def __init__(self, handle, **kwds):
kwds.pop('viewRect', None)
self.data = handle.read()
self.groupitem = pg.ItemGroup()
self.pipettes = {}
for dev in self.data.devices():
arrow = pg.ArrowItem()
self.pipettes[dev] = arrow
arrow.setParentItem(self.groupitem)
opts = {'movable': False, 'rotatable': False, 'handle': handle}
opts.update(kwds)
if opts.get('name') is None:
opts['name'] = handle.shortName()
CanvasItem.__init__(self, self.groupitem, **opts)
self._timeSliderResolution = 10. # 10 ticks per second on the time slider
self._mpCtrlWidget = MultiPatchLogCtrlWidget()
self.layout.addWidget(self._mpCtrlWidget, self.layout.rowCount(), 0, 1,
2)
self._mpCtrlWidget.timeSlider.setMaximum(
self._timeSliderResolution *
(self.data.lastTime() - self.data.firstTime()))
self._mpCtrlWidget.timeSlider.valueChanged.connect(
self.timeSliderChanged)
self._mpCtrlWidget.createMarkersBtn.clicked.connect(
self.createMarkersClicked)
self.timeSliderChanged(0)
def __init__(self, **kwds):
kwds.pop('viewRect', None)
item = pg.ItemGroup()
opts = {'scalable': False, 'rotatable': False, 'movable': False}
opts.update(kwds)
CanvasItem.__init__(self, item, **opts)
self.params = pg.parametertree.Parameter.create(
name='Markers', type='group', addText='Add marker...')
self.params.addNew = self.addMarker
self.params.sigTreeStateChanged.connect(self._paramsChanged)
self._markerCtrl = MarkerItemCtrlWidget(self)
self.layout.addWidget(self._markerCtrl, self.layout.rowCount(), 0, 1,
2)
def __init__(self, camera, module):
CameraModuleInterface.__init__(self, camera, module)
self.module = module
self.view = module.getView()
self.hasQuit = False
self.boundaryItems = {}
## setup UI
self.ui = CameraInterfaceTemplate()
self.widget = dockarea.DockArea()
w = QtGui.QWidget()
self.ui.setupUi(w)
# takes care of displaying image data,
# contrast & background subtraction user interfaces
self.imagingCtrl = ImagingCtrl()
self.frameDisplay = self.imagingCtrl.frameDisplay
## Move control panels into docks
recDock = dockarea.Dock(name="Recording",
widget=self.imagingCtrl,
size=(100, 10),
autoOrientation=False)
devDock = dockarea.Dock(name="Device Control",
widget=self.ui.devCtrlWidget,
size=(100, 10),
autoOrientation=False)
dispDock = dockarea.Dock(name="Display Control",
widget=self.frameDisplay.contrastWidget(),
size=(100, 600),
autoOrientation=False)
bgDock = dockarea.Dock(name="Background Subtraction",
widget=self.frameDisplay.backgroundWidget(),
size=(100, 10),
autoOrientation=False)
self.widget.addDock(recDock)
self.widget.addDock(devDock, 'bottom', recDock)
self.widget.addDock(dispDock, 'bottom', devDock)
self.widget.addDock(bgDock, 'bottom', dispDock)
## Camera state variables
self.cam = camera
self.roi = None
self.exposure = 0.001
self.binning = 1
self.region = None
## set up item groups
self.cameraItemGroup = pg.ItemGroup(
) ## translated with scope, scaled with camera objective
self.imageItemGroup = pg.ItemGroup(
) ## translated and scaled as each frame arrives
self.view.addItem(self.imageItemGroup)
self.view.addItem(self.cameraItemGroup)
self.cameraItemGroup.setZValue(0)
self.imageItemGroup.setZValue(-2)
## video image item
self.imageItem = self.frameDisplay.imageItem()
self.view.addItem(self.imageItem)
self.imageItem.setParentItem(self.imageItemGroup)
self.imageItem.setZValue(-10)
## open camera, determine bit depth and sensor area
self.openCamera()
## Initialize values
self.lastCameraPosition = Point(self.camSize[0] * 0.5,
self.camSize[1] * 0.5)
self.lastCameraScale = Point(1.0, 1.0)
self.scopeCenter = [self.camSize[0] * 0.5, self.camSize[1] * 0.5]
self.cameraScale = [1, 1]
## Camera region-of-interest control
self.roi = CamROI(self.camSize, parent=self.cameraItemGroup)
self.roi.sigRegionChangeFinished.connect(self.regionWidgetChanged)
self.roi.setZValue(-1)
self.setRegion()
## Set up microscope objective borders
self.borders = CameraItemGroup(self.cam)
self.module.addItem(self.borders)
self.borders.setZValue(-1)
self.cam.sigGlobalTransformChanged.connect(self.globalTransformChanged)
self.globalTransformChanged()
# initially set binning and exposure from camera state
self.exposure = self.cam.getParam('exposure')
self.binning = self.cam.getParam('binning')[0]
## Initialize values/connections in Camera Dock
self.setUiBinning(self.binning)
self.ui.spinExposure.setValue(self.exposure)
self.ui.spinExposure.setOpts(dec=True,
step=1,
minStep=100e-6,
siPrefix=True,
suffix='s',
bounds=[0, 10])
#Signals from self.ui.btnSnap and self.ui.recordStackBtn are caught by the RecordThread
self.ui.btnFullFrame.clicked.connect(lambda: self.setRegion())
self.proxy1 = SignalProxy(self.ui.binningCombo.currentIndexChanged,
slot=self.binningComboChanged)
self.ui.spinExposure.valueChanged.connect(
self.setExposure
) ## note that this signal (from acq4.util.SpinBox) is delayed.
## Signals from Camera device
self.cam.sigNewFrame.connect(self.newFrame)
self.cam.sigCameraStopped.connect(self.cameraStopped)
self.cam.sigCameraStarted.connect(self.cameraStarted)
self.cam.sigShowMessage.connect(self.showMessage)
self.frameDisplay.imageUpdated.connect(self.imageUpdated)
self.imagingCtrl.sigStartVideoClicked.connect(self.startAcquireClicked)
self.imagingCtrl.sigStopVideoClicked.connect(self.stopAcquireClicked)
self.imagingCtrl.ui.acquireFrameBtn.setEnabled(False)
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())
