carputilsGUI

openCARP examples GUI

Plot

Visualizer

Installation

Prerequisites

  • Install Docker version 19.03.5 or later.
  • For Linux users, additionally install Docker-compose 1.24.0 or later.
  • For macOS or Windows, you need administration rights for your machine during installation

carputilsGUI

Checkout the repository by using a command line terminal git clone git@git.opencarp.org:openCARP/carputilsgui.git or if you don't have an account on git.opencarp.org use git clone https://git.opencarp.org/openCARP/carputilsgui

Linux

Modify docker-compose.yml file as follows.

  1. Enter your carputilsGUI directory:
    cd path/to/folder/carputilsgui
  2. Open "docker-compose.yml" with your prefered editor. Comment this line by adding a # infront of the line:
    #- /usr/local/bin/docker:/usr/bin/docker
  3. And uncomment this by deleting the # infront of the line:
    - /usr/bin/docker:/usr/bin/docker

On Debian, you might also need to add permissions to resolve.conf sudo chmod o+r /etc/resolv.conf and add

{
    "dns": ["8.8.8.8"]
}

to /etc/docker/daemon.json and restart the Docker service: sudo service docker restart

macOS or Windows

Start the downloaded program "Docker Desktop".

All operating systems

Then, run docker-compose for building all images and volumes. Use sudo before docker-compose if required (Windows users need to login to Docker Desktop app with their Docker account):

cd path/to/folder/carputilsgui
docker-compose up 

The process takes a while, so please don't interrupt. When the process finishes and the terminal displays the message "flask | WSGI app 0 (mountpoint='')" (may be not the last entry), press Ctrl+c in the terminal for exit.

Usage

Starting the webApp containers

cd path/to/folder/carputilsgui
docker-compose start 

following a webrowser (checked for Chrome and Firefox) type:

    http://localhost/tutorials

You can follow the experiments at:

    https://opencarp.org/documentation/examples

The carputilsGUI runs the run.py steps of the experiments with the optional parameters and visualize the 2D or 3D results. The --visualize parameter is not required for the carputilsGUI.
If the experiment doesn't have a run.py step or has previous steps without it, you can open a new terminal tab and type:

docker exec -it opencarp /bin/bash
cd /tutorials

and follow this extra steps.

Stopping the webApp containers:

cd path/to/folder/carputilsgui
docker-compose stop

Optionally if you want to clear up all (remove) containers and volumes from app:

cd path/to/folder/carputilsgui
docker-compose down -v

Updating

If you want to update carputilsGUI and the underlying examples, stop the containers and delete the carputilsgui_app and carputilsgui_web_server images. Then, pull the updates and restart the containers.

docker-compose down -v
docker rmi carputilsgui_web_server carputilsgui_app
git pull
docker-compose up

Hints

  • In the ParaViewWeb Visualizer, the colormap is scaled to the range of the first time step by default, which can be very narrow if the tissue has not been depolarized yet (e.g., 1mV around the resting membrane voltage). In many cases it makes sense to rescale to the range of the entire simulation time. To do so, click on the file that is visualized (e.g., exp.case), then on the gear wheel next to the colorbar and then on the horizontal arrows and then on the clock icon. If you want to show the colorbar, click on the flag on the right side of the colorbar in the menu.

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