def _visualize(self, obj, **kwargs):
fnResults = self.protocol._getPath("results.txt")
if exists(fnResults):
X, Y, _, _ = self.protocol.getXYValues(False)
minX = min(X)
maxX = max(X)
step = (maxX - minX) / 50
xValues = np.arange(minX, maxX + step, step)
yValues = self.protocol.evalFunction(xValues)
plotter = EmPlotter(style='seaborn-whitegrid')
varNameX = self.protocol.labelX.get()
varNameY = self.protocol.labelY.get()
ax = plotter.createSubPlot(
"Regression Plot", "%s [%s]" %
(varNameX,
strUnit(
self.protocol.experiment.variables[varNameX].units.unit)),
"%s [%s]" %
(varNameY,
strUnit(
self.protocol.experiment.variables[varNameY].units.unit)))
ax.plot(xValues, yValues)
ax.plot(X, Y, 'o')
return [plotter]
else:
return [
self.errorMessage("Result file '%s' not produced yet. " %
fnResults)
]
def _onPlotClick(self, e=None):
sampleKeys = self.samplesTree.selection()
if sampleKeys:
if self.plotter is None or self.plotter.isClosed():
self.plotter = EmPlotter(style='seaborn-whitegrid',
figure=self.reuseFigure())
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 or not doShow:
x, y = self.getPlotValues(s)
label = s.sampleName
if not doShow:
label += " " + self.getTimeVarName(
) + " vs " + self.getMeasureVarName()
ax.plot(x, y, label=label)
self.plotDict[s.sampleName] = True
leg = ax.legend()
if leg:
leg.set_draggable(True)
if doShow:
self.plotter.show()
else:
self.plotter.draw()
else:
self.showInfo("Please select some sample(s) to plot.")
def paint(self, labels):
for label in labels:
labelValue = self.monitor.getData()[label[0]]
color = label[1]
if label == 'standard_deviation':
self.lines[label[0]], = self.ax2.plot(labelValue,
'-o',
label=label[0],
color=color)
if label == 'ratio1':
self.lines[label[0]], = self.ax.plot(
labelValue, '-o', label='97.5/2.5 percentile', color=color)
if label == 'ratio2':
self.lines[label[0]], = self.ax.plot(
labelValue, '-*', label='max/97.5 percentile', color=color)
self.legend()
anim = animation.FuncAnimation(self.fig,
self.animate,
interval=self.monitor.samplingInterval *
1000) # miliseconds
self.fig.canvas.mpl_connect('scroll_event', self.onscroll)
self.fig.canvas.mpl_connect('key_press_event', self.press)
EmPlotter.show(self)
def visualize(self, obj, **kwargs):
prot = obj
fnProfiles = prot._getPath("profiles.txt")
fh = open(fnProfiles,"r")
state = 0
legends = ['Iliver', 'Iinlet', 'Isys']
for line in fh:
if state==0:
tokens = line.split("::")
title = tokens[1].strip()
I3=[]
state=1
elif state==1:
tokens=line.strip().split()
if len(tokens)==0:
plotter = EmPlotter(style='seaborn-whitegrid')
ax = plotter.createSubPlot("Simulation", "t [h]", "[I] [mg/mL]")
t = np.asarray(I3[0],dtype=np.float64)/60
for n in range(1,len(I3)):
y = np.asarray(I3[n],dtype=np.float64)
ax.plot(t, y, label=legends[n-1])
ax.legend()
plotter.show()
state=0
else:
if len(I3)==0:
for n in range(len(tokens)):
I3.append([])
for n in range(len(tokens)):
I3[n].append(tokens[n])
fh.close()
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 = list(self.experiment.samples.values())
xmin = 1e38
xmax = -1e38
for s in samples:
xValues, _ = self.getPlotValues(s)
xmin = min(xmin, min(xValues))
xmax = max(xmax, max(xValues))
dataDict = {} # key will be time values
xrange = np.arange(xmin, xmax, (xmax - xmin) / 300.0)
for s in samples:
xValues, yValues = self.getPlotValues(s)
xValuesUnique, yValuesUnique = uniqueFloatValues(
xValues, yValues)
B = InterpolatedUnivariateSpline(xValuesUnique,
yValuesUnique,
k=1)
yrange = B(xrange)
for x, y in izip(xrange, yrange):
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(style='seaborn-whitegrid',
figure=self.reuseFigure())
# *** Pending
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.grid(True)
ax.legend()
plotter.show()
def press(self, event):
sys.stdout.flush()
if event.key == 'S':
self.stop = True
self.ax.set_title('Plot is Stopped. Press C to continue plotting')
elif event.key == 'C':
self.ax.set_title(self._getTitle())
self.stop = False
self.animate()
EmPlotter.show(self)
def onscroll(self, event):
if event.button == 'up':
self.win += self.step
else:
self.win -= self.step
if self.win < self.step:
self.win = self.step
if self.oldWin != self.win:
self.ax.set_title(self._getTitle())
self.oldWin = self.win
self.animate()
EmPlotter.show(self)
def _plot(varLabelX, varLabelY, x, y, yp):
plotter = EmPlotter(style='seaborn-whitegrid',
figure=self.reuseFigure())
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.set_draggable(True)
plotter.show()
def paint(self, labels):
for label in labels:
labelValue = self.monitor.getData()[label]
color = self.color[label]
self.lines[label], = self.ax.plot(labelValue,
'-',
label=label,
color=color)
self.ax.legend()
anim = animation.FuncAnimation(self.fig,
self.animate,
interval=self.monitor.samplingInterval *
1000) # miliseconds
self.fig.canvas.mpl_connect('scroll_event', self.onscroll)
self.fig.canvas.mpl_connect('key_press_event', self.press)
EmPlotter.show(self)
def __init__(self, monitor):
EmPlotter.__init__(self, windowTitle="Movie Gain Monitor")
self.monitor = monitor
self.y2 = 0.
self.y1 = 100.
self.win = 250 # number of samples to be plotted
self.step = 50 # self.win will be modified in steps of this size
self.createSubPlot(self._getTitle(), "", "")
self.fig = self.getFigure()
self.ax = self.getLastSubPlot()
self.ax2 = self.ax.twinx()
self.ax2.margins(0.05)
self.oldWin = self.win
self.lines = {}
self.init = True
self.stop = False
def __init__(self, monitor):
EmPlotter.__init__(self, windowTitle="CTF Monitor")
self.monitor = monitor
self.y2 = 0.
self.y1 = 100.
self.win = 250 # number of samples to be ploted
self.step = 50 # self.win will be modified in steps of this size
self.createSubPlot(self._getTitle(), "Micrographs", "Defocus (A)")
self.fig = self.getFigure()
self.ax = self.getLastSubPlot()
self.ax.margins(0.05)
self.ax.grid(True)
self.oldWin = self.win
self.lines = {}
self.init = True
self.stop = False
def __init__(self, monitor, nifName=None):
EmPlotter.__init__(self, windowTitle="system Monitor")
self.monitor = monitor
self.y2 = 0.
self.y1 = 100.
self.win = 250 # number of samples to be ploted
self.step = 50 # self.win will be modified in steps of this size
self.createSubPlot(self._getTitle(), "time (hours)",
"percentage (or MB for IO or NetWork)")
self.fig = self.getFigure()
self.ax = self.getLastSubPlot()
self.ax.margins(0.05)
self.ax.grid(True)
self.oldWin = self.win
self.lines = {}
self.init = True
self.stop = False
self.nifName = nifName
def plotResults(self):
if self.plotter is None or self.plotter.isClosed():
self.plotter = EmPlotter(style='seaborn-whitegrid')
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 visualize(self, obj, **kwargs):
model = PKPDAllometricScale()
model.load(obj.fnScale.get())
x = np.log10(np.asarray(model.X))
xlabel = "%s [%s]" % (model.predictor, model.predictorUnits)
for varName, varUnits in model.scaled_vars:
plotter = EmPlotter(style='seaborn-whitegrid')
y = np.log10(np.asarray(model.Y[varName]))
ylabel = "%s [%s]" % (varName, varUnits)
ax = plotter.createSubPlot(varName, xlabel, ylabel)
ax.plot(x, y, '.', label='Species')
ax.plot(x,
np.log10(model.models[varName][0]) +
x * model.models[varName][1],
'r',
label='R2=%f' % model.qualifiers[varName][0])
leg = ax.legend(loc='upper right')
if leg:
leg.draggable()
plotter.show()
for varName, varUnits in model.averaged_vars:
plotter = EmPlotter(style='seaborn-whitegrid')
y = np.asarray(model.Y[varName])
ylabel = "%s [%s]" % (varName, varUnits)
ax = plotter.createSubPlot("Scatter Plot", xlabel, ylabel)
ax.plot(x, y, '.', label='Species')
ax.plot(x,
model.models[varName][0] * np.ones(x.shape),
'r',
label='Std=%f' % model.qualifiers[varName][0])
leg = ax.legend(loc='upper right')
if leg:
leg.draggable()
plotter.show()
def _onPlotClick(self, e=None):
selection = self.tree.selection()
n = len(selection)
if n < 1 or n > 2:
self.showError("Select one or two variables to plot.")
else:
plotter = EmPlotter(style='seaborn-whitegrid')
varX = self._variables[selection[0]]
xValues = self.observations[:, varX.index]
def _label(var):
return "%s [%s]" % (var.varName, var.unitStr)
if n == 1:
plotter.createSubPlot("Histogram", _label(varX), "Count")
plotter.plotHist(xValues, 50)
else: # n == 2
varY = self._variables[selection[1]]
yValues = self.observations[:, varY.index]
ax = plotter.createSubPlot("Scatter Plot", _label(varX),
_label(varY))
ax.plot(xValues, yValues, '.')
plotter.show()
def __init__(self, x=1, y=1, mainTitle="", **kwargs):
EmPlotter.__init__(self, x, y, mainTitle, **kwargs)
def press(self, event):
def numericKey(key):
self.colorChanged = True
number = int(key)
index = 3 + number * 3
if (index + 3) > self.lenPlots:
return
if self.color['gpuMem_%d' % number] != 'w':
self.oldColor['gpuMem_%d' % number] = \
self.color['gpuMem_%d' % number]
self.oldColor['gpuUse_%d' % number] = \
self.color['gpuUse_%d' % number]
self.oldColor['gpuTem_%d' % number] = \
self.color['gpuTem_%d' % number]
self.color['gpuMem_%d' % number] = "w"
self.color['gpuUse_%d' % number] = "w"
self.color['gpuTem_%d' % number] = "w"
else:
self.color['gpuMem_%d' % number] = \
self.oldColor['gpuMem_%d' % number]
self.color['gpuUse_%d' % number] = \
self.oldColor['gpuUse_%d' % number]
self.color['gpuTem_%d' % number] = \
self.oldColor['gpuTem_%d' % number]
def cpuKey(key):
self.colorChanged = True
if self.color['cpu'] != 'w':
self.oldColor['cpu'] = self.color['cpu']
self.oldColor['mem'] = self.color['mem']
self.oldColor['swap'] = self.color['swap']
self.color['cpu'] = "w"
self.color['mem'] = "w"
self.color['swap'] = "w"
else:
self.color['cpu'] = self.oldColor['cpu']
self.color['swap'] = self.oldColor['swap']
self.color['mem'] = self.oldColor['mem']
def netKey(key):
self.colorChanged = True
if self.color['%s_send' % self.nifName] != 'w':
self.oldColor['%s_send' % self.nifName] = \
self.color['%s_send' % self.nifName]
self.oldColor['%s_recv' % self.nifName] = \
self.color['%s_recv' % self.nifName]
self.color['%s_send' % self.nifName] = "w"
self.color['%s_recv' % self.nifName] = "w"
else:
self.color['%s_send' % self.nifName] = \
self.oldColor['%s_send' % self.nifName]
self.color['%s_recv' % self.nifName] = \
self.oldColor['%s_recv' % self.nifName]
def diskKey(key):
self.colorChanged = True
if self.color['disk_read'] != 'w':
self.oldColor['disk_read'] = self.color['disk_read']
self.oldColor['disk_write'] = self.color['disk_write']
self.color['disk_read'] = "w"
self.color['disk_write'] = "w"
else:
self.color['disk_read'] = self.oldColor['disk_read']
self.color['disk_write'] = self.oldColor['disk_write']
sys.stdout.flush()
if event.key == 'S':
self.stop = True
self.ax.set_title('Plot has been Stopped. '
'Press C to continue plotting')
elif event.key == 'C':
self.ax.set_title(self._getTitle())
self.stop = False
self.animate()
elif event.key.isdigit():
numericKey(event.key)
self.animate()
elif event.key == 'c':
cpuKey(event.key)
self.animate()
elif event.key == 'n':
netKey(event.key)
self.animate()
elif event.key == 'd':
diskKey(event.key)
self.animate()
EmPlotter.show(self)
def visualize(self, obj, **kwargs):
prot = obj
auc = np.genfromtxt(prot._getExtraPath('errorAUC.txt'))
cmax = np.genfromtxt(prot._getExtraPath('errorCmax.txt'))
plotter = EmPlotter(style='seaborn-whitegrid')
plotter.createSubPlot("Histogram of error AUC0t", "Error AUC0t", "Count")
plotter.plotHist(auc[~np.isnan(auc)], 50)
plotter.show()
plotter = EmPlotter(style='seaborn-whitegrid')
plotter.createSubPlot("Histogram of error Cmax", "Error Cmax", "Count")
plotter.plotHist(cmax[~np.isnan(cmax)], 50)
plotter.show()
sortedTimeTrue, Ytrue = self.getSummary(prot.inputExperiment.get().fnPKPD)
sortedTimeSimulated, Ysimulated = self.getSummary(prot.inputSimulated.get().fnPKPD)
plotter = EmPlotter(style='seaborn-whitegrid')
ax = plotter.createSubPlot("Summary Plot", self.timeVarName, self.CVarName)
ax.plot(sortedTimeTrue, Ytrue[:, 0], 'r--', label="Minimum In-vivo", linewidth=2)
ax.plot(sortedTimeTrue, Ytrue[:, 1], 'b--', label="25% In-vivo", linewidth=2)
ax.plot(sortedTimeTrue, Ytrue[:, 2], 'g', label="50% (Median) In-vivo", linewidth=2)
ax.plot(sortedTimeTrue, Ytrue[:, 3], 'b--', label="75% In-vivo", linewidth=2)
ax.plot(sortedTimeTrue, Ytrue[:, 4], 'r--', label="Maximum In-vivo", linewidth=2)
ax.plot(sortedTimeSimulated, Ysimulated[:, 0], 'r--', label="Minimum Simulated")
ax.plot(sortedTimeSimulated, Ysimulated[:, 1], 'b--', label="25% Simulated")
ax.plot(sortedTimeSimulated, Ysimulated[:, 2], 'g', label="50% (Median) Simulated")
ax.plot(sortedTimeSimulated, Ysimulated[:, 3], 'b--', label="75% Simulated")
ax.plot(sortedTimeSimulated, Ysimulated[:, 4], 'r--', label="Maximum Simulated")
ax.grid(True)
ax.legend()
plotter.show()
plotter = EmPlotter(style='seaborn-whitegrid')
ax = plotter.createSubPlot("Mean Plot", self.timeVarName, self.CVarName)
ax.plot(sortedTimeTrue, Ytrue[:, 2], 'g', label="50% (Median) In-vivo", linewidth=2)
ax.plot(sortedTimeSimulated, Ysimulated[:, 2], 'g', label="50% (Median) Simulated")
ax.grid(True)
ax.legend()
plotter.show()
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()
if 'title' in self.experiment.general:
self._titleVar.set(self.experiment.general['title'])
else:
self._titleVar.set("")
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')
if 'comment' in self.experiment.general:
commentText.setText(self.experiment.general['comment'])
else:
commentText.setText("")
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')
if len(choices) == 0:
choices = ['']
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,
list(set(measureVars + timeVars)))
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.useCurrentPlotVar = tk.IntVar()
self.useCurrentPlot = tk.Checkbutton(plotFrame,
text='Use current plot',
variable=self.useCurrentPlotVar)
self.useCurrentPlot.grid(row=1, column=0, sticky='nw', padx=5, pady=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 reuseFigure(self):
return None if not self.useCurrentPlotVar.get() else 'active'
def _onPlotClick(self, e=None):
sampleKeys = self.samplesTree.selection()
if sampleKeys:
if self.plotter is None or self.plotter.isClosed():
self.plotter = EmPlotter(style='seaborn-whitegrid',
figure=self.reuseFigure())
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 or not doShow:
x, y = self.getPlotValues(s)
label = s.sampleName
if not doShow:
label += " " + self.getTimeVarName(
) + " vs " + self.getMeasureVarName()
ax.plot(x, y, label=label)
self.plotDict[s.sampleName] = True
leg = ax.legend()
if leg:
leg.set_draggable(True)
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 = list(self.experiment.samples.values())
xmin = 1e38
xmax = -1e38
for s in samples:
xValues, _ = self.getPlotValues(s)
xmin = min(xmin, min(xValues))
xmax = max(xmax, max(xValues))
dataDict = {} # key will be time values
xrange = np.arange(xmin, xmax, (xmax - xmin) / 300.0)
for s in samples:
xValues, yValues = self.getPlotValues(s)
xValuesUnique, yValuesUnique = uniqueFloatValues(
xValues, yValues)
B = InterpolatedUnivariateSpline(xValuesUnique,
yValuesUnique,
k=1)
yrange = B(xrange)
for x, y in izip(xrange, yrange):
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(style='seaborn-whitegrid',
figure=self.reuseFigure())
# *** Pending
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.grid(True)
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(style='seaborn-whitegrid',
figure=self.reuseFigure())
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.set_draggable(True)
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)
def visualize(self, obj, **kwargs):
self.prot = obj
plotter = EmPlotter(style='seaborn-whitegrid')
title = "Summary plot" if self.prot.showSummary else "Individual plots"
ax = plotter.createSubPlot("Summary Plot", self.prot.X1.get(),
self.prot.Y1.get())
if self.prot.twoExperiments.get() == 0:
X2 = self.prot.X1.get() if self.prot.X2.get(
) == "" else self.prot.X2.get()
Y2 = self.prot.Y1.get() if self.prot.Y2.get(
) == "" else self.prot.Y2.get()
sortedX1, Y1 = self.getData(
self.prot.inputExperiment1.get().fnPKPD, self.prot.X1.get(),
self.prot.Y1.get())
sortedX2, Y2 = self.getData(
self.prot.inputExperiment2.get().fnPKPD, X2, Y2)
if self.prot.showSummary:
ax.plot(sortedX1,
Y1[:, 0],
'r--',
label="Minimum Exp1",
linewidth=2)
ax.plot(sortedX1,
Y1[:, 1],
'b--',
label="25% Exp1",
linewidth=2)
ax.plot(sortedX1,
Y1[:, 2],
'g',
label="50% (Median) Exp1",
linewidth=2)
ax.plot(sortedX1,
Y1[:, 3],
'b--',
label="75% Exp1",
linewidth=2)
ax.plot(sortedX1,
Y1[:, 4],
'r--',
label="Maximum Exp1",
linewidth=2)
ax.plot(sortedX2, Y2[:, 0], 'r--', label="Minimum Exp2")
ax.plot(sortedX2, Y2[:, 1], 'b--', label="25% Exp2")
ax.plot(sortedX2, Y2[:, 2], 'g', label="50% (Median) Exp2")
ax.plot(sortedX2, Y2[:, 3], 'b--', label="75% Exp2")
ax.plot(sortedX2, Y2[:, 4], 'r--', label="Maximum Exp2")
else:
ax.plot(sortedX1, Y1, linewidth=2, label="Exp1")
ax.plot(sortedX2, Y2, label="Exp2")
else:
listColors = ['b', 'g', 'r', 'k', 'c', 'm', 'y']
for idx, experimentPtr in enumerate(self.prot.inputExperiments):
sortedX, Y = self.getData(experimentPtr.get().fnPKPD,
self.prot.X1.get(),
self.prot.Y1.get())
if self.prot.showSummary:
ax.plot(sortedX,
Y[:, 0],
linestyle='--',
color=listColors[idx],
label="Minimum Exp%d" % idx)
ax.plot(sortedX,
Y[:, 1],
linestyle='--',
color=listColors[idx],
label="25%% Exp%d" % idx)
ax.plot(sortedX,
Y[:, 2],
color=listColors[idx],
label="50%% (Median) Exp%d" % idx)
ax.plot(sortedX,
Y[:, 3],
linestyle='--',
color=listColors[idx],
label="75%% Exp%d" % idx)
ax.plot(sortedX,
Y[:, 4],
linestyle='--',
color=listColors[idx],
label="Maximum Exp%d" % idx)
else:
ax.plot(sortedX,
Y[:, 0],
color=listColors[idx],
label="Exp%d" % idx)
ax.plot(sortedX, Y[:, 1:], color=listColors[idx])
ax.legend()
ax.grid(True)
plotter.show()
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().items():
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(style='seaborn-whitegrid')
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)
def visualize(self, obj, **kwargs):
prot = obj
fn = prot._getExtraPath('D11.txt')
if os.path.exists(fn):
D11 = genfromtxt(fn)
plotter = EmPlotter(style='seaborn-whitegrid')
plotter.createSubPlot("Histogram of D11", "D11", "Count")
plotter.plotHist(D11[~isnan(D11)], 50)
plotter.show()
fn = prot._getExtraPath('D12.txt')
if os.path.exists(fn):
D12 = genfromtxt(fn)
plotter = EmPlotter(style='seaborn-whitegrid')
plotter.createSubPlot("Histogram of D12", "D12", "Count")
plotter.plotHist(D12[~isnan(D12)], 50)
plotter.show()
def visualize(self, obj, **kwargs):
prot = obj
fnProfiles = prot._getPath("profiles.txt")
fh = open(fnProfiles, "r")
Rtype = []
Rlegends = []
R = []
state = 0
for line in fh:
if state == 0:
tokens = line.split("::")
Rtype.append(tokens[0])
Rlegends.append(tokens[1].strip())
Ri = []
state = 1
elif state == 1:
tokens = line.strip().split()
if len(tokens) == 0:
R.append(Ri)
state = 0
else:
if len(Ri) == 0:
for n in range(len(tokens)):
Ri.append([])
for n in range(len(tokens)):
Ri[n].append(tokens[n])
fh.close()
plotter = None
previousType = ""
for legend, Ri, Rtypei in izip(Rlegends, R, Rtype):
if plotter is None or Rtypei != previousType:
if previousType != "":
self.addLimits(plotter, previousType, minX, maxX)
plotter = EmPlotter(style='seaborn-whitegrid')
doShow = True
if Rtypei == "ReversibleLiver" or Rtypei == "TimeDependentLiver" or Rtypei == "InductionLiver" or Rtypei == "StaticLiver" or Rtypei == "TransporterLiver":
Ilabel = "[Ih] [uM]"
elif Rtypei == "ReversibleGut" or Rtypei == "TimeDependentGut" or Rtypei == "InductionGut" or Rtypei == "StaticGut" or Rtypei == "TransporterGut":
Ilabel = "[Ig] [uM]"
elif Rtypei == "TransporterRenal":
Ilabel = "[Cmax] [uM]"
ax = plotter.createSubPlot("Plot", Ilabel, "R")
previousType = Rtypei
minX = None
maxX = None
else:
doShow = False
ax = plotter.getLastSubPlot()
x = np.asarray(Ri[0], dtype=np.float64)
if len(Ri) == 2:
y = np.asarray(Ri[1], dtype=np.float64)
else:
y = np.asarray(Ri[2], dtype=np.float64)
ax.plot(x, y, label=legend)
minXi = np.min(x)
maxXi = np.max(x)
if minX == None:
minX = minXi
maxX = maxXi
minX = min(minXi, minX)
maxX = min(maxXi, maxX)
leg = ax.legend()
if leg:
leg.draggable()
if doShow:
plotter.show()
else:
plotter.draw()
self.addLimits(plotter, previousType, minX, maxX)
def visualize(self, obj, **kwargs):
prot = obj
f1 = genfromtxt(prot._getExtraPath('f1.txt'))
f2 = genfromtxt(prot._getExtraPath('f2.txt'))
plotter = EmPlotter(style='seaborn-whitegrid')
plotter.createSubPlot("Histogram of f1", "f1", "Count")
plotter.plotHist(f1[~isnan(f1)], 50)
plotter.show()
plotter = EmPlotter(style='seaborn-whitegrid')
plotter.createSubPlot("Histogram of f2", "f2", "Count")
plotter.plotHist(f2[~isnan(f2)], 50)
plotter.show()