def update(self):
pos = self.dev.getPosition()
for i in range(3):
if i not in self.posLabels:
continue
text = pg.siFormat(pos[i], suffix='m', precision=5)
self.posLabels[i].setText(text)
def valueString(self, param):
units = param.opts.get('units', None)
if isinstance(units, basestring) and len(units) > 0:
val = pg.siFormat(param.value(), suffix=units, space='*', precision=5, allowUnicode=False)
else:
val = '%0.5g' % param.value()
return val
def update(self):
pos = self.dev.getPosition()
#for i in [0,1,2]:
#if pos[i] < self.limit
text = [pg.siFormat(x, suffix='m', precision=5) for x in pos]
self.ui.xPosLabel.setText(text[0])
self.ui.yPosLabel.setText(text[1])
self.ui.zPosLabel.setText(text[2])
def update(self):
pos = self.dev.getPosition()
#for i in [0,1,2]:
#if pos[i] < self.limit
text = [pg.siFormat(x, suffix='m', precision=5) for x in pos]
self.ui.xPosLabel.setText(text[0])
self.ui.yPosLabel.setText(text[1])
self.ui.zPosLabel.setText(text[2])
def valueString(self, param):
units = param.opts.get('units', None)
if isinstance(units, basestring) and len(units) > 0:
val = pg.siFormat(param.value(),
suffix=units,
space='*',
precision=5,
allowUnicode=False)
else:
val = '%0.5g' % param.value()
return val
def sendStatusMessage(self, iter, maxIter, depthIndex, depths):
if maxIter == 0:
itermsg = 'iter=%d' % (iter+1)
else:
itermsg = 'iter=%d/%s' % (iter+1, maxIter)
if depthIndex is None:
depthmsg = ''
else:
depthstr = pg.siFormat(depths[depthIndex], suffix='m')
depthmsg = 'depth=%s %d/%d' % (depthstr, depthIndex+1, len(depths))
self.sigMessage.emit('[ running %s %s ]' % (itermsg, depthmsg))
def updateLimits(self):
limits = self.dev.getLimits()
cap = self.dev.capabilities()
for axis in (0, 1, 2):
if not cap['limits'][axis]:
continue
for i, limit in enumerate(limits[axis]):
check = self.limitChecks[axis][i]
pfx = ('Min:', 'Max:')[i]
if limit is None:
check.setText(pfx)
check.setChecked(False)
else:
check.setText(pfx + ' %s' % pg.siFormat(limit, suffix='m'))
check.setChecked(True)
def paint(self, p, *args):
pg.LineSegmentROI.paint(self, p, *args)
h1 = self.handles[0]['item'].pos()
h2 = self.handles[1]['item'].pos()
p1 = p.transform().map(h1)
p2 = p.transform().map(h2)
vec = pg.Point(h2) - pg.Point(h1)
length = vec.length()
angle = vec.angle(pg.Point(1, 0))
pvec = p2 - p1
pvecT = pg.Point(pvec.y(), -pvec.x())
pos = 0.5 * (p1 + p2) + pvecT * 40 / pvecT.length()
p.resetTransform()
txt = pg.siFormat(length, suffix='m') + '\n%0.1f deg' % angle
p.drawText(QtCore.QRectF(pos.x() - 50,
pos.y() - 50, 100, 100),
QtCore.Qt.AlignCenter | QtCore.Qt.AlignVCenter, txt)
def update(self):
pos = self.dev.getPosition()
text = [pg.siFormat(x, suffix='m', precision=5) for x in pos]
self.label.setText(", ".join(text))
def valueChanged(self, param, val):
strs = tuple([pg.siFormat(x, suffix='m') for x in val])
self.setText(1, '[%s, %s, %s]' % strs)
def update(self):
pos = self.dev.getPosition()
for i in range(3):
text = pg.siFormat(pos[i], suffix="m", precision=5)
self.posLabels[i].setText(text)
def showErrorAnalysis(self):
if not hasattr(self, 'errorMap'):
filename = self.dev.configFileName('error_map.np')
self.errorMap = np.load(open(filename, 'rb'))[np.newaxis][0]
err = self.errorMap
imx = pg.image(err['err'][..., 0].transpose(1, 0, 2), title='X error')
imy = pg.image(err['err'][..., 1], title='Y error')
imz = pg.image(err['err'][..., 2], title='Z error')
# get N,3 array of offset values used to randomize hysteresis
off = np.vstack(err['offsets'])
sh = err['err'].shape
# Get N,3 array of measured position errors
errf = err['err'].reshape(sh[0] * sh[1] * sh[2], 3)[err['order']]
# Display histogram of errors
win = pg.GraphicsWindow(title="%s error" % self.dev.name())
# subtract out slow drift
normErr = errf - scipy.ndimage.gaussian_filter(errf, (20, 0))
# calculate magnitude of error
absErr = (normErr**2).sum(axis=1)**0.5
# errPlot.plot(absErr)
title = "Error Histogram (mean=%s)" % pg.siFormat(absErr.mean(),
suffix='m')
errPlot = win.addPlot(row=0,
col=0,
title=title,
labels={'bottom': ('Position error', 'm')})
hist = np.histogram(absErr, bins=50)
errPlot.plot(hist[1], hist[0], stepMode=True)
# display drift and hysteresis plots
driftPlot = win.addPlot(row=0,
col=1,
rowspan=1,
colspan=2,
title="Pipette Drift",
labels={
'left': ('Position error', 'm'),
'bottom': ('Time', 's')
})
driftPlot.plot(np.linspace(0, err['time'], errf.shape[0]),
errf[:, 0],
pen='r')
driftPlot.plot(np.linspace(0, err['time'], errf.shape[0]),
errf[:, 1],
pen='g')
driftPlot.plot(np.linspace(0, err['time'], errf.shape[0]),
errf[:, 2],
pen='b')
xhplot = win.addPlot(row=1,
col=0,
title='X Hysteresis',
labels={
'left': ('Position error', 'm'),
'bottom': ('Last pipette movement', 'm')
})
xhplot.plot(-off[:, 0], errf[:, 0], pen=None, symbol='o')
yhplot = win.addPlot(row=1,
col=1,
title='Y Hysteresis',
labels={
'left': ('Position error', 'm'),
'bottom': ('Last pipette movement', 'm')
})
yhplot.plot(-off[:, 1], errf[:, 1], pen=None, symbol='o')
zhplot = win.addPlot(row=1,
col=2,
title='Z Hysteresis',
labels={
'left': ('Position error', 'm'),
'bottom': ('Last pipette movement', 'm')
})
zhplot.plot(-off[:, 2], errf[:, 2], pen=None, symbol='o')
# Print best fit for manipulator axes
expPos = err['inds'] * err['stepSize']
measPos = expPos + off
guess = np.array([[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 1, 0]],
dtype='float')
def errFn(v):
return ((measPos -
np.dot(expPos, v.reshape(3, 4))[:, :3])**2).sum()
fit = scipy.optimize.minimize(errFn, guess)
print("Pipette position transform:", fit)
self.errorMapAnalysis = (imx, imy, imz, win)
def __init__(self, dev):
self.dev = dev
Qt.QWidget.__init__(self)
self.layout = Qt.QVBoxLayout()
self.setLayout(self.layout)
chans = self.dev.listChannels()
self.widgets = {}
#self.uis = {}
self.defaults = {}
row = 0
for ch in chans:
wid = Qt.QWidget()
ui = DeviceTemplate.Ui_Form()
ui.setupUi(wid)
self.layout.addWidget(wid)
ui.analogCtrls = [
ui.scaleDefaultBtn, ui.scaleSpin, ui.offsetDefaultBtn,
ui.offsetSpin, ui.scaleLabel, ui.offsetLabel
]
#ui.channel = ch
for s in dir(ui):
i = getattr(ui, s)
if isinstance(i, Qt.QWidget):
i.channel = ch
self.widgets[ch] = ui
ui.nameLabel.setText(str(ch))
ui.channelCombo.addItem("%s (%s)" % (ch, chans[ch]['channel']))
holding = chans[ch].get('holding', 0)
if chans[ch]['type'] in ['ao', 'ai']:
ui.inputRadio.setEnabled(False)
ui.outputRadio.setEnabled(False)
ui.invertCheck.hide()
scale = chans[ch].get('scale', 1)
units = chans[ch].get('units', 'V')
offset = chans[ch].get('offset', 0)
ui.offsetSpin.setOpts(suffix='V',
siPrefix=True,
dec=True,
step=1.0,
minStep=1e-4)
ui.offsetSpin.setValue(offset)
ui.offsetSpin.sigValueChanged.connect(self.offsetSpinChanged)
ui.offsetDefaultBtn.setText("Default (%s)" %
siFormat(offset, suffix='V'))
ui.offsetDefaultBtn.clicked.connect(
self.offsetDefaultBtnClicked)
if chans[ch]['type'] == 'ao':
ui.outputRadio.setChecked(True)
ui.scaleDefaultBtn.setText(
"Default (%s)" % siFormat(scale, suffix='V/' + units))
ui.scaleSpin.setOpts(suffix='V/' + units,
siPrefix=True,
dec=True,
step=1.0,
minStep=1e-9)
ui.holdingSpin.setOpts(suffix=units,
siPrefix=True,
step=0.01)
ui.holdingSpin.setValue(holding)
ui.holdingSpin.sigValueChanged.connect(
self.holdingSpinChanged)
elif chans[ch]['type'] == 'ai':
ui.inputRadio.setChecked(True)
ui.holdingLabel.hide()
ui.holdingSpin.hide()
ui.scaleDefaultBtn.setText(
"Default (%s)" % siFormat(scale, suffix=units + '/V'))
#ui.scaleDefaultBtn.clicked.connect(self.scaleDefaultBtnClicked)
ui.scaleSpin.setOpts(suffix=units + '/V',
siPrefix=True,
dec=True)
ui.scaleSpin.setValue(scale)
ui.scaleDefaultBtn.clicked.connect(self.scaleDefaultBtnClicked)
ui.scaleSpin.sigValueChanged.connect(self.scaleSpinChanged)
self.defaults[ch] = {'scale': scale, 'offset': offset}
elif chans[ch]['type'] in ['do', 'di']:
for item in ui.analogCtrls:
item.hide()
if chans[ch].get('invert', False):
ui.invertCheck.setChecked(True)
if chans[ch]['type'] == 'do':
ui.outputRadio.setChecked(True)
ui.holdingSpin.setOpts(bounds=[0, 1], step=1)
ui.holdingSpin.setValue(holding)
ui.holdingSpin.sigValueChanged.connect(
self.holdingSpinChanged)
elif chans[ch]['type'] == 'di':
ui.inputRadio.setChecked(True)
ui.holdingLabel.hide()
ui.holdingSpin.hide()
ui.invertCheck.toggled.connect(self.invertToggled)
#Qt.QObject.connect(self.dev, Qt.SIGNAL('holdingChanged'), self.holdingChanged)
self.dev.sigHoldingChanged.connect(self.holdingChanged)
def showCell(**kwds):
pw2.clear()
reloadData = kwds.get('reloadData', False)
#global lock
#if lock:
#return
#lock = True
Qt.QApplication.processEvents() ## prevents double-spin
#lock = False
cell = cells[cellCombo.currentIndex() - 1]
dh = cell #db.getDir('Cell', cell)
loadCell(dh, reloadData=reloadData)
try:
image.setImage(dh['morphology.png'].read())
gv.setRange(image.sceneBoundingRect())
except:
image.setImage(np.zeros((2, 2)))
pass
ev, numExSites, numInSites = events[cell]
ev2 = select(ev, ex=True)
ev3 = select(ev, ex=False)
if colorCheck.isChecked():
sp1.hide()
sp2.hide()
sp3.hide()
sp4.show()
start = postRgnStart()
stop = postRgnStop()
ev2post = ev2[(ev2['fitTime'] > start) * (ev2['fitTime'] < stop)]
ev3post = ev3[(ev3['fitTime'] > start) * (ev3['fitTime'] < stop)]
ev4 = np.concatenate([ev2post, ev3post])
yMax = ev4['dorsal'].max()
yMin = ev4['dorsal'].min()
brushes = []
for i in range(len(ev4)):
hue = 0.6 * ((ev4[i]['dorsal'] - yMin) / (yMax - yMin))
brushes.append(pg.hsvColor(hue, 1.0, 1.0, 0.3))
#pts.append({
#'pos': (ev4[i]['fitDecayTau'], ev4[i]['fitAmplitude']),
#'brush': pg.hsvColor(hue, 1, 1, 0.3),
#'data': ev4[i]
#})
sp4.setData(x=ev4['fitDecayTau'],
y=ev4['fitAmplitude'],
symbolBrush=brushes,
data=ev4)
else:
sp1.show()
sp2.show()
#sp3.show()
sp4.hide()
## excitatory
if separateCheck.isChecked():
pre = ev2[ev2['fitTime'] < preRgnStop()]
post = ev2[(ev2['fitTime'] > postRgnStart()) *
(ev2['fitTime'] < postRgnStop())]
else:
pre = ev2
sp1.setData(x=pre['fitDecayTau'], y=pre['fitAmplitude'], data=pre)
#print "Cell ", cell
#print " excitatory:", np.median(ev2['fitDecayTau']), np.median(ev2['fitAmplitude'])
## inhibitory
if separateCheck.isChecked():
pre = ev3[ev3['fitTime'] < preRgnStop()]
post2 = ev3[(ev3['fitTime'] > postRgnStart()) *
(ev3['fitTime'] < postRgnStop())]
post = np.concatenate([post, post2])
else:
pre = ev3
sp2.setData(x=pre['fitDecayTau'], y=pre['fitAmplitude'], data=pre)
#print " inhibitory:", np.median(ev2['fitDecayTau']), np.median(ev2['fitAmplitude'])
if separateCheck.isChecked():
sp3.setData(x=post['fitDecayTau'],
y=post['fitAmplitude'],
data=post)
sp3.show()
else:
sp3.hide()
try:
typ = ev2[0]['CellType']
except:
typ = ev3[0]['CellType']
sr = spontRate(ev2, numExSites)
sri = spontRate(ev3, numInSites)
title = "%s -- %s --- <span style='color: #99F;'>ex:</span> %s %s %s %0.1fHz --- <span style='color: #F99;'>in:</span> %s %s %s %0.1fHz" % (
dh.name(relativeTo=dh.parent().parent().parent()), typ,
pg.siFormat(np.median(ev2['fitTimeToPeak']),
error=np.std(ev2['fitTimeToPeak']),
space=False,
suffix='s'),
pg.siFormat(np.median(ev2['fitDecayTau']),
error=np.std(ev2['fitDecayTau']),
space=False,
suffix='s'),
pg.siFormat(np.median(ev2['fitAmplitude']),
error=np.std(ev2['fitAmplitude']),
space=False,
suffix='A'), sr,
pg.siFormat(np.median(ev3['fitTimeToPeak']),
error=np.std(ev3['fitTimeToPeak']),
space=False,
suffix='s'),
pg.siFormat(np.median(ev3['fitDecayTau']),
error=np.std(ev3['fitDecayTau']),
space=False,
suffix='s'),
pg.siFormat(np.median(ev3['fitAmplitude']),
error=np.std(ev3['fitAmplitude']),
space=False,
suffix='A'), sri)
print(re.sub(r'<[^>]+>', '', title))
pw1.setTitle(title)
### show cell in atlas
#rec = db.select('CochlearNucleus_Cell', where={'CellDir': cell})
#pts = []
#if len(rec) > 0:
#pos = (rec[0]['right'], rec[0]['anterior'], rec[0]['dorsal'])
#pts = [{'pos': pos, 'size': 100e-6, 'color': (0.7, 0.7, 1.0, 1.0)}]
### show event positions
evSpots = {}
for rec in ev:
p = (rec['right'], rec['anterior'], rec['dorsal'])
evSpots[p] = None
pos = np.array(list(evSpots.keys()))
atlasPoints.setData(pos=pos, )
def update(self):
pos = self.dev.getPosition()
text = [pg.siFormat(x, suffix="m", precision=5) for x in pos]
self.label.setText(", ".join(text))
def __init__(self, dev):
self.dev = dev
QtGui.QWidget.__init__(self)
self.layout = QtGui.QVBoxLayout()
self.setLayout(self.layout)
chans = self.dev.listChannels()
self.widgets = {}
#self.uis = {}
self.defaults = {}
row = 0
for ch in chans:
wid = QtGui.QWidget()
ui = DeviceTemplate.Ui_Form()
ui.setupUi(wid)
self.layout.addWidget(wid)
ui.analogCtrls = [ui.scaleDefaultBtn, ui.scaleSpin, ui.offsetDefaultBtn, ui.offsetSpin, ui.scaleLabel, ui.offsetLabel]
#ui.channel = ch
for s in dir(ui):
i = getattr(ui, s)
if isinstance(i, QtGui.QWidget):
i.channel = ch
self.widgets[ch] = ui
ui.nameLabel.setText(str(ch))
ui.channelCombo.addItem("%s (%s)" % (ch, chans[ch]['channel']))
holding = chans[ch].get('holding', 0)
if chans[ch]['type'] in ['ao', 'ai']:
ui.inputRadio.setEnabled(False)
ui.outputRadio.setEnabled(False)
ui.invertCheck.hide()
scale = chans[ch].get('scale', 1)
units = chans[ch].get('units', 'V')
offset = chans[ch].get('offset', 0)
ui.offsetSpin.setOpts(suffix = 'V', siPrefix=True, dec=True, step=1.0, minStep=1e-4)
ui.offsetSpin.setValue(offset)
ui.offsetSpin.sigValueChanged.connect(self.offsetSpinChanged)
ui.offsetDefaultBtn.setText("Default (%s)" % siFormat(offset, suffix='V'))
ui.offsetDefaultBtn.clicked.connect(self.offsetDefaultBtnClicked)
if chans[ch]['type'] == 'ao':
ui.outputRadio.setChecked(True)
ui.scaleDefaultBtn.setText("Default (%s)" % siFormat(scale, suffix='V/'+units))
ui.scaleSpin.setOpts(suffix= 'V/'+units, siPrefix=True, dec=True, step=1.0, minStep=1e-9)
ui.holdingSpin.setOpts(suffix=units, siPrefix=True, step=0.01)
ui.holdingSpin.setValue(holding)
ui.holdingSpin.sigValueChanged.connect(self.holdingSpinChanged)
elif chans[ch]['type'] == 'ai':
ui.inputRadio.setChecked(True)
ui.holdingLabel.hide()
ui.holdingSpin.hide()
ui.scaleDefaultBtn.setText("Default (%s)" % siFormat(scale, suffix=units+'/V'))
#ui.scaleDefaultBtn.clicked.connect(self.scaleDefaultBtnClicked)
ui.scaleSpin.setOpts(suffix= units+'/V', siPrefix=True, dec=True)
ui.scaleSpin.setValue(scale)
ui.scaleDefaultBtn.clicked.connect(self.scaleDefaultBtnClicked)
ui.scaleSpin.sigValueChanged.connect(self.scaleSpinChanged)
self.defaults[ch] = {
'scale': scale,
'offset': offset}
elif chans[ch]['type'] in ['do', 'di']:
for item in ui.analogCtrls:
item.hide()
if chans[ch].get('invert', False):
ui.invertCheck.setChecked(True)
if chans[ch]['type'] == 'do':
ui.outputRadio.setChecked(True)
ui.holdingSpin.setOpts(bounds=[0,1], step=1)
ui.holdingSpin.setValue(holding)
ui.holdingSpin.sigValueChanged.connect(self.holdingSpinChanged)
elif chans[ch]['type'] == 'di':
ui.inputRadio.setChecked(True)
ui.holdingLabel.hide()
ui.holdingSpin.hide()
ui.invertCheck.toggled.connect(self.invertToggled)
#QtCore.QObject.connect(self.dev, QtCore.SIGNAL('holdingChanged'), self.holdingChanged)
self.dev.sigHoldingChanged.connect(self.holdingChanged)
def handleNewFrame(self, frame):
prof = Profiler('PatchWindow.handleNewFrame', disabled=True)
with self.paramLock:
mode = self.params['mode']
data = frame['data'][self.clampName]
if mode == 'vc':
self.ui.patchPlot.setLabel('left', units='A')
else:
self.ui.patchPlot.setLabel('left', units='V')
prof.mark('1')
self.patchCurve.setData(data.xvals('Time'), data['primary'])
prof.mark('2')
if self.redrawCommand > 0:
self.redrawCommand -= 1
#print "set command curve"
self.commandCurve.setData(data.xvals('Time'), data['command'])
if mode == 'vc':
self.ui.commandPlot.setLabel('left', units='V')
else:
self.ui.commandPlot.setLabel('left', units='A')
prof.mark('3')
#self.ui.patchPlot.replot()
#self.ui.commandPlot.replot()
if frame['analysis']['fitTrace'] is not None:
self.patchFitCurve.show()
self.patchFitCurve.setData(data.xvals('Time'),
frame['analysis']['fitTrace'])
else:
self.patchFitCurve.hide()
prof.mark('4')
for k in self.analysisItems:
if k in frame['analysis']:
self.analysisData[k].append(frame['analysis'][k])
prof.mark('5')
for r in ['input', 'access']:
res = r + 'Resistance'
label = getattr(self.ui, res + 'Label')
resistance = frame['analysis'][res]
label.setText(siFormat(resistance) + u'Ω')
prof.mark('6')
self.ui.restingPotentialLabel.setText(
siFormat(frame['analysis']['restingPotential'],
error=frame['analysis']['restingPotentialStd'],
suffix='V'))
self.ui.restingCurrentLabel.setText(
siFormat(frame['analysis']['restingCurrent'],
error=frame['analysis']['restingCurrentStd'],
suffix='A'))
self.ui.capacitanceLabel.setText(
'%sF' % siFormat(frame['analysis']['capacitance']))
self.ui.fitErrorLabel.setText('%7.2g' % frame['analysis']['fitError'])
prof.mark('7')
start = data._info[-1]['DAQ']['command']['startTime']
if self.startTime is None:
self.startTime = start
if self.ui.recordBtn.isChecked() and self.storageFile is not None:
self.storageFile.setInfo({'startTime': self.startTime})
self.analysisData['time'].append(start - self.startTime)
prof.mark('8')
self.updateAnalysisPlots()
prof.mark('9')
## Record to disk if requested.
if self.ui.recordBtn.isChecked():
arr = self.makeAnalysisArray(lastOnly=True)
#print "appending array", arr.shape
if self.storageFile is None:
self.newFile(arr)
else:
arr.write(self.storageFile.name(), appendAxis='Time')
prof.mark('10')
prof.finish()
def handleNewFrame(self, frame):
prof = Profiler('PatchWindow.handleNewFrame', disabled=True)
with self.paramLock:
mode = self.params['mode']
data = frame['data'][self.clampName]
if mode == 'vc':
self.ui.patchPlot.setLabel('left', units='A')
else:
self.ui.patchPlot.setLabel('left', units='V')
prof.mark('1')
self.patchCurve.setData(data.xvals('Time'), data['primary'])
prof.mark('2')
if self.redrawCommand > 0:
self.redrawCommand -= 1
#print "set command curve"
self.commandCurve.setData(data.xvals('Time'), data['command'])
if mode == 'vc':
self.ui.commandPlot.setLabel('left', units='V')
else:
self.ui.commandPlot.setLabel('left', units='A')
prof.mark('3')
#self.ui.patchPlot.replot()
#self.ui.commandPlot.replot()
if frame['analysis']['fitTrace'] is not None:
self.patchFitCurve.show()
self.patchFitCurve.setData(data.xvals('Time'), frame['analysis']['fitTrace'])
else:
self.patchFitCurve.hide()
prof.mark('4')
for k in self.analysisItems:
if k in frame['analysis']:
self.analysisData[k].append(frame['analysis'][k])
prof.mark('5')
for r in ['input', 'access']:
res = r+'Resistance'
label = getattr(self.ui, res+'Label')
resistance = frame['analysis'][res]
label.setText(siFormat(resistance) + u'Ω')
prof.mark('6')
self.ui.restingPotentialLabel.setText(siFormat(frame['analysis']['restingPotential'], error=frame['analysis']['restingPotentialStd'], suffix='V'))
self.ui.restingCurrentLabel.setText(siFormat(frame['analysis']['restingCurrent'], error=frame['analysis']['restingCurrentStd'], suffix='A'))
self.ui.capacitanceLabel.setText('%sF' % siFormat(frame['analysis']['capacitance']))
self.ui.fitErrorLabel.setText('%7.2g' % frame['analysis']['fitError'])
prof.mark('7')
start = data._info[-1]['DAQ']['command']['startTime']
if self.startTime is None:
self.startTime = start
if self.ui.recordBtn.isChecked() and self.storageFile is not None:
self.storageFile.setInfo({'startTime': self.startTime})
self.analysisData['time'].append(start - self.startTime)
prof.mark('8')
self.updateAnalysisPlots()
prof.mark('9')
## Record to disk if requested.
if self.ui.recordBtn.isChecked():
arr = self.makeAnalysisArray(lastOnly=True)
#print "appending array", arr.shape
if self.storageFile is None:
self.newFile(arr)
else:
arr.write(self.storageFile.name(), appendAxis='Time')
prof.mark('10')
prof.finish()
def showCell(**kwds):
pw2.clear()
reloadData = kwds.get('reloadData', False)
#global lock
#if lock:
#return
#lock = True
QtGui.QApplication.processEvents() ## prevents double-spin
#lock = False
cell = cells[cellCombo.currentIndex()-1]
dh = cell #db.getDir('Cell', cell)
loadCell(dh, reloadData=reloadData)
try:
image.setImage(dh['morphology.png'].read())
gv.setRange(image.sceneBoundingRect())
except:
image.setImage(np.zeros((2,2)))
pass
ev, numExSites, numInSites = events[cell]
ev2 = select(ev, ex=True)
ev3 = select(ev, ex=False)
if colorCheck.isChecked():
sp1.hide()
sp2.hide()
sp3.hide()
sp4.show()
start = postRgnStart()
stop = postRgnStop()
ev2post = ev2[(ev2['fitTime']>start) * (ev2['fitTime']<stop)]
ev3post = ev3[(ev3['fitTime']>start) * (ev3['fitTime']<stop)]
ev4 = np.concatenate([ev2post, ev3post])
yMax = ev4['dorsal'].max()
yMin = ev4['dorsal'].min()
brushes = []
for i in range(len(ev4)):
hue = 0.6*((ev4[i]['dorsal']-yMin) / (yMax-yMin))
brushes.append(pg.hsvColor(hue, 1.0, 1.0, 0.3))
#pts.append({
#'pos': (ev4[i]['fitDecayTau'], ev4[i]['fitAmplitude']),
#'brush': pg.hsvColor(hue, 1, 1, 0.3),
#'data': ev4[i]
#})
sp4.setData(x=ev4['fitDecayTau'], y=ev4['fitAmplitude'], symbolBrush=brushes, data=ev4)
else:
sp1.show()
sp2.show()
#sp3.show()
sp4.hide()
## excitatory
if separateCheck.isChecked():
pre = ev2[ev2['fitTime']< preRgnStop()]
post = ev2[(ev2['fitTime'] > postRgnStart()) * (ev2['fitTime'] < postRgnStop())]
else:
pre = ev2
sp1.setData(x=pre['fitDecayTau'], y=pre['fitAmplitude'], data=pre);
#print "Cell ", cell
#print " excitatory:", np.median(ev2['fitDecayTau']), np.median(ev2['fitAmplitude'])
## inhibitory
if separateCheck.isChecked():
pre = ev3[ev3['fitTime']< preRgnStop()]
post2 = ev3[(ev3['fitTime'] > postRgnStart()) * (ev3['fitTime'] < postRgnStop())]
post = np.concatenate([post, post2])
else:
pre = ev3
sp2.setData(x=pre['fitDecayTau'], y=pre['fitAmplitude'], data=pre);
#print " inhibitory:", np.median(ev2['fitDecayTau']), np.median(ev2['fitAmplitude'])
if separateCheck.isChecked():
sp3.setData(x=post['fitDecayTau'], y=post['fitAmplitude'], data=post)
sp3.show()
else:
sp3.hide()
try:
typ = ev2[0]['CellType']
except:
typ = ev3[0]['CellType']
sr = spontRate(ev2, numExSites)
sri = spontRate(ev3, numInSites)
title = "%s -- %s --- <span style='color: #99F;'>ex:</span> %s %s %s %0.1fHz --- <span style='color: #F99;'>in:</span> %s %s %s %0.1fHz" % (
dh.name(relativeTo=dh.parent().parent().parent()),
typ,
pg.siFormat(np.median(ev2['fitTimeToPeak']), error=np.std(ev2['fitTimeToPeak']), space=False, suffix='s'),
pg.siFormat(np.median(ev2['fitDecayTau']), error=np.std(ev2['fitDecayTau']), space=False, suffix='s'),
pg.siFormat(np.median(ev2['fitAmplitude']), error=np.std(ev2['fitAmplitude']), space=False, suffix='A'),
sr,
pg.siFormat(np.median(ev3['fitTimeToPeak']), error=np.std(ev3['fitTimeToPeak']), space=False, suffix='s'),
pg.siFormat(np.median(ev3['fitDecayTau']), error=np.std(ev3['fitDecayTau']), space=False, suffix='s'),
pg.siFormat(np.median(ev3['fitAmplitude']), error=np.std(ev3['fitAmplitude']), space=False, suffix='A'),
sri)
print re.sub(r'<[^>]+>', '', title)
pw1.setTitle(title)
### show cell in atlas
#rec = db.select('CochlearNucleus_Cell', where={'CellDir': cell})
#pts = []
#if len(rec) > 0:
#pos = (rec[0]['right'], rec[0]['anterior'], rec[0]['dorsal'])
#pts = [{'pos': pos, 'size': 100e-6, 'color': (0.7, 0.7, 1.0, 1.0)}]
### show event positions
evSpots = {}
for rec in ev:
p = (rec['right'], rec['anterior'], rec['dorsal'])
evSpots[p] = None
pos = np.array(evSpots.keys())
atlasPoints.setData(pos=pos, )