Skip to content

Conversation

@sanjayankur31
Copy link
Member

Adds more morphology related plots

`pytest` is called in `test-ghactions.sh` already
Required to correctly load the hoc files by NEURON
and not in each iteration of the loop

CC @pgleeson
Otherwise plots remain open and consume memory. matplotlib warns:

```
.../pyneuroml/plot/PlotMorphology.py:986:
RuntimeWarning: More than 20 figures have been opened. Figures created
through the pyplot interface (`matplotlib.pyplot.figure`) are retained
until explicitly closed and may consume too much memory. (To control
this warning, see the rcParam `figure.max_open_warning`).

```
@sanjayankur31 sanjayankur31 marked this pull request as ready for review March 15, 2023 14:05
@sanjayankur31
Copy link
Member Author

This one is also ready for review. It adds an interactive vispy based viewer which is fairly performant. Screencast for a good sized model:

$ pynml-summary Balanced_610cells_0conns.net.nml 
pyNeuroML >>> INFO - Loading NeuroML2 file: Balanced_610cells_0conns.net.nml
*******************************************************
* NeuroMLDocument: Balanced_610cells_0conns
*
*  ExpTwoSynapse: ['synAmpa1', 'synGaba1']
*  PoissonFiringSynapse: ['psf1']
*  Property: ['Network seed = 1234']
*
*  Network: Balanced_610cells_0conns (temperature: 32degC)
*
*   610 cells in 3 populations 
*     Population: popBBP with 10 components of type cADpyr229_L23_PC_5ecbf9b163_0_0
*       Locations: [(-135.6341, 183.0145, 367.6131), ...]
*       Properties: color=0 .8 0; 
*     Population: popExc with 400 components of type HH_477127614
*       Locations: [(573.1628, 70.3663, 104.4949), ...]
*       Properties: color=.8 0 0; 
*     Population: popInh with 200 components of type HH_476686112
*       Locations: [(273.6470, 115.2328, 162.9573), ...]
*       Properties: color=0 0 .8; 
*
*   0 connections in 0 projections 
*
*   400 inputs in 1 input lists 
*     Input list: Stim0 to popExc, component psf1
*       400 inputs: [(Input 0: 0:0(0.500000)), ...]
*
*******************************************************
pynml-plotmorph-interactive3d.webm

Things we still need to do:

  • plot inputs in both 2d and 3d plots: this requires some more thought since we'll need to parse the target strings, which can be provided in multiple formats, in the input lists to get the target segments and then get the locations from the segments

@sanjayankur31 sanjayankur31 added the S: ready for review Status: ready for review label Mar 15, 2023
@pgleeson pgleeson mentioned this pull request May 2, 2023
3 tasks
@pgleeson pgleeson merged commit c1095a6 into development May 3, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

S: ready for review Status: ready for review T: enhancement Type: enhancement

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants