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patient.py
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patient.py
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import datetime
from dateutil.relativedelta import relativedelta
from diagnosis import Diagnosis
from disease_groups import *
class Patient:
def __init__(self, number, sex, birth_date, death_date=None):
self.number = number
self.sex = sex
self.birth_date = birth_date
self.death_date = death_date
self.diagnoses = DiagnosesDict({})
self.strokes = []
self.care_range = (datetime.date(datetime.MAXYEAR, 12, 31), datetime.date(datetime.MINYEAR, 1, 1)) # TODO Unused
self.medications = {}
def __repr__(self):
return "({}, {}, {}, {}\nDiseases: {})".format(self.number, self.sex, self.birth_date, self.death_date,
len(self.diagnoses.keys()))
def __eq__(self, other):
return (self.number == other.number and self.sex == other.sex and
self.birth_date == other.birth_date and self.death_date == other.death_date)
def add_diagnosis(self, diagnosis):
self.diagnoses.add(diagnosis)
if self.death_date is not None and self.death_date is not datetime.date(datetime.MAXYEAR, 12, 31):
if diagnosis.start_date > self.death_date:
self.death_date = diagnosis.start_date
def get_current_diseases(self, timestamp): # Unused
current_diseases = set()
for diagnosis in self.diagnoses.iter_diagnoses():
if diagnosis.start_date <= timestamp <= diagnosis.end_date:
current_diseases.add(diagnosis.disease)
return current_diseases
def has_disease(self, disease, timestamp, chronic=False):
if disease not in self.diagnoses:
return False
for d in self.diagnoses[disease]:
if (chronic and d.start_date <= timestamp) or d.start_date <= timestamp <= d.end_date:
return True
return False
def has_disease_group(self, group, timestamp, chronic=False):
return any(map(lambda d: self.has_disease(d, timestamp, chronic=chronic), group))
def days_since_diagnosis(self, disease, timestamp):
if disease not in self.diagnoses:
return 0
days = [(timestamp - d.start_date).days for d in self.diagnoses[disease]
if (timestamp - d.start_date).days >= 0]
if not days:
return 0
return min(days)
def days_since_last_diagnosis(self, timestamp):
last_diagnosis = self.diagnoses.last_diagnosis
if last_diagnosis is None:
raise Exception("No Diagnoses")
return (timestamp - last_diagnosis.start_date).days
def calculate_age(self, timestamp):
age = timestamp.year - self.birth_date.year
if timestamp.month < self.birth_date.month:
age -= 1
elif timestamp.month == self.birth_date.month and self.birth_date.day > timestamp.day:
age -= 1
return age
def is_female(self):
return self.sex.lower() == "v" or self.sex.lower() == "f"
def calculate_chads_vasc(self, timestamp):
score = sum([
1 if self.has_disease_group(chads_vasc_c, timestamp, chronic=True) else 0,
1 if self.has_disease_group(chads_vasc_h, timestamp, chronic=True) else 0,
1 if self.has_disease_group(chads_vasc_d, timestamp, chronic=True) else 0,
2 if self.has_disease_group(chads_vasc_s, timestamp, chronic=True) else 0,
1 if self.has_disease_group(chads_vasc_v, timestamp, chronic=True) else 0
])
age = self.calculate_age(timestamp)
if age >= 75:
score += 2
elif age >= 65:
score += 1
if self.is_female():
score += 1
return score
def should_have_AC(self, timestamp, method, **kwargs):
return method(self, timestamp, **kwargs)
def is_alive(self, timestamp):
if self.birth_date <= timestamp < self.death_date:
return True
return False
def find_strokes(self):
timestamps = []
for s in stroke_diseases:
if s not in self.diagnoses:
continue
for d in self.diagnoses[s]:
timestamps.append(d.start_date)
self.strokes = timestamps
def add_medication(self, medication):
if medication.code not in self.medications:
self.medications[medication.code] = []
self.medications[medication.code].append(medication)
def has_medication(self, medication_code, sim_date):
for m in self.medications[medication_code]:
if m.start_date <= sim_date <= m.end_date:
return True
return False
def has_medication_group(self, starts_with, sim_date, which=False):
last = None
last_date = datetime.date(datetime.MINYEAR, 1, 1)
for code, medications in self.medications.items():
if not code.startswith(starts_with):
continue
for m in medications:
if m.start_date <= sim_date <= m.end_date:
if not which:
return True
elif m.start_date > last_date:
last_date = m.start_date
last = code
if which and last is not None:
return last
return False
def set_care_range(self, extra_months=0):
first_date, last_date = self.care_range
for diagnosis in self.diagnoses.iter_diagnoses():
if diagnosis.start_date < first_date:
first_date = diagnosis.start_date
if diagnosis.end_date > last_date:
last_date = diagnosis.end_date
for atc_group in self.medications.values():
for m in atc_group:
if m.start_date < first_date:
first_date = m.start_date
if m.end_date != datetime.date(datetime.MAXYEAR, 12, 31) and \
m.end_date > last_date:
last_date = m.end_date
if first_date == datetime.date(datetime.MAXYEAR, 1, 1) or last_date == datetime.date(datetime.MINYEAR, 1, 1):
raise ValueError("No patient information")
self.care_range = (first_date, last_date + relativedelta(months=extra_months))
class DiagnosesDict(dict):
def __init__(self, *args, **kw):
super(DiagnosesDict, self).__init__(*args, **kw)
self.last_diagnosis = None
def add(self, diagnosis):
if not type(diagnosis) is Diagnosis:
raise(TypeError, "Type is not a Diagnosis")
disease = diagnosis.disease
if disease not in self.keys():
super(DiagnosesDict, self).__setitem__(disease, [])
self[disease].append(diagnosis)
if self.last_diagnosis is None or self.last_diagnosis < diagnosis:
self.last_diagnosis = diagnosis
def iter_diagnoses(self):
for diagnoses in self.values():
for diagnosis in diagnoses:
yield diagnosis