-
Notifications
You must be signed in to change notification settings - Fork 253
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
QWidget: Must construct a QApplication before a QWidget #601
Comments
Hello, Are you able to post the full trace-back for the error you got? Also, did you run Kilosort4 through the GUI or with a script/notebook? |
I'm getting the same error, full traceback:
|
Hi Kilosort experts, We got the similar error recently. The specific errors varies according to the input parameter, but always point to the same code line (IndexError), below is an example. 17:52:59.582 [E] init:62 An error has occurred (IndexError): index 14 is out of bounds for axis 0 with size 14 QWidget: Must construct a QApplication before a QWidget Since we currently don't have a good sense of the working mechanism about these parameters, we'd very much appreciated if you can suggest some initial parameters for the 24 channels data processing, which seems to be critical for the sorting quality. Many thanks! |
These look like Phy errors. The install instructions on your readme are now out of date for the current state of Phy. Phy now recommends to install from source rather than with a pip install. |
Hello, I still haven't been able to reproduce this myself, but based on the traceback I think it's related to one of two things:
For 1), please try pulling the latest copy of the repo and see if that fixes the issue, that change has been reverted. Or, if you don't want to wait for the sorting to run again, you can rename For 2), please follow the install instructions at https://github.com/cortex-lab/phy for installing Phy. I will update our readme to avoid confusion about that. Please let me know if any of you continue to have issues after trying that. |
@zm711 I had followed your instructions for phy install from source using .yml and an older version of python and got the same issue with only ks4, not ks2.5. |
Jacob, Thanks @ckwalters! |
From feedback in #604 it looks like the most recent changes to the code have fixed this issue, so if any of you haven't tried pulling the new version yet that would be my suggestion. Thanks for catching this! |
Jacob, 12:27:55.580 [E] init:62 An error has occurred (IndexError): index 395 is out of bounds for axis 0 with size 394 QWidget: Must construct a QApplication before a QWidget Tnanks for catching this! |
@jacobpennington Hi Jacob! Both of your fixes (duplicating the .npy file and re-installing kilosort) worked for me to allow me to open results in phy, but as of this morning 3/5 the setup.py file in the current repo is not working for me. I ended up using the setup.py file from the old repo which worked fine. |
@ckwalters What issue are you having with the setup file? |
@AlchemsitY Just double checking, did you reinstall from source after pulling the new version, or install in editable mode? |
It was a setuptools_scm problem:
|
I excitedly found the version updated and tried the new one. Now I have established the solo environment for Phy, but new error is reported as the Traceback shows.Thanks for catching this. Traceback (most recent call last): |
@AlchemsitY, I have a PR open to fix this. But Phy can not be used with python 3.12 because of the removal of imp for importlib. So you need the env to be <3.12. This error is due to this. |
@ckwalters Which command are you using to install? I can only reproduce that error using |
@jacobpennington I was using the instructions as written in the ks4 documentation, |
@carsen-stringer Any ideas on the |
hi, zm711. Thanks for catching this. May I ask where is your PR about this error? I'd like to hava a try. Thanks a lot! |
@AlchemsitY here |
Thanks a lot! |
The setuptools error can happen I believe if the repo folder is not actually a git clone, but a zipped git folder or a copied folder without a .git folder. What might be easier to recommend for non-developers is this command to install the git version (the user does need to have git installed): |
The original issue appears to be resolved. If you continue to have trouble with installation, please let us know in a new issue. |
Describe the issue:
hello , I have tried to compare results from different versions of Kilosort . The problem is when I run Phy on KS4 results, I get this error
" IndexError: index 232 is out of bounds for axis 0 with size 232
QWidget: Must construct a QApplication before a QWidget .
while it doesnt give the error when I run the Phy on same data for KS2 and KS2.5 results .
The text was updated successfully, but these errors were encountered: