# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
# * Carlos Oscar Sorzano (info@kinestat.com)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * 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 tkinter as tk
import tkinter.ttk as ttk
from pyworkflow.wizard import Wizard
import pyworkflow.gui.dialog as dialog
from pyworkflow.gui.tree import TreeProvider, BoundTree
from pyworkflow.gui.dialog import ListDialog
import pyworkflow.gui as gui
from pkpd.protocols import *
from pkpd.viewers.tk_ode import PKPDODEDialog, PKPDFitDialog
[docs]class VariablesProvider(dialog.Dialog):
"""
This class create a frame with the pkpd variables
"""
def __init__(self, parent, title, **kwargs):
""" From kwargs:
message: message tooltip to show when browsing.
selected: the item that should be selected.
validateSelectionCallback: a callback function to validate selected items.
"""
self.targetProtocol = kwargs['targetProtocol']
self.params = kwargs['params']
self.values = []
self.oldValues = {}
self.experiment = kwargs['experiment']
self.provider = kwargs['provider']
dialog.Dialog.__init__(self, parent, title,
buttons=[('Select', dialog.RESULT_YES),
('Cancel', dialog.RESULT_CANCEL)])
[docs] def body(self, bodyFrame):
bodyFrame.config(bg='white')
gui.configureWeigths(bodyFrame)
self._createContent(bodyFrame)
def _createContent(self, content):
"""
Create the wizard content
"""
# Create the variables
frame = tk.Frame(content, bg='white')
variables = tk.LabelFrame(frame, text="Parameters", bg='white')
variables.grid(row=0, column=0, sticky='news', padx=5, pady=5)
self.samplesTree = self._addBoundTree(variables,
self.provider, 4)
# Create the content
parameteres = tk.LabelFrame(frame, text="Variables", bg='white')
parameteres.grid(row=1, column=0, sticky='news', padx=5, pady=5)
self._insertParameters(parameteres)
frame.grid(row=0, column=0, sticky='news', padx=5, pady=5)
gui.configureWeigths(frame)
def _insertParameters(self, content):
row = 0
for param in self.params:
paramValue = self._createVariablesValue(content, param)
paramValue.grid(row=row, column=0, sticky='news', padx=5, pady=5)
row += 1
def _createVariablesValue(self, frame, paramName):
"""
Create the wizard variables with the values
"""
def _fillVariableValues(paramName, varValue, cbox):
self._objects = self.provider.getObjects()
index = 0
valueIndex = -1
valuesList = []
for obj in self._objects:
objDict = self.provider.getObjectInfo(obj)
if objDict is not None:
key = objDict.get('key')
# text = objDict.get('text', key)
# parent = objDict.get('parent', None)
valuesList.append(key)
if key == varValue:
valueIndex = index
index += 1
cbox['values'] = valuesList
if valueIndex != -1:
cbox.current(valueIndex)
else:
_selection_changed(None, paramName, valuesList[0])
cbox.current(0)
def _selection_changed(event, param, newValue):
for value in self.values:
if value[0].lower() == param:
value[1].set(newValue)
paramValueFrame = tk.Frame(frame, bg='white')
gui.configureWeigths(paramValueFrame)
label = tk.Label(paramValueFrame, text=(str(self.targetProtocol.getParam(paramName).label) + ': '))
label.grid(row=0, column=0, sticky='news')
combobox = ttk.Combobox(paramValueFrame, name=paramName.lower(), state="readonly")
combobox.grid(row=0, column=1, sticky='news')
combobox.bind("<<ComboboxSelected>>", lambda event: _selection_changed(event,
combobox._name,
combobox['value'][combobox.current()]))
varValue = getattr(self.targetProtocol, paramName, None)
self.values.append((paramName, varValue))
self.oldValues[paramName] = varValue.get()
_fillVariableValues(paramName, varValue, combobox)
return paramValueFrame
def _addBoundTree(self, parent, provider, height):
bt = BoundTree(parent, provider, height=height)
bt.grid(row=0, column=0, sticky='news', padx=5, pady=5)
gui.configureWeigths(parent)
return bt
[docs] def restartValues(self, restartAll=False):
if restartAll:
for value in self.values:
self.oldValues[value[0]] = value[1].get()
else:
for key, oldValue in self.oldValues.items():
for value in self.values:
if value[0] == key:
value[1].set(pwobj.String(oldValue))
[docs]class FilterVariablesTreeProvider(TreeProvider):
""" Simplified view of VariablesTreeProvider with less columns.
Additionally, we can filter by a given function. """
def __init__(self, experiment, filter=None):
self.params = params
self.experiment = experiment
self.filter = filter or self._noFilter
def _noFilter(self, v):
return True
[docs] def getColumns(self):
return [('Name', 100), ('Unit', 100), ('Comment', 300)]
[docs] def getObjects(self):
sortedVars = []
for key in sorted(self.experiment.variables.keys()):
v = self.experiment.variables[key]
if self.filter(v):
sortedVars.append(v)
return sortedVars
[docs] def getObjectInfo(self, obj):
key = obj.varName
return {'key': key, 'text': key,
'values': (obj.getUnitsString(),
obj.comment)}
[docs]class PKPDChooseVariableWizard(Wizard):
_targets = [(ProtPKPDRegressionLabel, ['labelX', 'labelY']),
(ProtPKPDChangeUnits, ['labelToChange']),
(ProtPKPDStatsExp1Subgroups2Mean, ['labelToCompare']),
(ProtPKPDExponentialFit, ['predictor', 'predicted']),
(ProtPKPDDissolutionFit, ['predictor', 'predicted']),
(ProtPKPDExportToCSV, ['tVar', 'xVar']),
(ProtPKPDEliminationRate, ['predictor', 'predicted']),
(ProtPKPDMonoCompartment, ['predictor', 'predicted']),
(ProtPKPDMonoCompartmentConv, ['predictor', 'predicted']),
(ProtPKPDMonoCompartmentUrine, ['predictor', 'predicted',
'Au']),
(ProtPKPDMonoCompartmentClint,['predictor', 'predicted']),
(ProtPKPDMonoCompartmentLinkPD, ['predictor', 'predicted',
'E']),
(ProtPKPDMonoCompartmentPD, ['predictor', 'predicted', 'E']),
(ProtPKPDNCANumeric, ['xVar']),
(ProtPKPDTwoCompartments, ['predictor', 'predicted']),
(ProtPKPDTwoCompartmentsConv, ['predictor', 'predicted']),
(ProtPKPDTwoCompartmentsUrine, ['predictor', 'predicted', 'Au']),
(ProtPKPDTwoCompartmentsClint, ['predictor', 'predicted']),
(ProtPKPDTwoCompartmentsClintCl, ['predictor', 'predicted']),
(ProtPKPDTwoCompartmentsClintMetabolite, ['predictor',
'predicted',
'metabolite']),
(ProtPKPDTwoCompartmentsAutoinduction, ['predictor',
'predicted']),
(ProtPKPDTwoCompartmentsBoth, ['predictor', 'predicted',
'Cperipheral']),
(ProtPKPDTwoCompartmentsBothPD, ['predictor', 'predicted',
'Cperipheral', 'E']),
(ProtPKPDThreeCompartments, ['predictor', 'predicted']),
(ProtPKPDMonoCompartmentUrine, ['predicted']),
(ProtPKPDSimulateGenericPD, ['predictor']),
]
[docs] def show(self, form, *params):
protocol = form.protocol
fullParams = self._getAllParams(protocol)
experiment = protocol.getAttributeValue('inputExperiment', None)
if experiment is None:
form.showError("Select input experiment first.")
else:
experiment.load()
filterFunc = getattr(protocol, 'filterVarForWizard', None)
provider = FilterVariablesTreeProvider(experiment)
dlg = VariablesProvider(form.root, self.getTitle(),
targetProtocol=protocol,
params=fullParams,
experiment=experiment,
provider=provider)
if dlg.resultYes():
for label in fullParams:
for value in dlg.values:
if value[0] == label:
self.setFormValues(form, label, value[1])
break
dlg.restartValues(restartAll=True)
else:
dlg.restartValues()
[docs] def getTitle(self):
return "Choose variable"
[docs] def getSelectMode(self):
return "browse"
def _getAllParams(self, protocol):
""" Return the list of all target parameters associated with this
protocol. This function is useful when more than one parameter is
associated to the wizard in the same protocol. """
for k, v in self._targets:
if k.__name__ == protocol.getClassName():
return v
return []
[docs]class DoseTreeProvider(TreeProvider):
def __init__(self, experiment):
self.params = params
self.experiment = experiment
[docs] def getColumns(self):
return [('Name', 100)]
[docs] def getObjects(self):
sortedDoses = []
for key in sorted(self.experiment.doses.keys()):
d = self.experiment.doses[key]
sortedDoses.append(d)
return sortedDoses
[docs] def getObjectInfo(self, obj):
key = obj.doseName
return {'key': key, 'text': key}
[docs]class PKPDChooseDoseWizard(Wizard):
_targets = [(ProtPKPDChangeVia, ['doseName', 'doseVia']),
]
[docs] def show(self, form, *params):
protocol = form.protocol
fullParams = self._getAllParams(protocol)
experiment = protocol.getAttributeValue('inputExperiment', None)
if experiment is None:
form.showError("Select input experiment first.")
else:
experiment.load()
provider = DoseTreeProvider(experiment)
dlg = VariablesProvider(form.root, "Choose dose name",
targetProtocol=protocol,
params=fullParams,
experiment=experiment,
provider=provider,
selectmode=self.getSelectMode())
if dlg.resultYes():
for label in fullParams:
for value in dlg.values:
if value[0] == label:
self.setFormValues(form, label, value[1])
break
dlg.restartValues(restartAll=True)
else:
dlg.restartValues()
[docs] def getSelectMode(self):
return "browse"
def _getAllParams(self, protocol):
""" Return the list of all target parameters associated with this
protocol. This function is useful when more than one parameter is
associated to the wizard in the same protocol. """
for k, v in self._targets:
if k.__name__ == protocol.getClassName():
return v
return []
[docs]class PKPDChooseSeveralVariableWizard(PKPDChooseVariableWizard):
_targets = [(ProtPKPDDropMeasurements, ['varsToDrop']),
(ProtPKPDScaleToCommonDose, ['measurementsToChange'])]
[docs] def getTitle(self):
return "Choose variable(s)"
[docs] def getSelectMode(self):
return "extended"
[docs]class SimpleListTreeProvider(TreeProvider):
""" A simple TreeProvider over the elements of a string list """
def __init__(self, strList, name='Name', width=100):
self.objects = [pwobj.String(value=s) for s in strList]
self.columns = [(name, width)]
[docs] def getColumns(self):
return self.columns
[docs] def getObjects(self):
return self.objects
[docs] def getObjectInfo(self, obj):
key = obj.get()
return {'key': key, 'text': key,
'values': ()}
[docs]class PKPDVariableTemplateWizard(Wizard):
_targets = [(ProtPKPDImportFromText, ['variables'])]
[docs] def show(self, form, *params):
protocol = form.protocol
labels = self._getAllParams(protocol)
fnCSV = protocol.getAttributeValue('inputFile', "")
if not os.path.exists(fnCSV):
form.showError("Select a valid CSV input file first.")
else:
varNames = getVarNamesFromCSVfile(fnCSV)
tp = SimpleListTreeProvider(varNames, name="Variables")
dlg = dialog.ListDialog(form.root, "Choose variable(s)", tp,
selectmode='extended')
if dlg.resultYes():
strToAdd = ""
for value in dlg.values:
strToAdd += ("\n%s ; [Units/none] ; [numeric/text] ; "
"[time/label/measurement] ; [Comment]"
% (value.get()))
if strToAdd != "":
for label in labels:
currentValue = protocol.getAttributeValue(label, "")
form.setVar(label, currentValue+strToAdd)
def _getAllParams(self, protocol):
""" Return the list of all target parameters associated with this
protocol. This function is useful when more than one parameter is
associated to the wizard in the same protocol. """
for k, v in self._targets:
if k.__name__ == protocol.getClassName():
return v
return []
[docs]class PKPDDoseTemplateWizard(Wizard):
_targets = [(ProtPKPDImportFromText, ['doses']),
(ProtPKPDODESimulate, ['doses'])
]
[docs] def show(self, form, *params):
label = params[0]
protocol = form.protocol
currentValue = protocol.getAttributeValue(label, "")
template = ("\nInfusion0 ; via=Intravenous; infusion; t=0.5:0.75 h; "
"d=60*weight/1000 mg\n Bolus1 ; via=Oral; bolus; t=2 h; "
"d=100 mg\n Treatment ; via=Oral; repeated_bolus; "
"t=0:8:48 h; d=100 mg")
form.setVar(label, currentValue+template)
[docs]class PKPDDosesToSamplesTemplateWizard(Wizard):
_targets = [(ProtPKPDImportFromText, ['dosesToSamples'])
]
[docs] def show(self, form, *params):
label = params
protocol = form.protocol
fnCSV = protocol.getAttributeValue('inputFile', "")
if not os.path.exists(fnCSV):
form.showError("Select a valid CSV input file first.")
else:
doseNames = []
for line in protocol.doses.get().replace('\n',';;').split(';;'):
tokens = line.split(';')
if len(tokens)==4:
doseNames.append(tokens[0].strip())
sampleNamesInCSV = getSampleNamesFromCSVfile(fnCSV)
currentValue = protocol.getAttributeValue(label, "")
sampleNamesAssigned = []
for line in currentValue.replace('\n',';;').split(';;'):
tokens = line.split(';')
if len(tokens)==2:
sampleNamesAssigned.append(tokens[0].strip())
dlg = MultiListDialog(form.root, "Test",
[SimpleListTreeProvider(list(set(sampleNamesInCSV)-set(sampleNamesAssigned)),
name="Samples"),
SimpleListTreeProvider(doseNames,
name="Doses")],
selectmode='extended')
if dlg.resultYes():
sampleList = dlg.values[0]
doseList = dlg.values[1]
for sample in sampleList:
if currentValue!="":
currentValue+="\n"
currentValue+="%s; "%sample.get().strip()
doseNo = 1
for dose in doseList:
if doseNo!=1:
currentValue+=", %s"%dose.get()
else:
currentValue+="%s"%dose.get()
doseNo += 1
if currentValue!="":
form.setVar(label, currentValue)
[docs]class PKPDODEWizard(Wizard):
_targets = [(ProtPKPDMonoCompartment, ['bounds']),
(ProtPKPDMonoCompartmentConv, ['bounds']),
(ProtPKPDMonoCompartmentUrine, ['bounds']),
(ProtPKPDMonoCompartmentClint, ['bounds']),
(ProtPKPDMonoCompartmentLinkPD, ['bounds']),
(ProtPKPDMonoCompartmentPD, ['bounds']),
(ProtPKPDTwoCompartments, ['bounds']),
(ProtPKPDTwoCompartmentsConv, ['bounds']),
(ProtPKPDTwoCompartmentsUrine, ['bounds']),
(ProtPKPDTwoCompartmentsBoth, ['bounds']),
(ProtPKPDTwoCompartmentsBothPD, ['bounds']),
(ProtPKPDTwoCompartmentsClint, ['bounds']),
(ProtPKPDTwoCompartmentsClintCl, ['bounds']),
(ProtPKPDTwoCompartmentsClintMetabolite, ['bounds']),
(ProtPKPDTwoCompartmentsAutoinduction, ['bounds']),
(ProtPKPDThreeCompartments, ['bounds']),
(ProtPKPDGenericFit, ['bounds'])]
_nonODE = [ProtPKPDGenericFit]
[docs] def show(self, form, *params):
protocol = form.protocol
labels = self._getAllParams(protocol)
experiment = protocol.getAttributeValue('inputExperiment', None)
if experiment is None:
form.showError("Select the input experiment first.")
else:
# try:
protocol.setInputExperiment() # this load the experiment
if not type(protocol) in PKPDODEWizard._nonODE:
protocol.clearGroupParameters()
protocol.getXYvars()
if not type(protocol) in PKPDODEWizard._nonODE:
protocol.configureSource(protocol.createDrugSource())
protocol.setupModel()
if not type(protocol) in PKPDODEWizard._nonODE:
protocol.model.drugSource = protocol.drugSource
i = 0
for sampleName, sample in protocol.experiment.samples.items():
sample.interpretDose()
if i == 0:
if not type(protocol) in PKPDODEWizard._nonODE:
protocol.model.drugSource.setDoses(sample.parsedDoseList,0,1) # Needed to correctly identify the parameters of the source
protocol.model.setSample(sample)
protocol.calculateParameterUnits(sample)
i += 1
if not type(protocol) in PKPDODEWizard._nonODE:
dlg = PKPDODEDialog(form.root, "Select Parameter Bounds",
targetProtocol=protocol,
varNameX=protocol.predictor.get(),
varNameY=protocol.predicted.get())
else:
dlg = PKPDFitDialog(form.root, "Select Parameter Bounds",
targetProtocol=protocol,
varNameX=protocol.predictor.get(),
varNameY=protocol.predicted.get())
if dlg.resultYes():
boundStr = ""
i = 1
for bound in dlg.getBoundsList():
if i > 1:
boundStr += "; "
boundStr += str(bound)
i += 1
if boundStr != "":
for label in labels:
form.setVar(label, boundStr)
protocol.unsetExperiment()
# except Exception as e:
# pass
# form.showError("Error: %s" % str(e))
def _getAllParams(self, protocol):
""" Return the list of all target parameters associated with this
protocol. This function is useful when more than one parameter is
associated to the wizard in the same protocol. """
for k, v in self._targets:
if k.__name__ == protocol.getClassName():
return v
return []
[docs]class MultiListDialog(ListDialog):
"""
Select elements among several lists.
"""
def _createTree(self, parent):
treeFrame = tk.Frame(parent)
treeFrame.grid(row=0, column=0, sticky='news')
treeFrame.rowconfigure(0, weight=1)
self.trees = []
self.tree = None
for i, p in enumerate(self.provider):
t = BoundTree(treeFrame, p,
selectmode=self._selectmode)
t.grid(row=0, column=i, padx=5, pady=5, sticky='news')
treeFrame.columnconfigure(i, weight=1)
self.trees.append(t)
[docs] def apply(self):
self.values = []
for t in self.trees:
self.values.append(t.getSelectedObjects())