def roiChanged(self, roi):
if isinstance(roi, int):
roi = self.currentRoi
self.plot.clearPlots()
c = 0
lineScans = []
for imgSet in self.data:
data = roi.getArrayRegion(imgSet['procMean'], self.view.imageItem, axes=(1,2))
m = data.mean(axis=1).mean(axis=1)
lineScans.append(data.mean(axis=2))
spacer = np.empty((lineScans[-1].shape[0], 1), dtype = lineScans[-1].dtype)
spacer[:] = lineScans[-1].min()
lineScans.append(spacer)
data = roi.getArrayRegion(imgSet['procStd'], self.view.imageItem, axes=(1,2))
s = data.mean(axis=1).mean(axis=1)
self.plot.plot(m, pen=pg.hsvColor(c*0.2, 1.0, 1.0))
self.plot.plot(m-s, pen=pg.hsvColor(c*0.2, 1.0, 0.4))
self.plot.plot(m+s, pen=pg.hsvColor(c*0.2, 1.0, 0.4))
c += 1
lineScan = np.hstack(lineScans)
self.getElement('Line Scan').setImage(lineScan)
self.currentRoi = roi
def updateAnalysis(self):
roi = self.currentRoi
plot = self.getElement('Trial Plot')
plot.clearPlots()
c = 0
for img in self.normData:
#img = img.mean(axis=1)
rgn = self.lr.getRegion()
img = img[:, rgn[0]:rgn[1]].mean(axis=1)
data = roi.getArrayRegion(img, self.view.imageItem, axes=(1,2))
m = data.mean(axis=1).mean(axis=1)
#data = roi.getArrayRegion(img, self.view.imageItem, axes=(1,2))
#s = data.mean(axis=1).mean(axis=1)
plot.plot(m, pen=pg.hsvColor(c*0.2, 1.0, 1.0))
#self.plot.plot(m-s, pen=pg.hsvColor(c*0.2, 1.0, 0.4))
#self.plot.plot(m+s, pen=pg.hsvColor(c*0.2, 1.0, 0.4))
c += 1
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, )
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, )