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gui_hcs.py
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# set QT_API environment variable
import os
os.environ["QT_API"] = "pyqt5"
import serial
import time
from typing import Optional
# qt libraries
from qtpy.QtCore import *
from qtpy.QtWidgets import *
from qtpy.QtGui import *
from control._def import *
# app specific libraries
import control.widgets as widgets
import pyqtgraph.dockarea as dock
import squid.abc
import squid.logging
import squid.config
import squid.stage.utils
import control.microscope
from control.microscope import LightSourceType, IntensityControlMode, ShutterControlMode, IlluminationController
log = squid.logging.get_logger(__name__)
import control.filterwheel as filterwheel
if USE_PRIOR_STAGE:
import squid.stage.prior
else:
import squid.stage.cephla
if CAMERA_TYPE == "Toupcam":
try:
import control.camera_toupcam as camera
except:
log.warning("Problem importing Toupcam, defaulting to default camera")
import control.camera as camera
elif CAMERA_TYPE == "FLIR":
try:
import control.camera_flir as camera
except:
log.warning("Problem importing FLIR camera, defaulting to default camera")
import control.camera as camera
elif CAMERA_TYPE == "Hamamatsu":
try:
import control.camera_hamamatsu as camera
except:
log.warning("Problem importing Hamamatsu camera, defaulting to default camera")
import control.camera as camera
elif CAMERA_TYPE == "iDS":
try:
import control.camera_ids as camera
except:
log.warning("Problem importing iDS camera, defaulting to default camera")
import control.camera as camera
elif CAMERA_TYPE == "Tucsen":
try:
import control.camera_tucsen as camera
except:
log.warning("Problem importing Tucsen camera, defaulting to default camera")
import control.camera as camera
else:
import control.camera as camera
if FOCUS_CAMERA_TYPE == "Toupcam":
try:
import control.camera_toupcam as camera_fc
except:
log.warning("Problem importing Toupcam for focus, defaulting to default camera")
import control.camera as camera_fc
elif FOCUS_CAMERA_TYPE == "FLIR":
try:
import control.camera_flir as camera_fc
except:
log.warning("Problem importing FLIR camera for focus, defaulting to default camera")
import control.camera as camera_fc
else:
import control.camera as camera_fc
import control.core.core as core
import control.microcontroller as microcontroller
import control.serial_peripherals as serial_peripherals
if ENABLE_STITCHER:
import control.stitcher as stitcher
if SUPPORT_LASER_AUTOFOCUS:
import control.core_displacement_measurement as core_displacement_measurement
SINGLE_WINDOW = True # set to False if use separate windows for display and control
if USE_JUPYTER_CONSOLE:
from control.console import JupyterWidget
class MovementUpdater(QObject):
position_after_move = Signal(squid.abc.Pos)
position = Signal(squid.abc.Pos)
def __init__(self, stage: squid.abc.AbstractStage, movement_threshhold_mm=0.0001, *args, **kwargs):
super().__init__(*args, **kwargs)
self.stage = stage
self.movement_threshhold_mm = movement_threshhold_mm
self.previous_pos = None
self.sent_after_stopped = False
def do_update(self):
pos = self.stage.get_pos()
# Doing previous_pos initialization like this means we technically miss the first real update,
# but that's okay since this is intended to be run frequently in the background.
if not self.previous_pos:
self.previous_pos = pos
return
abs_delta_x = abs(self.previous_pos.x_mm - pos.x_mm)
abs_delta_y = abs(self.previous_pos.y_mm - pos.y_mm)
if (
abs_delta_y < self.movement_threshhold_mm
and abs_delta_x < self.movement_threshhold_mm
and not self.stage.get_state().busy
):
# In here, send all the signals that must be sent once per stop of movement. AKA once per arriving at a
# new position for a while.
self.sent_after_stopped = True
self.position_after_move.emit(pos)
else:
self.sent_after_stopped = False
# Here, emit all the signals that want higher fidelity movement updates.
self.position.emit(pos)
self.previous_pos = pos
class HighContentScreeningGui(QMainWindow):
fps_software_trigger = 100
def __init__(self, is_simulation=False, live_only_mode=False, *args, **kwargs):
super().__init__(*args, **kwargs)
self.microcontroller: Optional[microcontroller.Microcontroller] = None
self.log = squid.logging.get_logger(self.__class__.__name__)
self.live_only_mode = live_only_mode or LIVE_ONLY_MODE
self.is_live_scan_grid_on = False
self.performance_mode = False
self.napari_connections = {}
self.loadObjects(is_simulation)
self.setupHardware()
self.setup_movement_updater()
self.loadWidgets()
self.setupLayout()
self.makeConnections()
self.microscope = control.microscope.Microscope(self.stage, self, is_simulation=is_simulation)
# TODO(imo): Why is moving to the cached position after boot hidden behind homing?
if HOMING_ENABLED_X and HOMING_ENABLED_Y and HOMING_ENABLED_Z:
if cached_pos := squid.stage.utils.get_cached_position():
self.stage.move_x_to(cached_pos.x_mm)
self.stage.move_y_to(cached_pos.y_mm)
self.stage.move_z_to(cached_pos.z_mm)
if ENABLE_WELLPLATE_MULTIPOINT:
self.wellplateMultiPointWidget.init_z()
self.flexibleMultiPointWidget.init_z()
# Create the menu bar
menubar = self.menuBar()
settings_menu = menubar.addMenu("Settings")
if SUPPORT_SCIMICROSCOPY_LED_ARRAY:
led_matrix_action = QAction("LED Matrix", self)
led_matrix_action.triggered.connect(self.openLedMatrixSettings)
settings_menu.addAction(led_matrix_action)
if USE_JUPYTER_CONSOLE:
# Create namespace to expose to Jupyter
self.namespace = {
'microscope': self.microscope,
}
# Create Jupyter widget as a dock widget
self.jupyter_dock = QDockWidget("Jupyter Console", self)
self.jupyter_widget = JupyterWidget(namespace=self.namespace)
self.jupyter_dock.setWidget(self.jupyter_widget)
self.addDockWidget(Qt.LeftDockWidgetArea, self.jupyter_dock)
def loadObjects(self, is_simulation):
self.illuminationController = None
if is_simulation:
self.loadSimulationObjects()
else:
try:
self.loadHardwareObjects()
except Exception:
self.log.error("---- !! ERROR CONNECTING TO HARDWARE !! ----", stack_info=True, exc_info=True)
raise
# Common object initialization
self.objectiveStore = core.ObjectiveStore(parent=self)
self.configurationManager = core.ConfigurationManager(filename="./channel_configurations.xml")
self.contrastManager = core.ContrastManager()
self.streamHandler = core.StreamHandler(display_resolution_scaling=DEFAULT_DISPLAY_CROP / 100)
self.liveController = core.LiveController(
self.camera, self.microcontroller, self.configurationManager, self.illuminationController, parent=self
)
if USE_PRIOR_STAGE:
self.stage: squid.abc.AbstractStage = squid.stage.prior.PriorStage(sn=PRIOR_STAGE_SN)
else:
self.stage: squid.abc.AbstractStage = squid.stage.cephla.CephlaStage(
microcontroller=self.microcontroller, stage_config=squid.config.get_stage_config()
)
self.slidePositionController = core.SlidePositionController(
self.stage, self.liveController, is_for_wellplate=True
)
self.autofocusController = core.AutoFocusController(
self.camera, self.stage, self.liveController, self.microcontroller
)
self.slidePositionController = core.SlidePositionController(
self.stage, self.liveController, is_for_wellplate=True
)
self.autofocusController = core.AutoFocusController(
self.camera, self.stage, self.liveController, self.microcontroller
)
self.imageSaver = core.ImageSaver()
self.imageDisplay = core.ImageDisplay()
if ENABLE_TRACKING:
self.trackingController = core.TrackingController(
self.camera,
self.microcontroller,
self.stage,
self.configurationManager,
self.liveController,
self.autofocusController,
self.imageDisplayWindow,
)
if WELLPLATE_FORMAT == "glass slide":
self.navigationViewer = core.NavigationViewer(self.objectiveStore, sample="4 glass slide")
else:
self.navigationViewer = core.NavigationViewer(self.objectiveStore, sample=WELLPLATE_FORMAT)
self.scanCoordinates = core.ScanCoordinates(
objectiveStore=self.objectiveStore, navigationViewer=self.navigationViewer, stage=self.stage
)
self.multipointController = core.MultiPointController(
self.camera,
self.stage,
self.microcontroller,
self.liveController,
self.autofocusController,
self.configurationManager,
scanCoordinates=self.scanCoordinates,
parent=self,
)
if SUPPORT_LASER_AUTOFOCUS:
self.configurationManager_focus_camera = core.ConfigurationManager(
filename="./focus_camera_configurations.xml"
)
self.streamHandler_focus_camera = core.StreamHandler()
self.liveController_focus_camera = core.LiveController(
self.camera_focus,
self.microcontroller,
self.configurationManager_focus_camera,
self,
control_illumination=False,
for_displacement_measurement=True,
)
self.multipointController = core.MultiPointController(
self.camera,
self.stage,
self.microcontroller,
self.liveController,
self.autofocusController,
self.configurationManager,
scanCoordinates=self.scanCoordinates,
parent=self,
)
self.imageDisplayWindow_focus = core.ImageDisplayWindow(
draw_crosshairs=True, show_LUT=False, autoLevels=False
)
self.displacementMeasurementController = core_displacement_measurement.DisplacementMeasurementController()
self.laserAutofocusController = core.LaserAutofocusController(
self.microcontroller,
self.camera_focus,
self.liveController_focus_camera,
self.stage,
has_two_interfaces=HAS_TWO_INTERFACES,
use_glass_top=USE_GLASS_TOP,
look_for_cache=False,
)
if USE_SQUID_FILTERWHEEL:
self.squid_filter_wheel = filterwheel.SquidFilterWheelWrapper(self.microcontroller)
def loadSimulationObjects(self):
self.log.debug("Loading simulated hardware objects...")
self.microcontroller = microcontroller.Microcontroller(existing_serial=microcontroller.SimSerial())
# Initialize simulation objects
if ENABLE_SPINNING_DISK_CONFOCAL:
self.xlight = serial_peripherals.XLight_Simulation()
if ENABLE_NL5:
import control.NL5 as NL5
self.nl5 = NL5.NL5_Simulation()
if ENABLE_CELLX:
self.cellx = serial_peripherals.CellX_Simulation()
if SUPPORT_LASER_AUTOFOCUS:
self.camera_focus = camera_fc.Camera_Simulation()
if USE_LDI_SERIAL_CONTROL:
self.ldi = serial_peripherals.LDI_Simulation()
self.illuminationController = control.microscope.IlluminationController(
self.microcontroller, self.ldi.intensity_mode, self.ldi.shutter_mode, LightSourceType.LDI, self.ldi
)
self.camera = camera.Camera_Simulation(rotate_image_angle=ROTATE_IMAGE_ANGLE, flip_image=FLIP_IMAGE)
self.camera.set_pixel_format(DEFAULT_PIXEL_FORMAT)
if USE_ZABER_EMISSION_FILTER_WHEEL:
self.emission_filter_wheel = serial_peripherals.FilterController_Simulation(
115200, 8, serial.PARITY_NONE, serial.STOPBITS_ONE
)
if USE_OPTOSPIN_EMISSION_FILTER_WHEEL:
self.emission_filter_wheel = serial_peripherals.Optospin_Simulation(SN=None)
if USE_SQUID_FILTERWHEEL:
self.squid_filter_wheel = filterwheel.SquidFilterWheelWrapper_Simulation(None)
def loadHardwareObjects(self):
# Initialize hardware objects
try:
self.microcontroller = microcontroller.Microcontroller(version=CONTROLLER_VERSION, sn=CONTROLLER_SN)
except Exception:
self.log.error(f"Error initializing Microcontroller")
raise
if ENABLE_SPINNING_DISK_CONFOCAL:
try:
self.xlight = serial_peripherals.XLight(XLIGHT_SERIAL_NUMBER, XLIGHT_SLEEP_TIME_FOR_WHEEL)
except Exception:
self.log.error("Error initializing Spinning Disk Confocal")
raise
if ENABLE_NL5:
try:
import control.NL5 as NL5
self.nl5 = NL5.NL5()
except Exception:
self.log.error("Error initializing NL5")
raise
if ENABLE_CELLX:
try:
self.cellx = serial_peripherals.CellX(CELLX_SN)
for channel in [1, 2, 3, 4]:
self.cellx.set_modulation(channel, CELLX_MODULATION)
self.cellx.turn_on(channel)
except Exception:
self.log.error("Error initializing CellX")
raise
if USE_LDI_SERIAL_CONTROL:
try:
self.ldi = serial_peripherals.LDI()
self.illuminationController = IlluminationController(
self.microcontroller, self.ldi.intensity_mode, self.ldi.shutter_mode, LightSourceType.LDI, self.ldi
)
except Exception:
self.log.error("Error initializing LDI")
raise
if USE_CELESTA_ETHENET_CONTROL:
try:
import control.celesta
self.celesta = control.celesta.CELESTA()
self.illuminationController = IlluminationController(
self.microcontroller,
IntensityControlMode.Software,
ShutterControlMode.TTL,
LightSourceType.CELESTA,
self.celesta,
)
except Exception:
self.log.error("Error initializing CELESTA")
raise
if SUPPORT_LASER_AUTOFOCUS:
try:
sn_camera_focus = camera_fc.get_sn_by_model(FOCUS_CAMERA_MODEL)
self.camera_focus = camera_fc.Camera(sn=sn_camera_focus)
self.camera_focus.open()
self.camera_focus.set_pixel_format("MONO8")
except Exception:
self.log.error(f"Error initializing Laser Autofocus Camera")
raise
try:
sn_camera_main = camera.get_sn_by_model(MAIN_CAMERA_MODEL)
self.camera = camera.Camera(sn=sn_camera_main, rotate_image_angle=ROTATE_IMAGE_ANGLE, flip_image=FLIP_IMAGE)
self.camera.open()
self.camera.set_pixel_format(DEFAULT_PIXEL_FORMAT)
except Exception:
self.log.error("Error initializing Main Camera")
raise
if USE_ZABER_EMISSION_FILTER_WHEEL:
try:
self.emission_filter_wheel = serial_peripherals.FilterController(
FILTER_CONTROLLER_SERIAL_NUMBER, 115200, 8, serial.PARITY_NONE, serial.STOPBITS_ONE
)
except Exception:
self.log.error("Error initializing Zaber Emission Filter Wheel")
raise
if USE_OPTOSPIN_EMISSION_FILTER_WHEEL:
try:
self.emission_filter_wheel = serial_peripherals.Optospin(SN=FILTER_CONTROLLER_SERIAL_NUMBER)
except Exception:
self.log.error("Error initializing Optospin Emission Filter Wheel")
raise
def setupHardware(self):
# Setup hardware components
if USE_ZABER_EMISSION_FILTER_WHEEL:
self.emission_filter_wheel.start_homing()
if USE_OPTOSPIN_EMISSION_FILTER_WHEEL:
self.emission_filter_wheel.set_speed(OPTOSPIN_EMISSION_FILTER_WHEEL_SPEED_HZ)
if not self.microcontroller:
raise ValueError("Microcontroller must be none-None for hardware setup.")
try:
if HOMING_ENABLED_Z:
self.stage.home(x=False, y=False, z=True, theta=False)
if HOMING_ENABLED_X and HOMING_ENABLED_Y:
self.stage.home(x=False, y=True, z=False, theta=False)
self.stage.home(x=True, y=False, z=False, theta=False)
self.slidePositionController.homing_done = True
if USE_ZABER_EMISSION_FILTER_WHEEL:
self.emission_filter_wheel.wait_for_homing_complete()
# TODO(imo): Why do we move to 20 after homing here?
if HOMING_ENABLED_X and HOMING_ENABLED_Y:
self.stage.move_x(20)
self.stage.move_y(20)
if ENABLE_OBJECTIVE_PIEZO:
OUTPUT_GAINS.CHANNEL7_GAIN = OBJECTIVE_PIEZO_CONTROL_VOLTAGE_RANGE == 5
div = 1 if OUTPUT_GAINS.REFDIV else 0
gains = sum(getattr(OUTPUT_GAINS, f"CHANNEL{i}_GAIN") << i for i in range(8))
self.microcontroller.configure_dac80508_refdiv_and_gain(div, gains)
self.microcontroller.set_dac80508_scaling_factor_for_illumination(ILLUMINATION_INTENSITY_FACTOR)
except TimeoutError as e:
# If we can't recover from a timeout, at least do our best to make sure the system is left in a safe
# and restartable state.
self.log.error("Setup timed out, resetting microcontroller before failing gui setup")
self.microcontroller.reset()
raise e
self.camera.set_software_triggered_acquisition()
self.camera.set_callback(self.streamHandler.on_new_frame)
self.camera.enable_callback()
if CAMERA_TYPE == "Toupcam":
self.camera.set_reset_strobe_delay_function(self.liveController.reset_strobe_arugment)
if SUPPORT_LASER_AUTOFOCUS:
self.camera_focus.set_software_triggered_acquisition() # self.camera.set_continuous_acquisition()
self.camera_focus.set_callback(self.streamHandler_focus_camera.on_new_frame)
self.camera_focus.enable_callback()
self.camera_focus.start_streaming()
if USE_SQUID_FILTERWHEEL:
if SQUID_FILTERWHEEL_HOMING_ENABLED:
self.squid_filter_wheel.homing()
def waitForMicrocontroller(self, timeout=5.0, error_message=None):
try:
self.microcontroller.wait_till_operation_is_completed(timeout)
except TimeoutError as e:
self.log.error(error_message or "Microcontroller operation timed out!")
raise e
def loadWidgets(self):
# Initialize all GUI widgets
if ENABLE_SPINNING_DISK_CONFOCAL:
self.spinningDiskConfocalWidget = widgets.SpinningDiskConfocalWidget(self.xlight, self.configurationManager)
if ENABLE_NL5:
import control.NL5Widget as NL5Widget
self.nl5Wdiget = NL5Widget.NL5Widget(self.nl5)
if CAMERA_TYPE == "Toupcam":
self.cameraSettingWidget = widgets.CameraSettingsWidget(
self.camera,
include_gain_exposure_time=False,
include_camera_temperature_setting=True,
include_camera_auto_wb_setting=False,
)
else:
self.cameraSettingWidget = widgets.CameraSettingsWidget(
self.camera,
include_gain_exposure_time=False,
include_camera_temperature_setting=False,
include_camera_auto_wb_setting=True,
)
self.liveControlWidget = widgets.LiveControlWidget(
self.streamHandler,
self.liveController,
self.configurationManager,
show_display_options=True,
show_autolevel=True,
autolevel=True,
)
self.navigationWidget = widgets.NavigationWidget(
self.stage, self.slidePositionController, widget_configuration=f"{WELLPLATE_FORMAT} well plate"
)
self.dacControlWidget = widgets.DACControWidget(self.microcontroller)
self.autofocusWidget = widgets.AutoFocusWidget(self.autofocusController)
self.piezoWidget = widgets.PiezoWidget(self.microcontroller)
self.objectivesWidget = widgets.ObjectivesWidget(self.objectiveStore)
if USE_ZABER_EMISSION_FILTER_WHEEL or USE_OPTOSPIN_EMISSION_FILTER_WHEEL:
self.filterControllerWidget = widgets.FilterControllerWidget(
self.emission_filter_wheel, self.liveController
)
if USE_SQUID_FILTERWHEEL:
self.squidFilterWidget = widgets.SquidFilterWidget(self)
self.recordingControlWidget = widgets.RecordingWidget(self.streamHandler, self.imageSaver)
self.wellplateFormatWidget = widgets.WellplateFormatWidget(
self.stage, self.navigationViewer, self.streamHandler, self.liveController
)
if WELLPLATE_FORMAT != "1536 well plate":
self.wellSelectionWidget = widgets.WellSelectionWidget(WELLPLATE_FORMAT, self.wellplateFormatWidget)
else:
self.wellSelectionWidget = widgets.Well1536SelectionWidget()
self.scanCoordinates.add_well_selector(self.wellSelectionWidget)
self.focusMapWidget = widgets.FocusMapWidget(
self.stage, self.navigationViewer, self.scanCoordinates, core.FocusMap()
)
if SUPPORT_LASER_AUTOFOCUS:
if FOCUS_CAMERA_TYPE == "Toupcam":
self.cameraSettingWidget_focus_camera = widgets.CameraSettingsWidget(
self.camera_focus,
include_gain_exposure_time=False,
include_camera_temperature_setting=True,
include_camera_auto_wb_setting=False,
)
else:
self.cameraSettingWidget_focus_camera = widgets.CameraSettingsWidget(
self.camera_focus,
include_gain_exposure_time=False,
include_camera_temperature_setting=False,
include_camera_auto_wb_setting=True,
)
self.liveControlWidget_focus_camera = widgets.LiveControlWidget(
self.streamHandler_focus_camera,
self.liveController_focus_camera,
self.configurationManager_focus_camera,
stretch=False,
) # ,show_display_options=True)
self.waveformDisplay = widgets.WaveformDisplay(N=1000, include_x=True, include_y=False)
self.displacementMeasurementWidget = widgets.DisplacementMeasurementWidget(
self.displacementMeasurementController, self.waveformDisplay
)
self.laserAutofocusControlWidget: widgets.LaserAutofocusControlWidget = widgets.LaserAutofocusControlWidget(
self.laserAutofocusController
)
self.imageDisplayWindow_focus = core.ImageDisplayWindow(draw_crosshairs=True)
self.imageDisplayTabs = QTabWidget()
if self.live_only_mode:
if ENABLE_TRACKING:
self.imageDisplayWindow = core.ImageDisplayWindow(
self.liveController, self.contrastManager, draw_crosshairs=True
)
self.imageDisplayWindow.show_ROI_selector()
else:
self.imageDisplayWindow = core.ImageDisplayWindow(
self.liveController, self.contrastManager, draw_crosshairs=True, show_LUT=True, autoLevels=True
)
self.imageDisplayTabs = self.imageDisplayWindow.widget
self.napariMosaicDisplayWidget = None
else:
self.setupImageDisplayTabs()
self.flexibleMultiPointWidget = widgets.FlexibleMultiPointWidget(
self.stage,
self.navigationViewer,
self.multipointController,
self.objectiveStore,
self.configurationManager,
self.scanCoordinates,
self.focusMapWidget,
)
self.wellplateMultiPointWidget = widgets.WellplateMultiPointWidget(
self.stage,
self.navigationViewer,
self.multipointController,
self.objectiveStore,
self.configurationManager,
self.scanCoordinates,
self.focusMapWidget,
self.napariMosaicDisplayWidget,
)
self.sampleSettingsWidget = widgets.SampleSettingsWidget(self.objectivesWidget, self.wellplateFormatWidget)
if ENABLE_TRACKING:
self.trackingControlWidget = widgets.TrackingControllerWidget(
self.trackingController,
self.configurationManager,
show_configurations=TRACKING_SHOW_MICROSCOPE_CONFIGURATIONS,
)
if ENABLE_STITCHER:
self.stitcherWidget = widgets.StitcherWidget(self.configurationManager, self.contrastManager)
self.recordTabWidget = QTabWidget()
self.setupRecordTabWidget()
self.cameraTabWidget = QTabWidget()
self.setupCameraTabWidget()
def setupImageDisplayTabs(self):
if USE_NAPARI_FOR_LIVE_VIEW:
self.napariLiveWidget = widgets.NapariLiveWidget(
self.streamHandler,
self.liveController,
self.stage,
self.configurationManager,
self.contrastManager,
self.wellSelectionWidget,
)
self.imageDisplayTabs.addTab(self.napariLiveWidget, "Live View")
else:
if ENABLE_TRACKING:
self.imageDisplayWindow = core.ImageDisplayWindow(
self.liveController, self.contrastManager, draw_crosshairs=True
)
self.imageDisplayWindow.show_ROI_selector()
else:
self.imageDisplayWindow = core.ImageDisplayWindow(
self.liveController, self.contrastManager, draw_crosshairs=True, show_LUT=True, autoLevels=True
)
self.imageDisplayTabs.addTab(self.imageDisplayWindow.widget, "Live View")
if not self.live_only_mode:
if USE_NAPARI_FOR_MULTIPOINT:
self.napariMultiChannelWidget = widgets.NapariMultiChannelWidget(
self.objectiveStore, self.contrastManager
)
self.imageDisplayTabs.addTab(self.napariMultiChannelWidget, "Multichannel Acquisition")
else:
self.imageArrayDisplayWindow = core.ImageArrayDisplayWindow()
self.imageDisplayTabs.addTab(self.imageArrayDisplayWindow.widget, "Multichannel Acquisition")
if USE_NAPARI_FOR_MOSAIC_DISPLAY:
self.napariMosaicDisplayWidget = widgets.NapariMosaicDisplayWidget(
self.objectiveStore, self.contrastManager
)
self.imageDisplayTabs.addTab(self.napariMosaicDisplayWidget, "Mosaic View")
if SUPPORT_LASER_AUTOFOCUS:
dock_laserfocus_image_display = dock.Dock("Focus Camera Image Display", autoOrientation=False)
dock_laserfocus_image_display.showTitleBar()
dock_laserfocus_image_display.addWidget(self.imageDisplayWindow_focus.widget)
dock_laserfocus_image_display.setStretch(x=100, y=100)
dock_laserfocus_liveController = dock.Dock("Focus Camera Controller", autoOrientation=False)
dock_laserfocus_liveController.showTitleBar()
dock_laserfocus_liveController.addWidget(self.liveControlWidget_focus_camera)
dock_laserfocus_liveController.setStretch(x=100, y=100)
dock_laserfocus_liveController.setFixedWidth(self.liveControlWidget_focus_camera.minimumSizeHint().width())
dock_waveform = dock.Dock("Displacement Measurement", autoOrientation=False)
dock_waveform.showTitleBar()
dock_waveform.addWidget(self.waveformDisplay)
dock_waveform.setStretch(x=100, y=40)
dock_displayMeasurement = dock.Dock("Displacement Measurement Control", autoOrientation=False)
dock_displayMeasurement.showTitleBar()
dock_displayMeasurement.addWidget(self.displacementMeasurementWidget)
dock_displayMeasurement.setStretch(x=100, y=40)
dock_displayMeasurement.setFixedWidth(self.displacementMeasurementWidget.minimumSizeHint().width())
laserfocus_dockArea = dock.DockArea()
laserfocus_dockArea.addDock(dock_laserfocus_image_display)
laserfocus_dockArea.addDock(
dock_laserfocus_liveController, "right", relativeTo=dock_laserfocus_image_display
)
if SHOW_LEGACY_DISPLACEMENT_MEASUREMENT_WINDOWS:
laserfocus_dockArea.addDock(dock_waveform, "bottom", relativeTo=dock_laserfocus_liveController)
laserfocus_dockArea.addDock(dock_displayMeasurement, "bottom", relativeTo=dock_waveform)
self.imageDisplayTabs.addTab(laserfocus_dockArea, "Laser-Based Focus")
def setupRecordTabWidget(self):
if ENABLE_WELLPLATE_MULTIPOINT:
self.recordTabWidget.addTab(self.wellplateMultiPointWidget, "Wellplate Multipoint")
if ENABLE_FLEXIBLE_MULTIPOINT:
self.recordTabWidget.addTab(self.flexibleMultiPointWidget, "Flexible Multipoint")
if ENABLE_TRACKING:
self.recordTabWidget.addTab(self.trackingControlWidget, "Tracking")
if ENABLE_RECORDING:
self.recordTabWidget.addTab(self.recordingControlWidget, "Simple Recording")
self.recordTabWidget.currentChanged.connect(lambda: self.resizeCurrentTab(self.recordTabWidget))
self.resizeCurrentTab(self.recordTabWidget)
def setupCameraTabWidget(self):
if not USE_NAPARI_FOR_LIVE_CONTROL or self.live_only_mode:
self.cameraTabWidget.addTab(self.navigationWidget, "Stages")
if ENABLE_OBJECTIVE_PIEZO:
self.cameraTabWidget.addTab(self.piezoWidget, "Piezo")
if ENABLE_NL5:
self.cameraTabWidget.addTab(self.nl5Wdiget, "NL5")
if ENABLE_SPINNING_DISK_CONFOCAL:
self.cameraTabWidget.addTab(self.spinningDiskConfocalWidget, "Confocal")
if USE_ZABER_EMISSION_FILTER_WHEEL or USE_OPTOSPIN_EMISSION_FILTER_WHEEL:
self.cameraTabWidget.addTab(self.filterControllerWidget, "Emission Filter")
if USE_SQUID_FILTERWHEEL:
self.cameraTabWidget.addTab(self.squidFilterWidget, "Squid Filter")
self.cameraTabWidget.addTab(self.cameraSettingWidget, "Camera")
self.cameraTabWidget.addTab(self.autofocusWidget, "Contrast AF")
if SUPPORT_LASER_AUTOFOCUS:
self.cameraTabWidget.addTab(self.laserAutofocusControlWidget, "Laser AF")
self.cameraTabWidget.addTab(self.focusMapWidget, "Focus Map")
self.cameraTabWidget.currentChanged.connect(lambda: self.resizeCurrentTab(self.cameraTabWidget))
self.resizeCurrentTab(self.cameraTabWidget)
def setupLayout(self):
layout = QVBoxLayout()
if USE_NAPARI_FOR_LIVE_CONTROL and not self.live_only_mode:
layout.addWidget(self.navigationWidget)
else:
layout.addWidget(self.liveControlWidget)
layout.addWidget(self.cameraTabWidget)
if SHOW_DAC_CONTROL:
layout.addWidget(self.dacControlWidget)
layout.addWidget(self.recordTabWidget)
if ENABLE_STITCHER:
layout.addWidget(self.stitcherWidget)
self.stitcherWidget.hide()
layout.addWidget(self.sampleSettingsWidget)
layout.addWidget(self.navigationViewer)
# Add performance mode toggle button
if not self.live_only_mode:
self.performanceModeToggle = QPushButton("Enable Performance Mode")
self.performanceModeToggle.setCheckable(True)
self.performanceModeToggle.setChecked(self.performance_mode)
self.performanceModeToggle.clicked.connect(self.togglePerformanceMode)
layout.addWidget(self.performanceModeToggle)
self.centralWidget = QWidget()
self.centralWidget.setLayout(layout)
self.centralWidget.setFixedWidth(self.centralWidget.minimumSizeHint().width())
if SINGLE_WINDOW:
self.setupSingleWindowLayout()
else:
self.setupMultiWindowLayout()
def setupSingleWindowLayout(self):
main_dockArea = dock.DockArea()
dock_display = dock.Dock("Image Display", autoOrientation=False)
dock_display.showTitleBar()
dock_display.addWidget(self.imageDisplayTabs)
dock_display.setStretch(x=100, y=100)
main_dockArea.addDock(dock_display)
self.dock_wellSelection = dock.Dock("Well Selector", autoOrientation=False)
self.dock_wellSelection.showTitleBar()
if not USE_NAPARI_WELL_SELECTION or self.live_only_mode:
self.dock_wellSelection.addWidget(self.wellSelectionWidget)
self.dock_wellSelection.setFixedHeight(self.dock_wellSelection.minimumSizeHint().height())
main_dockArea.addDock(self.dock_wellSelection, "bottom")
dock_controlPanel = dock.Dock("Controls", autoOrientation=False)
dock_controlPanel.addWidget(self.centralWidget)
dock_controlPanel.setStretch(x=1, y=None)
dock_controlPanel.setFixedWidth(dock_controlPanel.minimumSizeHint().width())
main_dockArea.addDock(dock_controlPanel, "right")
self.setCentralWidget(main_dockArea)
desktopWidget = QDesktopWidget()
height_min = 0.9 * desktopWidget.height()
width_min = 0.96 * desktopWidget.width()
self.setMinimumSize(int(width_min), int(height_min))
self.onTabChanged(self.recordTabWidget.currentIndex())
def setupMultiWindowLayout(self):
self.setCentralWidget(self.centralWidget)
self.tabbedImageDisplayWindow = QMainWindow()
self.tabbedImageDisplayWindow.setCentralWidget(self.imageDisplayTabs)
self.tabbedImageDisplayWindow.setWindowFlags(self.windowFlags() | Qt.CustomizeWindowHint)
self.tabbedImageDisplayWindow.setWindowFlags(self.windowFlags() & ~Qt.WindowCloseButtonHint)
desktopWidget = QDesktopWidget()
width = 0.96 * desktopWidget.height()
height = width
self.tabbedImageDisplayWindow.setFixedSize(int(width), int(height))
self.tabbedImageDisplayWindow.show()
def makeConnections(self):
self.streamHandler.signal_new_frame_received.connect(self.liveController.on_new_frame)
self.streamHandler.packet_image_to_write.connect(self.imageSaver.enqueue)
if ENABLE_STITCHER:
self.multipointController.signal_stitcher.connect(self.startStitcher)
if ENABLE_FLEXIBLE_MULTIPOINT:
self.flexibleMultiPointWidget.signal_acquisition_started.connect(self.toggleAcquisitionStart)
if ENABLE_STITCHER:
self.flexibleMultiPointWidget.signal_stitcher_widget.connect(self.toggleStitcherWidget)
self.flexibleMultiPointWidget.signal_acquisition_channels.connect(
self.stitcherWidget.updateRegistrationChannels
)
self.flexibleMultiPointWidget.signal_stitcher_z_levels.connect(
self.stitcherWidget.updateRegistrationZLevels
)
if ENABLE_WELLPLATE_MULTIPOINT:
self.wellplateMultiPointWidget.signal_acquisition_started.connect(self.toggleAcquisitionStart)
if ENABLE_STITCHER:
self.wellplateMultiPointWidget.signal_stitcher_widget.connect(self.toggleStitcherWidget)
self.wellplateMultiPointWidget.signal_acquisition_channels.connect(
self.stitcherWidget.updateRegistrationChannels
)
self.wellplateMultiPointWidget.signal_stitcher_z_levels.connect(
self.stitcherWidget.updateRegistrationZLevels
)
self.liveControlWidget.signal_newExposureTime.connect(self.cameraSettingWidget.set_exposure_time)
self.liveControlWidget.signal_newAnalogGain.connect(self.cameraSettingWidget.set_analog_gain)
if not self.live_only_mode:
self.liveControlWidget.signal_start_live.connect(self.onStartLive)
self.liveControlWidget.update_camera_settings()
self.connectSlidePositionController()
self.navigationViewer.signal_coordinates_clicked.connect(self.move_from_click_mm)
self.objectivesWidget.signal_objective_changed.connect(self.navigationViewer.on_objective_changed)
if ENABLE_FLEXIBLE_MULTIPOINT:
self.objectivesWidget.signal_objective_changed.connect(self.flexibleMultiPointWidget.update_fov_positions)
# TODO(imo): Fix position updates after removal of navigation controller
self.movement_updater.position_after_move.connect(self.navigationViewer.draw_fov_current_location)
if WELLPLATE_FORMAT == "glass slide":
# TODO(imo): This well place logic is duplicated below in onWellPlateChanged. We should change it to only exist in 1 location.
# self.movement_updater.sent_after_stopped.connect(self.wellplateMultiPointWidget.set_live_scan_coordinates)
self.movement_updater.position_after_move.connect(self.wellplateMultiPointWidget.update_live_coordinates)
self.is_live_scan_grid_on = True
self.multipointController.signal_register_current_fov.connect(self.navigationViewer.register_fov)
self.multipointController.signal_current_configuration.connect(self.liveControlWidget.set_microscope_mode)
self.multipointController.signal_z_piezo_um.connect(self.piezoWidget.update_displacement_um_display)
self.recordTabWidget.currentChanged.connect(self.onTabChanged)
if not self.live_only_mode:
self.imageDisplayTabs.currentChanged.connect(self.onDisplayTabChanged)
if USE_NAPARI_FOR_LIVE_VIEW and not self.live_only_mode:
self.multipointController.signal_current_configuration.connect(self.napariLiveWidget.set_microscope_mode)
self.autofocusController.image_to_display.connect(
lambda image: self.napariLiveWidget.updateLiveLayer(image, from_autofocus=True)
)
self.streamHandler.image_to_display.connect(
lambda image: self.napariLiveWidget.updateLiveLayer(image, from_autofocus=False)
)
self.multipointController.image_to_display.connect(
lambda image: self.napariLiveWidget.updateLiveLayer(image, from_autofocus=False)
)
self.napariLiveWidget.signal_coordinates_clicked.connect(self.move_from_click_image)
self.liveControlWidget.signal_live_configuration.connect(self.napariLiveWidget.set_live_configuration)
if USE_NAPARI_FOR_LIVE_CONTROL:
self.napariLiveWidget.signal_newExposureTime.connect(self.cameraSettingWidget.set_exposure_time)
self.napariLiveWidget.signal_newAnalogGain.connect(self.cameraSettingWidget.set_analog_gain)
self.napariLiveWidget.signal_autoLevelSetting.connect(self.imageDisplayWindow.set_autolevel)
else:
self.streamHandler.image_to_display.connect(self.imageDisplay.enqueue)
self.imageDisplay.image_to_display.connect(self.imageDisplayWindow.display_image)
self.autofocusController.image_to_display.connect(self.imageDisplayWindow.display_image)
self.multipointController.image_to_display.connect(self.imageDisplayWindow.display_image)
self.liveControlWidget.signal_autoLevelSetting.connect(self.imageDisplayWindow.set_autolevel)
self.imageDisplayWindow.image_click_coordinates.connect(self.move_from_click_image)
self.makeNapariConnections()
self.wellplateFormatWidget.signalWellplateSettings.connect(self.navigationViewer.update_wellplate_settings)
self.wellplateFormatWidget.signalWellplateSettings.connect(self.scanCoordinates.update_wellplate_settings)
self.wellplateFormatWidget.signalWellplateSettings.connect(self.wellSelectionWidget.onWellplateChanged)
self.wellplateFormatWidget.signalWellplateSettings.connect(
lambda format_, *args: self.onWellplateChanged(format_)
)
self.wellSelectionWidget.signal_wellSelectedPos.connect(self.move_to_mm)
if ENABLE_WELLPLATE_MULTIPOINT:
self.wellSelectionWidget.signal_wellSelected.connect(self.wellplateMultiPointWidget.update_well_coordinates)
self.objectivesWidget.signal_objective_changed.connect(self.wellplateMultiPointWidget.update_coordinates)
if SUPPORT_LASER_AUTOFOCUS:
self.liveControlWidget_focus_camera.signal_newExposureTime.connect(
self.cameraSettingWidget_focus_camera.set_exposure_time
)
self.liveControlWidget_focus_camera.signal_newAnalogGain.connect(
self.cameraSettingWidget_focus_camera.set_analog_gain
)
self.liveControlWidget_focus_camera.update_camera_settings()
self.streamHandler_focus_camera.signal_new_frame_received.connect(
self.liveController_focus_camera.on_new_frame
)
self.streamHandler_focus_camera.image_to_display.connect(self.imageDisplayWindow_focus.display_image)
self.streamHandler_focus_camera.image_to_display.connect(
self.displacementMeasurementController.update_measurement
)
self.displacementMeasurementController.signal_plots.connect(self.waveformDisplay.plot)
self.displacementMeasurementController.signal_readings.connect(
self.displacementMeasurementWidget.display_readings
)
self.laserAutofocusController.image_to_display.connect(self.imageDisplayWindow_focus.display_image)
self.camera.set_callback(self.streamHandler.on_new_frame)
def setup_movement_updater(self):
# We provide a few signals about the system's physical movement to other parts of the UI. Ideally, they other
# parts would register their interest (instead of us needing to know that they want to hear about the movements
# here), but as an intermediate pumping it all from one location is better than nothing.
self.movement_updater = MovementUpdater(self.stage)
self.movement_update_timer = QTimer()
self.movement_update_timer.setInterval(100)
self.movement_update_timer.timeout.connect(self.movement_updater.do_update)
self.movement_update_timer.start()
def makeNapariConnections(self):
"""Initialize all Napari connections in one place"""
self.napari_connections = {
"napariLiveWidget": [],
"napariMultiChannelWidget": [],
"napariMosaicDisplayWidget": [],
}
# Setup live view connections
if USE_NAPARI_FOR_LIVE_VIEW and not self.live_only_mode:
self.napari_connections["napariLiveWidget"] = [
(self.multipointController.signal_current_configuration, self.napariLiveWidget.set_microscope_mode),
(
self.autofocusController.image_to_display,
lambda image: self.napariLiveWidget.updateLiveLayer(image, from_autofocus=True),
),
(
self.streamHandler.image_to_display,
lambda image: self.napariLiveWidget.updateLiveLayer(image, from_autofocus=False),
),
(
self.multipointController.image_to_display,
lambda image: self.napariLiveWidget.updateLiveLayer(image, from_autofocus=False),
),
(self.napariLiveWidget.signal_coordinates_clicked, self.move_from_click_image),
(self.liveControlWidget.signal_live_configuration, self.napariLiveWidget.set_live_configuration),
]
if USE_NAPARI_FOR_LIVE_CONTROL:
self.napari_connections["napariLiveWidget"].extend(
[
(self.napariLiveWidget.signal_newExposureTime, self.cameraSettingWidget.set_exposure_time),
(self.napariLiveWidget.signal_newAnalogGain, self.cameraSettingWidget.set_analog_gain),
(self.napariLiveWidget.signal_autoLevelSetting, self.imageDisplayWindow.set_autolevel),
]
)
else:
# Non-Napari display connections
self.streamHandler.image_to_display.connect(self.imageDisplay.enqueue)
self.imageDisplay.image_to_display.connect(self.imageDisplayWindow.display_image)
self.autofocusController.image_to_display.connect(self.imageDisplayWindow.display_image)
self.multipointController.image_to_display.connect(self.imageDisplayWindow.display_image)
self.liveControlWidget.signal_autoLevelSetting.connect(self.imageDisplayWindow.set_autolevel)
self.imageDisplayWindow.image_click_coordinates.connect(self.move_from_click_image)
if not self.live_only_mode:
# Setup multichannel widget connections
if USE_NAPARI_FOR_MULTIPOINT:
self.napari_connections["napariMultiChannelWidget"] = [
(self.multipointController.napari_layers_init, self.napariMultiChannelWidget.initLayers),