[MRG] ENH: Custom section colors in Cell.plot_morphology

[ntolley]

I'd like to make a few additions to the visualization functions that will make animating HNN simulations more straight forward. The main change is allowing a custom color for each cell section in Cell.plot_morphology like so:

from hnn_core import jones_2009_model
net = jones_2009_model()
sections = list(net.cell_types['L5_pyramidal'].sections.keys())
section_color = {sect_name: f'C{idx}' for idx, sect_name in enumerate(sections)}
net.cell_types['L5_pyramidal'].plot_morphology(color=section_color)

The other addition will be a plot_network_morphology function (alternate name suggestions are appreciated!) that simply calls Cell.plot_morphology and places the cells in their appropriate 3D position.

With these two functions the code to make animations is pretty slim and could be added as an example to the main website. Let me know what you guys think! @rythorpe @jasmainak @chenghuzi

[ntolley]

Also I don't think cell_types is used anywhere? @jasmainak

[jasmainak]

I thought this was a method of Network object so you can loop over the cell_types in a network objec ... I remember a student was working on this but not sure if it ever got merged

[ntolley]

Yeah I think that ended up getting dropped, the tests are passing so I think it's safe to remove for now

[codecov-commenter]

Codecov Report

Merging #646 (cb71a54) into master (c91fdcc) will increase coverage by 0.10%.
The diff coverage is 100.00%.

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@@            Coverage Diff             @@
##           master     #646      +/-   ##
==========================================
+ Coverage   91.79%   91.90%   +0.10%     
==========================================
  Files          22       22              
  Lines        4316     4323       +7     
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+ Hits         3962     3973      +11     
+ Misses        354      350       -4     

Impacted Files	Coverage Δ
hnn_core/cell.py	96.95% <100.00%> (ø)
hnn_core/viz.py	89.37% <100.00%> (+0.13%)	⬆️

... and 1 file with indirect coverage changes

[ntolley]

Honestly the code for plotting the sections with different colors is pretty self contained. I think it would be better to bring this to merge to keep the diff small, and then I'll open the PR for plotting the network with the true cell morphologies

[rythorpe]

I'm guessing you want granular control over section colors in order to map the section voltage to a color map for each frame?

Re: the network plotting function, you can probably pull some of the logic from #499 since @mjpelah was working on a similar problem. My preference would be to name it Network.plot_cell_morphologies() with the option of either plotting each cell type in Network.cell_types or plotting the whole network. (Maybe we could also change Network.plot_cells(), which plots the location of all cell somas, to Network.plot_cell_positions to be more consistent).

Then, Network.plot_cell_morphologies() could call Cell.plot_morphology(...pos=(x, y, z)) with a new argument that allows you to set the 3D position of the soma (recall that one of the main issues @mjpelah was working on was how to plot multiple cells on the same axes without overlap).

[ntolley]

The 'b-' is redundant now since the color 'b' is explicitly set when None is passed to color

[jasmainak]

merge button is yours @rythorpe !

don't forget to update whats_new.rst @ntolley

[rythorpe]

Looks good @ntolley!

[ntolley]

@rythorpe that's exactly right! Since the voltages recorded for each section are stored in a dictionary, it's really easy to convert that to cell colors