Inheritance diagram for microscope.cameras.ximea.XimeaCamera:

Public Member Functions
None	__init__ (self, typing.Optional[str] serial_number=None, **kwargs)

	abort (self)

None	initialize (self)

None	set_exposure_time (self, float value)

float	get_exposure_time (self)

	get_cycle_time (self)

None	soft_trigger (self)

microscope.TriggerMode	trigger_mode (self)

microscope.TriggerType	trigger_type (self)

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

Public Member Functions inherited from microscope.abc.Camera
	set_readout_mode (self, description)

	get_transform (self)

	set_transform (self, transform)

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
None	trigger (self)

Public Member Functions inherited from microscope.abc.DataDevice
	__del__ (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)

	grab_next_data (self, bool soft_trigger=True)

None	receiveData (self, data, timestamp)

Public Member Functions inherited from microscope.abc.Device
bool	get_is_enabled (self)

None	shutdown (self)

None	add_setting (self, name, dtype, get_func, set_func, values, typing.Optional[typing.Callable[[], bool]] readonly=None)

	get_setting (self, str name)

	get_all_settings (self)

None	set_setting (self, str name, value)

	describe_setting (self, str name)

	describe_settings (self)

Public Attributes
	trigger_mode

	trigger_type

Public Attributes inherited from microscope.abc.Camera
	set_readout_mode

	get_roi

	set_roi

Public Attributes inherited from microscope.abc.DataDevice
bool	enabled = False

bool	_fetch_thread = True

bool	_dispatch_thread = True

None	_fetch_thread_run = self._fetch_data()

Public Attributes inherited from microscope.abc.Device
bool	enabled = False

Protected Member Functions
typing.Optional[np.ndarray]	_fetch_data (self)

	_do_disable (self)

	_do_enable (self)

typing.Tuple[int, int]	_get_sensor_shape (self)

None	_do_trigger (self)

microscope.Binning	_get_binning (self)

bool	_set_binning (self, microscope.Binning binning)

microscope.ROI	_get_roi (self)

bool	_set_roi (self, microscope.ROI roi)

None	_do_shutdown (self)

Protected Member Functions inherited from microscope.abc.Camera
	_process_data (self, data)

	_set_readout_transform (self, new_transform)

Protected Member Functions inherited from microscope.abc.TriggerTargetMixin
Protected Member Functions inherited from microscope.abc.DataDevice
	_send_data (self, client, data, timestamp)

None	_dispatch_loop (self)

None	_fetch_loop (self)

	_client (self)

	_client (self, val)

None	_put (self, data, timestamp)

Protected Member Functions inherited from microscope.abc.Device

Protected Attributes
bool	_acquiring = False

	_handle = xiapi.Camera()

	_img = xiapi.Image()

	_serial_number = serial_number

tuple	_sensor_shape = (0, 0)

str	_roi = microscope.ROI(None, None, None, None)

	_binning = microscope.Binning(1, 1)

Protected Attributes inherited from microscope.abc.Camera
list	_readout_modes = ["default"]

int	_readout_mode = 0

tuple	_readout_transform = (False, False, False)

tuple	_client_transform = (False, False, False)

tuple	_transform = (False, False, False)

Protected Attributes inherited from microscope.abc.DataDevice
	_fetch_thread = None

bool	_fetch_thread_run = False

bool	_using_callback = False

list	_clientStack = []

	_liveClients = set()

	_dispatch_thread = None

	_dispatch_buffer = queue.Queue(maxsize=buffer_length)

bool	_acquiring = False

	_new_data_condition = threading.Condition()

	_client = None

tuple	_new_data = (data, timestamp)

Protected Attributes inherited from microscope.abc.Device
dict	_settings = {}

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

Ximea cameras

Args:
    serial_number: the serial number of the camera to connect to.
        It can be set to `None` if there is only camera on the
        system.

Definition at line 176 of file ximea.py.

Constructor & Destructor Documentation

◆ init()

None microscope.cameras.ximea.XimeaCamera.__init__	(		self,
		typing.Optional[str]	buffer_length = None,
		**	kwargs )

Derived.__init__ must call this at some point.

Reimplemented from microscope.abc.Camera.

Definition at line 186 of file ximea.py.

    ) -> None:
        super().__init__(**kwargs)
        self._acquiring = False
        self._handle = xiapi.Camera()
        self._img = xiapi.Image()
        self._serial_number = serial_number
        self._sensor_shape = (0, 0)
        self._roi = microscope.ROI(None, None, None, None)
        self._binning = microscope.Binning(1, 1)
 
        # When using the Settings system, enums are not really enums
        # and even when using lists we get indices sent back and forth
        # (works fine only when using EnumInt.  The gymnastic here
        # makes it work with the rest of enums which are there to make
        # it work with TriggerTargetMixin.
        trg_source_names = [x.name for x in TrgSourceMap]
 
        def _trigger_source_setter(index: int) -> None:
            trigger_mode = TrgSourceMap[trg_source_names[index]].value
            self.set_trigger(trigger_mode, self.trigger_mode)
 
        self.add_setting(
            "trigger source",
            "enum",
            lambda: TrgSourceMap(self.trigger_type).name,
            _trigger_source_setter,
            trg_source_names,
        )
 
        self.initialize()
 

Member Function Documentation

◆ _do_disable()

microscope.cameras.ximea.XimeaCamera._do_disable ( self )

protected

Do any device-specific work on disable.

Subclasses should override this method rather than modify
`disable`.

Reimplemented from microscope.abc.Device.

Definition at line 335 of file ximea.py.

    def _do_disable(self):
        self.abort()
 

◆ _do_enable()

microscope.cameras.ximea.XimeaCamera._do_enable ( self )

protected

Do any device specific work on enable.

Subclasses should override this method, rather than modify
`enable`.

Reimplemented from microscope.abc.Device.

Definition at line 338 of file ximea.py.

    def _do_enable(self):
        _logger.info("Preparing for acquisition.")
        if self._acquiring:
            self.abort()
        # actually start camera
        self._handle.start_acquisition()
        self._acquiring = True
        _logger.info("Acquisition enabled.")
        return True
 

◆ _do_shutdown()

None microscope.cameras.ximea.XimeaCamera._do_shutdown ( self )

protected

Private method - actual shutdown of the device.

Users should be calling :meth:`shutdown` and not this method.
Concrete implementations should implement this method instead
of `shutdown`.

Reimplemented from microscope.abc.Device.

Definition at line 423 of file ximea.py.

    def _do_shutdown(self) -> None:
        if self._acquiring:
            self._handle.stop_acquisition()
        if self._handle.CAM_OPEN:
            # We check CAM_OPEN instead of try/catch an exception
            # because if the camera failed initialisation, XiApi fails
            # hard with error code -1009 (unknown) since the internal
            # device handler is NULL.
            self._handle.close_device()
 

◆ _do_trigger()

None microscope.cameras.ximea.XimeaCamera._do_trigger ( self )

protected

Actual trigger of the device.

Classes implementing this interface should implement this
method instead of `trigger`.

Reimplemented from microscope.abc.TriggerTargetMixin.

Definition at line 368 of file ximea.py.

    def _do_trigger(self) -> None:
        # Value for set_trigger_software() has no meaning.  See
        # https://github.com/python-microscope/vendor-issues/issues/3
        self._handle.set_trigger_software(1)
 

◆ _fetch_data()

typing.Optional[np.ndarray] microscope.cameras.ximea.XimeaCamera._fetch_data ( self )

protected

Poll for data and return it, with minimal processing.

If the device uses buffering in software, this function should
copy the data from the buffer, release or recycle the buffer,
then return a reference to the copy.  Otherwise, if the SDK
returns a data object that will not be written to again, this
function can just return a reference to the object.  If no
data is available, return `None`.

Reimplemented from microscope.abc.DataDevice.

Definition at line 219 of file ximea.py.

    def _fetch_data(self) -> typing.Optional[np.ndarray]:
        if not self._acquiring:
            return None
 
        try:
            self._handle.get_image(self._img, timeout=1)
        except xiapi.Xi_error as err:
            # err.status may not exist so use getattr (see
            # https://github.com/python-microscope/vendor-issues/issues/2)
            if getattr(err, "status", None) == _XI_TIMEOUT:
                return None
            elif (
                getattr(err, "status", None) == _XI_ACQUISITION_STOPED
                and not self._acquiring
            ):
                # We can end up here during disable if self._acquiring
                # was True but is now False.
                return None
            else:
                raise
 
        data: np.ndarray = self._img.get_image_data_numpy()
        _logger.info(
            "Fetched imaged with dims %s and size %s.", data.shape, data.size
        )
        return data
 

◆ _get_binning()

microscope.Binning microscope.cameras.ximea.XimeaCamera._get_binning ( self )

protected

Return the current binning.

Reimplemented from microscope.abc.Camera.

Definition at line 373 of file ximea.py.

    def _get_binning(self) -> microscope.Binning:
        return self._binning
 

◆ _get_roi()

microscope.ROI microscope.cameras.ximea.XimeaCamera._get_roi ( self )

protected

Return the ROI as it is on hardware.

Reimplemented from microscope.abc.Camera.

Definition at line 385 of file ximea.py.

    def _get_roi(self) -> microscope.ROI:
        assert self._roi == microscope.ROI(
            self._handle.get_offsetX(),
            self._handle.get_offsetY(),
            self._handle.get_width(),
            self._handle.get_height(),
        ), "ROI attribute is out of sync with internal camera setting"
        return self._roi
 

◆ _get_sensor_shape()

typing.Tuple[int, int] microscope.cameras.ximea.XimeaCamera._get_sensor_shape ( self )

protected

Return a tuple of `(width, height)` indicating shape in pixels.

Reimplemented from microscope.abc.Camera.

Definition at line 362 of file ximea.py.

    def _get_sensor_shape(self) -> typing.Tuple[int, int]:
        return self._sensor_shape
 

◆ _set_binning()

bool microscope.cameras.ximea.XimeaCamera._set_binning	(		self,
		microscope.Binning	binning )

protected

Set binning along both axes.  Return `True` if successful.

Reimplemented from microscope.abc.Camera.

Definition at line 376 of file ximea.py.

    def _set_binning(self, binning: microscope.Binning) -> bool:
        if binning == self._binning:
            return True
        # We don't have a ximea camera that supports binning so we
        # can't write support for this (a camera without this feature
        # will raise error 100).  When writing this, careful and check
        # what XiAPI does when mixing ROI and binning.
        raise NotImplementedError()
 

◆ _set_roi()

bool microscope.cameras.ximea.XimeaCamera._set_roi	(		self,
		microscope.ROI	roi )

protected

Set the ROI on the hardware.  Return `True` if successful.

Reimplemented from microscope.abc.Camera.

Definition at line 394 of file ximea.py.

    def _set_roi(self, roi: microscope.ROI) -> bool:
        if (
            roi.width + roi.left > self._sensor_shape[0]
            or roi.height + roi.top > self._sensor_shape[1]
        ):
            raise ValueError(
                "ROI %s does not fit in sensor shape %s"
                % (roi, self._sensor_shape)
            )
        try:
            # These methods will fail if the width/height plus their
            # corresponding offsets are higher than the sensor size.
            # So we start by setting the offset to zero.  Cases to
            # think off: 1) shrinking ROI size, 2) increasing ROI
            # size, 3) resetting ROI and so can't trust self._roi as
            # the current state (see this exception handling).
            with _disabled_camera(self):
                self._handle.set_offsetX(0)
                self._handle.set_offsetY(0)
                self._handle.set_width(roi.width)
                self._handle.set_height(roi.height)
                self._handle.set_offsetX(roi.left)
                self._handle.set_offsetY(roi.top)
        except Exception:
            self._set_roi(self._roi)  # set it back to whatever was before
            raise
        self._roi = roi
        return True
 

◆ abort()

microscope.cameras.ximea.XimeaCamera.abort ( self )

Stop acquisition as soon as possible.

Reimplemented from microscope.abc.DataDevice.

Definition at line 246 of file ximea.py.

    def abort(self):
        _logger.info("Disabling acquisition.")
        if self._acquiring:
            # We set acquiring before calling stop_acquisition because
            # the fetch loop is still running and will raise errors 45
            # otherwise.
            self._acquiring = False
            try:
                self._handle.stop_acquisition()
            except Exception:
                self._acquiring = True
                raise
 

◆ get_cycle_time()

microscope.cameras.ximea.XimeaCamera.get_cycle_time ( self )

Return the cycle time in seconds.

Reimplemented from microscope.abc.Camera.

Definition at line 359 of file ximea.py.

    def get_cycle_time(self):
        return 1.0 / self._handle.get_framerate()
 

◆ get_exposure_time()

float microscope.cameras.ximea.XimeaCamera.get_exposure_time ( self )

Return the current exposure time in seconds.

Reimplemented from microscope.abc.Camera.

Definition at line 355 of file ximea.py.

    def get_exposure_time(self) -> float:
        # exposure times are in us, so multiple by 1E-6 to get seconds.
        return self._handle.get_exposure() * 1.0e-6
 

◆ initialize()

None microscope.cameras.ximea.XimeaCamera.initialize ( self )

Initialise the camera.

Open the connection, connect properties and populate settings dict.

Reimplemented from microscope.abc.Device.

Definition at line 259 of file ximea.py.

    def initialize(self) -> None:
        """Initialise the camera.
 
        Open the connection, connect properties and populate settings dict.
        """
        n_cameras = self._handle.get_number_devices()
 
        if self._serial_number is None:
            if n_cameras > 1:
                raise TypeError(
                    "more than one Ximea camera found but the"
                    " serial_number argument was not specified"
                )
            _logger.info(
                "serial_number is not specified but there is only one"
                " camera on the system"
            )
            self._handle.open_device()
        else:
            _logger.info(
                "opening camera with serial number '%s'", self._serial_number
            )
            self._handle.open_device_by_SN(self._serial_number)
 
        self._sensor_shape = (
            self._handle.get_width_maximum()
            + self._handle.get_offsetX_maximum(),
            self._handle.get_height_maximum()
            + self._handle.get_offsetY_maximum(),
        )
        self._roi = microscope.ROI(
            left=0,
            top=0,
            width=self._sensor_shape[0],
            height=self._sensor_shape[1],
        )
        self.set_roi(self._roi)
 
        self.set_trigger(
            microscope.TriggerType.SOFTWARE, microscope.TriggerMode.ONCE
        )
 
        # Add settings for the different temperature sensors.
        for temp_param_name in [
            "chip_temp",
            "hous_temp",
            "hous_back_side_temp",
            "sensor_board_temp",
        ]:
            get_temp_method = getattr(self._handle, "get_" + temp_param_name)
            # Not all cameras have temperature sensors in all
            # locations.  We can't query if the sensor is there, we
            # can only try to read the temperature and skip that
            # temperature sensor if we get an exception.
            try:
                get_temp_method()
            except xiapi.Xi_error as err:
                # Depending on XiAPI version, camera model, and
                # selected sensor, we might get any of these errors as
                # meaning that it's not available.  See
                # https://github.com/python-microscope/vendor-issues/issues/6
                if err.status not in [
                    _XI_NOT_SUPPORTED,
                    _XI_NOT_IMPLEMENTED,
                    _XI_UNKNOWN_PARAM,
                ]:
                    raise
            else:
                self.add_setting(
                    temp_param_name,
                    "float",
                    get_temp_method,
                    None,
                    values=tuple(),
                )
 

◆ set_exposure_time()

None microscope.cameras.ximea.XimeaCamera.set_exposure_time	(		self,
		float	value )

Set the exposure time on the device in seconds.

Reimplemented from microscope.abc.Camera.

Definition at line 348 of file ximea.py.

    def set_exposure_time(self, value: float) -> None:
        # exposure times are set in us.
        try:
            self._handle.set_exposure_direct(int(value * 1000000))
        except Exception as err:
            _logger.debug("set_exposure_time exception: %s", err)
 

◆ set_trigger()

None microscope.cameras.ximea.XimeaCamera.set_trigger	(		self,
		microscope.TriggerType	ttype,
		microscope.TriggerMode	tmode )

Set device for a specific trigger.

Reimplemented from microscope.abc.TriggerTargetMixin.

Definition at line 455 of file ximea.py.

    ) -> None:
        if tmode is not microscope.TriggerMode.ONCE:
            raise microscope.UnsupportedFeatureError(
                "%s not supported (only TriggerMode.ONCE)" % tmode
            )
 
        try:
            trg_source = TrgSourceMap(ttype)
        except ValueError:
            raise microscope.UnsupportedFeatureError(
                "no support for trigger type %s" % ttype
            )
 
        if trg_source.name != self._handle.get_trigger_source():
            # Changing trigger source requires stopping acquisition.
            with _disabled_camera(self):
                self._handle.set_trigger_source(trg_source.name)

◆ soft_trigger()

None microscope.cameras.ximea.XimeaCamera.soft_trigger ( self )

Definition at line 365 of file ximea.py.

    def soft_trigger(self) -> None:
        self.trigger()
 

◆ trigger_mode()

microscope.TriggerMode microscope.cameras.ximea.XimeaCamera.trigger_mode ( self )

Reimplemented from microscope.abc.TriggerTargetMixin.

Definition at line 434 of file ximea.py.

    def trigger_mode(self) -> microscope.TriggerMode:
        trg_selector = self._handle.get_trigger_selector()
        try:
            tmode = TrgSelectorMap[trg_selector]
        except KeyError:
            raise Exception(
                "somehow set to unsupported trigger mode %s" % trg_selector
            )
        return tmode.value
 

◆ trigger_type()

microscope.TriggerType microscope.cameras.ximea.XimeaCamera.trigger_type ( self )

Reimplemented from microscope.abc.TriggerTargetMixin.

Definition at line 445 of file ximea.py.

    def trigger_type(self) -> microscope.TriggerType:
        trg_source = self._handle.get_trigger_source()
        try:
            ttype = TrgSourceMap[trg_source]
        except KeyError:
            raise Exception(
                "somehow set to unsupported trigger type %s" % trg_source
            )
        return ttype.value
 

Member Data Documentation

◆ _acquiring

bool microscope.cameras.ximea.XimeaCamera._acquiring = False

protected

Definition at line 190 of file ximea.py.

◆ _binning

microscope.cameras.ximea.XimeaCamera._binning = microscope.Binning(1, 1)

protected

Definition at line 196 of file ximea.py.

◆ _handle

microscope.cameras.ximea.XimeaCamera._handle = xiapi.Camera()

protected

Definition at line 191 of file ximea.py.

◆ _img

microscope.cameras.ximea.XimeaCamera._img = xiapi.Image()

protected

Definition at line 192 of file ximea.py.

◆ _roi

str microscope.cameras.ximea.XimeaCamera._roi = microscope.ROI(None, None, None, None)

protected

Definition at line 195 of file ximea.py.

◆ _sensor_shape

microscope.cameras.ximea.XimeaCamera._sensor_shape = (0, 0)

protected

Definition at line 194 of file ximea.py.

◆ _serial_number

microscope.cameras.ximea.XimeaCamera._serial_number = serial_number

protected

Definition at line 193 of file ximea.py.

◆ trigger_mode

microscope.cameras.ximea.XimeaCamera.trigger_mode

Definition at line 207 of file ximea.py.

◆ trigger_type

microscope.cameras.ximea.XimeaCamera.trigger_type

Definition at line 212 of file ximea.py.

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

BioImager/PythonMicroscope/microscope/cameras/ximea.py

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ _do_disable()

◆ _do_enable()

◆ _do_shutdown()

◆ _do_trigger()

◆ _fetch_data()

◆ _get_binning()

◆ _get_roi()

◆ _get_sensor_shape()

◆ _set_binning()

◆ _set_roi()

◆ abort()

◆ get_cycle_time()

◆ get_exposure_time()

◆ initialize()

◆ set_exposure_time()

◆ set_trigger()

◆ soft_trigger()

◆ trigger_mode()

◆ trigger_type()

Member Data Documentation

◆ _acquiring

◆ _binning

◆ _handle

◆ _img

◆ _roi

◆ _sensor_shape

◆ _serial_number

◆ trigger_mode

◆ trigger_type

◆ init()