def run(self):
# Returns True to close config dialog box, False or None otherwise.
# Check if the user is set to save to an already-existing file.
if self.savePath and os.path.exists(self.savePath):
if not guiUtils.getUserPermission(
("The file:\n%s\nalready exists. " % self.savePath) +
"Are you sure you want to overwrite it?"):
return False
global lastExperiment
lastExperiment = self
self.sanityCheckEnvironment()
self.prepareHandlers()
self.cameraToReadoutTime = {
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)
# Indicate any frame transfer cameras for reset at start of table.
for camera in self.cameras:
if camera.getExposureMode(
) == cockpit.handlers.camera.TRIGGER_AFTER:
self.cameraToIsReady[camera] = False
self.createValidActionTable()
if self.numReps > 1 and self.repDuration < self.table.lastActionTime / 1000:
warning = "Repeat duration is less than the time required to run " \
"one repeat. Choose:" \
"\n 'OK' to run repeats as fast as possible;" \
"\n 'Cancel' to go back and change parameters."
if not guiUtils.getUserPermission(warning):
return False
# ToDo: check duration of action table against timelapse settings
# display appropriate warnings.
self.lastMinuteActions()
self._run_thread = threading.Thread(target=self.execute,
name="Experiment-execute")
self._run_thread.start()
saveThread = None
if self.savePath and max(self.cameraToImageCount.values()):
cameraToExcitation = {c: 0.0 for c in self.cameras}
for cameras, lightTimePairs in self.exposureSettings:
## If there's multiple light sources for the same
## camera pick the one with highest wavelength. Main
## case of multiple light sources is single molecule
## localisation where a lower wavelength is doing the
## pumping while but excitation for fluorescence is
## with the higher wavelength.
if lightTimePairs:
max_wavelength = max(
[l.wavelength for l, t in lightTimePairs])
else:
max_wavelength = 0.0
for camera in cameras:
if camera not in self.cameras:
continue
cameraToExcitation[camera] = max(
cameraToExcitation[camera], max_wavelength)
saver = dataSaver.DataSaver(self.cameras, self.numReps,
self.cameraToImageCount,
self.cameraToIgnoredImageIndices,
self._run_thread,
self.savePath, self.sliceHeight,
self.generateTitles(),
cameraToExcitation)
saver.startCollecting()
saveThread = threading.Thread(target=saver.executeAndSave,
name="Experiment-execute-save")
saveThread.start()
generatedFilenames.append(saver.getFilenames())
cleanup_thread = threading.Thread(target=self.cleanup,
args=[self._run_thread, saveThread],
name="Experiment-cleanup")
cleanup_thread.start()
return True
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)))
if lightTimePairs == []:
if not guiUtils.getUserPermission(
("No enabled light has a define exposure time.") +
"Are you sure you want to continue?"):
return True
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()