def ifaceTransformChanged(self, iface):
# imaging device moved; update viewport and tracked group.
# This is only used when the camera is not running--
# if the camera is running, then this is taken care of in drawFrame to
# ensure that the image remains stationary on screen.
prof = Profiler()
if not self.cam.isRunning():
tr = pg.SRTTransform(self.cam.globalTransform())
self.updateTransform(tr)
def newFrame(self, iface, frame):
#sys.stdout.write('+')
if not self.roiPlotCheck.isChecked():
return
imageItem = iface.getImageItem()
prof = Profiler('CameraWindow.addPlotFrame', disabled=True)
if imageItem.width() is None:
return
## Get rid of old frames
minTime = None
now = pg.time()
#if len(self.frameBuffer) > 0:
#while len(self.frameBuffer) > 0 and self.frameBuffer[0][1]['time'] < (now-self.ui.spinROITime.value()):
#self.frameBuffer.pop(0)
for r in self.ROIs:
#print " >>", r['times'], now, frame[1]['time'], self.ui.spinROITime.value(), now-self.ui.spinROITime.value()
while len(r['times']) > 0 and r['times'][0] < (now-self.roiTimeSpin.value()):
r['times'].pop(0)
r['vals'].pop(0)
#print " <<", r['times']
if len(r['times']) > 0 and (minTime is None or r['times'][0] < minTime):
minTime = r['times'][0]
if minTime is None:
minTime = frame.info()['time']
prof.mark('remove old frames')
## add new frame
draw = False
if self.lastPlotTime is None or now - self.lastPlotTime > 0.05:
draw = True
self.lastPlotTime = now
for r in self.ROIs:
d = r['roi'].getArrayRegion(frame.data(), imageItem, axes=(0,1))
prof.mark('get array rgn')
if d is None:
continue
if d.size < 1:
val = 0
else:
val = d.mean()
r['vals'].append(val)
r['times'].append(frame.info()['time'])
prof.mark('append')
if draw:
r['plot'].setData(np.array(r['times'])-minTime, r['vals'])
prof.mark('draw')
prof.finish()
def newFrame(self, iface, frame):
"""New frame has arrived; update ROI plot if needed.
"""
if not self.roiPlotCheck.isChecked():
return
imageItem = iface.getImageItem()
prof = Profiler('CameraWindow.addPlotFrame', disabled=True)
if imageItem.width() is None:
return
# Get rid of old frames
minTime = None
now = pg.time()
for r in self.ROIs:
while len(r['times']) > 0 and r['times'][0] < (now-self.roiTimeSpin.value()):
r['times'].pop(0)
r['vals'].pop(0)
if len(r['times']) > 0 and (minTime is None or r['times'][0] < minTime):
minTime = r['times'][0]
if minTime is None:
minTime = frame.info()['time']
prof.mark('remove old frames')
# add new frame
draw = False
if self.lastPlotTime is None or now - self.lastPlotTime > 0.05:
draw = True
self.lastPlotTime = now
for r in self.ROIs:
if isinstance(r['roi'], pg.graphicsItems.ROI.RulerROI):
continue
d = r['roi'].getArrayRegion(frame.data(), imageItem, axes=(0,1))
prof.mark('get array rgn')
if d is None:
continue
if d.size < 1:
val = 0
else:
val = d.mean()
r['vals'].append(val)
r['times'].append(frame.info()['time'])
prof.mark('append')
if draw:
r['plot'].setData(np.array(r['times'])-minTime, r['vals'])
prof.mark('draw')
prof.finish()
def drawFrame(self):
if self.hasQuit:
return
#sys.stdout.write('+')
try:
## If we last drew a frame < 1/30s ago, return.
t = ptime.time()
if (self.lastDrawTime is not None) and (t - self.lastDrawTime < .033333):
#sys.stdout.write('-')
return
## if there is no new frame and no controls have changed, just exit
if not self.updateFrame and self.nextFrame is None:
#sys.stdout.write('-')
return
self.updateFrame = False
## If there are no new frames and no previous frames, then there is nothing to draw.
if self.currentFrame is None and self.nextFrame is None:
#sys.stdout.write('-')
return
prof = Profiler()
## We will now draw a new frame (even if the frame is unchanged)
if self.lastDrawTime is not None:
fps = 1.0 / (t - self.lastDrawTime)
self.ui.displayFpsLabel.setValue(fps)
self.lastDrawTime = t
prof()
## Handle the next available frame, if there is one.
if self.nextFrame is not None:
self.currentFrame = self.nextFrame
self.nextFrame = None
data = self.currentFrame.data()
info = self.currentFrame.info()
prof()
## divide the background out of the current frame if needed
if self.ui.divideBgBtn.isChecked():
bg = self.getBackgroundFrame()
if bg is not None and bg.shape == data.shape:
data = data / bg
elif self.ui.subtractBgBtn.isChecked():
bg = self.getBackgroundFrame()
if bg is not None and bg.shape == data.shape:
data = data - bg
prof()
## Set new levels if auto gain is enabled
if self.ui.btnAutoGain.isChecked():
cw = self.ui.spinAutoGainCenterWeight.value()
(w,h) = data.shape
center = data[w/2.-w/6.:w/2.+w/6., h/2.-h/6.:h/2.+h/6.]
minVal = data.min() * (1.0-cw) + center.min() * cw
maxVal = data.max() * (1.0-cw) + center.max() * cw
## If there is inf/nan in the image, strip it out before computing min/max
if any([np.isnan(minVal), np.isinf(minVal), np.isnan(minVal), np.isinf(minVal)]):
nanMask = np.isnan(data)
infMask = np.isinf(data)
valid = data[~nanMask * ~infMask]
minVal = valid.min() * (1.0-cw) + center.min() * cw
maxVal = valid.max() * (1.0-cw) + center.max() * cw
## Smooth min/max range to avoid noise
if self.lastMinMax is None:
minVal = minVal
maxVal = maxVal
else:
s = 1.0 - 1.0 / (self.ui.spinAutoGainSpeed.value()+1.0)
minVal = self.lastMinMax[0] * s + minVal * (1.0-s)
maxVal = self.lastMinMax[1] * s + maxVal * (1.0-s)
self.lastMinMax = [minVal, maxVal]
## and convert fraction of previous range into new levels
bl = self.autoGainLevels[0] * (maxVal-minVal) + minVal
wl = self.autoGainLevels[1] * (maxVal-minVal) + minVal
self.ignoreLevelChange = True
try:
self.ui.histogram.setLevels(bl, wl)
self.ui.histogram.setHistogramRange(minVal, maxVal, padding=0.05)
finally:
self.ignoreLevelChange = False
prof()
## update image in viewport
self.imageItem.updateImage(data)#, levels=[bl, wl])
self.imageItem.setOpacity(self.alpha)
self.imageItem.setTransform(self.currentFrame.frameTransform().as2D())
prof()
## Update viewport to correct for scope movement/scaling
tr = pg.SRTTransform(self.currentFrame.cameraTransform())
self.updateTransform(tr)
self.imageItemGroup.setTransform(tr)
prof()
prof()
prof.finish()
except:
printExc('Error while drawing new frames:')
finally:
pass
def storeToDB(self):
## collect list of cells and scans under this slice,
## read all positions with userTransform corrections
prof = Profiler("Atlas.storeToDB", disabled=True)
loaded = self.host.getLoadedFiles()
cells = []
prots = []
for f in loaded:
if not f.isDir() or not f.isGrandchildOf(self.sliceDir):
continue
if self.dataModel.dirType(f) == 'Cell':
info = f.info()
if 'userTransform' not in info:
continue
cells.append((f, info['userTransform']['pos']))
elif self.dataModel.dirType(f) == 'Protocol':
info = f.info()
scanInfo = info.get('Scanner', None)
if scanInfo is None:
continue
tr = pg.SRTTransform(info.get('userTransform', None))
pos = tr.map(*scanInfo['position'])
prots.append((f, pos))
elif self.dataModel.dirType(f) == 'ProtocolSequence':
info = f.info()
tr = pg.SRTTransform(info.get('userTransform', None))
for subName in f.subDirs():
subf = f[subName]
scanInfo = subf.info().get('Scanner', None)
if scanInfo is None:
continue
pos = tr.map(*scanInfo['position'])
prots.append((subf, pos))
prof.mark("made list of positions")
for ident, dirType, positions in [('_cell', 'Cell', cells),
('_protocol', 'Protocol', prots)]:
## map positions, build data tables
data, fields = self.generateDataArray(positions, dirType)
prof.mark("got data arrays for %s" % dirType)
#dirColumn = dirType + 'Dir'
#data = np.empty(len(positions), dtype=[('SliceDir', object), (dirColumn, object), ('right', float), ('anterior', float), ('dorsal', float)])
#for i in range(len(positions)):
#dh, pos = positions[i]
#mapped = self.atlas.mapToAtlas(pg.Point(pos))
##print dh, pos
##print " right:", mapped.x()
##print " anter:", mapped.y()
##print " dorsl:", mapped.z()
#data[i] = (self.sliceDir, dh, mapped.x(), mapped.y(), mapped.z())
## write to DB
db = self.ui.dbWidget.getDb()
prof.mark('got db')
table = self.ui.dbWidget.getTableName(self.atlas.DBIdentity +
ident)
prof.mark('got table')
#fields = collections.OrderedDict([
#('SliceDir', 'directory:Slice'),
#(dirColumn, 'directory:'+dirType),
#('right', 'real'),
#('anterior', 'real'),
#('dorsal', 'real'),
#])
## Make sure target table exists and has correct columns
db.checkTable(table,
owner=self.atlas.DBIdentity + ident,
columns=fields,
create=True)
prof.mark('checked table')
## delete old -- This is the slow part!
old = db.select(table,
where={'SliceDir': self.sliceDir},
toArray=True)
if old is not None: ## only do deleting if there is already data stored for this slice -- try to speed things up
for source in set(data[dirType + 'Dir']):
if source in old[
dirType +
'Dir']: ## check that source is in the old data before we delete it - try to speed things up
db.delete(table, where={dirType + 'Dir': source})
prof.mark('deleted old data')
## write new
db.insert(table, data)
prof.mark("added %s data to db" % dirType)
prof.finish()
def storeToDB(self):
## collect list of cells and scans under this slice,
## read all positions with userTransform corrections
prof = Profiler("Atlas.storeToDB", disabled=True)
loaded = self.host.getLoadedFiles()
cells = []
prots = []
for f in loaded:
if not f.isDir() or not f.isGrandchildOf(self.sliceDir):
continue
if self.dataModel.dirType(f) == 'Cell':
info = f.info()
if 'userTransform' not in info:
continue
cells.append((f, info['userTransform']['pos']))
elif self.dataModel.dirType(f) == 'Protocol':
info = f.info()
scanInfo = info.get('Scanner', None)
if scanInfo is None:
continue
tr = pg.SRTTransform(info.get('userTransform', None))
pos = tr.map(*scanInfo['position'])
prots.append((f, pos))
elif self.dataModel.dirType(f) == 'ProtocolSequence':
info = f.info()
tr = pg.SRTTransform(info.get('userTransform', None))
for subName in f.subDirs():
subf = f[subName]
scanInfo = subf.info().get('Scanner', None)
if scanInfo is None:
continue
pos = tr.map(*scanInfo['position'])
prots.append((subf, pos))
prof.mark("made list of positions")
for ident, dirType, positions in [('_cell', 'Cell', cells), ('_protocol', 'Protocol', prots)]:
## map positions, build data tables
data, fields = self.generateDataArray(positions, dirType)
prof.mark("got data arrays for %s" %dirType)
#dirColumn = dirType + 'Dir'
#data = np.empty(len(positions), dtype=[('SliceDir', object), (dirColumn, object), ('right', float), ('anterior', float), ('dorsal', float)])
#for i in range(len(positions)):
#dh, pos = positions[i]
#mapped = self.atlas.mapToAtlas(pg.Point(pos))
##print dh, pos
##print " right:", mapped.x()
##print " anter:", mapped.y()
##print " dorsl:", mapped.z()
#data[i] = (self.sliceDir, dh, mapped.x(), mapped.y(), mapped.z())
## write to DB
db = self.ui.dbWidget.getDb()
prof.mark('got db')
table = self.ui.dbWidget.getTableName(self.atlas.DBIdentity+ident)
prof.mark('got table')
#fields = collections.OrderedDict([
#('SliceDir', 'directory:Slice'),
#(dirColumn, 'directory:'+dirType),
#('right', 'real'),
#('anterior', 'real'),
#('dorsal', 'real'),
#])
## Make sure target table exists and has correct columns
db.checkTable(table, owner=self.atlas.DBIdentity+ident, columns=fields, create=True)
prof.mark('checked table')
## delete old -- This is the slow part!
old = db.select(table, where={'SliceDir':self.sliceDir}, toArray=True)
if old is not None: ## only do deleting if there is already data stored for this slice -- try to speed things up
for source in set(data[dirType+'Dir']):
if source in old[dirType+'Dir']: ## check that source is in the old data before we delete it - try to speed things up
db.delete(table, where={dirType+'Dir': source})
prof.mark('deleted old data')
## write new
db.insert(table, data)
prof.mark("added %s data to db" %dirType)
prof.finish()
def generateDataArray(self, positions, dirType):
prof = Profiler("A1Atlas.generateDataArray", disabled=True)
if self.atlas.state is None:
self.saveState()
prof.mark('saved atlas state')
dirColumn = dirType + 'Dir'
if dirType == 'Protocol':
data = np.empty(len(positions), dtype=[('SliceDir', object),
(dirColumn, object),
#('layer', float),
#('depth', float),
('yPosSlice', float),
('yPosCell', float),
('percentDepth', float),
('xPosSlice', float),
('xPosCell', float),
('modXPosSlice', float),
('modXPosCell', float)])
fields = collections.OrderedDict([
('SliceDir', 'directory:Slice'),
(dirColumn, 'directory:'+dirType),
('yPosSlice', 'real'),
('yPosCell', 'real'),
('percentDepth', 'real'),
('xPosSlice', 'real'),
('xPosCell', 'real'),
('modXPosSlice', 'real'),
('modXPosCell', 'real')])
prof.mark("defined Protocol data array")
for i in range(len(positions)):
dh, pos = positions[i]
cellPos = self.dataModel.getCellInfo(dh)['userTransform']['pos']
mapped = self.atlas.mapToAtlas(pg.Point(pos)) ## needs to return %depth and modXPosSlice
#data[i] = (self.sliceDir, dh, mapped.x(), mapped.y(), mapped.z())
data[i]['SliceDir'] = self.sliceDir
data[i][dirColumn] = dh
data[i]['yPosSlice'] = pos[1]
data[i]['yPosCell'] = pos[1]-cellPos[1]
data[i]['percentDepth'] = mapped[1]
data[i]['xPosSlice'] = pos[0]
data[i]['xPosCell'] = pos[0]-cellPos[0]
data[i]['modXPosSlice'] = mapped[0]
data[i]['modXPosCell'] = mapped[0]-self.atlas.mapToAtlas(pg.Point(cellPos))[0]
prof.mark("filled protocol data array")
elif dirType == 'Cell':
data = np.empty(len(positions), dtype=[('SliceDir', object),
(dirColumn, object),
#('layer', float),
#('depth', float),
('yPosSlice', float),
#('yPosCell', float),
('percentDepth', float),
('xPosSlice', float),
#('xPosCell', float),
('modXPosSlice', float),
#('modXPosCell', float)
])
fields = collections.OrderedDict([
('SliceDir', 'directory:Slice'),
(dirColumn, 'directory:'+dirType),
('yPosSlice', 'real'),
('percentDepth', 'real'),
('xPosSlice', 'real'),
('modXPosSlice', 'real')])
prof.mark("defined cell data array")
for i in range(len(positions)):
dh, pos = positions[i]
#cellPos = self.dataModel.getCellInfo(dh)['pos']
mapped = self.atlas.mapToAtlas(pg.Point(pos)) ## needs to return %depth and modXPosSlice
#data[i] = (self.sliceDir, dh, mapped.x(), mapped.y(), mapped.z())
data[i]['SliceDir'] = self.sliceDir
data[i][dirColumn] = dh
data[i]['yPosSlice'] = pos[1]
#data['yPosCell'] = pos[1]-cellPos[1]
data[i]['percentDepth'] = mapped[1]
data[i]['xPosSlice'] = pos[0]
#data['xPosCell'] = pos[0]-cellPos[0]
data[i]['modXPosSlice'] = mapped[0]
#data['modXPosCell'] = mapped[0]-self.atlas.mapToAtlas(pg.Point(cellPos))[0]
prof.mark("filled cell data array")
else:
prof.finish()
raise Exception("Not sure how to structure data array for dirType=%s"%dirType)
prof.finish()
return data, fields