def application(output_folder="output", stdout_filename="test.txt", property_report_name="PropertyReportEnvironmental.json", insetchart_name="InsetChart.json", config_filename="config.json", campaign_filename="campaign.json", report_name=sft.sft_output_filename, debug=False): if debug: print("output_folder: " + output_folder) print("stdout_filename: " + stdout_filename + "\n") print("property_report_name: " + property_report_name + "\n") print("insetchart_name: " + insetchart_name + "\n") print("config_filename: " + config_filename + "\n") print("campaign_filename: " + campaign_filename + "\n") print("report_name: " + report_name + "\n") print("debug: " + str(debug) + "\n") sft.wait_for_done(stdout_filename) config_obj = hint_support.load_config_parameters(config_filename, config_keys, debug) campaign_obj = hint_support.load_campaign_file(campaign_filename, debug) stdout_df = parse_stdout_file(stdout_filename, config_obj[ConfigKeys.Simulation_Timestep], debug) demo_path = "Assets" if stdout_filename == "StdOut.txt" else "" property_list = hint_support.load_demo_mr_overlay_file( config_obj[ConfigKeys.Demographics_Filenames][1], demo_path, debug) property_keys = hint_support.build_channel_string_for_property(property_list, channels, debug) property_df = hint_support.parse_property_report_json(property_report_name, output_folder, property_keys, debug) property_obj = property_list[0] # this test only has one property object inset_chart_obj = General_Support.parse_inset_chart(output_folder, insetchart_name, inset_channels, debug) create_report_file(config_obj, campaign_obj, stdout_df, property_df, property_obj, inset_chart_obj, insetchart_name, property_report_name, report_name, debug)
def application(output_folder="output", stdout_filename="test.txt", insetchart_name="InsetChart.json", config_filename="config.json", report_name=sft.sft_output_filename, debug=False): if debug: print("output_folder: " + output_folder) print("insetchart_name: " + insetchart_name + "\n") print("config_filename: " + config_filename + "\n") print("report_name: " + report_name + "\n") print("debug: " + str(debug) + "\n") sft.wait_for_done(stdout_filename) config_obj = hint_support.load_config_parameters(config_filename, config_keys, debug) inset_chart_obj = General_Support.parse_inset_chart(output_folder, insetchart_name, channels, debug) create_report_file(config_obj, inset_chart_obj, report_name, insetchart_name, debug)
def application(output_folder="output", stdout_filename="test.txt", insetchart_name="InsetChart.json", config_filename="config.json", report_name=sft.sft_output_filename, debug=False): if debug: print("output_folder: " + output_folder) print("insetchart_name: " + insetchart_name + "\n") print("config_filename: " + config_filename + "\n") print("report_name: " + report_name + "\n") print("debug: " + str(debug) + "\n") sft.wait_for_done(stdout_filename) config_obj = hint_support.load_config_parameters(config_filename, config_keys, debug) inset_chart_obj = General_Support.parse_inset_chart(output_folder, insetchart_name, channels, debug) create_report_file(config_obj, inset_chart_obj, report_name, insetchart_name, debug)
def application(output_folder="output", stdout_filename="test.txt", property_report_name="PropertyReportEnvironmental.json", insetchart_name="InsetChart.json", config_filename="config.json", campaign_filename="campaign.json", report_name=sft.sft_output_filename, debug=False): if debug: print("output_folder: " + output_folder) print("stdout_filename: " + stdout_filename + "\n") print("property_report_name: " + property_report_name + "\n") print("insetchart_name: " + insetchart_name + "\n") print("config_filename: " + config_filename + "\n") print("campaign_filename: " + campaign_filename + "\n") print("report_name: " + report_name + "\n") print("debug: " + str(debug) + "\n") sft.wait_for_done(stdout_filename) config_obj = hint_support.load_config_parameters(config_filename, config_keys, debug) campaign_obj = hint_support.load_campaign_file(campaign_filename, debug) stdout_df = parse_stdout_file(stdout_filename, config_obj[ConfigKeys.Simulation_Timestep], debug) demo_path = "Assets" if stdout_filename == "StdOut.txt" else "" property_list = hint_support.load_demo_mr_overlay_file( config_obj[ConfigKeys.Demographics_Filenames][1], demo_path, debug) property_keys = hint_support.build_channel_string_for_property( property_list, channels, debug) property_df = hint_support.parse_property_report_json( property_report_name, output_folder, property_keys, debug) property_obj = property_list[0] # this test only has one property object inset_chart_obj = General_Support.parse_inset_chart( output_folder, insetchart_name, inset_channels, debug) create_report_file(config_obj, campaign_obj, stdout_df, property_df, property_obj, inset_chart_obj, insetchart_name, property_report_name, report_name, debug)
def application(report_file, debug=True): sft.wait_for_done() """ Parse this line from test.txt: 00:00:00 [0] [V] [IndividualTyphoid] amplification calculated as 0.997059: day of year=1, start=360.000000, end=365.000000, ramp_up=30.000000, ramp_down=170.000000, cutoff=160.000000. 00:00:00 [0] [V] [IndividualTyphoid] Exposing individual 2 age 8582.488281 on route 'environment': prob=0.000000, infects=0.000008, immunity=1.000000, num_exposures=0, exposure=0.997059, environment=1.000000, iv_mult=1.000000. """ #print( "Post-processing: " + report_file ) # get params from config.json cdj = json.loads( open( "config.json" ).read() )["parameters"] ncdr = cdj["Node_Contagion_Decay_Rate"] start_time=cdj["Start_Time"] lines = [] timestep=start_time count =0 amp = {} exposure = {} environment = {} cum_shedding = cum = 0 cum_shedding_all = {} Statpop = [] with open( "test.txt" ) as logfile: for line in logfile: if "Update(): Time:" in line: # store the accumulated shedding and reset the counter at the end of each time step. cum_shedding_all[timestep] = cum_shedding pop = float(sft.get_val("StatPop: ", line)) Statpop.append(pop) # environmental cp decay cum_shedding *= 1.0 - ncdr # resetting shedding variables shedding = 0 #calculate time step timestep += 1 line = "TimeStep: " + str(timestep) + " " + line lines.append(line) elif "amplification calculated as" in line: count += 1 line = "TimeStep: " + str(timestep) + " " + line lines.append(line) amp[timestep] = float(sft.get_val("amplification calculated as ", line)) elif ("Exposing" in line) and ("environment" in line): line = "TimeStep: " + str(timestep) + " " + line lines.append(line) if timestep not in exposure: exposure[timestep] = float(sft.get_val("exposure=", line)) environment[timestep] = float(sft.get_val("environment=", line)) elif ("depositing" in line) and ("route environment" in line): # get shedding of contact route and add it to accumulated shedding shedding = float(sft.get_val("depositing ", line)) cum_shedding += shedding line = "TimeStep: " + str(timestep) + " " + line lines.append(line) if debug: with open("DEBUG_filtered_line.txt","w") as filter_file: filter_file.write("".join(lines)) #more params from config file rud=cdj["Environmental_Ramp_Up_Duration"] rdd=cdj["Environmental_Ramp_Down_Duration"] ecd=cdj["Environmental_Cutoff_Days"] eps=cdj["Environmental_Peak_Start"] peak_duration=365-rud-rdd-ecd # for eps > 365 peak_starttime = eps % 365 peak_endtime = peak_starttime + peak_duration cutoff_starttime = peak_starttime + peak_duration + rdd #cutoff_endtime = peak_starttime + peak_duration + rdd + ecd success = True expected_e_contagion = {} environmental_amp = {} inset_chart_obj = general_support.parse_inset_chart("output", "InsetChart.json", insetkey_list=[InsetKeys.ChannelsKeys.Environmental_Contagion_Population]) with open( sft.sft_output_filename, "w" ) as report_file: report_file.write("Peak_Start={0}, Peak_Duration={1}, Peak_End={2}, Ramp_Down={3}, Ramp_Up={4}," "Cutoff_Start={5}, Cutoff_Duration={6}.\n".format(peak_starttime, peak_duration, peak_endtime, rdd, rud, cutoff_starttime, ecd)) if ncdr != 1: report_file.write("WARNING: Node_Contagion_Decay_Rate is {}, suggest to set it to 1.\n".format( ncdr )) if count == 0: success = False report_file.write( "Found no data matching test case.\n" ) elif peak_duration < 0: success = False report_file.write("BAD: Environmental peak duration should be larger or equal to 0, the actual value is {}." "\n The ramp durations and cutoff days need to follow a rule where: ramp_up_duration + " "ramp_down_duration + cutoff_days < 365.\n".format(peak_duration)) else: # adjust the times so that the ramp up starts at time 0, which means the cut off ends at time 0 too. adjust_time = peak_starttime - rud peak_starttime -= adjust_time peak_endtime -= adjust_time cutoff_starttime -= adjust_time # cutoff_endtime -= adjust_time with open("DEBUG_contagion_data.txt", "w") as debug_file: for t in range(timestep - 2): amplification = environmental_amplification = None if t in amp: TimeStep = t - adjust_time day_in_year = TimeStep%365 amplification = amp[t] # Environment Ramp Up if day_in_year < peak_starttime: environmental_amplification = day_in_year/float(rud) # Environment peak elif peak_starttime <= day_in_year <= peak_endtime: environmental_amplification = 1 # Environment Ramp Down elif peak_endtime < day_in_year < cutoff_starttime: environmental_amplification = (cutoff_starttime - day_in_year) / float(rdd) # Environment cutoff elif day_in_year >= cutoff_starttime: environmental_amplification = 0 if math.fabs(amplification - environmental_amplification) > 5e-2 * environmental_amplification: success =False report_file.write("BAD: at time {0}, day of year = {1}, the environmental amplification is {2}," " expected {3}.\n".format(t, t%365, amplification, environmental_amplification)) environmental_amp[t] = environmental_amplification if t in exposure: exposure_t = exposure[t] if amplification is not None: environment_contagion = cum_shedding_all[t-start_time] / Statpop[t -start_time] expected_exposure = environment_contagion * amplification if math.fabs(expected_exposure - exposure_t) > 5e-2 * expected_exposure: success =False report_file.write("BAD: at time {0}, day of year = {1}, the amount of environmental contagion " "that individual is exposed is {2}, expected {3}" ".\n".format(t, t%365, exposure_t, expected_exposure)) expected_e_contagion[t] = expected_exposure if debug: environment_t = environment[t] inserchart_contagion_e = inset_chart_obj \ [InsetKeys.ChannelsKeys.Environmental_Contagion_Population][t] debug_file.write("At time step {0}: environment={1}, exposure={2} from loggind, " "{3}={4} from InsetChart, expected value={5}." "accumulated shedding after decay={6} calculated from logging, " "environmental amplification={7}.\n".format( t, environment_t,exposure_t, InsetKeys.ChannelsKeys.Environmental_Contagion_Population, inserchart_contagion_e, expected_exposure, environment_contagion, amplification )) sft.plot_data(amp.values(), environmental_amp.values(), label1="Actual Seasonal Attenuation", label2="Expected Seasonal Attenuation", title="Seasonal Attenuation", xlabel="Time", ylabel="Attenuation", category='seasonal_attenuation') for t in range(len(amp)): if t not in exposure: exposure[t] = 0 expected_e_contagion[t] = 0 sft.plot_data([exposure[key] for key in sorted(exposure.keys())], [expected_e_contagion[key] for key in sorted(expected_e_contagion.keys())], label1="exposure contagion(from StdOut)", label2="Expected", title="Environmental Contagion", xlabel="Time", ylabel="Environmental Contagion", category='Environmental_Contagion') report_file.write( sft.format_success_msg( success ) )
def parse_inset_chart(self, output_folder, insetchart_name, debug): return General_Support.parse_inset_chart( output_folder=output_folder, insetchart_name=insetchart_name, insetkey_list=self.chart_channels, debug=debug)