add reporting of simulation progress to terminal if simulation not visualised

Author: paulvangentcom

config.py

@@ -11,7 +11,7 @@ class config_error(Exception):
 class Configuration():
  def __init__(self, *args, **kwargs):
  #simulation variables
- self.verbose = False #whether to print infections, recoveries and fatalities to the terminal
+ self.verbose = True #whether to print infections, recoveries and fatalities to the terminal
  self.simulation_steps = 10000 #total simulation steps performed
  self.tstep = 0 #current simulation timestep
  self.save_data = False #whether to dump data at end of simulation

infection.py

@@ -196,7 +196,7 @@ def infect(population, Config, frame, send_to_location=False,
  new_infections.append(np.int32(person[0]))
 
  if len(new_infections) > 0 and Config.verbose:
- print('at timestep %i these people got sick: %s' %(frame, new_infections))
+ print('\nat timestep %i these people got sick: %s' %(frame, new_infections))
 
  if len(destinations) == 0:
  return population
@@ -298,9 +298,9 @@ def recover_or_die(population, frame, Config):
  recovered.append(np.int32(infected_people[infected_people[:,0] == idx][:,0][0]))
 
  if len(fatalities) > 0 and Config.verbose:
- print('at timestep %i these people died: %s' %(frame, fatalities))
+ print('\nat timestep %i these people died: %s' %(frame, fatalities))
  if len(recovered) > 0 and Config.verbose:
- print('at timestep %i these people recovered: %s' %(frame, recovered))
+ print('\nat timestep %i these people recovered: %s' %(frame, recovered))
 
  #put array back into population
  population[population[:,6] == 1] = infected_people

simulation.py

@@ -14,7 +14,7 @@
 from path_planning import go_to_location, set_destination, check_at_destination,\
 keep_at_destination, reset_destinations
 from population import initialize_population, initialize_destination_matrix,\
-set_destination_bounds, save_data, Population_trackers
+set_destination_bounds, save_data, save_population, Population_trackers
 from visualiser import build_fig, draw_tstep, set_style
 
 #set seed for reproducibility
@@ -119,10 +119,19 @@ def tstep(self):
  self.pop_tracker.update_counts(self.population)
 
  #visualise
- draw_tstep(self.Config, self.population, self.pop_tracker, self.frame, 
- self.fig, self.spec, self.ax1, self.ax2)
- 
-
+ if self.Config.visualise:
+ draw_tstep(self.Config, self.population, self.pop_tracker, self.frame, 
+ self.fig, self.spec, self.ax1, self.ax2)
+ else:
+ #report stuff to console
+ sys.stdout.write('\r')
+ sys.stdout.write('%i: healthy: %i, infected: %i, immune: %i, in treatment: %i, \
+dead: %i, of total: %i' %(self.frame, self.pop_tracker.susceptible[-1], self.pop_tracker.infectious[-1],
+ self.pop_tracker.recovered[-1], len(self.population[self.population[:,10] == 1]),
+ self.pop_tracker.fatalities[-1], self.Config.pop_size))
+ #save popdata if required
+ if self.Config.save_pop and (self.frame % self.Config.save_pop_freq) == 0:
+ save_population(self.population, self.frame, self.Config.save_pop_folder)
  #run callback
  self.callback()
 
@@ -145,18 +154,34 @@ def callback(self):
 
 
  def run(self):
- for t in range(self.Config.simulation_steps):
+ while self.frame < self.Config.simulation_steps:
  try:
  sim.tstep()
- sys.stdout.write('\r')
- sys.stdout.write('%i / %i' %(t, self.Config.simulation_steps))
  except KeyboardInterrupt:
  print('\nCTRL-C caught, exiting')
  sys.exit(1)
 
+ #check whether to end if no infecious persons remain.
+ #check if self.frame is above some threshold to prevent early breaking when simulation
+ #starts initially with no infections.
+ if self.Config.endif_no_infections and self.frame >= 500:
+ if len(self.population[(self.population[:,6] == 1) | 
+ (self.population[:,6] == 4)]) == 0:
+ self.frame = self.Config.simulation_steps
+
  if self.Config.save_data:
  save_data(self.population, self.pop_tracker)
 
+ #report outcomes
+ print('\n-----stopping-----\n')
+ print('total dead: %i' %len(self.population[self.population[:,6] == 3]))
+ print('total recovered: %i' %len(self.population[self.population[:,6] == 2]))
+ print('total infected: %i' %len(self.population[self.population[:,6] == 1]))
+ print('total infectious: %i' %len(self.population[(self.population[:,6] == 1) |
+ (self.population[:,6] == 4)]))
+ print('total unaffected: %i' %len(self.population[self.population[:,6] == 0]))
+
+
 
 if __name__ == '__main__':
 
@@ -175,8 +200,8 @@ def run(self):
  #sim.Config.colorblind_type = 'deuteranopia'
 
  #set reduced interaction
- sim.Config.set_reduced_interaction()
- sim.population_init()
+ #sim.Config.set_reduced_interaction()
+ #sim.population_init()
 
  #set lockdown scenario
  #sim.Config.set_lockdown(lockdown_percentage = 0.1, lockdown_compliance = 0.95)