local variable 'con_methods' referenced before assignment

[pasadesh]

Describe the bug

local variable 'con_methods' referenced before assignment (line 1120 in the spectral_connectivity_epochs function).

Steps to reproduce

Here I run the following code:

con_methods = ['pli', 'wpli2_debiased', 'ciplv']
con = spectral_connectivity_epochs(label_ts, method=con_methods, mode='multitaper', sfreq=sfreq, fmin=fmin, fmax=fmax,
                                    faverage=True, mt_adaptive=True, n_jobs=1)

as it is in the example (https://mne.tools/mne-connectivity/dev/auto_examples/mne_inverse_label_connectivity.html) and I get the following error... local variable 'con_methods' referenced before assignment (line 1120 in the spectral_connectivity_epochs function).

Expected results

Actual results

Additional information

[ruuskas]

Have you tried downloading the example and running it with the latest version?

I tried and wasn't able to reproduce the problem.

[pasadesh]

I downloaded your data and ran the code, it worked but again I ran only the following line of the codes with your data and got the same error... local variable 'con_methods' referenced before assignment

[ruuskas]

What do you mean by running only that one line of code? All code in the script should be run to assign values for the arguments to spectral_connectivity_epochs.

[pasadesh]

I mean after running the entire code, (and watching the nice plot) I run only this line >

con_methods = ['pli', 'wpli2_debiased', 'ciplv']
con = spectral_connectivity_epochs(label_ts, method=con_methods, mode='multitaper', sfreq=sfreq, fmin=fmin, fmax=fmax,
                                    faverage=True, mt_adaptive=True, n_jobs=1)
It should work, because no argument is changed... but I got the error (I checked with mine and with your data too)

[adam2392]

What is the output for mne.sys_info?

[pasadesh]

function mne.utils.config.sys_info(fid=None, show_paths=False, *, dependencies='user')

[adam2392]

What is the output of running it?

https://mne.tools/dev/generated/mne.sys_info.html

[pasadesh]

Platform: Windows-10-10.0.19044-SP0 Python: 3.10.6 | packaged by conda-forge | (main, Oct 24 2022, 16:02:16) [MSC v.1916 64 bit (AMD64)] Executable: e:\ZNZ\eeg_resting-state.venv\python.exe CPU: Intel64 Family 6 Model 60 Stepping 3, GenuineIntel: 8 cores Memory: 7.9 GB

[pasadesh]

Output exceeds the size limit. Open the full output data in a text editor Platform: Windows-10-10.0.19044-SP0 Python: 3.10.6 | packaged by conda-forge | (main, Oct 24 2022, 16:02:16) [MSC v.1916 64 bit (AMD64)] Executable: e:\ZNZ\eeg_resting-state.venv\python.exe CPU: Intel64 Family 6 Model 60 Stepping 3, GenuineIntel: 8 cores Memory: 7.9 GB

mne: 1.2.1 numpy: 1.21.6 {OpenBLAS 0.3.17 with 8 threads} scipy: 1.9.1 matplotlib: 3.6.2 {backend=module://matplotlib_inline.backend_inline}

sklearn: 1.1.2 numba: 0.55.0 nibabel: 4.0.2 nilearn: 0.9.2 dipy: 1.5.0 openmeeg: Not found cupy: Not found pandas: 1.4.4 pyvista: 0.36.1 {OpenGL 4.3.0 - Build 20.19.15.4835 via Intel(R) HD Graphics 4600} pyvistaqt: 0.9.0 ipyvtklink: 0.2.3 vtk: 9.2.2 qtpy: 2.2.0 {PyQt5=5.15.2} ipympl: Not found ... mne_features: Not found mne_qt_browser: 0.4.0 mne_connectivity: 0.5.0.dev0 mne_icalabel: Not found

[ruuskas]

Hi @pasadesh!

The problem is that label_ts is a generator, which gets exhausted when spectral_connectivity_epochs is called for the first time.

If you want to run spectral_connectivity_epochs multiple times, you should replace this:

label_ts = mne.extract_label_time_course(
    stcs, labels, src, mode='mean_flip', return_generator=True)

with this:

label_ts = mne.extract_label_time_course(
    stcs, labels, src, mode='mean_flip', return_generator=False)

This is not a bug in the code but rather a Python feature.

[adam2392]

Closing as this is not a bug. Feel free to re-open if you disagree @pasadesh