def load_burnin_x_temp(cb, x_temp):
# burnin_id_dict = {2:"8f334a00-dd2c-e911-a2c5-c4346bcb7273",
# 3:"90334a00-dd2c-e911-a2c5-c4346bcb7273",
# 4:"91334a00-dd2c-e911-a2c5-c4346bcb7273",
# 5:"92334a00-dd2c-e911-a2c5-c4346bcb7273",
# 6:"93334a00-dd2c-e911-a2c5-c4346bcb7273",
# 7:"94334a00-dd2c-e911-a2c5-c4346bcb7273",
# 8:"95334a00-dd2c-e911-a2c5-c4346bcb7273",
# 9:"96334a00-dd2c-e911-a2c5-c4346bcb7273",
# 10:"97334a00-dd2c-e911-a2c5-c4346bcb7273"}
burnin_id_dict = {2:"f80b7373-da2d-e911-a2c5-c4346bcb7273",
3:"f90b7373-da2d-e911-a2c5-c4346bcb7273",
4:"fa0b7373-da2d-e911-a2c5-c4346bcb7273",
5:"fb0b7373-da2d-e911-a2c5-c4346bcb7273",
6:"fc0b7373-da2d-e911-a2c5-c4346bcb7273",
7:"fd0b7373-da2d-e911-a2c5-c4346bcb7273",
8:"fe0b7373-da2d-e911-a2c5-c4346bcb7273",
9:"000c7373-da2d-e911-a2c5-c4346bcb7273",
10:"010c7373-da2d-e911-a2c5-c4346bcb7273"}
sim = retrieve_simulation(burnin_id_dict[x_temp])
serialized_file_path = sim.get_path()
cb.update_params({
'Serialized_Population_Path': os.path.join(serialized_file_path, 'output'),
# 'Serialized_Population_Filenames': ['state-19710.dtk']
'Serialized_Population_Filenames': ['state-19710-000.dtk', 'state-19710-001.dtk']
})
return {"x_temp": x_temp}
def add_simulation(self, simulation):
from simtools.DataAccess.Schema import Simulation
if not isinstance(simulation, Simulation):
simulation = retrieve_simulation(simulation)
self.filter_simulations([simulation])
self.experiments.add(simulation.experiment)
def draw_from_burnin(cb, burnin_sim_id):
sim = retrieve_simulation(burnin_sim_id)
serialized_file_path = sim.get_path()
cb.update_params({
'Serialized_Population_Path': os.path.join(serialized_file_path, 'output'),
'Serialized_Population_Filenames': ['state-19710-000.dtk', 'state-19710-001.dtk']
})
def draw_from_burnin(cb, burnin_sim_id):
sim = retrieve_simulation(burnin_sim_id)
serialized_file_path = sim.get_path()
cb.update_params({
'Serialized_Population_Path':
os.path.join(serialized_file_path, 'output'),
'Serialized_Population_Filenames':
['state-{}.dtk'.format(str(time).zfill(5)) for time in [200]]
})
def add_simulation(self, simulation):
from simtools.DataAccess.Schema import Simulation
if not isinstance(simulation, Simulation):
simulation = retrieve_simulation(simulation)
experiment = simulation.experiment
if experiment.exp_id not in self.experiments_simulations:
self.experiments_simulations[experiment.exp_id] = [simulation]
else:
self.experiments_simulations[experiment.exp_id].append(simulation)
def draw_from_burnin(cb, burnin_sim_id, t, n_cores=2):
sim = retrieve_simulation(burnin_sim_id)
serialized_file_path = sim.get_path()
if n_cores == 1:
raise NotImplementedError()
cb.update_params({
'Serialized_Population_Path':
os.path.join(serialized_file_path, 'output'),
'Serialized_Population_Filenames': [
'state-{}-{}.dtk'.format(str(t).zfill(5),
str(c).zfill(3)) for c in range(n_cores)
]
})
def retrieve_item(itemid):
"""
Return the object identified by id.
Can be an experiment, a suite or a batch.
If it is a suite, all experiments with this suite_id will be returned.
"""
# First try to get an experiment
from simtools.Utilities.Experiments import retrieve_experiment
from simtools.DataAccess.DataStore import DataStore
from simtools.Utilities.COMPSUtilities import exps_for_suite_id
from simtools.Utilities.Experiments import retrieve_simulation
# Try experiments first
try:
return retrieve_experiment(itemid)
except:
pass
# This was not an experiment, maybe a batch ?
batch = DataStore.get_batch_by_id(itemid)
if batch: return batch
batch = DataStore.get_batch_by_name(itemid)
if batch: return batch
# Still no item found -> test the suites
exps = DataStore.get_experiments_by_suite(itemid)
if exps: return exps
# Still no item found -> test the simulations
sim = DataStore.get_simulation(itemid)
if sim: return sim
# Still not -> last chance is a COMPS suite
exps = exps_for_suite_id(itemid)
if exps: return [retrieve_experiment(str(exp.id)) for exp in exps]
# Nothing, consider COMPS simulation
try:
return retrieve_simulation(itemid)
except:
pass
# Didnt find anything sorry
raise (Exception('Could not find any item corresponding to %s' % itemid))
def collect_experiments_simulations(ids):
experiments = dict()
simulations = dict()
if not ids: return experiments, simulations
# For each, treat it differently depending on what it is
for itemid in ids:
item = retrieve_item(itemid)
# We got back a list of experiment (itemid was a suite)
if isinstance(item, list):
experiments.update({i.exp_id: i for i in item})
elif isinstance(item, Experiment):
experiments[item.exp_id] = item
elif isinstance(item, Simulation):
simulations[item.id] = item
elif isinstance(item, Batch):
# We have to retrieve_experiment even if we already have the experiment object
# to make sure we are loading the simulations associated with it
experiments.update({i.exp_id: retrieve_experiment(i.exp_id) for i in item.experiments})
simulations.update({i.id: retrieve_simulation(i.id) for i in item.simulations})
return experiments, simulations
set(sims_this_rd["id"]) & set(available_sims["id"]))
sims_so_far["sample"] = list(
set(sims_this_rd["sample"]) & set(available_sims["sample"]))
rounds_so_far.append(r)
print(
"For all rounds included so far: {} -- there are {} sims that fit all criteria."
.format(rounds_so_far, len(sims_so_far["id"])))
available_sims = sims_so_far.copy()
print("Samples : {}".format(available_sims["sample"]))
if len(available_sims) > 0:
am = AnalyzeManager()
for sim_id in available_sims["id"]:
am.add_simulation(retrieve_simulation(sim_id))
am.add_analyzer(
comparison_channel_plotter(
"Blood Smear Parasite Prevalence",
filenames=['output/ReportMalariaFilteredCatchment.json'],
reference_data=prev_ref_data,
ref_date=ref_date,
legend=False,
working_dir=catch_folder,
save_type="other",
save_name="excl_prev_test"))
am.analyze()
plt.figure()
