Error when starting FLIKA - Assertion Error

[flika-org]

Error when starting FLIKA - Assertion Error

[HollyASmith488]

I think I solved this by installing a different version of sci-kit image...

pip install scikit-image==0.18.0
Seemed ok after that

[HollyASmith488]

Now I get this error when I try to open Script Editor

2022-12-05` 22:36:48,467 - ERROR - Uncaught exception
Traceback (most recent call last):
  File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\app\application.py", line 301, in <lambda>
    return lambda : ScriptEditor.importScript(script)
  File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\app\script_editor.py", line 214, in importScript
    ScriptEditor.show()
  File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\app\script_editor.py", line 282, in show
    ScriptEditor.gui = ScriptEditor()
  File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\app\script_editor.py", line 86, in __init__
    from .terminal import ipython_terminal
  File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\app\terminal.py", line 23, in <module>
    from ipykernel import find_connection_file
ImportError: cannot import name 'find_connection_file' from 'ipykernel' (C:\Users\has54.PHARM\Anaconda3\lib\site-packages\ipykernel\__init__.py)

[gddickinson]

Hi Holly, I think Kyle forwarded your email to me... or maybe I'm just on the subscribed list. Anyway, I've been using Flika a lot recently and I think your issues are likely due to incompatibility between newer libraries/python versions and older Flika code. I had a similar issue with sci-kit and fixed it the same way - by downgrading to 0.18. Could your new error be due to the version of Python you have installed? What version of Python are you using to run Flika? A possible quick-fix could be to create a new conda environment with python 3.7 and use pip to install flika (specifying scikit=0.18) in the new environment. best, George

…

On Mon, Dec 5, 2022 at 3:41 PM HollyASmith488 ***@***.***> wrote: Now I get this error when I try to open Script Editor 2022-12-05 22:36:48,467 - ERROR - Uncaught exception Traceback (most recent call last): File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\app\application.py", line 301, in return lambda : ScriptEditor.importScript(script) File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\app\script_editor.py", line 214, in importScript ScriptEditor.show() File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\app\script_editor.py", line 282, in show ScriptEditor.gui = ScriptEditor() File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\app\script_editor.py", line 86, in *init* from .terminal import ipython_terminal File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\app\terminal.py", line 23, in from ipykernel import find_connection_file ImportError: cannot import name 'find_connection_file' from 'ipykernel' (C:\Users\has54.PHARM\Anaconda3\lib\site-packages\ipykernel_*init*_.py)` — Reply to this email directly, view it on GitHub <#53 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABY57YZWAOWPW6NJXRBRW7TWLZVQLANCNFSM6AAAAAASUWO77U> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[HollyASmith488]

Hi George,

Thanks so much for your message! Yes I think the newer version of Python (3.9) was definitely the problem. I managed to make a virtual environment running Python 3.6.6 and used pip to install FLIKA with scikit image 0.17.2. That seems to be working now. Thanks again for your help!

Best wishes,
Holly

[gddickinson]

Hi Holly,Happy to hear that you were able to fix the problem! Best of luck with your research.George On Dec 6, 2022, at 3:58 AM, HollyASmith488 ***@***.***> wrote: Hi George, Thanks so much for your message! Yes I think the newer version of Python (3.9) was definitely the problem. I managed to make a virtual environment running Python 3.6.6 and used pip to install FLIKA with scikit image 0.17.2. That seems to be working now. Thanks again for your help! Best wishes, Holly —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: ***@***.***>