Unicode Decode Error when applying stimulus

Question

For some reason, I get the following error when applying a stimulus to a whole-heart mesh. Would anyone have any ideas on why this might be occurring? I tried looking through the .pts and .elem files for any non-ASCII characters but I couldn't find any.

File "/usr/local/lib/python3.10/dist-packages/carputils/divertoutput.py", line 116, in call
    for line in iter(proc.stdout.readline, ''):
  File "/usr/lib/python3.10/codecs.py", line 322, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xeb in position 6: invalid continuation byte

Comments

I am getting the same error on my simulation attempts, however I want to contribute by stressing the fact that when I use -stim[0].crct.type 0 I get the error on time 0. When I use 1 I do not get the error, simulation runs normally. When I use 2 I get the error on time 2.

Answer 1

Could it be that you saved your stimulus text file with latin1 encoding instead of utf8?

If this is not the problem, please share a minimum example to reproduce. Otherwise it will be hard to provide help.

Comments

Ahh i think the error was in the mesh itself. I deleted the carp_txt mesh and then reconverted it from the vtk  and it worked just fine!

edit: There may have been something deeper, it periodically was working and then stopped however I think I figured out the root cause- When the radius is large enough (>200) the simulation starts working perfectly fine.

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Hi Brayden,

I am having the same error. Can you please tell us what you mean by radius large enough?

Best,

Kocak

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Hi, I am getting a similar error: UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe8 in position 5: invalid continuation byte. For me it seems to be ionic model specific, i.e. for the exact same mesh and stimulus input, works fine for  Courtemanche but not Bondarenko

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Thanks for following up. Could you share a working example to reproduce this issue?

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Thank you for your help. The only change that causes the error is changing (OHara used here, but other works fine too':     
    imp_reg = ['-num_imp_regions',1,
               '-imp_region[0].im','OHara',
               '-imp_region[0].num_IDs', 1,
               '-imp_region[0].ID[0]', "1"]

Too:


imp_reg = ['-num_imp_regions',1,
               '-imp_region[0].im','Bondarenko',
               '-imp_region[0].num_IDs', 1,
               '-imp_region[0].ID[0]', "1"]

As it seems others have identified this issue when applying stimuli, this is my stimulus:

    E1_lower_bound = nplist([x/2-res, y/2 - res, 0])
    E1_upper_bound = nplist([x/2 + res, y/2 + res, res])

    electrode1 = mesh.block_region(geom, 'stimulus', 0, E1_lower_bound,E1_upper_bound, False)

    electrode = electrode1

    stim = ['-num_stim',1,
            '-stimulus[0].stimtype', 0,
            '-stimulus[0].strength',200.0,
            '-stimulus[0].duration', 2,
            '-stimulus[0].start',5,
            '-stimulus[0].npls', 1]

The full error is below and indeed happens on time of stimlus (i.e. if i change to start at 0ms, 10ms this is when the error occurs):
Traceback (most recent call last):
  File "/home/osheac/Desktop/OMTool/./mouse.py", line 125, in <module>
    run()
  File "/usr/local/lib/python3.10/dist-packages/carputils/tools.py", line 542, in wrapped
    ret = run(args, job)
  File "/home/osheac/Desktop/OMTool/./mouse.py", line 122, in run
    job.carp(cmd)
  File "/usr/local/lib/python3.10/dist-packages/carputils/job/job.py", line 380, in carp
    self.mpi(cmd, msg, *args, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/carputils/job/job.py", line 262, in mpi
    self.register(MPICommand(cmd, message), *args, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/carputils/job/job.py", line 119, in register
    self._queue.pop(0).execute()
  File "/usr/local/lib/python3.10/dist-packages/carputils/job/command.py", line 288, in execute
    divertoutput.call(self._cmd, interactive, timeout, stderr=stderr)
  File "/usr/local/lib/python3.10/dist-packages/carputils/divertoutput.py", line 43, in wrapped
    return func(cmd, *args, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/carputils/divertoutput.py", line 116, in call
    for line in iter(proc.stdout.readline, ''):
  File "/usr/lib/python3.10/codecs.py", line 322, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xc0 in position 5: invalid start byte

Answer 2

I think the error actually happens when the solver diverges.

I can reproduce the error, and when I run the experiment using the openCARP executable directly, I get the following output:

    *** Launching simulation ***

PROG    -----     ----    -------    -------|
time    %%comp    time     ctime       ETA  |
0.00    0.0    0.0    0:00:00    0:00:00
0.10    2.0    0.0    0:00:00    0:00:01
L5 : (??'?U solver diverged. Reason: NaN or inf encountered.

As we see, the name of the solver is corrupted, and that is actually causing the Python error.
We are investigating  this issue.

Answer 3

The issue should now be fixed in the master branch, via the merge request https://git.opencarp.org/openCARP/openCARP/-/merge_requests/180 .