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'], 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 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
