def __init__(self, id, session, managerlocation, **kwargs):
node.Node.__init__(self, id, session, managerlocation, **kwargs)
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[
'beam shift'] = calibrationclient.BeamShiftCalibrationClient(self)
self.calclients[
'image beam shift'] = calibrationclient.ImageBeamShiftCalibrationClient(
self)
self.pcal = calibrationclient.PixelSizeCalibrationClient(self)
self.presetsclient = presets.PresetsClient(self)
self.stagelocations = []
self.getLocationsFromDB()
self.correlator = correlator.Correlator()
self.peakfinder = peakfinder.PeakFinder()
self.oldimagedata = None
self.newimagedata = None
self.oldstate = None
self.newstate = None
self.addEventInput(event.MoveToTargetEvent, self.handleMoveEvent)
self.start()
def __init__(self, id, session, managerlocation, **kwargs):
targetfinder.ClickTargetFinder.__init__(self, id, session,
managerlocation, **kwargs)
self.userpause = threading.Event()
self.currentindex = None
self.presetsclient = presets.PresetsClient(self)
self.ancestorpreset = self.settings['ancestor preset']
# Focus target disabled for now
# self.ancestortargetnames = ['acquisition','focus']
self.ancestortargetnames = ['acquisition']
self.targetrelation2display = {
'acquisition': 'c_acquisition',
# 'focus':'c_focus',
'transformed': 'transformed',
}
self.targetrelation2original = {
'c_acquisition': 'acquisition',
# 'c_focus':'focus',
'transformed': 'transformed',
}
self.childtargetnames = self.targetrelation2original.keys()
self.displayedtargetnames = self.ancestortargetnames + self.childtargetnames
self.imageids = None
self.start()
def __init__(self, id, session, managerlocation, **kwargs):
self.grids = Grids(self)
self.insertion = None
node.Node.__init__(self, id, session, managerlocation, **kwargs)
targethandler.TargetWaitHandler.__init__(self)
self.instrument = instrument.Proxy(self.objectservice, self.session)
self.presetsclient = presets.PresetsClient(self)
self.abortevent = threading.Event()
calibrationclients = {
'image shift': calibrationclient.ImageShiftCalibrationClient,
'stage position': calibrationclient.StageCalibrationClient,
'modeled stage position':
calibrationclient.ModeledStageCalibrationClient,
'image beam shift':
calibrationclient.ImageBeamShiftCalibrationClient,
}
self.calibrationclients = {}
for i, clientclass in calibrationclients.items():
self.calibrationclients[i] = clientclass(self)
self.projectdata = None
try:
self.projectdata = project.ProjectData()
except Exception, e:
self.logger.warning(
'Failed to connect to the project database: %s' % e)
def __init__(self, *args, **kwargs):
try:
watch = kwargs['watchfor']
except KeyError:
watch = []
kwargs['watchfor'] = watch + [event.ReferenceTargetPublishEvent]
watcher.Watcher.__init__(self, *args, **kwargs)
targethandler.TargetHandler.__init__(self)
self.instrument = instrument.Proxy(self.objectservice, self.session)
self.calibration_clients = {
'image shift':
calibrationclient.ImageShiftCalibrationClient(self),
'stage position':
calibrationclient.StageCalibrationClient(self),
'modeled stage position':
calibrationclient.ModeledStageCalibrationClient(self),
'image beam shift':
calibrationclient.ImageBeamShiftCalibrationClient(self),
'beam shift':
calibrationclient.BeamShiftCalibrationClient(self),
}
self.presets_client = presets.PresetsClient(self)
self.player = player.Player(callback=self.onPlayer)
self.panel.playerEvent(self.player.state())
self.lock = threading.RLock()
self.reference_target = None
self.last_processed = None
if self.__class__ == Reference:
self.start()
def __init__(self, id, session, managerlocation, **kwargs): TargetMaker.__init__(self, id, session, managerlocation, **kwargs) self.pixelsizecalclient = calibrationclient.PixelSizeCalibrationClient(self) self.addEventInput(event.MakeTargetListEvent, self._makeAtlas) self.presetsclient = presets.PresetsClient(self) self.publishargs = None self.start()
def __init__(self, id, session, managerlocation, **kwargs): node.Node.__init__(self, id, session, managerlocation, **kwargs) self.instrument = instrument.Proxy(self.objectservice, self.session, self.panel) self.presetsclient = presets.PresetsClient(self) self.player = player.Player(callback=self.onPlayer) self.panel.playerEvent(self.player.state()) self.lock = threading.RLock() self.addEventInput(event.MakeTargetListEvent, self.onProcessing) self.userpause = threading.Event() self.endlocation = None self.start()
def __init__(self, *args, **kwargs):
self.publishargs = None
node.Node.__init__(self, *args, **kwargs)
self.instrument = instrument.Proxy(self.objectservice, self.session)
self.calibrationclients = {
'stage position': calibrationclient.StageCalibrationClient(self),
}
self.presetsclient = presets.PresetsClient(self)
self.addEventInput(event.MakeTargetListEvent, self._makeAtlas)
self.start()
def __init__(self, id, session, managerlocation, **kwargs):
watchfor = [event.DriftMonitorRequestEvent]
watcher.Watcher.__init__(self, id, session, managerlocation, watchfor,
**kwargs)
self.correlator = correlator.Correlator()
self.peakfinder = peakfinder.PeakFinder()
self.instrument = instrument.Proxy(self.objectservice, self.session,
self.panel)
self.pixsizeclient = calibrationclient.PixelSizeCalibrationClient(self)
self.presetsclient = presets.PresetsClient(self)
self.abortevent = threading.Event()
self.start()
def __init__(self, id, session, managerlocation, **kwargs):
imagewatcher.ImageWatcher.__init__(self, id, session, managerlocation,
**kwargs)
targethandler.TargetWaitHandler.__init__(self)
self.instrument = instrument.Proxy(self.objectservice, self.session)
self.presetsclient = presets.PresetsClient(self)
self.calclients = {
'image shift': calibrationclient.ImageShiftCalibrationClient(self),
'stage position': calibrationclient.StageCalibrationClient(self),
'modeled stage position':
calibrationclient.ModeledStageCalibrationClient(self)
}
self.parent_imageid = None
self.focusing_targetlist = None
self.resetLastFocusedTargetList(None)
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()
def __init__(self, *args, **kwargs):
targetfilter.TargetFilter.__init__(self, *args, **kwargs)
self.instrument = instrument.Proxy(self.objectservice, self.session)
self.presetsclient = presets.PresetsClient(self)
self.calclients = {
'image shift': calibrationclient.ImageShiftCalibrationClient(self),
'stage position': calibrationclient.StageCalibrationClient(self),
'modeled stage position':
calibrationclient.ModeledStageCalibrationClient(self)
}
self.targetdata = None
self.fromtarget = None
self.donetargetids = []
self.is_odd = True
if self.__class__ == RasterTargetFilter:
self.start()
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 __init__(self, id, session, managerlocation, **kwargs):
imagewatcher.ImageWatcher.__init__(self, id, session, managerlocation,
**kwargs)
targethandler.TargetWaitHandler.__init__(self)
self.instrument = instrument.Proxy(self.objectservice, self.session)
self.presetsclient = presets.PresetsClient(self)
self.calclients = {
'image shift': calibrationclient.ImageShiftCalibrationClient(self),
'stage position': calibrationclient.StageCalibrationClient(self),
'modeled stage position':
calibrationclient.ModeledStageCalibrationClient(self),
'beam size':
calibrationclient.BeamSizeCalibrationClient(self)
}
self.parent_imageid = None
self.current_image_pixelsize = None
self.focusing_targetlist = None
self.last_acq_node = None
self.next_acq_node = None
self.targetimagevector = (0,0)
self.targetbeamradius = 0
self.resetLastFocusedTargetList(None)
def __init__(self, id, session, managerlocation, **kwargs):
self.mosaicselectionmapping = {}
targetfinder.ClickTargetFinder.__init__(self, id, session,
managerlocation, **kwargs)
self.calclients = {
'image shift':
calibrationclient.ImageShiftCalibrationClient(self),
'stage position':
calibrationclient.StageCalibrationClient(self),
'modeled stage position':
calibrationclient.ModeledStageCalibrationClient(self)
}
self.images = {
'Original': None,
'Extra Crispy': None,
'Filtered': None,
'Thresholded': None
}
parameter = self.settings['calibration parameter']
self.mosaic = mosaic.EMMosaic(self.calclients[parameter])
self.mosaicimagelist = None
self.mosaicimage = None
self.mosaicimagescale = None
self.mosaicimagedata = None
self.convolver = convolver.Convolver()
self.currentposition = []
self.mosaiccreated = threading.Event()
self.presetsclient = presets.PresetsClient(self)
self.mosaic.setCalibrationClient(self.calclients[parameter])
self.existing_targets = {}
self.clearTiles()
self.reference_target = None
if self.__class__ == MosaicClickTargetFinder:
self.start()
def __init__(self, id, session, managerlocation, **kwargs):
node.Node.__init__(self, id, session, managerlocation, **kwargs)
self.cortypes = ['cross', 'phase']
self.instrument = instrument.Proxy(self.objectservice, self.session,
self.panel)
self.presetsclient = presets.PresetsClient(self)
