microscope.cameras.atmcd.AndorAtmcd Class Reference

Inheritance diagram for microscope.cameras.atmcd.AndorAtmcd:

Public Member Functions
def	__init__ (self, index=0, **kwargs)
def	__enter__ (self)
def	__exit__ (self, exc_type, exc_value, traceback)
def	abort (self)
def	initialize (self)
def	get_id (self)
def	set_exposure_time (self, value)
def	get_exposure_time (self)
def	get_cycle_time (self)
def	soft_trigger (self)
microscope.TriggerMode	trigger_mode (self)
microscope.TriggerType	trigger_type (self)
None	set_trigger (self, microscope.TriggerType ttype, microscope.TriggerMode tmode)
None	__init__ (self, int index, **kwargs)
str	get_id (self)
Public Member Functions inherited from microscope.abc.Camera
None	__init__ (self, **kwargs)
def	set_readout_mode (self, description)
def	get_transform (self)
def	set_transform (self, transform)
None	set_exposure_time (self, float value)
float	get_exposure_time (self)
float	get_cycle_time (self)
typing.Tuple[int, int]	get_sensor_shape (self)
microscope.Binning	get_binning (self)
None	set_binning (self, microscope.Binning binning)
microscope.ROI	get_roi (self)
None	set_roi (self, microscope.ROI roi)
Public Member Functions inherited from microscope.abc.TriggerTargetMixin
microscope.TriggerMode	trigger_mode (self)
microscope.TriggerType	trigger_type (self)
None	set_trigger (self, microscope.TriggerType ttype, microscope.TriggerMode tmode)
None	trigger (self)
Public Member Functions inherited from microscope.abc.DataDevice
None	__init__ (self, int buffer_length=0, **kwargs)
def	__del__ (self)
None	abort (self)
None	enable (self)
None	disable (self)
None	set_client (self, new_client)
None	update_settings (self, settings, bool init=False)
None	receiveClient (self, str client_uri)
def	grab_next_data (self, bool soft_trigger=True)
None	receiveData (self, data, timestamp)
Public Member Functions inherited from microscope.abc.Device
None	__init__ (self)
None	__del__ (self)
bool	get_is_enabled (self)
None	disable (self)
None	enable (self)
None	initialize (self)
None	shutdown (self)
None	add_setting (self, name, dtype, get_func, set_func, values, typing.Optional[typing.Callable[[], bool]] readonly=None)
def	get_setting (self, str name)
def	get_all_settings (self)
None	set_setting (self, str name, value)
def	describe_setting (self, str name)
def	describe_settings (self)
def	update_settings (self, incoming, bool init=False)

Public Attributes
	amplifiers
Public Attributes inherited from microscope.abc.DataDevice
	enabled
Public Attributes inherited from microscope.abc.Device
	enabled

Additional Inherited Members
Static Public Attributes inherited from microscope.abc.Camera
list	ALLOWED_TRANSFORMS = [p for p in itertools.product(*3 * [[False, True]])]
Static Public Attributes inherited from microscope.abc.DataDevice
	set_setting = keep_acquiring(Device.set_setting)

Detailed Description

Implements CameraDevice interface for Andor ATMCD library.

Definition at line 1364 of file atmcd.py.

Constructor & Destructor Documentation

__init__()

def microscope.cameras.atmcd.AndorAtmcd.__init__	(		self,
			index = 0,
		**	kwargs
	)

Reimplemented from microscope.abc.FloatingDeviceMixin.

Definition at line 1370 of file atmcd.py.

    def __init__(self, index=0, **kwargs):
        super().__init__(index=index, **kwargs)
        # Recursion depth for context manager behaviour.
        self._rdepth = 0
        # The handle used by the DLL to identify this camera.
        self._handle = None
        # The following parameters will be populated after hardware init.
        self._roi = None
        self._binning = None
        self.initialize()
 

Member Function Documentation

__enter__()

def microscope.cameras.atmcd.AndorAtmcd.__enter__

(

self

)

Context manager entry code.

The camera class is also a context manager that ensures DLL calls act
on this camera by obtaining the _dll_lock.

We could use RLock to give re-entrant behaviour, but we track recursion
ourselves so that we know when we must call SetCurrentCamera.

Definition at line 1391 of file atmcd.py.

    def __enter__(self):
        """Context manager entry code.
 
        The camera class is also a context manager that ensures DLL calls act
        on this camera by obtaining the _dll_lock.
 
        We could use RLock to give re-entrant behaviour, but we track recursion
        ourselves so that we know when we must call SetCurrentCamera.
        """
        if self._rdepth == 0:
            _dll_lock.acquire()
            SetCurrentCamera(self._handle)
        self._rdepth += 1
 

References microscope.cameras.atmcd.AndorAtmcd._handle, microscope.cameras.ximea.XimeaCamera._handle, and microscope.cameras.atmcd.AndorAtmcd._rdepth.

__exit__()

def microscope.cameras.atmcd.AndorAtmcd.__exit__	(		self,
			exc_type,
			exc_value,
			traceback
	)

Context manager exit code.

Definition at line 1405 of file atmcd.py.

    def __exit__(self, exc_type, exc_value, traceback):
        """Context manager exit code."""
        self._rdepth -= 1
        if self._rdepth == 0:
            _dll_lock.release()
 

References microscope.cameras.atmcd.AndorAtmcd._rdepth.

abort()

def microscope.cameras.atmcd.AndorAtmcd.abort

(

self

)

Abort acquisition.

Reimplemented from microscope.abc.DataDevice.

Definition at line 1424 of file atmcd.py.

    def abort(self):
        """Abort acquisition."""
        _logger.debug("Disabling acquisition.")
        try:
            with self:
                AbortAcquisition()
        except AtmcdException as e:
            if e.status != DRV_IDLE:
                raise
 

Referenced by microscope.simulators.SimulatedCamera.abort(), microscope.cameras.andorsdk3.AndorSDK3.get_id(), microscope.cameras.atmcd.AndorAtmcd.get_id(), microscope.cameras.picam.PiCamera.initialize(), microscope.cameras.ximea.XimeaCamera.initialize(), microscope.cameras.andorsdk3.AndorSDK3.set_trigger(), and microscope.abc.Device.update_settings().

get_cycle_time()

def microscope.cameras.atmcd.AndorAtmcd.get_cycle_time

(

self

)

Determine the minimum time between exposures.

Reimplemented from microscope.abc.Camera.

Definition at line 1717 of file atmcd.py.

    def get_cycle_time(self):
        """Determine the minimum time between exposures."""
        with self:
            exposure, accumulate, kinetic = GetAcquisitionTimings()
            readout = GetReadOutTime()
            # IMD 20210422 DeepSIM timing is wrong as the keepclear cycles are
            # not accounted for.
            # return exposure + readout
            # This appears to allow the correct time between trigger pulses.
            return kinetic
 

References microscope.abc.Camera._readout_modes, microscope.cameras.atmcd.AndorAtmcd._readout_modes, and microscope.cameras.pvcam.PVCamera._readout_modes.

get_exposure_time()

def microscope.cameras.atmcd.AndorAtmcd.get_exposure_time

(

self

)

Query the actual exposure time.

Reimplemented from microscope.abc.Camera.

Definition at line 1711 of file atmcd.py.

    def get_exposure_time(self):
        """Query the actual exposure time."""
        with self:
            exposure, accumulate, kinetic = GetAcquisitionTimings()
        return exposure
 

get_id()

def microscope.cameras.atmcd.AndorAtmcd.get_id

(

self

)

Return the device's unique identifier.

Reimplemented from microscope.abc.FloatingDeviceMixin.

Definition at line 1618 of file atmcd.py.

    def get_id(self):
        """Return the device's unique identifier."""
        with self:
            return GetCameraSerialNumber()
 

References microscope.abc.DataDevice._acquiring, microscope.cameras.andorsdk3.AndorSDK3._acquiring(), microscope.cameras.atmcd.AndorAtmcd._acquiring(), microscope.cameras.picam.PiCamera._acquiring, microscope.cameras.pvcam.PVCamera._acquiring, microscope.cameras.ximea.XimeaCamera._acquiring, microscope.simulators.SimulatedCamera._acquiring, microscope.cameras.atmcd.AndorAtmcd._binning, microscope.cameras.ximea.XimeaCamera._binning, microscope.simulators.SimulatedCamera._binning, microscope.cameras.atmcd.AndorAtmcd._roi, microscope.cameras.ximea.XimeaCamera._roi, microscope.simulators.SimulatedCamera._roi, microscope.cameras.atmcd.AndorAtmcd._set_image(), microscope.abc.DataDevice.abort(), microscope.cameras.andorsdk3.AndorSDK3.abort(), microscope.cameras.atmcd.AndorAtmcd.abort(), microscope.cameras.picam.PiCamera.abort(), microscope.cameras.pvcam.PVCamera.abort(), microscope.cameras.ximea.XimeaCamera.abort(), microscope.simulators.SimulatedCamera.abort(), and microscope.abc.Device.get_setting().

Referenced by microscope.cameras.atmcd.AndorAtmcd.initialize().

initialize()

def microscope.cameras.atmcd.AndorAtmcd.initialize

(

self

)

Initialize the library and hardware and create Setting objects.

Reimplemented from microscope.abc.Device.

Definition at line 1442 of file atmcd.py.

    def initialize(self):
        """Initialize the library and hardware and create Setting objects."""
        _logger.info("Initializing ...")
        num_cams = GetAvailableCameras()
        if self._index >= num_cams:
            msg = "Requested camera %d, but only found %d cameras" % (
                self._index,
                num_cams,
            )
            raise microscope.InitialiseError(msg)
        self._handle = GetCameraHandle(self._index)
 
        with self:
            # Initialize the library and connect to camera.
            Initialize(b"")
            # Initialise ROI to full sensor area and binning to single-pixel.
            self._set_roi(microscope.ROI(0, 0, 0, 0))
            self._set_binning(microscope.Binning(1, 1))
            # Check info bits to see if initialization successful.
            info = GetCameraInformation(self._index)
            if not info & 1 << 2:
                raise microscope.InitialiseError("... initialization failed.")
            self._caps = GetCapabilities()
            model = GetHeadModel()
            serial = self.get_id()
            # Populate amplifiers
            if GetNumberAmp() > 1:
                if self._caps.ulCameraType == AC_CAMERATYPE_CLARA:
                    self.amplifiers = IntEnum(
                        "Amplifiers",
                        (("CONVENTIONAL", 0), ("EXTENDED_NIR", 1)),
                    )
                else:
                    self.amplifiers = IntEnum(
                        "Amplifiers", (("EMCCD", 0), ("CONVENTIONAL", 1))
                    )
            # Populate readout modes
            self._readout_modes = []
            for ch in range(GetNumberADChannels()):
                for amp in self.amplifiers:
                    for s in range(GetNumberHSSpeeds(ch, amp.value)):
                        speed = GetHSSpeed(ch, amp.value, s)
                        self._readout_modes.append(
                            ReadoutMode(ch, amp, s, speed)
                        )
            _logger.info("... initilized %s s/n %s", model, serial)
        # Add settings. Some are write-only, so we set defaults here.
        # Mode
        name = "readout mode"
        if self._readout_modes:
            self.add_setting(
                name,
                "enum",
                None,
                self._set_readout_mode,
                lambda: [str(mode) for mode in self._readout_modes],
            )
            self.set_setting(name, 0)
        # TriggerMode
        name = "TriggerMode"
        self.add_setting(
            name, "enum", None, self._bind(SetTriggerMode), TriggerMode
        )
        if self._caps.ulTriggerModes & AC_TRIGGERMODE_EXTERNAL:
            self.set_setting(name, TriggerMode.EXTERNAL)
        elif self._caps.ulTriggerModes & AC_TRIGGERMODE_CONTINUOUS:
            self.set_setting(name, TriggerMode.SOFTWARE)
        # Gain - device will use either EMGain or MCPGain
        name = "gain"
        getter, setter, vrange = None, None, None
        if self._caps.ulGetFunctions & AC_GETFUNCTION_EMCCDGAIN:
            getter = self._bind(GetEMCCDGain)
        elif self._caps.ulGetFunctions & AC_GETFUNCTION_MCPGAIN:
            getter = self._bind(GetMCPGain)
        if self._caps.ulSetFunctions & AC_SETFUNCTION_EMCCDGAIN:
            setter = self._bind(SetEMCCDGain)
            vrange = self._bind(GetEMGainRange)
        elif self._caps.ulSetFunctions & AC_SETFUNCTION_MCPGAIN:
            setter = self._bind(SetMCPGain)
            vrange = self._bind(GetMCPGainRange)
        if getter or setter:
            self.add_setting(name, "int", getter, setter, vrange)
        # Temperature
        name = "TemperatureSetPoint"
        getter, setter, vrange = None, None, None
        if self._caps.ulSetFunctions & AC_SETFUNCTION_TEMPERATURE:
            setter = self._bind(SetTemperature)
        if self._caps.ulGetFunctions & AC_GETFUNCTION_TEMPERATURERANGE:
            vrange = self._bind(GetTemperatureRange)
        if setter:
            self.add_setting(name, "int", None, setter, vrange)
        # Set a conservative default temperature set-point.
        self.set_setting(name, -20)
        # Fan control
        name = "Temperature"
        self.add_setting(
            name, "int", self._get_sensor_temperature, None, (None, None)
        )
        name = "Fan mode"
        self.add_setting(
            name,
            "enum",
            None,  # Can't query fan mode
            self._bind(SetFanMode),
            {0: "full", 1: "low", 2: "off"},
        )
        # Cooler control
        name = "Cooler Enabled"
        self.add_setting(name, "bool", None, self._set_cooler_state, None)
        self.set_setting(name, True)
        # Binning
        name = "Binning"
        self.add_setting(
            name, "tuple", self.get_binning, self.set_binning, None
        )
        # Roi
        name = "Roi"
        self.add_setting(
            name, "tuple", self.get_roi, lambda roi: self.set_roi(*roi), None
        )
        # BaselineClamp
        name = "BaselineClamp"
        if self._caps.ulSetFunctions & AC_SETFUNCTION_BASELINECLAMP:
            self.add_setting(
                name, "bool", None, self._bind(SetBaselineClamp), None
            )
            self.set_setting(name, False)
        # BaselineOffset
        name = "BaselineOffset"
        if self._caps.ulSetFunctions & AC_SETFUNCTION_BASELINEOFFSET:
            self.add_setting(
                name, "int", None, self._bind(SetBaselineOffset), (-1000, 1000)
            )
            self.set_setting(name, 0)
        # EMAdvanced
        name = "EMAdvanced"
        if self._caps.ulSetFunctions & AC_SETFUNCTION_EMADVANCED:
            self.add_setting(
                name, "bool", None, self._bind(SetEMAdvanced), None
            )
            self.set_setting(name, False)
        # GateMode
        name = "GateMode"
        if self._caps.ulSetFunctions & AC_SETFUNCTION_GATEMODE:
            vrange = range(
                0, [5, 6][self._caps.ulCameraType & AC_CAMERATYPE_ISTAR]
            )
            self.add_setting(
                name, "int", None, self._bind(SetGateMode), vrange
            )
        # HighCapacity
        name = "HighCapacity"
        if self._caps.ulSetFunctions & AC_SETFUNCTION_HIGHCAPACITY:
            self.add_setting(
                name, "bool", None, self._bind(SetHighCapacity), None
            )
 

References microscope.cameras.atmcd.AndorAtmcd._bind(), microscope.cameras.atmcd.AndorAtmcd._binning, microscope.cameras.ximea.XimeaCamera._binning, microscope.simulators.SimulatedCamera._binning, microscope.cameras.atmcd.AndorAtmcd._caps, microscope.cameras.atmcd.AndorAtmcd._get_sensor_temperature(), microscope.cameras.atmcd.AndorAtmcd._handle, microscope.cameras.ximea.XimeaCamera._handle, microscope.abc.FloatingDeviceMixin._index, microscope.abc.Camera._readout_modes, microscope.cameras.atmcd.AndorAtmcd._readout_modes, microscope.cameras.pvcam.PVCamera._readout_modes, microscope.cameras.atmcd.AndorAtmcd._roi, microscope.cameras.ximea.XimeaCamera._roi, microscope.simulators.SimulatedCamera._roi, microscope.cameras.andorsdk3.AndorSDK3._set_binning(), microscope.cameras.atmcd.AndorAtmcd._set_binning(), microscope.cameras.pvcam.PVCamera._set_binning(), microscope.simulators.SimulatedCamera._set_binning(), microscope.cameras.picam.PiCamera._set_binning(), microscope.abc.Camera._set_binning(), microscope.cameras.ximea.XimeaCamera._set_binning(), microscope.cameras.atmcd.AndorAtmcd._set_cooler_state(), microscope.cameras.atmcd.AndorAtmcd._set_readout_mode(), microscope.cameras.picam.PiCamera._set_roi(), microscope.abc.Camera._set_roi(), microscope.cameras.ximea.XimeaCamera._set_roi(), microscope.cameras.andorsdk3.AndorSDK3._set_roi(), microscope.cameras.atmcd.AndorAtmcd._set_roi(), microscope.cameras.pvcam.PVCamera._set_roi(), microscope.simulators.SimulatedCamera._set_roi(), microscope.abc.Device.add_setting(), microscope.cameras.atmcd.AndorAtmcd.amplifiers, microscope.abc.Camera.get_binning(), microscope.abc.FloatingDeviceMixin.get_id(), microscope.cameras.andorsdk3.AndorSDK3.get_id(), microscope.cameras.atmcd.AndorAtmcd.get_id(), microscope.cameras.pvcam.PVCamera.get_id(), microscope.filterwheels.aurox.Clarity.get_id(), microscope.stages.linkam._LinkamBase.get_id(), microscope.testsuite.devices.TestFloatingDevice.get_id(), microscope.abc.Camera.get_roi(), microscope.abc.Camera.set_binning(), microscope.abc.Camera.set_roi(), microscope.abc.Device.set_setting(), and microscope.abc.DataDevice.set_setting.

Referenced by microscope.cameras.picam.PiCamera.__init__(), microscope.cameras.ximea.XimeaCamera.__init__(), and microscope.cameras.picam.PiCamera.initialize().

set_exposure_time()

def microscope.cameras.atmcd.AndorAtmcd.set_exposure_time	(		self,
			value
	)

Set exposure time.

Reimplemented from microscope.abc.Camera.

Definition at line 1706 of file atmcd.py.

    def set_exposure_time(self, value):
        """Set exposure time."""
        with self:
            SetExposureTime(value)
 

set_trigger()

None microscope.cameras.atmcd.AndorAtmcd.set_trigger	(		self,
		microscope.TriggerType	ttype,
		microscope.TriggerMode	tmode
	)

Set device for a specific trigger.

Reimplemented from microscope.abc.TriggerTargetMixin.

Definition at line 1768 of file atmcd.py.

    ) -> None:
        try:
            atmcd_mode = TRIGGER_TO_ATMCD_MODE[(ttype, tmode)]
        except KeyError:
            raise microscope.UnsupportedFeatureError(
                "no ATMCD mode for %s and %s" % (ttype, tmode)
            )
        self.set_setting("TriggerMode", atmcd_mode)
 

References microscope.cameras.atmcd.AndorAtmcd._binning, microscope.cameras.ximea.XimeaCamera._binning, microscope.simulators.SimulatedCamera._binning, microscope.cameras.atmcd.AndorAtmcd._roi, microscope.cameras.ximea.XimeaCamera._roi, microscope.simulators.SimulatedCamera._roi, microscope.abc.Device.set_setting(), and microscope.abc.DataDevice.set_setting.

Referenced by microscope.cameras.picam.PiCamera.__init__(), microscope.cameras.ximea.XimeaCamera.__init__(), and microscope.cameras.ximea.XimeaCamera.initialize().

soft_trigger()

def microscope.cameras.atmcd.AndorAtmcd.soft_trigger

(

self

)

Send a software trigger signal.

Deprecated, use trigger().

Definition at line 1752 of file atmcd.py.

    def soft_trigger(self):
        """Send a software trigger signal.
 
        Deprecated, use trigger().
        """
        with self:
            SendSoftwareTrigger()
 

References microscope.abc.Device.get_setting(), and microscope.abc.TriggerTargetMixin.trigger().

Referenced by microscope.cameras.picam.PiCamera.get_cycle_time().

trigger_mode()

microscope.TriggerMode microscope.cameras.atmcd.AndorAtmcd.trigger_mode

(

self

)

Reimplemented from microscope.abc.TriggerTargetMixin.

Definition at line 1761 of file atmcd.py.

    def trigger_mode(self) -> microscope.TriggerMode:
        return ATMCD_MODE_TO_TRIGGER[self.get_setting("TriggerMode")][1]
 

Referenced by microscope.cameras.picam.PiCamera.__init__(), and microscope.cameras.ximea.XimeaCamera.__init__().

trigger_type()

microscope.TriggerType microscope.cameras.atmcd.AndorAtmcd.trigger_type

(

self

)

Reimplemented from microscope.abc.TriggerTargetMixin.

Definition at line 1765 of file atmcd.py.

    def trigger_type(self) -> microscope.TriggerType:
        return ATMCD_MODE_TO_TRIGGER[self.get_setting("TriggerMode")][0]
 

Referenced by microscope.cameras.ximea.XimeaCamera.__init__(), microscope.abc.DeformableMirror.apply_pattern(), and microscope.abc.TriggerTargetMixin.trigger().

Member Data Documentation

amplifiers

microscope.cameras.atmcd.AndorAtmcd.amplifiers

Definition at line 1470 of file atmcd.py.

Referenced by microscope.cameras.atmcd.AndorAtmcd.initialize().

---

The documentation for this class was generated from the following file:

• F:/repos/BioImager/BioImager/PythonMicroscope/microscope/cameras/atmcd.py