Using PyJAMAS in headless mode

Some times it can be convenient to create a PyJAMAS instance within a notebook, or in an environment in which no display is available, to use a PyJAMAS object and the associated functionality. While these should work with no problem, creating the PyJAMAS object could printout warnings related to the lack of a display. To get around these issues, it is possible to create the PyJAMAS object in headless mode. In headless mode, PyJAMAS uses Qt offscreen rendering capabilities to avoid the need for a display. This is done by setting the environment variable QT_QPA_PLATFORM to offscreen before creating the PyJAMAS object. Please, note that once a headless PyJAMAS object is created, it is not possible to create a non-headless PyJAMAS object in the same Python session (e.g. notebook), and vice versa.

This code block illustrates how to create a PyJAMAS object in headless mode, how to use the headless PyJAMAS object to load annotations onto a virtual image (notice the second parameter passed on to cbLoadAnnotations), and how to plot the trajectories of the fiducials loaded (this time using a static PyJAMAS method, plotly_trajectories):.

from pyjamas.pjscore import PyJAMAS
from pyjamas.rutils import RUtils

apjs = PyJAMAS(headless=True)  # headless!!

thepath = 'path/to/your/annotations.pjs'

apjs.io.cbLoadAnnotations([thepath], '')  # no display

fig_trajectories = RUtils.plotly_trajectories(apjs.fiducials, xy_res, t_res)
fig_trajectories.show()