error when running tutorial example: working-with-seeg-data

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1

Dear,
I am trying to running this tutorial example:
https://mne.tools/stable/auto_tutorials/clinical/20_seeg.html?highlight=seeg#working-with-seeg-data
however, it showed me error message as below:
AttributeError: '_Renderer' object has no attribute '_window_close_connect'

Also when I am trying to run another tutorial example:
https://mne.tools/stable/auto_tutorials/clinical/10_ieeg_localize.html
it also give me error message as: AttributeError: ā€˜_Rendererā€™ object has no attribute ā€˜plotterā€™
I think it might be package version problem. I am using python3.7.11, mayavi-4.7.4, vtk-9.1.0, numpy 1.21.4.
Could you please advise?

2

I think this might have something to do with the version of mayavi and vtk.
have a try with

vtk==8.1.2

Or much more recommended, use

conda create --name=mne --channel=conda-forge mne

which is recommended by MNE officially to install all the packages working well with MNE.

1 Like
3

Hello @Long, as @BarryLiu97 pointed out, weā€™d suggest to create an entirely new Python environment for MNE in a situation like this. Please follow the official installation instructions you can find on our website.

Best wishes,
Richard

4

Thanks for your help on this. As suggested, I install MNE with conda using:

conda create --name=mne --channel=conda-forge mne

However, when I walk through this example: https://mne.tools/stable/auto_tutorials/clinical/10_ieeg_localize.html, when I am trying to locate the ieeg with command:

gui = mne.gui.locate_ieeg(raw_ecog.info, subj_trans_ecog, CT_aligned_ecog,
subject=ā€˜sample_ecogā€™,
subjects_dir=op.join(misc_path, ā€˜ecogā€™))

There is no plot showed up, and I can see some message in the console as:

qt.qpa.drawing: Layer-backing can not be explicitly controlled on 10.14 when built against the 10.14 SDK
qt.qpa.window: <QNSWindow: 0x7f945f391c60; contentView=<QNSView: 0x7f945cdf0460; QCocoaWindow(0x6000029563c0, window=QWidgetWindow(0x600003a33c60, name="QWidgetClassWindow"))>> has active key-value observers (KVO)! These will stop working now that the window is recreated, and will result in exceptions when the observers are removed. Break in QCocoaWindow::recreateWindowIfNeeded to debug.
qt.qpa.window: <QNSWindow: 0x7f945f396aa0; contentView=<QNSView: 0x7f945f396690; QCocoaWindow(0x6000029421b0, window=QWidgetWindow(0x600003af1c20, name="QWidgetClassWindow"))>> has active key-value observers (KVO)! These will stop working now that the window is recreated, and will result in exceptions when the observers are removed. Break in QCocoaWindow::recreateWindowIfNeeded to debug.

Plot seems stucked through I can see the MNE icon showed up in my mac dock but canā€™t be clicked to open.

5

Hello @Long, which version of macOS is that?

6

Itā€™s Monterey 12.0.1.

7

Iā€™m using 12.1, I can try to run your example later today and check if it works for me. The warnings you see actually shouldnā€™t be the problemā€¦

8

I will try to upgrade to 12.1 and see. And yes, this message doesnā€™t looks like the error msg, but still the plot get stucked in my dock and wouldnā€™t come out. Other plots are working just fine.

9

I just upgraded to 12.1, not working either. The same result.

10

Dear Richard,
Have you tried on your machine yet? I am still facing the same problem. Appreciate any feedback.

11

Could you provide the information returned by mne.sys_info()?
I suspect you are running on old versions of Python/PyQt5.

12

Here is the output:

mne.sys_info()
Platform:       macOS-12.1-x86_64-i386-64bit
Python:         3.9.7 | packaged by conda-forge | (default, Sep 29 2021, 20:33:18)  [Clang 11.1.0 ]
Executable:     /Users/long/opt/anaconda3/envs/mne/bin/python
CPU:            i386: 4 cores
Memory:         16.0 GB
mne:            0.24.1
numpy:          1.21.4 {blas=NO_ATLAS_INFO, lapack=lapack}
scipy:          1.7.3
matplotlib:     3.5.0 {backend=MacOSX}
sklearn:        1.0.1
numba:          0.53.1
nibabel:        3.2.1
nilearn:        0.8.1
dipy:           1.4.1
cupy:           Not found
pandas:         1.3.4
mayavi:         4.7.2
pyvista:        0.32.1 {OpenGL 4.1 INTEL-18.3.5 via Intel(R) Iris(TM) Plus Graphics 640}
pyvistaqt:      0.5.0
ipyvtklink:     Not found
vtk:            9.0.3
PyQt5:          5.12.3
ipympl:         Not found
mne_qt_browser: 0.1.7
pooch:          v1.5.2
13

I just update the PyQt5, but sitll canā€™t open the plot. Here is the new sys_info():

mne.sys_info()
Platform:       macOS-12.1-x86_64-i386-64bit
Python:         3.9.7 | packaged by conda-forge | (default, Sep 29 2021, 20:33:18)  [Clang 11.1.0 ]
Executable:     /Users/long/opt/anaconda3/envs/mne/bin/python
CPU:            i386: 4 cores
Memory:         16.0 GB
mne:            0.24.1
numpy:          1.21.4 {blas=NO_ATLAS_INFO, lapack=lapack}
scipy:          1.7.3
matplotlib:     3.5.0 {backend=MacOSX}
sklearn:        1.0.1
numba:          0.53.1
nibabel:        3.2.1
nilearn:        0.8.1
dipy:           1.4.1
cupy:           Not found
pandas:         1.3.4
mayavi:         4.7.2
pyvista:        0.32.1 {OpenGL 4.1 INTEL-18.3.5 via Intel(R) Iris(TM) Plus Graphics 640}
pyvistaqt:      0.5.0
ipyvtklink:     Not found
vtk:            9.0.3
PyQt5:          5.15.6
ipympl:         Not found
mne_qt_browser: 0.1.7
pooch:          v1.5.2
14

I think I know where goes wrong.
When I finish plotting the first plot with viewer = T1.orthoview() and close it, error msg will show up as:

Traceback (most recent call last):
  File "/Users/long/opt/anaconda3/envs/mne/lib/python3.9/site-packages/matplotlib/cbook/__init__.py", line 287, in process
    func(*args, **kwargs)
TypeError: _cleanup() takes 1 positional argument but 2 were given

Then I run mne.gui.locate_ieeg, and it will never show up. However, if I donā€™t close the first plot, and then go ahead and run the locate_ieeg, this ieeg plot will show up. But since the first plot is always active, I canā€™t actually bring the second plot forward. So we still need to find a way to close the first plot and working on the second one.
Appreciate any help here.

15

Ok, so the version of Python is fine; and the previous version of PyQt5 was also fine.
You now have updated outside the limits for MNE: pyqt5>=5.10,<5.14; platform_system == "Darwin".

I have a macOS install on Big Sur, so itā€™s not 12.xx but I can give it a shot later today and see if Iā€™m able to reproduce.

16

Never mind, I can reproduce this TypeError: _cleanup() takes 1 positional argument but 2 were given on Windows as well with the current dev version of MNE, but it looks like a bug in nibabel: AttributeError raised in OrthoSlicer3D Ā· Issue #920 Ā· nipy/nibabel Ā· GitHub
Maybe you could try older versions of matplotlibā€¦ Or comment this line to skip this problematic plot.

I donā€™t get the last part however:

But since the first plot is always active, I canā€™t actually bring the second plot forward. So we still need to find a way to close the first plot and working on the second one.

Each plot opens in a separate free window, for my case I could close the figure and continueā€¦ and then when trying to use mne.gui.locate_ieeg I had wrong versions for some dependencies and broke my VTK install :sweat_smile:

17

I tried go ahead and call mne.gui.locate_ieeg, however no plot will show up if I do not call the first problematic plot. Very strange. Can you please try on you machine?

For the last part, I mean when I had the problematic plot and locate_ieeg open at the same time, the first problematic plot will always keep active and stay on top of the other plots even after I click on the locate_ieeg plot.

I will try old version matplotlib later.

18

I have tried matplotlib from 3.1 to 3.5. None of them work well for this tutorial example. Actually, the _cleanup() error doesnā€™t bother me, what I really want is the mne.git.locate_ieeg.