示例#1
0
class PKPDResponsiveDialog(dialog.Dialog):
    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.values = []
        self.plotter = None
        self.targetProtocol = kwargs['targetProtocol']
        self.experiment = self.targetProtocol.experiment
        self.varNameX = kwargs['varNameX']
        self.varNameY = kwargs['varNameY']
        self.provider = SamplesTreeProvider(self.experiment)
        self.model = self.loadModel()
        self.validateSelectionCallback = kwargs.get('validateSelectionCallback', None)
        self.setLabels()

        dialog.Dialog.__init__(self, parent, title,
                        buttons=[('Select', dialog.RESULT_YES),
                                 ('Cancel', dialog.RESULT_CANCEL)])

    def setLabels(self):
        pass

    def loadModel(self):
        model = self.targetProtocol.createModel()
        model.setExperiment(self.experiment)
        # if hasattr(self.protODE, "deltaT"):
        #     model.deltaT = self.protODE.deltaT.get()
        model.setXVar(self.varNameX)
        model.setYVar(self.varNameY)
        return model

    def body(self, bodyFrame):
        bodyFrame.config(bg='white')
        gui.configureWeigths(bodyFrame)
        self._createSamplesFrame(bodyFrame)
        self._createSlidersFrame(bodyFrame)
        self._createLogsFrame(bodyFrame)

    def _createSamplesFrame(self, content):
        frame = tk.Frame(content, bg='white')
        #frame = tk.LabelFrame(content, text='General')
        lfSamples = tk.LabelFrame(frame, text="Samples", bg='white')
        gui.configureWeigths(frame)
        lfSamples.grid(row=0, column=0, sticky='news', padx=5, pady=5)
        self.samplesTree = self._addBoundTree(lfSamples,
                                                  self.provider, 10)
        self.samplesTree.itemClick = self._onSampleChanged

        frame.grid(row=0, column=0, sticky='news', padx=5, pady=5)

    def _createSlidersFrame(self, content):
        frame = tk.Frame(content, bg='white')
        lfBounds = tk.LabelFrame(frame, text="Parameter Bounds", bg='white')
        gui.configureWeigths(frame)

        i = 0
        self.sliders = {}
        paramUnits = self.targetProtocol.parameterUnits
        for paramName, bounds in self.targetProtocol.getParameterBounds().iteritems():
            bounds = bounds or (0, 1)
            slider = MinMaxSlider(lfBounds, "%s [%s]"%(paramName,strUnit(paramUnits[i])),
                                  bounds[0], bounds[1],
                                  callback=self._onVarChanged)
            slider.grid(row=i, column=0, padx=5, pady=5)
            self.sliders[paramName] = slider
            i += 1

        lfBounds.grid(row=0, column=0, sticky='news', padx=5, pady=5)
        frame.grid(row=0, column=1, sticky='news', padx=5, pady=5)

    def _createLogsFrame(self, content):
        frame = tk.Frame(content)

        def addVar(text, col, varName):
            varFrame = tk.Frame(frame)
            varFrame.grid(row=0, column=col, sticky='new')
            label = tk.Label(varFrame, text=text)#, font=self.fontBold)
            label.grid(row=0, column=0, padx=5, pady=2, sticky='nw')
            combo = tk.Label(varFrame, text=varName, width=10)
            combo.grid(row=0, column=1, sticky='nw', padx=5, pady=5)
            radioVar = tk.IntVar()
            radio = tk.Checkbutton(varFrame, text='Log10', variable=radioVar)
            radio.grid(row=0, column=2, sticky='nw', padx=5, pady=5)
            return combo, radio, radioVar

        self.timeWidget = addVar('Time variable', 0, self.varNameX)
        self.timeWidget[2].trace('w', self._onLogChanged)
        self.measureWidget = addVar('Measure variable', 1, self.varNameY)
        measureVar = self.measureWidget[2]
        measureVar.set(True)
        measureVar.trace('w', self._onLogChanged)
        frame.grid(row=1, column=0, columnspan=2, sticky='news', padx=5, pady=5)

    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

    def apply(self):
        self.values = []

    def _onVarChanged(self, *args):
        sampleKeys = self.samplesTree.selection()

        if sampleKeys:
            self.computeFit()
            self.plotResults()
        else:
            dialog.showInfo("Warning","Please select some sample(s) to plot.",self)

    def computeFit(self):
        currentParams = []
        for paramName in self.targetProtocol.getParameterNames():
            currentParams.append(self.sliders[paramName].getValue())

        self.targetProtocol.setParameters(currentParams)
        self.ypValues = self.targetProtocol.forwardModel(currentParams, self.xpValues)

    def getBoundsList(self):
        boundList = []
        for paramName in self.targetProtocol.getParameterNames():
            boundList.append(self.sliders[paramName].getMinMax())
        return boundList

    def useTimeLog(self):
        return self.timeWidget[2].get()

    def useMeasureLog(self):
        return self.measureWidget[2].get()

    def getUnits(self, varName):
        return self.experiment.variables[varName].getUnitsString()

    def getLabel(self, varName, useLog):
        varLabel = '%s [%s]' % (varName, self.getUnits(varName))
        if useLog:
            varLabel = "log10(%s)" % varLabel
        return varLabel

    def getTimeLabel(self):
        return self.getLabel(self.varNameX, self.useTimeLog())

    def getMeasureLabel(self):
        return self.getLabel(self.varNameY, self.useMeasureLog())

    def computePlotValues(self, xValues, yValues):
        useMeasureLog = self.useMeasureLog()
        useTimeLog = self.useTimeLog()

        if not (useMeasureLog or useTimeLog):
            newXValues = xValues
            newYValues = yValues
        else:
            # If log will be used either for time or measure var
            # we need to filter elements larger than 0
            newXValues = []
            newYValues = []

            def _value(v, useLog):
                if useLog:
                    return math.log10(v) if v > 0 else None
                return v

            for x, y in izip(xValues, yValues):
                x = _value(x, useTimeLog)
                y = _value(y, useMeasureLog)

                if x is not None and y is not None:
                    newXValues.append(x)
                    newYValues.append(y)

        return newXValues, newYValues

    def _updateModel(self):
        """ This function should be called whenever the sample changes """
        pass

    def _onLogChanged(self, *args):
        # We will treat a log change as a sample change to plot
        self._onSampleChanged()

    def _onSampleChanged(self, e=None):
        sampleKeys = self.samplesTree.selection()

        if sampleKeys:
            # When the sample is changed we need to re-compute (with log or not)
            # the x, y values
            self.sample = self.experiment.samples[sampleKeys[0]]
            self.xValues, self.yValues = self.sample.getXYValues(self.varNameX,
                                                                 self.varNameY)
            self.newXValues, self.newYValues = self.computePlotValues(self.xValues[0],
                                                                      self.yValues[0])
            self._updateModel()
            self.computeFit()
            self.plotResults()
        else:
            dialog.showInfo("Warning","Please select some sample(s) to plot.",self)

    def plotResults(self):
        if self.plotter is None or self.plotter.isClosed():
            self.plotter = EmPlotter()
            doShow = True
        else:
            doShow = False
            ax = self.plotter.getLastSubPlot()
            self.plotter.clear()

        ax = self.plotter.createSubPlot("Sample: %s" % self.sample.sampleName,
                                        self.getTimeLabel(),
                                        self.getMeasureLabel())
        self.newXPValues, self.newYPValues = self.computePlotValues(self.xpValues[0],
                                                                    self.ypValues[0])
        ax.plot(self.newXValues, self.newYValues, 'x', label="Observations")
        ax.plot(self.newXPValues, self.newYPValues, label="Fit")
        ax.legend()

        if doShow:
            self.plotter.show()
        else:
            self.plotter.draw()

    def destroy(self):
        """Destroy the window"""
        if not (self.plotter is None or self.plotter.isClosed()):
            self.plotter.close()
        dialog.Dialog.destroy(self)
示例#2
0
class ExperimentWindow(gui.Window):
    """ This class creates a Window that will display some Point's
    contained in a Data object.
    It will allow to launch 1D, 2D and 3D plots by selecting any
    combination of the x1, x2...xn from the Point dimension.
    Points can be selected by either Click and Drag in the Scatter plot or..
    by creating an Expression.
    Finally, there is a button 'Create Cluster' that will call a callback
    fuction to take care of it.
    """
    def __init__(self, **kwargs):
        gui.Window.__init__(self,  minsize=(420, 200), **kwargs)
        self.experiment = kwargs.get('experiment')
        self.fitting = kwargs.get('fitting', None)
        self.callback = kwargs.get('callback', None)
        content = tk.Frame(self.root)
        self._createContent(content)
        content.grid(row=0, column=0, sticky='news')
        content.columnconfigure(0, weight=1)
        content.rowconfigure(0, weight=1)
        self.plotter = None

    def _createContent(self, content):
        # Create and fill the frame containing the Experiment
        # info, variables and doses
        p = tk.PanedWindow(content, orient=tk.VERTICAL, bg='white')

        p.grid(row=0, column=0, sticky='news', padx=5, pady=5)

        self._createTopFrame(p)
        # Create the middle frame containing the Samples Box
        self._createSamplesFrame(p)
        # Create the last frame with the buttons
        self._createButtonsFrame(content)
        #self._updateSelectionLabel()

    def _createTopFrame(self, content):
        frame = tk.Frame(content)
        frame.columnconfigure(0, weight=1)
        frame.rowconfigure(0, weight=1)

        tab = ttk.Notebook(frame)
        tab.grid(row=0, column=0, sticky='news', padx=5, pady=5)

        def addTab(label):
            lf = tk.Frame(tab)
            tab.add(lf, text=label)
            return lf

        lfGeneral = addTab('General')
        self._addLabel(lfGeneral, 'Title', 0, 0)
        self._titleVar = tk.StringVar()
        self._titleVar.set(self.experiment.general['title'])
        titleEntry = tk.Entry(lfGeneral, width=26, textvariable=self._titleVar,
                              bg='white')
        titleEntry.grid(row=0, column=1, sticky='nw', padx=5, pady=(5, 0))
        self._addLabel(lfGeneral, 'Comment', 1, 0)
        commentText = gui.text.Text(lfGeneral, width=30, height=3, bg='white')
        commentText.setText(self.experiment.general['comment'])
        commentText.grid(row=1, column=1, sticky='nw', padx=5, pady=(5, 0))
        self._commentText = commentText

        lfVars = addTab('Variables')
        self.varsTree = self._addBoundTree(lfVars, VariablesTreeProvider, 5)

        lfVias = addTab('Vias')
        self.viasTree = self._addBoundTree(lfVias, ViasTreeProvider, 5)

        lfDoses = addTab('Doses')
        self.dosesTree = self._addBoundTree(lfDoses, DosesTreeProvider, 5)

        lfGroups = addTab('Groups')
        self.groupsTree = self._addBoundTree(lfGroups, GroupsTreeProvider, 5)

        # Fitting tab
        if self.fitting:
            tabFitting = addTab('Fitting')
            t = TaggedText(tabFitting, width=80, height=10, bg='white')
            t.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
            t.setText('Select one of the samples to see more information.')
            t.setReadOnly(True)
            self.fittingText = t
            # Buttons for fitting
            buttonsFrame = self._createFittingButtonsFrame(tabFitting)
            buttonsFrame.grid(row=0, column=1, sticky='news', padx=5, pady=5)

        #frame.grid(row=0, column=0, sticky='news', padx=5, pady=(10, 5))
        content.add(frame, sticky='news', padx=5, pady=5)

    def _createSamplesFrame(self, content):
        frame = tk.Frame(content)
        #frame = tk.LabelFrame(content, text='General')
        lfSamples = tk.LabelFrame(frame, text='Samples')
        gui.configureWeigths(frame)
        lfSamples.grid(row=0, column=0, sticky='news', padx=5, pady=5)
        self.samplesTree = self._addBoundTree(lfSamples, SamplesTreeProvider,
                                              10, fitting=self.fitting)
        self.samplesTree.itemDoubleClick = self._onSampleDoubleClick
        self.samplesTree.itemClick = self._onSampleClick

        plotFrame = tk.Frame(lfSamples)
        plotFrame.grid(row=1, column=0, sticky='ws', padx=5, pady=5)

        # Add a combobox with the variable for time
        timeVars = [v.varName for v in self.experiment.variables.values()
                    if v.role == v.ROLE_TIME]
        timeVars += [v.varName for v in self.experiment.variables.values()
                    if v.role == v.ROLE_MEASUREMENT]

        measureVars = [v.varName for v in self.experiment.variables.values()
                    if v.role == v.ROLE_MEASUREMENT]

        def addVar(text, col, choices):
            varFrame = tk.Frame(plotFrame)
            varFrame.grid(row=0, column=col, sticky='new')
            label = tk.Label(varFrame, text=text, font=self.fontBold)
            label.grid(row=0, column=0, padx=5, pady=2, sticky='nw')
            combo = ComboBox(varFrame, choices, width=10)
            combo.grid(row=0, column=1, sticky='nw', padx=5, pady=5)
            radioVar = tk.IntVar()
            radio = tk.Checkbutton(varFrame, text='Log10', variable=radioVar)
            radio.grid(row=0, column=2, sticky='nw', padx=5, pady=5)
            return combo, radio, radioVar

        self.timeWidget = addVar('Time variable', 0, timeVars)
        self.measureWidget = addVar('Measure variable', 1, measureVars)
        self.measureWidget[2].set(True)

        self.plotButton = Button(plotFrame, '   Plot   ', font=self.fontBold,
                                 command=self._onPlotClick,
                                 tooltip='Select one or more samples to plot '
                                         'their measures of the selected '
                                         'variables (optionally in log).')

        self.plotButton.grid(row=0, column=2, sticky='ne', padx=5)

        self.plotSummaryButton = Button(plotFrame, ' Summary Plot ',
                                        font=self.fontBold,
                                        command=self._onPlotSummaryClick,
                                        tooltip='Select several samples to plot'
                                                ' their statistics'
                                                ' (min, max, avg and std).')

        self.plotSummaryButton.grid(row=1, column=2, sticky='ne',
                                    padx=5, pady=5)

        #frame.grid(row=1, column=0, sticky='news', padx=5, pady=5)
        content.add(frame, sticky='news', padx=5, pady=5)

    def _createButtonsFrame(self, content):
        frame = tk.Frame(content)
        gui.configureWeigths(frame)
        buttonsFrame = tk.Frame(frame)
        buttonsFrame.grid(row=0, column=0, sticky='ne')
        closeButton = Button(buttonsFrame, 'Close', command=self.close,
                             imagePath='fa-times.png')
        closeButton.grid(row=0, column=0, sticky='ne', padx=5)
        self.newButton = HotButton(buttonsFrame, '   New Experiment   ',
                                   command=self._onCreateClick,
                                   tooltip='Create a new experiment with the '
                                            'selected samples. You can also edit'
                                            'title and comment.')

        self.newButton.grid(row=0, column=1, sticky='ne', padx=5)

        frame.grid(row=1, column=0, sticky='news', padx=5, pady=5)

    def _createFittingButtonsFrame(self, content):
        buttonsFrame = tk.Frame(content)
        buttonsFrame.grid(row=0, column=0, sticky='ne')

        plotValuesButton = Button(buttonsFrame, 'Plot Fit',
                                  command=self._onPlotFitClick)
        plotValuesButton.grid(row=0, column=0, sticky='sew', padx=5, pady=5)

        openValuesButton = Button(buttonsFrame, 'Open Fit',
                                  command=self._onOpenFitClick)
        openValuesButton.grid(row=1, column=0, sticky='sew', padx=5, pady=5)

        return buttonsFrame


    def _addLabel(self, parent, text, r, c):
        label = tk.Label(parent, text=text, font=self.fontBold)
        label.grid(row=r, column=c, padx=5, pady=5, sticky='ne')
        return label

    def _addBoundTree(self, parent, ProviderClass, height, **kwargs):
        bt = BoundTree(parent, ProviderClass(self.experiment, **kwargs),
                       height=height)
        bt.grid(row=0, column=0, sticky='news', padx=5, pady=5)
        gui.configureWeigths(parent)
        return bt

    def getUnits(self, varName):
        return self.experiment.variables[varName].getUnitsString()

    def getLabel(self, varName, useLog):
        varLabel = '%s [%s]' % (varName, self.getUnits(varName))
        if useLog:
            varLabel = "log10(%s)" % varLabel
        return varLabel

    def getTimeVarName(self):
        return self.timeWidget[0].getText()

    def useTimeLog(self):
        return self.timeWidget[2].get()

    def getTimeLabel(self):
        return self.getLabel(self.getTimeVarName(), self.useTimeLog())

    def getMeasureVarName(self):
        return self.measureWidget[0].getText()

    def useMeasureLog(self):
        return self.measureWidget[2].get()

    def getMeasureLabel(self):
        return self.getLabel(self.getMeasureVarName(), self.useMeasureLog())

    def getPlotValues(self, sample):
        xValues, yValues = sample.getXYValues(self.getTimeVarName(),
                                  self.getMeasureVarName())
        xValues=xValues[0] # From [array(...)] to array(...)
        yValues=yValues[0]

        useMeasureLog = self.useMeasureLog()
        useTimeLog = self.useTimeLog()

        if not (useMeasureLog or useTimeLog):
            return xValues, yValues

        # If log will be used either for time or measure var
        # we need to filter elements larger than 0
        newXValues = []
        newYValues = []

        def _value(v, useLog):
            if useLog:
                return math.log10(v) if v > 0 else None
            return v

        for x, y in izip(xValues, yValues):
            x = _value(x, useTimeLog)
            y = _value(y, useMeasureLog)

            if x is not None and y is not None:
                newXValues.append(x)
                newYValues.append(y)

        return newXValues, newYValues

    def _onPlotClick(self, e=None):
        sampleKeys = self.samplesTree.selection()

        if sampleKeys:
            if self.plotter is None or self.plotter.isClosed():
                self.plotter = EmPlotter()
                doShow = True
                ax = self.plotter.createSubPlot("Plot", self.getTimeLabel(),
                                                self.getMeasureLabel())
                self.plotDict = {}
            else:
                doShow = False
                ax = self.plotter.getLastSubPlot()

            samples = [self.experiment.samples[k] for k in sampleKeys]
            for s in samples:
                if not s.sampleName in self.plotDict:
                    x, y = self.getPlotValues(s)
                    ax.plot(x, y, label=s.sampleName)
                    self.plotDict[s.sampleName] = True
            leg = ax.legend()
            if leg:
                leg.draggable()

            if doShow:
                self.plotter.show()
            else:
                self.plotter.draw()
        else:
            self.showInfo("Please select some sample(s) to plot.")

    def _onPlotSummaryClick(self, e=None):
        sampleKeys = self.samplesTree.selection()
        n = len(sampleKeys)

        if n == 1:
            self.showInfo("Please select several samples to plot.")
        else:
            if n > 1:
                samples = [self.experiment.samples[k] for k in sampleKeys]
            else:
                samples = self.experiment.samples.values()

            dataDict = {} # key will be time values
            for s in samples:
                xValues, yValues = self.getPlotValues(s)
                for x, y in izip(xValues, yValues):
                    if x in dataDict:
                        dataDict[x].append(y)
                    else:
                        dataDict[x] = [y]

            sortedTime = sorted(dataDict.keys())
            # We will store five values (min, 25%, 50%, 75%, max)
            # for each of the time entries computed
            percentileList = [0, 25, 50, 75, 100]
            Y = np.zeros((len(sortedTime), 5))
            for i, t in enumerate(sortedTime):
                Y[i,:] = np.percentile(dataDict[t], percentileList)

            plotter = EmPlotter()
            ax = plotter.createSubPlot("Summary Plot", self.getTimeLabel(),
                                       self.getMeasureLabel())
            ax.plot(sortedTime, Y[:, 0], 'r--', label="Minimum")
            ax.plot(sortedTime, Y[:, 1], 'b--', label="25%")
            ax.plot(sortedTime, Y[:, 2], 'g', label="50% (Median)")
            ax.plot(sortedTime, Y[:, 3], 'b--', label="75%")
            ax.plot(sortedTime, Y[:, 4], 'r--', label="Maximum")

            ax.legend()
            plotter.show()

    def _onCreateClick(self, e=None):
        sampleKeys = self.samplesTree.selection()
        if sampleKeys and self.callback:
            self.callback()
        else:
            self.showInfo("Please select some sample(s) to create a new experiment.")

    def _onSampleClick(self, obj):
        # In fitting mode we need to display some information for
        # the given sample fit
        if self.fitting:
            selection = self.samplesTree.selection()
            if selection:
                sampleKey = selection[0]
                sampleFit = self.fitting.getSampleFit(sampleKey)
                textMsg = sampleFit.getBasicInfo()
            else:
                textMsg = 'Select one of the samples to see more information.'

            self.fittingText.setReadOnly(False)
            self.fittingText.setText(textMsg)
            self.fittingText.setReadOnly(True)

        if not (self.plotter is None or self.plotter.isClosed()):
            self._onPlotClick()

    def _onSampleDoubleClick(self, obj):
        sampleKeys = self.samplesTree.selection()
        if sampleKeys:
            MeasureWindow(masterWindow=self,
                          sample=self.experiment.samples[sampleKeys[0]]).show()

    def _onPlotFitClick(self, e=None):
        sampleKeys = self.samplesTree.selection()

        if sampleKeys:
            def _value(v, useLog):
                if useLog:
                    return math.log10(v) if v > 0 else None
                return v

            def _values(values, useLog=self.useMeasureLog()):
                return [_value(float(x), useLog) for x in values]

            def _plot(varLabelX, varLabelY, x, y, yp):
                plotter = EmPlotter()
                ax = plotter.createSubPlot("Plot", varLabelX, varLabelY)
                xValues = _values(x, useLog=self.useTimeLog())
                ax.plot(xValues, _values(y), 'x', label="Observations")
                idx = np.argsort(xValues)
                ypValues = _values(yp)
                ax.plot(np.asarray(xValues)[idx], np.asarray(ypValues)[idx], 'g', label="Fit")
                leg = ax.legend()
                if leg:
                    leg.draggable()

                plotter.show()

            # Get first selected element
            fit = self.fitting.getSampleFit(sampleKeys[0])
            if fit==None:
                return
            varLabelX = self.getLabel(self.fitting.predictor.varName,
                                      self.useTimeLog())
            if type(self.fitting.predicted)==list:
                i=0
                for v in self.fitting.predicted:
                    varLabelY = self.getLabel(v.varName, self.useMeasureLog())
                    _plot(varLabelX, varLabelY, fit.x[i], fit.y[i], fit.yp[i])
                    i+=1
            else:
                varLabelY = self.getLabel(self.fitting.predicted.varName,
                                          self.useMeasureLog())
                _plot(varLabelX, varLabelY, fit.x[0], fit.y[0], fit.yp[0])

        else:
            self.showInfo("Please select some sample(s) to plot.")

    def _onOpenFitClick(self, e=None):
        sampleKeys = self.samplesTree.selection()

        if sampleKeys:
            # Get first selected element
            fit = self.fitting.getSampleFit(sampleKeys[0])
            FitWindow(masterWindow=self,
                      fitting=self.fitting, sampleFit=fit).show()
        else:
            self.showInfo("Please select some sample(s) to plot.")

    def _onClosing(self):
        if self.plotter:
            self.plotter.close()
        gui.Window._onClosing(self)
示例#3
0
class PKPDResponsiveDialog(dialog.Dialog):
    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.values = []
        self.plotter = None
        self.targetProtocol = kwargs['targetProtocol']
        self.experiment = self.targetProtocol.experiment
        self.varNameX = kwargs['varNameX']
        self.varNameY = kwargs['varNameY']
        self.provider = SamplesTreeProvider(self.experiment)
        self.model = self.loadModel()
        self.validateSelectionCallback = kwargs.get(
            'validateSelectionCallback', None)
        self.setLabels()

        dialog.Dialog.__init__(self,
                               parent,
                               title,
                               buttons=[('Select', dialog.RESULT_YES),
                                        ('Cancel', dialog.RESULT_CANCEL)])

    def setLabels(self):
        pass

    def loadModel(self):
        model = self.targetProtocol.createModel()
        model.setExperiment(self.experiment)
        # if hasattr(self.protODE, "deltaT"):
        #     model.deltaT = self.protODE.deltaT.get()
        model.setXVar(self.varNameX)
        model.setYVar(self.varNameY)
        return model

    def body(self, bodyFrame):
        bodyFrame.config(bg='white')
        gui.configureWeigths(bodyFrame)
        self._createSamplesFrame(bodyFrame)
        self._createSlidersFrame(bodyFrame)
        self._createLogsFrame(bodyFrame)

    def _createSamplesFrame(self, content):
        frame = tk.Frame(content, bg='white')
        #frame = tk.LabelFrame(content, text='General')
        lfSamples = tk.LabelFrame(frame, text="Samples", bg='white')
        gui.configureWeigths(frame)
        lfSamples.grid(row=0, column=0, sticky='news', padx=5, pady=5)
        self.samplesTree = self._addBoundTree(lfSamples, self.provider, 10)
        self.samplesTree.itemClick = self._onSampleChanged

        frame.grid(row=0, column=0, sticky='news', padx=5, pady=5)

    def _createSlidersFrame(self, content):
        frame = tk.Frame(content, bg='white')
        lfBounds = tk.LabelFrame(frame, text="Parameter Bounds", bg='white')
        gui.configureWeigths(frame)

        i = 0
        self.sliders = {}
        paramUnits = self.targetProtocol.parameterUnits
        for paramName, bounds in self.targetProtocol.getParameterBounds(
        ).iteritems():
            bounds = bounds or (0, 1)
            slider = MinMaxSlider(lfBounds,
                                  "%s [%s]" %
                                  (paramName, strUnit(paramUnits[i])),
                                  bounds[0],
                                  bounds[1],
                                  callback=self._onVarChanged)
            slider.grid(row=i, column=0, padx=5, pady=5)
            self.sliders[paramName] = slider
            i += 1

        lfBounds.grid(row=0, column=0, sticky='news', padx=5, pady=5)
        frame.grid(row=0, column=1, sticky='news', padx=5, pady=5)

    def _createLogsFrame(self, content):
        frame = tk.Frame(content)

        def addVar(text, col, varName):
            varFrame = tk.Frame(frame)
            varFrame.grid(row=0, column=col, sticky='new')
            label = tk.Label(varFrame, text=text)  #, font=self.fontBold)
            label.grid(row=0, column=0, padx=5, pady=2, sticky='nw')
            combo = tk.Label(varFrame, text=varName, width=10)
            combo.grid(row=0, column=1, sticky='nw', padx=5, pady=5)
            radioVar = tk.IntVar()
            radio = tk.Checkbutton(varFrame, text='Log10', variable=radioVar)
            radio.grid(row=0, column=2, sticky='nw', padx=5, pady=5)
            return combo, radio, radioVar

        self.timeWidget = addVar('Time variable', 0, self.varNameX)
        self.timeWidget[2].trace('w', self._onLogChanged)
        self.measureWidget = addVar('Measure variable', 1, self.varNameY)
        measureVar = self.measureWidget[2]
        measureVar.set(True)
        measureVar.trace('w', self._onLogChanged)
        frame.grid(row=1,
                   column=0,
                   columnspan=2,
                   sticky='news',
                   padx=5,
                   pady=5)

    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

    def apply(self):
        self.values = []

    def _onVarChanged(self, *args):
        sampleKeys = self.samplesTree.selection()

        if sampleKeys:
            self.computeFit()
            self.plotResults()
        else:
            dialog.showInfo("Warning", "Please select some sample(s) to plot.",
                            self)

    def computeFit(self):
        currentParams = []
        for paramName in self.targetProtocol.getParameterNames():
            currentParams.append(self.sliders[paramName].getValue())

        self.targetProtocol.setParameters(currentParams)
        self.ypValues = self.targetProtocol.forwardModel(
            currentParams, self.xpValues)

    def getBoundsList(self):
        boundList = []
        for paramName in self.targetProtocol.getParameterNames():
            boundList.append(self.sliders[paramName].getMinMax())
        return boundList

    def useTimeLog(self):
        return self.timeWidget[2].get()

    def useMeasureLog(self):
        return self.measureWidget[2].get()

    def getUnits(self, varName):
        return self.experiment.variables[varName].getUnitsString()

    def getLabel(self, varName, useLog):
        varLabel = '%s [%s]' % (varName, self.getUnits(varName))
        if useLog:
            varLabel = "log10(%s)" % varLabel
        return varLabel

    def getTimeLabel(self):
        return self.getLabel(self.varNameX, self.useTimeLog())

    def getMeasureLabel(self):
        return self.getLabel(self.varNameY, self.useMeasureLog())

    def computePlotValues(self, xValues, yValues):
        useMeasureLog = self.useMeasureLog()
        useTimeLog = self.useTimeLog()

        if not (useMeasureLog or useTimeLog):
            newXValues = xValues
            newYValues = yValues
        else:
            # If log will be used either for time or measure var
            # we need to filter elements larger than 0
            newXValues = []
            newYValues = []

            def _value(v, useLog):
                if useLog:
                    return math.log10(v) if v > 0 else None
                return v

            for x, y in izip(xValues, yValues):
                x = _value(x, useTimeLog)
                y = _value(y, useMeasureLog)

                if x is not None and y is not None:
                    newXValues.append(x)
                    newYValues.append(y)

        return newXValues, newYValues

    def _updateModel(self):
        """ This function should be called whenever the sample changes """
        pass

    def _onLogChanged(self, *args):
        # We will treat a log change as a sample change to plot
        self._onSampleChanged()

    def _onSampleChanged(self, e=None):
        sampleKeys = self.samplesTree.selection()

        if sampleKeys:
            # When the sample is changed we need to re-compute (with log or not)
            # the x, y values
            self.sample = self.experiment.samples[sampleKeys[0]]
            self.xValues, self.yValues = self.sample.getXYValues(
                self.varNameX, self.varNameY)
            self.newXValues, self.newYValues = self.computePlotValues(
                self.xValues[0], self.yValues[0])
            self._updateModel()
            self.computeFit()
            self.plotResults()
        else:
            dialog.showInfo("Warning", "Please select some sample(s) to plot.",
                            self)

    def plotResults(self):
        if self.plotter is None or self.plotter.isClosed():
            self.plotter = EmPlotter()
            doShow = True
        else:
            doShow = False
            ax = self.plotter.getLastSubPlot()
            self.plotter.clear()

        ax = self.plotter.createSubPlot("Sample: %s" % self.sample.sampleName,
                                        self.getTimeLabel(),
                                        self.getMeasureLabel())
        self.newXPValues, self.newYPValues = self.computePlotValues(
            self.xpValues[0], self.ypValues[0])
        ax.plot(self.newXValues, self.newYValues, 'x', label="Observations")
        ax.plot(self.newXPValues, self.newYPValues, label="Fit")
        ax.legend()

        if doShow:
            self.plotter.show()
        else:
            self.plotter.draw()

    def destroy(self):
        """Destroy the window"""
        if not (self.plotter is None or self.plotter.isClosed()):
            self.plotter.close()
        dialog.Dialog.destroy(self)