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()