Source code for pkpd.protocols.protocol_pkpd_dissolution_wagner_nelson

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# * Authors:     Carlos Oscar Sorzano (
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# * Kinestat Pharma
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import numpy as np
from scipy.interpolate import InterpolatedUnivariateSpline

import pyworkflow.protocol.params as params
from .protocol_pkpd import ProtPKPD
from pkpd.objects import PKPDExperiment, PKPDSample, PKPDVariable
from pkpd.pkpd_units import createUnit
from pkpd.utils import uniqueFloatValues, calculateAUC0t, smoothPchip

# tested in

[docs]class ProtPKPDDeconvolutionWagnerNelson(ProtPKPD): """ Calculate the absorption profile of an in vivo concentration profile using the Wagner-Nelson approach. This is only valid for profiles that have been modelled with a monocompartment PK model. The formula is Fabs(t)=(Cp(t)+Ke*AUC0t(t))/(Ke*AUC0inf) where Ke=Cl/V In this implementation it is assumed that AUC0inf is the last AUC0t observed, meaning that Cp(t) has almost vanished in the last samples""" _label = 'deconvolution Wagner Nelson' #--------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addSection('Input') form.addParam('inputExperiment', params.PointerParam, label="In-vivo profiles", pointerClass='PKPDExperiment', help='Make sure that it has a clearance parameter (Cl) and central volume (V)') form.addParam('timeVar', params.StringParam, label="Time variable", default="t", help='Which variable contains the time stamps.') form.addParam('concVar', params.StringParam, label="Concentration variable", default="Cp", help='Which variable contains the plasma concentration.') form.addParam('resampleT', params.FloatParam, label="Resample profiles (time step)", default=-1, help='Resample the input profiles at this time step (make sure it is in the same units as the input). ' 'Leave it to -1 for no resampling') form.addParam('smooth', params.BooleanParam, label="Monotonic smooth", default=True, help='Apply a Pchip interpolation to make sure that the Adissolved is monotonically increasing') #--------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): self._insertFunctionStep('deconvolve',self.inputExperiment.get().getObjId()) self._insertFunctionStep('createOutputStep') #--------------------------- STEPS functions --------------------------------------------
[docs] def addSample(self, sampleName, t, y): newSample = PKPDSample() newSample.sampleName = sampleName newSample.variableDictPtr = self.outputExperiment.variables newSample.descriptors = {} newSample.addMeasurementPattern(["A"]) newSample.addMeasurementColumn("t", t) newSample.addMeasurementColumn("A",y) self.outputExperiment.samples[sampleName] = newSample
[docs] def deconvolve(self, objId1): self.experiment = self.readExperiment(self.inputExperiment.get().fnPKPD) # Create output object self.outputExperiment = PKPDExperiment() tvar = PKPDVariable() tvar.varName = "t" tvar.varType = PKPDVariable.TYPE_NUMERIC tvar.role = PKPDVariable.ROLE_TIME tvar.units = createUnit(self.experiment.getTimeUnits().unit) Avar = PKPDVariable() Avar.varName = "A" Avar.varType = PKPDVariable.TYPE_NUMERIC Avar.role = PKPDVariable.ROLE_MEASUREMENT Avar.units = createUnit("none") self.outputExperiment.variables[tvar.varName] = tvar self.outputExperiment.variables[Avar.varName] = Avar self.outputExperiment.general["title"]="Deconvolution of the amount released" self.outputExperiment.general["comment"]="Amount released at any time t" timeRange = self.experiment.getRange(self.timeVar.get()) for sampleName, sample in self.experiment.samples.items(): # Get t, Cp t=np.asarray(sample.getValues(self.timeVar.get()),dtype=np.float64) Cp=np.asarray(sample.getValues(self.concVar.get()),dtype=np.float64) Cp=np.clip(Cp,0.0,None) t=np.insert(t,0,0) # Add (0,0) to the profile Cp=np.insert(Cp,0,0) t, Cp = uniqueFloatValues(t, Cp) if self.resampleT.get()>0: B = InterpolatedUnivariateSpline(t, Cp, k=1) t = np.arange(np.min(t),np.max(t)+self.resampleT.get(),self.resampleT.get()) Cp = B(t) # Calculate AUC0t AUC0t=calculateAUC0t(t,Cp) # Deconvolve Cl=float(sample.descriptors['Cl']) V=float(sample.descriptors['V']) Ke=Cl/V AUC0inf = float(AUC0t[-1]) A = (Cp + Ke * AUC0t) / (Ke * AUC0inf) * 100 A = np.clip(A,0,100) if self.smooth: if t[0]>0: t = np.insert(t, 0, 0) A = np.insert(A, 0, 0) A = np.clip(smoothPchip(t, A),0,100) self.addSample(sampleName,t,A) self.outputExperiment.write(self._getPath("experiment.pkpd"))
[docs] def createOutputStep(self): self._defineOutputs(outputExperiment=self.outputExperiment) self._defineSourceRelation(self.inputExperiment.get(), self.outputExperiment)
def _validate(self): return [] def _summary(self): retval = [] return retval