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Avoiding when optical density is run

It's common to want a feature to turn off, or more generally change behaviour, when a sensitive optical density reading is taken. For example, if running an air bubbler, you may want to turn it off before an OD reading is taken, and then turn if back on after.

This behaviour is so common, we've added a helper class to take care of it for you. In pioreactor.background_jobs.base is the class BackgroundJobWithDodgingContrib that implements most of the "dodging" behaviour for you. you'll only need to do three things:

  1. Inherit from BackgroundJobWithDodgingContrib, instead of BackgroundJobContrib
from pioreactor.background_jobs.base import BackgroundJobWithDodgingContrib

class JustPause(BackgroundJobWithDodgingContrib):
    ...
  1. Fill in what to do before, and after, an OD reading takes place by implementing method action_to_do_before_od_reading and action_to_do_after_od_reading, respectively.
class JustPause(BackgroundJobWithDodgingContrib):

    ...


    def action_to_do_before_od_reading(self):
        # example
        self.logger.debug("Pausing")
        self.stop_pumping()

    def action_to_do_after_od_reading(self):
        # example
        self.logger.debug("Unpausing")
        self.start_pumping()

  1. We also want some "buffer" time before and after an OD reading. For example, if using a bubbler, we want the bubbles to dissipate completely before taking an OD reading. We should stop bubbling early then. To set these times, add the following to your config.ini:
[<job_name>]
pre_delay_duration=<float>
post_delay_duration=<float>
enable_dodging_od=1 # 1 if you want the behaviour, 0 to disable it.

The diagram of timing, actions, and OD reading, looks like the following:

And you're done!