Error when starting FLIKA - Assertion Error

[HollyASmith488]

Hi Kyle,

I'm guessing it is a while since you have been working on FLIKA, so I hope you're still able to get this message. I have been using FLIKA for a while but just recently I got this error on Anaconda prompt which I have never seen before. I've tried uninstalling and reinstalling both flika and anaconda but I still get the same problem. I have no idea where else to go with this as I am not in any way proficient with code, I have just been using FLIKA in the same way in the lab since the start of my PhD!! It would be great if you could take a look. Many thanks, Holly

Starting flika 2022-12-05 20:25:55,140 - ERROR - Uncaught exception Traceback (most recent call last): File "C:\Users\has54.PHARM\Anaconda3\lib\runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "C:\Users\has54.PHARM\Anaconda3\lib\runpy.py", line 87, in _run_code exec(code, runglobals) File "C:\Users\has54.PHARM\Anaconda3\Scripts\flika.exe__main__.py", line 7, in sys.exit(exec()) File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\flika.py", line 123, in exec_ fa = start_flika(sys.argv[1:]) File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\flika.py", line 115, in startflika fa = FlikaApplication() File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\app\application.py", line 153, in init from ..process.file import open_file, open_file_from_gui, open_image_sequence_from_gui, open_points, save_file, save_movie_gui, save_points, save_rois File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\process__init.py", line 7, in from .filters import * File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\process\filters.py", line 89, in gaussian_blur = Gaussian_blur() File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\process\filters.py", line 32, in init assert 'gaussian' in skimage.filters.dict__ # Make sure your version of skimage is >= 0.12.3 AssertionError

[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_connectionfile' from 'ipykernel' (C:\Users\has54.PHARM\Anaconda3\lib\site-packages\ipykernelinit_.py)`

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[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

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