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)