Problems with encoding using non-Slicer Python environment

Support
1

Hi!

I’m developing an extension for Slicer with a segmentation module. In my “Module.py” file I want to make a call to a python3.py file of my own (outside Slicer-Python environment) using conda environment. I tried different ways to make the call, until I find the last question of the article ( “How to run Python script using a non-Slicer Python environment”) and noticed that I had the same problem described there. But now I have a problem with encodings: hhis is the piece of my code:

command_line = ["/home/dloopz/miniconda3/bin/python", "--version"]
from subprocess import check_output
command_result = check_output(command_line, env=slicer.util.startupEnvironment())
print(command_result)

and this is the output:

command_result = check_output(command_line, env=slicer.util.startupEnvironment())
  File "/home/dloopz/SoftsLaburo/Slicer-4.10.2-linux-amd64/lib/Python/lib/python2.7/subprocess.py", line 212, in check_output
    process = Popen(stdout=PIPE, *popenargs, **kwargs)
  File "/home/dloopz/SoftsLaburo/Slicer-4.10.2-linux-amd64/lib/Python/lib/python2.7/subprocess.py", line 390, in __init__
    errread, errwrite)
  File "/home/dloopz/SoftsLaburo/Slicer-4.10.2-linux-amd64/lib/Python/lib/python2.7/subprocess.py", line 1024, in _execute_child
    raise child_exception
UnicodeEncodeError: 'ascii' codec can't encode character u'\xf3' in position 9: ordinal not in range(128)

The problems I had before were similar, but with the “init.py” file of Slicer.
Any idea of how to solve this?

Best regards,
Lucca Dellazoppa

2

It seems that Python subprocess expects ascii input and/or output. This seems to cause issues quite often (see for example here).

One solution is to only use ascii file and folder names and command-line arguments; or you may implement some of the workarounds suggested in various Python forums.

Slicer-4.10 used Python 2, but Preview Release uses Python 3. If this problem was fixed in Python 3 then you may consider switching to using a Slicer Preview Release.

3

Thanks Andras, I’ll look around to the works you mentioned and try to fix it. If I find a solution I post it here.

Lucca

1 Like
4

Hi again!

I can’t find how to solve the problem yet, and need to use the last version of Slicer. I noticed that reinstalling Slicer allows me to run external python3 files, in my miniconda env, but after a day or two, it crashes again. Always the same error, no matter what command_line I use:

command_result = check_output(command_line, env=slicer.util.startupEnvironment())
  File "/home/dloopz/SoftsLaburo/Slicer-4.10.2-linux-amd64/lib/Python/lib/python2.7/subprocess.py", line 212, in check_output
    process = Popen(stdout=PIPE, *popenargs, **kwargs)
  File "/home/dloopz/SoftsLaburo/Slicer-4.10.2-linux-amd64/lib/Python/lib/python2.7/subprocess.py", line 390, in __init__
    errread, errwrite)
  File "/home/dloopz/SoftsLaburo/Slicer-4.10.2-linux-amd64/lib/Python/lib/python2.7/subprocess.py", line 1024, in _execute_child
    raise child_exception
UnicodeEncodeError: 'ascii' codec can't encode character u'\xf3' in position 9: ordinal not in range(128)

I don’t even know where is that character u’\xf3’ in position 9, if my command_line was, for example:

command_line = ["/home/dloopz/miniconda3/bin/python", "--version"]

Any advice?

Thanks again!
Lucca

5

Try recent Slicer preview releases. They use Python3, which probably does not have this Python2 error anymore.