def normalize(self):
'''Normalizes timecourse.'''
factor, unit = self.remove_substance_dimension()
if unit:
if ureg(unit) != ureg(self.unit):
for key, value in self.norm_fields.items():
if value is not None:
list_norm_values = list(factor * np.array(value))
setattr(self, key, list_norm_values)
self.unit = unit
else:
self.unit = str(ureg(self.unit).u)
if not self.is_norm:
for key, value in self.norm_fields.items():
if value is not None:
list_norm_values = list(
self.measurement_type.normalize(value,
self.unit).magnitude)
setattr(self, key, list_norm_values)
self.unit = self.measurement_type.norm_unit(self.unit).__str__()
# for time_unit
if not self.time_unit == TIME_NORM_UNIT:
p_time_unit = self.measurement_type.p_unit(self.time_unit)
times = p_time_unit * self.time
norm_times = times.to(TIME_NORM_UNIT)
self.time = list(norm_times.m)
self.time_unit = TIME_NORM_UNIT
def p_unit(unit):
try:
return ureg(unit)
except (UndefinedUnitError, AttributeError):
if unit == "%":
raise ValueError(f"unit: [{unit}] has to written as 'percent'")
raise ValueError(
f"unit [{unit}] is not defined in unit registry or not allowed."
)
def p_unit(self):
return ureg(self.name).u
def is_norm_unit(self, unit):
return ureg(unit) in self.n_p_units
def get_pharmacokinetic_variables(self):
"""Get data for pharmacokinetics calculation
:return: dict of data for calculation of pharmacokinetics
"""
# TODO: This should be refactored in the pharmacokinetics module
pk_dict = {}
# substance
pk_dict["compound"] = self.substance.name
# bodyweight
bodyweight = self.get_bodyweight().first()
# time
pk_dict["t"] = pd.Series(self.time)
pk_dict["t_unit"] = self.time_unit
# concentration
# FIXME: the timecourse data must be filtered based on the dosing times
# (or alternatively this should be handled in the pk calculation)
pk_dict["c_unit"] = self.unit
if self.mean:
pk_dict["c"] = pd.Series(self.mean)
pk_dict["c_type"] = "mean"
elif self.median:
pk_dict["c"] = pd.Series(self.median)
pk_dict["c_type"] = "median"
elif self.value:
pk_dict["c"] = pd.Series(self.value)
pk_dict["c_type"] = "value"
# dosing
dosing = self.get_dosing()
restricted_dosing_units = [
'g',
'g/kg',
'mol',
'mol/kg',
]
MeasurementType()
if dosing:
if MeasurementType.objects.get(
name="restricted dosing").is_valid_unit(dosing.unit):
p_unit_dosing = self.measurement_type.p_unit(dosing.unit)
p_unit_concentration = self.measurement_type.p_unit(
pk_dict["c_unit"])
vd_unit = p_unit_dosing / p_unit_concentration
pk_dict["vd_unit"] = str(vd_unit)
pk_dict["dose"] = dosing.value
if dosing.time:
pk_dict["intervention_time"] = (
ureg(dosing.time_unit) * dosing.time).to(
self.time_unit).magnitude
pk_dict["dose_unit"] = dosing.unit
# bodyweight dependent values
if bodyweight:
pk_dict["bodyweight_unit"] = bodyweight.unit
if bodyweight.value:
pk_dict["bodyweight"] = bodyweight.value
pk_dict["bodyweight_type"] = "value"
elif bodyweight.mean:
pk_dict["bodyweight"] = bodyweight.mean
pk_dict["bodyweight_type"] = "mean"
elif bodyweight.median:
pk_dict["bodyweight"] = bodyweight.median
pk_dict["bodyweight_type"] = "median"
return pk_dict