# **************************************************************************
# *
# * 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 copy
import numpy as np
from scipy.interpolate import InterpolatedUnivariateSpline
import pyworkflow.protocol.params as params
from pkpd.objects import PKPDExperiment, PKPDSample, PKPDVariable
from pkpd.utils import computeXYmean, twoWayUniqueFloatValues
from .protocol_pkpd import ProtPKPD
[docs]class ProtPKPDDissolutionLevyPlotJoin(ProtPKPD):
""" Join several Levy plots into a single one. The strategy is to compute the average of all the plots involved in the
Levy plot process: 1) tvivo -> tvitro """
_label = 'dissol levyplot join avg'
#--------------------------- DEFINE param functions --------------------------------------------
def _defineParams(self, form):
form.addSection('Input')
form.addParam('inputLevyplots', params.MultiPointerParam, label="Levy plots",
pointerClass='PKPDExperiment', help='Choose experiments with IVIV correlations (only the Fabs experiments)')
#--------------------------- INSERT steps functions --------------------------------------------
def _insertAllSteps(self):
self._insertFunctionStep('calculateAllLevy')
self._insertFunctionStep('createOutputStep')
#--------------------------- STEPS functions --------------------------------------------
[docs] def calculateAllLevy(self):
L1=[]
for ptrExperiment in self.inputLevyplots:
experiment=PKPDExperiment()
experiment.load(ptrExperiment.get().fnPKPD.get())
x,y = experiment.getXYMeanValues("tvivo","tvitro")
L1.append((x,y))
tvivo, tvitro = computeXYmean(L1, common=True)
x, y = twoWayUniqueFloatValues(tvivo, tvitro)
Bt=InterpolatedUnivariateSpline(x, y, k=1)
vtvitroReinterpolated = np.zeros(len(tvivo))
for i in range(len(tvivo)):
tvivoi = tvivo[i]
vtvitroReinterpolated[i]=Bt(tvivoi)
tvitroReinterpolatedVar=experiment.variables["tvitro"]
tvivoVar=experiment.variables["tvivo"]
self.outputExperimentSingle = PKPDExperiment()
self.outputExperimentSingle.variables[tvitroReinterpolatedVar.varName] = tvitroReinterpolatedVar
self.outputExperimentSingle.variables[tvivoVar.varName] = tvivoVar
self.outputExperimentSingle.general["title"] = "Levy plot"
self.outputExperimentSingle.general["comment"] = "tvitro vs tvivo"
sampleName="jointLevyPlot"
newSampleSingle = PKPDSample()
newSampleSingle.sampleName = sampleName
newSampleSingle.variableDictPtr = self.outputExperimentSingle.variables
newSampleSingle.descriptors = {}
newSampleSingle.addMeasurementColumn("tvitro", vtvitroReinterpolated)
newSampleSingle.addMeasurementColumn("tvivo", tvivo)
self.outputExperimentSingle.samples[sampleName] = newSampleSingle
self.outputExperimentSingle.addLabelToSample(sampleName, "from", "individual---vesel", "meanVivo---meanVitro")
self.outputExperimentSingle.write(self._getPath("experiment.pkpd"))
[docs] def createOutputStep(self):
self._defineOutputs(outputExperiment=self.outputExperimentSingle)
for ptrExperiment in self.inputLevyplots:
self._defineSourceRelation(ptrExperiment.get(), self.outputExperimentSingle)
def _summary(self):
return []