def makeGroup(self, dev, subdev):
grp = DeviceTreeItemGroup.makeGroup(self, dev, subdev)
if dev is self.device:
bound = QtGui.QGraphicsPathItem(self.device.getBoundary(globalCoords=False))
bound.setParentItem(grp)
bound.setPen(pg.mkPen(40, 150, 150))
return grp
def setRelativeDepth(self, depth):
# adjust the apparent depth of the target
dist = depth * 255 / 50e-6
color = (np.clip(dist + 256, 0, 255), np.clip(256 - dist, 0, 255), 0)
self.pen = pg.mkPen(color)
self._picture = None
self.update()
def makeGroup(self, dev, subdev):
grp = DeviceTreeItemGroup.makeGroup(self, dev, subdev)
if dev is self.device:
bound = QtGui.QGraphicsPathItem(self.device.getBoundary(globalCoords=False))
bound.setParentItem(grp)
bound.setPen(pg.mkPen(40, 150, 150))
return grp
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 addROI(self, roiType):
pen = pg.mkPen(pg.intColor(len(self.ROIs)))
center = self.view.viewRect().center()
#print 'camerawindow.py: addROI:: ', self.view.viewPixelSize()
size = [x * 50 for x in self.view.viewPixelSize()]
if roiType == 'rect':
roi = PlotROI(center, size)
elif roiType == 'ellipse':
roi = pg.EllipseROI(center, size, removable=True)
elif roiType == 'polygon':
pts = [
center, center + pg.Point(0, size[1]),
center + pg.Point(size[0], 0)
]
roi = pg.PolyLineROI(pts, closed=True, removable=True)
elif roiType == 'ruler':
pts = [center, center + pg.Point(size[0], size[1])]
roi = RulerROI(pts, removable=True)
else:
raise ValueError("Invalid ROI type %s" % roiType)
roi.setZValue(40000)
roi.setPen(pen)
self.view.addItem(roi)
plot = self.roiPlot.plot(pen=pen)
self.ROIs.append({'roi': roi, 'plot': plot, 'vals': [], 'times': []})
roi.sigRemoveRequested.connect(self.removeROI)
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 start(self, canvas, plot):
"""Add graphics items to *view* showing the path of the scanner.
"""
self.clear()
self.path = pg.PlotCurveItem()
self.spot = QtGui.QGraphicsEllipseItem(QtCore.QRectF(-1, -1, 2, 2))
self.spot.scale(1e-6, 1e-6)
self.spot.setPen(pg.mkPen('y'))
self.data = self.program.generatePositionArray()
self.laserMask = self.program.generateLaserMask()
self.lastTime = pg.ptime.time()
self.index = 0
self.sampleRate = self.program.sampleRate
self.timeline = pg.InfiniteLine(angle=90)
self.timeline.setZValue(100)
if canvas is not None:
canvas.addItem(self.path)
canvas.addItem(self.spot)
if plot is not None:
self.plot = plot
self.plotTimeline(plot)
plot.addItem(self.timeline)
self.timer.start(16)
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, **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 paint(self, p, *args):
p.setPen(pg.mkPen(0.3))
#p.drawRect(self.boundingRect()) # causes artifacts at large scale
br = self.boundingRect()
# p.drawPolygon(QtGui.QPolygonF([br.topLeft(), br.topRight(), br.bottomRight(), br.bottomLeft()]))
p.drawLine(br.topLeft(), br.topRight())
p.drawLine(br.bottomLeft(), br.bottomRight())
p.drawLine(br.topLeft(), br.bottomLeft())
p.drawLine(br.bottomRight(), br.topRight())
pg.ROI.paint(self, p, *args)
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 addROI(self):
pen = pg.mkPen(pg.intColor(len(self.ROIs)))
center = self.view.viewRect().center()
#print 'camerawindow.py: addROI:: ', self.view.viewPixelSize()
size = [x*50 for x in self.view.viewPixelSize()]
roi = PlotROI(center, size)
roi.setZValue(40000)
roi.setPen(pen)
self.view.addItem(roi)
plot = self.roiPlot.plot(pen=pen)
self.ROIs.append({'roi': roi, 'plot': plot, 'vals': [], 'times': []})
roi.sigRemoveRequested.connect(self.removeROI)
def __init__(self, pos, state=None):
ROI.PolyLineROI.__init__(self, [[0, 0], [2, 0], [2, 1], [0, 1]],
pos=pos,
closed=True,
pen=pg.mkPen(50, 50, 255, 200))
## don't let the user add handles to the sides, only to the top and bottom
self.segments[0].setAcceptedMouseButtons(QtCore.Qt.NoButton)
#self.segments[1].setAcceptedMouseButtons(QtCore.Qt.NoButton) ## there was a change in PolylineROI that affected the order of segments, so now 0 and 2 are the sides instead of 1 and 3 (2013.12.12)
self.segments[2].setAcceptedMouseButtons(QtCore.Qt.NoButton)
#self.segments[3].setAcceptedMouseButtons(QtCore.Qt.NoButton)
if state is not None:
self.setState(state)
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 plotData():
rate = 1e3
nPts = 100
plot.clear()
params = {}
paramSpace = sg.listSequences()
for k in paramSpace:
params[k] = range(len(paramSpace[k]))
global seqPlots
seqPlots = []
SequenceRunner.runSequence(lambda p: seqPlots.append(sg.getSingle(rate, nPts, p)), params, params.keys())
for i, w in enumerate(seqPlots):
if w is not None:
plot.plot(w, pen=pg.intColor(i, len(seqPlots)*1.5))
data = sg.getSingle(rate, nPts)
plot.plot(data, pen=pg.mkPen('w', width=2))
def plotData():
rate = 1e3
nPts = 100
plot.clear()
params = {}
paramSpace = sg.listSequences()
for k in paramSpace:
params[k] = range(len(paramSpace[k]))
global seqPlots
seqPlots = []
SequenceRunner.runSequence(
lambda p: seqPlots.append(sg.getSingle(rate, nPts, p)), params,
list(params.keys()))
for i, w in enumerate(seqPlots):
if w is not None:
plot.plot(w, pen=pg.intColor(i, len(seqPlots) * 1.5))
data = sg.getSingle(rate, nPts)
plot.plot(data, pen=pg.mkPen('w', width=2))
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 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
def setPen(self, pen):
pen = pg.mkPen(pen)
self.pen = pen
for t in self.times:
t.setPen(pen)
def __init__(self, dev, taskRunner):
TaskGui.__init__(self, dev, taskRunner)
self.ui = Ui_Form()
self.ui.setupUi(self)
dm = getManager()
self.targets = None
self.items = {}
self.haveCalibration = True ## whether there is a calibration for the current combination of laser/optics
self.currentOpticState = None
self.currentCamMod = None
self.displaySize = {} ## maps (laser,opticState) : display size
## since this setting is remembered for each objective.
# Make sure DQ appears in this task
daqName = dev.getDaqName()
taskRunner.getDevice(daqName)
## Populate module/device lists, auto-select based on device defaults
self.defCam = None
if 'defaultCamera' in self.dev.config:
self.defCam = self.dev.config['defaultCamera']
defLaser = None
if 'defaultLaser' in self.dev.config:
defLaser = self.dev.config['defaultLaser']
daqDev = dev.getDaqName()
self.daqUI = taskRunner.getDevice(daqDev)
self.ui.cameraCombo.setTypes(['cameraModule'])
self.ui.laserCombo.setTypes(['laser'])
self.positionCtrlGroup = PositionCtrlGroup()
self.positionCtrlGroup.sigAddNewRequested.connect(self.addPositionCtrl)
self.ui.itemTree.setParameters(self.positionCtrlGroup, showTop=False)
self.positionCtrlGroup.sigChildRemoved.connect(self.positionCtrlRemoved)
self.ui.spotSequenceGroup.setCollapsed(True)
self.ui.spotDisplayGroup.setCollapsed(True)
self.scanProgram = ScanProgram()
self.scanProgram.setDevices(scanner=self.dev)
self.ui.programTree.setParameters(self.scanProgram.ctrlParameter(), showTop=False)
## Set up SpinBoxes
self.ui.minTimeSpin.setOpts(dec=True, step=1, minStep=1e-3, siPrefix=True, suffix='s', bounds=[0, 50])
self.ui.minDistSpin.setOpts(dec=True, step=1, minStep=1e-6, siPrefix=True, suffix='m', bounds=[0, 10e-3])
self.ui.sizeSpin.setOpts(dec=True, step=1, minStep=1e-6, siPrefix=True, suffix='m', bounds=[1e-9, 1e-3])
## Create state group for saving/restoring state
self.stateGroup = pg.WidgetGroup([
(self.ui.cameraCombo,),
(self.ui.laserCombo,),
(self.ui.minTimeSpin, 'minTime'),
(self.ui.minDistSpin, 'minDist'),
(self.ui.simulateShutterCheck, 'simulateShutter'),
(self.ui.sizeSpin, 'spotSize'),
(self.ui.enablePosCtrlCheck, 'enablePosCtrl'),
(self.ui.enableScanProgCheck, 'enableScanProg'),
])
self.stateGroup.setState({'minTime': 10, 'minDist': 500e-6, 'sizeSpin':100e-6})
self.tdPlot = self.ui.tdPlotWidget.plotItem
self.tdPlot.setLabel('bottom', text="Distance", units='m')
self.tdPlot.setLabel('left', text="Wait time", units='s')
self.ui.scanProgramSplitter.setSizes([600, 100])
self.ui.programTimeline.setDownsampling(True)
## Note we use lambda functions for all these clicks to strip out the arg sent with the signal
self.ui.showPosCtrlCheck.toggled.connect(self.showPosCtrls)
self.ui.cameraCombo.currentIndexChanged.connect(self.camModChanged)
self.ui.laserCombo.currentIndexChanged.connect(self.laserDevChanged)
self.ui.sizeFromCalibrationRadio.toggled.connect(self.updateSpotSizes)
self.ui.sizeSpin.valueChanged.connect(self.sizeSpinEdited)
self.ui.minTimeSpin.valueChanged.connect(self.sequenceChanged)
self.ui.minDistSpin.valueChanged.connect(self.sequenceChanged)
self.ui.recomputeBtn.clicked.connect(self.recomputeClicked)
self.ui.loadConfigBtn.clicked.connect(self.loadConfiguration)
self.ui.previewBtn.toggled.connect(self.previewProgram)
self.ui.enablePosCtrlCheck.toggled.connect(self.enablePosCtrlToggled)
self.ui.enableScanProgCheck.toggled.connect(self.enableScanProgToggled)
self.ui.showLastSpotCheck.toggled.connect(self.showLastSpotToggled)
self.ui.programPreviewSlider.valueChanged.connect(self.previewRateChanged)
self.dev.sigGlobalSubdeviceChanged.connect(self.opticStateChanged)
self.testTarget = TargetPoint(name="Test", ptSize=100e-6)
self.testTarget.setPen(Qt.QPen(Qt.QColor(255, 200, 200)))
self.spotMarker = TargetPoint(name="Last", ptSize=100e-6, movable=False)
self.spotMarker.setPen(pg.mkPen(color=(255,255,255), width = 2))
self.spotMarker.hide()
self.laserDevChanged() # also updates spot sizes
self.camModChanged()
self.updateTDPlot()
#self.ui.simulateShutterCheck.setChecked(False)
if 'offVoltage' not in self.dev.config: ## we don't have a voltage for virtual shuttering
self.ui.simulateShutterCheck.setChecked(False)
self.ui.simulateShutterCheck.setEnabled(False)
self.daqChanged(self.daqUI.currentState())
self.daqUI.sigChanged.connect(self.daqChanged)
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, six.string_types):
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
def show(dh=None):
"""
Display a graphic of the currently selected slice / cell
"""
global v, g, atlas
if dh is None:
dh = man.currentFile
v.clear()
if 'cell' in dh.shortName().lower():
cd = dh
sd = cd.parent()
else:
sd = dh
cd = None
atlas.loadState(sd)
g = atlas.schematicGraphicsItems()
v.addItem(g)
if cd is not None:
## 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)
g.cellImg1 = mimg1
## larger image to be displayed above
cellGroup = pg.ItemGroup()
g.cellGroup = cellGroup
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)
cellScale = 50.
cellGroup.scale(cellScale, cellScale)
g.cellImg2 = mimg2
## reposition image above slice schematic
b1 = g.atlasGroup.mapRectToParent(g.atlasGroup.childrenBoundingRect())
b2 = g.sliceClip.mapRectToParent(g.sliceClip.boundingRect())
bounds = b1 | b2
cellGroup.setParentItem(g)
imgBounds = g.mapRectFromItem(mimg2, mimg2.boundingRect())
pos = pg.Point(bounds.center().x() - imgBounds.center().x(), bounds.top()-imgBounds.bottom())
cellGroup.setPos(pos)
## add scale bar
sbLength = 25e-6
g.cellScale = Qt.QGraphicsLineItem(0.0, 0.0, sbLength, 0.0)
g.cellScale.setPen(pg.mkPen(color=0.0, width=100e-6/cellScale, cosmetic=False))
g.cellScale.setParentItem(cellGroup)
g.cellScale.setZValue(10)
g.cellScale.text = pg.TextItem(u"25 µm", anchor=(0.5, 1), color=(0,0,0))
g.cellScale.text.setParentItem(g.cellScale)
g.cellScale.text.setPos(sbLength*0.5, -50e-6/cellScale)
corner = mimg2.mapToParent(mimg2.boundingRect()).boundingRect().bottomRight()
g.cellScale.setPos(corner + pg.Point(-sbLength/2., -sbLength/3.))
cell = dh
sl = cell.parent()
day = sl.parent()
name = day.shortName() + "_" + sl.shortName() + "_" + cell.shortName()
g.cellName = pg.TextItem(name, color=(0,0,0))
g.cellName.setParentItem(cellGroup)
g.cellName.setPos(corner + pg.Point(-sbLength*4,-sbLength/4.))
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 __init__(self, dev, taskRunner):
TaskGui.__init__(self, dev, taskRunner)
self.ui = Ui_Form()
self.ui.setupUi(self)
dm = getManager()
self.targets = None
self.items = {}
self.haveCalibration = True ## whether there is a calibration for the current combination of laser/optics
self.currentOpticState = None
self.currentCamMod = None
self.programCtrls = []
self.displaySize = {} ## maps (laser,opticState) : display size
## since this setting is remembered for each objective.
## Populate module/device lists, auto-select based on device defaults
self.defCam = None
if 'defaultCamera' in self.dev.config:
self.defCam = self.dev.config['defaultCamera']
defLaser = None
if 'defaultLaser' in self.dev.config:
defLaser = self.dev.config['defaultLaser']
self.ui.cameraCombo.setTypes(['cameraModule'])
self.ui.laserCombo.setTypes(['laser'])
self.positionCtrlGroup = PositionCtrlGroup()
self.positionCtrlGroup.sigAddNewRequested.connect(self.addPositionCtrl)
self.ui.itemTree.setParameters(self.positionCtrlGroup, showTop=False)
self.positionCtrlGroup.sigChildRemoved.connect(self.positionCtrlRemoved)
self.programCtrlGroup = ProgramCtrlGroup()
self.programCtrlGroup.sigAddNewRequested.connect(self.addProgramCtrl)
self.ui.programTree.setParameters(self.programCtrlGroup, showTop=False)
self.programCtrlGroup.sigChildRemoved.connect(self.programCtrlRemoved)
## Set up SpinBoxes
self.ui.minTimeSpin.setOpts(dec=True, step=1, minStep=1e-3, siPrefix=True, suffix='s', bounds=[0, 50])
self.ui.minDistSpin.setOpts(dec=True, step=1, minStep=1e-6, siPrefix=True, suffix='m', bounds=[0, 10e-3])
self.ui.sizeSpin.setOpts(dec=True, step=1, minStep=1e-6, siPrefix=True, suffix='m', bounds=[1e-9, 1e-3])
## Create state group for saving/restoring state
self.stateGroup = pg.WidgetGroup([
(self.ui.cameraCombo,),
(self.ui.laserCombo,),
(self.ui.minTimeSpin, 'minTime'),
(self.ui.minDistSpin, 'minDist'),
(self.ui.simulateShutterCheck, 'simulateShutter'),
(self.ui.sizeSpin, 'spotSize'),
])
self.stateGroup.setState({'minTime': 10, 'minDist': 500e-6, 'sizeSpin':100e-6})
self.tdPlot = self.ui.tdPlotWidget.plotItem
self.tdPlot.setLabel('bottom', text="Distance", units='m')
self.tdPlot.setLabel('left', text="Wait time", units='s')
## Note we use lambda functions for all these clicks to strip out the arg sent with the signal
self.ui.hideCheck.toggled.connect(self.showInterface)
self.ui.hideMarkerBtn.clicked.connect(self.hideSpotMarker)
self.ui.cameraCombo.currentIndexChanged.connect(self.camModChanged)
self.ui.laserCombo.currentIndexChanged.connect(self.laserDevChanged)
self.ui.sizeFromCalibrationRadio.toggled.connect(self.updateSpotSizes)
self.ui.sizeSpin.valueChanged.connect(self.sizeSpinEdited)
self.ui.minTimeSpin.valueChanged.connect(self.sequenceChanged)
self.ui.minDistSpin.valueChanged.connect(self.sequenceChanged)
self.ui.recomputeBtn.clicked.connect(self.recomputeClicked)
self.ui.loadConfigBtn.clicked.connect(self.loadConfiguration)
self.dev.sigGlobalSubdeviceChanged.connect(self.opticStateChanged)
self.testTarget = TargetPoint(name="Test", ptSize=100e-6)
self.testTarget.setPen(QtGui.QPen(QtGui.QColor(255, 200, 200)))
self.spotMarker = TargetPoint(name="Last", ptSize=100e-6, movable=False)
self.spotMarker.setPen(pg.mkPen(color=(255,255,255), width = 2))
self.spotMarker.hide()
self.updateSpotSizes()
self.camModChanged()
self.updateTDPlot()
#self.ui.simulateShutterCheck.setChecked(False)
if 'offVoltage' not in self.dev.config: ## we don't have a voltage for virtual shuttering
self.ui.simulateShutterCheck.setChecked(False)
self.ui.simulateShutterCheck.setEnabled(False)
def recolor(self):
for i, s in enumerate(self.segments):
if i % 2 == 0:
s.setPen(self.pen)
else:
s.setPen(pg.mkPen([75, 200, 75]))
## 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()
atlas.addItem(atlasPoints)
win.show()
win.resize(1000, 800)
sp1 = pw1.scatterPlot([],
pen=pg.mkPen(None),
brush=(200, 200, 255, 70),
identical=True,
size=8)
sp2 = pw1.scatterPlot([],
pen=pg.mkPen(None),
brush=(255, 200, 200, 70),
identical=True,
size=8)
sp3 = pw1.scatterPlot([],
pen=pg.mkPen(None),
brush=(100, 255, 100, 70),
identical=True,
size=8)
sp4 = pw1.scatterPlot([], pen=pg.mkPen(None), size=8)
def __init__(self, pos, state=None):
ROI.PolyLineROI.__init__(self, [[0,0], [2,0], [2,1], [0,1]], pos=pos, closed=True, pen=pg.mkPen(50,50, 255, 200))
## don't let the user add handles to the sides, only to the top and bottom
self.segments[0].setAcceptedMouseButtons(QtCore.Qt.NoButton)
#self.segments[1].setAcceptedMouseButtons(QtCore.Qt.NoButton) ## there was a change in PolylineROI that affected the order of segments, so now 0 and 2 are the sides instead of 1 and 3 (2013.12.12)
self.segments[2].setAcceptedMouseButtons(QtCore.Qt.NoButton)
#self.segments[3].setAcceptedMouseButtons(QtCore.Qt.NoButton)
if state is not None:
self.setState(state)
## 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()
atlas.addItem(atlasPoints)
win.show()
win.resize(1000,800)
sp1 = pw1.scatterPlot([], pen=pg.mkPen(None), brush=(200,200,255,70), identical=True, size=8)
sp2 = pw1.scatterPlot([], pen=pg.mkPen(None), brush=(255,200,200,70), identical=True, size=8)
sp3 = pw1.scatterPlot([], pen=pg.mkPen(None), brush=(100,255,100,70), identical=True, size=8)
sp4 = pw1.scatterPlot([], pen=pg.mkPen(None), size=8)
print "Reading cell list..."
#import os, pickle
#md = os.path.abspath(os.path.split(__file__)[0])
#cacheFile = os.path.join(md, 'eventCache.p')
#if os.path.isfile(cacheFile):
#print "Read from cache..."
#ev = pickle.load(open(cacheFile, 'r'))
def setPen(self, pen):
pen = pg.mkPen(pen)
self.pen = pen
for t in self.times:
t.setPen(pen)
def show(dh=None):
"""
Display a graphic of the currently selected slice / cell
"""
global v, g, atlas
if dh is None:
dh = man.currentFile
v.clear()
if 'cell' in dh.shortName().lower():
cd = dh
sd = cd.parent()
else:
sd = dh
cd = None
atlas.loadState(sd)
g = atlas.schematicGraphicsItems()
v.addItem(g)
if cd is not None:
## 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)
g.cellImg1 = mimg1
## larger image to be displayed above
cellGroup = pg.ItemGroup()
g.cellGroup = cellGroup
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)
cellScale = 50.
cellGroup.scale(cellScale, cellScale)
g.cellImg2 = mimg2
## reposition image above slice schematic
b1 = g.atlasGroup.mapRectToParent(g.atlasGroup.childrenBoundingRect())
b2 = g.sliceClip.mapRectToParent(g.sliceClip.boundingRect())
bounds = b1 | b2
cellGroup.setParentItem(g)
imgBounds = g.mapRectFromItem(mimg2, mimg2.boundingRect())
pos = pg.Point(bounds.center().x() - imgBounds.center().x(), bounds.top()-imgBounds.bottom())
cellGroup.setPos(pos)
## add scale bar
sbLength = 25e-6
g.cellScale = pg.QtGui.QGraphicsLineItem(0.0, 0.0, sbLength, 0.0)
g.cellScale.setPen(pg.mkPen(color=0.0, width=100e-6/cellScale, cosmetic=False))
g.cellScale.setParentItem(cellGroup)
g.cellScale.setZValue(10)
g.cellScale.text = pg.TextItem(u"25 µm", anchor=(0.5, 1), color=(0,0,0))
g.cellScale.text.setParentItem(g.cellScale)
g.cellScale.text.setPos(sbLength*0.5, -50e-6/cellScale)
corner = mimg2.mapToParent(mimg2.boundingRect()).boundingRect().bottomRight()
g.cellScale.setPos(corner + pg.Point(-sbLength/2., -sbLength/3.))
cell = dh
sl = cell.parent()
day = sl.parent()
name = day.shortName() + "_" + sl.shortName() + "_" + cell.shortName()
g.cellName = pg.TextItem(name, color=(0,0,0))
g.cellName.setParentItem(cellGroup)
g.cellName.setPos(corner + pg.Point(-sbLength*4,-sbLength/4.))
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 recolor(self):
for i, s in enumerate(self.segments):
if i % 2 == 0:
s.setPen(self.pen)
else:
s.setPen(pg.mkPen([75, 200, 75]))
