from vivarium.core.process import Step
[docs]
class DivisionDetector(Step):
"""Calculates division threshold for inner simulation in EngineProcess.
Upon reaching threshold, sets a flag through the `division_trigger` port
that can be detected via a tunnel and used to initiate division.
By default, we forgo the dry mass threshold in favor of a boolean
threshold set by the MarkDPeriod Step in ecoli.processes.cell_division.
Users can revert to the mass threshold by setting d_period to False in
their config json.
"""
name = "division-detector"
defaults = {
"division_threshold": None,
"division_variable": None,
"chromosome_path": None,
"dry_mass_inc_dict": None,
"division_mass_multiplier": 1,
}
def __init__(self, config):
super().__init__(config)
self.division_threshold = self.parameters["division_threshold"]
self.dry_mass_inc_dict = self.parameters["dry_mass_inc_dict"]
self.division_mass_multiplier = self.parameters["division_mass_multiplier"]
[docs]
def ports_schema(self):
return {
"division_variable": {},
"division_trigger": {
"_default": False,
"_updater": "set",
"_divider": {"divider": "set_value", "config": {"value": False}},
},
"full_chromosomes": {},
"media_id": {},
"division_threshold": {
"_default": self.parameters["division_threshold"],
"_updater": "set",
"_divider": {
"divider": "set_value",
"config": {"value": self.parameters["division_threshold"]},
},
},
}
[docs]
def next_update(self, timestep, states):
update = {}
division_threshold = states["division_threshold"]
if division_threshold == "mass_distribution":
mass_inc = self.dry_mass_inc_dict[states["media_id"]]
division_threshold = (
states["division_variable"]
+ mass_inc.asNumber() * self.division_mass_multiplier
)
update["division_threshold"] = division_threshold
if (states["division_variable"] >= division_threshold) and (
states["full_chromosomes"]["_entryState"].sum() >= 2
):
update["division_trigger"] = True
return update