def application(output_folder="output",
stdout_filename="test.txt",
config_filename="config.json",
campaign_filename="campaign.json",
demographics_filename="../../demographics.json",
propertyreport_name="PropertyReport.json",
reportevenrecorder_name="ReportEventRecorder.csv",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder)
print("stdout_filename: " + stdout_filename + "\n")
print("config_filename: " + config_filename + "\n")
print("campaign_filename: " + campaign_filename + "\n")
print("demographics_filename: " + demographics_filename + "\n")
print("propertyreport_name: " + propertyreport_name + "\n")
print("reportevenrecorder_name: " + reportevenrecorder_name + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
report_data_obj = parse_json_report(output_folder, propertyreport_name,
debug)
csv_df = parse_excel_report(output_folder, reportevenrecorder_name)
create_report_file(report_data_obj, csv_df, report_name, debug)
def application( output_folder="output", stdout_filename="test.txt",
config_filename="config.json",
chart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=True):
if debug:
print( "output_folder: " + output_folder )
print( "stdout_filename: " + stdout_filename+ "\n" )
print( "config_filename: " + config_filename + "\n" )
print( "chart_name: " + chart_name + "\n" )
print( "report_name: " + report_name + "\n" )
print( "debug: " + str(debug) + "\n" )
sft.wait_for_done()
param_obj = load_emod_parameters(config_filename)
drug_start_timestep = param_obj[dts.ParamKeys.KEY_DrugStartTime]
tb_drug_relapse_rate_hiv = float(param_obj[dts.ConfigKeys.DrugParams.KEY_TbDrugRelapseRateHIV])
# Now process log output (probably) and compare to theory (not in this example) or to another report.
relapses, cum_relapses = parse_stdout_file(drug_start_timestep, stdout_filename, debug)
sft.plot_data( relapses, cum_relapses, label1="Relapses",
label2="Cumulative Relapses", title="Relapses vs. Cumulative Relapses over Time",
xlabel="Timestep", ylabel="Relapses",
category="Relapses_vs_Cumulative_Relapse", show=True, line = True)
active_TB_treatments = parse_json_report( output_folder, chart_name, debug)
mean_relapses = [x * tb_drug_relapse_rate_hiv for x in active_TB_treatments]
sft.plot_data( relapses[1:len(relapses) - 1], mean_relapses, label1="Relapses",
label2="calculated relapses", title="Relapses vs. calculated relapses over Time",
xlabel="Timestep", ylabel="Relapses",
category="Relapses_actual_vs_calculated", show=True, line=True, overlap=True )
# Now we've ingested all relevant inputs, let's do analysis
create_report_file( active_TB_treatments,relapses, tb_drug_relapse_rate_hiv,drug_start_timestep, report_name)
def application( output_folder="output", stdout_filename="test.txt",
property_report_name="PropertyReportEnvironmental.json",
report_event_recorder="ReportNodeEventRecorder.csv",
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("report_event_recorder: " + report_event_recorder+ "\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 = General_Support.load_config_parameters(config_filename, Diagnostic_Support.config_keys, debug)
demo_overlay_file = config_obj[ConfigKeys.Demographics_Filenames][-1]
campaign_obj = Diagnostic_Support.load_campaign_file(campaign_filename, debug)
demo_path = "Assets" if stdout_filename == "StdOut.txt" else ""
property_obj = HINT_Support.load_demo_mr_overlay_file(demo_overlay_file, demo_path, debug)[0]
ip_key_value = campaign_obj[CampaignKeys.EnvironmentalDiagnosticKeys.Environment_IP_Key_Value]
property_keys = []
for channel in Diagnostic_Support.channels:
property_keys.append("{0}:{1}".format(channel, ip_key_value))
property_df = HINT_Support.parse_property_report_json(property_report_name, output_folder, property_keys, debug)
stdout_df = Diagnostic_Support.parse_stdout_file(stdout_filename, config_obj[ConfigKeys.Simulation_Timestep], debug)
recorder_obj = Diagnostic_Support.parse_report_event_recorder(output_folder, report_event_recorder, debug)
create_report_file(config_obj, campaign_obj, property_obj, property_df, stdout_df, recorder_obj, report_name,
report_event_recorder, stdout_filename, debug)
def application(output_folder="output",
stdout_filename="test.txt",
config_filename="config.json",
insetchart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder)
print("stdout_filename: " + stdout_filename + "\n")
print("config_filename: " + config_filename + "\n")
print("insetchart_name: " + insetchart_name + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
#param_obj = load_emod_parameters("HIVMaleOverlay.json")
param_obj = load_emod_parameters("campaign.json")
#total_timesteps = param_obj[KEY_TOTAL_TIMESTEPS]
start_timestep = 0 # get from config
# Now process log output (probably) and compare to theory (not in this example) or to another report.
male_probs, female_probs = parse_stdout_file(start_timestep,
stdout_filename, debug)
inset_days = parse_json_report(start_timestep, output_folder,
insetchart_name, debug)
create_report_file(male_probs, female_probs, param_obj, report_name)
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",
config_filename="config.json",
insetchart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print( "output_folder: " + output_folder )
print( "stdout_filename: " + stdout_filename + "\n" )
print( "config_filename: " + config_filename + "\n" )
print( "insetchart_name: " + insetchart_name + "\n" )
print( "report_name: " + report_name + "\n" )
print( "debug: " + str(debug) + "\n" )
sft.wait_for_done()
param_obj = load_emod_parameters(config_filename)
parsed_data = parse_stdout_file(param_obj, stdout_filename, debug=debug)
inset_days = parse_json_report()
parsed_data.extend([param_obj[KEY_TYPHOID_ACUTE_INFECTIOUSNESS]])
data_to_graph = create_report_file(parsed_data, inset_days,
report_name=sft.sft_output_filename)
sft.plot_data_sorted(data_to_graph[0], data_to_graph[1], label1="Actual", label2="Expected",
title="Contact Dose Response Probability", xlabel="Occurrences",
ylabel="Dose Response",
category='contact_dose_response_probability_plot',
alpha=0.5, overlap=True)
sft.plot_data_sorted(data_to_graph[2], data_to_graph[3], label1="Actual", label2="Expected",
title="Environmental Dose Response Probability", xlabel="Occurrences",
ylabel="Dose Response",
category='environmental_dose_response_probability_plot',
alpha=0.5, overlap=True)
def application(output_folder="output",
stdout_filename="test.txt",
config_filename="config.json",
insetchart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder)
print("stdout_filename: " + stdout_filename + "\n")
print("config_filename: " + config_filename + "\n")
print("insetchart_name: " + insetchart_name + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
print("current dir = " + os.getcwd())
sft.wait_for_done()
param_obj, config_json = MM_Support.load_emod_parameters(config_filename)
if debug:
print(param_obj)
node_demo_df, human_migration_df = MM_Support.parse_output_files(
"output/ReportNodeDemographics.csv",
"output/ReportHumanMigrationTracking.csv", debug)
# for local testing
# node_demo_df, human_migration_df = MM_Support.parse_output_files("ReportNodeDemographics.csv", "ReportHumanMigrationTracking.csv", debug)
MM_Support.create_report_file(param_obj, node_demo_df, human_migration_df,
report_name, debug)
def application(report_file, debug=False):
# pdb.set_trace()
# print( "Post-processing: " + report_file )
sft.wait_for_done()
cdj = json.loads(open("config.json").read())["parameters"]
start_time = cdj["Start_Time"]
isj = json.loads(open(os.path.join("output",
"InsetChart.json")).read())["Channels"]
nonai = isj["Number of New Acute Infections"]["Data"]
count = 0
sum_count = 0
counts = []
with open("test.txt") as logfile:
for line in logfile:
if re.search("Update\(\): Time:", line):
counts.append(count)
sum_count += count
count = 0
if re.search("Infection stage transition", line) and re.search(
"->Acute", line):
count += 1
success = True
with open(sft.sft_output_filename, "w") as report_file:
if sum_count == 0:
# make sure there is at least one acute infection during the test
success = False
report_file.write("Found no Acute Infections in test case.\n")
else:
# #2890
# for i in range(1, len(counts)):
# count_log = counts[i]
# count_icj = nonai[i-1]
for i in range(0, len(counts)):
count_log = counts[i]
count_icj = nonai[i]
timestep = start_time + i
if count_log != count_icj:
success = False
report_file.write(
"BAD: At time {0}: new Acute infections is {1} from Stdout log, while it's"
" {2} from InsetChart.json.\n".format(
timestep, count_log, count_icj))
# #2890
# counts2 = counts[1:len(counts)-1]
# sft.plot_data(counts2, nonai, label1="New Acute from stdout", label2="New Acute from InsertChart",
sft.plot_data(counts,
nonai,
label1="New Acute from stdout",
label2="New Acute from InsertChart",
title="New Acute Infections (InsetChart Test)",
xlabel="Time",
ylabel="Number of New Acute Infections",
category='report_inset_chart_new_acute',
alpha=0.5,
overlap=True)
report_file.write(sft.format_success_msg(success))
def application(output_folder="output",
stdout_filename="test.txt",
config_filename="config.json",
insetchart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder)
print("stdout_filename: " + stdout_filename + "\n")
print("config_filename: " + config_filename + "\n")
print("insetchart_name: " + insetchart_name + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
param_obj = load_emod_parameters(config_filename)
parsed_data = parse_stdout_file(param_obj[KEY_START_TIME],
stdout_filename,
debug=debug)
inset_days = parse_json_report(param_obj[KEY_START_TIME], output_folder,
insetchart_name, debug)
processed_data = create_report_file(parsed_data,
inset_days,
report_name=sft.sft_output_filename)
graph_the_data(processed_data[0], processed_data[1])
def application(output_folder="output",
stdout_filename="test.txt",
reporter_filename="Report_TBHIV_ByAge.csv",
config_filename="config.json",
report_name=sft.sft_output_filename,
debug=True):
if debug:
print("output_folder: " + output_folder)
print("stdout_filename: " + stdout_filename + "\n")
print("reporter_filename: " + reporter_filename + "\n")
print("config_filename: " + config_filename + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
param_obj = trs.load_emod_parameters(config_filename, debug)
output_dict = parse_output_file(stdout_filename,
param_obj[trs.Config.simulation_timestep],
debug)
report_column_list = [
ReportColumn.year, ReportColumn.agebin, ReportColumn.active_sx,
ReportColumn.incidence
]
reporter_df = trs.parse_custom_reporter(
report_column_list,
reporter_path=output_folder,
reporter_filename=reporter_filename,
debug=debug)
trs.create_report_file_prevalence(ReportColumn.active_sx,
ReportColumn.year, param_obj,
output_dict, reporter_df, report_name,
debug)
def application(output_folder="output",
stdout_filename="test.txt",
config_filename="config.json",
insetchart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder)
print("stdout_filename: " + stdout_filename + "\n")
print("config_filename: " + config_filename + "\n")
print("insetchart_name: " + insetchart_name + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
param_obj = load_emod_parameters(config_filename)
parsed_data = parse_stdout_file()
inset_days = parse_json_report()
create_report_file([
report_name, parsed_data,
param_obj.get(TB_CD4_STRATA_I_S),
param_obj.get(TB_CD4_S),
param_obj.get(BASE_INF),
param_obj.get(TB_ACTIVE_PS_INF_MULT),
param_obj.get(TB_SMEAR_NEG_MULT)
])
def application(output_folder="output",
stdout_filename="test.txt",
initial_timestep=0,
insetchart_name="InsetChart.json",
config_filename="config.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder + "\n")
print("stdout_filename: " + stdout_filename + "\n")
print("initial_timestep: " + str(initial_timestep) + "\n")
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()
vles = VlesEnv()
inset_chart_obj = vles.parse_inset_chart(output_folder=output_folder,
insetchart_name=insetchart_name,
debug=debug)
attenuation = vles.parse_stdout_file(initial_timestep=initial_timestep,
stdout_filename=stdout_filename,
debug=debug)
vles.create_report_file(attenuation=attenuation,
inset_chart_obj=inset_chart_obj,
report_name=report_name,
debug=debug)
def application(output_folder="output",
stdout_filename="test.txt",
config_filename="config.json",
campaign_filename="campaign.json",
chart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=True):
if debug:
print("output_folder: " + output_folder)
print("stdout_filename: " + stdout_filename + "\n")
print("config_filename: " + config_filename + "\n")
print("chart_name: " + chart_name + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
param_obj = load_emod_parameters(config_filename, campaign_filename)
#total_timesteps = param_obj[KEY_TOTAL_TIMESTEPS]
drug_start_time = param_obj[dts.ParamKeys.KEY_DrugStartTime]
start_timestep = param_obj[dts.ConfigKeys.KEY_StartTime]
# duration_of_interest = param_obj[dts.ParamKeys.KEY_DrugRegimenLength]
drug_inactivation_rate = param_obj[
dts.ConfigKeys.DrugParams.KEY_TbDrugInactivationRateHIV]
cum_inactivations, inactivation_times, active_count, inactivations = parse_stdout_file(
drug_start_time, start_timestep, stdout_filename, debug)
# inset_days = parse_json_report(start_timestep, output_folder, chart_name, debug)
create_report_file(drug_start_time, inactivation_times, active_count,
inactivations, drug_inactivation_rate, report_name,
debug)
return None
def application( output_folder="output", stdout_filename="test.txt",
config_filename="config.json",campaign_filename="campaign.json",
chart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=True):
if debug:
print( "output_folder: " + output_folder )
print( "stdout_filename: " + stdout_filename+ "\n" )
print( "config_filename: " + config_filename + "\n" )
print( "chart_name: " + chart_name + "\n" )
print( "report_name: " + report_name + "\n" )
print( "debug: " + str(debug) + "\n" )
sft.wait_for_done()
param_obj = load_emod_parameters(config_filename,campaign_filename)
drug_mortality_rate_HIV = param_obj[dts.ConfigKeys.DrugParams.KEY_TbDrugMortalityRateHIV]
drug_start_timestep = param_obj[dts.ParamKeys.KEY_DrugStartTime]
duration_of_interest = param_obj[dts.ParamKeys.KEY_DrugRegimenLength]
cum_deaths, deaths, infected_individuals, death_times = parse_stdout_file(drug_start_timestep, duration_of_interest, stdout_filename, debug)
disease_deaths = parse_json_report(output_folder, chart_name, debug)
sft.plot_data( cum_deaths, disease_deaths,
label1="stdout", label2="insetchart",
title="Cumulative Deaths stdout vs. insetchart",
category="Cumulative_Deaths",
xlabel="Timestep", ylabel="Deaths", show=True, line=True, overlap=True)
# Now we've ingested all relevant inputs, let's do analysis
create_report_file(drug_start_timestep, disease_deaths, cum_deaths, deaths, infected_individuals, death_times, drug_mortality_rate_HIV, report_name)
def application( output_folder="output", stdout_filename="test.txt",
property_report_name="PropertyReport.json",
config_filename="config.json", campaign_filename="campaign.json",
report_name=sft.sft_output_filename,
debug=True):
if debug:
print( "output_folder: " + output_folder )
print( "stdout_filename: " + stdout_filename+ "\n" )
print( "property_report_name: " + property_report_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, hint_support.config_keys, debug)
campaign_obj = hint_support.load_campaign_file(campaign_filename, debug)
stdout_df = hint_support.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_overlay_file(
config_obj[ConfigKeys.Demographics_Filenames][1], demo_path, debug)
property_keys = hint_support.build_channel_string_for_property(property_list, hint_support.channels, debug)
property_df = hint_support.parse_property_report_json(property_report_name, output_folder, property_keys, debug)
create_report_file(config_obj, campaign_obj, stdout_df, property_df, property_list, report_name, debug)
def application(output_folder="output",
stdout_filename="test.txt",
config_filename="config.json",
campaign_filename="campaign.json",
insetchart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder)
print("stdout_filename: " + stdout_filename + "\n")
print("config_filename: " + config_filename + "\n")
print("campaign_filename: " + campaign_filename + "\n")
print("insetchart_name: " + insetchart_name + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
param_obj = dts.load_emod_parameters(config_filename, campaign_filename)
start_timestep = param_obj[ConfigKeys.Start_Time] # get from config
# Now process log output (probably) and compare to theory (not in this example) or to another report.
infections = dts.parse_stdout_file(stdout_filename, debug)
inset_summary = dts.parse_json_report(start_timestep, output_folder,
insetchart_name, debug)
dts.create_report_file(param_obj, infections, inset_summary, report_name)
def application(output_folder="output",
stdout_filename="test.txt",
config_filename="config.json",
property_report_name="PropertyReportEnvironmental.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("config_filename: " + config_filename + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done(stdout_filename)
config_obj = General_Support.load_config_parameters(
config_filename, config_keys, 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
create_report_file(config_obj, stdout_df, property_obj, property_df,
report_name, debug)
def application(output_folder="output", csv_name="ReportNodeDemographics.csv", config_filename="config.json",
report_name=sft.sft_output_filename, debug=False):
if debug:
print("output_folder: " + output_folder + "\n")
print("csv_name: " + csv_name + "\n")
print("config_name: " + config_filename + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
with open(config_filename) as infile:
test_config_name = json.load(infile)["parameters"]["Config_Name"]
sft.start_report_file(report_name, test_config_name)
all_data_df = pd.read_csv(path.join(output_folder, csv_name))
all_data_df.rename(columns={' NodeID': 'NodeID', ' Gender': 'Gender',
' AgeYears': 'AgeYears', ' NumIndividuals': 'NumIndividuals',
' NumInfected': 'NumInfected'}, inplace=True)
all_data_df.drop(['NumInfected'], axis=1, inplace=True)
if debug:
all_data_df.to_csv("DEBUG_all_data_cleaned.csv")
last_day_df = all_data_df.loc[all_data_df['Time']==399]
if debug:
last_day_df.to_csv("DEBUG_day_399_data_cleaned.csv")
northern_nodes = last_day_df[last_day_df['NodeID'].isin([1,2,3])]
southern_nodes = last_day_df[last_day_df['NodeID'].isin([7,8,9])]
eastern_nodes = last_day_df[last_day_df['NodeID'].isin([3,6,9])]
western_nodes = last_day_df[last_day_df['NodeID'].isin([1,4,7])]
create_report_file(sft_filename=report_name, n_nodes=northern_nodes,
s_nodes=southern_nodes, e_nodes=eastern_nodes,
w_nodes=western_nodes)
def application(output_folder="output",
config_filename="config.json",
jsonreport_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder + "\n")
print("config_filename: " + config_filename + "\n")
print("insetchart_name: " + jsonreport_name + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
config_object = dtk_iis.load_config_file(config_filename=config_filename,
debug=debug)
demographics_overlay_name = config_object[
dtk_iis.ConfigKeys.DEMOGRAPHIC_FILENAMES][-1]
campaign_name = config_object[dtk_iis.ConfigKeys.CAMPAIGN_FILENAME]
test_config_name = config_object[dtk_iis.ConfigKeys.CONFIG_NAME]
campaign_object = dtk_iis.load_campaign_file(campaign_name, debug)
outbreak_day = campaign_object[dtk_iis.CampaignKeys.START_DAY]
demographics_object = dtk_iis.load_demographics_file(
demographics_filename=demographics_overlay_name,
susceptibility_initialization_type=config_object[
dtk_iis.ConfigKeys.SUS_INIT_DIST_TYPE],
debug=debug)
average_immunity = demographics_object[
dtk_iis.DemographicFileKeys.KEY_AVERAGE_IMMUNITY]
sft.start_report_file(report_name, test_config_name)
report_data_object = dtk_iis.parse_json_report(output_folder=output_folder,
report_name=jsonreport_name,
debug=debug)
statistical_population_channel = report_data_object[
dtk_iis.InsetChannels.STATISTICAL_POPULATION]
new_infections_channel = report_data_object[
dtk_iis.InsetChannels.NEW_INFECTIONS]
expected_infections_obj = dtk_iis.get_expected_infections(
statistical_population_channel,
average_immunity,
campaign_object,
debug=debug)
actual_infections = dtk_iis.get_actual_infections(new_infections_channel,
outbreak_day)
dtk_iis.create_report_file(expected_infections_obj,
actual_infections,
outbreak_day,
report_name,
debug=debug)
def application(output_folder="output", stdout_filename=sft.sft_test_filename,
config_filename="config.json",
insetchart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
sft.wait_for_done()
stc = STC()
param_obj = stc.load_emod_parameters(config_filename=config_filename)
output_df = stc.parse_output_file(output_filename=sft.sft_test_filename,
start_time=param_obj[ConfigParameters.KEY_Start_Time], debug=False)
stc.create_report_file(param_obj, output_df, report_name=report_name, age_index_1=2, age_index_2=3)
def application(output_folder="output", config_filename="config.json",
jsonreport_name="InsetChart.json", stdout_filename="test.txt",
report_name=sft.sft_output_filename, debug=False):
if debug:
print("output_folder: " + output_folder)
print("config_filename: " + config_filename)
print("insetchart_name: " + jsonreport_name)
print("report_name: " + report_name)
print("debug: " + str(debug))
sft.wait_for_done()
config_object = dtk_iis.load_config_file(config_filename=config_filename,
debug=debug)
demographics_overlay_name = config_object[dtk_iis.ConfigKeys.DEMOGRAPHIC_FILENAMES][-1]
campaign_name = config_object[dtk_iis.ConfigKeys.CAMPAIGN_FILENAME]
test_config_name = config_object[dtk_iis.ConfigKeys.CONFIG_NAME]
campaign_object = dtk_iis.load_campaign_file(campaign_name, debug)
outbreak_day = campaign_object[dtk_iis.CampaignKeys.START_DAY]
demographics_object = dtk_iis.load_demographics_file(
demographics_filename=demographics_overlay_name,
susceptibility_initialization_type=config_object[dtk_iis.ConfigKeys.SUS_INIT_DIST_TYPE],
debug=debug)
average_immunity = demographics_object[dtk_iis.DemographicFileKeys.KEY_AVERAGE_IMMUNITY]
sft.start_report_file(report_name, test_config_name)
individual_df = dtk_iis.parse_stdout_file(stdout_filename, debug=debug)
dtk_iis.test_immunity_within_age_range(individual_df, max_age=365,
expected_immunity=0.0)
dtk_iis.test_immunity_within_age_range(individual_df, max_age=730,
expected_immunity=0.4)
report_data_object = dtk_iis.parse_json_report(output_folder=output_folder,
report_name=jsonreport_name,
debug=debug)
statistical_population_channel = report_data_object[dtk_iis.InsetChannels.STATISTICAL_POPULATION]
new_infections_channel = report_data_object[dtk_iis.InsetChannels.NEW_INFECTIONS]
expected_infections_obj = dtk_iis.get_expected_infections(statistical_population_channel,
average_immunity,
campaign_object,
debug=debug)
actual_infections = dtk_iis.get_actual_infections(new_infections_channel,
outbreak_day)
dtk_iis.create_report_file(expected_infections_obj, actual_infections,
outbreak_day, report_name,
debug=debug)
def application(output_folder="output",
stdout_filename="test.txt",
reporter_filename="Report_TBHIV_ByAge.csv",
inset_chart_filename="InsetChart.json",
migration_report_filename="ReportHumanMigrationTracking.csv",
config_filename="config.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder)
print("stdout_filename: " + stdout_filename + "\n")
print("reporter_filename: " + reporter_filename + "\n")
print("inset_chart_filename: " + inset_chart_filename + "\n")
print("migration_report_filename: " + migration_report_filename + "\n")
print("config_filename: " + config_filename + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
param_obj = tms.load_emod_parameters([
Config.config_name, Config.simulation_timestep, Config.duration,
Config.num_core, Config.demog_filename
], config_filename, debug)
demog_filename = param_obj[Config.demog_filename][-1]
node_list = tms.get_node_counts(demog_filename)
json_obj = tms.parse_json_report([InsetChart.disease_death],
inset_chart_filename, output_folder,
debug)
migration_df = tms.load_migration_report(migration_report_filename,
output_folder)
report_column_list = [
ReportColumn.year, ReportColumn.agebin, ReportColumn.hivdeaths,
ReportColumn.diseasedeaths
]
reporter_df = trs.parse_custom_reporter(
report_column_list,
reporter_path=output_folder,
reporter_filename=reporter_filename,
debug=debug)
create_report_file_incidence(ReportColumn.diseasedeaths,
ReportColumn.hivdeaths, ReportColumn.year,
json_obj, param_obj, reporter_df,
migration_df, node_list, stdout_filename,
report_name, debug)
def application( output_folder="output", stdout_filename="test.txt", config_filename="config.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print( "output_folder: " + output_folder )
print( "stdout_filename: " + stdout_filename+ "\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 = General_Support.load_config_parameters(config_filename, config_keys, debug)
stdout_df = parse_stdout_file(stdout_filename, config_obj[ConfigKeys.Simulation_Timestep], debug)
create_report_file(config_obj, stdout_df, report_name, debug)
def application(output_folder="output", stdout_filename="test.txt",
config_filename="config.json",
insetchart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print( "output_folder: " + output_folder )
print( "stdout_filename: " + stdout_filename+ "\n" )
print( "config_filename: " + config_filename + "\n" )
print( "insetchart_name: " + insetchart_name + "\n" )
print( "report_name: " + report_name + "\n" )
print( "debug: " + str(debug) + "\n" )
sft.wait_for_done()
param_obj = load_emod_parameters(config_filename)
parsed_data = parse_stdout_file(debug=True)
create_report_file([report_name, parsed_data, param_obj.get(TB_CD4_ACTIVATION_VECTOR)], debug=True)
def application(output_folder="output",
stdout_filename="test.txt",
config_filename="config.json",
chart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder)
print("stdout_filename: " + stdout_filename + "\n")
print("config_filename: " + config_filename + "\n")
print("chart_name: " + chart_name + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
param_obj = load_emod_parameters(config_filename)
drug_start_timestep = param_obj[dts.ParamKeys.KEY_DrugStartTime]
sim_start_timestep = param_obj[dts.ConfigKeys.KEY_StartTime]
# Now process log output (probably) and compare to theory (not in this example) or to another report.
duration_of_interest = param_obj[dts.ParamKeys.KEY_DrugRegimenLength]
cum_clears, clear_times, stdout_days = parse_stdout_file(
drug_start_timestep, duration_of_interest, stdout_filename, debug)
inset_days = parse_json_report(sim_start_timestep, debug=debug)
if debug:
print("trying to plot data\n")
sft.plot_data_sorted(
cum_clears,
label1="Cumulative Clearances",
title="Cumulative Clearances over Time from Drugs (HIV+/No ART)",
xlabel="Timestep",
ylabel="Clearances",
show=True)
else:
sft.plot_data(
cum_clears,
label1="Cumulative Clearances",
title="Cumulative Clearances over Time from Drugs (HIV+/No ART)",
xlabel="Timestep",
ylabel="Clearances")
#inset_days = parse_json_report(start_timestep, output_folder, chart_name, debug)
# Now we've ingested all relevant inputs, let's do analysis
if debug:
print("trying to create report file\n")
create_report_file(clear_times, param_obj, report_name, stdout_days,
inset_days, debug)
def application( output_folder="output", stdout_filename="test.txt", 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( "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()
param_obj = load_emod_parameters(config_filename, debug)
output_dict = parse_output_file(stdout_filename, debug)
create_report_file(param_obj, output_dict, 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",
config_filename="config.json",
campaign_filename="campaign.json",
demographics_filename="demographics_100_overlay.json",
insetchart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder)
print("config_filename: " + config_filename + "\n")
print("campaign_filename: " + campaign_filename + "\n")
print("demographics_filename: " + demographics_filename + "\n")
print("insetchart_name: " + insetchart_name + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
param_obj = ips.load_emod_parameters(config_filename, debug)
campaign_obj = ips.load_campaign_file(param_obj[KEY_CAMPAIGN_NAME], debug)
demographics_obj = ips.load_demographics_file(
param_obj[KEY_DEMOGRAPHICS_NAME][-1], debug)
report_data_obj = ips.parse_json_report(output_folder, insetchart_name,
debug)
sft.plot_data(report_data_obj[KEY_NEW_INFECTIONS],
title="new infections",
label1="New Infections",
label2="NA",
xlabel="time steps",
ylabel="new infection",
category='New_infections',
show=True)
sft.plot_data(report_data_obj[KEY_STATISTICAL_POPULATION],
title="Statistical Population",
label1="Statistical Population",
label2="NA",
xlabel="time steps",
ylabel="Statistical Population",
category='Statistical_population',
show=True,
line=True)
ips.create_report_file(param_obj, campaign_obj, demographics_obj,
report_data_obj, report_name, debug)
def application( output_folder="output", stdout_filename="test.txt",
config_filename="config.json",
insetchart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print( "output_folder: " + output_folder )
print( "stdout_filename: " + stdout_filename+ "\n" )
print( "config_filename: " + config_filename + "\n" )
print( "insetchart_name: " + insetchart_name + "\n" )
print( "report_name: " + report_name + "\n" )
print( "debug: " + str(debug) + "\n" )
sft.wait_for_done()
param_obj = isb_support.load_emod_parameters(config_filename)
simulation_timestep = param_obj[KEY_SIMULATION_TIMESTEP]
output_df = isb_support.parse_output_file(stdout_filename, simulation_timestep, debug)
report_df = isb_support.parse_json_report(output_folder, insetchart_name, debug)
isb_support.create_report_file(param_obj, output_df, report_df, report_name, debug)
def application( output_folder="output", stdout_filename="test.txt",
config_filename="config.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print( "output_folder: " + output_folder )
print( "stdout_filename: " + stdout_filename+ "\n" )
print( "config_filename: " + config_filename + "\n" )
print( "report_name: " + report_name + "\n" )
print( "debug: " + str(debug) + "\n" )
sft.wait_for_done()
param_obj = load_emod_parameters(config_filename,debug)
output_obj = parse_output_file(stdout_filename, debug)
multipliers = output_obj[matches[0]]
infectiousness = output_obj[matches[1]]
create_report_file(param_obj, multipliers, infectiousness, report_name, debug)
def application(output_folder="output", stdout_filename="test.txt",
config_filename="config.json",
insetchart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print( "output_folder: " + output_folder )
print( "stdout_filename: " + stdout_filename+ "\n" )
print( "config_filename: " + config_filename + "\n" )
print( "insetchart_name: " + insetchart_name + "\n" )
print( "report_name: " + report_name + "\n" )
print( "debug: " + str(debug) + "\n" )
sft.wait_for_done()
param_obj = load_emod_parameters(config_filename)
parsed_data = parse_stdout_file()
inset_days = parse_json_report()
create_report_file([report_name, parsed_data, param_obj.get(COINFECTION_MORTALITY_RATE_OFF_ART),
param_obj.get(COINFECTION_MORTALITY_RATE_ON_ART)])
def application( output_folder="output", stdout_filename="test.txt",
config_filename="config.json",
insetchart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print( "output_folder: " + output_folder )
print( "stdout_filename: " + stdout_filename+ "\n" )
print( "config_filename: " + config_filename + "\n" )
print( "insetchart_name: " + insetchart_name + "\n" )
print( "report_name: " + report_name + "\n" )
print( "debug: " + str(debug) + "\n" )
sft.wait_for_done()
param_obj = isb_support.load_emod_parameters(config_filename)
simulation_timestep = param_obj[KEY_SIMULATION_TIMESTEP]
output_df = isb_support.parse_output_file(stdout_filename, simulation_timestep, debug)
report_df = isb_support.parse_json_report(output_folder, insetchart_name, debug)
isb_support.create_report_file(param_obj, output_df, report_df, report_name, debug)
def application(output_folder="output",
stdout_filename="test.txt",
property_report_name="PropertyReportEnvironmental.json",
report_event_recorder="ReportNodeEventRecorder.csv",
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("report_event_recorder: " + report_event_recorder + "\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 = General_Support.load_config_parameters(
config_filename, Diagnostic_Support.config_keys, debug)
demo_overlay_file = config_obj[ConfigKeys.Demographics_Filenames][-1]
campaign_obj = Diagnostic_Support.load_campaign_file(
campaign_filename, debug)
demo_path = "Assets" if stdout_filename == "StdOut.txt" else ""
property_obj = HINT_Support.load_demo_mr_overlay_file(
demo_overlay_file, demo_path, debug)[0]
ip_key_value = campaign_obj[
CampaignKeys.EnvironmentalDiagnosticKeys.Environment_IP_Key_Value]
property_keys = []
for channel in Diagnostic_Support.channels:
property_keys.append("{0}:{1}".format(channel, ip_key_value))
property_df = HINT_Support.parse_property_report_json(
property_report_name, output_folder, property_keys, debug)
stdout_df = Diagnostic_Support.parse_stdout_file(
stdout_filename, config_obj[ConfigKeys.Simulation_Timestep], debug)
recorder_obj = Diagnostic_Support.parse_report_event_recorder(
output_folder, report_event_recorder, debug)
create_report_file(config_obj, campaign_obj, property_obj, property_df,
stdout_df, recorder_obj, report_name,
report_event_recorder, stdout_filename, debug)
def application(output_folder="output",
csv_name="ReportNodeDemographics.csv",
config_filename="config.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder + "\n")
print("csv_name: " + csv_name + "\n")
print("config_name: " + config_filename + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
with open(config_filename) as infile:
test_config_name = json.load(infile)["parameters"]["Config_Name"]
sft.start_report_file(report_name, test_config_name)
all_data_df = pd.read_csv(path.join(output_folder, csv_name))
all_data_df.rename(columns={
' NodeID': 'NodeID',
' Gender': 'Gender',
' AgeYears': 'AgeYears',
' NumIndividuals': 'NumIndividuals',
' NumInfected': 'NumInfected'
},
inplace=True)
all_data_df.drop(['NumInfected'], axis=1, inplace=True)
if debug:
all_data_df.to_csv("DEBUG_all_data_cleaned.csv")
last_day_df = all_data_df.loc[all_data_df['Time'] == 399]
if debug:
last_day_df.to_csv("DEBUG_day_399_data_cleaned.csv")
northern_nodes = last_day_df[last_day_df['NodeID'].isin([1, 2, 3])]
southern_nodes = last_day_df[last_day_df['NodeID'].isin([7, 8, 9])]
eastern_nodes = last_day_df[last_day_df['NodeID'].isin([3, 6, 9])]
western_nodes = last_day_df[last_day_df['NodeID'].isin([1, 4, 7])]
create_report_file(sft_filename=report_name,
n_nodes=northern_nodes,
s_nodes=southern_nodes,
e_nodes=eastern_nodes,
w_nodes=western_nodes)
def application( output_folder="output", stdout_filename="test.txt", reporter_filename="Report_TBHIV_ByAge.csv",
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( "reporter_filename: " + reporter_filename+ "\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()
param_obj = load_emod_parameters(config_filename, debug)
campaign_obj = load_campaign_file(campaign_filename, debug)
output_df = parse_output_file(stdout_filename, param_obj[Config.simulation_timestep], debug)
reporter = parse_custom_reporter(reporter_path=output_folder, reporter_filename=reporter_filename, debug=debug)
create_report_file(param_obj, campaign_obj, output_df, reporter, report_name, debug)
def application( output_folder="output", stdout_filename="test.txt",
config_filename="config.json",campaign_filename="campaign.json",
demographics_filename = "../../demographics.json",
propertyreport_name="PropertyReport.json",
report_name=sft.sft_output_filename,
debug=True):
if debug:
print( "output_folder: " + output_folder )
print( "stdout_filename: " + stdout_filename+ "\n" )
print( "config_filename: " + config_filename + "\n" )
print( "campaign_filename: " + campaign_filename + "\n" )
print( "demographics_filename: " + demographics_filename + "\n" )
print( "propertyreport_name: " + propertyreport_name + "\n" )
print( "report_name: " + report_name + "\n" )
print( "debug: " + str(debug) + "\n" )
sft.wait_for_done()
report_data_obj = parse_json_report(output_folder, propertyreport_name, debug)
create_report_file(report_data_obj, report_name, debug)
def application(output_folder="output",
stdout_filename="test.txt",
initial_timestep=0,
config_filename="config.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder)
print("stdout_filename: " + stdout_filename + "\n")
print("initial_timestep: " + str(initial_timestep) + "\n")
print("config_filename: " + config_filename + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
param_obj = load_emod_parameters(config_filename, debug)
stdout_data_obj = parse_stdout_file(initial_timestep, stdout_filename,
debug)
create_report_file(param_obj, stdout_data_obj, report_name, debug)
def application(report_file):
sft.wait_for_done()
# get params from config.json
cdj = json.loads(open("config.json").read())["parameters"]
# I don't use most of these yet, but they're pretty standard boilerplate for SFTs
start_time = cdj["Start_Time"]
lines = []
timestep = start_time
with open("test.txt") as logfile:
for line in logfile:
if "Update(): Time:" in line:
# calculate time step
timestep += 1
# This test uses the PropertyReport not stdout.
prt_json = json.loads( open( "output/PropertyReportTyphoid.json" ).read() )
geographic_zones = [ "A", "B", "C", "D", "E", "F", "G", "H", "I" ]
def application( output_folder="output", stdout_filename="test.txt", report_event_recorder="ReportNodeEventRecorder.csv",
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("report_event_recorder: " + report_event_recorder+ "\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 = General_Support.load_config_parameters(config_filename, Diagnostic_Support.config_keys, debug)
campaign_obj = Diagnostic_Support.load_campaign_file(campaign_filename, debug)
stdout_df = Diagnostic_Support.parse_stdout_file(stdout_filename, config_obj[ConfigKeys.Simulation_Timestep], debug)
recorder_obj = Diagnostic_Support.parse_report_event_recorder(output_folder, report_event_recorder, debug)
create_report_file(config_obj, campaign_obj, stdout_df, recorder_obj, report_name, report_event_recorder, debug)
def application(output_folder="output", config_filename="config.json",
jsonreport_name="InsetChart.json", stdout_filename="test.txt",
report_name=sft.sft_output_filename, debug=False):
if debug:
print("output_folder: " + output_folder + "\n")
print("config_filename: " + config_filename + "\n")
print("insetchart_name: " + jsonreport_name + "\n")
print("stdout filename:" + stdout_filename + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
sft.wait_for_done()
config_object = dtk_iis.load_config_file(config_filename=config_filename,
debug=debug)
demographics_overlay_name = config_object[dtk_iis.ConfigKeys.DEMOGRAPHIC_FILENAMES][-1]
campaign_name = config_object[dtk_iis.ConfigKeys.CAMPAIGN_FILENAME]
test_config_name = config_object[dtk_iis.ConfigKeys.CONFIG_NAME]
demographics_object = dtk_iis.load_demographics_file(
demographics_filename=demographics_overlay_name,
susceptibility_initialization_type=config_object[dtk_iis.ConfigKeys.SUS_INIT_DIST_TYPE],
debug=debug)
sft.start_report_file(report_name, test_config_name)
i_df = dtk_iis.parse_stdout_file(stdout_filename, debug=debug)
distribution_object = demographics_object[dtk_iis.DemographicFileKeys.SusceptibilityDistribution.KEY]
distro_values = \
distribution_object[dtk_iis.DemographicFileKeys.SusceptibilityDistribution.ComplexKeys.DistributionValues][0]
distro_results = \
distribution_object[dtk_iis.DemographicFileKeys.SusceptibilityDistribution.ComplexKeys.ResultValues][0]
if debug:
print("Sus distribution type: {0}\n".format(config_object[dtk_iis.ConfigKeys.SUS_INIT_DIST_TYPE]))
print("Distribution object: {0}\n".format(distribution_object))
print("Distro values: {0}\n".format(distro_values))
with open(report_name, "a") as outfile:
messages = dtk_iis.validate_complex_initialization_numpy(
individual_dataframe=i_df, susceptibility_distribution=distribution_object,
outfile=outfile, debug=debug)
pass
def application(output_folder="output",
config_filename="config.json", campaign_filename="campaign.json",
demographics_filename="demographics_100_overlay.json",
insetchart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder)
print("config_filename: " + config_filename+"\n")
print("campaign_filename: " + campaign_filename+"\n")
print("demographics_filename: " + demographics_filename+"\n")
print("insetchart_name: " + insetchart_name+"\n")
print("report_name: " + report_name+"\n")
print("debug: " + str(debug)+"\n")
sft.wait_for_done()
param_obj = ips.load_emod_parameters(config_filename, debug)
campaign_obj = ips.load_campaign_file(param_obj[KEY_CAMPAIGN_NAME], debug)
demographics_obj = ips.load_demographics_file(param_obj[KEY_DEMOGRAPHICS_NAME][-1], debug)
report_data_obj = ips.parse_json_report(output_folder, insetchart_name, debug)
sft.plot_data(report_data_obj[KEY_NEW_INFECTIONS],
title="new infections",
label1="New Infections",
label2="NA",
xlabel="time steps", ylabel="new infection",
category='New_infections',
show=True)
sft.plot_data(report_data_obj[KEY_STATISTICAL_POPULATION],
title="Statistical Population",
label1="Statistical Population",
label2="NA",
xlabel="time steps", ylabel="Statistical Population",
category='Statistical_population',
show=True, line=True)
ips.create_report_file(param_obj, campaign_obj, demographics_obj, report_data_obj, report_name,
debug)
def application(output_folder="output", stdout_filename="test.txt",
config_filename="config.json",
insetchart_name="InsetChart.json",
report_name=sft.sft_output_filename,
debug=False):
if debug:
print("output_folder: " + output_folder)
print("stdout_filename: " + stdout_filename + "\n")
print("config_filename: " + config_filename + "\n")
print("insetchart_name: " + insetchart_name + "\n")
print("report_name: " + report_name + "\n")
print("debug: " + str(debug) + "\n")
print("current dir = " + os.getcwd())
sft.wait_for_done()
param_obj, config_json = MM_Support.load_emod_parameters(config_filename)
if debug:
print (param_obj)
node_demog_df, human_migration_df = MM_Support.parse_output_files("output/ReportNodeDemographics.csv",
"output/ReportHumanMigrationTracking.csv", debug)
# for local testing
# node_demo_df, human_migration_df = MM_Support.parse_output_files("ReportNodeDemographics.csv", "ReportHumanMigrationTracking.csv", debug)
MM_Support.create_report_file_stationary_distribution(param_obj, node_demog_df, report_name, debug)
def application(output_folder="output", config_filename="config.json",
report_name=sft.sft_output_filename, debug=False):
if debug:
print("output_folder: {0}".format(output_folder))
print("config_filename: {0}".format(config_filename))
print("report_name: {0}".format(report_name))
print("debug: {0}".format(debug))
config_object = d_ss.load_config_file(config_filename=config_filename, debug=debug)
sft.start_report_file(output_filename=report_name,
config_name=config_object[d_ss.ConfigKeys.CONFIGNAME_KEY],
already_started=True)
sft.wait_for_done()
dtk_filename = path.join(output_folder, 'state-00005.dtk')
dtk_file = d_ss.DtkFile(dtk_filename)
dtk_file.write_node_to_disk(node_index=0)
dtk_file.write_simulation_to_disk()
infected_people_to_check = []
with open("DEBUG_found_infected_persons.json") as infile:
infected_people_to_check = json.load(infile)
if debug:
print(f"Infected_people_to_check: {infected_people_to_check}")
infected_people_first={}
infected_people_second={}
for suid in infected_people_to_check:
suid_int = int(suid)
print("Trying suid: {0}".format(suid_int))
infected_people_first[suid] = d_ss.SerializedHuman.from_file(f"human-{suid_int}-old.json")
dtk_file.write_human_to_disk(node_index=0, suid=suid_int, debug=debug)
infected_people_second[suid] = d_ss.SerializedHuman.from_file(f"human-{suid_int}-new.json")
# Make sure each individual is Simulation_Duration days older
messages = []
expected_age_delta = config_object[d_ss.ConfigKeys.Serialization.TIMESTEPS_KEY][0]
for person in infected_people_to_check:
infection_suid = infected_people_to_check[person]
if debug:
# print(f"X is: {x}")
print(f"person is: {person}")
print(f"infection is: {infection_suid}")
print(f"infected_people_first[person] = {infected_people_first[person]}")
print(f"infected_people_second[person] = {infected_people_second[person]}")
aging_messages = infected_people_first[person].compare_to_older(infected_people_second[person], expected_age_delta)
messages += aging_messages if aging_messages else [f"GOOD: human {person} checks out"]
older_infection = infected_people_first[person].get_infection_by_suid(infection_suid)
newer_infection = infected_people_second[person].get_infection_by_suid(infection_suid)
messages += newer_infection.compare_to_older(older_infection, expected_age_delta)
messages += newer_infection.validate_own_timers()
# Make sure each infection is Simulation_Duration days older
#TODO: compare the simulation objects
#TODO: compare the node objects
success_message_formatter = sft.format_success_msg
d_ss.generate_report_file(config_object, report_name, output_folder=output_folder,
messages=messages, success_formatter=success_message_formatter,
debug=debug)
d_ss.clean_serialization_test(debug)