Source code for pkpd.protocols.protocol_pkpd_dissolution_ivivc_internal_validity

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# * Authors:     Carlos Oscar Sorzano (info@kinestat.com)
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# * Kinestat Pharma
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import numpy as np
import pyworkflow.protocol.params as params
from .protocol_pkpd import ProtPKPD

# Tested in test_workflow_levyplot.py
# Tested in test_workflow_deconvolution2.py

[docs]class ProtPKPDIVIVCInternalValidity(ProtPKPD): """ This protocol compares the AUC and Cmax predicted from an in vitro-in vivo experiment and the AUC and Cmax of the in vivo population from which the IVIV correlation was estimated. There should not be differences larger than 15%% between the two sets of variables. Protocol created by http://www.kinestatpharma.com\n""" _label = 'ivivc internal validity' #--------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addSection('Input') form.addParam('inputExperiment', params.PointerParam, label="True in-vivo experiment", pointerClass='PKPDExperiment', help='Select the experiment with the measurements you want to analyze. It must have Cmax and AUC0t') form.addParam('inputSimulated', params.PointerParam, label="Simulated in-vivo experiment", pointerClass='PKPDExperiment', help='Select the experiment with the measurements you want to analyze. It must have Cmax and AUC0t' 'and it is the output of a IVIVC+PK simulation') #--------------------------- STEPS functions -------------------------------------------- def _insertAllSteps(self): self._insertFunctionStep('runAnalysis',self.inputExperiment.getObjId(),self.inputSimulated.getObjId())
[docs] def runAnalysis(self,objId1,objId2): trueExp = self.readExperiment(self.inputExperiment.get().fnPKPD,False) simExp = self.readExperiment(self.inputSimulated.get().fnPKPD,False) if not "AUC0t" in trueExp.variables or not "Cmax" in trueExp.variables: raise Exception("Cannot find AUC0t or Cmax in the in vivo experiment") if not "AUC0t" in simExp.variables or not "Cmax" in simExp.variables or not "from" in simExp.variables: raise Exception("Cannot find AUC0t, Cmax or from in the simulated experiment") trueAUC = {} trueCmax = {} for sampleName, sample in trueExp.samples.items(): try: trueAUC[sampleName]=float(sample.descriptors["AUC0t"]) trueCmax[sampleName]=float(sample.descriptors["Cmax"]) except: pass simAUC = {} simCmax = {} simNames = [] for sampleName, sample in simExp.samples.items(): fromNames=sample.descriptors["from"] sampleName=fromNames.split("---")[0] if not sampleName in simNames: simNames.append(sampleName) if not sampleName in simAUC: simAUC[sampleName]=[] simCmax[sampleName]=[] try: simAUC[sampleName].append(float(sample.descriptors["AUC0t"])) simCmax[sampleName].append(float(sample.descriptors["Cmax"])) except: pass errorAUC=[] errorCmax=[] for sampleName in trueAUC: tAUC = trueAUC[sampleName] tCmax = trueCmax[sampleName] if sampleName in simAUC: if tAUC>0: for sAUC in simAUC[sampleName]: errorAUC.append((tAUC-sAUC)/tAUC*100) if tCmax>0: for sCmax in simCmax[sampleName]: errorCmax.append((tCmax-sCmax)/tCmax*100) np.savetxt(self._getExtraPath("errorAUC.txt"),errorAUC) np.savetxt(self._getExtraPath("errorCmax.txt"),errorCmax) if len(errorAUC)==0: print("Cannot find any matching name between the true experiment (%s) and the simulated names (%s)"%\ (" ".join(trueExp.samples.keys())," ".join(simNames))) else: alpha_2 = (100-95)/2 limits = np.percentile(errorAUC,[alpha_2,100-alpha_2]) fhSummary=open(self._getPath("summary.txt"),"w") self.doublePrint(fhSummary,"error AUC (normalized to 100, (true-sim)/true) %f%% confidence interval=[%f,%f] mean=%f"%(95,limits[0],limits[1],np.mean(errorAUC))) limits = np.percentile(errorCmax,[alpha_2,100-alpha_2]) self.doublePrint(fhSummary,"error Cmax (normalized to 100, (true-sim)/true) %f%% confidence interval=[%f,%f] mean=%f"%(95,limits[0],limits[1],np.mean(errorCmax))) fhSummary.close()
#--------------------------- INFO functions -------------------------------------------- def _summary(self): msg=[] self.addFileContentToMessage(msg,self._getPath("summary.txt")) return msg