add_mosquito_release(cb, start_day=200, species='arabiensis', repetitions=1, number=number,
released_genome=[['X', 'X'], ['b0', 'b0']])
return {'Label': label, 'Number': number}
if __name__ == "__main__":
expname = 'vector_genetics_single_node_introgression'
sim_duration = 365 * 6
num_seeds = 50
SetupParser('HPC')
cb = DTKConfigBuilder.from_defaults('VECTOR_SIM')
set_climate_constant(cb)
set_species_param(cb, 'arabiensis', 'Larval_Habitat_Types',
{"CONSTANT": 11250000000})
set_species_param(cb, 'arabiensis', 'Male_Life_Expectancy', 5)
set_species_param(cb, 'arabiensis', 'Adult_Life_Expectancy', 10)
set_species_param(cb, 'arabiensis', 'Transmission_Rate', 0.5)
set_species_param(cb, 'arabiensis', 'Indoor_Feeding_Fraction', 1.0)
########################## VECTOR GENETICS ####################################################
# Add genes
genes = {'arabiensis': [{
"Alleles": {"a0": 1.0, "b0": 0.0},
"Mutations": {"a0:b0": 0.0, "b0:a0": 0.0}
}]
from simtools.ModBuilder import ModFn, ModBuilder
from malaria.reports.MalariaReport import add_patient_report, add_survey_report, add_summary_report
from dtk.interventions.input_EIR import add_InputEIR
# General --------------------------------------------------------------------------------------------------------
exp_name = 'PfPR_by_EIR_sweep_matching_regression_defaults'
years = 50 # length of simulation, in years
num_seeds = 5
report_start = years - 5
# Setup ----------------------------------------------------------------------------------------------------------
# config_path = os.path.join('.', 'inputs','config.json')
# cb = DTKConfigBuilder.from_files(config_path)
cb = DTKConfigBuilder.from_defaults('MALARIA_SIM')
cb.update_params({
"Demographics_Filenames":
["Namawala_single_node_demographics_balanced_pop_growth.json"],
"x_Base_Population":
1,
"Enable_Disease_Mortality":
0,
"Max_Individual_Infections":
10,
"Number_Basestrains":
1,
"Number_Substrains":
0,
"Maternal_Antibodies_Type":
print "migration off!!!"
cb.update_params(
{'Migration_Model': 'NO_MIGRATION'}
) #'NO_MIGRATION' is actually default for MALARIA_SIM, but might as well make sure it's off
if True:
exp_name = 'GridTest_v2'
location = 'HPC'
SetupParser.default_block = location
num_cores = 1
num_years = 2
cb = DTKConfigBuilder.from_defaults(
'MALARIA_SIM', #'VECTOR_SIM'
Num_Cores=num_cores,
Simulation_Duration=int(365 * num_years))
cb.set_experiment_executable('inputs/Eradication.exe')
cb.set_input_files_root('inputs')
cb.update_params({
'Enable_Spatial_Output':
1, # spatial reporting
'Spatial_Output_Channels': [
'Infectious_Vectors', 'Adult_Vectors', 'New_Infections',
'Population', 'Prevalence', 'New_Diagnostic_Prevalence',
'Daily_EIR', 'New_Clinical_Cases', 'Human_Infectious_Reservoir',
'Daily_Bites_Per_Human', 'Land_Temperature', 'Relative_Humidity',
'Rainfall', 'Air_Temperature'
]
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
# This block will be used unless overridden on the command-line
SetupParser.default_block = 'HPC'
cb = DTKConfigBuilder.from_defaults('VECTOR_SIM', Simulation_Duration=365)
configure_site(cb, 'Namawala')
# run_sim_args is what the `dtk run` command will look for
run_sim_args = {
'exp_name': 'ExampleSim',
'config_builder': cb
}
# If you prefer running with `python example_sim.py`, you will need the following block
if __name__ == "__main__":
SetupParser.init()
exp_manager = ExperimentManagerFactory.init()
exp_manager.run_simulations(**run_sim_args)
# Wait for the simulations to be done
exp_manager.wait_for_finished(verbose=True)
assert (exp_manager.succeeded())
foi_out = [
np.repeat(0, repeats=len(days_sim)) for ii in range(0, node_cnt)
]
for ss in range(0, node_cnt):
for yy in range(0, len(times[ss])):
times[ss][yy] = times[ss][yy] * len(days_sim)
foi_out[ss] = \
foi_out[ss] + \
heights[ss][yy] * \
sp.stats.norm(times[ss][yy], widths[ss][yy]).pdf(days_sim)
return foi_out
cb = DTKConfigBuilder.from_defaults(
'DENGUE_SIM') # should be from_files (check what cls means)
#configure_site(cb, 'Puerto_Rico')
cb.set_param('Koppen_Filename', "")
climate_file_path = 'D:\\Eradication/InputDataFiles/Colombia_dept_nodes_admin2/%s/' % site_name
cb.set_input_files_root(climate_file_path)
cb.set_experiment_executable('D:\\Eradication\\Executable\\Eradication.exe')
cb.set_dll_root('D:\\Eradication\\bin')
cb.set_param('Air_Temperature_Filename',
'%s_admin2_air_temperature_daily.bin' % site_name)
cb.set_param('Land_Temperature_Filename',
'%s_admin2_air_temperature_daily.bin' % site_name)
cb.set_param('Rainfall_Filename', '%s_admin2_rainfall_daily.bin' % site_name)
cb.set_param('Relative_Humidity_Filename',
'%s_admin2_humidity_daily.bin' % site_name)
demo_file_name = "%s_admin2_nodes_demographics.json" % site_name
mig_file_name = "%s_admin2_nodes_regional_migration_hi.bin" % site_name
from dtk.generic.serialization import add_SerializationTimesteps
from single_node_simulations.helper_functions import change_vector_params, update_config_params, add_reporters
if __name__ == "__main__":
dir = './'
geography = 'Burkina Faso'
prefix = 'single_node_simulations'
exp = 8.60
exp_name = "insecticide_resistance_single_node_serialization"
num_years = 40
num_seeds = 1
cb = DTKConfigBuilder.from_defaults('MALARIA_SIM',
Simulation_Duration=int(365 *
num_years))
update_config_params(cb, direc=dir, geography=geography)
add_SerializationTimesteps(cb, [num_years * 365], end_at_final=True)
########################## VECTOR GENETICS ####################################################
builder = ModBuilder.from_list([
[
ModFn(DTKConfigBuilder.set_param, 'Run_Number', seed),
ModFn(change_vector_params,
species='gambiae',
mutation_rate1=mutation_rate,
mutation_rate2=mutation_rate,
serialization_seed=seed)
def test_bad_simtype(self):
self.assertRaises(Exception, lambda: DTKConfigBuilder.from_defaults('NOT_A_SIM'))
def setUp(self):
self.cb = DTKConfigBuilder.from_defaults('MALARIA_SIM', Base_Air_Temperature=26)
def test_bad_kwargs(self):
self.assertRaises(Exception, lambda: DTKConfigBuilder.from_defaults('MALARIA_SIM', Not_A_Climate_Parameter=26))
cb = DTKConfigBuilder.from_defaults(
"MALARIA_SIM",
Simulation_Duration=int(365 * years),
Config_Name=sweep_name,
Birth_Rate_Dependence="FIXED_BIRTH_RATE",
Age_Initialization_Distribution_Type="DISTRIBUTION_COMPLEX",
Num_Cores=1,
# interventions
Valid_Intervention_States=[], # apparently a necessary parameter
# todo: do I need listed events?
Listed_Events=[
"Bednet_Discarded", "Bednet_Got_New_One", "Bednet_Using",
"Received_Vaccine"
],
Enable_Default_Reporting=1,
Enable_Demographics_Risk=1,
Enable_Vector_Species_Report=0,
# ento from prashanth
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,
)
'GENERIC_SIM_SIR', 'GENERIC_SIM_SEIR', 'GENERIC_SIM_SIRS',
'GENERIC_SIM_SEIRS', 'GENERIC_SIM_SI', 'GENERIC_SIM_SIS',
'GENERIC_SIM_SIR_Vaccinations_A', 'GENERIC_SIM_SIR_Vaccinations_B',
'GENERIC_SIM_SIR_Vaccinations_C'
]
if __name__ == '__main__':
# Initialize the SetupParser to use HPC
SetupParser.init(selected_block='HPC')
# Create an experiment manager
exp_mgr = ExperimentManagerFactory.init()
# For each generic simulations, create a config builder from the default and run it
for sim_example in generic_defaults:
cb = DTKConfigBuilder.from_defaults(sim_example)
cb.set_param("Config_Name", sim_example)
# Create a builder in order to run a single simulation
# This step is optional usually but it allows us to set tags on the simulation
builder = SingleSimulationBuilder()
builder.tags.update({"Simulation_Type": sim_example})
exp_mgr.run_simulations(config_builder=cb,
exp_builder=builder,
exp_name=experiment_name)
# Wait for the experiment to finish
exp_mgr.wait_for_finished()
print("Congratulations! they ran.")
from dtk.interventions.malaria_drug_campaigns import add_drug_campaign
from dtk.utils.analyzers.DownloadAnalyzer import DownloadAnalyzer
exp_name = 'Parasite Population Surveys'
testing = False
"""
Construct a baseline scenario with:
* Holoendemic Sahel initial immunity + seasonal force-of-infection
* Survey reporter into rainy season and through following dry season
"""
cb = DTKConfigBuilder.from_defaults('MALARIA_SIM',
Num_Cores=1,
Simulation_Duration=365 if testing else 365*3
)
configure_site_EIR(cb, 'Sugungum',
habitat=0.01 if testing else 1,
birth_cohort=False,
static=True, pop_scale=0.1)
cb.config['parameters']['Demographics_Filenames'].append(
'Garki_Single/immune_init/Sugungum/Garki_single_immune_init_Sugungum_x_1.0.json')
cb.set_param("Immunity_Initialization_Distribution_Type", "DISTRIBUTION_COMPLEX")
survey_day = 100 if testing else 365 + 280 # early October
add_survey_report(cb, survey_days=[survey_day],
# Set the simulation duration. Needs to be longer than the last timestep to serialize
Simulation_Duration = 365
# Choose at which timesteps we want to serialize. Here 5, 10 and 50
timesteps_to_serialize = [5, 10, 50]
# Which timesteps we want to reload from ?
timestep_to_reload = timesteps_to_serialize[-1] # Let's choose 50
if __name__ == "__main__":
# Initialize the SetupParser
SetupParser.init()
# Create a configbuilder for the simulation to serialize
cb_serializing = DTKConfigBuilder.from_defaults('VECTOR_SIM')
configure_site(cb_serializing, 'Namawala')
cb_serializing.set_param("Simulation_Duration", Simulation_Duration)
# Create an experiment manager
exp_manager = ExperimentManagerFactory.init()
# Set those timesteps
add_SerializationTimesteps(config_builder=cb_serializing, timesteps=timesteps_to_serialize, end_at_final=True)
# Run the simulation
exp_manager.run_simulations(config_builder=cb_serializing,
exp_name="Sample serialization test")
# Wait for it to finish
exp_manager.wait_for_finished()
