Merge pull request #82 from jxx123/fix_warning

Fix Random init bg does not work issue

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name="simglucose",
-    version="0.2.9",
+    version="0.2.10",
     description="A Type-1 Diabetes Simulator as a Reinforcement Learning Environment in OpenAI gym or rllab (python implementation of UVa/Padova Simulator)",
     url="https://github.com/jxx123/simglucose",
     author="Jinyu Xie",

simglucose/patient/t1dpatient.py

@@ -8,32 +8,28 @@
 
 logger = logging.getLogger(__name__)
 
-Action = namedtuple("patient_action", ['CHO', 'insulin'])
-Observation = namedtuple("observation", ['Gsub'])
+Action = namedtuple("patient_action", ["CHO", "insulin"])
+Observation = namedtuple("observation", ["Gsub"])
 
 PATIENT_PARA_FILE = pkg_resources.resource_filename(
-    'simglucose', 'params/vpatient_params.csv')
+    "simglucose", "params/vpatient_params.csv"
+)
 
 
 class T1DPatient(Patient):
     SAMPLE_TIME = 1  # min
     EAT_RATE = 5  # g/min CHO
 
-    def __init__(self,
-                 params,
-                 init_state=None,
-                 random_init_bg=False,
-                 seed=None,
-                 t0=0):
-        '''
+    def __init__(self, params, init_state=None, random_init_bg=False, seed=None, t0=0):
+        """
         T1DPatient constructor.
         Inputs:
             - params: a pandas sequence
             - init_state: customized initial state.
               If not specified, load the default initial state in
               params.iloc[2:15]
             - t0: simulation start time, it is 0 by default
-        '''
+        """
         self._params = params
         self._init_state = init_state
         self.random_init_bg = random_init_bg
@@ -43,26 +39,26 @@ def __init__(self,
 
     @classmethod
     def withID(cls, patient_id, **kwargs):
-        '''
+        """
         Construct patient by patient_id
         id are integers from 1 to 30.
         1  - 10: adolescent#001 - adolescent#010
         11 - 20: adult#001 - adult#001
         21 - 30: child#001 - child#010
-        '''
+        """
         patient_params = pd.read_csv(PATIENT_PARA_FILE)
         params = patient_params.iloc[patient_id - 1, :]
         return cls(params, **kwargs)
 
     @classmethod
     def withName(cls, name, **kwargs):
-        '''
+        """
         Construct patient by name.
         Names can be
             adolescent#001 - adolescent#010
             adult#001 - adult#001
             child#001 - child#010
-        '''
+        """
         patient_params = pd.read_csv(PATIENT_PARA_FILE)
         params = patient_params.loc[patient_params.Name == name].squeeze()
         return cls(params, **kwargs)
@@ -86,33 +82,33 @@ def step(self, action):
 
         # Detect eating or not and update last digestion amount
         if action.CHO > 0 and self._last_action.CHO <= 0:
-            logger.info('t = {}, patient starts eating ...'.format(self.t))
+            logger.info("t = {}, patient starts eating ...".format(self.t))
             self._last_Qsto = self.state[0] + self.state[1]  # unit: mg
             self._last_foodtaken = 0  # unit: g
             self.is_eating = True
 
         if to_eat > 0:
-            logger.debug('t = {}, patient eats {} g'.format(
-                self.t, action.CHO))
+            logger.debug("t = {}, patient eats {} g".format(self.t, action.CHO))
 
         if self.is_eating:
             self._last_foodtaken += action.CHO  # g
 
         # Detect eating ended
         if action.CHO <= 0 and self._last_action.CHO > 0:
-            logger.info('t = {}, Patient finishes eating!'.format(self.t))
+            logger.info("t = {}, Patient finishes eating!".format(self.t))
             self.is_eating = False
 
         # Update last input
         self._last_action = action
 
         # ODE solver
-        self._odesolver.set_f_params(action, self._params, self._last_Qsto,
-                                     self._last_foodtaken)
+        self._odesolver.set_f_params(
+            action, self._params, self._last_Qsto, self._last_foodtaken
+        )
         if self._odesolver.successful():
             self._odesolver.integrate(self._odesolver.t + self.sample_time)
         else:
-            logger.error('ODE solver failed!!')
+            logger.error("ODE solver failed!!")
             raise
 
     @staticmethod
@@ -136,8 +132,10 @@ def model(t, x, action, params, last_Qsto, last_foodtaken):
             aa = 5 / (2 * Dbar * (1 - params.b))
             cc = 5 / (2 * Dbar * params.d)
             kgut = params.kmin + (params.kmax - params.kmin) / 2 * (
-                np.tanh(aa * (qsto - params.b * Dbar)) -
-                np.tanh(cc * (qsto - params.d * Dbar)) + 2)
+                np.tanh(aa * (qsto - params.b * Dbar))
+                - np.tanh(cc * (qsto - params.d * Dbar))
+                + 2
+            )
         else:
             kgut = params.kmax
 
@@ -162,8 +160,7 @@ def model(t, x, action, params, last_Qsto, last_foodtaken):
 
         # glucose kinetics
         # plus dextrose IV injection input u[2] if needed
-        dxdt[3] = max(EGPt, 0) + Rat - Uiit - Et - \
-            params.k1 * x[3] + params.k2 * x[4]
+        dxdt[3] = max(EGPt, 0) + Rat - Uiit - Et - params.k1 * x[3] + params.k2 * x[4]
         dxdt[3] = (x[3] >= 0) * dxdt[3]
 
         Vmt = params.Vm0 + params.Vmx * x[6]
@@ -173,8 +170,12 @@ def model(t, x, action, params, last_Qsto, last_foodtaken):
         dxdt[4] = (x[4] >= 0) * dxdt[4]
 
         # insulin kinetics
-        dxdt[5] = -(params.m2 + params.m4) * x[5] + params.m1 * x[9] + params.ka1 * \
-            x[10] + params.ka2 * x[11]  # plus insulin IV injection u[3] if needed
+        dxdt[5] = (
+            -(params.m2 + params.m4) * x[5]
+            + params.m1 * x[9]
+            + params.ka1 * x[10]
+            + params.ka2 * x[11]
+        )  # plus insulin IV injection u[3] if needed
         It = x[5] / params.Vi
         dxdt[5] = (x[5] >= 0) * dxdt[5]
 
@@ -198,34 +199,33 @@ def model(t, x, action, params, last_Qsto, last_foodtaken):
         dxdt[11] = (x[11] >= 0) * dxdt[11]
 
         # subcutaneous glucose
-        dxdt[12] = (-params.ksc * x[12] + params.ksc * x[3])
+        dxdt[12] = -params.ksc * x[12] + params.ksc * x[3]
         dxdt[12] = (x[12] >= 0) * dxdt[12]
 
         if action.insulin > basal:
-            logger.debug('t = {}, injecting insulin: {}'.format(
-                t, action.insulin))
+            logger.debug("t = {}, injecting insulin: {}".format(t, action.insulin))
 
         return dxdt
 
     @property
     def observation(self):
-        '''
+        """
         return the observation from patient
         for now, only the subcutaneous glucose level is returned
         TODO: add heart rate as an observation
-        '''
+        """
         GM = self.state[12]  # subcutaneous glucose (mg/kg)
         Gsub = GM / self._params.Vg
         observation = Observation(Gsub=Gsub)
         return observation
 
     def _announce_meal(self, meal):
-        '''
+        """
         patient announces meal.
         The announced meal will be added to self.planned_meal
         The meal is consumed in self.EAT_RATE
         The function will return the amount to eat at current time
-        '''
+        """
         self.planned_meal += meal
         if self.planned_meal > 0:
             to_eat = min(self.EAT_RATE, self.planned_meal)
@@ -245,9 +245,9 @@ def seed(self, seed):
         self.reset()
 
     def reset(self):
-        '''
+        """
         Reset the patient state to default intial state
-        '''
+        """
         if self._init_state is None:
             self.init_state = self._params.iloc[2:15]
         else:
@@ -257,13 +257,17 @@ def reset(self):
         if self.random_init_bg:
             # Only randomize glucose related states, x4, x5, and x13
             mean = [
-                1.0 * self.init_state[3], 1.0 * self.init_state[4],
-                1.0 * self.init_state[12]
+                1.0 * self.init_state[3],
+                1.0 * self.init_state[4],
+                1.0 * self.init_state[12],
             ]
-            cov = np.diag([
-                0.1 * self.init_state[3], 0.1 * self.init_state[4],
-                0.1 * self.init_state[12]
-            ])
+            cov = np.diag(
+                [
+                    0.1 * self.init_state[3],
+                    0.1 * self.init_state[4],
+                    0.1 * self.init_state[12],
+                ]
+            )
             bg_init = self.random_state.multivariate_normal(mean, cov)
             self.init_state[3] = 1.0 * bg_init[0]
             self.init_state[4] = 1.0 * bg_init[1]
@@ -273,28 +277,28 @@ def reset(self):
         self._last_foodtaken = 0
         self.name = self._params.Name
 
-        self._odesolver = ode(self.model).set_integrator('dopri5')
+        self._odesolver = ode(self.model).set_integrator("dopri5")
         self._odesolver.set_initial_value(self.init_state, self.t0)
 
         self._last_action = Action(CHO=0, insulin=0)
         self.is_eating = False
         self.planned_meal = 0
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     logger.setLevel(logging.INFO)
     # create console handler and set level to debug
     ch = logging.StreamHandler()
     # ch.setLevel(logging.DEBUG)
     ch.setLevel(logging.INFO)
     # create formatter
-    formatter = logging.Formatter('%(name)s: %(levelname)s: %(message)s')
+    formatter = logging.Formatter("%(name)s: %(levelname)s: %(message)s")
     # add formatter to ch
     ch.setFormatter(formatter)
     # add ch to logger
     logger.addHandler(ch)
 
-    p = T1DPatient.withName('adolescent#001')
+    p = T1DPatient.withName("adolescent#001")
     basal = p._params.u2ss * p._params.BW / 6000  # U/min
     t = []
     CHO = []
@@ -316,6 +320,7 @@ def reset(self):
         p.step(act)
 
     import matplotlib.pyplot as plt
+
     fig, ax = plt.subplots(3, sharex=True)
     ax[0].plot(t, BG)
     ax[1].plot(t, CHO)