def solve(self, objId1):
self.experiment = self.readExperiment(self.inputExperiment.get().fnPKPD)
# Create output object
self.outputExperiment = None
timeRange = self.experiment.getRange(self.timeVar.get())
for sampleName, sample in self.experiment.samples.items():
# Get t, A
t=np.asarray(sample.getValues(self.timeVar.get()),dtype=np.float64)
A=np.asarray(sample.getValues(self.amountVar.get()),dtype=np.float64)
if t[0]>0:
t=np.insert(t,0,0) # Add (0,0) to the profile
A=np.insert(A,0,0)
t, A = uniqueFloatValues(t, A)
if self.resampleT.get()>0:
B = InterpolatedUnivariateSpline(t, A, k=1)
t = np.arange(np.min(t),np.max(t)+self.resampleT.get(),self.resampleT.get())
A = B(t)
# Find C and Cp
C, Cp = self.calculateConcentrations2(t,A)
if self.outputExperiment is None:
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)
Cvar = PKPDVariable()
Cvar.varName = "C"
Cvar.varType = PKPDVariable.TYPE_NUMERIC
Cvar.role = PKPDVariable.ROLE_MEASUREMENT
Lunits = createUnit("L")
Cvar.units = createUnit(divideUnits(self.experiment.getVarUnits(self.amountVar.get()),Lunits.unit))
Cvar.comment = "Concentration central compartment"
Cpvar = PKPDVariable()
Cpvar.varName = "Cp"
Cpvar.varType = PKPDVariable.TYPE_NUMERIC
Cpvar.role = PKPDVariable.ROLE_MEASUREMENT
Cpvar.units = createUnit(divideUnits(self.experiment.getVarUnits(self.amountVar.get()),Lunits.unit))
Cpvar.comment = "Concentration peripheral compartment"
self.outputExperiment.variables[tvar.varName] = tvar
self.outputExperiment.variables[Cvar.varName] = Cvar
self.outputExperiment.variables[Cpvar.varName] = Cpvar
self.outputExperiment.general["title"]="Inverse Loo-Riegelman"
self.outputExperiment.general["comment"]=""
self.addSample(sampleName,t,C,Cp)
self.outputExperiment.write(self._getPath("experiment.pkpd"))
def createOutputExperiment(self):
tvitroVar = PKPDVariable()
tvitroVar.varName = "tvitro"
tvitroVar.varType = PKPDVariable.TYPE_NUMERIC
tvitroVar.role = PKPDVariable.ROLE_TIME
tvitroVar.units = createUnit(self.experimentInVivo.getTimeUnits().unit)
tvitroVar.comment = "tvitro"
AdissolVar = PKPDVariable()
AdissolVar.varName = "Adissol"
AdissolVar.varType = PKPDVariable.TYPE_NUMERIC
AdissolVar.role = PKPDVariable.ROLE_MEASUREMENT
AdissolVar.units = createUnit(PKPDUnit.UNIT_NONE)
AdissolVar.comment = "Amount disolved in vitro"
self.outputExperiment = PKPDExperiment()
self.outputExperiment.variables[tvitroVar.varName] = tvitroVar
self.outputExperiment.variables[AdissolVar.varName] = AdissolVar
self.outputExperiment.general["title"] = "In-vitro target simulation"
self.outputExperiment.general["comment"] = ""
def runSimulation(self):
self.deposition = PKDepositionParameters()
self.deposition.setFiles(self.ptrDeposition.get().fnSubstance.get(),
self.ptrDeposition.get().fnLung.get(),
self.ptrDeposition.get().fnDeposition.get())
self.deposition.doseMultiplier = self.doseMultiplier.get()
self.deposition.read()
substanceParams = PKSubstanceLungParameters()
substanceParams.multiplier = [
float(x) for x in self.substanceMultiplier.get().split()
]
substanceParams.read(self.ptrDeposition.get().fnSubstance.get())
lungParams = PKPhysiologyLungParameters()
lungParams.multiplier = [
float(x) for x in self.physiologyMultiplier.get().split()
]
lungParams.read(self.ptrDeposition.get().fnLung.get())
pkParams = PKPDExperiment()
pkParams.load(self.ptrPK.get().fnPKPD)
pkLungParams = PKLung()
pkLungParams.prepare(
substanceParams, lungParams, pkParams,
[float(x) for x in self.pkMultiplier.get().split()],
self.ciliarySpeedType.get())
# diameters = np.concatenate((np.arange(0.1,1.1,0.1),np.arange(1.2,9.2,0.2))) # [um]
evalStr = "np.concatenate((" + ",".join([
"np.arange(" + x.strip() + ")"
for x in self.diameters.get().split(";")
]) + "))"
diameters = eval(evalStr, {'np': np})
Sbnd = self.volMultiplier.get() * diam2vol(diameters)
tt = np.arange(0,
self.simulationTime.get() + self.deltaT.get(),
self.deltaT.get())
sol = saturable_2D_upwind_IE(lungParams, pkLungParams, self.deposition,
tt, Sbnd)
# Postprocessing
depositionData = self.deposition.getData()
alvDose = np.sum(depositionData['alveolar'])
bronchDose = np.sum(depositionData['bronchial'])
lungDose = alvDose + bronchDose
Aalvsolid = sol['A']['alv']['solid']
Aalvfluid = sol['A']['alv']['fluid']
Aalvtissue = sol['A']['alv']['tissue']
AsysGut = sol['A']['sys']['gut']
AsysPer = sol['A']['sys']['per']
AsysCtr = sol['A']['sys']['ctr']
Atisbr = sol['A']['br']['tissue']
Abrtissue = Atisbr
Vtisbr = lungParams.getBronchial()['fVol'] * lungParams.getSystemic(
)['OWlung']
Cavgbr = Atisbr / Vtisbr
Abrcleared = sol['A']['br']['clear']
Abrcleared = np.reshape(Abrcleared, Abrcleared.size)
Abrsolid = sol['A']['br']['solid']
Abrfluid = sol['A']['br']['fluid']
Acleared = sol['A']['sys']['clear'] + AsysGut - AsysGut[0]
lungRetention = 100 * (lungDose - Acleared) / lungDose
# in percent of lung dose
Csysnmol = sol['C']['sys']['ctr']
Csys = Csysnmol * substanceParams.getData()['MW']
CsysPer = AsysPer * substanceParams.getData(
)['MW'] / pkLungParams.pkData['Vp']
# Create output
self.experimentLungRetention = PKPDExperiment()
self.experimentLungRetention.general["title"] = "Inhalation simulate"
tvar = PKPDVariable()
tvar.varName = "t"
tvar.varType = PKPDVariable.TYPE_NUMERIC
tvar.role = PKPDVariable.ROLE_TIME
tvar.units = createUnit("min")
Rvar = PKPDVariable()
Rvar.varName = "Retention"
Rvar.varType = PKPDVariable.TYPE_NUMERIC
Rvar.role = PKPDVariable.ROLE_MEASUREMENT
Rvar.units = createUnit("none")
Rvar.comment = "Lung retention (% lung dose)"
Cnmolvar = PKPDVariable()
Cnmolvar.varName = "Cnmol"
Cnmolvar.varType = PKPDVariable.TYPE_NUMERIC
Cnmolvar.role = PKPDVariable.ROLE_MEASUREMENT
Cnmolvar.units = createUnit("nmol/mL")
Cnmolvar.comment = "Central compartment concentration"
Cvar = PKPDVariable()
Cvar.varName = "C"
Cvar.varType = PKPDVariable.TYPE_NUMERIC
Cvar.role = PKPDVariable.ROLE_MEASUREMENT
Cvar.units = createUnit("g/mL")
Cvar.comment = "Central compartment concentration"
alvTissueVar = PKPDVariable()
alvTissueVar.varName = "alvTissue"
alvTissueVar.varType = PKPDVariable.TYPE_NUMERIC
alvTissueVar.role = PKPDVariable.ROLE_MEASUREMENT
alvTissueVar.units = createUnit("nmol")
alvTissueVar.comment = "Amount in alveoli"
alvSolidVar = PKPDVariable()
alvSolidVar.varName = "alvSolid"
alvSolidVar.varType = PKPDVariable.TYPE_NUMERIC
alvSolidVar.role = PKPDVariable.ROLE_MEASUREMENT
alvSolidVar.units = createUnit("nmol")
alvSolidVar.comment = "Amount undissolved in alveoli"
alvFluidVar = PKPDVariable()
alvFluidVar.varName = "alvFluid"
alvFluidVar.varType = PKPDVariable.TYPE_NUMERIC
alvFluidVar.role = PKPDVariable.ROLE_MEASUREMENT
alvFluidVar.units = createUnit("nmol")
alvFluidVar.comment = "Amount in alveolar lining fluid"
brTissueVar = PKPDVariable()
brTissueVar.varName = "brTissue"
brTissueVar.varType = PKPDVariable.TYPE_NUMERIC
brTissueVar.role = PKPDVariable.ROLE_MEASUREMENT
brTissueVar.units = createUnit("nmol")
brTissueVar.comment = "Amount in bronchii"
brSolidVar = PKPDVariable()
brSolidVar.varName = "brSolid"
brSolidVar.varType = PKPDVariable.TYPE_NUMERIC
brSolidVar.role = PKPDVariable.ROLE_MEASUREMENT
brSolidVar.units = createUnit("nmol")
brSolidVar.comment = "Amount undissolved in bronchii"
brFluidVar = PKPDVariable()
brFluidVar.varName = "brFluid"
brFluidVar.varType = PKPDVariable.TYPE_NUMERIC
brFluidVar.role = PKPDVariable.ROLE_MEASUREMENT
brFluidVar.units = createUnit("nmol")
brFluidVar.comment = "Amount in bronchial lining fluid"
brClvar = PKPDVariable()
brClvar.varName = "brClear"
brClvar.varType = PKPDVariable.TYPE_NUMERIC
brClvar.role = PKPDVariable.ROLE_MEASUREMENT
brClvar.units = createUnit("nmol")
brClvar.comment = "Cumulative amount cleared by mucociliary elevator"
brCTisvar = PKPDVariable()
brCTisvar.varName = "CbrTis"
brCTisvar.varType = PKPDVariable.TYPE_NUMERIC
brCTisvar.role = PKPDVariable.ROLE_MEASUREMENT
brCTisvar.units = createUnit("nmol/mL")
brCTisvar.comment = "Concentration in bronchial tissue"
sysGutVar = PKPDVariable()
sysGutVar.varName = "sysAbsorption"
sysGutVar.varType = PKPDVariable.TYPE_NUMERIC
sysGutVar.role = PKPDVariable.ROLE_MEASUREMENT
sysGutVar.units = createUnit("nmol")
sysGutVar.comment = "Amount in absorption compartment"
sysCtrVar = PKPDVariable()
sysCtrVar.varName = "sysCentral"
sysCtrVar.varType = PKPDVariable.TYPE_NUMERIC
sysCtrVar.role = PKPDVariable.ROLE_MEASUREMENT
sysCtrVar.units = createUnit("nmol")
sysCtrVar.comment = "Amount in central compartment"
sysPerVar = PKPDVariable()
sysPerVar.varName = "sysPeripheral"
sysPerVar.varType = PKPDVariable.TYPE_NUMERIC
sysPerVar.role = PKPDVariable.ROLE_MEASUREMENT
sysPerVar.units = createUnit("nmol")
sysPerVar.comment = "Amount in peripheral compartment"
CsysPerVar = PKPDVariable()
CsysPerVar.varName = "Cp"
CsysPerVar.varType = PKPDVariable.TYPE_NUMERIC
CsysPerVar.role = PKPDVariable.ROLE_MEASUREMENT
CsysPerVar.units = createUnit("g/mL")
CsysPerVar.comment = "Concentration in peripheral compartment"
doseNmolVar = PKPDVariable()
doseNmolVar.varName = "dose_nmol"
doseNmolVar.varType = PKPDVariable.TYPE_NUMERIC
doseNmolVar.role = PKPDVariable.ROLE_LABEL
doseNmolVar.units = createUnit("nmol")
doseNmolVar.comment = "Input dose in nmol"
doseThroatVar = PKPDVariable()
doseThroatVar.varName = "throat_dose_nmol"
doseThroatVar.varType = PKPDVariable.TYPE_NUMERIC
doseThroatVar.role = PKPDVariable.ROLE_LABEL
doseThroatVar.units = createUnit("nmol")
doseThroatVar.comment = "Throat dose in nmol"
doseLungVar = PKPDVariable()
doseLungVar.varName = "lung_dose_nmol"
doseLungVar.varType = PKPDVariable.TYPE_NUMERIC
doseLungVar.role = PKPDVariable.ROLE_LABEL
doseLungVar.units = createUnit("nmol")
doseLungVar.comment = "Lung dose in nmol"
doseBronchialVar = PKPDVariable()
doseBronchialVar.varName = "bronchial_dose_nmol"
doseBronchialVar.varType = PKPDVariable.TYPE_NUMERIC
doseBronchialVar.role = PKPDVariable.ROLE_LABEL
doseBronchialVar.units = createUnit("nmol")
doseBronchialVar.comment = "Bronchial dose in nmol"
doseAlveolarVar = PKPDVariable()
doseAlveolarVar.varName = "alveolar_dose_nmol"
doseAlveolarVar.varType = PKPDVariable.TYPE_NUMERIC
doseAlveolarVar.role = PKPDVariable.ROLE_LABEL
doseAlveolarVar.units = createUnit("nmol")
doseAlveolarVar.comment = "Alveolar dose in nmol"
mccClearedLungDoseFractionVar = PKPDVariable()
mccClearedLungDoseFractionVar.varName = "mcc_cleared_lung_dose_fraction"
mccClearedLungDoseFractionVar.varType = PKPDVariable.TYPE_NUMERIC
mccClearedLungDoseFractionVar.role = PKPDVariable.ROLE_LABEL
mccClearedLungDoseFractionVar.units = createUnit("None")
mccClearedLungDoseFractionVar.comment = "MCC cleared lung dose fraction"
self.experimentLungRetention.variables["t"] = tvar
self.experimentLungRetention.variables["Retention"] = Rvar
self.experimentLungRetention.variables["Cnmol"] = Cnmolvar
self.experimentLungRetention.variables["C"] = Cvar
self.experimentLungRetention.variables["alvTissue"] = alvTissueVar
self.experimentLungRetention.variables["alvFluid"] = alvFluidVar
self.experimentLungRetention.variables["alvSolid"] = alvSolidVar
self.experimentLungRetention.variables["brTissue"] = brTissueVar
self.experimentLungRetention.variables["brFluid"] = brFluidVar
self.experimentLungRetention.variables["brSolid"] = brSolidVar
self.experimentLungRetention.variables["brClear"] = brClvar
self.experimentLungRetention.variables["CbrTis"] = brCTisvar
self.experimentLungRetention.variables["sysCentral"] = sysCtrVar
self.experimentLungRetention.variables["sysAbsoprtion"] = sysGutVar
self.experimentLungRetention.variables["sysPeripheral"] = sysPerVar
self.experimentLungRetention.variables["Cp"] = CsysPerVar
self.experimentLungRetention.variables["dose_nmol"] = doseNmolVar
self.experimentLungRetention.variables[
"throat_dose_nmol"] = doseThroatVar
self.experimentLungRetention.variables["lung_dose_nmol"] = doseLungVar
self.experimentLungRetention.variables[
"bronchial_dose_nmol"] = doseBronchialVar
self.experimentLungRetention.variables[
"alveolar_dose_nmol"] = doseAlveolarVar
self.experimentLungRetention.variables[
"mcc_cleared_lung_dose_fraction"] = mccClearedLungDoseFractionVar
# Samples
simulationSample = PKPDSample()
simulationSample.sampleName = "simulation"
simulationSample.addMeasurementColumn("t", tt)
simulationSample.addMeasurementColumn("Retention", lungRetention)
simulationSample.addMeasurementColumn("Cnmol", Csysnmol)
simulationSample.addMeasurementColumn("C", Csys)
simulationSample.addMeasurementColumn("alvFluid", Aalvfluid)
simulationSample.addMeasurementColumn("alvTissue", Aalvtissue)
simulationSample.addMeasurementColumn("alvSolid", Aalvsolid)
simulationSample.addMeasurementColumn("brFluid", Abrfluid)
simulationSample.addMeasurementColumn("brTissue", Abrtissue)
simulationSample.addMeasurementColumn("brSolid", Abrsolid)
simulationSample.addMeasurementColumn("brClear", Abrcleared)
simulationSample.addMeasurementColumn("CbrTis", Cavgbr)
simulationSample.addMeasurementColumn("sysAbsorption", AsysGut)
simulationSample.addMeasurementColumn("sysCentral", AsysCtr)
simulationSample.addMeasurementColumn("sysPeripheral", AsysPer)
simulationSample.addMeasurementColumn("Cp", CsysPer)
simulationSample.setDescriptorValue("dose_nmol",
depositionData['dose_nmol'])
simulationSample.setDescriptorValue("throat_dose_nmol",
depositionData['throat'])
lungDose = depositionData['dose_nmol'] - depositionData['throat']
simulationSample.setDescriptorValue("lung_dose_nmol", lungDose)
simulationSample.setDescriptorValue("bronchial_dose_nmol", bronchDose)
simulationSample.setDescriptorValue("alveolar_dose_nmol", alvDose)
simulationSample.setDescriptorValue("mcc_cleared_lung_dose_fraction",
Abrcleared[-1] / lungDose)
self.experimentLungRetention.samples[
"simulmvarNameation"] = simulationSample
self.experimentLungRetention.write(self._getPath("experiment.pkpd"))
# Plots
import matplotlib.pyplot as plt
lungData = lungParams.getBronchial()
Xbnd = np.sort([0] + lungData['end_cm'].tolist() +
lungData['pos'].tolist())
Xctr = Xbnd[:-1] + np.diff(Xbnd) / 2
tvec = tt / 60
T = np.max(tvec)
Cflu = sol['C']['br']['fluid']
Cs = substanceParams.getData()['Cs_br']
plt.figure(figsize=(15, 9))
plt.title('Concentration in bronchial fluid (Cs=%f [uM])' % Cs)
plt.imshow(Cflu,
interpolation='bilinear',
aspect='auto',
extent=[np.min(Xctr), np.max(Xctr), T, 0])
plt.clim(0, Cs)
plt.xlim(np.min(Xctr), np.max(Xctr))
plt.ylim(0, T)
plt.colorbar()
plt.ylabel('Time [h]')
plt.xlabel('Distance from throat [cm]')
plt.savefig(self._getPath('concentrationBronchialFluid.png'))
Ctis = sol['C']['br']['fluid']
plt.figure(figsize=(15, 9))
plt.title('Concentration in bronchial tissue')
plt.imshow(Ctis,
interpolation='bilinear',
aspect='auto',
extent=[np.min(Xctr), np.max(Xctr), T, 0])
plt.xlim(np.min(Xctr), np.max(Xctr))
plt.ylim(0, T)
plt.colorbar()
plt.ylabel('Time [h]')
plt.xlabel('Distance from throat [cm]')
plt.savefig(self._getPath('concentrationBronchialTissue.png'))
def runSimulate(self, objId, X, Y, modelType, paramValues, reportX):
reportX = parseRange(self.reportX.get())
self.experiment = self.readExperiment(
self.inputExperiment.get().fnPKPD)
# Setup model
self.printSection("Model setup")
if self.modelType.get() == 0:
model = PDPolynomial1()
elif self.modelType.get() == 1:
model = PDLogLinear()
elif self.modelType.get() == 2:
model = PDSaturated()
elif self.modelType.get() == 3:
model = PDSigmoid()
elif self.modelType.get() == 4:
model = PDGompertz()
elif self.modelType.get() == 5:
model = PDLogistic1()
elif self.modelType.get() == 6:
model = PDLogistic2()
elif self.modelType.get() == 7:
model = PDLogistic3()
elif self.modelType.get() == 8:
model = PDLogistic4()
elif self.modelType.get() == 9:
model = PDRichards()
elif self.modelType.get() == 10:
model = PDMorgan()
elif self.modelType.get() == 11:
model = PDWeibull()
elif self.modelType.get() == 12:
model = PDPolynomial2()
elif self.modelType.get() == 13:
model = PDPolynomial3()
elif self.modelType.get() == 14:
model = PDPolynomial4()
elif self.modelType.get() == 15:
model = PDPolynomial5()
elif self.modelType.get() == 16:
model = PDPolynomial6()
elif self.modelType.get() == 17:
model = PDPolynomial7()
elif self.modelType.get() == 18:
model = PDPolynomial8()
elif self.modelType.get() == 19:
model = PDPolynomial9()
model.setExperiment(self.experiment)
model.setXVar(self.predictor.get())
model.printSetup()
# Create list of parameters
tokens = self.paramValues.get().split(';')
if len(tokens) != model.getNumberOfParameters():
raise Exception(
"The list of parameter values has not the same number of parameters as the model"
)
model.parameters = []
for token in tokens:
try:
model.parameters.append(float(token.strip()))
except:
raise Exception("Cannot convert %s to float" % token)
print("Simulated model: %s" % model.getEquation())
if self.noiseType.get() == 1:
print("Adding additive noise with sigma=%f" %
self.noiseSigma.get())
elif self.noiseType.get() == 2:
print("Adding multiplicative noise with sigma=%f*X" %
self.noiseSigma.get())
# Add new variable to experiment
newVariable = PKPDVariable()
newVariable.varName = self.predicted.get()
newVariable.varType = PKPDVariable.TYPE_NUMERIC
newVariable.displayString = "%f"
newVariable.role = PKPDVariable.ROLE_MEASUREMENT
newVariable.comment = self.predictedComment.get()
newVariable.units = PKPDUnit(self.predictedUnit.get())
self.experiment.variables[newVariable.varName] = newVariable
for sampleName, sample in self.experiment.samples.items():
model.x = np.array(sample.getValues(self.predictor.get()),
dtype=np.float)
y = model.forwardModel(model.parameters, model.x)
y = self.addNoise(y)
sample.addMeasurementColumn(newVariable.varName, y)
print("==========================================")
sample._printToStream(sys.stdout)
print("==========================================")
sample._printMeasurements(sys.stdout)
print(" ")
if reportX != None:
print("Evaluation of the model at specified values")
yReportX = model.forwardModel(model.parameters, reportX)
yReportX = self.addNoise(yReportX)
print("==========================================")
print("X Ypredicted log10(Ypredicted)")
print("==========================================")
for n in range(0, reportX.shape[0]):
print("%f %f %f" %
(reportX[n], yReportX[n], math.log10(yReportX[n])))
print(' ')
def createOutputExperiments(self, set):
tvitroVar = PKPDVariable()
tvitroVar.varName = "tvitro"
tvitroVar.varType = PKPDVariable.TYPE_NUMERIC
tvitroVar.role = PKPDVariable.ROLE_TIME
tvitroVar.units = createUnit(
self.experimentInVitro.getTimeUnits().unit)
tvitroVar.comment = "tvitro"
tvivoVar = PKPDVariable()
tvivoVar.varName = "tvivo"
tvivoVar.varType = PKPDVariable.TYPE_NUMERIC
tvivoVar.role = PKPDVariable.ROLE_TIME
tvivoVar.units = createUnit(self.experimentInVivo.getTimeUnits().unit)
tvivoVar.comment = "tvivo"
tvitroReinterpolatedVar = PKPDVariable()
tvitroReinterpolatedVar.varName = "tvitroReinterpolated"
tvitroReinterpolatedVar.varType = PKPDVariable.TYPE_NUMERIC
tvitroReinterpolatedVar.role = PKPDVariable.ROLE_TIME
tvitroReinterpolatedVar.units = createUnit(
self.experimentInVitro.getTimeUnits().unit)
tvitroReinterpolatedVar.comment = "tvitro reinterpolated"
tvivoReinterpolatedVar = PKPDVariable()
tvivoReinterpolatedVar.varName = "tvivoReinterpolated"
tvivoReinterpolatedVar.varType = PKPDVariable.TYPE_NUMERIC
tvivoReinterpolatedVar.role = PKPDVariable.ROLE_TIME
tvivoReinterpolatedVar.units = createUnit(
self.experimentInVivo.getTimeUnits().unit)
tvivoReinterpolatedVar.comment = "tvivo reinterpolated"
AdissolVar = PKPDVariable()
AdissolVar.varName = "Adissol"
AdissolVar.varType = PKPDVariable.TYPE_NUMERIC
AdissolVar.role = PKPDVariable.ROLE_MEASUREMENT
AdissolVar.units = createUnit(
self.experimentInVitro.getVarUnits(self.varNameY))
AdissolVar.comment = "Amount disolved in vitro"
FabsVar = PKPDVariable()
FabsVar.varName = "Fabs"
FabsVar.varType = PKPDVariable.TYPE_NUMERIC
FabsVar.role = PKPDVariable.ROLE_MEASUREMENT
FabsVar.units = createUnit(self.experimentInVivo.getVarUnits("A"))
FabsVar.comment = "Amount absorbed in vivo"
AdissolReinterpolatedVar = PKPDVariable()
AdissolReinterpolatedVar.varName = "AdissolReinterpolated"
AdissolReinterpolatedVar.varType = PKPDVariable.TYPE_NUMERIC
AdissolReinterpolatedVar.role = PKPDVariable.ROLE_MEASUREMENT
AdissolReinterpolatedVar.units = createUnit(
self.experimentInVitro.getVarUnits(self.varNameY))
AdissolReinterpolatedVar.comment = "Time reinterpolated amount disolved in vitro"
FabsReinterpolatedVar = PKPDVariable()
FabsReinterpolatedVar.varName = "FabsReinterpolated"
FabsReinterpolatedVar.varType = PKPDVariable.TYPE_NUMERIC
FabsReinterpolatedVar.role = PKPDVariable.ROLE_MEASUREMENT
FabsReinterpolatedVar.units = createUnit(
self.experimentInVivo.getVarUnits("A"))
FabsReinterpolatedVar.comment = "Time reinterpolated amount absorbed in vivo"
AdissolPredictedVar = PKPDVariable()
AdissolPredictedVar.varName = "AdissolPredicted"
AdissolPredictedVar.varType = PKPDVariable.TYPE_NUMERIC
AdissolPredictedVar.role = PKPDVariable.ROLE_MEASUREMENT
AdissolPredictedVar.units = createUnit(
self.experimentInVitro.getVarUnits(self.varNameY))
AdissolPredictedVar.comment = "Predicted amount disolved in vitro"
FabsPredictedVar = PKPDVariable()
FabsPredictedVar.varName = "FabsPredicted"
FabsPredictedVar.varType = PKPDVariable.TYPE_NUMERIC
FabsPredictedVar.role = PKPDVariable.ROLE_MEASUREMENT
FabsPredictedVar.units = createUnit(
self.experimentInVivo.getVarUnits("A"))
FabsPredictedVar.comment = "Predicted amount absorbed in vivo"
if set == 1:
self.outputExperimentFabs = PKPDExperiment()
self.outputExperimentFabs.variables[
tvitroReinterpolatedVar.varName] = tvitroReinterpolatedVar
self.outputExperimentFabs.variables[
AdissolReinterpolatedVar.varName] = AdissolReinterpolatedVar
self.outputExperimentFabs.variables[tvivoVar.varName] = tvivoVar
self.outputExperimentFabs.variables[FabsVar.varName] = FabsVar
self.outputExperimentFabs.variables[
FabsPredictedVar.varName] = FabsPredictedVar
self.outputExperimentFabs.general[
"title"] = "In-vitro In-vivo correlation"
self.outputExperimentFabs.general[
"comment"] = "Fabs vs Predicted Fabs"
self.outputExperimentAdissol = PKPDExperiment()
self.outputExperimentAdissol.variables[
tvivoReinterpolatedVar.varName] = tvivoReinterpolatedVar
self.outputExperimentAdissol.variables[
FabsReinterpolatedVar.varName] = FabsReinterpolatedVar
self.outputExperimentAdissol.variables[
tvitroVar.varName] = tvitroVar
self.outputExperimentAdissol.variables[
AdissolVar.varName] = AdissolVar
self.outputExperimentAdissol.variables[
AdissolPredictedVar.varName] = AdissolPredictedVar
self.outputExperimentAdissol.general[
"title"] = "In-vitro In-vivo correlation"
self.outputExperimentAdissol.general[
"comment"] = "Adissol vs Predicted Adissol"
else:
self.outputExperimentFabsSingle = PKPDExperiment()
self.outputExperimentFabsSingle.variables[
tvitroReinterpolatedVar.varName] = tvitroReinterpolatedVar
self.outputExperimentFabsSingle.variables[
AdissolReinterpolatedVar.varName] = AdissolReinterpolatedVar
self.outputExperimentFabsSingle.variables[
tvivoVar.varName] = tvivoVar
self.outputExperimentFabsSingle.variables[
FabsVar.varName] = FabsVar
self.outputExperimentFabsSingle.variables[
FabsPredictedVar.varName] = FabsPredictedVar
self.outputExperimentFabsSingle.general[
"title"] = "In-vitro In-vivo correlation"
self.outputExperimentFabsSingle.general[
"comment"] = "Fabs vs Predicted Fabs"