def __init__(self, lightToSequence, lightToIsOnDuringAcquisition,
**kwargs):
# Convert from light source names to light handlers.
self.lightToSequence = {}
for name, sequence in lightToSequence.items():
handler = depot.getHandlerWithName(name)
self.lightToSequence[handler] = sequence
self.lightToIsOnDuringAcquisition = {}
for name, isOn in lightToIsOnDuringAcquisition.items():
handler = depot.getHandlerWithName(name)
self.lightToIsOnDuringAcquisition[handler] = isOn
# Call the ZStackExperiment constructor with all of our remaining
# parameters, which are in the "kwargs" dictionary object.
super().__init__(**kwargs)
def augmentParams(self, params):
self.saveSettings()
params['settlingTime'] = guiUtils.tryParseNum(self.settlingTimeControl, float)
params['startV'] = guiUtils.tryParseNum(self.startVControl, float)
params['maxV'] = guiUtils.tryParseNum(self.maxVControl, float)
params['vSteps'] = guiUtils.tryParseNum(self.vStepsControl)
params['polarizerHandler'] = depot.getHandlerWithName('SI polarizer')
return params
def augmentParams(self, params):
self.saveSettings()
params['numAngles'] = 3
params['numPhases'] = 5
params['collectionOrder'] = self.siCollectionOrder.GetStringSelection()
params['angleHandler'] = depot.getHandlerWithName('SI angle')
params['phaseHandler'] = depot.getHandlerWithName('SI phase')
params['polarizerHandler'] = depot.getHandlerWithName('SI polarizer')
params['slmHandler'] = depot.getHandler('slm', depot.EXECUTOR)
compensations = {}
for i, light in enumerate(self.allLights):
val = guiUtils.tryParseNum(self.bleachCompensations[i], float)
if val:
# Convert from percentage to multiplier
compensations[light] = .01 * float(val)
else:
compensations[light] = 0
params['bleachCompensations'] = compensations
return params
def takeImage(self):
if not self.digitalClients:
# No triggered devices registered.
return
camlines = sum([1<<self.digitalClients[cam] for cam in self.activeCameras])
# We want to know if there are cameras using rolling shutter. If so, cameras must be triggered in advance
exposureStartTime = [cam.getTimeBetweenExposures() for cam in self.activeCameras
if cam.getShutteringMode() == ElectronicShutteringMode.ROLLING]
exposureStartTime = max(exposureStartTime, default=0)
if camlines == 0:
# No cameras to be triggered.
return
ltpairs = []
for light in self.activeLights:
lline = 1 << self.digitalClients[light]
ltime = light.getExposureTime()
ltpairs.append((lline, ltime))
# Sort by exposure time
ltpairs.sort(key = lambda item: item[1])
# Generate a sequence of (time, digital state)
# TODO: currently uses bulb exposure; should support other modes.
if ltpairs:
# Start by all active cameras and lights.
state = camlines | functools.reduce(operator.ior, list(zip(*ltpairs))[0])
if exposureStartTime != 0:
seq = [(0, camlines)]
seq.append((exposureStartTime, state))
# Switch off each light as its exposure time expires.
for lline, ltime in ltpairs:
state -= lline
seq.append((exposureStartTime + ltime, state))
else:
# No lights. Just trigger the cameras.
seq = [(0, camlines)]
# If there is an ambient light enabled, extend exposure as
# necessary (see issue #669).
ambient = depot.getHandlerWithName('Ambient')
if ambient is not None and ambient.getIsEnabled():
t = ambient.getExposureTime()
if t > seq[-1][0]:
seq.append((ambient.getExposureTime(), 0))
# Switch all lights and cameras off.
seq.append( (seq[-1][0] + 1, 0) )
if self.callbacks.get('runSequence', None):
self.callbacks['runSequence'](seq)
else:
self.softSequence(seq)
def takeImage(self):
if not self.digitalClients:
# No triggered devices registered.
return
camlines = sum(
[1 << self.digitalClients[cam] for cam in self.activeCameras])
if camlines == 0:
# No cameras to be triggered.
return
ltpairs = []
for light in self.activeLights:
lline = 1 << self.digitalClients[light]
ltime = light.getExposureTime()
ltpairs.append((lline, ltime))
# Sort by exposure time
ltpairs.sort(key=lambda item: item[1])
# Generate a sequence of (time, digital state)
# TODO: currently uses bulb exposure; should support other modes.
if ltpairs:
# Start by all active cameras and lights.
state = camlines | functools.reduce(operator.ior,
list(zip(*ltpairs))[0])
seq = [(0, state)]
# Switch off each light as its exposure time expires.
for lline, ltime in ltpairs:
state -= lline
seq.append((ltime, state))
else:
# No lights. Just trigger the cameras.
seq = [(0, camlines)]
ambient = depot.getHandlerWithName('ambient')
# If ambient light is enabled, extend exposure if necessary.
if ambient.getIsEnabled():
t = ambient.getExposureTime()
if t > seq[-1][0]:
seq.append((ambient.getExposureTime(), 0))
# Switch all lights and cameras off.
seq.append((seq[-1][0] + 1, 0))
if self.callbacks.get('runSequence', None):
self.callbacks['runSequence'](seq)
else:
self.softSequence(seq)
def setDetMode(self, mode):
for mirrorIndex, isUp in self.modeToFlips[mode]:
self.flipDownUp(mirrorIndex, isUp)
for button in self.detPathButtons:
button.setActive(button.GetLabel() == mode)
self.curDetMode = mode
#IMD 20150129 - flipping buttons for detection path also changes objective
# set correct pixel size and image orientation
objectiveHandler = depot.getHandlerWithName('objective')
if mode == 'with AO & 85 nm pixel size':
if (objectiveHandler.curObjective != '63x85nm'):
objectiveHandler.changeObjective('63x85nm')
print("Change objective 85 nm pixel")
elif mode == 'w/o AO & 209 nm pixel size':
if (objectiveHandler.curObjective != '63x209nm'):
objectiveHandler.changeObjective('63x209nm')
print("Change objective 209 nm pixel")
def onLoadExposureSettings(self, event=None):
dialog = wx.FileDialog(
self,
style=wx.FD_OPEN,
wildcard='*.txt',
message="Please select the settings file to load.",
defaultDir=cockpit.util.files.getUserSaveDir())
if dialog.ShowModal() != wx.ID_OK:
# User cancelled.
self.pathButton.setOption(self.currentPath)
return
handle = open(dialog.GetPath(), 'r')
modeName = os.path.splitext(os.path.basename(handle.name))[0]
#get name for new mode
# abuse get value dialog which will also return a string.
name = cockpit.gui.dialogs.getNumberDialog.getNumberFromUser(
parent=self.topPanel,
default=modeName,
title='New Path Name',
prompt='Name')
if name not in self.paths:
self.pathList.append(name)
self.paths[name] = json.loads('\n'.join(handle.readlines()))
handle.close()
events.publish('load exposure settings', self.paths[name])
#update button list
self.pathButton.setOptions(
map(lambda name: (name, lambda n=name: self.setPath(n)),
self.pathList))
#and set button value.
self.pathButton.setOption(name)
self.currentPath = name
# If we're using the listbox approach to show/hide light controls,
# then make sure all enabled lights are shown and vice versa.
if self.lightList is not None:
for i, name in enumerate(self.lightList.GetItems()):
handler = depot.getHandlerWithName(name)
self.lightList.SetStringSelection(name, handler.getIsEnabled())
self.onLightSelect()
def takeBurst(self, frameCount=10):
"""
Use the internal triggering of the camera to take a burst of images
Experimental
"""
cameraMask = 0
lightTimePairs = list()
maxTime = 0
for handler, line in self.handlerToDigitalLine.items():
if handler.name in self.activeLights:
maxTime = max(maxTime, handler.getExposureTime())
exposureTime = handler.getExposureTime()
lightTimePairs.append((line, exposureTime))
maxTime = max(maxTime, exposureTime)
for name, line in self.nameToDigitalLine.items():
if name in self.activeCameras:
cameraMask += line
handler = depot.getHandlerWithName(name)
handler.setExposureTime(maxTime)
sleep(5)
def executeRep(self, repNum):
# Get all light sources that the microscope has.
allLights = depot.getHandlersOfType(depot.LIGHT_TOGGLE)
# getHandlersOfType returns an unordered set datatype. If we want to
# index into allLights, we need to convert it to a list first.
allLights = list(allLights)
# Print the names of all light sources.
for light in allLights:
print(light.name)
# Get all power controls for light sources.
allLightPowers = depot.getHandlersOfType(depot.LIGHT_POWER)
# Get all camera handlers that the microscope has, and filter it
# down to the ones that are currently active.
allCameras = depot.getHandlersOfType(depot.CAMERA)
# Create a new empty list.
activeCams = []
for camera in allCameras:
if camera.getIsEnabled():
# Camera is enabled.
activeCams.append(camera)
# Get a specific light.
led650 = depot.getHandlerWithName("650 LED")
# Get a specific light's power control (ditto).
led650power = depot.getHandlerWithName("650 LED power")
# Set the output power to use for this light source, when it is active.
led650power.setPower(2.5)
# Set this light source to be continually exposing.
led650.setExposing(True)
# Wait for some time (1.5 seconds in this case).
time.sleep(1.5)
# Set this light source to stop continually exposing.
led650.setExposing(False)
# Get another light source.
laser488 = depot.getHandlerWithName("488 L")
# Set this light source to be enabled when we take images.
# Note: for lasers, an AOM in the laser box that acts as a light
# shutter is automatically adjusted when you enable/disable lights.
# I don't know how well enabling multiple lasers simultaneously works.
# Note: lasers, the DIA light source, and the EPI light source, are
# mutually exclusive as they use different shutters and only one
# shutter can be active at a time for some unknown reason.
laser488.setEnabled(True)
# Take images, using all current active camera views and light
# sources; wait for the image (and time of acquisition) from the named
# camera to be available.
# Note: The light sources selected automatically use the emission
# filter you have set in the UI. If multiple lights use the same
# emission filter, then they will expose simultaneously (if possible).
# Note: that if you try to wait for an image
# that will never arrive (e.g. for the wrong camera name) then your
# script will get stuck at this point.
# Note: you must have at least one light source enabled for any
# image to be taken!
eventName = 'new image %s' % activeCams[0].name
image, timestamp = events.executeAndWaitFor(
eventName, cockpit.interfaces.imager.takeImage, shouldBlock=True)
# Get the min, max, median, and standard deviation of the image
imageMin = image.min()
imageMax = image.max()
imageMedian = numpy.median(image)
imageStd = numpy.std(image)
print("Image stats:", imageMin, imageMax, imageMedian, imageStd)
# Some miscellaneous functions below.
# Get the current stage position; positions are in microns.
curX, curY, curZ = cockpit.interfaces.stageMover.getPosition()
# Move to a new Z position, and wait until we arrive.
cockpit.interfaces.stageMover.goToZ(curZ + 5, shouldBlock=True)
# Move to a new XY position.
# Note: the goToXY function expects a "tuple" for the position,
# hence the extra parentheses (i.e. "goToXY(x, y)" is invalid;
# "goToXY((x, y))" is correct).
cockpit.interfaces.stageMover.goToXY((curX + 50, curY - 50),
shouldBlock=True)
# Get the device responsible for the dichroics and light sources
lightsDevice = depot.getDevice(cockpit.devices.lights)
# Set a new filter/dichroic for the lower turret.
lightsDevice.setFilter(isFirstFilter=True, label="2-488 L")
# Set a new filter/dichroic for the upper turret.
lightsDevice.setFilter(isFirstFilter=False, label="6-600bp")
def executeRep(self, repNum):
# Get all light sources that the microscope has.
allLights = depot.getHandlersOfType(depot.LIGHT_TOGGLE)
# getHandlersOfType returns an unordered set datatype. If we want to
# index into allLights, we need to convert it to a list first.
allLights = list(allLights)
# Print the names of all light sources.
for light in allLights:
print(light.name)
# Get all power controls for light sources.
allLightPowers = depot.getHandlersOfType(depot.LIGHT_POWER)
# Get all light source filters.
allLightFilters = depot.getHandlersOfType(depot.LIGHT_FILTER)
# Get all camera handlers that the microscope has, and filter it
# down to the ones that are currently active.
allCameras = depot.getHandlersOfType(depot.CAMERA)
# Create a new empty list.
activeCams = []
for camera in allCameras:
if camera.getIsEnabled():
# Camera is enabled.
activeCams.append(camera)
# Get a specific light.
deepstar405 = depot.getHandlerWithName("488 Deepstar")
deepstar405power = depot.getHandlerWithName("488 Deepstar power")
# Set the output power to use for this light source, when it is active.
deepstar405power.setPower(15)
# Get another light source. The "\n" in the name is a newline, which
# was inserted (when this light source handler was created) to make
# the light control button look nice.
laser488 = depot.getHandlerWithName("488\nlight")
# Set this light source to be enabled when we take images.
laser488.setEnabled(True)
# Take images, using all current active camera views and light
# sources; wait for the image (and time of acquisition) from the named
# camera to be available.
# Note: that if you try to wait for an image
# that will never arrive (e.g. for the wrong camera name) then your
# script will get stuck at this point.
eventName = 'new image %s' % activeCams[0].name
image, timestamp = events.executeAndWaitFor(
eventName, cockpit.interfaces.imager.takeImage, shouldBlock=True)
# Get the min, max, median, and standard deviation of the image
imageMin = image.min()
imageMax = image.max()
imageMedian = numpy.median(image)
imageStd = numpy.std(image)
print("Image stats:", imageMin, imageMax, imageMedian, imageStd)
# Some miscellaneous functions below.
# Get the current stage position; positions are in microns.
curX, curY, curZ = cockpit.interfaces.stageMover.getPosition()
# Move to a new Z position, and wait until we arrive.
cockpit.interfaces.stageMover.goToZ(curZ + 5, shouldBlock=True)
# Move to a new XY position.
# Note: the goToXY function expects a "tuple" for the position,
# hence the extra parentheses (i.e. "goToXY(x, y)" is invalid;
# "goToXY((x, y))" is correct).
cockpit.interfaces.stageMover.goToXY((curX + 50, curY - 50),
shouldBlock=True)
def generateActions(self):
table = actionTable.ActionTable()
# Open all light sources for the duration of the experiment.
# Normally the delay generator logic would do this for us.
for cameras, exposures in self.exposureSettings:
for light, exposureTime in exposures:
table.addAction(0, light, True)
shutter = depot.getHandlerWithName('488 shutter')
delayGen = depot.getHandlerWithName('Delay generator trigger')
curTime = 0
table.addAction(curTime, shutter, True)
prevAltitude = None
numZSlices = int(math.ceil(self.zHeight / self.sliceHeight))
for zIndex in range(numZSlices):
# Move to the next position, then wait for the stage to
# stabilize.
zTarget = self.zStart + self.sliceHeight * zIndex
motionTime, stabilizationTime = 0, 0
if prevAltitude is not None:
motionTime, stabilizationTime = self.zPositioner.getMovementTime(
prevAltitude, zTarget)
table.addAction(curTime + motionTime, self.zPositioner, zTarget)
curTime += motionTime + stabilizationTime
prevAltitude = zTarget
# Trigger the delay generator. Do it slightly *after* the trigger
# of the cameras below, so that we ensure the first exposure, which
# may be very brief, is fully-contained in a camera exposure.
table.addToggle(curTime + decimal.Decimal('.5'), delayGen)
# Trigger the cameras twice. Lazy; only allow one set of cameras.
cameras = self.exposureSettings[0][0]
for camera in cameras:
table.addToggle(curTime, camera)
table.addToggle(curTime + self.exposureDelay, camera)
self.cameraToImageCount[camera] += 2
maxCamDelay = max(
c.getTimeBetweenExposures(isExact=True) for c in cameras)
# Wait for the exposure to complete and/or for the cameras to be
# ready again.
longExposureTime = self.exposureSettings[0][1][0][
1] * self.exposureMultiplier
curTime += self.exposureDelay + max(
maxCamDelay, self.exposureDelay + longExposureTime)
# Plus a little extra for the cameras to recover.
# \todo This seems a bit excessive; why do we need to wait so
# long for the Zyla to be ready?
curTime += decimal.Decimal('10')
# Hold the Z motion flat during the exposure.
table.addAction(curTime, self.zPositioner, zTarget)
# Close all light sources we opened at the start.
# Normally the delay generator logic would do this for us.
for cameras, exposures in self.exposureSettings:
for light, exposureTime in exposures:
table.addAction(curTime, light, False)
# Move back to the start so we're ready for the next rep.
motionTime, stabilizationTime = self.zPositioner.getMovementTime(
self.zHeight, 0)
curTime += motionTime
table.addAction(curTime, self.zPositioner, 0)
# Hold flat for the stabilization time, and any time needed for
# the cameras to be ready. Only needed if we're doing multiple
# reps, so we can proceed immediately to the next one.
cameraReadyTime = 0
if self.numReps > 1:
for cameras, lightTimePairs in self.exposureSettings:
for camera in cameras:
cameraReadyTime = max(
cameraReadyTime,
self.getTimeWhenCameraCanExpose(table, camera))
table.addAction(max(curTime + stabilizationTime, cameraReadyTime),
self.zPositioner, 0)
return table
