Source code for pkpd.protocols.protocol_pkpd_drop_measurements

# **************************************************************************
# *
# * Authors:     Carlos Oscar Sorzano (info@kinestat.com)
# *
# * Kinestat Pharma
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# * This program is free software; you can redistribute it and/or modify
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# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
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# *  All comments concerning this program package may be sent to the
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import pyworkflow.protocol.params as params
from .protocol_pkpd import ProtPKPD
from pkpd.objects import PKPDExperiment, PKPDSample


[docs]class ProtPKPDDropMeasurements(ProtPKPD): """ Filter measurements.\n Protocol created by http://www.kinestatpharma.com\n """ _label = 'drop measurements' #--------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addSection('Input') form.addParam('inputExperiment', params.PointerParam, label="Input experiment", important=True, pointerClass='PKPDExperiment', help='Select an experiment with samples') form.addParam('varsToDrop', params.StringParam, label="Variables to drop", default="", help='List of variable names to drop separated by commas') #--------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): self._insertFunctionStep('runDrop',self.inputExperiment.get().getObjId(), self.varsToDrop.get()) self._insertFunctionStep('createOutputStep') #--------------------------- STEPS functions --------------------------------------------
[docs] def runDrop(self, objId, varsToDrop): import copy experiment = self.readExperiment(self.inputExperiment.get().fnPKPD) self.printSection("Dropping variables") varsToDrop = [] for varName in self.varsToDrop.get().split(','): varsToDrop.append(varName.strip()) filteredExperiment = PKPDExperiment() filteredExperiment.general = copy.copy(experiment.general) filteredExperiment.variables = {} for varName, variable in experiment.variables.items(): if not varName in varsToDrop: filteredExperiment.variables[varName] = copy.copy(variable) filteredExperiment.samples = {} filteredExperiment.doses = copy.copy(experiment.doses) for sampleKey, sample in experiment.samples.items(): candidateSample = PKPDSample() candidateSample.variableDictPtr = filteredExperiment.variables candidateSample.doseDictPtr = filteredExperiment.doses candidateSample.sampleName = copy.copy(sample.sampleName) candidateSample.doseList = copy.copy(sample.doseList) candidateSample.descriptors = copy.copy(sample.descriptors) candidateSample.measurementPattern = [] for varName in sample.measurementPattern: if not varName in varsToDrop: candidateSample.measurementPattern.append(varName) exec("candidateSample.measurement_%s = copy.copy(sample.measurement_%s)"%(varName,varName)) filteredExperiment.samples[candidateSample.varName] = candidateSample self.writeExperiment(filteredExperiment,self._getPath("experiment.pkpd")) self.experiment = filteredExperiment
[docs] def createOutputStep(self): self._defineOutputs(outputExperiment=self.experiment) self._defineSourceRelation(self.inputExperiment, self.experiment)
#--------------------------- INFO functions -------------------------------------------- def _summary(self): msg=["Variables %s dropped"%self.varsToDrop.get()] return msg
[docs] def filterVarForWizard(self, v): """ Define the type of variables required (used in wizard). """ return v.isMeasurement()