def __init__(self, parent, configKey):
super().__init__(parent=parent)
self.configKey = configKey + self._CONFIG_KEY_SUFFIX
self.allLights = depot.getHandlersOfType(depot.LIGHT_TOGGLE)
self.settings = self.loadSettings()
sizer = wx.BoxSizer(wx.VERTICAL)
rowSizer = wx.BoxSizer(wx.HORIZONTAL)
text = wx.StaticText(self, -1, "Exposure bleach compensation (%):")
rowSizer.Add(text, 0, wx.ALL, 5)
## Ordered list of bleach compensation percentages.
self.bleachCompensations, subSizer = guiUtils.makeLightsControls(
self, [str(l.name) for l in self.allLights],
self.settings['bleachCompensations'])
rowSizer.Add(subSizer)
sizer.Add(rowSizer)
# Now a row for the collection order.
rowSizer = wx.BoxSizer(wx.HORIZONTAL)
self.siCollectionOrder = guiUtils.addLabeledInput(
self,
rowSizer,
label="Collection order",
control=wx.Choice(self, choices=sorted(COLLECTION_ORDERS.keys())),
helperString=
"What order to change the angle, phase, and Z step of the experiment. E.g. for \"Angle, Phase, Z\" Angle will change most slowly and Z will change fastest."
)
self.siCollectionOrder.SetSelection(self.settings['siCollectionOrder'])
sizer.Add(rowSizer)
self.SetSizerAndFit(sizer)
def __init__(self,
parent,
resizeCallback,
resetCallback,
configKey='singleSiteExperiment'):
super().__init__(parent,
style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER
| wx.TAB_TRAVERSAL)
self.parent = parent
self.configKey = configKey
self.resizeCallback = resizeCallback
self.resetCallback = resetCallback
## cockpit.experiment.Experiment subclass instance -- mostly preserved for
# debugging, so we can examine the state of the experiment.
self.runner = None
self.allLights = depot.getHandlersOfType(depot.LIGHT_TOGGLE)
self.allLights.sort(key=lambda l: l.wavelength)
self.allCameras = depot.getHandlersOfType(depot.CAMERA)
self.allCameras.sort(key=lambda c: c.name)
## Map of default settings as loaded from config.
self.settings = self.loadConfig()
self.SetSizer(wx.BoxSizer(wx.VERTICAL))
self.sizer = self.GetSizer()
# Section for settings that are universal to all experiment types.
universalSizer = wx.FlexGridSizer(2, 3, 5, 5)
## Maps experiment description strings to experiment modules.
self.experimentStringToModule = collections.OrderedDict()
for module in cockpit.experiment.experimentRegistry.getExperimentModules(
):
self.experimentStringToModule[module.EXPERIMENT_NAME] = module
self.experimentType = wx.Choice(
self, choices=list(self.experimentStringToModule.keys()))
self.experimentType.SetSelection(0)
guiUtils.addLabeledInput(self,
universalSizer,
label="Experiment type:",
control=self.experimentType)
self.numReps = guiUtils.addLabeledInput(
self,
universalSizer,
label="Number of reps:",
defaultValue=self.settings['numReps'])
self.numReps.SetValidator(guiUtils.INTVALIDATOR)
self.repDuration = guiUtils.addLabeledInput(
self,
universalSizer,
label="Rep duration (s):",
defaultValue=self.settings['repDuration'],
helperString="Amount of time that must pass between the start " +
"of each rep. Use 0 if you don't want any wait time.")
self.repDuration.SetValidator(guiUtils.FLOATVALIDATOR)
self.zPositionMode = wx.Choice(self, choices=Z_POSITION_MODES)
self.zPositionMode.SetSelection(0)
guiUtils.addLabeledInput(self,
universalSizer,
label="Z position mode:",
control=self.zPositionMode)
self.stackHeight = guiUtils.addLabeledInput(
self,
universalSizer,
label=u"Stack height (\u03bcm):",
defaultValue=self.settings['stackHeight'])
self.stackHeight.SetValidator(guiUtils.FLOATVALIDATOR)
self.sliceHeight = guiUtils.addLabeledInput(
self,
universalSizer,
label=u"Slice height (\u03bcm):",
defaultValue=self.settings['sliceHeight'])
self.sliceHeight.SetValidator(guiUtils.FLOATVALIDATOR)
self.sizer.Add(universalSizer, 0, wx.ALL, border=5)
## Maps experiment modules to ExperimentUI instances holding the
# UI for that experiment, if any.
self.experimentModuleToPanel = {}
for module in self.experimentStringToModule.values():
if not hasattr(module, 'ExperimentUI'):
# This experiment type has no special UI to set up.
continue
panel = module.ExperimentUI(self, self.configKey)
panel.Hide()
self.sizer.Add(panel)
self.experimentModuleToPanel[module] = panel
self.experimentType.Bind(wx.EVT_CHOICE, self.onExperimentTypeChoice)
self.onExperimentTypeChoice()
# Section for exposure settings. We allow either setting per-laser
# exposure times and activating all cameras as a group, or setting
# them per-laser and per-camera (and activating each camera-laser
# grouping in sequence).
exposureSizer = wx.BoxSizer(wx.VERTICAL)
## Controls which set of exposure settings we enable.
self.shouldExposeSimultaneously = wx.CheckBox(
self, label="Expose all cameras simultaneously")
exposureSizer.Add(self.shouldExposeSimultaneously, 0, wx.ALL, border=5)
## Panel for holding controls for when we expose every camera
# simultaneously.
self.simultaneousExposurePanel = wx.Panel(
self, name="simultaneous exposures")
simultaneousSizer = wx.BoxSizer(wx.VERTICAL)
simultaneousSizer.Add(
wx.StaticText(self.simultaneousExposurePanel, -1,
"Exposure times for light sources:"), 0, wx.ALL, 5)
## Ordered list of exposure times for simultaneous exposure mode.
self.lightExposureTimes, timeSizer = guiUtils.makeLightsControls(
self.simultaneousExposurePanel,
[str(l.name) for l in self.allLights],
self.settings['simultaneousExposureTimes'])
simultaneousSizer.Add(timeSizer)
useCurrentButton = wx.Button(self.simultaneousExposurePanel, -1,
"Use current settings")
useCurrentButton.SetToolTip(
wx.ToolTip(
"Use the same settings as are currently used to take images with the '+' button"
))
useCurrentButton.Bind(wx.EVT_BUTTON, self.onUseCurrentExposureSettings)
simultaneousSizer.Add(useCurrentButton)
self.simultaneousExposurePanel.SetSizerAndFit(simultaneousSizer)
exposureSizer.Add(self.simultaneousExposurePanel, 0, wx.ALL, border=5)
## Panel for when we expose each camera in sequence.
self.sequencedExposurePanel = wx.Panel(self,
name="sequenced exposures")
## Maps a camera handler to an ordered list of exposure times.
self.cameraToExposureTimes = {}
sequenceSizer = wx.FlexGridSizer(
len(self.settings['sequencedExposureSettings']) + 1,
len(self.settings['sequencedExposureSettings'][0]) + 1, 1, 1)
for label in [''] + [str(l.name) for l in self.allLights]:
sequenceSizer.Add(
wx.StaticText(self.sequencedExposurePanel, -1, label), 0,
wx.ALIGN_RIGHT | wx.ALL, 5)
for i, camera in enumerate(self.allCameras):
sequenceSizer.Add(
wx.StaticText(self.sequencedExposurePanel, -1,
str(camera.name)), 0, wx.TOP | wx.ALIGN_RIGHT, 8)
times = []
for (label, defaultVal) in zip(
[str(l.name) for l in self.allLights],
self.settings['sequencedExposureSettings'][i]):
exposureTime = wx.TextCtrl(self.sequencedExposurePanel,
size=(40, -1),
name="exposure: %s for %s" %
(label, camera.name))
exposureTime.SetValue(defaultVal)
# allowEmpty=True lets validator know this control may be empty.
exposureTime.SetValidator(guiUtils.FLOATVALIDATOR)
exposureTime.allowEmpty = True
sequenceSizer.Add(exposureTime, 0, wx.ALL, border=5)
times.append(exposureTime)
self.cameraToExposureTimes[camera] = times
self.sequencedExposurePanel.SetSizerAndFit(sequenceSizer)
exposureSizer.Add(self.sequencedExposurePanel, 0, wx.ALL, border=5)
self.sizer.Add(exposureSizer)
# Toggle which panel is displayed based on the checkbox.
self.shouldExposeSimultaneously.Bind(wx.EVT_CHECKBOX,
self.onExposureCheckbox)
self.shouldExposeSimultaneously.SetValue(
self.settings['shouldExposeSimultaneously'])
self.onExposureCheckbox()
self.filepath_panel = FilepathPanel(self)
self.filepath_panel.SetTemplate(self.settings['filenameTemplate'])
self.filepath_panel.UpdateFilename()
self.Sizer.Add(self.filepath_panel, wx.SizerFlags(1).Expand().Border())
# Save/load experiment settings buttons.
saveLoadPanel = wx.Panel(self)
rowSizer = wx.BoxSizer(wx.HORIZONTAL)
saveButton = wx.Button(saveLoadPanel, -1,
"Save experiment settings...")
saveButton.Bind(wx.EVT_BUTTON, self.onSaveExperiment)
rowSizer.Add(saveButton, 0, wx.ALL, 5)
loadButton = wx.Button(saveLoadPanel, -1,
"Load experiment settings...")
loadButton.Bind(wx.EVT_BUTTON, self.onLoadExperiment)
rowSizer.Add(loadButton, 0, wx.ALL, 5)
saveLoadPanel.SetSizerAndFit(rowSizer)
self.sizer.Add(saveLoadPanel, 0, wx.LEFT, 5)
self.SetSizerAndFit(self.sizer)
def __init__(self, parent):
super().__init__(parent,
title="OMX multi-site experiment",
style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER)
## Whether or not we should abort the current experiment.
self.shouldAbort = False
events.subscribe(events.USER_ABORT, self.onAbort)
## List of all light handlers.
self.allLights = depot.getHandlersOfType(depot.LIGHT_TOGGLE)
## List of booleans indicating which lights were active at the
# start of the experiment.
self.activeLights = [None for l in self.allLights]
## User's last-used inputs.
self.settings = cockpit.util.userConfig.getValue(
'multiSiteExperiment',
default={
'numCycles': '10',
'cycleDuration': '60',
'delayBeforeStarting': '0',
'delayBeforeImaging': '0',
'fileBase': '',
'shouldCustomizeLightFrequencies': False,
'shouldOptimizeSiteOrder': True,
'lightFrequencies': ['1' for l in self.allLights],
})
## Contains self.panel
self.sizer = wx.BoxSizer(wx.VERTICAL)
## Contains all UI widgets.
self.panel = wx.Panel(self)
## Sizer for self.panel.
self.panelSizer = wx.BoxSizer(wx.VERTICAL)
## Sizer for all controls except the start/cancel/reset buttons.
controlsSizer = wx.BoxSizer(wx.HORIZONTAL)
## Sizer for a single column of controls.
columnSizer = wx.BoxSizer(wx.VERTICAL)
## Panel for selecting sites to visit.
self.sitesPanel = cockpit.gui.dialogs.enumerateSitesPanel.EnumerateSitesPanel(
self.panel,
label="Sites to visit:",
size=(200, -1),
minSize=CONTROL_SIZE)
columnSizer.Add(self.sitesPanel)
self.numCycles = guiUtils.addLabeledInput(
self.panel,
columnSizer,
label="Number of cycles:",
defaultValue=self.settings['numCycles'],
size=FIELD_SIZE,
minSize=CONTROL_SIZE)
self.cycleDuration = guiUtils.addLabeledInput(
self.panel,
columnSizer,
label="Min cycle duration (s):",
defaultValue=self.settings['cycleDuration'],
size=FIELD_SIZE,
minSize=CONTROL_SIZE,
helperString=
"Minimum amount of time to pass between each cycle. If the " +
"cycle finishes early, then I will wait until this much " +
"time has passed. You can enter multiple values here " +
"separated by commas; I will then use each wait time in " +
"sequence; e.g. \"60,120,180\" means the first " +
"cycle takes one minute, the second two, the third three, " +
"the fourth one, the fifth two, and so on.")
self.delayBeforeStarting = guiUtils.addLabeledInput(
self.panel,
columnSizer,
label="Delay before starting (min):",
defaultValue=self.settings['delayBeforeStarting'],
size=FIELD_SIZE,
minSize=CONTROL_SIZE,
helperString=
"Amount of time to wait before starting the experiment. " +
"This is useful if you have a lengthy period to wait for " +
"your cells to reach the stage you're interested in, for " +
"example.")
self.delayBeforeImaging = guiUtils.addLabeledInput(
self.panel,
columnSizer,
label="Delay before imaging (s):",
defaultValue=self.settings['delayBeforeImaging'],
size=FIELD_SIZE,
minSize=CONTROL_SIZE,
helperString="Amount of time to wait after moving to a site before "
+ "I start imaging the site. This is mostly useful if " +
"your stage needs time to stabilize after moving.")
self.fileBase = guiUtils.addLabeledInput(
self.panel,
columnSizer,
label="Data file base name:",
defaultValue=self.settings['fileBase'],
size=FIELD_SIZE,
minSize=CONTROL_SIZE)
controlsSizer.Add(columnSizer, 0, wx.ALL, 5)
columnSizer = wx.BoxSizer(wx.VERTICAL)
## We don't necessarily have this option.
self.shouldPowerDownWhenDone = None
powerHandlers = depot.getHandlersOfType(depot.POWER_CONTROL)
if powerHandlers:
# There are devices that we could potentially turn off at end of
# experiment.
self.shouldPowerDownWhenDone = guiUtils.addLabeledInput(
self.panel,
columnSizer,
label="Power off devices when done:",
control=wx.CheckBox(self.panel),
labelHeightAdjustment=0,
border=3,
flags=wx.ALL,
helperString=
"If checked, then at the end of the experiment, I will " +
"power down all the devices I can.")
self.shouldOptimizeSiteOrder = guiUtils.addLabeledInput(
self.panel,
columnSizer,
label="Optimize route:",
defaultValue=self.settings['shouldOptimizeSiteOrder'],
control=wx.CheckBox(self.panel),
labelHeightAdjustment=0,
border=3,
flags=wx.ALL,
helperString=
"If checked, then I will calculate an ordering of the sites " +
"that will minimize the total time spent in transit; " +
"otherwise, I will use the order you specify.")
self.shouldCustomizeLightFrequencies = guiUtils.addLabeledInput(
self.panel,
columnSizer,
label="Customize light frequencies:",
defaultValue=self.settings['shouldCustomizeLightFrequencies'],
control=wx.CheckBox(self.panel),
labelHeightAdjustment=0,
border=3,
flags=wx.ALL,
helperString=
"This allows you to set up experiments where different " +
"light sources are enabled for different cycles. If you " +
"set a frequency of 5 for a given light, for example, " +
"then that light will only be used for every 5th pass " +
"(the 1st, 6th, 11th, etc. cycles). You can specify an " +
"offset, too: \"5 + 1\" would enable the light for the " +
"2nd, 7th, 12th, etc. cycles.")
self.shouldCustomizeLightFrequencies.Bind(
wx.EVT_CHECKBOX, self.onCustomizeLightFrequencies)
self.lightFrequenciesPanel = wx.Panel(self.panel,
style=wx.BORDER_SUNKEN
| wx.TAB_TRAVERSAL)
self.lightFrequencies, sizer = guiUtils.makeLightsControls(
self.lightFrequenciesPanel,
[str(l.wavelength) for l in self.allLights],
self.settings['lightFrequencies'])
self.lightFrequenciesPanel.SetSizerAndFit(sizer)
self.lightFrequenciesPanel.Show(
self.settings['shouldCustomizeLightFrequencies'])
columnSizer.Add(self.lightFrequenciesPanel, 0,
wx.LEFT | wx.RIGHT | wx.BOTTOM, 5)
controlsSizer.Add(columnSizer, 0, wx.ALL, 5)
self.panelSizer.Add(controlsSizer)
## Controls whether or not the scanning experiment's parameters are
# shown.
self.showScanButton = wx.Button(self.panel, -1,
"Show experiment settings")
self.showScanButton.Bind(wx.EVT_BUTTON, self.onShowScanButton)
self.panelSizer.Add(self.showScanButton, 0, wx.ALIGN_CENTER | wx.TOP,
5)
## This panel configures the experiment we perform when visiting sites.
self.experimentPanel = experimentConfigPanel.ExperimentConfigPanel(
self.panel,
resizeCallback=self.onExperimentPanelResize,
resetCallback=self.onExperimentPanelReset,
configKey='multiSiteExperimentPanel',
shouldShowFileControls=False)
self.panelSizer.Add(self.experimentPanel, 0, wx.ALIGN_CENTER | wx.ALL,
5)
self.experimentPanel.Hide()
buttonSizer = wx.BoxSizer(wx.HORIZONTAL)
button = wx.Button(self.panel, -1, "Reset")
button.SetToolTip(
wx.ToolTip("Reload this window with all default values"))
button.Bind(wx.EVT_BUTTON, self.onReset)
buttonSizer.Add(button, 0, wx.ALL, 5)
buttonSizer.Add((1, 0), 1, wx.EXPAND)
button = wx.Button(self.panel, wx.ID_CANCEL, "Cancel")
buttonSizer.Add(button, 0, wx.ALL, 5)
button = wx.Button(self.panel, wx.ID_OK, "Start")
button.SetToolTip(wx.ToolTip("Start the experiment"))
button.Bind(wx.EVT_BUTTON, self.onStart)
buttonSizer.Add(button, 0, wx.ALL, 5)
self.panelSizer.Add(buttonSizer, 0, wx.ALL, 5)
self.panel.SetSizerAndFit(self.panelSizer)
self.sizer.Add(self.panel)
self.SetSizerAndFit(self.sizer)
