def __init__(self, host, rec=None):
self.host = host ## host is the parent Photostim object
self.stubs = [] ## list of ScanStub objects for scans in the map that have not been loaded yet
self.scans = [] ## list of loaded Scan objects
self.scanItems = {} ## maps {scan: tree item}
#self.points = [] ## Holds all data: [ (position, [(scan, dh), ...], spotData), ... ]
self.pointsByFile = {} ## just a lookup dictionary
self.spots = [] ## holds all data {pos, size, [(scan, dh), ...]}; used to construct scatterplotitem
self.sPlotItem = pg.ScatterPlotItem(pxMode=False, pen=(50,50,50))
self.header = self.mapFields.keys()[2:]
self.item = QtGui.QTreeWidgetItem([""] * len(self.header))
self.item.setFlags(QtCore.Qt.ItemIsSelectable| QtCore.Qt.ItemIsEditable| QtCore.Qt.ItemIsEnabled)
self.item.map = self
self.item.setExpanded(True)
self.rowID = None
## If a DB record was supplied, that means this map already exists in the DB so
## we can reload the list of scans already included in the map
if rec is not None:
self.rowID = rec['rowid']
scans = rec['scans']
#del rec['scans']
#del rec['cell']
for i in range(len(self.header)):
self.item.setText(i, str(rec[self.header[i]]))
for fh,rowid in scans:
item = QtGui.QTreeWidgetItem([fh.shortName()])
#print "Create scan stub:", fh
self.stubs.append(ScanStub(fh, item, rowid)) ## rowid can be either a (table, rowid) pair or an integer implying ('ProtocolSequence', rowid)
item.handle = fh
self.item.addChild(item)
def __init__(self, name, ptSize, **args):
pg.CrosshairROI.__init__(self, pos=(0,0), size=args.get('size', [ptSize*4]*2), angle=args.get('angle', 0), **args)
self.name = name
self.params = pTypes.SimpleParameter(name=self.name, type='bool', value=True, removable=True, renamable=True, children=[
dict(name='layout', type='list', value=args.get('layout', 'Hexagonal'), values=['Square', 'Hexagonal']),
dict(name='spacing', type='float', value=args.get('spacing', ptSize), suffix='m', siPrefix=True, bounds=[1e-9, None], step=10e-6),
dict(name='Active Regions', type='group', addText="Add region...", addList=['Rectangle', 'Polygon'])
])
self.params.item = self
self.params.param('Active Regions').addNew = self.addActiveRegion
self.rgns = []
self.pointSize = ptSize
self._points = np.empty((0,2), dtype=float)
self._scene = None
self._scatter = pg.ScatterPlotItem(pxMode=False, brush=None, antialias=True)
self._scatter.setParentItem(self)
self._needScatterUpdate = False
self.params.param('layout').sigStateChanged.connect(self.invalidatePoints)
self.params.param('spacing').sigStateChanged.connect(self.invalidatePoints)
self.params.param('Active Regions').sigChildRemoved.connect(self.rgnRemoved)
self.sigRegionChanged.connect(self.invalidatePoints)
self.params.sigValueChanged.connect(self.toggled)
self.params.sigRemoved.connect(self.removed)
def __init__(self, name, ui):
self.scatter = pg.ScatterPlotItem(pxMode=False)
self.name = name
self.ui = weakref.ref(ui)
self.frames = []
self.spots = {'pos': [], 'size': [], 'color': []}
self.updateParams()
self.z = Task.z
Task.z += 1
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 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())
bTimes = [x[1] for x in l2]
print key, " \tcompute time:\t%0.1f \ttotal cost:\t%0.1f \tmax interval:\t%0.1f\t" % (
time.time()-start,
sum(bTimes),
max(bTimes)
)
#print " total cost:\t%0.1f" % sum(bTimes)
#print " max interval:\t%0.1f" % max(bTimes)
check(locs, l2)
vb = pg.ViewBox()
view.addItem(vb)
data = [{'pos': l2[i][0], 'brush': (i * 255/ len(l2),)*3} for i in range(len(l2))]
sp = pg.ScatterPlotItem(data, pen=0.3, pxMode=False, size=1e-4)
vb.addItem(sp)
## number spots
#for i in range(len(data)):
#t = QtGui.QGraphicsTextItem()
#t.setHtml('<span style="color: #f00">%d</span>'%i)
#t.setFlag(t.ItemIgnoresTransformations, True)
#t.setPos(*l2[i][0])
#vb.addItem(t)
vb.setRange(sp.boundingRect())
### show video of sequence
#img = np.zeros((n**2, n, n, 3), dtype=float)
#l3 = [x[0] for x in l2]
def __init__(self, **opts):
self.defaultSize = 1e-4 # set a default spot size as 100 um.
if 'handle' not in opts:
raise Exception(
"ScanCanvasItem must be initialized with 'handle' or 'handles' specified in opts"
)
## Top-level dirHandle tells us the default name of the item
## and may have a userTransform
dirHandle = opts['handle']
if 'name' not in opts:
opts['name'] = dirHandle.shortName()
## Get the specific list of subdirs to use from which to pull spot information
if 'subDirs' in opts:
dirs = opts['subDirs']
else:
model = acq4.Manager.getManager().dataModel
typ = model.dirType(dirHandle)
if typ == 'ProtocolSequence':
dirs = [dirHandle[d] for d in dirHandle.subDirs()]
elif typ == 'Protocol':
dirs = [dirHandle]
else:
raise Exception("Invalid dir type '%s'" % typ)
## Generate spot data and a scatterplotitem
pts = []
for d in dirs:
if 'Scanner' in d.info() and 'position' in d.info(
)['Scanner']: #Note: this is expected to fail (gracefully) when a protocol sequence is incomplete
pos = d.info()['Scanner']['position']
if 'spotSize' in d.info()['Scanner']:
size = d.info()['Scanner']['spotSize']
else:
size = self.defaultSize
pts.append({'pos': pos, 'size': size, 'data': d})
self.scatterPlotData = pts
if len(pts) == 0:
raise Exception(
"No data found in scan %s." %
dirHandle.name(relativeTo=dirHandle.parent().parent()))
gitem = pg.ScatterPlotItem(pts, pxMode=False, pen=(50, 50, 50, 200))
#citem = ScanCanvasItem(self, item, handle=dirHandle, **opts)
#self._addCanvasItem(citem)
#return [citem]
CanvasItem.__init__(self, gitem, **opts)
#self.scatterPlot = gitem
self.originalSpotSize = size
self._ctrlWidget = Qt.QWidget()
self.ui = ScanCanvasItemTemplate.Ui_Form()
self.ui.setupUi(self._ctrlWidget)
self.layout.addWidget(self._ctrlWidget, self.layout.rowCount(), 0, 1,
2)
self.ui.outlineColorBtn.setColor((50, 50, 50, 200))
#self.transformGui.mirrorImageBtn.clicked.connect(self.mirrorY)
self.ui.sizeSpin.setOpts(dec=True,
step=1,
minStep=1e-6,
siPrefix=True,
suffix='m',
bounds=[1e-6, None])
self.ui.sizeSpin.setValue(self.originalSpotSize)
self.ui.sizeSpin.valueChanged.connect(self.sizeSpinEdited)
self.ui.sizeFromCalibrationRadio.clicked.connect(self.updateSpotSize)
self.ui.outlineColorBtn.sigColorChanging.connect(self.updateOutline)
self.addScanImageBtn = self.ui.loadSpotImagesBtn
#self.createGradientBtn = self.ui.createGradientBtn
#self.removeGradientBtn = self.ui.removeGradientBtn
self.addScanImageBtn.connect(self.addScanImageBtn,
Qt.SIGNAL('clicked()'),
self.loadScanImage)