def pick_scenario():
while True:
print('Select scnenario:')
print('[1] Random Scnenario')
print('[2] Custom Scnenario')
input_value = input('>>>')
try:
selection = int(input_value)
except ValueError:
print('Please input an integer!')
continue
if selection < 1 or selection > 2:
print('Please input a number from the list!')
else:
break
if selection == 1:
while True:
input_value = input(
'Select random seed for random scenario [None]: ')
try:
seed = int(input_value)
break
except ValueError:
if input_value == '' or input_value == 'None':
seed = None
break
else:
print('Please input an integer!')
continue
scenario = RandomScenario(seed=seed)
elif selection == 2:
scenario = CustomScenario()
return scenario
def run_sim_PID_once(pname, runtime, meals, controller_params):
'''
Run the simulation a single time on a single patient with the PID controller.
Parameters
----------
pname: str
patient name
runtime: int
simulation time, in hours.
meals: (timedelta, int)
a tuple containing the time of meal (as referenced from simulation start) and the meal size, in grams.
targetBG: int
the target blood glucose for the controller, in mg/dl
lowBG: int
the pump suspension glucose for the controller, in mg/dl
Returns
-------
A pandas dataframe containing the simulation results.
axis=0: time, type datetime.datetime
axis=1: data category, type str
'''
sensor = CGMSensor.withName('Dexcom')
pump = InsulinPump.withName('Insulet')
scenario = CustomScenario(start_time = datetime(2020, 1, 1, 0,0,0), scenario=meals)
obj = SimObj(T1DSimEnv(T1DPatient.withName(pname),
sensor,
pump,
scenario),
controller.PIDController(controller_params, pname),
timedelta(hours=runtime),
animate=False,
path=None)
return sim(obj)
def __init__(self, patient_name=None, reward_fun=None):
'''
patient_name must be 'adolescent#001' to 'adolescent#010',
or 'adult#001' to 'adult#010', or 'child#001' to 'child#010'
'''
seeds = self._seed()
# have to hard code the patient_name, gym has some interesting
# error when choosing the patient
if patient_name is None:
patient_name = 'adolescent#001'
patient = T1DPatient.withName(patient_name)
sensor = CGMSensor.withName('Dexcom', seed=seeds[1])
hour = self.np_random.randint(low=0.0, high=24.0)
start_time = datetime(2018, 1, 1, hour, 0, 0)
# scenario = RandomScenario(start_time=start_time, seed=seeds[2])
# Added a custom scenario with no meals
# scen = [(7, 45), (12, 70), (16, 15), (18, 80), (23, 10)]
scen = [(0, 0)]
scenario = CustomScenario(start_time=start_time, scenario=scen)
pump = InsulinPump.withName('Insulet')
self.env = _T1DSimEnv(patient, sensor, pump, scenario)
self.reward_fun = reward_fun
# Added by Jonas -- state space is now 10 * sample_time = 30 minutes long
self.state_space_length = 10
self.insulin_history = np.zeros(4)
def test_batch_sim(self):
# specify start_time as the beginning of today
now = datetime.now()
start_time = datetime.combine(now.date(), datetime.min.time())
# --------- Create Random Scenario --------------
# Create a simulation environment
patient = T1DPatient.withName('adolescent#001')
sensor = CGMSensor.withName('Dexcom', seed=1)
pump = InsulinPump.withName('Insulet')
scenario = RandomScenario(start_time=start_time, seed=1)
env = T1DSimEnv(patient, sensor, pump, scenario)
# Create a controller
controller = BBController()
# Put them together to create a simulation object
s1 = SimObj(env, controller, timedelta(
days=2), animate=True, path=save_folder)
results1 = sim(s1)
# --------- Create Custom Scenario --------------
# Create a simulation environment
patient = T1DPatient.withName('adolescent#001')
sensor = CGMSensor.withName('Dexcom', seed=1)
pump = InsulinPump.withName('Insulet')
# custom scenario is a list of tuples (time, meal_size)
scen = [(7, 45), (12, 70), (16, 15), (18, 80), (23, 10)]
scenario = CustomScenario(start_time=start_time, scenario=scen)
env = T1DSimEnv(patient, sensor, pump, scenario)
# Create a controller
controller = BBController()
# Put them together to create a simulation object
s2 = SimObj(env, controller, timedelta(
days=2), animate=False, path=save_folder)
results2 = sim(s2)
# --------- batch simulation --------------
s1.reset()
s2.reset()
s1.animate = False
s = [s1, s2]
results_para = batch_sim(s, parallel=True)
s1.reset()
s2.reset()
s = [s1, s2]
results_serial = batch_sim(s, parallel=False)
assert_frame_equal(results_para[0], results1)
assert_frame_equal(results_para[1], results2)
for r1, r2 in zip(results_para, results_serial):
assert_frame_equal(r1, r2)
def run_sim_once(simtime, meals, controller, patients):
# times
run_time = timedelta(hours=simtime)
start_time = datetime(2020, 1, 1, 0,0,0)
scenario = CustomScenario(start_time = start_time, scenario=meals)
envs = build_envs(scenario, start_time, patients)
# must deepcopy controllers because they're dynamic
controllers = [copy.deepcopy(controller) for _ in range(len(envs))]
sim_instances = [SimObj(env, ctr, run_time, animate=False, path='./results') for (env, ctr) in zip(envs, controllers)]
# run simulations
results = batch_sim(sim_instances, parallel=False)
# create dataframe with results from 1 sim
return pd.concat(results, keys=[s.env.patient.name for s in sim_instances])
def run_sim_PID(no_runs, patients, runtime, meals, controller_params):
'''
Run the simulation a single time on a list of patients with the PID controller.
Parameters
----------
no_runs: int
the number of separate simulation runs.
patients: list of str
a list of patient name strings. Patient name strings can be found in the params/Quest.csv file inside simGlucose.
runtime: int
simulation time, in hours.
meals: (timedelta, int)
a tuple containing the time of meal (as referenced from simulation start) and the meal size, in grams.
targetBG: int
the target blood glucose for the controller, in mg/dl
lowBG: int
the pump suspension glucose for the controller, in mg/dl
Returns
-------
A pandas dataframe containing the simulation results.
axis=0: time, type datetime.datetime
axis=1: MultiIndex
level 0: data category, type str
level 1: patient id, type str
level 2: run number, type int (starts at 1)
'''
sensor = CGMSensor.withName('Dexcom')
pump = InsulinPump.withName('Insulet')
scenario = CustomScenario(start_time = datetime(2020, 1, 1, 0,0,0), scenario=meals)
sim_objs = []
keys = []
for run in range(0, no_runs):
for pname in patients:
sim_objs.append(SimObj(T1DSimEnv(T1DPatient.withName(pname),
sensor,
pump,
copy.deepcopy(scenario)), # because random numbers.
controller.PIDController(controller_params, pname),
timedelta(hours=runtime),
animate=False,
path=None))
keys.append((run + 1, pname))
p_start = time.time()
print('Running batch simulation of {} items...'.format(len(patients * no_runs)))
p = pathos.pools.ProcessPool()
results = p.map(sim, sim_objs)
print('Simulation took {} seconds.'.format(time.time() - p_start))
return pd.concat(results, axis=1, keys=keys)
def __init__(self,
patient_name=None,
reward_fun=None,
scen=None,
start_time=None,
sensor_name=None,
pump_name=None): #, scenario_tup=None, startTime=None
'''
patient_name must be 'adolescent#001' to 'adolescent#010',
or 'adult#001' to 'adult#010', or 'child#001' to 'child#010'
'''
seeds = self._seed()
# have to hard code the patient_name, gym has some interesting
# error when choosing the patient
if patient_name is None:
patient_name = 'adolescent#001'
if sensor_name is None:
sensor_name = 'Dexcom'
if pump_name is None:
pump_name = 'Insulet'
print(patient_name)
print(sensor_name)
print(pump_name)
print(scen)
patient = T1DPatient.withName(patient_name)
sensor = CGMSensor.withName(sensor_name, seed=seeds[1])
#hour = self.np_random.randint(low=0.0, high=24.0)
#start_time = datetime(2018, 1, 1, hour, 0, 0)
scenario = CustomScenario(
start_time=start_time, scenario=scen
) #RandomScenario(start_time=start_time, seed=seeds[2])
pump = InsulinPump.withName(pump_name)
self.env = _T1DSimEnv(patient, sensor, pump, scenario)
self.reward_fun = reward_fun
def pick_scenario(start_time=None):
while True:
print('Select scnenario:')
print('[1] Random Scnenario')
print('[2] Custom Scnenario')
input_value = input('>>>')
try:
selection = int(input_value)
except ValueError:
print('Please input an integer!')
continue
if selection < 1 or selection > 2:
print('Please input a number from the list!')
else:
break
if start_time is None:
start_time = pick_start_time()
if selection == 1:
while True:
input_value = input(
'Select random seed for random scenario [None]: ')
try:
seed = int(input_value)
break
except ValueError:
if input_value in ('', 'None'):
seed = None
break
print('Please input an integer!')
continue
scenario = RandomScenario(start_time, seed=seed)
else:
custom_scenario = input_custom_scenario()
scenario = CustomScenario(start_time, custom_scenario)
return scenario
def __init__(self, patient_name=None, reward_fun=None, Initial_Bg=0):
'''
patient_name must be 'adolescent#001' to 'adolescent#010',
or 'adult#001' to 'adult#010', or 'child#001' to 'child#010'
'''
seeds = self._seed()
# have to hard code the patient_name, gym has some interesting
# error when choosing the patient
if patient_name is None:
patient_name = 'adolescent#001'
patient = T1DPatient.withName(patient_name, Initial_Bg)
sensor = CGMSensor.withName('GuardianRT', seed=seeds[1]) #Dexcom
hour = 20 #self.np_random.randint(low=0.0, high=24.0)
start_time = datetime(2018, 1, 1, hour, 0, 0)
# scenario = RandomScenario(start_time=start_time, seed=seeds[2])
# custom scenario is a list of tuples (time, meal_size)
# scen = [(0,float(Initial_Bg)),(13, 45), (16, 10), (18, 35), (22, 10)]#, (23, 10)]
scen = [(13, 45), (16, 10), (18, 35), (22, 10)] #, (23, 10)]
scenario = CustomScenario(start_time=start_time, scenario=scen)
pump = InsulinPump.withName('Insulet')
self.env = _T1DSimEnv(patient, sensor, pump, scenario)
self.reward_fun = reward_fun
ki +=.000001
print('kp=' + str(ki))
# (kp, ki, kd, target, low)
PIDparams = (0.00025, round(ki, 7), 0, 120, 70)
dfs = run_sim_PID(n, adults, t, meals, PIDparams)
filename = 'dfs/' + 'p_' + str(PIDparams[0]) + ' i_' + str(PIDparams[1]) + ' d_' + str(PIDparams[2]) + ' target_' + str(PIDparams[3]) + '.bz2'
dfs.to_pickle(filename)
=======
pname = "adult#001"
t = 9
meals = [(timedelta(hours=2), 50)]
sensor = CGMSensor.withName('Dexcom')
pump = InsulinPump.withName('Insulet')
scenario = CustomScenario(start_time = datetime(2020, 1, 1, 0,0,0), scenario=meals)
keys = []
# forward horizon
horizon = 50
controller_params = (140, 80, horizon)
obj= SimObj(T1DSimEnv(T1DPatient.withName(pname),
sensor,
pump,
copy.deepcopy(scenario)), # because random numbers.
controller.MPCNaive(controller_params, pname),
timedelta(hours=t),
animate=False,
path=None)
keys.append((1, pname))
p_start = time.time()
results = sim(obj)
# Create a controller
controller = BBController()
# Put them together to create a simulation object
s1 = SimObj(env, controller, timedelta(days=1), animate=False, path=path)
results1 = sim(s1)
print(results1)
# --------- Create Custom Scenario --------------
# Create a simulation environment
patient = T1DPatient.withName('adolescent#001')
sensor = CGMSensor.withName('Dexcom', seed=1)
pump = InsulinPump.withName('Insulet')
# custom scenario is a list of tuples (time, meal_size)
scen = [(7, 45), (12, 70), (16, 15), (18, 80), (23, 10)]
scenario = CustomScenario(start_time=start_time, scenario=scen)
env = T1DSimEnv(patient, sensor, pump, scenario)
# Create a controller
controller = BBController()
# Put them together to create a simulation object
s2 = SimObj(env, controller, timedelta(days=1), animate=False, path=path)
results2 = sim(s2)
print(results2)
# --------- batch simulation --------------
# Re-initialize simulation objects
s1.reset()
s2.reset()
sim_pump = InsulinPump.withName('Insulet')
# env setup
RANDOM_SEED = 5550
RUN_TIME = 48
sim_start_time = datetime(2020, 1, 1, 0, 0, 0)
sim_run_time = timedelta(hours=RUN_TIME)
# random scenario
random_scen = RandomScenario(start_time=sim_start_time, seed=RANDOM_SEED)
# custom scenario
# meals is a list of tuples, each tuple containing a timedelta (time after start of sim) and a meal size, in g CHO.
meals = [(timedelta(hours=12), 100)]
# generate the custom scenario with the list of meals
custom_scen = CustomScenario(start_time=sim_start_time, scenario=meals)
# choose scenario
environment = T1DSimEnv(patient, sim_sensor, sim_pump, custom_scen)
# choose controller
controller = PController(gain=0.04, dweight=.5, pweight=1, target=120)
# script saves csv(s) into this path
results_path = './results/'
simulator = SimObj(environment,
controller,
sim_run_time,
animate=False,
path=results_path)
results = sim(simulator)