2

A way for us to reproduce and troubleshoot the issue:

• A minimum working code sample
• The entire traceback (if one occurred).

Traceback (most recent call last):
  File "xdataset.py", line 16, in <module>
  File "pydicom\dataset.py", line 1887, in pixel_array
  File "pydicom\dataset.py", line 1444, in convert_pixel_data
  File "pydicom\dataset.py", line 1556, in _convert_pixel_data_without_handler
  File "pydicom\dataset.py", line 1536, in _convert_pixel_data_without_handler
  File "pydicom\dataset.py", line 1563, in _do_pixel_data_conversion
  File "pydicom\pixel_data_handlers\pylibjpeg_handler.py", line 327, in get_pixeldata
  File "pydicom\pixel_data_handlers\pylibjpeg_handler.py", line 235, in generate_frames
RuntimeError: Unable to convert the Pixel Data as the 'pylibjpeg-libjpeg' plugin is not installed
[2716] Failed to execute script 'xdataset' due to unhandled exception!

It's also extremely helpful if you can include one of the following:

• The anonymized DICOM dataset, which can be attached to the issue as a zip archive, or

anonymized_dataset.zip

[darcymason]

If you've found a solution for this, please let us know.

It appears to be a pyinstaller problem (unable to find pylibjpeg-libjpeg dependency) rather than a pydicom issue, so I'm going to close the issue. But if you find there is a pydicom problem, feel free to re-open.

[BJladika]

If you've found a solution for this, please let us know.

Well, I found the solution (or more like, it was found by other people). It requires pyinstaller to clone some metada things from libs, due to them being optional dependency.

So in short you need to use such command

pyinstaller --hiddenimport=pydicom.encoders.gdcm --hiddenimport=pydicom.encoders.pylibjpeg --hiddenimport=pylibjpeg --copy-metadata=pylibjpeg-libjpeg --copy-metadata=numpy --hiddenimport=libjpeg --noconfirm --clean test.py

Where I've mentioned issue: pyinstaller/pyinstaller#7157

Hoping for simplier solution in the bright future. Cheers!