def configure(cb):
ModBuilder.metadata.update({'Config_Name': test_name})
test = DTKConfigBuilder.from_files(
os.path.join(self.regression_path, test_name, 'config.json'),
os.path.join(self.regression_path, test_name, 'campaign.json'))
cb.copy_from(test)
def configure_forest_system(years=100,
migration_start_day=91,
migration_type='one_season'):
# General
village_nodes = [1, 2]
forest_nodes = [3]
geog_name = "Ratanikiri_3node"
cb = DTKConfigBuilder.from_defaults('MALARIA_SIM')
standard_cb_updates(cb, years, geog_name)
update_vector_params(cb)
# For the forest: add Individual Properties so only some people travel to forest nodes
change_individual_property_at_age(cb,
'ForestGoing',
'LovesForest',
coverage=0.7,
change_age_in_days=15 * 365,
revert=20 * 365)
add_forest_migration(cb,
migration_start_day,
years,
forest_nodes,
village_nodes,
mig_type=migration_type)
recurring_outbreak(cb,
start_day=(91 + 30),
outbreak_fraction=0.2,
nodes={
"class": "NodeSetNodeList",
'Node_List': forest_nodes
})
return cb
def configure_sahel_intervention_system(years=100):
# General
cb = DTKConfigBuilder.from_defaults('MALARIA_SIM')
standard_cb_updates(cb, years)
update_vector_params(cb)
return cb
def test_add_ITN():
# cb = {}
cb = DTKConfigBuilder.from_defaults('MALARIA_SIM')
coverage_by_age = {'min': 0, 'max': 200, 'coverage': 1}
ITN_event = add_ITN(cb,
start=0,
coverage_by_ages=[coverage_by_age],
waning={},
nodeIDs=[])
print(ITN_event)
print(ITN_event.to_json())
def do_stuff():
SetupParser.default_block = 'HPC'
gen_cb = DTKConfigBuilder.from_defaults('GENERIC_SIM_SEIR')
gen_cb.params["Simulation_Duration"] = 200
exp_tags = {}
exp_tags['role'] = 'serialization_test'
exp_tags['model'] = 'generic'
s_ts = [5, 25, 150]
T = skt.SerializationKsTest(config_builder=gen_cb,
experiment_name='Generic serialization test',
experiment_tags=exp_tags,
timesteps_to_serialize=s_ts,
inset_channels=[
'New Infections', 'Infected',
'Statistical Population'
])
T.run_test()
def setUp(self):
current_dir = os.path.dirname(os.path.realpath(__file__))
input_dir = os.path.join(current_dir, 'input')
self.am_simtools = os.path.join(input_dir, 'am_simtools.ini')
# Adjust path sensitive parameters in the ini file
cp = ConfigParser()
cp.read(self.am_simtools)
cp.set('DEFAULT', 'path', input_dir)
cp.set('DEFAULT', 'example_dir',
os.path.join(current_dir, '..', '..', 'examples'))
cp.write(open(self.am_simtools, 'w'))
SetupParser.init(selected_block=self.SELECTED_BLOCK,
setup_file=self.am_simtools)
self.config_builder = DTKConfigBuilder.from_defaults('VECTOR_SIM')
configure_site(self.config_builder, 'Namawala')
self.config_builder.add_reports(BaseReport(type="VectorHabitatReport"))
def configure_VC_GM_intervention_system(prefix,
geography,
num_cores=1,
num_years=100,
migration_mul=1):
# General
cb = DTKConfigBuilder.from_defaults(
'MALARIA_SIM',
Num_Cores=num_cores,
Simulation_Duration=int(365 * num_years),
)
standard_cb_updates(cb, prefix, geography, migration_mul)
update_vector_params(cb)
return cb
def do_stuff():
SetupParser.default_block = 'HPC'
vec_cb = DTKConfigBuilder.from_defaults('VECTOR_SIM')
configure_site(vec_cb, 'Namawala')
exp_tags = {}
exp_tags['role'] = 'serialization_test'
exp_tags['model'] = 'vector'
s_ts = [5, 25, 150]
T = skt.SerializationKsTest(config_builder=vec_cb,
experiment_name='Vector serialization test',
experiment_tags=exp_tags,
timesteps_to_serialize=s_ts,
inset_channels=['Adult Vectors',
'New Infections',
'Infected',
'Statistical Population',
'Daily EIR'])
T.run_test()
def prepare_malariatherapy_configbuilder(config_path,
immunity_forcing=True,
years=1):
# Setup -------------------------------------------------------------------------------------------
cb = DTKConfigBuilder.from_files(config_path)
cb.update_params({
'Vector_Species_Names': [],
'Simulation_Duration':
365 * years,
'Demographics_Filenames': ['Malariatherapy_demographics.json']
})
set_climate_constant(cb)
# Add source of infection (challenge bite or forced EIR) ------------------------------------------
add_challenge_trial(cb, start_day=0)
# ---- CUSTOM REPORTS ----
add_patient_report(cb)
return cb
def test_listed_events(self):
from simtools.SetupParser import SetupParser
SetupParser.init()
# Create a builder based on the files
builder = DTKConfigBuilder.from_files(
os.path.join(self.input_path, 'customevents', 'configbad.json'),
os.path.join(self.input_path, 'customevents', 'campaign.json'))
# Call the file writter
def fake_write(name, content):
return
builder.file_writer(fake_write)
# Try if the listed events worked
self.assertEqual(
set(builder.config['parameters']['Listed_Events']),
set([
"Received_ITN", "TestedPositive", "Received_Campaign_Drugs",
"Received_Treatment", "Received_Test", "Received_Survey",
"Diagnostic_Survey_5", "Give_Drugs"
]))
from dtk.utils.core.DTKConfigBuilder import DTKConfigBuilder
from simtools.SetupParser import SetupParser
from simtools.ExperimentManager.ExperimentManagerFactory import ExperimentManagerFactory
# Run on HPC
SetupParser.default_block = "HPC"
# Tell this module how to find the config and campaign files to be used. Set campaign_file to None if not used.
input_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "input")
config_file = os.path.join(input_dir, 'config.json')
campaign_file = os.path.join(input_dir, 'campaign.json')
kwargs = {}
cb = DTKConfigBuilder.from_files(config_name=config_file,
campaign_name=campaign_file,
**kwargs)
cb.set_collection_id('71483975-57dc-e711-9414-f0921c16b9e5')
# Name of the experiment
exp_name = 'catalyst_comparison-MalariaSandbox'
# when run with 'dtk catalyst', run_sim_args['exp_name'] will have additional information appended.
run_sim_args = {
'exp_name': exp_name,
# 'exp_builder': builder, # users may have created one; this will be overridden in 'dtk catalyst'
'config_builder': cb
}
if __name__ == "__main__":
SetupParser.init()
def basic_gridded_config_builder(immunity_params="prashanth"):
cb = DTKConfigBuilder.from_defaults('MALARIA_SIM')
# Reduce StdOut size and prevent DTK from spitting out too many messages
cb.update_params({
"logLevel_default": "WARNING",
"Enable_Log_Throttling": 1,
"Memory_Usage_Warning_Threshold_Working_Set_MB": 50000,
"Memory_Usage_Halting_Threshold_Working_Set_MB": 60000,
"logLevel_JsonConfigurable": "WARNING",
"Disable_IP_Whitelist": 1
})
cb.update_params(immunity.params)
cb.update_params(infection.params)
cb.update_params(symptoms.params)
if immunity_params == 'prashanth':
cb.update_params({
'Antigen_Switch_Rate': pow(10, -9.116590124),
'Base_Gametocyte_Production_Rate': 0.06150582,
'Base_Gametocyte_Mosquito_Survival_Rate': 0.002011099,
'Falciparum_MSP_Variants': 32,
'Falciparum_Nonspecific_Types': 76,
'Falciparum_PfEMP1_Variants': 1070,
'Gametocyte_Stage_Survival_Rate': 0.588569307,
'MSP1_Merozoite_Kill_Fraction': 0.511735322,
'Max_Individual_Infections': 3,
'Nonspecific_Antigenicity_Factor': 0.415111634
})
elif immunity_params == "jaline":
cb.update_params({
'Base_Gametocyte_Production_Rate': 0.044,
"Gametocyte_Stage_Survival_Rate": 0.82,
'Antigen_Switch_Rate': 2.96e-9,
'Falciparum_PfEMP1_Variants': 1112,
'Falciparum_MSP_Variants': 7,
'MSP1_Merozoite_Kill_Fraction': 0.43,
'Falciparum_Nonspecific_Types': 90,
'Nonspecific_Antigenicity_Factor': 0.42,
'Base_Gametocyte_Mosquito_Survival_Rate': 0.00088,
"Max_Individual_Infections": 5
})
cb.update_params({
"Climate_Model":
"CLIMATE_CONSTANT",
"Base_Air_Temperature":
27,
"Base_Land_Temperature":
27,
"Migration_Model":
"NO_MIGRATION",
"Enable_Immunity_Distribution":
0,
"Enable_Immunity_Initialization_Distribution":
0,
"Immunity_Initialization_Distribution_Type":
"DISTRIBUTION_OFF"
})
cb.update_params({
"Enable_Demographics_Other": 1,
"Enable_Demographics_Builtin": 0,
"Valid_Intervention_States": [],
"Report_Detection_Threshold_PfHRP2": 40.0,
"Report_Detection_Threshold_Blood_Smear_Parasites": 0,
"Parasite_Smear_Sensitivity": 0.025,
"Birth_Rate_Dependence":
"FIXED_BIRTH_RATE", # Match demographics file for constant population size (with exponential age distribution)
"Enable_Nondisease_Mortality": 1,
})
# Intervention events
intervene_events_list = [
"Bednet_Got_New_One", "Bednet_Using", "Bednet_Discarded"
]
cb.update_params({
"Report_Event_Recorder": 0,
"Report_Event_Recorder_Ignore_Events_In_List": 0,
"Listed_Events": intervene_events_list,
"Report_Event_Recorder_Events": intervene_events_list
})
# Basic entomology
set_species_param(cb, 'arabiensis', 'Indoor_Feeding_Fraction', 0.5)
set_species_param(cb, 'arabiensis', 'Adult_Life_Expectancy', 20)
set_species_param(cb, 'arabiensis', 'Anthropophily', 0.65)
set_species_param(cb, 'funestus', "Indoor_Feeding_Fraction", 0.9)
set_species_param(cb, 'funestus', 'Adult_Life_Expectancy', 20)
set_species_param(cb, 'funestus', 'Anthropophily', 0.65)
return cb
# For quick test simulations, this is set to a very low value
static_params = {'Base_Population_Scale_Factor': 0.05}
cfg.set_params(static_params)
cpn.set_params(static_params)
# Prepare templates
templates = TemplateHelper()
table_base = {
'ACTIVE_TEMPLATES': [cfg, cpn, demog_pfa, demog_acc, demog_asrt],
'TAGS': {
'Scenario': 'StatusQuo_Baseline',
'pyOptimTool': None
}
}
config_builder = DTKConfigBuilder()
config_builder.ignore_missing = True
def constrain_sample(sample):
if 'Pr Ex Trns Male LOW' and 'Pr Ex Trns Male MED' in sample:
sample['Pr Ex Trns Male LOW'] = min(
[sample['Pr Ex Trns Male LOW'], sample['Pr Ex Trns Male MED']])
if 'Pr Ex Trns Fem LOW' and 'Pr Ex Trns Fem MED' in sample:
sample['Pr Ex Trns Fem LOW'] = min(
[sample['Pr Ex Trns Fem LOW'], sample['Pr Ex Trns Fem MED']])
return sample
def map_sample_to_model_input(config_builder, s):
SetupParser.init('HPC')
# Find experiment from whose config/campaigns we want to use (also get sweep params)
comparison_exp_id = "9945ae69-3106-e711-9400-f0921c16849c"
sim_name = 'Rerun_Rampup_MDA_Better_Diagnostic'
expt = retrieve_experiment(comparison_exp_id)
df = pd.DataFrame([x.tags for x in expt.simulations])
df['outpath'] = pd.Series([sim.get_path() for sim in expt.simulations])
# generate cb object from the first of these files (the only difference will be in the sweep params)
cb_dir = df['outpath'][0]
cb = DTKConfigBuilder.from_files(config_name=os.path.join(cb_dir, 'config.json'),
campaign_name=os.path.join(cb_dir, 'campaign.json'))
CompsDTKOutputParser.sim_dir_map = None
#cb.update_params({'Num_Cores': 1})
sites = [
MyanmarCalibSite()
]
# Here we are specifying the initial values for the next point data
initial_state = [{
'NodeIDs':[],
'Serialization':2007,
'Prevalence_date':2006,
'Prevalence_threshold':0.4,
'New_Duration': 1643, # Duration of second iteration
run_sets = []
for sweep in SWEEPS:
i = 0
for sim_id in os.listdir(path=simulation_input_files_dir):
# Create one experiment per base_simulationXsweep pairing. Each exp contains one sim per sweep setting.
i += 1
simulation_directory = os.path.join(simulation_input_files_dir, sim_id)
if not os.path.isdir(simulation_directory): # skip over Readme file
continue
# create a config builder for the current experiment, derived from the base simulation input files
config_filepath = os.path.join(simulation_directory, 'config.json')
campaign_filepath = os.path.join(
simulation_directory,
'campaign_Swaziland_v05Sep2018_FINAL_reftracktopup_2011_v2.json')
cb = DTKConfigBuilder.from_files(config_name=config_filepath,
campaign_name=campaign_filepath)
cb.set_input_files_root(
path=simulation_directory
) # discoverability of other input files, e.g. PFA_Overlay.json
exp_name = EXP_NAME_PATTERN % (sweep['name'], i)
# Create a generator of the per-simulation differences from the base simulation
builder = ModBuilder.from_combos(sweep['mods'])
# keep track of each run_sim_args dictionary, one per experiment
run_sets.append({
'exp_name': exp_name,
'exp_builder': builder,
'config_builder': cb,
'base_simulation_id': sim_id,
from malaria.reports.MalariaReport import add_filtered_report
from dtk.vector.species import set_larval_habitat
from simtools.SetupParser import SetupParser
from spline_functions import *
# from .spline_functions import get_spline_values_for_all_params, get_annual_representative_spline, \
# get_representative_spline_multipiers
from dtk.interventions.novel_vector_control import add_ATSB
from ATSBEntoCalibSite import ATSBEntoCalibSite
# Which simtools.ini block to use for this calibration
SetupParser.default_block = 'HPC'
# Start from a base MALARIA_SIM config builder
# This config builder will be modify by the different sites defined below
cb = DTKConfigBuilder.from_defaults('MALARIA_SIM')
update_species_param(cb, 'gambiae', 'Indoor_Feeding_Fraction', 0.5)
update_species_param(cb, 'funestus', 'Indoor_Feeding_Fraction', 0.9)
update_species_param(cb, 'gambiae', 'Vector_Sugar_Feeding_Frequency', 'VECTOR_SUGAR_FEEDING_EVERY_DAY', overwrite=False)
update_species_param(cb, 'gambiae', 'Anthropophily', 0.8)
update_species_param(cb, 'gambiae', 'Adult_Life_Expectancy', 20)
datadir = 'C:\\Users\\jkurlander\\Dropbox (IDM)'
# List of sites we want to calibrate on
throwaway = 1
species = 'gambiae'
reference_fname = 'cluster_mosquito_counts_per_house_by_month.csv'
reference_spline = 'Multi_year_calibration_by_HFCA_180404/best_180409/Panjane_funestus.csv'
irs_fn = os.path.join(datadir,
'Malaria Team Folder/projects/Mozambique/entomology_calibration/cluster_all_irs_events_pyrethroid_2014.csv')
BaseInputPath = load_input_path()
if not os.path.exists(BaseInputPath):
os.mkdir(BaseInputPath)
OutputPath = os.path.join(load_output_path(), ScenarioName)
if not os.path.exists(OutputPath):
os.mkdir(OutputPath)
if not os.path.exists(os.path.join(OutputPath, 'input_files')):
os.mkdir(os.path.join(OutputPath, 'input_files'))
#Name the input files
DemoFile = os.path.join(BaseInputPath, 'demographics.json')
CampaignFile = os.path.join(BaseInputPath, 'campaign.json')
ConfigFile = os.path.join(BaseInputPath, 'config.json')
SimDurationInYears = 1
TotalPopulation = 5e5
cb = DTKConfigBuilder.from_files(ConfigFile, campaign_name=CampaignFile)
cb.set_param('Simulation_Duration', SimDurationInYears * 365.0)
demoFile = DemographicsFile.from_file(DemoFile)
demoFile.content['Nodes'][0]['NodeAttributes'][
'InitialPopulation'] = TotalPopulation
#Fix this
if len(demoFile.nodes) == 1:
for node in demoFile.nodes.values():
node.pop = TotalPopulation
else:
raise ValueError('demographics.json assumed to have only one node')
demoFile = SetAgeDistribution(
demoFile,
def setUp(self):
self.cb = DTKConfigBuilder.from_defaults('VECTOR_SIM')
def setUp(self):
self.cb = DTKConfigBuilder.from_defaults('MALARIA_SIM')
from dtk.utils.core.DTKConfigBuilder import DTKConfigBuilder
from dtk.vector.study_sites import configure_site
from simtools.ExperimentManager.ExperimentManagerFactory import ExperimentManagerFactory
from simtools.SetupParser import SetupParser
from dtk.interventions.outbreakindividualdengue import add_OutbreakIndividualDengue
# This block will be used unless overridden on the command-line
SetupParser.default_block = 'HPC'
cb = DTKConfigBuilder.from_defaults('DENGUE_SIM')
configure_site(cb, 'Puerto_Rico')
cb.campaign["Campaign_Name"] = "Campaign - Outbreak"
add_OutbreakIndividualDengue(cb, 100, {'max': 1.725, 'min': 0}, 'Strain_1', [])
add_OutbreakIndividualDengue(cb, 5000, {}, 'Strain_2', [])
add_OutbreakIndividualDengue(cb, 5000, {}, 'Strain_3', [])
add_OutbreakIndividualDengue(cb, 5000, {}, 'Strain_4', [])
# cb.set_param('Simulation_Duration', 30*365)
run_sim_args = {
'exp_name': 'ExampleSim',
'config_builder': cb
}
if __name__ == "__main__":
SetupParser.init()
exp_manager = ExperimentManagerFactory.from_cb(config_builder=cb)
exp_manager.run_simulations(**run_sim_args)
def basic_gridded_config_builder(archetype="Southern"):
cb = DTKConfigBuilder.from_defaults('MALARIA_SIM')
cb.update_params(immunity.params)
cb.update_params(infection.params)
cb.update_params(symptoms.params)
cb.update_params({
'Antigen_Switch_Rate': pow(10, -9.116590124),
'Base_Gametocyte_Production_Rate': 0.06150582,
'Base_Gametocyte_Mosquito_Survival_Rate': 0.002011099,
'Falciparum_MSP_Variants': 32,
'Falciparum_Nonspecific_Types': 76,
'Falciparum_PfEMP1_Variants': 1070,
'Gametocyte_Stage_Survival_Rate': 0.588569307,
'MSP1_Merozoite_Kill_Fraction': 0.511735322,
'Max_Individual_Infections': 3,
'Nonspecific_Antigenicity_Factor': 0.415111634
})
cb.update_params({
"Climate_Model": "CLIMATE_BY_DATA",
"Migration_Model": "NO_MIGRATION",
"Enable_Immunity_Distribution": 0,
"Enable_Immunity_Initialization_Distribution": 0,
"Immunity_Initialization_Distribution_Type": "DISTRIBUTION_OFF",
"Enable_Demographics_Risk": 1
})
cb.update_params({
"Disable_IP_Whitelist": 1,
"Enable_Demographics_Other": 1,
"Enable_Demographics_Builtin": 0,
"Valid_Intervention_States": [],
"Report_Detection_Threshold_PfHRP2": 40.0,
"Report_Detection_Threshold_Blood_Smear_Parasites": 0,
"Parasite_Smear_Sensitivity": 0.025,
"Report_Detection_Threshold_True_Parasite_Density": 40,
"Birth_Rate_Dependence":
"FIXED_BIRTH_RATE", # Match demographics file for constant population size (with exponential age distribution)
"Enable_Nondisease_Mortality": 1,
})
# Intervention events
intervene_events_list = [
"Bednet_Got_New_One", "Bednet_Using", "Bednet_Discarded"
]
full_custom_events_list = [
"Bednet_Got_New_One", "Bednet_Using", "Bednet_Discarded",
"Received_Treatment", "Received_Campaign_Drugs", "Received_RCD_Drugs",
"Received_Test", "Received_SMC", "Took_Dose", "InfectionDropped",
"Received_Ivermectin", "Received_Primaquine",
"Received_Campaign_Drugs_Term_1", "Received_Campaign_Drugs_Term_2",
"Received_Campaign_Drugs_Term_3"
]
cb.set_param("Custom_Individual_Events", full_custom_events_list)
cb.update_params({
"Report_Event_Recorder": 0,
"Report_Event_Recorder_Ignore_Events_In_List": 0,
# "Listed_Events": full_custom_events_list, #intervene_events_list
"Report_Event_Recorder_Events":
full_custom_events_list #intervene_events_list
})
# Basic entomology
set_ento(cb, archetype=archetype
) # I think there just needs to be something set for now
return cb
def basic_cb(self):
SetupParser.default_block = self.parser_location
self.cb = DTKConfigBuilder.from_defaults('MALARIA_SIM')
self.cb.set_experiment_executable(
os.path.join(self.dropbox_base,
'bin/malaria_ongoing_build_185/Eradication.exe'))
self.cb.set_input_files_root(
os.path.join(self.dropbox_base, 'inputs/catchments/'))
# Tell config builder where to find dlls for specified Bamboo build of executable
self.cb.set_dll_root(
os.path.join(self.dropbox_base, 'bin/malaria_ongoing_build_185/'))
self.cb.set_param("Num_Cores", self.num_cores)
# Reduce StdOut size
self.cb.params['logLevel_default'] = "WARNING"
self.cb.params['Enable_Log_Throttling'] = 1
self.cb.params["Memory_Usage_Warning_Threshold_Working_Set_MB"] = 50000
self.cb.params["Memory_Usage_Halting_Threshold_Working_Set_MB"] = 60000
# Prevent DTK from spitting out too many messages
self.cb.params['logLevel_JsonConfigurable'] = "WARNING"
self.cb.params['Disable_IP_Whitelist'] = 1
# Latest parameters
# self.cb.update_params(immunity.params)
self.cb.update_params(infection.params)
self.cb.update_params(symptoms.params)
if self.immunity_params == 'prashanth':
self.cb.update_params({
'Antigen_Switch_Rate':
pow(10, -9.116590124),
'Base_Gametocyte_Production_Rate':
0.06150582,
'Base_Gametocyte_Mosquito_Survival_Rate':
0.002011099,
'Falciparum_MSP_Variants':
32,
'Falciparum_Nonspecific_Types':
76,
'Falciparum_PfEMP1_Variants':
1070,
'Gametocyte_Stage_Survival_Rate':
0.588569307,
'MSP1_Merozoite_Kill_Fraction':
0.511735322,
'Max_Individual_Infections':
3,
'Nonspecific_Antigenicity_Factor':
0.415111634
})
elif self.immunity_params == "jaline":
self.cb.update_params({
'Base_Gametocyte_Production_Rate': 0.044,
"Gametocyte_Stage_Survival_Rate": 0.82,
'Antigen_Switch_Rate': 2.96e-9,
'Falciparum_PfEMP1_Variants': 1112,
'Falciparum_MSP_Variants': 7,
'MSP1_Merozoite_Kill_Fraction': 0.43,
'Falciparum_Nonspecific_Types': 90,
'Nonspecific_Antigenicity_Factor': 0.42,
'Base_Gametocyte_Mosquito_Survival_Rate': 0.00088,
"Max_Individual_Infections": 5
})
from dtk.utils.core.DTKConfigBuilder import DTKConfigBuilder
from dtk.vector.study_sites import configure_site
from simtools.ExperimentManager.ExperimentManagerFactory import ExperimentManagerFactory
from simtools.SetupParser import SetupParser
from simtools.Utilities.Experiments import retrieve_simulation
from COMPS.Client import Client
Client.login("comps.idmod.org")
SetupParser.default_block = "HPC"
priority = "Highest"
coreset = "emod_32cores"
cb = DTKConfigBuilder.from_defaults('VECTOR_SIM', Simulation_Duration=365)
configure_site(cb, 'Namawala')
# Using dtk-tools example exe/dlls, which fits the DTKConfigBuilder.from_defaults call
cb.set_experiment_executable(
"C:/Users/jsuresh/Code/dtk-tools/examples/inputs/Eradication.exe")
cb.set_dll_root("C:/Users/jsuresh/Code/dtk-tools/examples/inputs/dlls")
# Serialization stuff:
# To write out a serialization file at a timestep
cb.set_param("Serialization_Time_Steps", [100, 200, 300])
# To draw from a serialized file:
def draw_from_burnin(cb, burnin_sim_id):
def setUp(self):
self.cb = DTKConfigBuilder.from_defaults('MALARIA_SIM')
self.input_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'input')
import os
from dtk.interventions.larvicides import add_larvicides
from dtk.utils.analyzers import TimeseriesAnalyzer, group_by_name
from dtk.utils.core.DTKConfigBuilder import DTKConfigBuilder
from simtools.ExperimentManager.ExperimentManagerFactory import ExperimentManagerFactory
from simtools.ModBuilder import ModBuilder, ModFn
from simtools.SetupParser import SetupParser
SetupParser.default_block = 'HPC'
# Create a config builder from set of input files
input_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..",
"inputs", "Sweeps")
cb = DTKConfigBuilder.from_files(os.path.join(input_dir, 'config.json'),
os.path.join(input_dir, 'campaign.json'))
# Change the duration of the simulations to 5 years
cb.set_param('Simulation_Duration', 5 * 365)
# Define a set_larvicides function in order for the builder to call with different values
# Functions passed to the builder needs to take a ConfigBuilder as first parameter
# Here we are interested on sweeping on the start date of the intervention.
def set_larvicides(cb, start):
# Add larvicides to the campaign held in the ConfigBuilder
add_larvicides(cb, start)
# Returns the tag we want our simulation to have
# In order to identify which value of the sweep we used, we are tagging our simulations
# with larvicide_start = start date of the larvicides intervention
'Testing1b': 'Works'
}], [[cfg, cpn_outbreak, demog_pfa], 1980, 0.50, 1.0e-3, {
'Testing2': None
}]]
# Initialize the template system
# ==============================
# Create an instance of the TemplateHelper helper class and, if desired, give it templates to work with.
# In this example, there's no need to set the campaign_template because it will be set dynamically from the table above.
templates = TemplateHelper()
# Give the header and table to the template helper
templates.set_dynamic_header_table(header, table)
# Let's use a standard DTKConfigBuilder.
config_builder = DTKConfigBuilder()
# ignore_missing is required when using templates
config_builder.ignore_missing = True
# Use the default COMPS 2.10 and the SamplesInput folder for input files
# See examples\AssetManagement\use_custom_executable.py for more information
config_builder.set_exe_collection('EMOD 2.10')
# For the experiment builder in the example, we use a ModBuilder from_combos to run
# each of the configurations for two separate run numbers.
# The first line needs to be the modifier functions coming from the templates
experiment_builder = ModBuilder.from_combos(
templates.get_modifier_functions(), # <-- Do this first!
[
ModFn(DTKConfigBuilder.set_param, 'Run_Number', rn)
for rn in range(2, 4)
from simtools.ModBuilder import ModBuilder, ModFn
from simtools.SetupParser import SetupParser
from single_node_simulations.helper_functions import change_vector_params, update_config_params, add_reporters, \
add_ITNs, add_insecticides
if __name__ == "__main__":
dir = './'
geography = 'Burkina Faso'
prefix = 'single_node_simulations'
exp_name = "insecticide_resistance_single_node"
extra = 0
num_years = 6 + extra
num_seeds = 50
cb = DTKConfigBuilder.from_defaults('MALARIA_SIM',
Simulation_Duration=int(365 * num_years))
update_config_params(cb, direc=dir, geography=geography)
add_insecticides(cb, pyrethroid_killing=0.125, carbamate_killing=0.25)
serialized_file_list = ['', '']
cb.update_params({
'Serialized_Population_Filenames': serialized_file_list
})
########################## VECTOR GENETICS ############################################
three_year_gap = [
[ModFn(DTKConfigBuilder.set_param, 'Run_Number', seed),
ModFn(change_vector_params, species='gambiae', mutation_rate1=mutation_rate1,
mutation_rate2=mutation_rate2, serialization_seed=0),
import os
import json
import math
import random
from dtk.utils.core.DTKConfigBuilder import DTKConfigBuilder
from dtk.utils.reports.BaseAgeHistReport import BaseAgeHistReport
from simtools.ModBuilder import ModBuilder, ModFn
from simtools.SetupParser import SetupParser
from simtools.ExperimentManager.ExperimentManagerFactory import ExperimentManagerFactory
from SetupFunctions import sample_point_fn
#Run on HPC
SetupParser.default_block = "HPC"
cb = DTKConfigBuilder.from_files(config_name='InputFiles\\config.json',
campaign_name='InputFiles\\basecampaign.json')
cb.set_param('Num_Cores', 1)
cb.set_experiment_executable(path='Executable\\Eradication.exe')
cb.add_demog_overlay(
name='demographics.json',
content=json.load(
open('InputFiles\\Nigeria_Ward_smaller_minpop5000_demographics.json')))
cb.experiment_files.add_file(
path='InputFiles\\Nigeria_Ward_smaller_minpop5000_air_migration.bin')
cb.experiment_files.add_file(
path='InputFiles\\Nigeria_Ward_smaller_minpop5000_air_migration.bin.json')
cb.experiment_files.add_file(
path='InputFiles\\Nigeria_Ward_smaller_minpop5000_local_migration.bin')
cb.experiment_files.add_file(
path='InputFiles\\Nigeria_Ward_smaller_minpop5000_local_migration.bin.json'
)
from dtk.utils.core.DTKConfigBuilder import DTKConfigBuilder
from dtk.vector.study_sites import configure_site
from simtools.ExperimentManager.ExperimentManagerFactory import ExperimentManagerFactory
from simtools.SetupParser import SetupParser
from dtk.interventions.incidence_counter import add_incidence_counter
from dtk.interventions.irs import add_node_IRS
from malaria.reports.MalariaReport import add_event_counter_report # you need to isntall the malaria package
# This block will be used unless overridden on the command-line
# this means that simtools.ini local block will be used
SetupParser.default_block = 'LOCAL'
cb = DTKConfigBuilder.from_defaults('VECTOR_SIM')
configure_site(cb, 'Namawala')
# event counter can help you keep track of events that are happening
add_event_counter_report(
cb,
["HappyBirthday", "Party", "PartyHarder", "IRS_Blackout_Event_Trigger"])
# adding an incidence counter, which starts on day 20, and counts "Happy Birthday" events for 30 days. the default
# thresholds are 10 and 100 event counts and default events being sent out when the threshold is reached are Action1 and Action2
add_incidence_counter(
cb,
start_day=20,
count_duration=30,
count_triggers=['HappyBirthday'],
threshold_type=
'COUNT', #this is the default, we can also look at % per eligible population
thresholds=[13, 254],
triggered_events=['Party', 'PartyHarder'])
## Execute directly: 'python example_sweep.py'
## or via the dtk.py script: 'dtk run example_sweep.py'
import numpy as np
from dtk.utils.core.DTKConfigBuilder import DTKConfigBuilder
from dtk.utils.builders.sweep import GenericSweepBuilder
from dtk.vector.study_sites import configure_site
from simtools.SetupParser import SetupParser
from simtools.ExperimentManager.ExperimentManagerFactory import ExperimentManagerFactory
# Run on HPC
SetupParser.default_block = "HPC"
# Configure a default 5 years simulation
cb = DTKConfigBuilder.from_defaults('MALARIA_SIM', Simulation_Duration=365 * 5)
# Set it in Namawala
configure_site(cb, 'Namawala')
# Name of the experiment
exp_name = 'ExampleSweep'
# Create a builder to sweep over the birth rate multiplier
builder = GenericSweepBuilder.from_dict({'x_Birth': np.arange(1, 1.5, .1)})
run_sim_args = {
'exp_name': exp_name,
'exp_builder': builder,
'config_builder': cb
}
