def __init__(self,
name,
groupName,
callbacks,
wavelength,
exposureTime,
trigHandler=None,
trigLine=None):
# Note we assume all light sources are eligible for experiments.
# However there's no associated callbacks for a light source.
super().__init__(name, groupName, True, callbacks, depot.LIGHT_TOGGLE)
self.wavelength = float(wavelength or 0)
self.defaultExposureTime = exposureTime
self.exposureTime = exposureTime
# Current enabled state
self.state = deviceHandler.STATES.disabled
# Set up trigger handling.
if trigHandler and trigLine:
h = trigHandler.registerDigital(self, trigLine)
self.triggerNow = h.triggerNow
if 'setExposing' not in callbacks:
cb = lambda name, state: trigHandler.setDigital(
trigLine, state)
callbacks['setExposing'] = cb
else:
self.triggerNow = lambda: None
# Most lasers use bulb-type triggering. Ensure they're not left on after
# an abort event.
if trigHandler and trigLine:
onAbort = lambda *args: trigHandler.setDigital(trigLine, False)
events.subscribe(events.USER_ABORT, onAbort)
def __init__(self, parent):
wx.Frame.__init__(self, parent, title = "Camera views",
style=wx.FRAME_NO_TASKBAR | wx.CAPTION)
self.numCameras = len(depot.getHandlersOfType(depot.CAMERA))
self.panel = wx.Panel(self)
# Make a 2xN grid of camera canvases, with menus above for selecting
# which camera to use in that location.
self.sizer = wx.FlexGridSizer(2, 5, 5)
## List of ViewPanels we contain.
self.views = []
for i in range(self.numCameras):
view = viewPanel.ViewPanel(self.panel)
self.views.append(view)
self.SetPosition((675, 280))
events.subscribe(events.CAMERA_ENABLE, self.onCameraEnableEvent)
events.subscribe("image pixel info", self.onImagePixelInfo)
cockpit.gui.keyboard.setKeyboardHandlers(self)
self.Bind(wx.EVT_CLOSE, self.onClose)
self.resetGrid()
self.SetDropTarget(cockpit.gui.viewFileDropTarget.ViewFileDropTarget(self))
def __init__(self, name, config):
super().__init__(name, config)
## Connection to the XYZ stage controller (serial.Serial instance)
self.xyzConnection = None
## Lock around sending commands to the XYZ stage controller.
self.xyzLock = threading.Lock()
## Cached copy of the stage's position. Initialized to an impossible
# value; this will be modified in initialize.
self.xyzPositionCache = (10 ** 100, 10 ** 100, 10 ** 100)
## Target positions for movement in X, Y and Z, or None if that ch is
# not moving.
self.xyzMotionTargets = [None, None, None]
## If there is a config section for the smaractMCS2, grab the config and
# subscribe to events.
try :
limitString = config.get('softlimits')
parsed = re.search(LIMITS_PAT, limitString)
if not parsed:
# Could not parse config entry.
raise Exception('Bad config: smaractMCS2XYZ Limits.')
# No transform tuple
else:
lstr = parsed.groupdict()['limits']
self.softlimits=eval(lstr)
except:
print ("No softlimits section setting default limits")
self.softlimits = ((-15000, -15000, -15000), (15000, 15000, 15000))
events.subscribe(events.USER_ABORT, self.onAbort)
def __init__(self, name, config={}):
super().__init__(name, config)
## Connection to the XY stage controller (serial.Serial instance).
self._proxy = Pyro4.Proxy(config.get('uri'))
## Lock around sending commands to the XY stage controller.
self.xyLock = threading.Lock()
## Cached copy of the stage's position.
self.positionCache = (None, None)
## Target positions for movement in X and Y.
self.motionTargets = [None, None]
## Flag to show that sendPositionUpdates is running.
self.sendingPositionUpdates = False
## Status dict updated by remote.
self.status = {}
## Keys for status items that should be logged
self.logger = valueLogger.ValueLogger(
name, keys=list(map('t_'.__add__, self._temperature_names)))
try:
xlim = self._proxy.get_value_limits('MotorSetpointX')
ylim = self._proxy.get_value_limits('MotorSetpointY')
except:
xlim, ylim = zip(*DEFAULT_LIMITS)
# _proxy may return (0,0) if it can't query the hardware.
if not any(xlim):
xlim, _ = zip(*DEFAULT_LIMITS)
if not any(ylim):
_, ylim = zip(*DEFAULT_LIMITS)
self.hardlimits = tuple(zip(xlim, ylim))
self.softlimits = self.hardlimits
events.subscribe(events.USER_ABORT, self.onAbort)
def makeUI(self, parent):
# TODO - this should probably live in a base deviceHandler.
self.panel = wx.Panel(parent)
sizer = wx.BoxSizer(wx.VERTICAL)
# Readout mode control
sizer.Add(wx.StaticText(self.panel, label="Readout mode"))
modeButton = wx.Choice(self.panel, choices=self._modenames)
self.updateModeButton(modeButton)
sizer.Add(modeButton, flag=wx.EXPAND)
events.subscribe(events.SETTINGS_CHANGED % self,
lambda: self.updateModeButton(modeButton))
modeButton.Bind(wx.EVT_CHOICE,
lambda evt: self.setReadoutMode(evt.GetSelection()))
sizer.AddSpacer(4)
# Gain control
sizer.Add(wx.StaticText(self.panel, label="Gain"))
gainButton = wx.Button(self.panel,
label="%s" % self.settings.get('gain', None))
if 'gain' not in self.settings:
gainButton.Disable()
gainButton.Bind(wx.EVT_BUTTON, self.onGainButton)
sizer.Add(gainButton, flag=wx.EXPAND)
events.subscribe(
events.SETTINGS_CHANGED % self, lambda: gainButton.SetLabel(
"%s" % self.settings.get('gain', None)))
sizer.AddSpacer(4)
# Settings button
adv_button = wx.Button(parent=self.panel, label='Settings')
adv_button.Bind(wx.EVT_LEFT_UP, self.showSettings)
sizer.Add(adv_button)
self.panel.SetSizerAndFit(sizer)
return self.panel
def __init__(self):
## Maps axis to the handlers for that axis, sorted by their range of
# motion.
self.axisToHandlers = depot.getSortedStageMovers()
## XXX: We have a single index for all axis, even though each
## axis may have a different number of stages. While we don't
## refactor this assumption, we just make copies of the movers
## with the most precise movement (issues #413 and #415)
self.n_stages = max([len(s) for s in self.axisToHandlers.values()])
for axis, stages in self.axisToHandlers.items():
stages.extend([stages[-1]] * (self.n_stages - len(stages)))
## Indicates which stage handler is currently under control.
self.curHandlerIndex = 0
## Maps Site unique IDs to Site instances.
self.idToSite = {}
## Maps handler names to events indicating if those handlers
# have stopped moving.
self.nameToStoppedEvent = {}
events.subscribe("stage mover", self.onMotion)
events.subscribe("stage stopped", self.onStop)
## Device-speficic primitives to draw on the macrostage.
self.primitives = set()
for h in depot.getHandlersOfType(depot.STAGE_POSITIONER):
ps = h.getPrimitives()
if ps:
self.primitives.update(ps)
self.primitives.discard(None)
def __init__(self, name, config):
super().__init__(name, config)
self.STAGE_CAL = config.get('cal') # e.g. 13.750
self.PICO_CONTROLLER = config.get('ipaddress') # e.g. 172.16.0.30'
self.PICO_PORT = config.get('port') # e.g. 23
## Maps the cockpit's axis ordering (0: X, 1: Y, 2: Z) to the
# XY stage's ordering which is
#x controller 1, motor 1 - '1>1'
#y controller 1, motor 2 - '1>2'
#z controller 2, motor 1 - '2>1'
#Needs moving to config file!
self.axisMapper = {0: '1>1', 1: '1>2', 2: '2>1'}
## Connection to the Z piezo controller (Pyro4.Proxy of a
# telnetlib.Telnet instance)
self.zConnection = None
## Lock around sending commands to the Z piezo controller.
self.zLock = threading.Lock()
## Connection to the XY stage controller (serial.Serial instance)
self.xyConnection = None
## Lock around sending commands to the XY stage controller.
self.xyLock = threading.Lock()
## Cached copy of the stage's position. Initialized to an impossible
# value; this will be modified in initialize.
self.xyPositionCache = [10**100, 10**100, 7500]
events.subscribe(events.USER_ABORT, self.onAbort)
def __init__(self, name, config={}):
super().__init__(name, config)
try:
limitString = config.get('softlimits', '')
parsed = re.search(LIMITS_PAT, limitString)
if not parsed:
# Could not parse config entry.
raise Exception('Bad config: Aerotech Limits.')
# No transform tuple
else:
lstr = parsed.groupdict()['limits']
self.softlimits = eval(lstr)
except:
print("No softlimits section setting default limits")
self.softlimits = (-30000, 7000)
# Subscribe to abort events.
events.subscribe(events.USER_ABORT, self.onAbort)
# The cockpit axis does this stage moves along.
self.axis = int(config.get('axis', 2))
# Socket used to communicate with controller.
self.socket = None
# Last known position (microns)
self.position = None
# Axis acceleration (mm / s^2)
self.acceleration = 200
# Axis maximum speed (mm / s^2)
self.speed = 20
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
## Handle of the current camera we're controlling.
self.curCamera = None
## Position of the currently displayed image - only updated on dbl-click.
self.imagePos = None
columnSizer = wx.BoxSizer(wx.VERTICAL)
## Clickable text box showing the name of the currently-selected
# camera.
self.selector = wx.StaticText(self,
style=wx.RAISED_BORDER | wx.ALIGN_CENTRE
| wx.ST_NO_AUTORESIZE,
size=(VIEW_WIDTH, 30))
self.selector.Bind(wx.EVT_LEFT_DOWN, self.onSelector)
self.selector.SetDoubleBuffered(True)
columnSizer.Add(self.selector, 0)
## Panel for holding our canvas.
self.canvasPanel = wx.Panel(self)
self.canvasPanel.SetMinSize((VIEW_WIDTH, VIEW_HEIGHT))
columnSizer.Add(self.canvasPanel)
self.SetSizerAndFit(columnSizer)
## Canvas we paint the camera's view onto. Created when we connect a
# camera, and destroyed after.
self.canvas = None
self.disable()
events.subscribe("filter change", self.onFilterChange)
self.Bind(wx.EVT_LEFT_DCLICK, self.onMouse)
def __init__(self, name, groupName, callbacks, dlines=None, alines=None):
# \param name: handler name
# \param groupname: handler and device group name
# \param callbacks: callbacks, as above
# \param dlines: optional, number of digital lines
# \param alines: optional, number of analogue lines
# Note that even though this device is directly involved in running
# experiments, it is never itself a part of an experiment, so
# we pass False for isEligibleForExperiments here.
super().__init__(name, groupName, False, callbacks, depot.EXECUTOR)
# Base class contains empty dicts used by mixins so that methods like
# getNumRunnableLines can be implemented here for all mixin combos. This
# works just great, but is probably a horrible abuse of OOP. It might be
# cleaner to have a single list of clients.
self.digitalClients = {}
self.analogClients = {}
# Number of digital and analogue lines.
self._dlines = dlines
self._alines = alines
if not isinstance(self, DigitalMixin):
self.registerDigital = self._raiseNoDigitalException
self.getDigital = self._raiseNoDigitalException
self.setDigital = self._raiseNoDigitalException
self.readDigital = self._raiseNoDigitalException
self.writeDigital = self._raiseNoDigitalException
self.triggerDigital = self._raiseNoDigitalException
if not isinstance(self, AnalogMixin):
self.registerAnalog = self._raiseNoAnalogException
self.setAnalog = self._raiseNoAnalogException
self.getAnalog = self._raiseNoAnalogException
self.setAnalogClient = self._raiseNoAnalogException
self.getAnalogClient = self._raiseNoAnalogException
events.subscribe(events.PREPARE_FOR_EXPERIMENT, self.onPrepareForExperiment)
events.subscribe(events.CLEANUP_AFTER_EXPERIMENT, self.cleanupAfterExperiment)
def __init__(self,
name,
groupName,
callbacks,
wavelength,
minPower,
maxPower,
curPower,
isEnabled=True,
units='mW'):
# Validation:
required = set(['getPower', 'setPower'])
missing = required.difference(callbacks)
if missing:
e = Exception('%s %s missing callbacks: %s.' %
(self.__class__.__name__, name, ' '.join(missing)))
raise e
super().__init__(name, groupName, False, callbacks, depot.LIGHT_POWER)
LightPowerHandler._instances.append(self)
self.wavelength = wavelength
self.minPower = minPower
self.maxPower = maxPower
self.lastPower = curPower
self.powerSetPoint = None
self.isEnabled = isEnabled
self.units = units
events.subscribe('save exposure settings', self.onSaveSettings)
events.subscribe('load exposure settings', self.onLoadSettings)
def __init__(self,
name,
groupName,
callbacks,
exposureMode,
trigHandler=None,
trigLine=None):
# Note we assume that cameras are eligible for experiments.
deviceHandler.DeviceHandler.__init__(self, name, groupName, True,
callbacks, depot.CAMERA)
## True if the camera is currently receiving images.
self.isEnabled = False
self._exposureMode = exposureMode
self.wavelength = None
self.dye = None
# Set up trigger handling.
if trigHandler and trigLine:
h = trigHandler.registerDigital(self, trigLine)
self.triggerNow = h.triggerNow
else:
softTrigger = self.callbacks.get('softTrigger', None)
self.triggerNow = lambda: softTrigger
if softTrigger:
depot.addHandler(
cockpit.handlers.imager.ImagerHandler(
"%s imager" % name, "imager",
{'takeImage': softTrigger}))
#subscribe to save and load setting calls to enabvle saving and
#loading of configurations.
events.subscribe('save exposure settings', self.onSaveSettings)
events.subscribe('load exposure settings', self.onLoadSettings)
def run(self):
# For debugging purposes
experiment.lastExperiment = self
self.sanityCheckEnvironment()
self.prepareHandlers()
self.cameraToReadoutTime = dict([(c, c.getTimeBetweenExposures(isExact = True)) for c in self.cameras])
for camera, readTime in self.cameraToReadoutTime.items():
if type(readTime) is not decimal.Decimal:
raise RuntimeError("Camera %s did not provide an exact (decimal.Decimal) readout time" % camera.name)
for camera, func in self.camToFunc.items():
events.subscribe(events.NEW_IMAGE % camera.name, func)
for exposureTime in self.exposureTimes:
if self.shouldAbort:
break
self.camToImages = {}
self.camToNumImagesReceived = {}
self.camToLock = {}
for camera in self.cameras:
# Prepare a memory buffer to store images in.
width, height = camera.getImageSize()
self.camToImages[camera] = numpy.zeros((self.numExposures, height, width))
self.camToNumImagesReceived[camera] = 0
self.camToLock[camera] = threading.Lock()
# Indicate any frame transfer cameras for reset at start of
# table.
if camera.getExposureMode() == cockpit.handlers.camera.TRIGGER_AFTER:
self.cameraToIsReady[camera] = False
self.table = self.generateActions(exposureTime)
self.table.sort()
self.examineActions()
self.table.sort()
self.table.enforcePositiveTimepoints()
self.lastMinuteActions()
self.doneReceivingThread = threading.Thread(target = self.waiter)
self.doneReceivingThread.start()
self.execute()
if self.shouldAbort:
break
# Wait until it's been a short time after the last received image.
self.doneReceivingThread.join()
progress = cockpit.gui.progressDialog.ProgressDialog("Processing images",
"Processing images for exposure time %.4f" % exposureTime,
parent = None)
self.processImages(exposureTime)
progress.Destroy()
for camera, func in self.camToFunc.items():
events.unsubscribe(events.NEW_IMAGE % camera.name, func)
self.save()
self.showResults()
self.cleanup()
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
## Whether or not to draw the mosaic tiles
self.shouldDrawMosaic = True
## True if we're in the processing of changing the soft motion limits.
self.amSettingSafeties = False
## Position the mouse first clicked when setting safeties, or None if
# we aren't setting safeties.
self.firstSafetyMousePos = None
## Last seen mouse position
self.lastMousePos = [0, 0]
primitive_specs = wx.GetApp().Config['stage'].getlines('primitives', [])
self._primitives = [Primitive.factory(spec) for spec in primitive_specs]
hardLimits = cockpit.interfaces.stageMover.getHardLimits()
self.minX, self.maxX = hardLimits[0]
self.minY, self.maxY = hardLimits[1]
## X extent of the stage, in microns.
stageWidth = self.maxX - self.minX
## Y extent of the stage, in microns.
stageHeight = self.maxY - self.minY
## Max of X or Y stage extents.
self.maxExtent = max(stageWidth, stageHeight)
## X and Y view extent.
if stageHeight > stageWidth:
self.viewExtent = 1.2 * stageHeight
self.viewDeltaY = stageHeight * 0.1
else:
self.viewExtent = 1.05 * stageWidth
self.viewDeltaY = stageHeight * 0.05
# Push out the min and max values a bit to give us some room around
# the stage to work with. In particular we need space below the display
# to show our legend.
self.centreX = ((self.maxX - self.minX) / 2) + self.minX
self.centreY = ((self.maxY - self.minY) / 2) + self.minY
self.minX = self.centreX - self.viewExtent / 2
self.maxX = self.centreX + self.viewExtent / 2
self.minY = self.centreY - self.viewExtent / 2 - self.viewDeltaY
self.maxY = self.centreY + self.viewExtent / 2 - self.viewDeltaY
## Size of text to draw. I confess I don't really understand how this
# corresponds to anything, but it seems to work out.
self.textSize = .004
self.Bind(wx.EVT_MOTION, self.OnMouseMotion)
self.Bind(wx.EVT_LEFT_UP, self.OnLeftClick)
self.Bind(wx.EVT_LEFT_DCLICK, self.OnLeftDoubleClick)
self.Bind(wx.EVT_RIGHT_UP, self.OnRightClick)
self.Bind(wx.EVT_RIGHT_DCLICK, self.OnRightDoubleClick)
# Bind context menu event to None to prevent main window context menu
# being displayed in preference to our own.
self.Bind(wx.EVT_CONTEXT_MENU, lambda event: None)
events.subscribe("soft safety limit", self.onSafetyChange)
events.subscribe('objective change', self.onObjectiveChange)
self.SetToolTip(wx.ToolTip("Left double-click to move the stage. " +
"Right click for gotoXYZ and double-click to toggle displaying of mosaic " +
"tiles."))
def __init__(self, name="dummy XY stage", config={}):
super().__init__(name, config)
# List of 2 doubles indicating our X/Y position.
self.curPosition = [1000, 1000]
events.subscribe(events.USER_ABORT, self.onAbort)
# Is this device in use?
self.active = False
self.deviceType = "stage positioner"
self.axes = [0, 1]
def startCollecting(self):
for camera in self.cameras:
def func(data, timestamp, camera=camera):
return self.onImage(self.cameraToIndex[camera], data, timestamp)
self.lambdas.append(func)
events.subscribe(events.NEW_IMAGE % camera.name, func)
self.minMaxVals.append((float('inf'), float('-inf')))
events.subscribe(events.USER_ABORT, self.onAbort)
self.statusThread.start()
def exposureMode(self, triggerType):
"""Set exposure mode.
If the device set a softTrigger handler, subscribe to "dummy take image"
if exposureMode is TRIGGER_SOFT, otherwise unsubscribe."""
self._exposureMode = triggerType
softTrigger = self.callbacks.get('softTrigger', None)
events.unsubscribe("dummy take image", softTrigger)
if softTrigger:
events.subscribe("dummy take image", softTrigger)
def finalizeInitialization(self):
if self.excitation:
self.setExMode(self.excitation[0])
self.temperatureConnection.connect(self.receiveTemperatureData)
# self.setStageMode('Inverted')
#set default emission path
#IMD 20170316 comment out as this is a hack for OMXT
# self.setDetMode('w/o AO & 209 nm pixel size')
#Subscribe to objective change to map new detector path to new pixel sizes via fake objective
events.subscribe('objective change', self.onObjectiveChange)
def __init__(self, parent, size, id=-1, *args, **kwargs):
super().__init__(parent, id, size=size, *args, **kwargs)
## WX context for drawing.
self.context = wx.glcanvas.GLContext(self)
## Whether or not we have done some one-time-only logic.
self.haveInitedGL = False
## Whether or not we should try to draw
self.shouldDraw = True
## Font for drawing text
try:
self.font = ftgl.TextureFont(cockpit.gui.FONT_PATH)
self.font.setFaceSize(18)
except Exception as e:
print("Failed to make font:", e)
## X values below this are off the canvas. We leave it up to children
# to fill in proper values for these.
self.minX = 0
## X values above this are off the canvas
self.maxX = 1000
## Y values below this are off the canvas
self.minY = 0
## Y values above this are off the canvas
self.maxY = 1000
## (X, Y, Z) vector describing the stage position as of the last
# time we drew ourselves. We need this to display motion deltas.
self.prevStagePosition = numpy.zeros(3)
## As above, but for the current position.
self.curStagePosition = numpy.zeros(3)
## Event used to indicate when drawing is done, so we can update
# the above.
self.drawEvent = threading.Event()
##objective offset info to get correct position and limits
self.objective = depot.getHandlersOfType(depot.OBJECTIVE)[0]
self.listObj = list(self.objective.nameToOffset.keys())
self.listOffsets = list(self.objective.nameToOffset.values())
self.offset = self.objective.getOffset()
## Boolean to just force a redraw.
self.shouldForceRedraw = False
## Thread that ensures we don't spam redisplaying ourselves.
self.redrawTimerThread = threading.Thread(target=self.refreshWaiter,
name="macrostage-refresh")
self.redrawTimerThread.start()
self.Bind(wx.EVT_PAINT, self.onPaint)
self.Bind(wx.EVT_SIZE, lambda event: event)
self.Bind(wx.EVT_ERASE_BACKGROUND,
lambda event: event) # Do nothing, to avoid flashing
events.subscribe(events.STAGE_POSITION, self.onMotion)
events.subscribe("stage step index", self.onStepIndexChange)
def __init__(self, device, parent=None, handler=None):
wx.Frame.__init__(self,
parent,
wx.ID_ANY,
style=wx.FRAME_FLOAT_ON_PARENT)
self.device = device
self.SetTitle("%s settings" % device.name)
self.settings = {}
self.current = {}
self.handler = handler
#self.handler.addListener(self)
#self.panel = wx.Panel(self, wx.ID_ANY, style=wx.WANTS_CHARS)
sizer = wx.BoxSizer(wx.VERTICAL)
self.grid = wx.propgrid.PropertyGrid(
self, style=wx.propgrid.PG_SPLITTER_AUTO_CENTER)
self.grid.SetColumnProportion(0, 2)
self.grid.SetColumnProportion(1, 1)
self.populateGrid()
self.Bind(wx.propgrid.EVT_PG_CHANGED, self.onPropertyChange)
sizer.Add(self.grid, 1, wx.EXPAND | wx.ALIGN_LEFT | wx.ALIGN_TOP)
sizer.AddSpacer(2)
buttonSizer = wx.BoxSizer(wx.HORIZONTAL)
#saveButton = wx.Button(self, id=wx.ID_SAVE)
#saveButton.SetToolTip(wx.ToolTip("Save current settings as defaults."))
#saveButton.Bind(wx.EVT_BUTTON, self.onSave)
#buttonSizer.Add(saveButton, 0, wx.ALIGN_RIGHT, 0, 0)
okButton = wx.Button(self, id=wx.ID_OK)
okButton.Bind(wx.EVT_BUTTON, self.onClose)
okButton.SetToolTip(
wx.ToolTip("Apply settings and close this window."))
buttonSizer.Add(okButton, 0, wx.ALIGN_RIGHT)
cancelButton = wx.Button(self, id=wx.ID_CANCEL)
cancelButton.Bind(wx.EVT_BUTTON, self.onClose)
cancelButton.SetToolTip(
wx.ToolTip("Close this window without applying settings."))
buttonSizer.Add(cancelButton, 0, wx.ALIGN_RIGHT)
applyButton = wx.Button(self, id=wx.ID_APPLY)
applyButton.SetToolTip(wx.ToolTip("Apply these settings."))
applyButton.Bind(wx.EVT_BUTTON,
lambda evt: self.device.updateSettings(self.current))
buttonSizer.Add(applyButton, 0, wx.ALIGN_RIGHT)
sizer.Add(buttonSizer, 0, wx.ALIGN_CENTER, 0, 0)
self.SetSizerAndFit(sizer)
self.SetMinSize((256, -1))
events.subscribe(events.SETTINGS_CHANGED % self.device,
self.updateGrid)
self.Bind(wx.EVT_SHOW, lambda evt: self.updateGrid())
def toggleSyncViews(self, event=None):
self.syncViews = not self.syncViews
if self.syncViews:
events.subscribe(
events.SYNCED_VIEW,
self.setView,
)
else:
events.unsubscribe(
events.SYNCED_VIEW,
self.setView,
)
def __init__(self, name, groupName, isEligibleForExperiments, callbacks,
cameras, lights):
super().__init__(name, groupName, isEligibleForExperiments, callbacks,
depot.LIGHT_FILTER)
self.cameras = cameras or []
self.lights = lights or []
self.lastFilter = None
#subscribe to save and load setting calls to enabvle saving and
#loading of configurations.
events.subscribe('save exposure settings', self.onSaveSettings)
events.subscribe('load exposure settings', self.onLoadSettings)
def __init__(self, images, title, *args, **kwargs):
super().__init__(*args, **kwargs)
self.images = images
self.title = title
## Current image/pixel under examination.
self.curViewIndex = numpy.zeros(5, dtype=numpy.int)
## Panel for holding UI widgets.
self.panel = wx.Panel(self)
self.panel.SetBackgroundColour(wx.WHITE)
# Set up our UI -- just a collection of sliders to change the
# image we show, plus some keyboard shortcuts.
## Maps axes to the Sliders for those axes.
self.axisToSlider = dict()
sizer = wx.BoxSizer(wx.VERTICAL)
sliderSizer = wx.BoxSizer(wx.HORIZONTAL)
for i, label in enumerate(['Wavelength', 'Time', 'Z']):
if self.images.shape[i] > 1:
# We need a slider for this dimension.
sliderSizer.Add(self.makeSlider(i, label))
sizer.Add(sliderSizer)
self.canvas = cockpit.gui.imageViewer.viewCanvas.ViewCanvas(
self.panel,
size=(self.images.shape[-1], self.images.shape[-2] + 40))
sizer.Add(self.canvas)
self.panel.SetSizerAndFit(sizer)
temp = wx.BoxSizer(wx.VERTICAL)
temp.Add(self.panel)
self.SetSizerAndFit(temp)
self.Show()
# For some reason, if we don't do this, then the first time we try
# to access curViewIndex in self.setCurImage we get strange values.
self.setCurImage()
events.subscribe('image pixel info', self.onImagePixelInfo)
self.Bind(wx.EVT_CLOSE, self.onClose)
accelTable = wx.AcceleratorTable([(wx.ACCEL_NORMAL,
wx.WXK_NUMPAD_MULTIPLY, 1),
(wx.ACCEL_NORMAL, wx.WXK_LEFT, 2),
(wx.ACCEL_NORMAL, wx.WXK_RIGHT, 3),
(wx.ACCEL_NORMAL, wx.WXK_UP, 4),
(wx.ACCEL_NORMAL, wx.WXK_DOWN, 5)])
self.SetAcceleratorTable(accelTable)
self.Bind(wx.EVT_MENU, self.onRescale, id=1)
for id, delta in [(2, (0, -1)), (3, (0, 1)), (4, (-1, 0)),
(5, (1, 0))]:
self.Bind(wx.EVT_MENU,
lambda event, delta=delta: self.shiftView(delta),
id=id)
def __init__(self,
name,
groupName,
settings=None,
settingIndex=None,
callbacks={}):
super().__init__(name, groupName, False, callbacks, depot.DRAWER)
self.settings = settings
self.settingIndex = settingIndex
## List of ToggleButtons, one per setting.
self.buttons = []
# Last thing to do is update UI to show default selections.
events.subscribe('cockpit initialization complete', self.changeDrawer)
def __init__(self, name="dummy XY stage", config={}):
config['primitives'] = \
"r 12500 6000 3000 3000\n" \
"c 5000 6000 3000\n" \
"c 20000, 6000, 3000\n"
super(DummyMover, self).__init__(name, config)
# List of 2 doubles indicating our X/Y position.
self.curPosition = [1000, 1000]
events.subscribe('user abort', self.onAbort)
# Is this device in use?
self.active = False
self.deviceType = "stage positioner"
self.axes = [0, 1]
def __init__(self, name, groupName, nameToPixelSize, nameToTransform, nameToOffset, nameToColour, nameToLensID, curObjective,
callbacks = {}):
super().__init__(name, groupName, False, {}, depot.OBJECTIVE)
self.nameToPixelSize = nameToPixelSize
self.nameToTransform = nameToTransform
self.nameToOffset = nameToOffset
self.nameToColour = nameToColour
self.nameToLensID = nameToLensID
self.curObjective = curObjective
self.callbacks = callbacks
## List of ToggleButtons, one per objective.
self.buttons = []
events.subscribe('save exposure settings', self.onSaveSettings)
events.subscribe('load exposure settings', self.onLoadSettings)
def enable(self, camera):
self.selector.SetLabel(camera.descriptiveName)
self.selector.SetBackgroundColour(camera.color)
self.selector.Refresh()
self.curCamera = camera
# NB the 512 here is the largest texture size our graphics card can
# gracefully handle.
self.canvas = cockpit.gui.imageViewer.viewCanvas.ViewCanvas(
self.canvasPanel, size=(VIEW_WIDTH, VIEW_HEIGHT))
self.canvas.SetSize((VIEW_WIDTH, VIEW_HEIGHT))
self.canvas.resetView()
# Subscribe to new image events only after canvas is prepared.
events.subscribe(events.NEW_IMAGE % self.curCamera.name, self.onImage)
def __init__(self):
## Maps axis to the handlers for that axis, sorted by their range of
# motion.
self.axisToHandlers = depot.getSortedStageMovers()
if set(self.axisToHandlers.keys()) != {0, 1, 2}:
raise ValueError('stage mover requires 3 axis: X, Y, and Z')
# FIXME: we should have sensible defaults.
self._saved_top = userConfig.getValue('savedTop', default=3010.0)
self._saved_bottom = userConfig.getValue('savedBottom', default=3000.0)
## XXX: We have a single index for all axis, even though each
## axis may have a different number of stages. While we don't
## refactor this assumption, we just make copies of the movers
## with the most precise movement (issues #413 and #415)
self.n_stages = max([len(s) for s in self.axisToHandlers.values()])
for axis, stages in self.axisToHandlers.items():
stages.extend([stages[-1]] * (self.n_stages - len(stages)))
## Indicates which stage handler is currently under control.
self.curHandlerIndex = 0
## Maps Site unique IDs to Site instances.
self.idToSite = {}
# Compute the hard motion limits for each axis as the
# summation of all limits for handlers on that axis.
hard_limits = [None] * 3
for axis in range(3):
lower = 0.0
upper = 0.0
# We need set() to avoid duplicated handlers, and we might
# have duplicated handlers because of the hack to meet
# cockpit requirements that all axis have the same number
# of handlers (see comments on issue #413).
for handler in set(self.axisToHandlers[axis]):
handler_limits = handler.getHardLimits()
lower += handler_limits[0]
upper += handler_limits[1]
hard_limits[axis] = (lower, upper)
# Use a tuple to prevent changes to it, and assemble it like
# this to enable static code analysis.
self._hard_limits = (hard_limits[0], hard_limits[1], hard_limits[2])
## Maps handler names to events indicating if those handlers
# have stopped moving.
self.nameToStoppedEvent = {}
events.subscribe(events.STAGE_MOVER, self.onMotion)
events.subscribe(events.STAGE_STOPPED, self.onStop)
def __init__(self, parent):
wx.Frame.__init__(self, parent, title = "Status information",
style = wx.RESIZE_BORDER | wx.CAPTION | wx.FRAME_NO_TASKBAR)
self.panel = wx.Panel(self)
## Maps status light names to the lights themselves. Each light is
# a ToggleButton instance.
self.nameToLight = {}
events.subscribe('new status light', self.onNewLight)
events.subscribe('update status light', self.onNewStatus)
# Some lights that we know we need.
self.onNewLight('image count', '')
self.onNewLight('device waiting', '')
self.Show()
def __init__(self, parent, size, id=-1, *args, **kwargs):
super().__init__(parent, id, size=size, *args, **kwargs)
## WX context for drawing.
self.context = wx.glcanvas.GLContext(self)
## Whether or not we have done some one-time-only logic.
self.haveInitedGL = False
## Whether or not we should try to draw
self.shouldDraw = True
## Font for drawing text
self.face = cockpit.gui.freetype.Face(18)
## X values below this are off the canvas. We leave it up to children
# to fill in proper values for these.
self.minX = 0
## X values above this are off the canvas
self.maxX = 1000
## Y values below this are off the canvas
self.minY = 0
## Y values above this are off the canvas
self.maxY = 1000
## (X, Y, Z) vector describing the stage position as of the last
# time we drew ourselves. We need this to display motion deltas.
self.prevStagePosition = numpy.zeros(3)
## As above, but for the current position.
self.curStagePosition = numpy.zeros(3)
## Event used to indicate when drawing is done, so we can update
# the above.
self.drawEvent = threading.Event()
## Boolean to just force a redraw.
self.shouldForceRedraw = False
## Thread that ensures we don't spam redisplaying ourselves.
self.redrawTimerThread = threading.Thread(target=self.refreshWaiter,
name="macrostage-refresh",
daemon=True)
self.redrawTimerThread.start()
self.Bind(wx.EVT_PAINT, self.onPaint)
self.Bind(wx.EVT_SIZE, lambda event: event)
self.Bind(wx.EVT_ERASE_BACKGROUND,
lambda event: event) # Do nothing, to avoid flashing
events.subscribe(events.STAGE_POSITION, self.onMotion)
events.subscribe("stage step index", self.onStepIndexChange)
