These are the docker configuration files to make a baseline user environment for 3D Slicer.
It includes:
- base: a gui-less debian with file management via webdav
- x11: a basic gui environment with noVNC
- slicer-dev: pre-installed developer environment to build Slicer
- slicer: a binary distribution version of Slicer you can connect to
- slicer-chronicle: an example of a customized slicer
The build.sh script shows how to make the dockers (change the account from stevepieper to your docker hub name)
Then run the container with a command like this:
docker run -d -p 8080:8080 --name slicer stevepieper/slicer-chronicle
then open localhost:8080 in your browser and click the "X11 Session" button.
Close the container down again with:
docker rm -f slicer
The push.sh script sends the new images to hub.docker.com.
The script below can be run in an instance and can be used as a template for more sophisticated analysis scripts.
"""
Here's a simple proof of concept example to run a slicer based script
in a docker instance.
Note that this runs in a full virtualized desktop envionment, so anything
that works in Slicer on a desktop should also work in the docker instance,
including rendering operations.
First create a directory called /tmp/shared that will serve as the bridge
between the host and the instance.
Then copy this file myScript.py into /tmp/shared
Run this script with a command like the following:
docker run -v /tmp/shared:/tmp/shared -p 8080:8080 --rm -it --env SLICER_ARGUMENTS="--python-script /tmp/shared/myScript.py" stevepieper/slicer
it should print some diagnostic info and then exit.
After it runs you will have a copy of the MRHead.nrrd sample data in the /tmp/shared directory.
"""
# as an example, download data and save it locally
import SampleData
mrHeadVolume = SampleData.downloadSample("MRHead")
slicer.util.saveNode(mrHeadVolume, "/tmp/MRHead-from-docker.nrrd")
import os
# use sudo to copy into the shared folder
os.system("sudo cp /tmp/MRHead-from-docker.nrrd /tmp/shared/MRHead-from-docker.nrrd")
# gracefully shut down the docker instance
os.system('sudo kill -s SIGTERM 1')