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 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"
]))
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
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()
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,
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'
)
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,
force_immunity = True
debug = False
def set_immune_forcing_builder(transition_matrix=None,
scale_factor_array=[2, 5, 10, 100]):
"""Creates an experiment builder setting up immunity based on scale factor"""
builder = ModBuilder.from_combos([
ModFn(set_transition_matrix, transition_matrix, scale_factor)
for scale_factor in scale_factor_array
])
return builder
# Setup -------------------------------------------------------------------------------------------
cb = DTKConfigBuilder.from_files(config_filename)
cb.update_params({
'Vector_Species_Names': [],
'Simulation_Duration': 365,
'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)
if debug:
print(f"DEBUG: config builder created")
from malaria.interventions.malaria_challenge import add_challenge_trial
from malaria.reports.MalariaReport import add_patient_report
from analyze_infection_durations import DurationsAnalyzer
from immunity_transitions_configuration import set_transition_matrix
# General
working_dir = './'
exp_name = 'Malariatherapy_2pt0_infections'
years = 1 # length of simulation, in years
immunity_forcing_on = 1
config_path = os.path.join(working_dir, 'input/from-cfg.json')
# 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)
analyzers = [DurationsAnalyzer()
]
# Specify immune parameters --------------------------------------------------------------------------------------
if immunity_forcing_on == 1:
#Pull the naive transition matrix values from the config
transition_matrix = cb.config['parameters']['Parasite_Peak_Density_Probabilities']
#Specify the scaling of the transitio matrix to be applied (representing increasing immune pressure)
scale_factor_array = [2,5,10,100]
