Good for serialization computing, parallel not ready

.gitignore

@@ -0,0 +1,9 @@
+# Compiled python modules.
+*.pyc
+
+# Setuptools distribution folder.
+/dist/
+
+# Python egg metadata, regenerated from source files by setuptools.
+/*.egg-info
+/*.egg

MANIFEST.in

@@ -0,0 +1 @@
+include simglucose/params/*.csv

setup.py

@@ -0,0 +1,19 @@
+from setuptools import setup
+
+
+setup(name='simglucose',
+      version='0.1',
+      description='A Type-1 Diabetes simulator as an OpenAI gym environment',
+      url='',
+      author='Jinyu Xie',
+      author_email='[email protected]',
+      license='MIT',
+      packages=['simglucose'],
+      install_requires=[
+          'pandas',
+          'numpy',
+          'scipy',
+          'matplotlib',
+      ],
+      include_package_data=True,
+      zip_safe=False)

simglucose/analysis/risk.py

@@ -0,0 +1,14 @@
+import numpy as np
+
+
+def risk_index(BG, horizon):
+    # BG is in mg/dL
+    # horizon in samples
+    BG_to_compute = BG[-horizon:]
+    fBG = 1.509 * (np.log(BG_to_compute)**1.084 - 5.381)
+    rl = 10 * fBG[fBG < 0]**2
+    rh = 10 * fBG[fBG > 0]**2
+    LBGI = np.nan_to_num(np.mean(rl))
+    HBGI = np.nan_to_num(np.mean(rh))
+    RI = LBGI + HBGI
+    return (LBGI, HBGI, RI)

simglucose/controller/basal_bolus_ctrller.py

@@ -0,0 +1,53 @@
+from .base import Controller
+from .base import Action
+import numpy as np
+import pandas as pd
+import pkg_resources
+import logging
+
+logger = logging.getLogger(__name__)
+CONTROL_QUEST = pkg_resources.resource_filename(
+    'simglucose', 'params/Quest.csv')
+PATIENT_PARA_FILE = pkg_resources.resource_filename(
+    'simglucose', 'params/vpatient_params.csv')
+
+
+class BBController(Controller):
+    def __init__(self, target=140):
+        self.quest = pd.read_csv(CONTROL_QUEST)
+        self.patient_params = pd.read_csv(
+            PATIENT_PARA_FILE)
+        self.target = target
+
+    def policy(self, observation, **kwargs):
+        sample_time = kwargs.get('sample_time', 1)
+        pname = kwargs.get('patient_name')
+        action = self._bb_policy(
+            pname, observation.CHO, observation.CGM, sample_time)
+        return action
+
+    def _bb_policy(self, name, meal, glucose, env_sample_time):
+        if any(self.quest.Name.str.match(name)):
+            q = self.quest[self.quest.Name.str.match(name)]
+            params = self.patient_params[self.patient_params.Name.str.match(
+                name)]
+            u2ss = np.asscalar(params.u2ss.values)
+            BW = np.asscalar(params.BW.values)
+        else:
+            q = pd.DataFrame([['Average', 1 / 15, 1 / 50, 50, 30]],
+                             columns=['Name', 'CR', 'CF', 'TDI', 'Age'])
+            u2ss = 1.43
+            BW = 57.0
+
+        basal = u2ss * BW / 6000
+        if meal > 0:
+            logger.info('Calculating bolus ...')
+            logger.debug('glucose = {}'.format(glucose))
+            bolus = np.asscalar(meal / q.CR.values + (glucose > 150)
+                                * (glucose - self.target) / q.CF.values)
+        else:
+            bolus = 0
+
+        bolus = bolus / env_sample_time
+        action = Action(basal=basal, bolus=bolus)
+        return action

simglucose/controller/base.py

@@ -0,0 +1,13 @@
+from collections import namedtuple
+
+Action = namedtuple('ctrller_action', ['basal', 'bolus'])
+
+
+class Controller(object):
+    def __init__(self, init_state):
+        self.state = init_state
+
+    def policy(self, observation, **kwargs):
+        self.state = observation
+        action = self.state[0]
+        return action

simglucose/params/Quest.csv

@@ -0,0 +1,31 @@
+Name,CR,CF,Age,TDI
+adolescent#001,12,15.0360283441,18,36.7339146827
+adolescent#002,5,13.1750891807,19,62.031042736
+adolescent#003,23,33.5259913553,15,24.2427803659
+adolescent#004,14,21.8224838663,17,35.2528665417
+adolescent#005,12,20.9084301999,16,34.0047207467
+adolescent#006,7,17.6966328214,14,49.5812925714
+adolescent#007,8,12.4931832305,16,43.638064
+adolescent#008,4,11.9355179763,14,63.3866974592
+adolescent#009,21,20.013934775,19,24.0781667718
+adolescent#010,14,31.8684843717,17,33.1735076937
+adult#001,10,8.77310657487,61,50.416652
+adult#002,8,9.21276345633,65,57.86877688
+adult#003,9,17.9345522688,27,56.4297186222
+adult#004,16,42.6533755134,66,33.8079423727
+adult#005,5,8.23126750783,52,68.315922352
+adult#006,10,18.21328135,26,61.38880928
+adult#007,22,26.1530845971,35,42.0066074109
+adult#008,13,12.2505850562,48,42.7787865846
+adult#009,5,7.64317583896,68,67.211482912
+adult#010,5,10.69260456,68,64.448546656
+child#001,25,42.7177301243,9,17.4729287744
+child#002,23,36.9153947641,9,18.1778368801
+child#003,22,31.0525488428,8,16.0218757795
+child#004,25,40.7235040865,12,19.8151389176
+child#005,7,33.6312561084,10,40.9345323552
+child#006,19,39.9807063565,8,20.2240173973
+child#007,8,24.9969862972,9,36.2128538724
+child#008,15,30.8823307429,10,21.4944284585
+child#009,25,35.3170388027,7,17.3942110251
+child#010,18,29.222745246,12,20.6516964887

simglucose/params/pump_params.csv

@@ -0,0 +1,3 @@
+Name,min_bolus,max_bolus,inc_bolus,min_basal,max_basal,inc_basal,sample_time
+Cozmo,0.0,75.0,0.05,0.0,35.0,0.05,1.0
+Insulet,0.0,30.0,0.05,0.0,30.0,0.05,1.0

simglucose/params/sensor_params.csv

@@ -0,0 +1,4 @@
+Name,PACF,gamma,lambda,delta,xi,sample_time,min,max
+Dexcom,0.7,-0.5444,15.9574,1.6898,-5.47,3.0,39.0,600.0
+GuardianRT,0.7,-0.5444,15.9574,1.6898,-5.47,5.0,39.0,600.0
+Navigator,0.7,-0.5444,15.9574,1.6898,-5.47,1.0,32.0,600.0