Issue Opening simba

[GettyScience2]

Hello,

I have successfully installed simba, but when I try to open it I get the following error message:

(simba_trial) C:\Users\giraf>simba
Traceback (most recent call last):
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\matplotlib\backends\qt_compat.py", line 64, in
QT_API = _ETS[QT_API_ENV]
KeyError: 'pyside6'

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

Traceback (most recent call last):
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\runpy.py", line 193, in run_module_as_main
"main", mod_spec)
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\runpy.py", line 85, in run_code
exec(code, run_globals)
File "C:\Users\giraf\anaconda3\envs\simba_trial\Scripts\simba.exe_main.py", line 4, in
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\simba\SimBA.py", line 28, in
from simba.bounding_box_tools.boundary_menus import BoundaryMenus
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\simba\bounding_box_tools\boundary_menus.py", line 9, in
from simba.bounding_box_tools.agg_boundary_stats import
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\simba\bounding_box_tools\agg_boundary_stats.py", line 13, in
from simba.mixins.config_reader import ConfigReader
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\simba\mixins_init.py", line 1, in
from simba.utils.data import get_library_version
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\simba\utils\data.py", line 19, in
from pylab import *
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\pylab.py", line 1, in
from matplotlib.pylab import *
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\matplotlib\pylab.py", line 35, in
from matplotlib import cbook, mlab, pyplot as plt
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\matplotlib\pyplot.py", line 2336, in
switch_backend(rcParams["backend"])
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\matplotlib_init_.py", line 703, in getitem
plt.switch_backend(rcsetup._auto_backend_sentinel)
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\matplotlib\pyplot.py", line 256, in switch_backend
switch_backend(candidate)
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\matplotlib\pyplot.py", line 276, in switch_backend
class backend_mod(matplotlib.backend_bases.Backend):
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\matplotlib\pyplot.py", line 277, in backend_mod
locals().update(vars(importlib.import_module(backend_name)))
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\importlib_init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\matplotlib\backends\backend_qt5agg.py", line 11, in
from .backend_qt5 import (
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\matplotlib\backends\backend_qt5.py", line 16, in
import matplotlib.backends.qt_editor.figureoptions as figureoptions
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\matplotlib\backends\qt_editor\figureoptions.py", line 11, in
from matplotlib.backends.qt_compat import QtGui
File "C:\Users\giraf\anaconda3\envs\simba_trial\lib\site-packages\matplotlib\backends\qt_compat.py", line 69, in
"'pyside'") from err
RuntimeError: The environment variable QT_API has the unrecognized value {!r};valid values are 'pyqt5', 'pyside2', 'pyqt', and 'pyside'

Any suggestions?

[GettyScience2]

See #517 for the same issue and some suggestions.

[sronilsson]

Hey @GettyScience2 - thanks for reporting this, not sure why this keeps popping up. I will take a look asap and get back to you.

[sronilsson]

@GettyScience2 as this issue was happening for at least two people, I decided to dig for a more permanent fix and update the code.

It would be super helpful if you could test it out. If you install the latest simba in a new conda environment, does it work now?

Thanks again for reporting 🚀

[GettyScience2]

I made a new conda environment with python 3.6 and put in "pip install simba-uw-tf-dev". Installed correctly. But when I put in "simba", I got the same error message.

[sronilsson]

Got it thanks @GettyScience2 I'll give it another go tomorrow 👍🏼👍🏼👍🏼

[sronilsson]

Hey @GettyScience2 - can you give it one more go, and see if the error persist?

Again, thank you appreciate the help 🙏🏼🙏🏼

[GettyScience2]

Hi!
It is no problem at all, happy to help. I made a new environment with python 3.6 and entered "pip install simba-uw-tf-dev". It ran for a bit and installed correctly. When I put in "simba", I no longer got the RuntimeError. Instead, I got the same "packaging" error where I just needed to pip install that module. After that installation, simba opened with no issues!

[sronilsson]

Got it cheers! One more question, which version of packaging do you see with pip show packaging ?

[GettyScience2]

Name: packaging
Version: 21.3
Summary: Core utilities for Python packages
Home-page: https://github.com/pypa/packaging
Author: Donald Stufft and individual contributors
Author-email: donald@stufft.io
License: BSD-2-Clause or Apache-2.0
Location: c:\users\giraf\anaconda3\envs\simba_trial\lib\site-packages
Requires: pyparsing
Required-by:

[sronilsson]

thx 💯

[GettyScience2]

Quick, unrelated, question. My lab is interested in knowing the number of times and amount of time an individual animal in a social defeat assay does a set of behaviours. From my understanding of the walkthroughs, simba provides information on the behaviours irrespective of who is doing the behaviour. Is that correct? If it is correct, how would you suggest parsing which individual did what behaviour apart? For example, we would want to know how many times one fish bit the other fish, not simply how many bites occurred total. Or we want to know how much time an individual spent chasing another fish (and vice versa how much time the other fish spent fleeing an approaching fish).

Thank you,

[GettyScience2]

Also, does simba work for deeplabcut pose estimation files that contain an x, y, and z coordinate?

[sronilsson]

Hey @GettyScience2 - regarding the first question, it's is a little more involved unfortunately, but I will get back to you tomorrow. There should be other discussions about this on the issues/gitter.

The second question: no sorry, I've had a few people reach out about this, but, the issue has most often been about data quality / amount of data the labs that reach out have. The code exist, but not very well written or exposed in the GUI, as most labs seem to just have vaguer plans to collect 3D data in the end. Understandable, I work mostly with 3d data myself and I know how much more involved and fiddly it is compared to 2d data.