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)