# **************************************************************************
# *
# * 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.
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# * This program is distributed in the hope that it will be useful,
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# * GNU General Public License for more details.
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# * 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
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# * 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 PKDepositionParameters
# Tested in test_workflow_inhalation1
[docs]class ProtPKPDInhImportDepositionProperties(ProtPKPD):
""" Read deposition parameters associated to some substance\n
See Hartung2020.
Protocol created by http://www.kinestatpharma.com\n """
_label = 'deposition pattern'
#--------------------------- DEFINE param functions --------------------------------------------
def _defineParams(self, form):
# Default parameters from
# Hartung2020_MATLAB/physiol_subst/properties_subst.m
form.addSection('Input')
form.addParam('substance', params.PointerParam, pointerClass='PKSubstanceLungParameters', label="Substance")
form.addParam('lungModel', params.PointerParam, pointerClass='PKPhysiologyLungParameters', label="Lung model")
form.addParam('depositionFile', params.FileParam, label="Deposition pattern",
help='This file is generated by MPPD software')
#--------------------------- INSERT steps functions --------------------------------------------
def _insertAllSteps(self):
self._insertFunctionStep('createOutputStep')
#--------------------------- STEPS functions --------------------------------------------
[docs] def createOutputStep(self):
self.deposition = PKDepositionParameters()
self.deposition.setFiles(self.substance.get().fnSubst.get(),
self.lungModel.get().fnPhys.get(),
self.depositionFile.get())
self._defineOutputs(outputDeposition=self.deposition)
def _citations(self):
return ['Hartung2020']