# **************************************************************************
# *
# * 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
[docs]class ProtPKPDCumulatedDose(ProtPKPD):
""" Create label with the cumulated dose between two time points.\n
Protocol created by http://www.kinestatpharma.com\n """
_label = 'cumulated dose'
#--------------------------- 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('labelToAdd', params.StringParam, label="Label to add", default="CumulatedDose",
help='Name of the variable to add')
form.addParam('fromTime', params.FloatParam, label="From (h)", default=0)
form.addParam('toTime', params.FloatParam, label="To (h)", default=1)
#--------------------------- INSERT steps functions --------------------------------------------
def _insertAllSteps(self):
self._insertFunctionStep('runCreate',self.inputExperiment.get().getObjId(), self.labelToAdd.get(),
self.fromTime.get(), self.toTime.get())
self._insertFunctionStep('createOutputStep')
#--------------------------- STEPS functions --------------------------------------------
[docs] def runCreate(self, objId, labelToAdd, fromTime, toTime):
self.experiment = self.readExperiment(self.inputExperiment.get().fnPKPD)
labelToAdd = self.labelToAdd.get().replace(' ',"_")
fromTime*=60
toTime*=60
comment = "Cumulated dose between %s and %s"%(fromTime,toTime)
for sampleName, sample in self.experiment.samples.items():
sample.interpretDose()
Dunits = sample.getDoseUnits()
varValue = sample.getCumulatedDose(fromTime,toTime)
self.experiment.addParameterToSample(sampleName, labelToAdd, Dunits, comment, varValue)
self.writeExperiment(self.experiment,self._getPath("experiment.pkpd"))
[docs] def createOutputStep(self):
self._defineOutputs(outputExperiment=self.experiment)
self._defineSourceRelation(self.inputExperiment, self.experiment)
#--------------------------- INFO functions --------------------------------------------
def _summary(self):
msg=["Cumulated dose between %s and %s"%(self.fromTime.get(),self.toTime.get())]
return msg