def plotClicked(plt, pts):
pt = pts[0]
#(id, fn, time) = pt.data
#[['SourceFile', 'ProtocolSequenceDir', 'fitTime']]
#fh = db.getDir('ProtocolSequence', id)[fn]
fh = pt.data()['SourceFile']
id = pt.data()['ProtocolSequenceDir']
time = pt.data()['fitTime']
data = fh.read()['Channel':'primary']
data = fn.besselFilter(data, 8e3)
p = pw2.plot(data, clear=True)
pos = time / data.xvals('Time')[-1]
arrow = pg.CurveArrow(p, pos=pos)
xr = pw2.viewRect().left(), pw2.viewRect().right()
if time < xr[0] or time > xr[1]:
w = xr[1]-xr[0]
pw2.setXRange(time-w/5., time+4*w/5., padding=0)
fitLen = pt.data()['fitDecayTau']*pt.data()['fitLengthOverDecay']
x = np.linspace(time, time+fitLen, fitLen * 50e3)
v = [pt.data()['fitAmplitude'], pt.data()['fitTime'], pt.data()['fitRiseTau'], pt.data()['fitDecayTau']]
y = fn.pspFunc(v, x, risePower=2.0) + data[np.argwhere(data.xvals('Time')>time)[0]-1]
pw2.plot(x, y, pen='b')
def processEventFits(events, startEvent, stopEvent, opts):
## This function does all the processing work for EventFitter.
dt = opts['dt']
origTau = opts['tau']
multiFit = opts['multiFit']
waveform = opts['waveform']
tvals = opts['tvals']
nFields = len(events.dtype.fields)
dtype = [(n, events[n].dtype) for n in events.dtype.names]
output = np.empty(len(events), dtype=dtype + [
('fitAmplitude', float),
('fitTime', float),
('fitRiseTau', float),
('fitDecayTau', float),
('fitTimeToPeak', float),
('fitError', float),
('fitFractionalError', float),
('fitLengthOverDecay', float),
])
offset = 0 ## not all input events will produce output events; offset keeps track of the difference.
outputState = {
'guesses': [],
'eventData': [],
'indexes': [],
'xVals': [],
'yVals': []
}
for i in range(startEvent, stopEvent):
start = events[i]['time']
#sliceLen = 50e-3
sliceLen = dt*300. ## Ca2+ events are much longer than 50ms
if i+1 < len(events):
nextStart = events[i+1]['time']
sliceLen = min(sliceLen, nextStart-start)
guessLen = events[i]['len']*dt
tau = origTau
if tau is not None:
guessLen += tau*2.
#print i, guessLen, tau, events[i]['len']*dt
#sliceLen = 50e-3
sliceLen = guessLen
if i+1 < len(events): ## cut slice back if there is another event coming up
nextStart = events[i+1]['time']
sliceLen = min(sliceLen, nextStart-start)
## Figure out from where to pull waveform data that will be fitted
startIndex = np.argwhere(tvals>=start)[0][0]
stopIndex = startIndex + int(sliceLen/dt)
eventData = waveform[startIndex:stopIndex]
times = tvals[startIndex:stopIndex]
#print i, startIndex, stopIndex, dt
if len(times) < 4: ## PSP fit requires at least 4 points; skip this one
offset += 1
continue
## reconvolve this chunk of the signal if it was previously deconvolved
if tau is not None:
eventData = functions.expReconvolve(eventData, tau=tau, dt=dt)
#print i, len(eventData)
## Make guesses as to the shape of the event
mx = eventData.max()
mn = eventData.min()
if mx > -mn:
peakVal = mx
else:
peakVal = mn
guessAmp = peakVal * 2 ## fit converges more reliably if we start too large
guessRise = guessLen/4.
guessDecay = guessLen/2.
guessStart = times[0]
zc = functions.zeroCrossingEvents(eventData - (peakVal/3.))
## eliminate events going the wrong direction
if len(zc) > 0:
if guessAmp > 0:
zc = zc[zc['peak']>0]
else:
zc = zc[zc['peak']<0]
#print zc
## measure properties for the largest event within 10ms of start
zc = zc[zc['index'] < 10e-3/dt]
if len(zc) > 0:
if guessAmp > 0:
zcInd = np.argmax(zc['sum']) ## the largest event in this clip
else:
zcInd = np.argmin(zc['sum']) ## the largest event in this clip
zcEv = zc[zcInd]
#guessLen = dt*zc[zcInd]['len']
guessRise = .1e-3 #dt*zcEv['len'] * 0.2
guessDecay = dt*zcEv['len'] * 0.8
guessStart = times[0] + dt*zcEv['index'] - guessRise*3.
## cull down the data set if possible
cullLen = zcEv['index'] + zcEv['len']*3
if len(eventData) > cullLen:
eventData = eventData[:cullLen]
times = times[:cullLen]
## fitting to exponential rise * decay
## parameters are [amplitude, x-offset, rise tau, fall tau]
guess = [guessAmp, guessStart, guessRise, guessDecay]
#guess = [amp, times[0], guessLen/4., guessLen/2.] ## careful!
bounds = [
sorted((guessAmp * 0.1, guessAmp)),
sorted((guessStart-min(guessRise, 0.01), guessStart+guessRise*2)),
sorted((dt*0.5, guessDecay)),
sorted((dt*0.5, guessDecay * 50.))
]
yVals = eventData.view(np.ndarray)
fit = functions.fitPsp(times, yVals, guess=guess, bounds=bounds, multiFit=multiFit)
computed = functions.pspFunc(fit, times)
peakTime = functions.pspMaxTime(fit[2], fit[3])
diff = (yVals - computed)
err = (diff**2).sum()
fracError = diff.std() / computed.std()
lengthOverDecay = (times[-1] - fit[1]) / fit[3] # ratio of (length of data that was fit : decay constant)
output[i-offset] = tuple(events[i]) + tuple(fit) + (peakTime, err, fracError, lengthOverDecay)
#output['fitTime'] += output['time']
#print fit
#self.events.append(eventData)
outputState['guesses'].append(guess)
outputState['eventData'].append(eventData)
outputState['indexes'].append(i)
outputState['xVals'].append(times)
outputState['yVals'].append(computed)
if offset > 0:
output = output[:-offset]
outputState['output'] = output
return outputState
def process(self, waveform, events, display=True):
self.deletedFits = []
for item in self.plotItems:
try:
item.sigClicked.disconnect(self.fitClicked)
except:
pass
self.plotItems = []
tau = waveform.infoCopy(-1).get('expDeconvolveTau', None)
dt = waveform.xvals(0)[1] - waveform.xvals(0)[0]
opts = {
'dt': dt, 'tau': tau, 'multiFit': self.ctrls['multiFit'].isChecked(),
'waveform': waveform.view(np.ndarray),
'tvals': waveform.xvals('Time'),
}
#if not self.ctrls['parallel'].isChecked():
output = processEventFits(events, startEvent=0, stopEvent=len(events), opts=opts)
guesses = output['guesses']
eventData = output['eventData']
indexes = output['indexes']
xVals = output['xVals']
yVals = output['yVals']
output = output['output']
#else:
#print "parallel:", self.pool, self.poolSize
#results = []
#nProcesses = self.ctrls['nProcesses'].value()
#evPerProcess = int(len(events) / nProcesses)
#start = 0
#for i in range(nProcesses):
#stop = start + evPerProcess
#if stop > len(events):
#stop = len(events)
#args = (events, start, stop, opts)
#results.append(self.pool.apply_async(processEventFits, args))
#print "started process", start, stop
#start = stop
#data = []
#guesses = []
#eventData = []
#indexes = []
#xVals = []
#yVals = []
#for res in results: ## reconstruct results here
#print "getting result", res
#output = res.get(10)
#data.append(output['output'])
#guesses.extend(output['guesses'])
#eventData.extend(output['eventData'])
#indexes.extend(output['indexes'])
#xVals.extend(output['xVals'])
#yVals.extend(output['yVals'])
#output = np.concatenate(data)
for i in range(len(indexes)):
if display and self['plot'].isConnected():
if self.ctrls['plotFits'].isChecked():
item = pg.PlotDataItem(x=xVals[i], y=yVals[i], pen=(0, 0, 255), clickable=True)
item.setZValue(100)
self.plotItems.append(item)
item.eventIndex = indexes[i]
item.sigClicked.connect(self.fitClicked)
item.deleted = False
if self.ctrls['plotGuess'].isChecked():
item2 = pg.PlotDataItem(x=xVals[i], y=functions.pspFunc(guesses[i], xVals[i]), pen=(255, 0, 0))
item2.setZValue(100)
self.plotItems.append(item2)
if self.ctrls['plotEvents'].isChecked():
item2 = pg.PlotDataItem(x=xVals[i], y=eventData[i], pen=(0, 255, 0))
item2.setZValue(100)
self.plotItems.append(item2)
#plot = self.plot.connections().keys()[0].node().getPlot()
#plot.addItem(item)
self.outputData = output
return {'output': output, 'plot': self.plotItems}
def displayData(self, fh, plot, pen, evTime=None, eventFilter=None):
"""
Display data for a single site in a plot--ephys trace, detected events
Returns all items added to the plot.
"""
pen = pg.mkPen(pen)
items = []
if isinstance(fh, basestring):
fh = self.source()[fh]
if fh.isDir():
fh = self.dataModel.getClampFile(fh)
## plot all data, incl. events
data = fh.read()['primary']
data = fn.besselFilter(data, 4e3)
pc = plot.plot(data, pen=pen, clear=False)
items.append(pc)
## mark location of event if an event index was given
if evTime is not None:
#pos = float(index)/len(data)
pos = evTime / data.xvals('Time')[-1]
#print evTime, data.xvals('Time')[-1], pos
#print index
arrow = pg.CurveArrow(pc, pos=pos)
plot.addItem(arrow)
items.append(arrow)
events = self.getEvents(fh)['events']
if eventFilter is not None:
events = eventFilter(events)
## draw ticks over all detected events
if len(events) > 0:
if 'fitTime' in events.dtype.names:
times = events['fitTime']
ticks = pg.VTickGroup(times, [0.9, 1.0], pen=pen)
plot.addItem(ticks)
items.append(ticks)
#self.mapTicks.append(ticks)
## draw event fits
evPen = pg.mkPen(pen)
c = evPen.color()
c.setAlpha(c.alpha()/2)
evPen.setColor(c)
for ev in events:
time = ev['fitTime']
try:
fitLen = ev['fitDecayTau']*ev['fitLengthOverDecay']
except IndexError:
fitLen = ev['fitDecayTau']*4.
x = np.linspace(time, time+fitLen, fitLen * 50e3)
v = [ev['fitAmplitude'], ev['fitTime'], ev['fitRiseTau'], ev['fitDecayTau']]
y = fn.pspFunc(v, x, risePower=2.0) + data[np.argwhere(data.xvals('Time')>time)[0]-1]
evc = plot.plot(x, y, pen=evPen)
evc.setZValue(pc.zValue()-100)
return items