Gamma tutorial issues

[asoplata]

There are a few outstanding issues with the new CoreGUI Gamma tutorial specifically:

• Due to the recent change to the default morlet wavelet cycle divisor (see hotfix: Change Morlet cycles for better alpha hnn-core#928 ), a simulation tstop of 250 no longer produces any spectrogram. I will make PRs to extend the time length of simulation so this is avoided, both in here in hnn-tutorials and in the related file in hnn-data.

• Figures 7, 9.B, 19, and 21.B, all of which use the PSD Layers plot, do not actually display the PSDs of each layer plus the aggregate. This is a known issue (see GUI: PSD Layers plot does not plot PSD of layers hnn-core#954 ). This can wait to be fixed until the GUI issue is resolved.

• Figure 12 is incorrect:

There is a step missing between Figure 11 and Figure 12. This section may have to be partially rewritten. If I follow the CoreGUI tutorial exactly, instead of Figure 12, I get the following output:

This appears to be due to a difference in the tonic drive strength. In the original tutorial https://jonescompneurolab.github.io/hnn-tutorials/gamma/gamma near Figure 11, the L5 Pyr tonic drive is set to 6.0 nA (but in the newest CoreGUI tutorial, it is only set to 2.0 nA). If I make the changes necessary for the gamma_L5weak_tonic_02 simulation in the CoreGUI tutorial, but ALSO increase the L5 Pyr tonic drive from 2 to 6, only then do I get the output exactly as shown in Figure 12.A:

• Figures 22.A-C no longer show increased variability in the spectral peaks. This is possibly due to the change in default wavelet cycle divisor. Instead of 22.C, I get something resembling shown below:

• Update all spectrogram plots: Now that the wavelet cycle divisor has been changed (see above), all the spectrograms figures come out looking a bit different than their versions in the current tutorial. However, changing this can wait until we make further GUI changes and regenerate all the existing figures.

[dylansdaniels]

Sounds like the right path forward on all items. I think you're totally right that there's a step missing between Figs 11/12