[MRG] add method to plot cell morphologies #319

jasmainak · 2021-04-23T22:21:52Z

Plots the cell morphology

codecov-commenter · 2021-04-24T00:09:11Z

Codecov Report

Merging #319 (caed5ff) into master (eb17311) will increase coverage by 0.10%.
The diff coverage is 95.34%.

❗ Current head caed5ff differs from pull request most recent head 83360c1. Consider uploading reports for the commit 83360c1 to get more accurate results

@@            Coverage Diff             @@
##           master     #319      +/-   ##
==========================================
+ Coverage   90.43%   90.53%   +0.10%     
==========================================
  Files          14       14              
  Lines        2425     2493      +68     
==========================================
+ Hits         2193     2257      +64     
- Misses        232      236       +4

Impacted Files	Coverage Δ
hnn_core/cell.py	`95.45% <ø> (-0.14%)`	⬇️
hnn_core/network.py	`92.47% <66.66%> (-0.58%)`	⬇️
hnn_core/viz.py	`87.50% <93.33%> (+1.11%)`	⬆️
hnn_core/basket.py	`100.00% <100.00%> (ø)`
hnn_core/params_default.py	`100.00% <100.00%> (ø)`
hnn_core/pyramidal.py	`98.13% <100.00%> (-0.11%)`	⬇️
hnn_core/cell_response.py	`83.73% <0.00%> (+2.48%)`	⬆️

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hnn_core/viz.py

hnn_core/params_default.py

ntolley · 2021-04-26T01:07:18Z

doc/whats_new.rst

@@ -16,6 +16,8 @@ Changelog
 ~~~~~~~~~
 - Store all connectivity information under :attr:`~hnn_core.Network.connectivity` before building the network, by `Nick Tolley`_ in `#276 <https://github.com/jonescompneurolab/hnn-core/pull/276>`_

+- Add new function :func:`~hnn_core.viz.plot_cell_morphology` to visualize cell morphology in `#319 <https://github.com/jonescompneurolab/hnn-core/pull/319>`_


Suggested change

- Add new function :func:`~hnn_core.viz.plot_cell_morphology` to visualize cell morphology in `#319 <https://github.com/jonescompneurolab/hnn-core/pull/319>`_

- Add new function :func:`~hnn_core.viz.plot_cell_morphology` to visualize cell morphology, by `Mainak Jas`_ in `#319 <https://github.com/jonescompneurolab/hnn-core/pull/319>`_

ntolley · 2021-04-26T01:11:46Z

hnn_core/network.py

+        ----------
+        axes : list of instance of Axes3D
+            Matplotlib 3D axis
+        cell_types : 'L5Pyr' | 'L5Basket' | list


Suggested change

cell_types : 'L5Pyr' | 'L5Basket' | list

cell_types : str | list of str

ntolley · 2021-04-26T01:12:59Z

hnn_core/network.py

+        axes : list of instance of Axes3D
+            Matplotlib 3D axis
+        cell_types : 'L5Pyr' | 'L5Basket' | list
+            The cell types.


Suggested change

The cell types.

The cell types. Valid strings include: 'L5Pyr', 'L2Pyr'

hnn_core/viz.py

ntolley · 2021-04-26T01:20:00Z

hnn_core/viz.py

+    ----------
+    axes : list of instance of Axes3D
+        Matplotlib 3D axis
+    cell_types : 'L5Pyr' | 'L5Basket' | list


Suggested change

cell_types : 'L5Pyr' | 'L5Basket' | list

cell_types : str | list of str

ntolley · 2021-04-26T01:20:31Z

hnn_core/viz.py

+    axes : list of instance of Axes3D
+        Matplotlib 3D axis
+    cell_types : 'L5Pyr' | 'L5Basket' | list
+        The cell types.


Suggested change

The cell types.

The cell types. Valid strings include: 'L5Pyr', 'L2Pyr'

cjayb · 2021-04-26T14:55:17Z

I like the barebones first pass at (any!) visualisation. This could clearly be improved on in future PRs.

Could we make this 2D? The 3rd dimension is super confusing: rotating the axes isn't stable with effectively two degrees of freedom. As long as our basal oblique dendrites are in the same plane, I think we should plot them in a XZ-system, where Z is the cortical depth direction. The NEURON sections are defined as (x, z, y), which no doubt has a historical reason.

I'd also advocate fixing the Z-range to always start from 0 (white matter begins). That way the size difference between L2/3 and L5 pyramidals becomes obvious, as does their relative depth in cortex.

jasmainak · 2021-04-26T15:57:37Z

okay starting in reverse order with comments. @cjayb better?

it's still a matplotlib 3D plot but since axes are turned off, I don't anticipate users to interact with. It also keeps the door open for future additions where there is a non-zero projection of a dendrite along the third axis

cjayb · 2021-04-26T16:01:25Z

I guess I prefer the new axes-less plot, yes. Emphasises relative size and location, which are important.

jasmainak · 2021-04-26T19:24:45Z

hnn_core/basket.py

+    def secs(self):
+        return _secs_Basket()
+
+    def set_geometry(self):


this should be unified with Pyramidal class set_geometry but I would keep this for a followup PR

cjayb · 2021-04-27T17:48:09Z

As mentioned in #202, could we please agree on our axes? I think this PR should be relatable to the output of net.plot_cells(). Ultimately they will perhaps merge, but for now, what are the axes labels on each?

The above is clearly rotated to align the apical dendrites with the Z-direction (which intuitively makes more sense to me...)

jasmainak · 2021-04-28T15:47:01Z

@rythorpe see caed5ff which gives

now I do concede that the sections are not cylindrical but you don't realize that until you interact with this figure. Personally, for me, this is good enough for the use case I outlined above (educational). Cylindrical is possible although probably not worth it currently

cjayb · 2021-04-28T16:16:18Z

I like this, +1 for merge and iterate later

hnn_core/pyramidal.py

cjayb

I see I hadn't submitted this, sorry... @jasmainak see my one question in the test, otherwise good to merge?

cjayb · 2021-04-28T16:13:38Z

hnn_core/tests/test_viz.py

+    with pytest.raises(ValueError, match='Unrecognized cell type'):
+        plot_cell_morphology(cell_types='blah')
+    axes = plot_cell_morphology(cell_types='L2Pyr')
+    len(axes) == 1


Missing assert?

@jasmainak could you confirm this before I merge?

oops indeed, fixed now

cjayb · 2021-04-29T14:45:02Z

Go @jasmainak !

VIZ add method to plot cell morphologies

1d4e701

jasmainak force-pushed the plot_morphology branch from 1740d3c to 1d4e701 Compare April 23, 2021 22:23

jasmainak changed the title ~~ENH WIP add method to plot cell morphologies~~ [MRG] add method to plot cell morphologies Apr 23, 2021

TST: add test for 3d viz of cells

8d57230

jasmainak force-pushed the plot_morphology branch from 697f6b2 to 8d57230 Compare April 23, 2021 22:31

jasmainak added 2 commits April 23, 2021 18:33

ENH: whats new

4f75e91

PEP8 ignore

1bb8390

jasmainak requested review from ntolley and rythorpe April 24, 2021 00:10

rythorpe reviewed Apr 26, 2021

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ntolley reviewed Apr 26, 2021

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ENH: better alignment

3dfc3fa

jasmainak added 2 commits April 26, 2021 15:17

ENH: extend viz to basket cells

1832227

FIX address comments

c5b5078

jasmainak commented Apr 26, 2021

View reviewed changes

jasmainak force-pushed the plot_morphology branch from 7796c4c to 050e609 Compare April 26, 2021 19:26

Cosmit

2a2d519

jasmainak force-pushed the plot_morphology branch from 050e609 to 2a2d519 Compare April 26, 2021 19:29

ENH: add diameter

caed5ff

rythorpe reviewed Apr 28, 2021

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rythorpe approved these changes Apr 29, 2021

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jasmainak mentioned this pull request Apr 29, 2021

[MRG] Improve cell classes #322

Merged

6 tasks

cjayb approved these changes Apr 29, 2021

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ENH: missing assert

83360c1

cjayb merged commit 4cbc4b3 into jonescompneurolab:master Apr 29, 2021

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[MRG] add method to plot cell morphologies #319

[MRG] add method to plot cell morphologies #319

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cjayb commented Apr 29, 2021

	- Add new function :func:`~hnn_core.viz.plot_cell_morphology` to visualize cell morphology in `#319 <https://github.com/jonescompneurolab/hnn-core/pull/319>`_
	- Add new function :func:`~hnn_core.viz.plot_cell_morphology` to visualize cell morphology, by `Mainak Jas`_ in `#319 <https://github.com/jonescompneurolab/hnn-core/pull/319>`_

	cell_types : 'L5Pyr' \| 'L5Basket' \| list
	cell_types : str \| list of str

	The cell types.
	The cell types. Valid strings include: 'L5Pyr', 'L2Pyr'

[MRG] add method to plot cell morphologies #319

[MRG] add method to plot cell morphologies #319

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