pingu_98/cara
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Merge branch 'feature/no_computing_before_first_time' into 'master'

Browse source 
Model optimisation: avoid computing before first presence time

See merge request cara/cara!254
This commit is contained in:
Philip Elson 2021-09-13 12:00:07 +02:00
commit 743d4ab706
2 changed files with 17 additions and 1 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

14
cara/models.py
View file

@ -776,6 +776,14 @@ class ConcentrationModel:
state_change_times.update(self.ventilation.transition_times()) state_change_times.update(self.ventilation.transition_times())
return sorted(state_change_times) return sorted(state_change_times)
@method_cache
def _first_presence_time(self) -> float:
"""
First presence time. Before that, the concentration is zero.
"""
return self.infected.presence.boundaries()[0][0]
def last_state_change(self, time: float) -> float: def last_state_change(self, time: float) -> float:
""" """
Find the most recent/previous state change. Find the most recent/previous state change.
@ -823,7 +831,9 @@ class ConcentrationModel:
Note that time is not vectorised. You can only pass a single float Note that time is not vectorised. You can only pass a single float
to this method. to this method.
""" """
if time == 0: # The model always starts at t=0, but we avoid running concentration calculations
# before the first presence as an optimisation.
if time <= self._first_presence_time():
return 0.0 return 0.0
next_state_change_time = self._next_state_change(time) next_state_change_time = self._next_state_change(time)
IVRR = self.infectious_virus_removal_rate(next_state_change_time) IVRR = self.infectious_virus_removal_rate(next_state_change_time)
@ -841,6 +851,8 @@ class ConcentrationModel:
""" """
Get the integrated concentration dose between the times start and stop. Get the integrated concentration dose between the times start and stop.
""" """
if stop <= self._first_presence_time():
return 0.0
state_change_times = self.state_change_times() state_change_times = self.state_change_times()
req_start, req_stop = start, stop req_start, req_stop = start, stop
total_concentration = 0. total_concentration = 0.

4
cara/tests/models/test_concentration_model.py
View file

@ -121,6 +121,10 @@ def test_next_state_change_time_out_of_range(simple_conc_model: models.Concentra
simple_conc_model._next_state_change(3.1) simple_conc_model._next_state_change(3.1)
def test_first_presence_time(simple_conc_model):
assert simple_conc_model._first_presence_time() == 0.5
def test_integrated_concentration(simple_conc_model): def test_integrated_concentration(simple_conc_model):
c1 = simple_conc_model.integrated_concentration(0, 2) c1 = simple_conc_model.integrated_concentration(0, 2)
c2 = simple_conc_model.integrated_concentration(0, 1) c2 = simple_conc_model.integrated_concentration(0, 1)