def step(self):
# decide how much to advance preview
data = self.data
now = pg.ptime.time()
dt = (now - self.lastTime) * self.rate
index = self.index + dt * self.sampleRate
npts = data.shape[0]
end = min(index, npts-1)
va = data[:end]
self.index = index
self.lastTime = now
# draw path
self.path.setData(va[:,0], va[:,1])
self.timeline.setValue(end / self.sampleRate)
self.spot.setPos(va[-1,0], va[-1,1])
if self.laserMask[end]:
self.spot.setBrush(pg.mkBrush('y'))
else:
self.spot.setBrush(pg.mkBrush('k'))
# Stop preview and delete path data if we reached the end
if end >= npts-1:
self.timer.stop()
self.data = None
self.laserMask = None
def paint(self, p, *args):
p.setRenderHint(p.Antialiasing)
w, h = self._pxLen
p.setPen(pg.mkPen('y'))
p.setBrush(pg.mkBrush(255, 255, 0, 100))
p.scale(w, h)
p.drawPath(self._path)
def __init__(self):
pg.GraphicsObject.__init__(self)
self.times = []
self.yRange = (0.1, 0.2)
self.xRange = [float('inf'), float('-inf')]
self.pen = pg.mkPen(None)
self.brush = pg.mkBrush((200, 200, 255, 200))
def __init__(self):
pg.GraphicsObject.__init__(self)
self.times = []
self.yRange=(0.1, 0.2)
self.xRange=[float('inf'), float('-inf')]
self.pen = pg.mkPen(None)
self.brush = pg.mkBrush((200,200,255,200))
def paintEvent(self, event):
p = QtGui.QPainter(self)
brush = pg.mkBrush(0.0)
p.fillRect(self.rect(), brush)
center = self.rect().center()
r = QtCore.QPoint(70, 30)
self.cancelRect = QtCore.QRect(center-r, center+r)
p.setPen(pg.mkPen(150, 0, 0))
f = p.font()
f.setPointSize(18)
p.setFont(f)
if self.cancelPressed:
p.fillRect(self.cancelRect, pg.mkBrush(80, 0, 0))
p.drawRect(self.cancelRect)
p.drawText(self.cancelRect, QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter, "Cancel")
p.end()
def update_sequence_analysis(self):
xvals = []
yvals = []
brushes = []
avg_x = []
avg_y = []
noise_values = []
for i in range(len(self.img_data)):
img_data = self.img_arrays[i]
img_t = self.img_data[i][0].xvals('Time')
base_starti, base_stopi, test_starti, test_stopi = self.time_indices(
img_t)
base = img_data[:, base_starti:base_stopi]
base_mean = base.mean(axis=1)
test = img_data[:, test_starti:test_stopi]
test_mean = test.mean(axis=1)
roi1, roi2 = self.rois # roi1 is signal, roi2 is background
base_rgn1 = roi1.getArrayRegion(base_mean, self.img1, axes=(1, 2))
base_rgn2 = roi2.getArrayRegion(base_mean, self.img1, axes=(1, 2))
test_rgn1 = roi1.getArrayRegion(test_mean, self.img1, axes=(1, 2))
test_rgn2 = roi2.getArrayRegion(test_mean, self.img1, axes=(1, 2))
# Use the temporal profile in roi2 in order to remove changes in LED brightness over time
# Then use the difference between baseline and test time regions to determine change in fluorescence
baseline1 = base_rgn1.mean(axis=1).mean(axis=1)
signal1 = test_rgn1.mean(axis=1).mean(axis=1)
baseline2 = base_rgn2.mean(axis=1).mean(axis=1)
signal2 = test_rgn2.mean(axis=1).mean(axis=1)
dff = ((signal1 - signal2) -
(baseline1 - baseline2)) / (baseline1 - baseline2)
x = self.seqParams[0][1][i]
xvals.extend([x] * len(dff))
yvals.extend(list(dff))
color = pg.mkColor(self.seqColors[i])
color.setAlpha(50)
brushes.extend([pg.mkBrush(color)] * len(dff))
avg_x.append(x)
avg_y.append(dff.mean())
self.plt3.clear()
if self.seqParams[0][0] is None:
self.plt3.plot(range(len(xvals)), yvals, pen='w')
else:
self.plt3.plot(xvals,
yvals,
symbol='o',
pen=None,
symbolBrush=brushes,
symbolPen=None)
self.plt3.plot(avg_x, avg_y, pen='w', antialias=True)
def __init__(self, **opts):
if 'scale' not in opts:
opts['scale'] = [20e-6, 20e-6]
item = QtGui.QGraphicsEllipseItem(-0.5, -0.5, 1., 1.)
item.setPen(pg.mkPen((255, 255, 255)))
item.setBrush(pg.mkBrush((0, 100, 255)))
opts.setdefault('scalable', False)
opts.setdefault('rotatable', False)
CanvasItem.__init__(self, item, **opts)
self.selectBox.addTranslateHandle([0.5, 0.5])
def paint(self, p, *args):
p.setRenderHint(p.Antialiasing)
w, h = self._pxLen
# r = QtCore.QRectF(-w, -h, w*2, h*2)
p.setPen(pg.mkPen('y'))
p.setBrush(pg.mkBrush(255, 255, 0, 100))
# p.drawEllipse(r)
# p.drawLine(pg.Point(-w*2, 0), pg.Point(w*2, 0))
# p.drawLine(pg.Point(0, -h*2), pg.Point(0, h*2))
p.scale(w, h)
p.drawPath(self._path)
def __init__(self, **opts):
if 'scale' not in opts:
opts['scale'] = [20e-6, 20e-6]
#opts['size'] = [20e-6, 20e-6]
#opts['scale'] = [1., 1.]
item = QtGui.QGraphicsEllipseItem(-0.5, -0.5, 1., 1.)
item.setPen(pg.mkPen((255,255,255)))
item.setBrush(pg.mkBrush((0,100,255)))
opts['scalable'] = False
opts['rotatable'] = False
CanvasItem.__init__(self, item, **opts)
self.selectBox.addTranslateHandle([0.5,0.5])
def update_sequence_analysis(self):
analysis = self.params['sequence', 'analysis']
xvals = []
yvals = []
noise = []
brushes = []
avg_x = []
avg_y = []
avg_noise = []
for i in range(len(self.img_data)):
img_data = self.img_arrays[i]
img_t = self.img_data[i][0].xvals('Time')
base_starti, base_stopi, test_starti, test_stopi, noise_starti, noise_stopi = self.time_indices(img_t)
dff = self.measure_dff(img_data, img_t, (base_starti, base_stopi, test_starti, test_stopi))
x = self.seqParams[0][1][i]
xvals.extend([x] * len(dff))
yvals.extend(list(dff))
if analysis in ('SNR', 'noise'):
noise_dff = self.measure_dff(img_data, img_t, (base_starti, base_stopi, noise_starti, noise_stopi))
noise.extend(list(noise_dff))
avg_noise.append(noise_dff.mean())
color = pg.mkColor(self.seqColors[i])
color.setAlpha(50)
brushes.extend([pg.mkBrush(color)] * len(dff))
avg_x.append(x)
avg_y.append(dff.mean())
if analysis == 'SNR':
noise = np.std(noise)
yvals = np.array(yvals) / noise
avg_y = np.array(avg_y) / noise
elif analysis == 'noise':
yvals = noise
avg_y = avg_noise
self.plt3.clear()
self.plt3.setLabels(left=analysis)
if self.seqParams[0][0] is None:
self.plt3.plot(range(len(xvals)), yvals, pen='w')
else:
self.plt3.plot(xvals, yvals, symbol='o', pen=None, symbolBrush=brushes, symbolPen=None)
self.plt3.plot(avg_x, avg_y, pen='w', antialias=True)
lin = stats.linregress(avg_x, avg_y)
self.plt3.setTitle("slope: %0.2g" % lin[0])
def addScan(self, scanDict):
plot = pg.ScatterPlotItem(pen=QtGui.QPen(QtCore.Qt.NoPen), brush=pg.mkBrush((255, 255, 255, 100)))
self.plot.addItem(plot)
plot.sigClicked.connect(self.plotClicked)
if not isinstance(scanDict, dict):
scanDict = {'key':scanDict}
#print "Adding:", scan.name
for scan in scanDict.values():
item = QtGui.QTreeWidgetItem([scan.name()])
item.setCheckState(0, QtCore.Qt.Checked)
item.scan = scan
self.scanList.addTopLevelItem(item)
self.scans[scan] = [plot, item, False]
self.updateScan(scan)
scan.sigEventsChanged.connect(self.invalidateScan)
def addScan(self, scanDict):
plot = pg.ScatterPlotItem(pen=QtGui.QPen(QtCore.Qt.NoPen),
brush=pg.mkBrush((255, 255, 255, 100)))
self.plot.addItem(plot)
plot.sigClicked.connect(self.plotClicked)
if not isinstance(scanDict, dict):
scanDict = {'key': scanDict}
#print "Adding:", scan.name
for scan in scanDict.values():
item = QtGui.QTreeWidgetItem([scan.name()])
item.setCheckState(0, QtCore.Qt.Checked)
item.scan = scan
self.scanList.addTopLevelItem(item)
self.scans[scan] = [plot, item, False]
self.updateScan(scan)
scan.sigEventsChanged.connect(self.invalidateScan)
def paint(self, p, *args):
p.setRenderHint(p.Antialiasing)
px = self.pixelLength(pg.Point(1, 0))
py = self.pixelLength(pg.Point(0, 1))
w = 5 * px
h = 5 * py
r = QtCore.QRectF(-w, -h, w * 2, h * 2)
p.setPen(pg.mkPen('y'))
p.setBrush(pg.mkBrush(0, 0, 255, 100))
p.drawEllipse(r)
p.drawLine(pg.Point(-w * 2, 0), pg.Point(w * 2, 0))
p.drawLine(pg.Point(0, -h * 2), pg.Point(0, h * 2))
if self.label is not None:
angle = self.labelAngle * np.pi / 180.
pos = p.transform().map(QtCore.QPointF(
0, 0)) + 15 * QtCore.QPointF(np.cos(angle), -np.sin(angle))
p.resetTransform()
p.drawText(QtCore.QRectF(pos.x() - 10,
pos.y() - 10, 20, 20),
QtCore.Qt.AlignCenter | QtCore.Qt.AlignVCenter,
self.label)
def showMap(dh=None):
"""
Display a graphic of an input map for the currently selected cell
"""
global v, g, atlas
if dh is None:
dh = man.currentFile
db = man.getModule('Data Manager').currentDatabase()
v.clear()
cd = dh
sd = cd.parent()
atlas.loadState(sd)
g = atlas.schematicGraphicsItems(contours=False, sliceScale=10, cellDir=cd)
v.addItem(g)
cellGroup = pg.ItemGroup()
g.cellGroup = cellGroup
cellScale = 10.
cellGroup.scale(cellScale, cellScale)
cellGroup.setParentItem(g)
g.atlasScale.hide()
g.arrowGroup.hide()
## reposition/rescale atlas group
b1 = g.atlasGroup.mapRectToParent(g.atlasGroup.childrenBoundingRect())
b2 = g.sliceClip.mapRectToParent(g.sliceClip.boundingRect())
g.atlasGroup.setPos(b2.right()-b1.left()+0.001, b2.top()-b1.top())
b1 = g.atlasGroup.mapRectToParent(g.atlasGroup.childrenBoundingRect())
bounds = b1 | b2
if cd.exists('morphology.png'):
## small image to go over slice schematic
imgf = cd['morphology.png']
imgd = pg.colorToAlpha(imgf.read(), np.array([255,255,255]))
mimg1 = pg.ImageItem(imgd)
tr = pg.SRTTransform(imgf.info()['userTransform'])
mimg1.setTransform(tr)
mimg1.setParentItem(g.sliceGroup)
mimg1.setZValue(100)
g.cellImg1 = mimg1
## larger image to be displayed above
mimg2 = pg.ImageItem(imgd)
mimg2.setParentItem(cellGroup)
mimg2.setTransform(tr * g.sliceGroup.transform())
mimg2.scale(1.0 / g.sliceScaleFactor, 1.0 / g.sliceScaleFactor)
#angle = pg.SRTTransform(g.sliceGroup.transform()).getRotation()
#mimg2.rotate(angle)
g.cellImg2 = mimg2
cellGroup.scale(5,5)
## reposition next to slice schematic
imgBounds = g.mapRectFromItem(mimg2, mimg2.boundingRect())
pos = pg.Point(bounds.right()-imgBounds.left(), bounds.bottom()-imgBounds.bottom())
cellGroup.setPos(pos)
## add scale bar
sbLength = 50e-6
g.cellScale = pg.QtGui.QGraphicsLineItem(0.0, 0.0, sbLength, 0.0)
g.cellScale.setPen(pg.mkPen(color=0.0, width=5))
g.cellScale.setZValue(10)
g.cellScale.text = pg.TextItem(u"%d µm" % int(sbLength*1e6), anchor=(0.5, 1), color=(0,0,0))
g.cellScale.text.setParentItem(g.cellScale)
g.cellScale.text.setPos(sbLength*0.5, -50e-6/cellScale)
#g.cellScale = pg.ScaleBar(sbLength)
g.cellScale.setParentItem(cellGroup)
corner = mimg2.mapToParent(mimg2.boundingRect()).boundingRect().bottomRight()
g.cellScale.setPos(corner + pg.Point(-sbLength/2., -sbLength/3.))
pos = pg.SRTTransform(cd.info()['userTransform']).map(pg.Point(0,0))
size = pg.Point(30e-6, 30e-6)
g.cellMarker = pg.QtGui.QGraphicsEllipseItem(pg.QtCore.QRectF(pos-size, pos+size))
g.cellMarker.setBrush(pg.mkBrush(100,100,255,150))
g.cellMarker.setPen(pg.mkPen('k', width=0.5))
g.cellMarker.setParentItem(g.sliceGroup)
g.cellMarker.setZValue(90)
sites = db.select('map_site_view', ['ProtocolDir', 'HasInput'], where={'CellDir': cd})
if len(sites) > 0:
tr = sites[0]['ProtocolDir'].parent().info().get('userTransform', None)
if tr is None:
tr = pg.SRTTransform()
else:
tr = pg.SRTTransform(tr)
pos = []
size = sites[0]['ProtocolDir'].info()['Scanner']['spotSize']
brushes = []
for site in sites:
pd = site['ProtocolDir']
x,y = pd.info()['Scanner']['position']
p2 = tr.map(pg.Point(x,y))
pos.append((p2.x(), p2.y()))
if site['HasInput']:
brushes.append(pg.mkBrush('w'))
else:
brushes.append(pg.mkBrush(None))
inputMap = pg.ScatterPlotItem(pos=np.array(pos), size=size, brush=brushes, pen=(0,0,0,50), pxMode=False, antialias=True)
g.sliceGroup.addItem(inputMap)
g.inputMap = inputMap
inputMap.setZValue(50)
cell = dh
sl = cell.parent()
day = sl.parent()
name = day.shortName() + "_" + sl.shortName() + "_" + cell.shortName()
rec = db.select('DirTable_Cell', '*', where={'Dir': cd})[0]
name += "\nType: " + str(rec['CellType']) + " Temp: " + str(rec['Temperature']) + " Internal: " + str(rec['Internal']) + " Age:" + str(rec['Age']) + " Raccess: " + str(rec['AccessResistance'])
name += "\nDirect Area: %s>0pA %s>20pA %s>100pA" % (str(rec['DirectAreaGt0']), str(rec['DirectAreaGt20']), str(rec['DirectAreaGt100']))
name += " Direct n spikes: " + str(rec['DirectNSpikes'])
name += "\nSpont Ex Decay: %s Spont In Decay: %s" % (str(rec['SpontExDecay1']), str(rec['SpontInDecay']))
name += "\nExcitatory input" if (rec['EvokedExDecay'] is not None or rec['EvokedExAmp'] is not None) else ""
print rec
#name += '\nDirect Slow Decay: %s %s' % (str(rec['DirectAreaGT0']), str(rec['DirectAreaGT0']))
g.cellName = pg.TextItem(name, color=(0,0,0))
g.cellName.setParentItem(g)
g.cellName.setPos(0, bounds.bottom())
def paintEvent(self, event):
p = QtGui.QPainter(self)
brush = pg.mkBrush(0.0)
p.fillRect(self.rect(), brush)
p.end()
pw1.setLabel('left', 'Amplitude', 'A')
pw1.setLabel('bottom', 'Decay Tau', 's')
spl2 = Qt.QSplitter()
spl2.setOrientation(Qt.Qt.Horizontal)
spl1.addWidget(spl2)
pw2 = pg.PlotWidget(labels={'bottom': ('time', 's')})
spl2.addWidget(pw2)
tab = Qt.QTabWidget()
spl2.addWidget(tab)
## For viewing cell morphology
gv = pg.GraphicsView()
gv.setBackgroundBrush(pg.mkBrush('w'))
image = pg.ImageItem()
gv.addItem(image)
gv.enableMouse()
gv.setAspectLocked(True)
tab.addTab(gv, 'Morphology')
## 3D atlas
import acq4.analysis.atlas.CochlearNucleus as CN
atlas = CN.CNAtlasDisplayWidget()
atlas.showLabel('DCN')
atlas.showLabel('AVCN')
atlas.showLabel('PVCN')
tab.addTab(atlas, 'Atlas')
atlasPoints = gl.GLScatterPlotItem()
def setBrush(self, brush):
brush = pg.mkBrush(brush)
self.brush = brush
for t in self.times:
t.setBrush(brush)
def showMap(dh=None):
"""
Display a graphic of an input map for the currently selected cell
"""
global v, g, atlas
if dh is None:
dh = man.currentFile
db = man.getModule('Data Manager').currentDatabase()
v.clear()
cd = dh
sd = cd.parent()
atlas.loadState(sd)
g = atlas.schematicGraphicsItems(contours=False, sliceScale=10, cellDir=cd)
v.addItem(g)
cellGroup = pg.ItemGroup()
g.cellGroup = cellGroup
cellScale = 10.
cellGroup.scale(cellScale, cellScale)
cellGroup.setParentItem(g)
g.atlasScale.hide()
g.arrowGroup.hide()
## reposition/rescale atlas group
b1 = g.atlasGroup.mapRectToParent(g.atlasGroup.childrenBoundingRect())
b2 = g.sliceClip.mapRectToParent(g.sliceClip.boundingRect())
g.atlasGroup.setPos(b2.right()-b1.left()+0.001, b2.top()-b1.top())
b1 = g.atlasGroup.mapRectToParent(g.atlasGroup.childrenBoundingRect())
bounds = b1 | b2
if cd.exists('morphology.png'):
## small image to go over slice schematic
imgf = cd['morphology.png']
imgd = pg.colorToAlpha(imgf.read(), np.array([255,255,255]))
mimg1 = pg.ImageItem(imgd)
tr = pg.SRTTransform(imgf.info()['userTransform'])
mimg1.setTransform(tr)
mimg1.setParentItem(g.sliceGroup)
mimg1.setZValue(100)
g.cellImg1 = mimg1
## larger image to be displayed above
mimg2 = pg.ImageItem(imgd)
mimg2.setParentItem(cellGroup)
mimg2.setTransform(tr * g.sliceGroup.transform())
mimg2.scale(1.0 / g.sliceScaleFactor, 1.0 / g.sliceScaleFactor)
#angle = pg.SRTTransform(g.sliceGroup.transform()).getRotation()
#mimg2.rotate(angle)
g.cellImg2 = mimg2
cellGroup.scale(5,5)
## reposition next to slice schematic
imgBounds = g.mapRectFromItem(mimg2, mimg2.boundingRect())
pos = pg.Point(bounds.right()-imgBounds.left(), bounds.bottom()-imgBounds.bottom())
cellGroup.setPos(pos)
## add scale bar
sbLength = 50e-6
g.cellScale = Qt.QGraphicsLineItem(0.0, 0.0, sbLength, 0.0)
g.cellScale.setPen(pg.mkPen(color=0.0, width=5))
g.cellScale.setZValue(10)
g.cellScale.text = pg.TextItem(u"%d µm" % int(sbLength*1e6), anchor=(0.5, 1), color=(0,0,0))
g.cellScale.text.setParentItem(g.cellScale)
g.cellScale.text.setPos(sbLength*0.5, -50e-6/cellScale)
#g.cellScale = pg.ScaleBar(sbLength)
g.cellScale.setParentItem(cellGroup)
corner = mimg2.mapToParent(mimg2.boundingRect()).boundingRect().bottomRight()
g.cellScale.setPos(corner + pg.Point(-sbLength/2., -sbLength/3.))
pos = pg.SRTTransform(cd.info()['userTransform']).map(pg.Point(0,0))
size = pg.Point(30e-6, 30e-6)
g.cellMarker = Qt.QGraphicsEllipseItem(Qt.QRectF(pos-size, pos+size))
g.cellMarker.setBrush(pg.mkBrush(100,100,255,150))
g.cellMarker.setPen(pg.mkPen('k', width=0.5))
g.cellMarker.setParentItem(g.sliceGroup)
g.cellMarker.setZValue(90)
sites = db.select('map_site_view', ['ProtocolDir', 'HasInput'], where={'CellDir': cd})
if len(sites) > 0:
tr = sites[0]['ProtocolDir'].parent().info().get('userTransform', None)
if tr is None:
tr = pg.SRTTransform()
else:
tr = pg.SRTTransform(tr)
pos = []
size = sites[0]['ProtocolDir'].info()['Scanner']['spotSize']
brushes = []
for site in sites:
pd = site['ProtocolDir']
x,y = pd.info()['Scanner']['position']
p2 = tr.map(pg.Point(x,y))
pos.append((p2.x(), p2.y()))
if site['HasInput']:
brushes.append(pg.mkBrush('w'))
else:
brushes.append(pg.mkBrush(None))
inputMap = pg.ScatterPlotItem(pos=np.array(pos), size=size, brush=brushes, pen=(0,0,0,50), pxMode=False, antialias=True)
g.sliceGroup.addItem(inputMap)
g.inputMap = inputMap
inputMap.setZValue(50)
cell = dh
sl = cell.parent()
day = sl.parent()
name = day.shortName() + "_" + sl.shortName() + "_" + cell.shortName()
rec = db.select('DirTable_Cell', '*', where={'Dir': cd})[0]
name += "\nType: " + str(rec['CellType']) + " Temp: " + str(rec['Temperature']) + " Internal: " + str(rec['Internal']) + " Age:" + str(rec['Age']) + " Raccess: " + str(rec['AccessResistance'])
name += "\nDirect Area: %s>0pA %s>20pA %s>100pA" % (str(rec['DirectAreaGt0']), str(rec['DirectAreaGt20']), str(rec['DirectAreaGt100']))
name += " Direct n spikes: " + str(rec['DirectNSpikes'])
name += "\nSpont Ex Decay: %s Spont In Decay: %s" % (str(rec['SpontExDecay1']), str(rec['SpontInDecay']))
name += "\nExcitatory input" if (rec['EvokedExDecay'] is not None or rec['EvokedExAmp'] is not None) else ""
print(rec)
#name += '\nDirect Slow Decay: %s %s' % (str(rec['DirectAreaGT0']), str(rec['DirectAreaGT0']))
g.cellName = pg.TextItem(name, color=(0,0,0))
g.cellName.setParentItem(g)
g.cellName.setPos(0, bounds.bottom())
def update_sequence_analysis(self):
analysis = self.params['sequence', 'analysis']
xvals = []
yvals = []
noise = []
brushes = []
avg_x = []
avg_y = []
avg_noise = []
for i in range(len(self.img_data)):
img_data = self.img_arrays[i]
img_t = self.img_data[i][0].xvals('Time')
base_starti, base_stopi, test_starti, test_stopi, noise_starti, noise_stopi = self.time_indices(
img_t)
dff = self.measure_dff(
img_data, img_t,
(base_starti, base_stopi, test_starti, test_stopi))
x = self.seqParams[0][1][i]
xvals.extend([x] * len(dff))
yvals.extend(list(dff))
if analysis in ('SNR', 'noise'):
noise_dff = self.measure_dff(
img_data, img_t,
(base_starti, base_stopi, noise_starti, noise_stopi))
noise.extend(list(noise_dff))
avg_noise.append(noise_dff.mean())
color = pg.mkColor(self.seqColors[i])
color.setAlpha(50)
brushes.extend([pg.mkBrush(color)] * len(dff))
avg_x.append(x)
avg_y.append(dff.mean())
if analysis == 'SNR':
noise = np.std(noise)
yvals = np.array(yvals) / noise
avg_y = np.array(avg_y) / noise
elif analysis == 'noise':
yvals = noise
avg_y = avg_noise
self.plt3.clear()
self.plt3.setLabels(left=analysis)
if self.seqParams[0][0] is None:
self.plt3.plot(range(len(xvals)), yvals, pen='w')
else:
self.plt3.plot(xvals,
yvals,
symbol='o',
pen=None,
symbolBrush=brushes,
symbolPen=None)
self.plt3.plot(avg_x, avg_y, pen='w', antialias=True)
lin = stats.linregress(avg_x, avg_y)
self.plt3.setTitle("slope: %0.2g" % lin[0])
def mapErrors(self,
nSteps=(5, 5, 7),
stepSize=(50e-6, 50e-6, 50e-6),
padding=60e-6,
threshold=0.4,
speed='slow',
show=False,
intermediateDist=60e-6):
"""Move pipette tip randomly to locations in a grid and measure the position error
at each location.
All tip locations must be within the field of view.
"""
startTime = time.time()
start = np.array(self.dev.globalPosition())
npts = nSteps[0] * nSteps[1] * nSteps[2]
inds = np.mgrid[0:nSteps[0], 0:nSteps[1], 0:nSteps[2]].reshape(
(3, npts)).transpose()
order = np.arange(npts)
np.random.shuffle(order)
err = np.zeros(nSteps + (3, ))
stepSize = np.array(stepSize)
if show:
imv = pg.image()
mark1 = pg.QtGui.QGraphicsEllipseItem(
pg.QtCore.QRectF(-5, -5, 10, 10))
mark1.setBrush(pg.mkBrush(255, 255, 0, 100))
mark1.setZValue(100)
imv.addItem(mark1)
mark2 = pg.QtGui.QGraphicsEllipseItem(
pg.QtCore.QRectF(-5, -5, 10, 10))
mark2.setBrush(pg.mkBrush(255, 0, 0, 100))
mark2.setZValue(100)
imv.addItem(mark2)
# loop over all points in random order, and such that we do heavy computation while
# pipette is moving.
images = []
offsets = []
try:
with pg.ProgressDialog("Acquiring error map...", 0,
len(order)) as dlg:
for i in range(len(order) + 1):
if i > 0:
lastPos = pos
if i < len(order):
ind = inds[order[i]]
pos = start.copy() + (stepSize * ind)
# Jump to position + a random 20um offset to avoid hysteresis
offset = np.random.normal(size=3)
offset *= intermediateDist / (offset**2).sum()**0.5
offsets.append(offset)
mfut = self.dev._moveToGlobal(pos + offset, speed)
ffut = self.dev.scopeDevice().setFocusDepth(
pos[2], speed)
if i > 0:
ind = inds[order[i - 1]]
print("Frame: %d %s" % (i - 1, lastPos))
err[tuple(ind)] = self.measureError(
padding=padding,
threshold=threshold,
frame=frame,
pos=lastPos)
print(" error: %s" % err[tuple(ind)])
dlg += 1
if show:
imv.setImage(frame.data()[0])
p1 = frame.globalTransform().inverted()[0].map(
pg.Vector(lastPos))
p2 = frame.globalTransform().inverted()[0].map(
pg.Vector(lastPos + err[tuple(ind)]))
mark1.setPos(p1.x(), p1.y())
mark2.setPos(p2.x(), p2.y())
# wait for previous moves to complete
mfut.wait(updates=True)
ffut.wait(updates=True)
# step back to actual target position
self.dev._moveToGlobal(pos, speed).wait(updates=True)
frame = self.takeFrame()
if dlg.wasCanceled():
return None
finally:
self.dev._moveToGlobal(start, 'fast')
self.dev.scopeDevice().setFocusDepth(start[2], 'fast')
self.errorMap = {
'err': err,
'nSteps': nSteps,
'stepSize': stepSize,
'order': order,
'inds': inds,
'offsets': offsets,
'time': time.time() - startTime,
}
filename = self.dev.configFileName('error_map.np')
np.save(open(filename, 'wb'), self.errorMap)
return self.errorMap
def setBrush(self, brush):
brush = pg.mkBrush(brush)
self.brush = brush
for t in self.times:
t.setBrush(brush)
pw1.setLabel('bottom', 'Decay Tau', 's')
spl2 = QtGui.QSplitter()
spl2.setOrientation(QtCore.Qt.Horizontal)
spl1.addWidget(spl2)
pw2 = pg.PlotWidget(labels={'bottom': ('time', 's')})
spl2.addWidget(pw2)
tab = QtGui.QTabWidget()
spl2.addWidget(tab)
## For viewing cell morphology
gv = pg.GraphicsView()
gv.setBackgroundBrush(pg.mkBrush('w'))
image = pg.ImageItem()
gv.addItem(image)
gv.enableMouse()
gv.setAspectLocked(True)
tab.addTab(gv, 'Morphology')
## 3D atlas
import acq4.analysis.atlas.CochlearNucleus as CN
atlas = CN.CNAtlasDisplayWidget()
atlas.showLabel('DCN')
atlas.showLabel('AVCN')
atlas.showLabel('PVCN')
tab.addTab(atlas, 'Atlas')
atlasPoints = gl.GLScatterPlotItem()
