Zhong scenarios generator

Author: khvilaboa

epidemic_zhong_et_al/generator/model_generator.py

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+
+import argparse
+
+parser = argparse.ArgumentParser(description='Auxiliar script to generate Zhong-based CA models')
+
+parser.add_argument('-i', '--incubation_steps', type=int, default=2, help='Number of days for the incubation state')
+parser.add_argument('-f', '--infected_steps', type=int, default=2, help='Number of days for the infected state')
+parser.add_argument('-l', '--latent_steps', type=int, default=2, help='Number of days for the latent state')
+parser.add_argument('-r', '--recovered_steps', type=int, default=3, help='Number of days for the recovered state')
+parser.add_argument('-t', '--template_ma', type=str, default="template_sirs_zhong_ma", help='Path to zhong .ma template')
+parser.add_argument('-m', '--template_macros', type=str, default="template_sirs_zhong_macros", help='Path to zhong macros template')
+parser.add_argument('-o', '--out_ma_file', type=str, default="out.ma", help='Output path of the .ma file')
+parser.add_argument('-p', '--out_macros_file', type=str, default="sirs_zhong_macros.inc", help='Output path of the macros file')
+
+args = parser.parse_args()
+
+i = 1
+states = ["sus_0"]
+neighbors = ["(1,0)", "(0,-1)", "(0,1)", "(-1,0)"]
+
+while i <= args.incubation_steps:
+    states.append("inc_%d" % i)
+    i += 1
+
+while i <= args.incubation_steps + args.infected_steps:
+    states.append("inf_%d" % i)
+    i += 1
+
+while i <= args.incubation_steps + args.infected_steps + args.latent_steps:
+    states.append("lat_%d" % i)
+    i += 1
+
+while i <= args.incubation_steps + args.infected_steps + args.latent_steps + args.recovered_steps:
+    states.append("rec_%d" % i)
+    i += 1
+
+##############################
+# GENERATION OF THE .MA FILE
+##############################
+content = ""
+with open(args.template_ma, "r") as f:
+    content = f.read()
+
+content = content.replace("[[internal_vars]]", " ".join(["i_%s" % s for s in states]))
+content = content.replace("[[internal_vars_values]]", " ".join(["1.0"] + ["0.0"] * (len(states)-1)))
+update_ports_str = " ".join(["~%s := $i_%s;" % (s, s) for s in states])
+content = content.replace("[[initial_ports_set_up]]", update_ports_str)
+content = content.replace("[[update_ports_step]]", update_ports_str)
+content = content.replace("[[ports]]", " ".join(states))
+
+update_rules = ""
+idx_first_rec = len(states)-args.recovered_steps
+for i in range(len(states)-1, idx_first_rec, -1):
+    update_rules += "$i_%s := $i_%s;\n" % (states[i], states[i-1])
+update_rules += "$i_%s := $i_%s + #macro(local_cured);\n\n" % (states[idx_first_rec], states[idx_first_rec-1])
+
+for i in range(idx_first_rec-1, 1, -1):
+    update_rules += "$i_%s := trunc(min((1 - $cured_rate) * $i_%s, 1)*100)/100;\n" % (states[i], states[i - 1])
+update_rules += "$i_%s := #macro(internal_infected) + #macro(external_infected);\n\n" % states[1]
+
+update_rules += "$i_%s := 1 " % states[0]
+update_rules += " ".join(["- $i_%s" % s for s in states[1:]])
+update_rules += ";\n"
+
+content = content.replace("[[update_vars_step]]", update_rules)
+
+with open(args.out_ma_file, "w") as f:
+    f.write(content)
+
+#################################
+# GENERATION OF THE MACROS FILE
+#################################
+
+content = ""
+with open(args.template_macros, "r") as f:
+    content = f.read()
+
+local_cured_rules = []
+for i in range(idx_first_rec-2, 0, -1):
+    local_cured_rules.append("trunc(min($cured_rate * $i_%s, 1)*100)" % states[i])
+
+content = content.replace("[[local_cured]]", "(( %s ) / 100 )" % " +\n".join(local_cured_rules))
+content = content.replace("[[infected_vars]]", " + ".join(["i_%s" % s for s in states[idx_first_rec:0]]))
+
+external_infected_comp = \
+"""( trunc(min(( $connection *
+$contact_rate * 
+(($i_sus_0 * $population) / $area) *
+$i_sus_0 * 
+([[external_infected]])
+) / $p, 1)*100) / 100 )
+"""
+
+external_infected_rules = []
+for nei in neighbors:
+    inf = " + ".join(["%s~%s" % (nei, s) for s in states[idx_first_rec-1:0:-1]])
+    external_infected_rules.append(external_infected_comp.replace("[[external_infected]]", inf))
+
+content = content.replace("[[external_infected]]", "+\n".join(external_infected_rules))
+
+with open(args.out_macros_file, "w") as f:
+    f.write(content)

epidemic_zhong_et_al/generator/template_sirs_zhong_ma

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+#include(sirs_zhong_macros.inc)
+[top]
+components : area
+
+[area]
+type : cell
+width : 50
+height : 50
+delay : transport
+defaultDelayTime : 1
+border : wrapped
+neighbors : 			area(-1,0)
+neighbors : area(0,-1)  area(0,0)  area(0,1)
+neighbors : 			area(1,0)
+initialvalue : -1
+
+localtransition : sirs-zhong-rule
+
+statevariables: population area p connection contact_rate cured_rate t_i t_p t_l t_r [[internal_vars]]
+statevalues: 100 1 500 1 1 0.00 2 2 2 3 [[internal_vars_values]]
+initialvariablesvalue: sirs_zhong.var
+
+neighborports : initial pop [[ports]]
+
+[sirs-zhong-rule]
+rule : {~initial := 0; ~pop := $population; [[initial_ports_set_up]]}
+ 1 {(0,0)~initial = -1}
+
+rule : {
+~pop := $population; [[update_ports_step]]
+}
+{
+[[update_vars_step]]
+}
+1 { (0,0)~initial != -1 }
+
+
+
+
+
+
+
+
+

epidemic_zhong_et_al/generator/template_sirs_zhong_macros

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+
+#BeginMacro(local_cured) 
+[[local_cured]]
+#EndMacro
+
+#BeginMacro(internal_infected) 
+( trunc(min(($contact_rate * 
+(($i_sus_0 * $population) / $area) *
+$i_sus_0 *
+($i_lat_6 + $i_lat_5 + $i_inf_4 + $i_inf_3 + $i_inc_2 + $i_inc_1)
+) / $p, 1) * 100) / 100 )
+#EndMacro
+
+#BeginMacro(external_infected) 
+[[external_infected]]
+#EndMacro