def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.ui = dashboard.Dashboard(limit=config.get('limit', None),
filter_defaults=config.get(
'filters', None))
self.ui.resize(1600, 900)
self.ui.show()
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.man = manager
self.win = QtGui.QMainWindow()
self.cw = DataTreeWidget()
self.win.setCentralWidget(self.cw)
self.win.show()
self.man.sigTaskCreated.connect(self.showTask)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.ui = submit_expt.ExperimentSubmitUi()
self.ui.resize(1600, 900)
self.ui.show()
self.load_from_dm_btn = QtGui.QPushButton("load from data manager")
self.ui.left_layout.insertWidget(0, self.load_from_dm_btn)
self.load_from_dm_btn.clicked.connect(self.load_from_dm_clicked)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.ui = vimaging.VImagingAnalyzer()
self.ui.resize(1600, 900)
self.ui.show()
self.load_from_dm_btn = QtGui.QPushButton("load from data manager")
self.ui.layout.addWidget(self.load_from_dm_btn, self.ui.layout.rowCount(), 0)
self.load_from_dm_btn.clicked.connect(self.load_from_dm_clicked)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.ui = submit_expt.ExperimentSubmitUi()
self.ui.resize(1600, 900)
self.ui.show()
self.load_from_dm_btn = QtGui.QPushButton("load from data manager")
self.ui.left_layout.insertWidget(0, self.load_from_dm_btn)
self.load_from_dm_btn.clicked.connect(self.load_from_dm_clicked)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.ui = multipatch_nwb_viewer.MultipatchNwbViewer()
self.ui.resize(1600, 900)
self.ui.show()
self.load_from_dm_btn = QtGui.QPushButton("load from data manager")
self.ui.vsplit.insertWidget(0, self.load_from_dm_btn)
self.load_from_dm_btn.clicked.connect(self.load_from_dm_clicked)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.ui = multipatch_nwb_viewer.MultipatchNwbViewer()
self.ui.resize(1600, 900)
self.ui.show()
self.load_from_dm_btn = QtGui.QPushButton("load from data manager")
self.ui.vsplit.insertWidget(0, self.load_from_dm_btn)
self.load_from_dm_btn.clicked.connect(self.load_from_dm_clicked)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.ui = vimaging.VImagingAnalyzer()
self.ui.resize(1600, 900)
self.ui.show()
self.load_from_dm_btn = QtGui.QPushButton("load from data manager")
self.ui.layout.addWidget(self.load_from_dm_btn,
self.ui.layout.rowCount(), 0)
self.load_from_dm_btn.clicked.connect(self.load_from_dm_clicked)
def quit(self):
if self.img is not None:# clear the image ovelay if it exists
self.cameraModule.window().removeItem(self.img)
self.img = None
for obj in self.objectiveROImap: # remove the ROI's for all objectives.
try:
self.cameraModule.window().removeItem(self.objectiveROImap[obj])
except:
pass
Module.quit(self)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.ui = vimaging.VImagingAnalyzer2()
self.ui.resize(1600, 900)
self.ui.show()
self.load_from_dm_btn = QtGui.QPushButton("load from data manager")
self.load_from_dm_btn.setParent(self.ui)
self.load_from_dm_btn.resize(160, 30)
self.load_from_dm_btn.show()
self.load_from_dm_btn.clicked.connect(self.load_from_dm_clicked)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.ui = vimaging.VImagingAnalyzer2()
self.ui.resize(1600, 900)
self.ui.show()
self.load_from_dm_btn = QtGui.QPushButton("load from data manager")
self.load_from_dm_btn.setParent(self.ui)
self.load_from_dm_btn.resize(160, 30)
self.load_from_dm_btn.show()
self.load_from_dm_btn.clicked.connect(self.load_from_dm_clicked)
def __init__(self, manager, name, config):
from aiccf.data import CCFAtlasData
from aiccf.viewer import AtlasViewer
Module.__init__(self, manager, name, config)
self.man = manager
self.win = AtlasViewer()
self.win.show()
self.win.setWindowTitle(name)
resolution = config.get('resolution', None)
self.atlas_data = CCFAtlasData(resolution=resolution)
self.win.set_data(self.atlas_data)
def __init__(self, manager, name, config):
from pycsf.editor import SolutionEditorWindow
from pycsf.core import SolutionDatabase
Module.__init__(self, manager, name, config)
self.man = manager
self.db = SolutionDatabase()
self.win = SolutionEditorWindow(db=self.db)
if 'recipeFile' in config:
self.win.loadFile(config['recipeFile'])
else:
self.db.loadDefault()
self.win.show()
self.win.tabs.setCurrentIndex(2)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.man = manager
self.win = QtGui.QMainWindow()
self.cw = QtGui.QSplitter()
self.taskTree = DataTreeWidget()
self.resultTree = DataTreeWidget()
self.win.setCentralWidget(self.cw)
self.cw.addWidget(self.taskTree)
self.cw.addWidget(self.resultTree)
self.win.show()
self.win.setWindowTitle('Task Monitor')
self.man.sigTaskCreated.connect(self.showTask)
self.taskTimer = QtCore.QTimer()
self.taskTimer.timeout.connect(self.checkResult)
def quit(self):
self.abortTask()
# if self.imageItem is not None and self.imageItem.scene() is not None:
# self.imageItem.scene().removeItem(self.imageItem)
# for obj,item in self.objectiveROImap.items(): # remove the ROI's for all objectives.
# try:
# if item.scene() is not None:
# item.scene().removeItem(item)
# except:
# pass
# if self.tileRoi is not None:
# if self.tileRoi.scene() is not None:
# self.tileRoi.scene().removeItem(self.tileRoi)
# self.tileRoi = None
self.camModInterface.quit()
self.imagingCtrl.quit()
self.imageItem = None
Module.quit(self)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.dataModel = None # left over from old analysis system..
self.editor = MosaicEditor(self)
self.win = MosaicEditorWindow(self.editor, name)
self.win.show()
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.win = MultiPatchWindow(self)
self.win.show()
def quit(self):
self.startBtn.setChecked(False)
Module.quit(self)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.recordDir = None
self.recordWritable = False
self.running = False
self.win = Qt.QSplitter()
self.ctrlWidget = pg.LayoutWidget()
self.win.addWidget(self.ctrlWidget)
self.newBtn = Qt.QPushButton('New Record')
self.loadBtn = Qt.QPushButton('Load Record')
self.startBtn = Qt.QPushButton('Start')
self.startBtn.setCheckable(True)
self.fileLabel = Qt.QLabel()
self.ctrlWidget.addWidget(self.newBtn, 0, 0)
self.ctrlWidget.addWidget(self.loadBtn, 1, 0)
self.ctrlWidget.addWidget(self.startBtn, 2, 0)
self.ctrlWidget.addWidget(self.fileLabel, 3, 0)
self.newBtn.clicked.connect(self.newRecord)
self.loadBtn.clicked.connect(self.loadClicked)
self.startBtn.toggled.connect(self.startToggled)
self.params = pg.parametertree.Parameter.create(
name='params',
type='group',
children=[
dict(name='interval',
type='float',
value=10,
suffix='s',
siPrefix=True,
limits=[0.001, None],
step=1.0),
dict(name='trace duration',
type='float',
value=1.0,
suffix='s',
siPrefix=True,
limits=[0.001, None],
step=0.1),
dict(name='sample rate',
type='int',
value=1e6,
suffix='Hz',
siPrefix=True,
limits=[100, None],
step=1e5),
])
self.ptree = pg.parametertree.ParameterTree()
self.ptree.setParameters(self.params)
self.ctrlWidget.addWidget(self.ptree, 4, 0)
self.channelLayout = Qt.QSplitter()
self.win.addWidget(self.channelLayout)
self.channels = collections.OrderedDict()
self.win.show()
self.timer = Qt.QTimer()
self.timer.timeout.connect(self.runOnce)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.win = ImagerWindow(self) # make the main window - mostly to catch window close event...
self.ui = Ui_Form()
self.testMode = False # set to True to just display the scan signals
self.win.show()
self.win.setWindowTitle('Multiphoton Imager V 1.01')
self.win.resize(1200, 900) # make the window big enough to use on a large monitor...
self.w1 = QtGui.QSplitter() # divide l, r
self.w1.setOrientation(QtCore.Qt.Horizontal)
self.w2s = QtGui.QSplitter()
self.w2s.setOrientation(QtCore.Qt.Vertical)
self.win.setCentralWidget(self.w1) # w1 is the "main window" splitter
self.w1.addWidget(self.w2s) # now we add w2s, the spliter on the left
self.ui.setupUi(self.w2s) # put the ui on the top
# create the user interface
self.tree = PT.ParameterTree()
self.w2s.addWidget(self.tree) # put the parameters on the bottom
self.w2s.setSizes([1,1,900]) # Ui top widget has multiple splitters itself - force small space..
self.view = ImagerView()
self.w1.addWidget(self.view) # add the view to the right of w1
self.originalROI = None
self.currentStack = None
self.currentStackLength = 0
self.roi = None # no current ROI
self.regionCtrl = None
self.currentRoi = None
self.tileRoi = None
self.tileRoiVisible = False
self.tilexPos = 0.
self.tileyPos = 0.
self.tileWidth = 2e-4
self.tileHeight = 2e-4
self.img = None # overlay image in the camera Window...
self.dwellTime = 0. # "pixel dwell time" computed from scan time and points.
self.fieldSize = 63.0*120e-6 # field size for 63x, will be scaled for others
# we assume that you are not going to change the current camera or scope while running
# ... not just yet anyway.
# if this is to be allowed on a system, the change must be signaled to this class,
# and we need to pick up the device in a routine that handles the change.
try:
self.cameraModule = self.manager.getModule(config['cameraModule'])
except:
self.manager.loadDefinedModule(config['cameraModule'])
pg.QtGui.QApplication.processEvents()
self.cameraModule = self.manager.getModule(config['cameraModule'])
#self.scopeDev = self.camdev.scopeDev
self.laserDev = self.manager.getDevice(config['laser'])
self.scannerDev = self.manager.getDevice(config['scanner'])
#self.scannerDev.sigGlobalSubdeviceChanged.connect(self.objectiveUpdate)
#self.scannerDev.sigGlobalTransformChanged.connect(self.transformUpdate)
# find first scope device that is parent of scanner
dev = self.scannerDev
while dev is not None and not isinstance(dev, Microscope):
dev = dev.parentDevice()
self.scopeDev = dev
if dev is not None:
self.scopeDev.sigObjectiveChanged.connect(self.objectiveUpdate)
self.scopeDev.sigGlobalTransformChanged.connect(self.transformChanged)
self.detectorDev = self.manager.getDevice(config['detector'][0])
self.detectorChannel = config['detector'][1]
self.attenuatorDev = self.manager.getDevice(config['attenuator'][0])
self.attenuatorChannel = config['attenuator'][1]
self.objectiveROImap = {} # this is a dict that we will populate with the name
# of the objective and the associated ROI object .
# That way, each objective has a scan region appopriate for it's magnification.
self.ui.hide_check.stateChanged.connect(self.hideOverlayImage)
self.ui.alphaSlider.valueChanged.connect(self.imageAlphaAdjust)
self.ui.snap_Button.clicked.connect(self.PMT_SnapClicked)
self.ui.snap_Standard_Button.clicked.connect(self.PMT_Snap_std)
self.ui.snap_High_Button.clicked.connect(self.PMT_Snap_high)
self.ui.video_button.clicked.connect(self.toggleVideo)
self.ui.video_std_button.clicked.connect(self.toggleVideo_std)
self.ui.video_fast_button.clicked.connect(self.toggleVideo_fast)
self.ui.record_button.toggled.connect(self.recordToggled)
self.ui.run_button.clicked.connect(self.PMT_Run)
self.ui.stop_button.clicked.connect(self.PMT_Stop)
self.ui.set_TilesButton.clicked.connect(self.setTilesROI)
#self.ui.cameraSnapBtn.clicked.connect(self.cameraSnap)
self.ui.restoreROI.clicked.connect(self.restoreROI)
self.ui.saveROI.clicked.connect(self.saveROI)
self.ui.Align_to_Camera.clicked.connect(self.reAlign)
self.param = PT.Parameter(name = 'param', children=[
dict(name="Preset", type='list', value='StandardDef',
values=['StandardDef', 'HighDef', 'video-std', 'video-fast',
'video-ultra']),
dict(name='Store', type='bool', value=True),
dict(name='Blank Screen', type='bool', value=True),
dict(name='Sample Rate', type='float', value=1.0e6, suffix='Hz', dec = True, minStep=100., step=0.5, limits=[10e3, 5e6], siPrefix=True),
dict(name='Downsample', type='int', value=1, limits=[1,None]),
dict(name='Frame Time', type='float', readonly=True, value=0.0),
dict(name='Average', type='int', value=1, limits=[1,100]),
dict(name='Pockels', type='float', value= 0.03, suffix='V', dec=True, minStep=1e-3, limits=[0, 1.5], step=0.1, siPrefix=True),
dict(name='Wavelength', type='float', value= 700, suffix = 'nm', readonly = True),
dict(name='Power', type='float', value = 0.00, suffix = 'W', readonly = True),
dict(name='Objective', type='str', value='Unknown', readonly=True),
dict(name='Follow Stage', type='bool', value=True),
dict(name='Image Width', type='int', value=500, readonly=False),
dict(name='Image Height', type='int', value=500, readonly=False),
dict(name='xSpan', type='float', value = 1.0, limits=[0.01, 2.5]), #limits=[0., 20.e-3], step=10e-6, siPrefix=True, readonly=True), # True image width and height, in microns
dict(name='ySpan', type = 'float', value = 1.0, limits=[0.01, 2.5]), # limits=[0., 20.e-3], step=10e-6, siPrefix=True, readonly=True),
dict(name='Bidirectional', type='bool', value=True),
dict(name='Decomb', type='bool', value=True, children=[
dict(name='Auto', type='bool', value=True),
dict(name='Shift', type='float', value=100e-6, suffix='s', step=10e-6, siPrefix=True),
]),
dict(name='Overscan', type='float', value=25.0, suffix='%'),
dict(name='Scope Device', type='interface', interfaceTypes=['microscope']),
dict(name='Scanner Device', type='interface', interfaceTypes=['scanner']),
dict(name='Laser Device', type='interface', interfaceTypes=['laser']),
dict(name='Camera Module', type='interface', interfaceTypes=['cameraModule']),
dict(name="Tiles", type="bool", value=False, children=[
dict(name='Stage', type='interface', interfaceTypes='stage'),
dict(name="X0", type="float", value=-100., suffix='um', dec=True, minStep=1, step=1, limits=[-2.5e3,2.5e3], siPrefix=True),
dict(name="X1", type="float", value=100., suffix='um', dec=True, minStep=1, step=1, limits=[-2.5e3,2.5e3], siPrefix=True),
dict(name="Y0", type="float", value=-100., suffix='um', dec=True, minStep=1, step=1, limits=[-2.5e3,2.5e3], siPrefix=True),
dict(name="Y1", type="float", value=100., suffix='um', dec=True, minStep=1, step=1, limits=[-2.5e3,2.5e3], siPrefix=True),
dict(name="StepSize", type="float", value=100, suffix='um', dec=True, minStep=1e-5, step=0.5, limits=[1e-5,1e3], siPrefix=True),
]),
dict(name="Z-Stack", type="bool", value=False, children=[
dict(name='Stage', type='interface', interfaceTypes='stage'),
dict(name="Step Size", type="float", value=5e-6, suffix='m', dec=True, minStep=1e-7, step=0.5, limits=[1e-9,1], siPrefix=True),
dict(name="Steps", type='int', value=10, step=1, limits=[1,None]),
dict(name="Depth", type="float", value=0, readonly=True, suffix='m', siPrefix=True)
]),
dict(name="Timed", type="bool", value=False, children=[
dict(name="Interval", type="float", value=5.0, suffix='s', dec=True, minStep=0.1, step=0.5, limits=[0.1,30], siPrefix=True),
dict(name="N Intervals", type='int', value=10, step=1, limits=[1,None]),
dict(name="Duration", type="float", value=0, readonly=True, suffix='s', siPrefix = True),
dict(name="Current Frame", type='int', value = 0, readonly=True),
]),
dict(name='Show PMT V', type='bool', value=False),
dict(name='Show Mirror V', type='bool', value=False),
])
self.stopFlag = False
self.tree.setParameters(self.param)
self.Manager = manager
# insert an ROI into the camera image that corresponds to our scan area
self.objectiveUpdate() # force update of objective information and create appropriate ROI
# check the devices...
self.update() # also force update now to make sure all parameters are synchronized
self.param.sigTreeStateChanged.connect(self.update)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.win = ImagerWindow(self) # make the main window - mostly to catch window close event...
self.win.show()
self.win.setWindowTitle('Multiphoton Imager V 1.01')
self.win.resize(500, 900) # make the window big enough to use on a large monitor...
self.w1 = QtGui.QSplitter() # divide l, r
self.w1.setOrientation(QtCore.Qt.Horizontal)
self.win.setCentralWidget(self.w1) # w1 is the "main window" splitter
self.dockarea = pg.dockarea.DockArea()
self.w1.addWidget(self.dockarea)
self.w2s = QtGui.QWidget()
self.w2sl = QtGui.QVBoxLayout()
self.w2s.setLayout(self.w2sl)
self.w2sl.setContentsMargins(0, 0, 0, 0)
self.w2sl.setSpacing(0)
self.ctrlWidget = QtGui.QWidget()
self.ui = Ui_Form()
self.ui.setupUi(self.ctrlWidget) # put the ui on the top
self.w2sl.addWidget(self.ctrlWidget)
# create the parameter tree for controlling device behavior
self.tree = PT.ParameterTree()
self.w2sl.addWidget(self.tree)
# takes care of displaying image data,
# contrast & background subtraction user interfaces
self.imagingCtrl = imaging.ImagingCtrl()
self.frameDisplay = self.imagingCtrl.frameDisplay
self.imageItem = self.frameDisplay.imageItem()
# create docks for imaging, contrast, and background subtraction
recDock = pg.dockarea.Dock(name="Acquisition Control", widget=self.imagingCtrl, size=(250, 10), autoOrientation=False)
scanDock = pg.dockarea.Dock(name="Device Control", widget=self.w2s, size=(250, 800), autoOrientation=False)
dispDock = pg.dockarea.Dock(name="Display Control", widget=self.frameDisplay.contrastWidget(), size=(250, 800), autoOrientation=False)
bgDock = pg.dockarea.Dock(name="Background Subtraction", widget=self.frameDisplay.backgroundWidget(), size=(250, 10), autoOrientation=False)
self.dockarea.addDock(recDock)
self.dockarea.addDock(dispDock, 'right', recDock)
self.dockarea.addDock(scanDock, 'bottom', recDock)
self.dockarea.addDock(bgDock, 'bottom', dispDock)
# TODO: resurrect this for situations when the camera module can't be used
# self.view = ImagerView()
# self.w1.addWidget(self.view) # add the view to the right of w1
self.blanker = ScreenBlanker()
self.blanker.sigCancelClicked.connect(self.blankerCancelClicked)
self.abort = False
self.storedROI = None
self.currentRoi = None
self.ignoreRoiChange = False
self.lastFrame = None
self.fieldSize = 63.0*120e-6 # field size for 63x, will be scaled for others
self.scanVoltageCache = None # cached scan protocol computed by generateScanProtocol
self.objectiveROImap = {} # this is a dict that we will populate with the name
# of the objective and the associated ROI object .
# That way, each objective has a scan region appopriate for it's magnification.
# we assume that you are not going to change the current camera or scope while running
# ... not just yet anyway.
# if this is to be allowed on a system, the change must be signaled to this class,
# and we need to pick up the device in a routine that handles the change.
try:
self.cameraModule = self.manager.getModule(config['cameraModule'])
except:
self.manager.loadDefinedModule(config['cameraModule'])
pg.QtGui.QApplication.processEvents()
self.cameraModule = self.manager.getModule(config['cameraModule'])
self.laserDev = self.manager.getDevice(config['laser'])
self.scannerDev = self.manager.getDevice(config['scanner'])
self.imagingThread = ImagingThread(self.laserDev, self.scannerDev)
self.imagingThread.sigNewFrame.connect(self.newFrame)
self.imagingThread.sigVideoStopped.connect(self.videoStopped)
self.imagingThread.sigAborted.connect(self.imagingAborted)
# connect user interface to camera module
self.camModInterface = ImagerCamModInterface(self, self.cameraModule)
self.cameraModule.window().addInterface(self.name, self.camModInterface)
# find first scope device that is parent of scanner
dev = self.scannerDev
while dev is not None and not isinstance(dev, Microscope):
dev = dev.parentDevice()
self.scopeDev = dev
if dev is not None:
self.scopeDev.sigObjectiveChanged.connect(self.objectiveUpdate)
self.scopeDev.sigGlobalTransformChanged.connect(self.transformChanged)
# config may specify a single detector device (dev, channel) or a list of devices
# to select from [(dev1, channel1), ...]
self.detectors = config.get('detectors', [config.get('detector')])
self.attenuatorDev = self.manager.getDevice(config['attenuator'][0])
self.attenuatorChannel = config['attenuator'][1]
self.laserMonitor = QtCore.QTimer()
self.laserMonitor.timeout.connect(self.updateLaserInfo)
self.laserMonitor.start(3000)
self.frameDisplay.imageUpdated.connect(self.imageUpdated)
self.imagingCtrl.sigAcquireFrameClicked.connect(self.acquireFrameClicked)
self.imagingCtrl.sigStartVideoClicked.connect(self.startVideoClicked)
self.imagingCtrl.sigStopVideoClicked.connect(self.stopVideoClicked)
# Add custom imaging modes
for mode in FrameModes:
self.imagingCtrl.addFrameButton(mode)
for mode in VideoModes:
self.imagingCtrl.addVideoButton(mode)
# Connect other UI controls
# self.ui.run_button.clicked.connect(self.PMT_Run)
# self.ui.stop_button.clicked.connect(self.PMT_Stop)
# self.ui.set_TilesButton.clicked.connect(self.setTilesROI)
#self.ui.cameraSnapBtn.clicked.connect(self.cameraSnap)
self.ui.restoreROI.clicked.connect(self.restoreROI)
self.ui.saveROI.clicked.connect(self.saveROI)
self.ui.Align_to_Camera.clicked.connect(self.reAlign)
self.scanProgram = ScanProgram()
self.scanProgram.addComponent('rect')
self.param = PT.Parameter(name = 'param', children=[
dict(name='Scan Control', type='group', children=[
dict(name='Pockels', type='float', value=0.03, suffix='V', step=0.005, limits=[0, 1.5], siPrefix=True),
dict(name='Sample Rate', type='int', value=2.0e6, suffix='Hz', dec=True, minStep=100., step=0.5, limits=[10e3, 50e6], siPrefix=True),
dict(name='Downsample', type='int', value=1, limits=[1,None]),
dict(name='Average', type='int', value=1, limits=[1,100]),
dict(name='Blank Screen', type='bool', value=True),
dict(name='Image Width', type='int', value=500, readonly=False, limits=[1, None]),
dict(name='Image Height', type='int', value=500, readonly=False, limits=[1, None]),
dict(name='Bidirectional', type='bool', value=True),
dict(name='Overscan', type='float', value=50e-6, suffix='s', siPrefix=True, limits=[0, None], step=10e-6),
dict(name='Photodetector', type='list', values=self.detectors),
dict(name='Follow Stage', type='bool', value=True),
]),
dict(name='Scan Properties', type='group', children=[
dict(name='Frame Time', type='float', value=50e-3, suffix='s', siPrefix=True, readonly=True, dec=True, step=0.5, minStep=100e-6),
dict(name='Pixel Size', type='float', value=1e-6, suffix='m', siPrefix=True, readonly=True),
dict(name='Scan Speed', type='float', value=0.00, suffix='m/s', siPrefix=True, readonly=True),
dict(name='Exposure per Frame', type='float', value=0.00, suffix='s/um^2', siPrefix=True, readonly=True),
dict(name='Total Exposure', type='float', value=0.00, suffix='s/um^2', siPrefix=True, readonly=True),
dict(name='Wavelength', type='float', value=700, suffix='nm', readonly=True),
dict(name='Power', type='float', value=0.00, suffix='W', readonly=True),
dict(name='Objective', type='str', value='Unknown', readonly=True),
]),
dict(name='Image Control', type='group', children=[
dict(name='Decomb', type='float', value=20e-6, suffix='s', siPrefix=True, bounds=[0, 1e-3], step=2e-7, decimals=5, children=[
dict(name='Auto', type='action'),
dict(name='Subpixel', type='bool', value=False),
]),
dict(name='Camera Module', type='interface', interfaceTypes=['cameraModule']),
]),
# dict(name='Scope Device', type='interface', interfaceTypes=['microscope']),
# dict(name='Scanner Device', type='interface', interfaceTypes=['scanner']),
# dict(name='Laser Device', type='interface', interfaceTypes=['laser']),
# dict(name="Tiles", type="bool", value=False, children=[
# dict(name='Stage', type='interface', interfaceTypes='stage'),
# dict(name="X0", type="float", value=-100., suffix='um', dec=True, minStep=1, step=1, limits=[-2.5e3,2.5e3], siPrefix=True),
# dict(name="X1", type="float", value=100., suffix='um', dec=True, minStep=1, step=1, limits=[-2.5e3,2.5e3], siPrefix=True),
# dict(name="Y0", type="float", value=-100., suffix='um', dec=True, minStep=1, step=1, limits=[-2.5e3,2.5e3], siPrefix=True),
# dict(name="Y1", type="float", value=100., suffix='um', dec=True, minStep=1, step=1, limits=[-2.5e3,2.5e3], siPrefix=True),
# dict(name="StepSize", type="float", value=100, suffix='um', dec=True, minStep=1e-5, step=0.5, limits=[1e-5,1e3], siPrefix=True),
# ]),
# dict(name="Z-Stack", type="bool", value=False, children=[
# dict(name='Stage', type='interface', interfaceTypes='stage'),
# dict(name="Step Size", type="float", value=5e-6, suffix='m', dec=True, minStep=1e-7, step=0.5, limits=[1e-9,1], siPrefix=True),
# dict(name="Steps", type='int', value=10, step=1, limits=[1,None]),
# dict(name="Depth", type="float", value=0, readonly=True, suffix='m', siPrefix=True)
# ]),
# dict(name="Timed", type="bool", value=False, children=[
# dict(name="Interval", type="float", value=5.0, suffix='s', dec=True, minStep=0.1, step=0.5, limits=[0.1,30], siPrefix=True),
# dict(name="N Intervals", type='int', value=10, step=1, limits=[1,None]),
# dict(name="Duration", type="float", value=0, readonly=True, suffix='s', siPrefix = True),
# dict(name="Current Frame", type='int', value = 0, readonly=True),
# ]),
# dict(name='Show PMT V', type='bool', value=False),
# dict(name='Show Mirror V', type='bool', value=False),
])
self.tree.setParameters(self.param, showTop=False)
# insert an ROI into the camera image that corresponds to our scan area
self.objectiveUpdate() # force update of objective information and create appropriate ROI
# check the devices...
self.updateParams() # also force update now to make sure all parameters are synchronized
self.param.child('Scan Control').sigTreeStateChanged.connect(self.updateParams)
self.param.child('Image Control').sigTreeStateChanged.connect(self.updateDecomb)
self.param.child('Image Control', 'Decomb', 'Auto').sigActivated.connect(self.autoDecomb)
self.manager.sigAbortAll.connect(self.abortTask)
self.updateImagingProtocol()
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.ui = dashboard.Dashboard(limit=config.get('limit', None), filter_defaults=config.get('filters', None))
self.ui.resize(1600, 900)
self.ui.show()
