--visualize not plotting graph

Question

Hi there,

I am a new user so please excuse for asking relatively very basic question.

I have installed opencarp by pulling opencarp docker container. I am using docker on windows. As part of my first experiment of a single cell electrophysiology,  I tried to run 01_basic_bench experiments. The file run.py runs fine. However once I try to run python run.py - - visualize, the plot or visualization doesn't pop up. What possible mistake I am making ? Is the - - visualize parameter saving the plot some where else. If yes, then which folder is it saving to and how to access this folder in order to plot the graph?

Thanks

Answer 1

the --visualize flag in the experiments directly launches the visualization tool. For single cell experiments, this is matplotlib: https://git.opencarp.org/openCARP/experiments/-/blob/master/tutorials/01_EP_single_cell/01_basic_bench/run.py#L271

I don't think Docker provides a graphical interface off the shelf. What you could probably do is to change the output of matplotlib from on-screen rendering to output directly to a file. Alternatively, carputilsGUI provides a Docker-powered way to plot via the browser: https://git.opencarp.org/openCARP/carputilsgui

Comments

Thanks Axel. Your answer helped. I mounted the working dir in docker. Now using a small matlab script to plot action potential

data=importdata('C:\path\to\exp_TT2__bcl_500_ms_duration_500_ms\Trace_0.dat');
plot(data(:,1),data(:,17));