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 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 = 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 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())