# **************************************************************************
# *
# * Authors: Carlos Oscar Sorzano (info@kinestat.com)
# *
# * Kinestat Pharma
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'info@kinestat.com'
# *
# **************************************************************************
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()