def setup(self, unused_timeout=15):
'''
create a ConceptExtractor and initialize the patient status
the list here is the complete list
'''
'''
self.ce1 = CE.ConceptExtractor("Concept_List_1.csv")
self.ce1.StatusInit()
self.ce2 = CE.ConceptExtractor("Concept_List_2.csv")
self.ce2.StatusInit()
'''
vcl = pd.read_csv(self.exlist)
blackboard = Blackboard()
self.sce = CE.CEWithoutMM(self.slist, self.intlist,\
AllinOne_SS = self.aio_ss, AllinOne_Int = self.aio_int,\
neg_res = self.neg_res, WDistance = self.WDistance, aio_only = self.aio_only)
self.sce.StatusInit()
for item in vcl:
self.sce.SpecificInit(item)
self.vce = CE.ConceptExtractor(self.vlist)
#self.vce.StatusInit()
#self.ice = CE.ConceptExtractor(self.intlist)
#self.ice.StatusInit()
if self.inC:
self.vce.ConceptWrapper(self.inC)
blackboard.Signs = self.sce.Status
blackboard.Vitals = self.vce.Status
blackboard.Inters = self.sce.Interventions
blackboard.ConcLog = []
return True
def setup(self, unused_timeout = 15):
'''
create a ConceptExtractor and initialize the patient status
the list here is the complete list
'''
'''
self.ce1 = CE.ConceptExtractor("Concept_List_1.csv")
self.ce1.StatusInit()
self.ce2 = CE.ConceptExtractor("Concept_List_2.csv")
self.ce2.StatusInit()
'''
vcl = pd.read_csv(self.exlist)
blackboard = Blackboard()
self.sce = CE.ConceptExtractor(self.slist)
self.sce.StatusInit()
for item in vcl:
self.sce.SpecificInit(item)
self.vce = CE.ConceptExtractor(self.vlist)
#self.vce.StatusInit()
self.ice = CE.ConceptExtractor(self.intlist)
self.ice.StatusInit()
if self.inC:
self.vce.ConceptWrapper(self.inC)
blackboard.Signs = self.sce.Status
blackboard.Vitals = self.vce.Status
blackboard.Inters = self.ice.Status
blackboard.ConcLog = []
return True
def setup(self, unused_timeout=15):
'''
create a ConceptExtractor and initialize the patient status
the list here is the complete list
'''
'''
self.ce1 = CE.ConceptExtractor("Concept_List_1.csv")
self.ce1.StatusInit()
self.ce2 = CE.ConceptExtractor("Concept_List_2.csv")
self.ce2.StatusInit()
'''
vcl = pd.read_csv(self.exlist)
blackboard = Blackboard()
# Signs and Symptoms Concept Extractor
self.sce = CE.ConceptExtractor(self.slist)
self.sce.StatusInit()
for item in vcl:
self.sce.SpecificInit(item)
# Vital Signs Concept Extractor
self.vce = CE.ConceptExtractor(self.vlist)
#self.vce.StatusInit()
# Interventions Concept Extractor
self.ice = CE.ConceptExtractor(self.intlist)
self.ice.StatusInit()
self.vce.StatusInit()
if self.inC:
self.vce.ConceptWrapper(self.inC)
# The list of vital signs we support (from RAA data)
pool = ['Pulse', 'Resp', 'BP', 'GCS', 'Glucose', 'SPO2', 'Pain', 'EKG']
for item in pool:
self.vce.SpecificInit(item)
blackboard.Signs = self.sce.Status
blackboard.Vitals = self.vce.Status
blackboard.Inters = self.ice.Status
blackboard.ConcLog = []
return True
def Vital2Symptom(self):
'''
pulse-85 tachy > 100 extreme tachy >150 bradicardia <= 50
resp-16 8 - 24 fast slow normal
bp-164/101 hyper age + 100 hypo < 70 normal mbp = (sbp + 2*dbp)/3
gcs-15 decreased mental status <= 14
glucose-101 hyper >300 hypo <60
spo2-100 94 - 99
pain-9 pain severity
'''
# pulse to bradycardia or tachycardia
if len(self.vce.Status['pulse'].content) > 0:
if self.vce.Status['pulse'].value and self.vce.Status['pulse'].value.isdigit():
pr = int(self.vce.Status['pulse'].value)
if pr > 100:
self.sce.Status['tachycardia'] = CE.PatientStatus('tachycardia',True,str(pr),'pulse')
self.sce.Status['tachycardia'].score = self.vce.Status['pulse'].score
elif pr <= 50:
self.sce.Status['bradycardia'] = CE.PatientStatus('bradycardia',True,str(pr),'pulse')
self.sce.Status['bradycardia'].score = self.vce.Status['pulse'].score
# resp rate symptoms
if len(self.vce.Status['resp'].content) > 0:
if self.vce.Status['resp'].value and self.vce.Status['resp'].value.isdigit():
rr = int(self.vce.Status['resp'].value)
if rr > 24:
self.sce.Status['tachypnea'] = CE.PatientStatus('tachypnea',True,str(rr),'resp')
self.sce.Status['tachypnea'].score = self.vce.Status['resp'].score
elif rr < 8:
self.sce.Status['bradypnea'] = CE.PatientStatus('bradypnea',True,str(rr),'resp')
self.sce.Status['bradypnea'].score = self.vce.Status['resp'].score
# blood pressure symptoms
if len(self.vce.Status['bp'].content) > 0:
if self.vce.Status['bp'].value and '/' in self.vce.Status['bp'].value:
temp = self.vce.Status['bp'].value.strip().split('/')
if temp[0] and temp[1] and temp[0].isdigit() and temp[1].isdigit():
bp = [int(temp[0]), int(temp[1])]
mbp = (bp[0] + 2 * bp[1])/3
if bp[0] >= 140 or bp[1] >= 90:
self.sce.Status['hypertension'] = CE.PatientStatus('hypertension',True,str(bp[0]),'bp')
self.sce.Status['hypertension'].score = self.vce.Status['bp'].score
elif mbp < 70:
self.sce.Status['hypotension'] = CE.PatientStatus('hypotension',True,str(mbp),'bp')
self.sce.Status['hypotension'].score = self.vce.Status['bp'].score
# gcs symptoms
if len(self.vce.Status['gcs'].content) > 0:
if self.vce.Status['gcs'].value and self.vce.Status['gcs'].value.isdigit():
gcs = int(self.vce.Status['gcs'].value)
if gcs < 15:
self.sce.Status['decreased mental status'] = CE.PatientStatus('decreased mental status',True,str(gcs),'gcs')
self.sce.Status['decreased mental status'].score = self.vce.Status['gcs'].score
# glucose symptoms
if len(self.vce.Status['glucose'].content) > 0:
if self.vce.Status['glucose'].value and self.vce.Status['glucose'].value.isdigit():
glu = int(self.vce.Status['glucose'].value)
if glu > 300:
self.sce.Status['hyperglycemia'] = CE.PatientStatus('hyperglycemia',True,str(glu),'glucose')
self.sce.Status['hyperglycemia'].score = self.vce.Status['glucose'].score
elif glu < 60:
self.sce.Status['hypoglycemia'] = CE.PatientStatus('hypoglycemia',True,str(glu),'glucose')
self.sce.Status['hypoglycemia'].score = self.vce.Status['glucose'].score
# spo2 symptoms
if len(self.vce.Status['spo2'].content) > 0:
if self.vce.Status['spo2'].value and self.vce.Status['spo2'].value.isdigit():
spo2 = int(self.vce.Status['spo2'].value)
if spo2 < 94:
self.sce.Status['hypoxemia'] = CE.PatientStatus('hypoxemia',True,str(spo2),'spo2')
self.sce.Status['hypoxemia'].score = self.vce.Status['spo2'].score
# pain
if len(self.vce.Status['pain'].content) > 0:
if self.vce.Status['pain'].value and self.vce.Status['pain'].value.isdigit():
ps = int(self.vce.Status['pain'].value)
self.sce.Status['pain severity'] = CE.PatientStatus('pain severity',True,str(ps),'pain')
self.sce.Status['pain severity'].score = self.vce.Status['pain'].score
# ekg symptoms
if len(self.vce.Status['ekg'].content) > 0:
ekg = self.vce.Status['ekg'].value
if "Sinus_Arrhythmia" in ekg:
self.sce.Status['dysrhythmia'] = CE.PatientStatus('dysrhythmia',True,ekg,'ekg')
self.sce.Status['dysrhythmia'].score = self.vce.Status['ekg'].score
else:
self.sce.Status['dysrhythmia'] = CE.PatientStatus('dysrhythmia',False,ekg,'ekg')
self.sce.Status['dysrhythmia'].score = self.vce.Status['ekg'].score
if "_Bradycardia" in ekg:
self.sce.Status['bradycardia'] = CE.PatientStatus('bradycardia',True,ekg,'ekg')
self.sce.Status['bradycardia'].score = self.vce.Status['ekg'].score
if "_Tachycardia" in ekg:
self.sce.Status['tachycardia'] = CE.PatientStatus('tachycardia',True,ekg,'ekg')
self.sce.Status['tachycardia'].score = self.vce.Status['ekg'].score
return True
def Vital2Symptom(self):
'''
Rules for checking the values of vitals and transform them into signs and symptoms.
Pulse-85 tachy > 100 extreme tachy >150 bradicardia <= 50
Resp-16 8 - 24 fast slow normal
BP-164/101 hyper age + 100 hypo < 70 normal mbp = (sbp + 2*dbp)/3
GCS-15 decreased mental status <= 14
Glucose-101 hyper >300 hypo <60
SPO2-100 94 - 99
Pain-9 pain severity
'''
# Pulse to bradycardia or tachycardia
if len(self.vce.vtLog['Pulse']) > 0:
for v in self.vce.vtLog['Pulse']:
pr = int(v)
if pr > 100:
self.sce.Status['tachycardia'] = CE.PatientStatus(
'tachycardia', True, str(pr), 'Pulse')
self.sce.Status['tachycardia'].score = 1000.
elif pr <= 50:
self.sce.Status['bradycardia'] = CE.PatientStatus(
'bradycardia', True, str(pr), 'Pulse')
self.sce.Status['bradycardia'].score = 1000.
# Resp rate symptoms
if len(self.vce.vtLog['Resp']) > 0:
for v in self.vce.vtLog['Resp']:
rr = int(v)
if rr > 24:
self.sce.Status['tachypnea'] = CE.PatientStatus(
'tachypnea', True, str(rr), 'Resp')
self.sce.Status['tachypnea'].score = 1000.
elif rr < 8:
self.sce.Status['bradypnea'] = CE.PatientStatus(
'bradypnea', True, str(rr), 'Resp')
self.sce.Status['bradypnea'].score = 1000.
# blood pressure symptoms
if len(self.vce.vtLog['BP']) > 0:
for v in self.vce.vtLog['BP']:
if '/' not in v:
continue
bp = [int(n) for n in v.strip().split('/')]
mbp = (bp[0] + 2 * bp[1]) / 3
if bp[0] > 140 and bp[1] > 90:
self.sce.Status['hypertension'] = CE.PatientStatus(
'hypertension', True, str(bp[0]), 'BP')
self.sce.Status['hypertension'].score = 1000.
elif mbp < 70:
self.sce.Status['hypotension'] = CE.PatientStatus(
'hypotension', True, str(mbp), 'BP')
self.sce.Status['hypotension'].score = 1000.
# GCS symptoms
if len(self.vce.vtLog['GCS']) > 0:
for v in self.vce.vtLog['GCS']:
gcs = int(v)
if gcs < 15:
self.sce.Status[
'decreased mental status'] = CE.PatientStatus(
'decreased mental status', True, str(gcs), 'GCS')
self.sce.Status['decreased mental status'].score = 1000.
# glucose symptoms
if len(self.vce.vtLog['Glucose']) > 0:
for v in self.vce.vtLog['Pulse']:
glu = int(v)
if glu > 300:
self.sce.Status['hyperglycemia'] = CE.PatientStatus(
'hyperglycemia', True, str(glu), 'Glucose')
self.sce.Status['hyperglycemia'].score = 1000.
elif glu < 60:
self.sce.Status['hypoglycemia'] = CE.PatientStatus(
'hypoglycemia', True, str(glu), 'Glucose')
self.sce.Status['hypoglycemia'].score = 1000.
# spo2 symptoms
if len(self.vce.vtLog['SPO2']) > 0:
for v in self.vce.vtLog['SPO2']:
spo2 = int(v)
if spo2 < 94:
self.sce.Status['hypoxemia'] = CE.PatientStatus(
'hypoxemia', True, str(spo2), 'SPO2')
self.sce.Status['hypoxemia'].score = 1000.
# pain
if len(self.vce.vtLog['Pain']) > 0:
for v in self.vce.vtLog['Pain']:
ps = int(v)
self.sce.Status['pain severity'] = CE.PatientStatus(
'pain severity', True, str(ps), 'Pain')
self.sce.Status['pain severity'].score = 1000.
# EKG symptoms
if len(self.vce.vtLog['EKG']) > 0:
for v in self.vce.vtLog['Pulse']:
ekg = v
if "Sinus_Arrhythmia" in ekg:
self.sce.Status['dysrhythmia'] = CE.PatientStatus(
'dysrhythmia', True, ekg, 'EKG')
self.sce.Status['dysrhythmia'].score = 1000.
else:
self.sce.Status['dysrhythmia'] = CE.PatientStatus(
'dysrhythmia', False, ekg, 'EKG')
self.sce.Status['dysrhythmia'].score = 1000.
if "_Bradycardia" in ekg:
self.sce.Status['bradycardia'] = CE.PatientStatus(
'bradycardia', True, ekg, 'EKG')
self.sce.Status['bradycardia'].score = 1000.
if "_Tachycardia" in ekg:
self.sce.Status['tachycardia'] = CE.PatientStatus(
'tachycardia', True, ekg, 'EKG')
self.sce.Status['tachycardia'].score = 1000.
return True