def onAdd(self, event=None):
start = guiUtils.tryParseNum(self.startText, float)
stop = guiUtils.tryParseNum(self.stopText, float)
if start >= stop:
# No-op; easiest way for this to happen is for the stop text to
# have no value.
return
# Go through our list of sequences and see if we need to merge them
# together.
self.sequence.append([start, stop])
indexToDelete = len(self.sequence) - 1
didChange = True
while didChange:
didChange = False
for i, (altStart, altStop) in enumerate(self.sequence):
# Check for overlap.
if ((start < altStart and stop > altStart)
or (stop > altStop and start < altStop)):
# Merge the two entries.
start = min(start, altStart)
stop = max(stop, altStop)
self.sequence[i] = [start, stop]
didChange = True
# Destroy the old sequence as it's been merged with
# this one.
del self.sequence[indexToDelete]
indexToDelete = i
break
# Sort the sequence by start time.
self.sequence.sort(key=lambda s: s[0])
self.startText.SetValue('')
self.stopText.SetValue('')
self.updateDisplay()
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['numExposures'] = guiUtils.tryParseNum(self.responseArgs['responseMapNumExposures'])
tokens = self.responseArgs['responseMapExposureTimes'].GetValue()
tokens = tokens.split(',')
params['exposureTimes'] = map(float, tokens)
params['cosmicRayThreshold'] = guiUtils.tryParseNum(self.responseArgs['responseMapCosmicRayThreshold'])
params['shouldPreserveIntermediaryFiles'] = self.responseArgs['responseMapShouldPreserveIntermediaryFiles'].GetValue()
return params
def augmentParams(self, params):
self.saveSettings()
params['numExposures'] = guiUtils.tryParseNum(
self.correctionArgs['correctionNumExposures'])
params['numCollections'] = guiUtils.tryParseNum(
self.correctionArgs['correctionNumCollections'])
params['exposureMultiplier'] = guiUtils.tryParseNum(
self.correctionArgs['correctionExposureMultiplier'], float)
params['maxIntensity'] = guiUtils.tryParseNum(
self.correctionArgs['correctionMaxIntensity'])
params['cosmicRayThreshold'] = guiUtils.tryParseNum(
self.correctionArgs['correctionCosmicRayThreshold'], float)
params['shouldPreserveIntermediaryFiles'] = self.correctionArgs[
'correctionShouldPreserveIntermediaryFiles'].GetValue()
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 runExperiment(self):
# Returns True to close dialog box, None or False otherwise.
self.saveSettings()
# Find the Z mover with the smallest range of motion, assumed
# to be our experiment mover.
mover = depot.getSortedStageMovers()[2][-1]
# Only use active cameras and enabled lights.
# Must do list(filter) because we will iterate over the list
# many times.
cameras = list(
filter(lambda c: c.getIsEnabled(),
depot.getHandlersOfType(depot.CAMERA)))
if not cameras:
wx.MessageDialog(
self,
message=
"No cameras are enabled, so the experiment cannot be run.",
style=wx.ICON_EXCLAMATION | wx.STAY_ON_TOP
| wx.OK).ShowModal()
return True
exposureSettings = []
if self.shouldExposeSimultaneously.GetValue():
# A single exposure event with all cameras and lights.
lightTimePairs = []
for i, light in enumerate(self.allLights):
if (self.allLights[i].getIsEnabled()
and self.lightExposureTimes[i].GetValue()):
lightTimePairs.append(
(light,
guiUtils.tryParseNum(self.lightExposureTimes[i],
decimal.Decimal)))
exposureSettings = [(cameras, lightTimePairs)]
else:
# A separate exposure for each camera.
for camera in cameras:
cameraSettings = self.cameraToExposureTimes[camera]
settings = []
for i, light in enumerate(self.allLights):
if not light.getIsEnabled():
continue
timeControl = cameraSettings[i]
if timeControl.GetValue():
settings.append(
(light,
guiUtils.tryParseNum(timeControl,
decimal.Decimal)))
exposureSettings.append(([camera], settings))
altitude = cockpit.interfaces.stageMover.getPositionForAxis(2)
# Default to "current is bottom"
altBottom = altitude
zHeight = guiUtils.tryParseNum(self.stackHeight, float)
if self.zPositionMode.GetStringSelection() == 'Current is center':
altBottom = altitude - zHeight / 2
elif self.zPositionMode.GetStringSelection() == 'Use saved top/bottom':
altBottom = cockpit.interfaces.stageMover.mover.SavedBottom
zHeight = cockpit.interfaces.stageMover.mover.SavedTop - altBottom
sliceHeight = guiUtils.tryParseNum(self.sliceHeight, float)
if zHeight == 0:
# 2D mode.
zHeight = 1e-6
sliceHeight = 1e-6
try:
savePath = self.filepath_panel.GetPath()
except Exception:
cockpit.gui.ExceptionBox("Failed to get filename for data.",
parent=self)
return True
params = {
'numReps': guiUtils.tryParseNum(self.numReps),
'repDuration': guiUtils.tryParseNum(self.repDuration, float),
'zPositioner': mover,
'altBottom': altBottom,
'zHeight': zHeight,
'sliceHeight': sliceHeight,
'exposureSettings': exposureSettings,
'savePath': savePath
}
experimentType = self.experimentType.GetStringSelection()
module = self.experimentStringToModule[experimentType]
if module in self.experimentModuleToPanel:
# Add on the special parameters needed by this experiment type.
params = self.experimentModuleToPanel[module].augmentParams(params)
self.runner = module.EXPERIMENT_CLASS(**params)
return self.runner.run()
