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QWidget: Must construct a QApplication before a QWidget
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 .
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:
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "C:\Users\CKW\anaconda3\Scripts\phy.exe\__main__.py", line 7, in <module>
File "C:\Users\CKW\anaconda3\Lib\site-packages\click\core.py", line 1128, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\click\core.py", line 1053, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\click\core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\click\core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\click\core.py", line 754, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\click\decorators.py", line 26, in new_func
return f(get_current_context(), *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\phy\apps\__init__.py", line 244, in template_extract_waveforms
model = load_model(params_path)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\phylib\io\model.py", line 1433, in load_model
return TemplateModel(**get_template_params(params_path))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\phylib\io\model.py", line 339, in __init__
self._load_data()
File "C:\Users\CKW\anaconda3\Lib\site-packages\phylib\io\model.py", line 419, in _load_data
self.sparse_clusters = self.cluster_waveforms()
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\phylib\io\model.py", line 1323, in cluster_waveforms
data[clust, :, :] = self.sparse_templates.data[val[0], :, :]
~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\numpy\core\memmap.py", line 334, in __getitem__
res = super().__getitem__(index)
^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 250 is out of bounds for axis 0 with size 250
09:30:37.015 [E] __init__:62 An error has occurred (IndexError): index 250 is out of bounds for axis 0 with size 250
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "C:\Users\CKW\anaconda3\Scripts\phy.exe\__main__.py", line 7, in <module>
sys.exit(phycli())
^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\click\core.py", line 1128, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\click\core.py", line 1053, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\click\core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\click\core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\click\core.py", line 754, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\click\decorators.py", line 26, in new_func
return f(get_current_context(), *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\phy\apps\__init__.py", line 159, in cli_template_gui
template_gui(params_path, **kwargs)
File "C:\Users\CKW\anaconda3\Lib\site-packages\phy\apps\template\gui.py", line 209, in template_gui
model = load_model(params_path)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\phylib\io\model.py", line 1433, in load_model
return TemplateModel(**get_template_params(params_path))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\phylib\io\model.py", line 339, in __init__
self._load_data()
File "C:\Users\CKW\anaconda3\Lib\site-packages\phylib\io\model.py", line 419, in _load_data
self.sparse_clusters = self.cluster_waveforms()
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\phylib\io\model.py", line 1323, in cluster_waveforms
data[clust, :, :] = self.sparse_templates.data[val[0], :, :]
~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\Lib\site-packages\numpy\core\memmap.py", line 334, in __getitem__
res = super().__getitem__(index)
^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 250 is out of bounds for axis 0 with size 250
QWidget: Must construct a QApplication before a QWidget
Hi Kilosort experts,
We got the similar error recently. We're trying to using Kilosort 4 with Plexon's 24 linear channel data, were able to import, run the sorting processing, and make some plots using of your tutorials codes by modifying some parameters. However some attempts of the parameters would cause this type of error, which resulted in fail in launching the phy gui. [e.g. settings['nearest_templates'] = 10, or settings['nearest_chans'] = 1, or settings['cluster_pcs'] = 10 and so on.
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
Traceback (most recent call last):
File "C:\Users\xx..xx\anaconda3\envs\kilosort\lib\runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "C:\Users\xx..xx\anaconda3\envs\kilosort\lib\runpy.py", line 86, in run_code
exec(code, run_globals)
File "C:\Users\xx..xx\anaconda3\envs\kilosort\Scripts\phy.exe_main.py", line 7, in
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!
@jacobpennington,
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:
- a recent change in how variables were saved for phy
- differences in the Phy version being used.
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 spike_templates.npy in the KS4 results folder to spike_detection_templates.npy (or something else, it won't be used by Phy), then make a copy of spike_clusters.npy and rename it to spike_templates.npy.
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, One last annoying point for Phy is that their readme instructions are missing a couple packages for the conda install and I have a PR open to fix their requirements.txt but Cyrille is a little busy now for upkeep. So if people come to Kilosort for help with Phy stuff the best recommendation is to install with the environment.yaml in the repo, but edit such that python < 3.12. I know it's an annoying workaround, but since I'm helping out with the issue tracker these qt widget issues come up a lot and they can usually be solved.
Thanks @ckwalters! That's actually good to know. I wanted to make sure this was a ks4 issue and not a phy issue. So this puts the issue back on the KS side.
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!
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, I tried your new version 1 hour ago, but the same bug still exists. Here is my full traceback.
12:27:55.580 [E] init:62 An error has occurred (IndexError): index 395 is out of bounds for axis 0 with size 394
Traceback (most recent call last):
File "C:\Users\alche\anaconda3\envs\kilosort\lib\runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "C:\Users\alche\anaconda3\envs\kilosort\lib\runpy.py", line 87, in run_code
exec(code, run_globals)
File "C:\Users\alche\anaconda3\envs\kilosort\Scripts\phy.exe_main.py", line 7, in
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.
@AlchemsitY Just double checking, did you reinstall from source after pulling the new version, or install in editable mode?
@ckwalters What issue are you having with the setup file?
It was a setuptools_scm problem:
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [42 lines of output]
WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does
not contain a tool.setuptools_scm section'
Traceback (most recent call last):
File "C:\Users\CKW\anaconda3\envs\kilosort\Lib\site-packages\pip\_vendor\pyproje
ct_hooks\_in_process\_in_process.py", line 353, in <module>
main()
File "C:\Users\CKW\anaconda3\envs\kilosort\Lib\site-packages\pip\_vendor\pyproje
ct_hooks\_in_process\_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\anaconda3\envs\kilosort\Lib\site-packages\pip\_vendor\pyproje
ct_hooks\_in_process\_in_process.py", line 149, in prepare_metadata_for_build_wheel
return hook(metadata_directory, config_settings)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\AppData\Local\Temp\pip-build-env-181s35hz\overlay\Lib\site-pa
ckages\setuptools\build_meta.py", line 366, in prepare_metadata_for_build_wheel
self.run_setup()
File "C:\Users\CKW\AppData\Local\Temp\pip-build-env-181s35hz\overlay\Lib\site-pa
ckages\setuptools\build_meta.py", line 487, in run_setup
super().run_setup(setup_script=setup_script)
File "C:\Users\CKW\AppData\Local\Temp\pip-build-env-181s35hz\overlay\Lib\site-pa
ckages\setuptools\build_meta.py", line 311, in run_setup
exec(code, locals())
File "<string>", line 40, in <module>
File "C:\Users\CKW\AppData\Local\Temp\pip-build-env-181s35hz\overlay\Lib\site-pa
ckages\setuptools\__init__.py", line 103, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\CKW\AppData\Local\Temp\pip-build-env-181s35hz\overlay\Lib\site-pa
ckages\setuptools\_distutils\core.py", line 147, in setup
_setup_distribution = dist = klass(attrs)
^^^^^^^^^^^^
File "C:\Users\CKW\AppData\Local\Temp\pip-build-env-181s35hz\overlay\Lib\site-pa
ckages\setuptools\dist.py", line 303, in __init__
_Distribution.__init__(self, dist_attrs)
File "C:\Users\CKW\AppData\Local\Temp\pip-build-env-181s35hz\overlay\Lib\site-pa
ckages\setuptools\_distutils\dist.py", line 283, in __init__
self.finalize_options()
File "C:\Users\CKW\AppData\Local\Temp\pip-build-env-181s35hz\overlay\Lib\site-pa
ckages\setuptools\dist.py", line 654, in finalize_options
ep(self)
File "C:\Users\CKW\AppData\Local\Temp\pip-build-env-181s35hz\overlay\Lib\site-pa
ckages\setuptools\dist.py", line 674, in _finalize_setup_keywords
ep.load()(self, ep.name, value)
File "C:\Users\CKW\AppData\Local\Temp\pip-build-env-181s35hz\normal\Lib\site-pac
kages\setuptools_scm\_integration\setuptools.py", line 101, in version_keyword
_assign_version(dist, config)
File "C:\Users\CKW\AppData\Local\Temp\pip-build-env-181s35hz\normal\Lib\site-packages\setuptools_scm\_
integration\setuptools.py", line 56, in _assign_version
_version_missing(config)
File "C:\Users\CKW\AppData\Local\Temp\pip-build-env-181s35hz\normal\Lib\site-packages\setuptools_scm\_
get_version_impl.py", line 112, in _version_missing
raise LookupError(
LookupError: setuptools-scm was unable to detect version for C:\Users\CKW\Kilosort\Kilosort4_20240305.
Make sure you're either building from a fully intact git repository or PyPI tarballs. Most other sources
(such as GitHub's tarballs, a git checkout without the .git folder) don't contain the necessary metadata and
will not work.
For example, if you're using pip, instead of https://github.com/user/proj/archive/master.zip use git+htt
ps://github.com/user/proj.git#egg=proj
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
@AlchemsitY Just double checking, did you reinstall from source after pulling the new version, or install in editable mode?
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):
File "
@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 python setup.py, which is deprecated.
@jacobpennington I was using the instructions as written in the ks4 documentation,
python -m pip install .
But I'm seeing now there's a different suggested pip command in the readme
@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.
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!
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): pip install git+https://github.com/mouseland/kilosort.git
The original issue appears to be resolved. If you continue to have trouble with installation, please let us know in a new issue.