Inheritance diagram for microscope.abc.Camera:

Public Member Functions
None	__init__ (self, **kwargs)

	set_readout_mode (self, description)

	get_transform (self)

	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
	__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)

	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	initialize (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
	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

Static Public Attributes
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)

Protected Member Functions
	_process_data (self, data)

	_set_readout_transform (self, new_transform)

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

microscope.Binning	_get_binning (self)

	_set_binning (self, microscope.Binning binning)

microscope.ROI	_get_roi (self)

	_set_roi (self, microscope.ROI roi)

Protected Member Functions inherited from microscope.abc.TriggerTargetMixin
None	_do_trigger (self)

Protected Member Functions inherited from microscope.abc.DataDevice
None	_fetch_data (self)

	_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
	_do_disable (self)

	_do_enable (self)

None	_do_shutdown (self)

Protected Attributes
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 = {}

Detailed Description

Adds functionality to :class:`DataDevice` to support cameras.

Defines the interface for cameras.  Applies a transform to
acquired data in the processing step.

Definition at line 819 of file abc.py.

Constructor & Destructor Documentation

◆ init()

None microscope.abc.Camera.__init__	(		self,
		**	buffer_length )

Derived.__init__ must call this at some point.

Reimplemented from microscope.abc.DataDevice.

Reimplemented in microscope.cameras.picam.PiCamera, microscope.cameras.ximea.XimeaCamera, microscope.simulators.SimulatedCamera, microscope.simulators.stage_aware_camera.StageAwareCamera, and microscope.testsuite.devices.TestCamera.

Definition at line 829 of file abc.py.

    def __init__(self, **kwargs) -> None:
        super().__init__(**kwargs)
        # A list of readout mode descriptions.
        self._readout_modes = ["default"]
        # The index of the current readout mode.
        self._readout_mode = 0
        # Transforms to apply to data (fliplr, flipud, rot90)
        # Transform to correct for readout order.
        self._readout_transform = (False, False, False)
        # Transform supplied by client to correct for system geometry.
        self._client_transform = (False, False, False)
        # Result of combining client and readout transforms
        self._transform = (False, False, False)
        # A transform provided by the client.
        self.add_setting(
            "transform",
            "enum",
            lambda: Camera.ALLOWED_TRANSFORMS.index(self._transform),
            lambda index: self.set_transform(Camera.ALLOWED_TRANSFORMS[index]),
            Camera.ALLOWED_TRANSFORMS,
        )
        self.add_setting(
            "readout mode",
            "enum",
            lambda: self._readout_mode,
            self.set_readout_mode,
            lambda: self._readout_modes,
        )
        self.add_setting("roi", "tuple", self.get_roi, self.set_roi, None)
 

Member Function Documentation

◆ _get_binning()

microscope.Binning microscope.abc.Camera._get_binning ( self )

protected

Return the current binning.

Reimplemented in microscope.cameras.andorsdk3.AndorSDK3, microscope.cameras.atmcd.AndorAtmcd, microscope.cameras.picam.PiCamera, microscope.cameras.pvcam.PVCamera, microscope.cameras.ximea.XimeaCamera, and microscope.simulators.SimulatedCamera.

Definition at line 929 of file abc.py.

    def _get_binning(self) -> microscope.Binning:
        """Return the current binning."""
        pass
 

◆ _get_roi()

microscope.ROI microscope.abc.Camera._get_roi ( self )

protected

Return the ROI as it is on hardware.

Reimplemented in microscope.cameras.andorsdk3.AndorSDK3, microscope.cameras.atmcd.AndorAtmcd, microscope.cameras.picam.PiCamera, microscope.cameras.pvcam.PVCamera, microscope.cameras.ximea.XimeaCamera, and microscope.simulators.SimulatedCamera.

Definition at line 957 of file abc.py.

    def _get_roi(self) -> microscope.ROI:
        """Return the ROI as it is on hardware."""
        raise NotImplementedError()
 

◆ _get_sensor_shape()

typing.Tuple[int, int] microscope.abc.Camera._get_sensor_shape ( self )

protected

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

Reimplemented in microscope.cameras.andorsdk3.AndorSDK3, microscope.cameras.atmcd.AndorAtmcd, microscope.cameras.picam.PiCamera, microscope.cameras.pvcam.PVCamera, microscope.cameras.ximea.XimeaCamera, and microscope.simulators.SimulatedCamera.

Definition at line 916 of file abc.py.

    def _get_sensor_shape(self) -> typing.Tuple[int, int]:
        """Return a tuple of `(width, height)` indicating shape in pixels."""
        pass
 

◆ _process_data()

microscope.abc.Camera._process_data	(		self,
			data )

protected

Apply self._transform to data.

Reimplemented from microscope.abc.DataDevice.

Definition at line 859 of file abc.py.

    def _process_data(self, data):
        """Apply self._transform to data."""
        flips = (self._transform[0], self._transform[1])
        rot = self._transform[2]
 
        # Choose appropriate transform based on (flips, rot).
        # Do rotation
        data = numpy.rot90(data, rot)
        # Flip
        data = {
            (0, 0): lambda d: d,
            (0, 1): numpy.flipud,
            (1, 0): numpy.fliplr,
            (1, 1): lambda d: numpy.fliplr(numpy.flipud(d)),
        }[flips](data)
        return super()._process_data(data)
 

◆ _set_binning()

microscope.abc.Camera._set_binning	(		self,
		microscope.Binning	binning )

protected

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

Reimplemented in microscope.cameras.andorsdk3.AndorSDK3, microscope.cameras.atmcd.AndorAtmcd, microscope.cameras.picam.PiCamera, microscope.cameras.pvcam.PVCamera, microscope.cameras.ximea.XimeaCamera, and microscope.simulators.SimulatedCamera.

Definition at line 942 of file abc.py.

    def _set_binning(self, binning: microscope.Binning):
        """Set binning along both axes.  Return `True` if successful."""
        pass
 

◆ _set_readout_transform()

microscope.abc.Camera._set_readout_transform	(		self,
			new_transform )

protected

Update readout transform and update resultant transform.

Definition at line 897 of file abc.py.

    def _set_readout_transform(self, new_transform):
        """Update readout transform and update resultant transform."""
        self._readout_transform = [bool(int(t)) for t in new_transform]
        self.set_transform(self._client_transform)
 

◆ _set_roi()

microscope.abc.Camera._set_roi	(		self,
		microscope.ROI	roi )

protected

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

Reimplemented in microscope.cameras.andorsdk3.AndorSDK3, microscope.cameras.atmcd.AndorAtmcd, microscope.cameras.picam.PiCamera, microscope.cameras.pvcam.PVCamera, microscope.cameras.ximea.XimeaCamera, and microscope.simulators.SimulatedCamera.

Definition at line 970 of file abc.py.

    def _set_roi(self, roi: microscope.ROI):
        """Set the ROI on the hardware.  Return `True` if successful."""
        return False
 

◆ get_binning()

microscope.Binning microscope.abc.Camera.get_binning ( self )

Return the current binning corrected for transform.

Definition at line 933 of file abc.py.

    def get_binning(self) -> microscope.Binning:
        """Return the current binning corrected for transform."""
        binning = self._get_binning()
        if self._transform[2]:
            # 90 degree rotation
            binning = microscope.Binning(binning[1], binning[0])
        return binning
 

◆ get_cycle_time()

float microscope.abc.Camera.get_cycle_time ( self )

Return the cycle time in seconds.

Reimplemented in microscope.cameras.andorsdk3.AndorSDK3, microscope.cameras.atmcd.AndorAtmcd, microscope.cameras.picam.PiCamera, microscope.cameras.pvcam.PVCamera, microscope.cameras.ximea.XimeaCamera, and microscope.simulators.SimulatedCamera.

Definition at line 911 of file abc.py.

    def get_cycle_time(self) -> float:
        """Return the cycle time in seconds."""
        pass
 

◆ get_exposure_time()

float microscope.abc.Camera.get_exposure_time ( self )

Return the current exposure time in seconds.

Reimplemented in microscope.cameras.andorsdk3.AndorSDK3, microscope.cameras.atmcd.AndorAtmcd, microscope.cameras.picam.PiCamera, microscope.cameras.pvcam.PVCamera, microscope.cameras.ximea.XimeaCamera, and microscope.simulators.SimulatedCamera.

Definition at line 907 of file abc.py.

    def get_exposure_time(self) -> float:
        """Return the current exposure time in seconds."""
        pass
 

◆ get_roi()

microscope.ROI microscope.abc.Camera.get_roi ( self )

Return current ROI.

Definition at line 961 of file abc.py.

    def get_roi(self) -> microscope.ROI:
        """Return current ROI."""
        roi = self._get_roi()
        if self._transform[2]:
            # 90 degree rotation
            roi = microscope.ROI(roi[1], roi[0], roi[3], roi[2])
        return roi
 

◆ get_sensor_shape()

typing.Tuple[int, int] microscope.abc.Camera.get_sensor_shape ( self )

Return a tuple of `(width, height)` corrected for transform.

Definition at line 920 of file abc.py.

    def get_sensor_shape(self) -> typing.Tuple[int, int]:
        """Return a tuple of `(width, height)` corrected for transform."""
        shape = self._get_sensor_shape()
        if self._transform[2]:
            # 90 degree rotation
            shape = (shape[1], shape[0])
        return shape
 

◆ get_transform()

microscope.abc.Camera.get_transform ( self )

Return the current transform without readout transform.

Definition at line 880 of file abc.py.

    def get_transform(self):
        """Return the current transform without readout transform."""
        return self._client_transform
 

◆ set_binning()

None microscope.abc.Camera.set_binning	(		self,
		microscope.Binning	binning )

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

Definition at line 946 of file abc.py.

    def set_binning(self, binning: microscope.Binning) -> None:
        """Set binning along both axes.  Return `True` if successful."""
        h_bin, v_bin = binning
        if self._transform[2]:
            # 90 degree rotation
            binning = microscope.Binning(v_bin, h_bin)
        else:
            binning = microscope.Binning(h_bin, v_bin)
        return self._set_binning(binning)
 

◆ set_exposure_time()

None microscope.abc.Camera.set_exposure_time	(		self,
		float	value )

Set the exposure time on the device in seconds.

Reimplemented in microscope.cameras.andorsdk3.AndorSDK3, microscope.cameras.atmcd.AndorAtmcd, microscope.cameras.picam.PiCamera, microscope.cameras.pvcam.PVCamera, microscope.cameras.ximea.XimeaCamera, and microscope.simulators.SimulatedCamera.

Definition at line 903 of file abc.py.

    def set_exposure_time(self, value: float) -> None:
        """Set the exposure time on the device in seconds."""
        pass
 

◆ set_readout_mode()

microscope.abc.Camera.set_readout_mode	(		self,
			description )

Set the readout mode and _readout_transform.

Reimplemented in microscope.cameras.pvcam.PVCamera.

Definition at line 876 of file abc.py.

    def set_readout_mode(self, description):
        """Set the readout mode and _readout_transform."""
        pass
 

◆ set_roi()

None microscope.abc.Camera.set_roi	(		self,
		microscope.ROI	roi )

Set the ROI according to the provided rectangle.

Return True if ROI set correctly, False otherwise.

Definition at line 974 of file abc.py.

    def set_roi(self, roi: microscope.ROI) -> None:
        """Set the ROI according to the provided rectangle.
 
        Return True if ROI set correctly, False otherwise.
        """
        maxw, maxh = self.get_sensor_shape()
        binning = self.get_binning()
        left, top, width, height = roi
        if not width:  # 0 or None
            width = maxw // binning.h
        if not height:  # 0 or None
            height = maxh // binning.v
        if self._transform[2]:
            roi = microscope.ROI(left, top, height, width)
        else:
            roi = microscope.ROI(left, top, width, height)
        return self._set_roi(roi)
 
 

◆ set_transform()

microscope.abc.Camera.set_transform	(		self,
			transform )

Combine provided transform with readout transform.

Definition at line 884 of file abc.py.

    def set_transform(self, transform):
        """Combine provided transform with readout transform."""
        if isinstance(transform, str):
            transform = literal_eval(transform)
        self._client_transform = transform
        lr, ud, rot = (
            self._readout_transform[i] ^ transform[i] for i in range(3)
        )
        if self._readout_transform[2] and self._client_transform[2]:
            lr = not lr
            ud = not ud
        self._transform = (lr, ud, rot)
 

Member Data Documentation

◆ _client_transform

tuple microscope.abc.Camera._client_transform = (False, False, False)

protected

Definition at line 839 of file abc.py.

◆ _readout_mode

microscope.abc.Camera._readout_mode = 0

protected

Definition at line 834 of file abc.py.

◆ _readout_modes

microscope.abc.Camera._readout_modes = ["default"]

protected

Definition at line 832 of file abc.py.

◆ _readout_transform

tuple microscope.abc.Camera._readout_transform = (False, False, False)

protected

Definition at line 837 of file abc.py.

◆ _transform

tuple microscope.abc.Camera._transform = (False, False, False)

protected

Definition at line 841 of file abc.py.

◆ ALLOWED_TRANSFORMS

list microscope.abc.Camera.ALLOWED_TRANSFORMS = [p for p in itertools.product(*3 * [[False, True]])]

static

Definition at line 827 of file abc.py.

◆ get_roi

microscope.abc.Camera.get_roi

Definition at line 857 of file abc.py.

◆ set_readout_mode

microscope.abc.Camera.set_readout_mode

Reimplemented in microscope.cameras.pvcam.PVCamera.

Definition at line 854 of file abc.py.

◆ set_roi

microscope.abc.Camera.set_roi

Definition at line 857 of file abc.py.

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

BioImager/PythonMicroscope/microscope/abc.py

Public Member Functions

Public Attributes

Static Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ _get_binning()

◆ _get_roi()

◆ _get_sensor_shape()

◆ _process_data()

◆ _set_binning()

◆ _set_readout_transform()

◆ _set_roi()

◆ get_binning()

◆ get_cycle_time()

◆ get_exposure_time()

◆ get_roi()

◆ get_sensor_shape()

◆ get_transform()

◆ set_binning()

◆ set_exposure_time()

◆ set_readout_mode()

◆ set_roi()

◆ set_transform()

Member Data Documentation

◆ _client_transform

◆ _readout_mode

◆ _readout_modes

◆ _readout_transform

◆ _transform

◆ ALLOWED_TRANSFORMS

◆ get_roi

◆ set_readout_mode

◆ set_roi

◆ init()