error with interactive annotations

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1

hi everyone,

iā€™m trying to manually annotate parts of my data that are noisy. iā€™m importing my data and am going in interactive annotations as per the tutorial:

raw = mne.io.read_raw_fif(fifpath, allow_maxshield=True, preload=True, verbose=None)
raw_lowpass = raw.filter(h_freq=40, l_freq=None)
fig3 = raw_lowpass.plot(duration=30, n_channels=75, title='lowpass filter at 40hz', event_color='red', remove_dc=True, block=True, show=True)
fig3.fake_keypress('a')

i drag and drop to create a new annotation, but when i close the interactive figure i get an error:

AttributeError: ā€˜BrowserParamsā€™ object has no attribute ā€˜keyboard_shortcutsā€™

alternatively, if i try to edit an annotation while in the interactive window, i get another error:

AttributeError: ā€˜AnnotationDockā€™ object has no attribute ā€˜mainā€™

iā€™m using dataspell 2022.3 on a mac os 12.3.1 and my mne-base package is 1.2.3

thanks for your advice (:

1 Like
2

Hello,

From the code snippet, fig3.fake_keypress('a') is used in the tutorial to demonstrate the functionality.
In practice, you have to press on the A key of your keyboard to display the annotation menu. In an interactive python shell, after raw.plot(), the figure will open (using the old matplotlib backend if you donā€™t have mne-qt-browser installed, using the modern qt backend if you have it), and then you need to press on the A key of your keyboard and it will display the annotation menu.
Next step is to create an annotation by adding a description and finally mark the segments by click/drag on the traces.

Mathieu

3

Hi Mathieu,

Thanks for the reply. Yes, i should have taken this bit out. I do actually press the ā€˜aā€™ key once the figure comes up and go into annotation mode where i click and drag to create the annotations. However the first error doesnā€™t come until i click on the X to close the figure (from annotation mode) and the second error comes up when i try to click on ā€˜edit descriptionā€™ from the annotation menu. Itā€™s ok to ā€˜add descriptionā€™, but not to edit one.

bissera

4

From the text description, nothing that could explain this behavior comes to mind.
If possible, you could join the next Office Hours on January 6th (every 2 weeks usually) and share your screen on Discord.

Mathieu

5

Thanks, just joined discord. See you next year and enjoy the holidays (:

6

based on the error messages it sounds like the errors are coming from mne-qt-browser. I donā€™t know much about DataSpell, but if itā€™s capturing the plot into a panel of its UI that could be part of the issue. You could try using the matplotlib browser backend instead: add mne.viz.set_browser_backend('matplotlib') somewhere early in your script (before any calls to raw.plot()). Thereā€™s a chance that the matplotlib backend will integrate better with DataSpell.

Another option is running the script from a terminal instead of through your IDE; that can help us track down the source of the error too. So in a terminal, running something like ipython -i my_script.py (without making the browser_backend change suggested above) could also be informative.

1 Like
7

Hi Dan,

Happy new year!!

Thanks for your message. I tried to set the backend to matplotlib in which case the visualisation just didnā€™t show up. I wasnā€™t able to run my code via the terminal, because my packages are installed on conda virtual environment and my computer didnā€™t know how to find them and i didnā€™t know how to explain it via the terminal. However, i really donā€™t know whatā€™s changed, since i didnā€™t do any work over the holidays, but the qt gui is now not crashing when i add a new annotation. Sorry i couldnā€™t help you find the source of the problem, but iā€™m happy the problem is gone.

Best,
bissera

1 Like