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, *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):
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, id, session, managerlocation, **kwargs):
self.correlator = correlator.Correlator()
self.correlation_types = ['cross', 'phase']
self.tableau_types = ['beam tilt series-power', 'split image-power']
if not hide_incomplete:
self.tableau_types.append('beam tilt series-image')
self.tiltdelta = 5e-3
self.tabscale = None
manualfocuschecker.ManualFocusChecker.__init__(self, id, session,
managerlocation,
**kwargs)
self.parameter_choice = 'Beam Tilt X'
self.increment = 5e-4
self.btcalclient = calibrationclient.BeamTiltCalibrationClient(self)
self.imageshiftcalclient = calibrationclient.ImageShiftCalibrationClient(
self)
self.euclient = calibrationclient.EucentricFocusClient(self)
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):
self.focus_methods = ordereddict.OrderedDict((
('Manual', self.manualCheckLoop),
('Beam Tilt', self.autoFocus),
('Stage Tilt', self.autoStage),
('None', self.noMeasure),
))
self.correction_types = ordereddict.OrderedDict((
('Defocus', self.correctDefocusStig),
('Stage Z', self.correctZ),
('None', self.correctNone),
))
self.correlation_types = ['cross', 'phase']
self.default_setting = {
'switch': True,
'preset name': 'Grid',
'focus method': 'Beam Tilt',
'tilt': 0.01,
'correlation type': 'phase',
'fit limit': 1000,
'delta min': 0.0,
'delta max': 1e-3,
'correction type': 'Defocus',
'stig correction': False,
'stig defocus min': 2e-6,
'stig defocus max': 4e-6,
'check drift': False,
'drift threshold': 3e-10,
'reset defocus': None,
}
self.manualplayer = player.Player(callback=self.onManualPlayer)
manualfocuschecker.ManualFocusChecker.__init__(self, id, session,
managerlocation,
**kwargs)
self.btcalclient = calibrationclient.BeamTiltCalibrationClient(self)
self.stagetiltcalclient = calibrationclient.StageTiltCalibrationClient(
self)
self.imageshiftcalclient = calibrationclient.ImageShiftCalibrationClient(
self)
self.euclient = calibrationclient.EucentricFocusClient(self)
self.focus_sequence = self.researchFocusSequence()
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):
calibrator.Calibrator.__init__(self, id, session, managerlocation,
**kwargs)
self.parameters = {
'image shift': calibrationclient.ImageShiftCalibrationClient(self),
'beam shift': calibrationclient.BeamShiftCalibrationClient(self),
}
self.parameter = 'beam shift'
self.pixsizeclient = calibrationclient.PixelSizeCalibrationClient(self)
self.settle = {
'image shift': 5.0,
'beam shift': 1.0,
}
self.axislist = ['x', 'y']
self.aborted = 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),
'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()