Very small performance improvement

Makefile

@@ -5,7 +5,7 @@ test:
  python -m tests.run
 
 coverage:
- coverage run -m pytest
+ coverage run -m pytest && coverage xml
 
 report:
  coverage report

simulator/constants/keys.py

@@ -10,6 +10,8 @@
 WI_K = "work_to_individual_mapping"
 HA_K = "house_to_adult_mapping"
 HS_K = "house_to_store_mapping"
+IS_K = "individual_to_store_mapping"
+SI_K = "store_to_individual_mapping"
 ITI_K = "individual_transport_individual_mapping"
 
 HB_K = "house_to_block_mapping"

simulator/helper/dynamic.py

@@ -7,13 +7,13 @@ def update_infection_period(newly_infected_individuals_arg, virus_dic):
  for i in newly_infected_individuals_arg:
  if virus_dic[STA_K][i] == HEALTHY_V:
  virus_dic[STA_K][i] = INFECTED_V
- virus_dic[NC_K] = virus_dic[NC_K] + 1
+ virus_dic[NC_K] += 1
 
 
 def update_immunity_state(virus_dic):
  for i in get_immune_people(virus_dic):
  # Losing immunity
- virus_dic[IMM_K][i] = virus_dic[IMM_K][i] - 1
+ virus_dic[IMM_K][i] -= 1
  if virus_dic[IMM_K][i] == 0:
  virus_dic[STA_K][i] = HEALTHY_V
  virus_dic[CON_K][i] = virus_dic[CON_INIT_K][i]
@@ -42,9 +42,9 @@ def decide_life_immunity(env_dic, virus_dic, icu_factor):
 
 def decrement_virus_carrier_periods(virus_dic):
  for i in get_virus_carrier_people(virus_dic):
- virus_dic[CON_K][i] = virus_dic[CON_K][i] - 1
- virus_dic[HOS_K][i] = virus_dic[HOS_K][i] - 1
- virus_dic[DEA_K][i] = virus_dic[DEA_K][i] - 1
+ virus_dic[CON_K][i] -= 1
+ virus_dic[HOS_K][i] -= 1
+ virus_dic[DEA_K][i] -= 1
 
 
 def increment_pandemic_1_day(env_dic, virus_dic, available_beds):
@@ -189,14 +189,14 @@ def propagate_to_stores(env_dic, virus_dic, probability_store_infection_arg, sam
  # [(2, 0), (3, 1), (6, 2)] 2, 3 and 6 are infected and going to the stores 0, 1 and 2
  # we divide same_store_preference by behavior since high behavior value is bad behavior
  individuals_healthy_gotostore = [
- (i, choose_weight_order(env_dic[HS_K][env_dic[IH_K][i]], same_store_preference / env_dic[IBE_K][i]))
+ (i, choose_weight_order(env_dic[IS_K][i], same_store_preference / env_dic[IBE_K][i]))
  for i in individuals_gotostore if not is_contagious(i, virus_dic)
  ]
 
  # Stores that will be visited by a contagious person
  # [ (0, 1), (0, 1.3), (2, 1.2)] where stores 0 and 2 are infected with 1, 1.3 and 1.2 weights
  infected_stores = [
- (choose_weight_order(env_dic[HS_K][env_dic[IH_K][i]], same_store_preference / env_dic[IBE_K][i]), env_dic[IBE_K][i])
+ (choose_weight_order(env_dic[IS_K][i], same_store_preference / env_dic[IBE_K][i]), env_dic[IBE_K][i])
  for i in individuals_infected_gotostore
  ]
 

simulator/helper/environment.py

@@ -4,7 +4,8 @@
 from scipy import spatial
 
 from simulator.constants.keys import nindividual_key, store_per_house_key, nb_1d_block_key, store_nb_choice_key, \
- transport_contact_cap_key, IH_K, HI_K, IAD_K, IAG_K, IW_K, WI_K, HA_K, HS_K, ITI_K, HB_K, IBE_K, IDEA_K, IHOS_K
+ transport_contact_cap_key, IH_K, HI_K, IAD_K, IAG_K, IW_K, WI_K, HA_K, HS_K, ITI_K, HB_K, IBE_K, IDEA_K, IHOS_K, \
+ IS_K, SI_K
 from simulator.constants.parameters import TPE_MAX_EMPLOYEES, PME_MAX_EMPLOYEES, GE_MAX_EMPLOYEES, covid_mortality_rate, \
  covid_hospitalization_rate
 from simulator.constants.parameters import age_dist_adults_cs, age_dist_adults, \
@@ -38,6 +39,8 @@ def get_environment_simulation(params_arg):
  geo_store = build_geo_positions_store(int(len(house_indiv) / number_store_per_house_arg))
 
  house_store = build_house_store_map(geo_store, geo_house, nb_store_choice)
+ indiv_store = build_individual_store_map(indiv_house, house_store)
+ store_indiv = build_store_individual_map(indiv_store)
 
  house_block = build_block_assignment(geo_house, nb_1d_block_arg)
  workplace_block = build_block_assignment(geo_workplace, nb_1d_block_arg)
@@ -63,6 +66,8 @@ def get_environment_simulation(params_arg):
  WI_K: workplace_indiv,
  HA_K: house_adult,
  HS_K: house_store,
+ IS_K: indiv_store,
+ SI_K: store_indiv,
  ITI_K: indiv_transport_indiv,
  HB_K: house_block,
  IBE_K: indiv_behavior
@@ -188,6 +193,17 @@ def build_house_store_map(geo_position_store_arg, geo_position_house_arg, nb_sto
  return all_hou_sto
 
 
+def build_individual_store_map(indiv_house_arg, house_store_arg):
+ all_ind_sto = {}
+ for i in range(len(indiv_house_arg)):
+ all_ind_sto[i] = house_store_arg[indiv_house_arg[i]]
+ return all_ind_sto
+
+
+def build_store_individual_map(indiv_store_arg):
+ return invert_map_list(indiv_store_arg)
+
+
 def build_individual_work_map(individual_adult_map_arg):
  # Only adults work
  workers = list([ind for ind, is_adult in individual_adult_map_arg.items() if is_adult == 1])

tests/simulator/environment_test.py

@@ -5,8 +5,9 @@
 
 from simulator.helper.environment import build_individual_houses_map, build_individual_adult_map, \
  build_individual_age_map, build_house_adult_map, build_2d_item_behavior, build_1d_item_behavior, \
- build_house_store_map, build_individual_work_map, build_individual_workblock_map, \
- build_individual_individual_transport_map, build_individual_death_rate_map, build_individual_hospitalization_map
+ build_house_store_map, build_individual_work_map, build_individual_workblock_map, build_individual_store_map, \
+ build_individual_individual_transport_map, build_individual_death_rate_map, build_individual_hospitalization_map, \
+ build_store_individual_map
 from simulator.helper.utils import invert_map_list, invert_map
 from tests.utils import g_d
 
@@ -88,6 +89,31 @@ def test_build_house_store_map(self):
  4: [4, 3, 5],
  5: [5, 4, 3]})
 
+ def test_build_indiv_store_map(self):
+ ind_hou = g_d([0, 0, 0, 0, 1, 1, 1, 1, 2, 2])
+ hou_sto = g_d([[0, 1, 2], [1, 2, 3], [4, 5, 3]])
+ result = build_individual_store_map(ind_hou, hou_sto)
+ self.assertEqual(result, {0: [0, 1, 2],
+ 1: [0, 1, 2],
+ 2: [0, 1, 2],
+ 3: [0, 1, 2],
+ 4: [1, 2, 3],
+ 5: [1, 2, 3],
+ 6: [1, 2, 3],
+ 7: [1, 2, 3],
+ 8: [4, 5, 3],
+ 9: [4, 5, 3]})
+
+ def test_build_store_individual_map(self):
+ ind_sto = {0: [0, 1, 2], 1: [2, 3, 4]}
+ result = build_store_individual_map(ind_sto)
+ self.assertEqual(result, {0: [0], 1: [0], 2: [0, 1], 3: [1], 4: [1]})
+
+ def test_build_store_individual_map2(self):
+ ind_sto = {0: [0, 1], 1: [3, 4]}
+ result = build_store_individual_map(ind_sto)
+ self.assertEqual(result, {0: [0], 1: [0], 3: [1], 4: [1]})
+
  def test_build_individual_work_map(self):
  input_individual_adult_map = {
  0: 1, 1: 1, 2: 0, 3: 0,

tests/simulator/store_propagation_test.py

@@ -17,7 +17,9 @@ def test_propagate_to_stores_child(self):
  # he can't infect anyone
  env_dic = {
  HA_K: {0: [0, 1], 1: [4, 5], 2: [8, 9]},
- HS_K: {0: [0, 0, 0], 1: [1, 1, 1], 2: [0, 0, 0]},
+ IS_K: {0: [0, 0, 0], 1: [0, 0, 0], 2: [0, 0, 0], 3: [0, 0, 0],
+ 4: [1, 1, 1], 5: [1, 1, 1], 6: [1, 1, 1], 7: [1, 1, 1],
+ 8: [0, 0, 0], 9: [0, 0, 0]},
  IH_K: {0: 0, 1: 0, 2: 0, 3: 0, 4: 1, 5: 1, 6: 1, 7: 1, 8: 2, 9: 2},
  IBE_K: {0: 1, 1: 1, 2: 1, 3: 1, 4: 1, 5: 1, 6: 1, 7: 1, 8: 1, 9: 1},
  }
@@ -40,7 +42,9 @@ def test_propagate_to_stores_adult_notcontagious(self):
  # but i8 and i9 stay healthy
  env_dic = {
  HA_K: {0: [0, 1], 1: [4, 5], 2: [8, 9]},
- HS_K: {0: [0, 0, 0], 1: [1, 1, 1], 2: [0, 0, 0]},
+ IS_K: {0: [0, 0, 0], 1: [0, 0, 0], 2: [0, 0, 0], 3: [0, 0, 0],
+ 4: [1, 1, 1], 5: [1, 1, 1], 6: [1, 1, 1], 7: [1, 1, 1],
+ 8: [0, 0, 0], 9: [0, 0, 0]},
  IH_K: {0: 0, 1: 0, 2: 0, 3: 0, 4: 1, 5: 1, 6: 1, 7: 1, 8: 2, 9: 2},
  IBE_K: {0: 1, 1: 1, 2: 1, 3: 1, 4: 1, 5: 1, 6: 1, 7: 1, 8: 1, 9: 1},
  }
@@ -63,7 +67,9 @@ def test_propagate_to_stores_adult_contagious(self):
  # i9 becomes infected
  env_dic = {
  HA_K: {0: [0, 1], 1: [4, 5], 2: [8, 9]},
- HS_K: {0: [0, 0, 0], 1: [1, 1, 1], 2: [0, 0, 0]},
+ IS_K: {0: [0, 0, 0], 1: [0, 0, 0], 2: [0, 0, 0], 3: [0, 0, 0],
+ 4: [1, 1, 1], 5: [1, 1, 1], 6: [1, 1, 1], 7: [1, 1, 1],
+ 8: [0, 0, 0], 9: [0, 0, 0]},
  IH_K: {0: 0, 1: 0, 2: 0, 3: 0, 4: 1, 5: 1, 6: 1, 7: 1, 8: 2, 9: 2},
  IBE_K: {0: 1, 1: 1, 2: 1, 3: 1, 4: 1, 5: 1, 6: 1, 7: 1, 8: 1, 9: 1}
  }
@@ -86,7 +92,9 @@ def test_propagate_to_stores_adult_contagious_bad_gobal_behavior(self):
  # They meet and i1 contaminates i9
  env_dic = {
  HA_K: {0: [1, 0], 1: [4, 5], 2: [8, 9]},
- HS_K: {0: [1, 0, 0], 1: [1, 1, 1], 2: [1, 0, 0]},
+ IS_K: {0: [1, 0, 0], 1: [1, 0, 0], 2: [1, 0, 0], 3: [1, 0, 0],
+ 4: [1, 1, 1], 5: [1, 1, 1], 6: [1, 1, 1], 7: [1, 1, 1],
+ 8: [1, 0, 0], 9: [1, 0, 0]},
  IH_K: {0: 0, 1: 0, 2: 0, 3: 0, 4: 1, 5: 1, 6: 1, 7: 1, 8: 2, 9: 2},
  IBE_K: {0: 1, 1: 1, 2: 1, 3: 1, 4: 1, 5: 1, 6: 1, 7: 1, 8: 1, 9: 1}
  }
@@ -109,7 +117,9 @@ def test_propagate_to_stores_adult_contagious_bad_individual_behavior(self):
  # They meet and i1 contaminates i9
  env_dic = {
  HA_K: {0: [1, 0], 1: [4, 5], 2: [8, 9]},
- HS_K: {0: [1, 0, 0], 1: [1, 1, 1], 2: [0, 0, 0]},
+ IS_K: {0: [1, 0, 0], 1: [1, 0, 0], 2: [1, 0, 0], 3: [1, 0, 0],
+ 4: [1, 1, 1], 5: [1, 1, 1], 6: [1, 1, 1], 7: [1, 1, 1],
+ 8: [0, 0, 0], 9: [0, 0, 0]},
  IH_K: {0: 0, 1: 0, 2: 0, 3: 0, 4: 1, 5: 1, 6: 1, 7: 1, 8: 2, 9: 2},
  IBE_K: {0: 1, 1: 100, 2: 1, 3: 1, 4: 1, 5: 1, 6: 1, 7: 1, 8: 1, 9: 1}
  }
@@ -133,7 +143,9 @@ def test_propagate_to_stores_adult_contagious_bad_2individual_behavior(self):
  # They meet and i1 contaminates i9
  env_dic = {
  HA_K: {0: [0, 1], 1: [4, 5], 2: [8, 9]},
- HS_K: {0: [1, 0, 0], 1: [1, 1, 1], 2: [1, 0, 0]},
+ IS_K: {0: [1, 0, 0], 1: [1, 0, 0], 2: [1, 0, 0], 3: [1, 0, 0],
+ 4: [1, 1, 1], 5: [1, 1, 1], 6: [1, 1, 1], 7: [1, 1, 1],
+ 8: [1, 0, 0], 9: [1, 0, 0]},
  IH_K: {0: 0, 1: 0, 2: 0, 3: 0, 4: 1, 5: 1, 6: 1, 7: 1, 8: 2, 9: 2},
  IBE_K: {0: 100, 1: 1, 2: 1, 3: 1, 4: 1, 5: 1, 6: 1, 7: 1, 8: 1, 9: 100}
  }
@@ -155,7 +167,9 @@ def test_propagate_to_stores_child2(self):
  # he can't infect anyone
  env_dic = {
  HA_K: {0: [0, 1], 1: [4, 5], 2: [8, 9]},
- HS_K: {0: [0, 0, 0], 1: [1, 1, 1], 2: [0, 0, 0]},
+ IS_K: {0: [0, 0, 0], 1: [0, 0, 0], 2: [0, 0, 0], 3: [0, 0, 0],
+ 4: [1, 1, 1], 5: [1, 1, 1], 6: [1, 1, 1], 7: [1, 1, 1],
+ 8: [0, 0, 0], 9: [0, 0, 0]},
  IH_K: g_d([0, 0, 0, 0, 1, 1, 1, 1, 2, 2]),
  IBE_K: g_d([1, 1, 1, 1, 1, 1, 1, 1, 1, 1]),
  }
@@ -178,7 +192,9 @@ def test_propagate_to_stores_adult_notcontagious2(self):
  # but i8 and i9 stay healthy
  env_dic = {
  HA_K: {0: [0, 1], 1: [4, 5], 2: [8, 9]},
- HS_K: {0: [0, 0, 0], 1: [1, 1, 1], 2: [0, 0, 0]},
+ IS_K: {0: [0, 0, 0], 1: [0, 0, 0], 2: [0, 0, 0], 3: [0, 0, 0],
+ 4: [1, 1, 1], 5: [1, 1, 1], 6: [1, 1, 1], 7: [1, 1, 1],
+ 8: [0, 0, 0], 9: [0, 0, 0]},
  IH_K: g_d([0, 0, 0, 0, 1, 1, 1, 1, 2, 2]),
  IBE_K: g_d([1, 1, 1, 1, 1, 1, 1, 1, 1, 1]),
  }
@@ -201,7 +217,9 @@ def test_propagate_to_stores_adult_contagious2(self):
  # i9 becomes infected
  env_dic = {
  HA_K: {0: [0, 1], 1: [4, 5], 2: [8, 9]},
- HS_K: {0: [0, 0, 0], 1: [1, 1, 1], 2: [0, 0, 0]},
+ IS_K: {0: [0, 0, 0], 1: [0, 0, 0], 2: [0, 0, 0], 3: [0, 0, 0],
+ 4: [1, 1, 1], 5: [1, 1, 1], 6: [1, 1, 1], 7: [1, 1, 1],
+ 8: [0, 0, 0], 9: [0, 0, 0]},
  IH_K: g_d([0, 0, 0, 0, 1, 1, 1, 1, 2, 2]),
  IBE_K: g_d([1, 1, 1, 1, 1, 1, 1, 1, 1, 1])
  }
@@ -224,7 +242,9 @@ def test_propagate_to_stores_adult_contagious_bad_gobal_behavior2(self):
  # They meet and i1 contaminates i9
  env_dic = {
  HA_K: {0: [1, 0], 1: [4, 5], 2: [8, 9]},
- HS_K: {0: [1, 0, 0], 1: [1, 1, 1], 2: [1, 0, 0]},
+ IS_K: {0: [1, 0, 0], 1: [1, 0, 0], 2: [1, 0, 0], 3: [1, 0, 0],
+ 4: [1, 1, 1], 5: [1, 1, 1], 6: [1, 1, 1], 7: [1, 1, 1],
+ 8: [1, 0, 0], 9: [1, 0, 0]},
  IH_K: g_d([0, 0, 0, 0, 1, 1, 1, 1, 2, 2]),
  IBE_K: g_d([1, 1, 1, 1, 1, 1, 1, 1, 1, 1])
  }
@@ -247,7 +267,9 @@ def test_propagate_to_stores_adult_contagious_bad_individual_behavior2(self):
  # They meet and i1 contaminates i9
  env_dic = {
  HA_K: {0: [1, 0], 1: [4, 5], 2: [8, 9]},
- HS_K: {0: [1, 0, 0], 1: [1, 1, 1], 2: [0, 0, 0]},
+ IS_K: {0: [1, 0, 0], 1: [1, 0, 0], 2: [1, 0, 0], 3: [1, 0, 0],
+ 4: [1, 1, 1], 5: [1, 1, 1], 6: [1, 1, 1], 7: [1, 1, 1],
+ 8: [0, 0, 0], 9: [0, 0, 0]},
  IH_K: g_d([0, 0, 0, 0, 1, 1, 1, 1, 2, 2]),
  IBE_K: g_d([1, 100, 1, 1, 1, 1, 1, 1, 1, 1])
  }
@@ -272,7 +294,9 @@ def test_propagate_to_stores_adult_contagious_bad_2individual_behavior2(self):
  # They meet and i1 contaminates i9
  env_dic = {
  HA_K: {0: [1, 0], 1: [4, 5], 2: [8, 9]},
- HS_K: {0: [1, 0, 0], 1: [1, 1, 1], 2: [1, 0, 0]},
+ IS_K: {0: [1, 0, 0], 1: [1, 0, 0], 2: [1, 0, 0], 3: [1, 0, 0],
+ 4: [1, 1, 1], 5: [1, 1, 1], 6: [1, 1, 1], 7: [1, 1, 1],
+ 8: [1, 0, 0], 9: [1, 0, 0]},
  IH_K: g_d([0, 0, 0, 0, 1, 1, 1, 1, 2, 2]),
  IBE_K: g_d([1, 100, 1, 1, 1, 1, 1, 1, 1, 100])
  }