def researchMosaicTileData(self):
tilequery = leginondata.MosaicTileData(
session=self.session, list=leginondata.ImageListData())
mosaictiles = self.research(datainstance=tilequery)
mosaiclists = ordereddict.OrderedDict()
for tile in mosaictiles:
list = tile['list']
label = '(no label)'
if list['targets'] is not None:
if list['targets']['label']:
label = list['targets']['label']
key = '%s: %s' % (list.dbid, label)
if key not in mosaiclists:
mosaiclists[key] = []
mosaiclists[key].append(tile)
self.mosaicselectionmapping = mosaiclists
return mosaiclists
def __init__(self, id, session, managerlocation, **kwargs):
targetwatcher.TargetWatcher.__init__(self, id, session, managerlocation, **kwargs)
self.addEventInput(event.AcquisitionImagePublishEvent, self.handleDriftImage)
self.addEventInput(event.DriftMonitorResultEvent, self.handleDriftResult)
self.addEventInput(event.ImageProcessDoneEvent, self.handleImageProcessDone)
self.addEventInput(event.MakeTargetListEvent, self.setGrid)
self.driftdone = threading.Event()
self.driftimagedone = threading.Event()
self.instrument = instrument.Proxy(self.objectservice, self.session)
self.calclients = ordereddict.OrderedDict()
self.calclients['image shift'] = calibrationclient.ImageShiftCalibrationClient(self)
self.calclients['stage position'] = calibrationclient.StageCalibrationClient(self)
self.calclients['modeled stage position'] = calibrationclient.ModeledStageCalibrationClient(self)
self.calclients['image beam shift'] = calibrationclient.ImageBeamShiftCalibrationClient(self)
self.calclients['beam shift'] = calibrationclient.BeamShiftCalibrationClient(self)
self.calclients['beam tilt'] = calibrationclient.BeamTiltCalibrationClient(self)
self.presetsclient = presets.PresetsClient(self)
self.navclient = navigator.NavigatorClient(self)
self.doneevents = {}
self.onTarget = False
self.imagelistdata = None
self.simloopstop = threading.Event()
self.received_image_drift = threading.Event()
self.requested_drift = None
self.grid = None
self.acq_counter = itertools.cycle(range(0,5))
self.time0 = time.time()
self.times = []
self.intensities = []
self.alignzlp_bound = False
self.alignzlp_warned = False
self.duplicatetypes = ['acquisition', 'focus']
self.presetlocktypes = ['acquisition', 'target', 'target list']
if debug:
self.timedebug = {}
self.start()
def holeStatsTargets(self, holes):
targets = []
for hole in holes:
mean = float(hole.stats['hole_mean'])
tmean = self.icecalc.get_thickness(mean)
std = float(hole.stats['hole_std'])
tstd = self.icecalc.get_stdev_thickness(std, mean)
target = {}
target['x'] = hole.stats['center'][1]
target['y'] = hole.stats['center'][0]
target['stats'] = ordereddict.OrderedDict()
target['stats']['Mean Intensity'] = mean
target['stats']['Mean Thickness'] = tmean
target['stats']['S.D. Intensity'] = std
target['stats']['S.D. Thickness'] = tstd
targets.append(target)
return targets
def makeWellTargetsAndStats(self):
'''
Make targets to be set to gui.wx.TargetPanel.
The targets in the list have information
of the grid format raster and the plate well name coded in stats
'''
targets = []
for spot_number in range(1, len(self.spottargets) + 1):
spottarget = self.spottargets[spot_number]
spot = spottarget['coord']
spotmap = spottarget['map']
target = {}
target['x'] = spot[0]
target['y'] = spot[1]
target['stats'] = ordereddict.OrderedDict()
target['stats']['Raster Col'] = spotmap['spot position']['col']
target['stats']['Raster Row'] = spotmap['spot position']['row']
target['stats']['Well Name'] = spotmap['name']
targets.append(target)
return targets
def __init__(self, node, logger, threaded=True, queueclass=Queue.Queue, tcpport=None):
self.logger = logger
self.server = datatransport.Server(self, logger, tcpport=tcpport)
self.node = node
## this is a mapping of data class to function
## using list instead of dict to preserve order, and also
## because there may be more than one function for every
## data class
self.threaded = threaded
self.bindings = ordereddict.OrderedDict()
self.remotecallobjects = {}
## a queue to hold incoming data, and a thread
## to process data from the queue
self.exitedevent = threading.Event()
self.queue = queueclass()
t = threading.Thread(name='data binder queue thread',
target=self.handlerLoop)
#t.setDaemon(1)
t.start()
def __init__(self, id, session, managerlocation, **kwargs):
node.Node.__init__(self, id, session, managerlocation, **kwargs)
TargetTransformer.__init__(self)
self.correlator = correlator.Correlator()
self.peakfinder = peakfinder.PeakFinder()
self.instrument = instrument.Proxy(self.objectservice, self.session,
self.panel)
self.calclients = ordereddict.OrderedDict()
self.calclients['image shift'] = calibrationclient.ImageShiftCalibrationClient(self)
self.calclients['stage position'] = calibrationclient.StageCalibrationClient(self)
self.calclients['modeled stage position'] = calibrationclient.ModeledStageCalibrationClient(self)
self.calclients['image beam shift'] = calibrationclient.ImageBeamShiftCalibrationClient(self)
self.calclients['beam shift'] = calibrationclient.BeamShiftCalibrationClient(self)
self.pixsizeclient = calibrationclient.PixelSizeCalibrationClient(self)
self.presetsclient = presets.PresetsClient(self)
self.navclient = navigator.NavigatorClient(self)
self.target_to_transform = None
self.addEventInput(event.TransformTargetEvent, self.handleTransformTargetEvent)
self.registrations = {
'correlation': transformregistration.CorrelationRegistration(self),
}
if not hide_incomplete:
self.registrations.update({
'keypoints': transformregistration.KeyPointsRegistration(self),
'logpolar': transformregistration.LogPolarRegistration(self),
'identity': transformregistration.IdentityRegistration(self),
})
self.abortevent = threading.Event()
self.player = player.Player(callback=self.onPlayer)
self.panel.playerEvent(self.player.state())
self.start()